Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 118 of 320
Found at i:38611038 original size:40 final size:40
Alignment explanation
Indices: 38610959--38611216 Score: 342
Period size: 40 Copynumber: 6.5 Consensus size: 40
38610949 AAGCCAGGTA
* * * * *
38610959 CCTTCGGGATTTA-ACCAGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
38610998 CCTTCGGGACATAGCCCGGATGTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
38611038 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
38611078 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
38611118 CCTTCGGGGCTTAACCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * * **
38611158 CCTTCAGGACTTAGCTCGGA-ACTAGTCACTAGTGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
38611198 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
38611217 TTATCATCCG
Statistics
Matches: 195, Mismatches: 21, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
39 13 0.07
40 182 0.93
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:38618416 original size:9 final size:9
Alignment explanation
Indices: 38618402--38618427 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
38618392 CAAGTCCACA
38618402 TATTTCACT
1 TATTTCACT
38618411 TATTTCACT
1 TATTTCACT
38618420 TATTTCAC
1 TATTTCAC
38618428 ATTTTAGTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (9 bp):
TATTTCACT
Found at i:38621050 original size:42 final size:43
Alignment explanation
Indices: 38621004--38621100 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 43
38620994 ATCATGTCTA
* * * **
38621004 GGACATTGGCATC-GTATATGATTTCGTGTAAGACCCTGTATG
1 GGACATTGGCATCAATATATGATTACATGTAAGACCAAGTATG
* * *
38621046 GGACAGTGGCATCAATATTTGATTACATGTAAGACCAAGTCTG
1 GGACATTGGCATCAATATATGATTACATGTAAGACCAAGTATG
38621089 GGACATTGGCAT
1 GGACATTGGCAT
38621101 TGTAGGAGCT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 12 0.27
43 33 0.73
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (43 bp):
GGACATTGGCATCAATATATGATTACATGTAAGACCAAGTATG
Found at i:38624847 original size:28 final size:27
Alignment explanation
Indices: 38624815--38624877 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
38624805 CTCAAATACT
38624815 AAGTGCCATACTCAATATCTCGCACACC
1 AAGTGCCATACT-AATATCTCGCACACC
* * * * *
38624843 AAGTGCCATTCTTATATTTCTCACACT
1 AAGTGCCATACTAATATCTCGCACACC
38624870 AAGTGCCA
1 AAGTGCCA
38624878 CATATATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 19 0.63
28 11 0.37
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.29
Consensus pattern (27 bp):
AAGTGCCATACTAATATCTCGCACACC
Found at i:38626995 original size:25 final size:25
Alignment explanation
Indices: 38626949--38627019 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
38626939 GAGGAAGTGC
* *
38626949 AAAAGGGCTTTTGCCCTAGTTTACCG
1 AAAAGGGC-TTTGCCCCAGTTTACCA
* *
38626975 AAAAGGGCTTTGCCCCGGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
38627000 AAAAGAGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
38627020 ATTAAAAGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
25 31 0.79
26 8 0.21
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:38627274 original size:30 final size:31
Alignment explanation
Indices: 38627240--38627322 Score: 134
Period size: 30 Copynumber: 2.7 Consensus size: 31
38627230 CATTTACAGT
38627240 AAAGGCTTCGGCCCAGTGATATG-ATAATGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
* *
38627270 AAAGGCTTCGGCCCAGTGACATGAATAATGC
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
38627301 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
38627323 TTGAGATTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
30 26 0.53
31 23 0.47
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGA
Found at i:38627305 original size:31 final size:30
Alignment explanation
Indices: 38627240--38627317 Score: 129
Period size: 31 Copynumber: 2.6 Consensus size: 30
38627230 CATTTACAGT
*
38627240 AAAGGCTTCGGCCCAGTGATATGATAATGA
1 AAAGGCTTCGGCCCAGTGACATGATAATGA
*
38627270 AAAGGCTTCGGCCCAGTGACATGAATAATGC
1 AAAGGCTTCGGCCCAGTGACATG-ATAATGA
38627301 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
38627318 ATATGTTGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 22 0.49
31 23 0.51
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.21
Consensus pattern (30 bp):
AAAGGCTTCGGCCCAGTGACATGATAATGA
Found at i:38638911 original size:46 final size:46
Alignment explanation
Indices: 38638806--38638931 Score: 130
Period size: 46 Copynumber: 2.7 Consensus size: 46
38638796 GGTCACTTAT
* * **
38638806 GTAAGCCAGTGTAAGACCATGTCTGGGACACGGCATTGGCATTAAGAC
1 GTAAGCCAGTGT-AGAACATGTCTGGGACA-TGCATCAGCATTAAGAC
* * * *
38638854 G-AGTGCTAGTGTAGAACATGTCTGGTACATGCATCAGCCTTAAGAC
1 GTA-AGCCAGTGTAGAACATGTCTGGGACATGCATCAGCATTAAGAC
38638900 GTAAGCCAGTGTA-AGACATGTCTGGGACATGC
1 GTAAGCCAGTGTAGA-ACATGTCTGGGACATGC
38638932 GTTGCCTACG
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
45 1 0.02
46 38 0.59
47 17 0.27
48 8 0.12
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (46 bp):
GTAAGCCAGTGTAGAACATGTCTGGGACATGCATCAGCATTAAGAC
Found at i:38641452 original size:27 final size:27
Alignment explanation
Indices: 38641404--38641616 Score: 215
Period size: 27 Copynumber: 7.9 Consensus size: 27
38641394 GCGAGGCTGC
* *
38641404 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
38641431 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
38641457 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
38641484 CAGATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
38641511 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* * * *
38641538 CAGATAATCGTGGCATAGCCGCCAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
* *
38641565 CAAATATATGTGGCAGAGCCACCAAAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
38641592 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
38641617 GATGCTTCCT
Statistics
Matches: 155, Mismatches: 19, Indels: 24
0.78 0.10 0.12
Matches are distributed among these distances:
26 12 0.08
27 136 0.88
28 7 0.05
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:38641525 original size:81 final size:81
Alignment explanation
Indices: 38641422--38641616 Score: 240
Period size: 81 Copynumber: 2.4 Consensus size: 81
38641412 GTGACGAAGT
38641422 CACCAGATACAGATAT-TGTGGCAGAGCCACCAGAACAGATATAT-GTGGCAGAGCCACCA-GAT
1 CACCAGA-ACAGATATATGTGGCAGAGCCACCAGAACAGATA-ATCGTGGCAGAGCCACCAGGA-
* *
38641484 CAGATA-ATCGTGGCATAGC
63 CAAATATAT-GTGGCAGAGC
* * *
38641503 CACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCATAGCCGCCAGGACAA
1 CACCAGAACAGATATATGTGGCAGAGCCACCAGAACAGATAATCGTGGCAGAGCCACCAGGACAA
38641568 ATATATGTGGCAGAGC
66 ATATATGTGGCAGAGC
*
38641584 CACCA-AATCAGATA-ATTGTGGCATAGCCACCAG
1 CACCAGAA-CAGATATA-TGTGGCAGAGCCACCAG
38641617 GATGCTTCCT
Statistics
Matches: 102, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
80 13 0.13
81 85 0.83
82 4 0.04
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (81 bp):
CACCAGAACAGATATATGTGGCAGAGCCACCAGAACAGATAATCGTGGCAGAGCCACCAGGACAA
ATATATGTGGCAGAGC
Found at i:38641618 original size:54 final size:54
Alignment explanation
Indices: 38641422--38641616 Score: 311
Period size: 54 Copynumber: 3.6 Consensus size: 54
38641412 GTGACGAAGT
* *
38641422 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
38641476 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
* * *
38641530 CACCAGATCAGATAATCGTGGCATAGCCGCCAGGACAAATATATGTGGCAGAGC
1 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
* *
38641584 CACCAAATCAGATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATCGTGGCATAGCCACCAG
38641617 GATGCTTCCT
Statistics
Matches: 132, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
53 5 0.04
54 127 0.96
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (54 bp):
CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:38644254 original size:39 final size:39
Alignment explanation
Indices: 38644202--38644404 Score: 289
Period size: 39 Copynumber: 5.2 Consensus size: 39
38644192 TATGAGATTG
* *
38644202 AAAATATCCGGACATAAGGTCCGCAGGCTATATGCTGGA
1 AAAATATCCGGACATGAGATCCGCAGGCTATATGCTGGA
* *
38644241 AAAATATCTGGACATGAGATCCGTAGGCTATATGCTGGA
1 AAAATATCCGGACATGAGATCCGCAGGCTATATGCTGGA
*
38644280 AAAATATCCGGACATGAGATCCGCATGCTATATGCTGGA
1 AAAATATCCGGACATGAGATCCGCAGGCTATATGCTGGA
*
38644319 AAAATATCCGGACATGAGATCCGCAGGCTATATGCTAGA
1 AAAATATCCGGACATGAGATCCGCAGGCTATATGCTGGA
* * * * * **
38644358 AATATATCCGGACTTGAGGTCCACTGGCTACGTGCTGGA
1 AAAATATCCGGACATGAGATCCGCAGGCTATATGCTGGA
38644397 AAAATATC
1 AAAATATC
38644405 TGGGTTAAAG
Statistics
Matches: 146, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 146 1.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (39 bp):
AAAATATCCGGACATGAGATCCGCAGGCTATATGCTGGA
Found at i:38646408 original size:26 final size:26
Alignment explanation
Indices: 38646377--38646484 Score: 173
Period size: 26 Copynumber: 4.2 Consensus size: 26
38646367 TGAAATTTCC
38646377 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
38646403 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
38646429 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
38646455 ATCATGGAACATTTACCT-AACCTATT
1 ATCATGGAACATTTACCTAAACC-ATT
38646481 ATCA
1 ATCA
38646485 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
25 3 0.04
26 73 0.96
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:38651652 original size:27 final size:27
Alignment explanation
Indices: 38651604--38651816 Score: 224
Period size: 27 Copynumber: 7.9 Consensus size: 27
38651594 GCGAGGCTGC
* *
38651604 CAGATATTGTGAGGA-AGTCACCAGATA
1 CAGATATTGTG-GCATAGCCACCAGATA
* *
38651631 CAGATATTGTGGCAGAACCACCAGA-A
1 CAGATATTGTGGCATAGCCACCAGATA
*
38651657 TAGATATATGTGGCATAGCCACCAGAT-
1 CAGATAT-TGTGGCATAGCCACCAGATA
*
38651684 CAGATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCATAGCCACCAGATA
* *
38651711 CAGATATATGTGGCAGAGCCACTAGAT-
1 CAGATAT-TGTGGCATAGCCACCAGATA
*
38651738 CAGATAATTGTGGCATAGCCACCAG-GA
1 CAGAT-ATTGTGGCATAGCCACCAGATA
*
38651765 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCATAGCCACCAGATA
38651792 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCATAGCCACCAG
38651817 GATGCTTCCT
Statistics
Matches: 157, Mismatches: 17, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
26 13 0.08
27 138 0.88
28 6 0.04
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (27 bp):
CAGATATTGTGGCATAGCCACCAGATA
Found at i:38651725 original size:81 final size:81
Alignment explanation
Indices: 38651622--38651816 Score: 249
Period size: 81 Copynumber: 2.4 Consensus size: 81
38651612 GTGAGGAAGT
*
38651622 CACCAGATACAGATAT-TGTGGCAGAACCACCAGAAT-AGAT-ATATGTGGCATAGCCACCA-GA
1 CACCAGA-ACAGATATATGTGGCAGAGCCACCAG-ATCAGATAAT-TGTGGCATAGCCACCAGGA
*
38651683 TCAGATA-ATCGTGGCATAGC
63 -CAGATATAT-GTGGCAGAGC
*
38651703 CACCAGAACAGATATATGTGGCAGAGCCACTAGATCAGATAATTGTGGCATAGCCACCAGGACAG
1 CACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGGACAG
38651768 ATATATGTGGCAGAGC
66 ATATATGTGGCAGAGC
* *
38651784 CACCAGATCAGATA-ATTGTGGCATAGCCACCAG
1 CACCAGAACAGATATA-TGTGGCAGAGCCACCAG
38651817 GATGCTTCCT
Statistics
Matches: 102, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
80 11 0.11
81 85 0.83
82 6 0.06
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.19
Consensus pattern (81 bp):
CACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGGACAG
ATATATGTGGCAGAGC
Found at i:38651818 original size:54 final size:54
Alignment explanation
Indices: 38651622--38651816 Score: 311
Period size: 54 Copynumber: 3.6 Consensus size: 54
38651612 GTGAGGAAGT
* * * *
38651622 CACCAGATACAGAT-ATTGTGGCAGAACCACCAGAATAGATATATGTGGCATAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
*
38651676 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
* *
38651730 CACTAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
38651784 CACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAG
38651817 GATGCTTCCT
Statistics
Matches: 131, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
53 5 0.04
54 126 0.96
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.19
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:38653445 original size:26 final size:26
Alignment explanation
Indices: 38653414--38653521 Score: 166
Period size: 26 Copynumber: 4.2 Consensus size: 26
38653404 TGAAATGCCC
38653414 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
38653440 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
*
38653466 ATCATGG-ACTATTTACCTAATCCATT
1 ATCATGGAAC-ATTTACCTAAACCATT
38653492 ATCATGGAACATTTACCT-AACCTATT
1 ATCATGGAACATTTACCTAAACC-ATT
38653518 ATCA
1 ATCA
38653522 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
25 5 0.07
26 69 0.91
27 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:38656122 original size:33 final size:33
Alignment explanation
Indices: 38656085--38656180 Score: 106
Period size: 34 Copynumber: 2.9 Consensus size: 33
38656075 CTATGGGCCA
* *
38656085 TACTGTTATCTGAAAAGGGGCTGAGGCCCAGT-T
1 TACTGTTATCTGAAAA-GGGCTTAGGCCCAGTAC
* *
38656118 TACTG-TATTTTGAAAAGGGCTTCGGCCCAGTACC
1 TACTGTTA-TCTGAAAAGGGCTTAGGCCCAGTA-C
*
38656152 TACTGTTATCTGAATAGGGCTTAGGCCCA
1 TACTGTTATCTGAAAAGGGCTTAGGCCCA
38656181 ATGGGCTTGG
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
32 15 0.29
33 12 0.23
34 23 0.44
35 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (33 bp):
TACTGTTATCTGAAAAGGGCTTAGGCCCAGTAC
Found at i:38657274 original size:34 final size:35
Alignment explanation
Indices: 38657235--38657306 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
38657225 ATTCTATAGT
*
38657235 TAGGGAAATACTG-AAACTGTAGAA-ACTGAGACAG
1 TAGGGAAA-ACTGAAAACTGTAGAAGACTAAGACAG
* *
38657269 TAGGGAAAACTGAAAACTTTAGAAGACTAAGACTG
1 TAGGGAAAACTGAAAACTGTAGAAGACTAAGACAG
38657304 TAG
1 TAG
38657307 CTAGGATACG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 4 0.12
34 18 0.55
35 11 0.33
ACGTcount: A:0.44, C:0.11, G:0.25, T:0.19
Consensus pattern (35 bp):
TAGGGAAAACTGAAAACTGTAGAAGACTAAGACAG
Found at i:38659285 original size:46 final size:46
Alignment explanation
Indices: 38659210--38659381 Score: 161
Period size: 46 Copynumber: 3.7 Consensus size: 46
38659200 TGTAACCCGC
* * * * *
38659210 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT
* * * *
38659256 CCATGAGTGAACTCGGACTCAACTCAACGAGTTTGGATGCCTAATTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C-ATTTGCAT
* * **
38659306 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT
*
38659349 CCATAAGTGAAGTCGGACTCAACTCAACGAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTT
38659382 TGGATGCTCA
Statistics
Matches: 100, Mismatches: 19, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 55 0.55
47 26 0.26
48 3 0.03
49 2 0.02
50 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT
Found at i:38659376 original size:93 final size:93
Alignment explanation
Indices: 38659217--38659388 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
38659207 CGCCCATAAG
** * *
38659217 CGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
38659282 ACGAGTTTGGATGCCTAATTACATCTCA
66 ACGAGTTTGGATGCCTAATTACATCTCA
* * * *
38659310 CGAACTCGGACTCAACTCAACGAGTTCGAACATTTGCATCCATAAGTGAAGTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
38659375 ACGAGTTTGGATGC
66 ACGAGTTTGGATGC
38659389 TCAACCATCC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTTGGATGCCTAATTACATCTCA
Found at i:38659404 original size:46 final size:45
Alignment explanation
Indices: 38659261--38659404 Score: 116
Period size: 46 Copynumber: 3.1 Consensus size: 45
38659251 CGCATCCATG
*
38659261 AGTGAACTCGGACTCAACTCAACGAGTTTGGATGC-CTAATTACATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTTGGATGCTC-AA--CCATCT
* * * * * *
38659308 CA-CGAACTCGGACTCAACTCAACGAGTTCGAACAT-TTGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTTG--GATGCT-CAACCATCT
*
38659354 AGTGAAGTCGGACTCAACTCAACGAGTTTGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTTGGATGCTCAACCAT-CT
38659400 AGTGA
1 AGTGA
38659405 CATGTCACTT
Statistics
Matches: 74, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
44 8 0.11
45 2 0.03
46 30 0.41
47 29 0.39
48 1 0.01
49 3 0.04
50 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTTGGATGCTCAACCATCT
Found at i:38661338 original size:20 final size:20
Alignment explanation
Indices: 38661309--38661349 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
38661299 AAATTCCTTT
38661309 TCCTTAGTGCCGATTTCTTC
1 TCCTTAGTGCCGATTTCTTC
* *
38661329 TCCTTGGTGCTGATTTCTTC
1 TCCTTAGTGCCGATTTCTTC
38661349 T
1 T
38661350 TCCTCTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.07, C:0.27, G:0.17, T:0.49
Consensus pattern (20 bp):
TCCTTAGTGCCGATTTCTTC
Found at i:38664690 original size:31 final size:32
Alignment explanation
Indices: 38664573--38664722 Score: 214
Period size: 32 Copynumber: 4.8 Consensus size: 32
38664563 CACGACTTAC
* *
38664573 AGCCATCAGTAGCGGTAATATGATCGGCACAA
1 AGCCATCAGTAGCTGTAATATGATCGACACAA
** * *
38664605 AGAAAACAATAGCTGTAATATGATCGACACAA
1 AGCCATCAGTAGCTGTAATATGATCGACACAA
*
38664637 AGCCATCAGTAGCTATAATATGATCGACACAA
1 AGCCATCAGTAGCTGTAATATGATCGACACAA
*
38664669 AGCCATCAGTA-CTGTAATATGATCGGCACAA
1 AGCCATCAGTAGCTGTAATATGATCGACACAA
38664700 AGCCATCAGTA-CTGTAATATGAT
1 AGCCATCAGTAGCTGTAATATGAT
38664723 TGGTAACAAG
Statistics
Matches: 105, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
31 41 0.39
32 64 0.61
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (32 bp):
AGCCATCAGTAGCTGTAATATGATCGACACAA
Found at i:38667314 original size:35 final size:35
Alignment explanation
Indices: 38667266--38667332 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
38667256 TTTATAACAG
* *
38667266 TTCAATTACAAATAAACATATATAACTCAATTCAA
1 TTCAATAACAAATAAACATATATAACCCAATTCAA
* * *
38667301 TTCAATAATAAATAAGCATTTATAACCCAATT
1 TTCAATAACAAATAAACATATATAACCCAATT
38667333 TAAATACGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.49, C:0.16, G:0.01, T:0.33
Consensus pattern (35 bp):
TTCAATAACAAATAAACATATATAACCCAATTCAA
Found at i:38672493 original size:40 final size:40
Alignment explanation
Indices: 38672396--38672616 Score: 214
Period size: 40 Copynumber: 5.5 Consensus size: 40
38672386 TTGAATGCTG
* * * * * *
38672396 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
38672436 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
38672476 TCCAGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
** *
38672516 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTGAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
38672556 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
38672595 ACCGGGCTATGTCCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCA
38672617 CTTGAACGAG
Statistics
Matches: 155, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 32 0.21
40 115 0.74
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:38672638 original size:79 final size:80
Alignment explanation
Indices: 38672474--38672653 Score: 188
Period size: 79 Copynumber: 2.3 Consensus size: 80
38672464 CGAGATACTA
* * * *
38672474 AATCCAGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAT
1 AATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** ** *
38672539 TCGTGCGAGTTGTTG
66 TCGAACGAGGAGCTG
* * *
38672554 AATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCAC
1 AATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCA-
38672618 TT-GAACGAGGAGCT-
65 TTCGAACGAGGAGCTG
* *
38672632 ATATCC-GGTTAAATTCCGAAGG
1 A-ATCCGGGTTAAGTCCCGAAGG
38672654 TACGTGATTT
Statistics
Matches: 83, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
78 14 0.17
79 43 0.52
80 26 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
AATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
TCGAACGAGGAGCTG
Found at i:38679447 original size:40 final size:40
Alignment explanation
Indices: 38679392--38679547 Score: 206
Period size: 40 Copynumber: 3.9 Consensus size: 40
38679382 TTCGGCCTTT
* *
38679392 GTGCGAGATACTAAATCCAGGTTAAGTCCCGAAGGCATTC
1 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
*
38679432 GTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
** * *
38679472 GTGCGAGTTGTTGAATCCGGGTTATGTCCCGAAGGCATT-
1 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* * * *
38679511 GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCA
1 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCA
38679548 CTTGAACGAG
Statistics
Matches: 104, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 31 0.30
40 73 0.70
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
Found at i:38679569 original size:79 final size:80
Alignment explanation
Indices: 38679405--38679584 Score: 188
Period size: 79 Copynumber: 2.3 Consensus size: 80
38679395 CGAGATACTA
* * * *
38679405 AATCCAGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAT
1 AATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** ** *
38679470 TCGTGCGAGTTGTTG
66 TCGAACGAGGAGCTG
* * *
38679485 AATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCAC
1 AATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCA-
38679549 TT-GAACGAGGAGCT-
65 TTCGAACGAGGAGCTG
* *
38679563 ATATCC-GGTTAAATTCCGAAGG
1 A-ATCCGGGTTAAGTCCCGAAGG
38679585 TACGTGATTT
Statistics
Matches: 83, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
78 14 0.17
79 43 0.52
80 26 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
AATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
TCGAACGAGGAGCTG
Found at i:38682084 original size:27 final size:27
Alignment explanation
Indices: 38682030--38682140 Score: 136
Period size: 27 Copynumber: 4.1 Consensus size: 27
38682020 AGCATGGCTG
** * *
38682030 CCAGAACAGATAA-TGTGATAGGGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
38682056 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
*
38682083 CCAGAACAAAT-ATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* *
38682110 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
38682137 CCAG
1 CCAG
38682141 GACGCTTCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
26 15 0.20
27 57 0.77
28 2 0.03
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:38682289 original size:26 final size:27
Alignment explanation
Indices: 38682259--38682319 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
38682249 GGGTATAATG
* *
38682259 GTAATTT-TACACCTAGGGGTATATCAA
1 GTAATTTCCACACATAGGGGTAT-TCAA
*
38682286 -TAATTTCCATACATAGGGGTATTCAA
1 GTAATTTCCACACATAGGGGTATTCAA
38682312 GTAATTTC
1 GTAATTTC
38682320 ACTATTCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 10 0.34
27 19 0.66
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (27 bp):
GTAATTTCCACACATAGGGGTATTCAA
Found at i:38683356 original size:16 final size:16
Alignment explanation
Indices: 38683331--38683363 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
38683321 CCAAAAGAAA
38683331 AAGAAAAGATGAGCAG
1 AAGAAAAGATGAGCAG
*
38683347 AAGAAGAGATGAGCAG
1 AAGAAAAGATGAGCAG
38683363 A
1 A
38683364 GAATTCGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.33, T:0.06
Consensus pattern (16 bp):
AAGAAAAGATGAGCAG
Found at i:38686805 original size:40 final size:40
Alignment explanation
Indices: 38686749--38686901 Score: 209
Period size: 40 Copynumber: 3.8 Consensus size: 40
38686739 TATAACCACA
* * * *
38686749 AGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACT
*
38686789 TGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACT
* *
38686829 CGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACT
* *
38686869 AGCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
38686902 CATTCAAATG
Statistics
Matches: 101, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
39 1 0.01
40 96 0.95
41 4 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACT
Found at i:38701300 original size:42 final size:43
Alignment explanation
Indices: 38701198--38701338 Score: 142
Period size: 43 Copynumber: 3.3 Consensus size: 43
38701188 AGCTTGTTCA
* * *
38701198 ATGCCAATGTCCCAGACATGGTCATACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACATGGTCATACAGGAAATCAAATATCG
* * * *
38701241 ATGCC-ACTGTCCCAGACAGGGTCTTATAGGAAATCAAGTATC-
1 ATGCCAAC-GTCCCAGACATGGTCATACAGGAAATCAAATATCG
* * * *
38701283 ATGCCAACGTCCCAGACATGGTCATACACGTAAATCATAGATTG
1 ATGCCAACGTCCCAGACATGGTCATACA-GGAAATCAAATATCG
*
38701327 ATGCCAATGTCC
1 ATGCCAACGTCC
38701339 TGTACATGGT
Statistics
Matches: 78, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
42 23 0.29
43 44 0.56
44 11 0.14
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCATACAGGAAATCAAATATCG
Found at i:38707636 original size:34 final size:35
Alignment explanation
Indices: 38707578--38707649 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
38707568 CGTATCATAG
*
38707578 CTACAGTCTCAGTCTTCTAAAGTTTTCAGT-TTTCC
1 CTACAGTCTCAGTCTTCTAAAG-TTTCAGTATTACC
* *
38707613 CTACTGTCTCAGT-TTCTACAGTTTCAGTATTACC
1 CTACAGTCTCAGTCTTCTAAAGTTTCAGTATTACC
38707647 CTA
1 CTA
38707650 ACTACAGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 7 0.21
34 14 0.42
35 12 0.36
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (35 bp):
CTACAGTCTCAGTCTTCTAAAGTTTCAGTATTACC
Found at i:38710844 original size:65 final size:65
Alignment explanation
Indices: 38710740--38710870 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
38710730 AGTCTCACGC
* *
38710740 ATCAGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTT
1 ATCAGATAATAATAACATGGCATGCAGAAAATAGTAACAGTCAAACATCCATTCAGGTCAACCTT
38710805 ATCAGATAATAATAACATGGCATGCAGAAAATAGTAACAGTCAAACATCCATTCAGGTCAACCTT
1 ATCAGATAATAATAACATGGCATGCAGAAAATAGTAACAGTCAAACATCCATTCAGGTCAACCTT
38710870 A
1 A
38710871 ACCCTAGTGG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.24
Consensus pattern (65 bp):
ATCAGATAATAATAACATGGCATGCAGAAAATAGTAACAGTCAAACATCCATTCAGGTCAACCTT
Found at i:38714179 original size:34 final size:35
Alignment explanation
Indices: 38714127--38714192 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
38714117 CTATCTGCAA
*
38714127 TCTCAGTCTTCTAAAGTTTTCAGT-TTTCCCTACTG
1 TCTCAGTCTTCTAAAG-TTTCAGTATTACCCTACTG
*
38714162 TCTCAGT-TTCTACAGTTTCAGTATTACCCTA
1 TCTCAGTCTTCTAAAGTTTCAGTATTACCCTA
38714193 ACTACAGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 7 0.25
34 14 0.50
35 7 0.25
ACGTcount: A:0.20, C:0.26, G:0.11, T:0.44
Consensus pattern (35 bp):
TCTCAGTCTTCTAAAGTTTCAGTATTACCCTACTG
Found at i:38718008 original size:79 final size:79
Alignment explanation
Indices: 38717897--38718119 Score: 260
Period size: 79 Copynumber: 2.8 Consensus size: 79
38717887 GCTCCTCGTT
* * *
38717897 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCG
*
38717961 GATTTAGTAACTCGCA
64 GAATTAGTAACTCGCA
38717977 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
* *
38718040 AATTAGTATCTCGTA
65 AATTAGTAACTCGCA
* * * *
38718055 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCC
38718117 GGA
63 GGA
38718120 CATCATTCAA
Statistics
Matches: 126, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
78 45 0.36
79 57 0.45
80 23 0.18
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:38718014 original size:39 final size:40
Alignment explanation
Indices: 38717897--38718119 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
38717887 GCTCCTCGTT
* *
38717897 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
38717937 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
38717977 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
38718016 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
38718055 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
38718096 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
38718120 CATCATTCAA
Statistics
Matches: 164, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
38 2 0.01
39 88 0.54
40 64 0.39
41 10 0.06
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:38725393 original size:27 final size:27
Alignment explanation
Indices: 38725376--38725582 Score: 207
Period size: 27 Copynumber: 7.6 Consensus size: 27
38725366 ATATTAAGTC
38725376 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* *
38725403 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* * *
38725431 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* * *
38725458 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* * * *
38725486 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTCAGTGCTATATAATCAACT
* * *
38725513 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* * * *
38725541 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTCAGTGCTATATAATCAACT
*
38725568 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
38725583 GCACAATTTA
Statistics
Matches: 171, Mismatches: 6, Indels: 6
0.93 0.03 0.03
Matches are distributed among these distances:
27 92 0.54
28 79 0.46
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:38725460 original size:55 final size:55
Alignment explanation
Indices: 38725376--38725582 Score: 360
Period size: 55 Copynumber: 3.8 Consensus size: 55
38725366 ATATTAAGTC
* * * *
38725376 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
38725431 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
*
38725486 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
*
38725541 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
38725583 GCACAATTTA
Statistics
Matches: 147, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 147 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
Found at i:38732121 original size:51 final size:51
Alignment explanation
Indices: 38732047--38732160 Score: 183
Period size: 51 Copynumber: 2.2 Consensus size: 51
38732037 TTGATCACAT
*
38732047 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAACTAAAACTACCACTTATCAC
* *
38732098 TTATCACTTGTCACTGATGAGATAAGTGTAACTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAACTAAAACTACCACTTATCAC
* *
38732149 TTGTCGCTTGTC
1 TTATCACTTGTC
38732161 GCTTGTCACT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAACTAAAACTACCACTTATCAC
Found at i:38734961 original size:33 final size:34
Alignment explanation
Indices: 38734924--38734995 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 34
38734914 ATGGCAATTG
*
38734924 TGTGAAACGTAAGTATGGTATTTCC-TACCGAGC
1 TGTGAAACATAAGTATGGTATTTCCATACCGAGC
* * * *
38734957 TGTG-AACATAGGTATGGTGTTTCCATACTGAGT
1 TGTGAAACATAAGTATGGTATTTCCATACCGAGC
38734990 TGTGAA
1 TGTGAA
38734996 TCGTGGCACT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
32 17 0.53
33 14 0.44
34 1 0.03
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (34 bp):
TGTGAAACATAAGTATGGTATTTCCATACCGAGC
Found at i:38736800 original size:52 final size:53
Alignment explanation
Indices: 38736722--38736848 Score: 211
Period size: 53 Copynumber: 2.4 Consensus size: 53
38736712 AACAGAAGGT
*
38736722 AATTTTTTTTTAATACTCGTACTGGTGTTGG-CCATTACAAGGCCAGCACCAA
1 AATTTTTTTTTAATACTCGTACTGGTGTCGGCCCATTACAAGGCCAGCACCAA
*
38736774 AATTTTTTTTTAATACTCGTACTGGTGTCGGCCCATTATAAGGCCAGCACCAA
1 AATTTTTTTTTAATACTCGTACTGGTGTCGGCCCATTACAAGGCCAGCACCAA
*
38736827 AATTTTTTTTTAAGTTCTCGTA
1 AATTTTTTTTTAA-TACTCGTA
38736849 TTTTTGTATA
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
52 30 0.43
53 33 0.47
54 7 0.10
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (53 bp):
AATTTTTTTTTAATACTCGTACTGGTGTCGGCCCATTACAAGGCCAGCACCAA
Found at i:38738018 original size:31 final size:31
Alignment explanation
Indices: 38737960--38738018 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
38737950 AGTTAAGAGC
* **
38737960 TCAATGTGGGAACAATTGTCAAATTCAAACT
1 TCAATATGGGAACAATTACCAAATTCAAACT
*
38737991 TCAATATGGGAACAATTACCAAGTTCAA
1 TCAATATGGGAACAATTACCAAATTCAA
38738019 GGAATAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (31 bp):
TCAATATGGGAACAATTACCAAATTCAAACT
Found at i:38738247 original size:33 final size:36
Alignment explanation
Indices: 38738190--38738258 Score: 117
Period size: 34 Copynumber: 2.0 Consensus size: 36
38738180 CACCAAAAGT
38738190 TTTGTTCTTTTAAAAAAAACCCTCCTCTTT-GAAGA
1 TTTGTTCTTTTAAAAAAAACCCTCCTCTTTGGAAGA
38738225 TTTGTTC-TTTAAAAAAAA-CCTCCTCTTTGGAAGA
1 TTTGTTCTTTTAAAAAAAACCCTCCTCTTTGGAAGA
38738259 AGGTGAGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
33 10 0.30
34 16 0.48
35 7 0.21
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (36 bp):
TTTGTTCTTTTAAAAAAAACCCTCCTCTTTGGAAGA
Found at i:38738950 original size:6 final size:6
Alignment explanation
Indices: 38738931--38738966 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
38738921 ACAAATTTAG
*
38738931 AATTTT TATATTT AATTTT AATTTT AATTTT AATTT
1 AATTTT AAT-TTT AATTTT AATTTT AATTTT AATTT
38738967 CATATCATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
AATTTT
Found at i:38739537 original size:16 final size:16
Alignment explanation
Indices: 38739516--38739550 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
38739506 TAACATTGAA
*
38739516 GTATTGGATTAGAGTT
1 GTATTGGATTAGAGGT
38739532 GTATTGGATTAGAGGT
1 GTATTGGATTAGAGGT
38739548 GTA
1 GTA
38739551 ATAACAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.34, T:0.40
Consensus pattern (16 bp):
GTATTGGATTAGAGGT
Found at i:38739969 original size:112 final size:109
Alignment explanation
Indices: 38739767--38740036 Score: 293
Period size: 112 Copynumber: 2.4 Consensus size: 109
38739757 CATATTTATC
* * * *
38739767 ATAATTAT-TATAGATATATTATAATTAAAAATAGAATTTAATAAAATTCTAATAATCAATTTCT
1 ATAATTATAT-TAAATATATTATAATT-AAAATATATTTTAATAAAATTCTAATAATCAATATCT
*
38739831 TTATGAATTTACTCAAATAATAATATATGATTACTATAAATATAAATTAA
64 TTATGAATTTACTCAAATAATAATATATGA--A-TATAAA-AGAAATTAA
* *
38739881 CATAATT-TATT-AATATATTATAATTAAATATATATTTTAAT-AAATTCTTATAAT-TATATCT
1 -ATAATTATATTAAATATATTATAATTAAA-ATATATTTTAATAAAATTCTAATAATCAATATCT
* *
38739942 TATATG-ATTTACTCAAAATCATAATATATGAATATAAAAGAATTTAA
64 T-TATGAATTTACTC-AAATAATAATATATGAATATAAAAGAAATTAA
*
38739989 ATAATTATATTAAATATATTTTAATTAAAATATATGATTT-ATAAAATT
1 ATAATTATATTAAATATATTATAATTAAAATATAT--TTTAATAAAATT
38740037 TAAAATAATT
Statistics
Matches: 136, Mismatches: 10, Indels: 23
0.80 0.06 0.14
Matches are distributed among these distances:
107 6 0.04
108 17 0.12
109 24 0.18
110 9 0.07
111 14 0.10
112 34 0.25
113 23 0.17
114 2 0.01
115 7 0.05
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (109 bp):
ATAATTATATTAAATATATTATAATTAAAATATATTTTAATAAAATTCTAATAATCAATATCTTT
ATGAATTTACTCAAATAATAATATATGAATATAAAAGAAATTAA
Found at i:38751042 original size:30 final size:30
Alignment explanation
Indices: 38751008--38751068 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
38750998 TCCTTAACTC
38751008 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
38751038 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
38751068 A
1 A
38751069 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:38759016 original size:16 final size:17
Alignment explanation
Indices: 38758995--38759034 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
38758985 CTTTCATTAA
38758995 GTTTTTAAGATTCAATT
1 GTTTTTAAGATTCAATT
*
38759012 GTTTTTAAGATTCATTT
1 GTTTTTAAGATTCAATT
38759029 GTTTTT
1 GTTTTT
38759035 CTTTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.12, T:0.60
Consensus pattern (17 bp):
GTTTTTAAGATTCAATT
Found at i:38759679 original size:15 final size:15
Alignment explanation
Indices: 38759659--38759694 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
38759649 ATGTCAAAAT
38759659 GATTAAGGCACTTAG
1 GATTAAGGCACTTAG
*
38759674 GATTAAGGCATTTAG
1 GATTAAGGCACTTAG
38759689 GATTAA
1 GATTAA
38759695 CCCACTCATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (15 bp):
GATTAAGGCACTTAG
Found at i:38770691 original size:9 final size:9
Alignment explanation
Indices: 38770672--38770701 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
38770662 AATTAAATAT
38770672 ATGCATATTA
1 ATGC-TATTA
38770682 ATGCTATTA
1 ATGCTATTA
38770691 ATGCTATTA
1 ATGCTATTA
38770700 AT
1 AT
38770702 TTATTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.80
10 4 0.20
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (9 bp):
ATGCTATTA
Found at i:38780824 original size:21 final size:21
Alignment explanation
Indices: 38780800--38780842 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
38780790 TCTTTGACGT
38780800 ATTCATCAAGATTTCTTATTG
1 ATTCATCAAGATTTCTTATTG
38780821 ATTCATCAAGATTTCTTATTG
1 ATTCATCAAGATTTCTTATTG
38780842 A
1 A
38780843 ACTTCTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (21 bp):
ATTCATCAAGATTTCTTATTG
Found at i:38787089 original size:14 final size:16
Alignment explanation
Indices: 38787055--38787094 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
38787045 TTAAACATAT
38787055 ATATATCATCTATTTC
1 ATATATCATCTATTTC
*
38787071 CTATATCA-CT-TTTC
1 ATATATCATCTATTTC
38787085 ATATATCATC
1 ATATATCATC
38787095 GTTTCTTGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 11 0.52
15 3 0.14
16 7 0.33
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATATCATCTATTTC
Found at i:38789338 original size:14 final size:15
Alignment explanation
Indices: 38789292--38789361 Score: 79
Period size: 15 Copynumber: 4.7 Consensus size: 15
38789282 GAAATGACAT
*
38789292 GAAAACCAAGACAAA
1 GAAATCCAAGACAAA
*
38789307 GAAGTCCAAGACAAA
1 GAAATCCAAGACAAA
*
38789322 GAAATCCTAGA-AAA
1 GAAATCCAAGACAAA
* *
38789336 GAAATCCAAGATACA
1 GAAATCCAAGACAAA
*
38789351 GAAATCTAAGA
1 GAAATCCAAGA
38789362 TAAAATATCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
14 13 0.28
15 34 0.72
ACGTcount: A:0.57, C:0.17, G:0.16, T:0.10
Consensus pattern (15 bp):
GAAATCCAAGACAAA
Found at i:38800667 original size:23 final size:23
Alignment explanation
Indices: 38800641--38800687 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
38800631 GAGGAGAGAT
38800641 CTTTAGTCTTGATGATGAATCCC
1 CTTTAGTCTTGATGATGAATCCC
38800664 CTTTAGTCTTGATGATGAATCCC
1 CTTTAGTCTTGATGATGAATCCC
38800687 C
1 C
38800688 CTTTTCTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (23 bp):
CTTTAGTCTTGATGATGAATCCC
Found at i:38801743 original size:16 final size:15
Alignment explanation
Indices: 38801722--38801755 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
38801712 GTATACATAG
38801722 TTTTTTTTTCTTTTTC
1 TTTTTTTTTC-TTTTC
38801738 TTTTTTTTTCTTTTC
1 TTTTTTTTTCTTTTC
38801753 TTT
1 TTT
38801756 AAGAACAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTCTTTTC
Found at i:38802782 original size:21 final size:21
Alignment explanation
Indices: 38802758--38802800 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
38802748 CTGTGATAAA
38802758 ATCAGGAAATTTTTAGGGGAT
1 ATCAGGAAATTTTTAGGGGAT
38802779 ATCAGGAAATTTTTAGGGGAT
1 ATCAGGAAATTTTTAGGGGAT
38802800 A
1 A
38802801 AAATCACGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.33
Consensus pattern (21 bp):
ATCAGGAAATTTTTAGGGGAT
Found at i:38815303 original size:11 final size:11
Alignment explanation
Indices: 38815287--38815334 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
38815277 CTTTATATAC
38815287 TAATAAAATAA
1 TAATAAAATAA
*
38815298 TAATAAAATATCT
1 TAATAAAATA--A
* *
38815311 TATTAAAATAT
1 TAATAAAATAA
38815322 TAATAAAATAA
1 TAATAAAATAA
38815333 TA
1 TA
38815335 TTTATCTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 22 0.71
13 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:38815609 original size:31 final size:31
Alignment explanation
Indices: 38815571--38815629 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
38815561 CACCCTTAAA
**
38815571 ATATTTACACTATTAGTCC-TTAAATTTTTTC
1 ATATTTACACT-TTAACCCTTTAAATTTTTTC
38815602 ATATTTACACTTTAACCCTTTAAATTTT
1 ATATTTACACTTTAACCCTTTAAATTTT
38815630 GAGTATTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.51
Consensus pattern (31 bp):
ATATTTACACTTTAACCCTTTAAATTTTTTC
Found at i:38818340 original size:29 final size:29
Alignment explanation
Indices: 38818298--38818353 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
38818288 TGCCATAATG
* *
38818298 TCTTCCAACTATGGTCTTGTTCATTTCTA
1 TCTTCCAACCATGGTCTTATTCATTTCTA
*
38818327 TCTTTCAACCATGGTCTTATTCATTTC
1 TCTTCCAACCATGGTCTTATTCATTTC
38818354 CTGTCATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.18, C:0.25, G:0.09, T:0.48
Consensus pattern (29 bp):
TCTTCCAACCATGGTCTTATTCATTTCTA
Found at i:38818379 original size:46 final size:46
Alignment explanation
Indices: 38818325--38818529 Score: 295
Period size: 46 Copynumber: 4.5 Consensus size: 46
38818315 TGTTCATTTC
* *
38818325 TATCTTTCAACCATGGTCTTATTCATTTCCTGTCATGTTGCTATGG
1 TATCTTTCAACCATGGTCTTATTCATTTTCTGTCATGTTGCCATGG
* *
38818371 AATCTTTCAACCATGGTCTTATTCATTTTCTATCATGTTGCCATGG
1 TATCTTTCAACCATGGTCTTATTCATTTTCTGTCATGTTGCCATGG
*
38818417 TATCTTTCAACCATGGTCTTATTCATTTTCTGTCATGTTCCCATGG
1 TATCTTTCAACCATGGTCTTATTCATTTTCTGTCATGTTGCCATGG
* * * *
38818463 TATCTTTCAACCATGGTCTTATTCA-TATCTCGTCATATTACCATAG
1 TATCTTTCAACCATGGTCTTATTCATTTTCT-GTCATGTTGCCATGG
* *
38818509 TATATTTCAACTATGGTCTTA
1 TATCTTTCAACCATGGTCTTA
38818530 CATATCTGAA
Statistics
Matches: 145, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 4 0.03
46 141 0.97
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.44
Consensus pattern (46 bp):
TATCTTTCAACCATGGTCTTATTCATTTTCTGTCATGTTGCCATGG
Found at i:38818621 original size:45 final size:45
Alignment explanation
Indices: 38818513--38818621 Score: 164
Period size: 45 Copynumber: 2.4 Consensus size: 45
38818503 CCATAGTATA
* *
38818513 TTTCAACTATGGTCTTACATATCTGAATCGTGATGCCATAACGTC
1 TTTCAACTATGGTCTTACTTATCTGAATCGCGATGCCATAACGTC
* * *
38818558 TTTCAGCTATGGTCTTACTTGTCTGAATCGCGATGCCATAGCGTC
1 TTTCAACTATGGTCTTACTTATCTGAATCGCGATGCCATAACGTC
*
38818603 TTTCATCTATGGTCTTACT
1 TTTCAACTATGGTCTTACT
38818622 CCTTTCTGGA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (45 bp):
TTTCAACTATGGTCTTACTTATCTGAATCGCGATGCCATAACGTC
Found at i:38818638 original size:45 final size:42
Alignment explanation
Indices: 38818513--38818643 Score: 127
Period size: 45 Copynumber: 2.9 Consensus size: 42
38818503 CCATAGTATA
* * * *
38818513 TTTCAACTATGGTCTTACATATCTGAATCGTGATGCCATAACGTC
1 TTTCAGCTATGGTCTTACTTGTCTGAA---TGATGCCATAGCGTC
38818558 TTTCAGCTATGGTCTTACTTGTCTGAATCGCGATGCCATAGCGTC
1 TTTCAGCTATGGTCTTACTTGTCTGAAT---GATGCCATAGCGTC
* *
38818603 TTTCATCTATGGTCTTACTCCTTTCTGGAATGATGCCATAG
1 TTTCAGCTATGGTCTTACT--TGTCT-GAATGATGCCATAG
38818644 TCCAACTATG
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
42 1 0.01
45 65 0.88
47 4 0.05
48 4 0.05
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.37
Consensus pattern (42 bp):
TTTCAGCTATGGTCTTACTTGTCTGAATGATGCCATAGCGTC
Found at i:38818721 original size:33 final size:33
Alignment explanation
Indices: 38818684--38818761 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
38818674 TGGCGCAGCC
* *
38818684 ATGGTCTTACACTC-GTAGTGCCATATCCCAGAT
1 ATGGTCTTACACTCAGGA-TGCCATAGCCCAGAT
* *
38818717 ATGGTCTTATCA-TCAGGATGCCATAGCCTAGCT
1 ATGGTCTTA-CACTCAGGATGCCATAGCCCAGAT
38818750 ATGGTCTTACAC
1 ATGGTCTTACAC
38818762 ATATACTCCC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
32 2 0.05
33 32 0.84
34 4 0.11
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (33 bp):
ATGGTCTTACACTCAGGATGCCATAGCCCAGAT
Found at i:38820433 original size:32 final size:32
Alignment explanation
Indices: 38820375--38820447 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
38820365 CTTTATATAC
*
38820375 TAATAAAATAATAATATATCTTATTAAA-ATAT
1 TAATAAAATAATAATATATCTAATTAAATA-AT
*
38820407 TAATAAAATAAT-ATTTAATCTAATTAAATAAT
1 TAATAAAATAATAATAT-ATCTAATTAAATAAT
38820439 T-ATAAAATA
1 TAATAAAATA
38820448 TCAAAATATC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
31 11 0.30
32 25 0.68
33 1 0.03
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.40
Consensus pattern (32 bp):
TAATAAAATAATAATATATCTAATTAAATAAT
Found at i:38821452 original size:27 final size:27
Alignment explanation
Indices: 38821422--38821491 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
38821412 TTGACCAAAG
38821422 TTACCAAAATACCCCTAGTTTGTAAAA
1 TTACCAAAATACCCCTAGTTTGTAAAA
* *
38821449 TTACCAAAATACCCTTGGTTTGTAAAA
1 TTACCAAAATACCCCTAGTTTGTAAAA
*
38821476 TTACGAAAATACCCCT
1 TTACCAAAATACCCCT
38821492 GTAGGGTAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.30
Consensus pattern (27 bp):
TTACCAAAATACCCCTAGTTTGTAAAA
Found at i:38821803 original size:27 final size:27
Alignment explanation
Indices: 38821474--38821803 Score: 376
Period size: 27 Copynumber: 12.3 Consensus size: 27
38821464 TGGTTTGTAA
38821474 AATTA-CGAAAATACCCCTGTAGGGTAG
1 AATTACCG-AAATACCCCTGTAGGGTAG
* *
38821501 AATTACTGAAATACCCATGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
38821528 AATTACTGAAATACCCCTATAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
38821555 AATTATCGAAATA-CCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * * *
38821581 AATTACTAAAATACTCCTATAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
38821608 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
38821635 AATTACTAAAATACCCCTATAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
38821662 AATTACTGAAATGCCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
38821689 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
38821716 AATTACTGAAATACCCTTGTACGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
38821743 AAATATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * * *
38821770 AATTACCGAGATAACCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
38821797 AATTACC
1 AATTACC
38821804 ATTCTGCCTC
Statistics
Matches: 258, Mismatches: 43, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
26 21 0.08
27 236 0.91
28 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:38837490 original size:25 final size:25
Alignment explanation
Indices: 38837456--38837508 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
38837446 ATCTTGTCAC
*
38837456 ATGGTTTCTTCGCTTGACAATCTCA
1 ATGGTTTCTTCACTTGACAATCTCA
*
38837481 ATGGTTTCTTTACTTGACAATCTCA
1 ATGGTTTCTTCACTTGACAATCTCA
38837506 ATG
1 ATG
38837509 TAGCATACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.42
Consensus pattern (25 bp):
ATGGTTTCTTCACTTGACAATCTCA
Found at i:38839328 original size:18 final size:17
Alignment explanation
Indices: 38839300--38839333 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
38839290 GACCTTAGCC
38839300 CATTACAGAATAAGAAA
1 CATTACAGAATAAGAAA
*
38839317 CATTATCAGAATTAGAA
1 CATTA-CAGAATAAGAA
38839334 CCAAAATGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (17 bp):
CATTACAGAATAAGAAA
Found at i:38839351 original size:6 final size:6
Alignment explanation
Indices: 38839321--38839450 Score: 81
Period size: 6 Copynumber: 21.3 Consensus size: 6
38839311 AAGAAACATT
* * * *
38839321 ATCAGA ATTAGA ACCAAA ATGAGA ATCAGA ATCAGA ATCAGTA A-CAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAG-A ATCAGA
* * *
38839369 ATCAGA ATCAGA ATCA-A TATTAGTA A-CAGA ATCAGA ATTACGTG A-CAGA
1 ATCAGA ATCAGA ATCAGA -ATCAG-A ATCAGA ATCAGA ATCA-G-A ATCAGA
* *
38839418 ATCAGA ATTACGTG A-CAGA ATCAGA ATCAGA AT
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
38839451 GTGAATGCAA
Statistics
Matches: 94, Mismatches: 18, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
5 7 0.07
6 77 0.82
7 7 0.07
8 3 0.03
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:38839369 original size:24 final size:24
Alignment explanation
Indices: 38839342--38839425 Score: 98
Period size: 24 Copynumber: 3.5 Consensus size: 24
38839332 AACCAAAATG
38839342 AGAATCAGAATCAGAATCAGTAAC
1 AGAATCAGAATCAGAATCAGTAAC
* **
38839366 AGAATCAGAATCAGAATCAATATT
1 AGAATCAGAATCAGAATCAGTAAC
* *
38839390 AGTAA-CAGAATCAGAATTACGTGAC
1 AG-AATCAGAATCAGAATCA-GTAAC
38839415 AGAATCAGAAT
1 AGAATCAGAAT
38839426 TACGTGACAG
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
24 38 0.78
25 11 0.22
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (24 bp):
AGAATCAGAATCAGAATCAGTAAC
Found at i:38839394 original size:30 final size:30
Alignment explanation
Indices: 38839342--38839406 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
38839332 AACCAAAATG
38839342 AGAATCAGAATCAGAATCAGTAACAGAATC
1 AGAATCAGAATCAGAATCAGTAACAGAATC
*
38839372 AGAATCAGAATCA-ATATTAGTAACAGAATC
1 AGAATCAGAATCAGA-ATCAGTAACAGAATC
38839402 AGAAT
1 AGAAT
38839407 TACGTGACAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 32 0.97
ACGTcount: A:0.51, C:0.14, G:0.15, T:0.20
Consensus pattern (30 bp):
AGAATCAGAATCAGAATCAGTAACAGAATC
Found at i:38839418 original size:19 final size:19
Alignment explanation
Indices: 38839377--38839444 Score: 104
Period size: 19 Copynumber: 3.6 Consensus size: 19
38839367 GAATCAGAAT
*
38839377 CAGAATCA-ATATTA-GTAA
1 CAGAATCAGA-ATTACGTGA
38839395 CAGAATCAGAATTACGTGA
1 CAGAATCAGAATTACGTGA
38839414 CAGAATCAGAATTACGTGA
1 CAGAATCAGAATTACGTGA
38839433 CAGAATCAGAAT
1 CAGAATCAGAAT
38839445 CAGAATGTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
18 12 0.26
19 35 0.74
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.22
Consensus pattern (19 bp):
CAGAATCAGAATTACGTGA
Found at i:38839638 original size:27 final size:27
Alignment explanation
Indices: 38839567--38839641 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
38839557 CAGCATGGCT
* **
38839567 ACCAGAAT-AGAT-ATCGTGACAGATTC
1 ACCAGAATCAGATAAT-GTGGCAGAGCC
*
38839593 ACCAG-ATACAGATATTGTGGCAGAGCC
1 ACCAGAAT-CAGATAATGTGGCAGAGCC
38839620 ACCAGAATCAGATAATGTGGCA
1 ACCAGAATCAGATAATGTGGCA
38839642 AACCCACCTA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
25 2 0.05
26 5 0.12
27 30 0.75
28 3 0.08
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (27 bp):
ACCAGAATCAGATAATGTGGCAGAGCC
Found at i:38839648 original size:27 final size:27
Alignment explanation
Indices: 38839592--38839649 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
38839582 GTGACAGATT
* * *
38839592 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAACC
38839619 CACCAGA-ATCAGATAATGTGGCAAACC
1 CACCAGATA-CAGATAATGTGGCAAACC
38839646 CACC
1 CACC
38839650 TAACAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAACC
Found at i:38839854 original size:22 final size:22
Alignment explanation
Indices: 38839806--38839864 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
38839796 GTAAATACGT
*
38839806 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
38839828 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
38839850 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
38839865 TAATAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:38840031 original size:27 final size:26
Alignment explanation
Indices: 38839952--38840034 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
38839942 TCGATCGGTC
* * *
38839952 AACAGATATTGTGACAGAGTCACCAA
1 AACAGATATTGTGGCAGAGCCACCAG
38839978 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
38840005 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
38840032 AAC
1 AAC
38840035 GCTTCCTCCG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 8 0.16
27 43 0.84
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:38840263 original size:27 final size:27
Alignment explanation
Indices: 38840233--38840401 Score: 212
Period size: 27 Copynumber: 6.3 Consensus size: 27
38840223 GGGGCAAAAT
* * *
38840233 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
38840260 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
38840287 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
38840314 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
38840341 GGTAATTCTATCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
38840368 GGAAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
38840395 AGTAATT
1 GGTAATT
38840402 TCACAATCAA
Statistics
Matches: 122, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 122 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:38840436 original size:27 final size:27
Alignment explanation
Indices: 38840406--38840761 Score: 475
Period size: 27 Copynumber: 13.2 Consensus size: 27
38840396 GTAATTTCAC
*
38840406 AATCAAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
38840433 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
38840460 AA-CTGAGGGTAAACCAGTAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* * **
38840487 AATCAAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
38840514 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
38840541 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
38840568 AA-CTGAGGGTAAAATGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
** *
38840595 AATCGAGGGTAAAATAGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
38840622 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
*
38840649 AATCGAGGGTAAAACGTTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* **
38840676 AATCGAGGGTAAAACGGTAATTTTAAA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
38840703 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
38840730 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
38840757 AATCG
1 AATCG
38840762 GGAGTACTTT
Statistics
Matches: 288, Mismatches: 35, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
26 3 0.01
27 282 0.98
28 3 0.01
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:38844796 original size:24 final size:24
Alignment explanation
Indices: 38844746--38844799 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
38844736 AATCGAATTT
*
38844746 GCACACATAGTGCTCGTGACACTC
1 GCACACATAGTGCTAGTGACACTC
38844770 GCACACATAGTGCCATAGT-ACAC-C
1 GCACACATAGTG-C-TAGTGACACTC
38844794 GCACAC
1 GCACAC
38844800 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 19 0.70
25 5 0.19
26 3 0.11
ACGTcount: A:0.30, C:0.35, G:0.19, T:0.17
Consensus pattern (24 bp):
GCACACATAGTGCTAGTGACACTC
Found at i:38850611 original size:6 final size:6
Alignment explanation
Indices: 38850577--38850628 Score: 61
Period size: 6 Copynumber: 8.5 Consensus size: 6
38850567 AATAAAGTTC
* *
38850577 AAAATA GAAAA-A CAAAATA AACATG AAAATA AAAATA AAAATA AAAATA
1 AAAATA -AAAATA -AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
38850626 AAA
1 AAA
38850629 TAATTGGACT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
6 34 0.87
7 5 0.13
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.13
Consensus pattern (6 bp):
AAAATA
Found at i:38852027 original size:24 final size:24
Alignment explanation
Indices: 38852000--38852054 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
38851990 AATAATGACC
38852000 AATAAGACTAGAAAGAAACATATT
1 AATAAGACTAGAAAGAAACATATT
38852024 AATAAGACTAGAAAGAAACATATT
1 AATAAGACTAGAAAGAAACATATT
*
38852048 AACAAGA
1 AATAAGA
38852055 AAAGTTAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.60, C:0.09, G:0.13, T:0.18
Consensus pattern (24 bp):
AATAAGACTAGAAAGAAACATATT
Found at i:38852358 original size:17 final size:17
Alignment explanation
Indices: 38852293--38852358 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 17
38852283 AAATAAACTC
*
38852293 ATAATAATGACTAAAA-A
1 ATAATAA-GAATAAAATA
38852310 ATAATAAGAA-AACAATA
1 ATAATAAGAATAA-AATA
38852327 ATAATAAGGGAATAAAATA
1 ATAATAA--GAATAAAATA
*
38852346 ATACTAAGAATAA
1 ATAATAAGAATAA
38852359 TGATAAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
15 2 0.05
16 4 0.10
17 21 0.50
19 13 0.31
20 2 0.05
ACGTcount: A:0.65, C:0.05, G:0.09, T:0.21
Consensus pattern (17 bp):
ATAATAAGAATAAAATA
Found at i:38856177 original size:27 final size:27
Alignment explanation
Indices: 38856138--38856315 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
38856128 ATATTGAGTC
* * *
38856138 CGCACACTCAGTGCTATATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* * *
38856165 CACACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38856192 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
38856220 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
38856247 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
38856274 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38856301 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38856316 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:38878064 original size:28 final size:28
Alignment explanation
Indices: 38878001--38878154 Score: 229
Period size: 28 Copynumber: 5.5 Consensus size: 28
38877991 ATATTAAGTC
*
38878001 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
38878028 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
38878056 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
38878084 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
38878112 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
38878141 CGCACACTTAGTGC
1 CGCACACTTAGTGC
38878155 CAATCTCATG
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 21 0.18
28 76 0.66
29 19 0.16
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:38879866 original size:47 final size:47
Alignment explanation
Indices: 38879799--38880112 Score: 452
Period size: 47 Copynumber: 6.6 Consensus size: 47
38879789 GGTTGTCACA
*
38879799 ATGAATGTGAAAGTGTATATATATGTGATAA-GCCTAATGGACGATGTG
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTG
*
38879847 ATGAATGTG-AAGTGTATATATGTGATAAGGCCTAATAGCCGATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
* *
38879893 ATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
38879940 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTG
* *
38879989 ATTAATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
* * * * * *
38880036 ATGAATGTGAAAGTGTATATATGTGACAGGGCCGAATGGCCAACGTT
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
* *
38880083 ATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGAATGTGAAAGTGTATATATGTGATAAG
38880113 TCCCGAAGGG
Statistics
Matches: 241, Mismatches: 21, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
45 14 0.06
46 24 0.10
47 150 0.62
48 9 0.04
49 44 0.18
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
Found at i:38879986 original size:96 final size:94
Alignment explanation
Indices: 38879799--38880112 Score: 452
Period size: 96 Copynumber: 3.3 Consensus size: 94
38879789 GGTTGTCACA
*
38879799 ATGAATGTGAAAGTGTATATATATGTGATAA-GCCTAATGGACGATGTGATGAATGTG-AAGTGT
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
*
38879862 ATATATGTGATAAGGCCTAATAGCCGATGTG
64 ATATATGTGATAAGGCCTAATGGCCGATGTG
* *
38879893 ATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTAT
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
38879958 ATATATGTGATAAGGCCTAATGGCCGATGTG
64 ATATATGTGATAAGGCCTAATGGCCGATGTG
* *
38879989 ATTAATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* * * * * *
38880054 ATATGTGACAGGGCCGAATGGCCAACGTT
66 ATATGTGATAAGGCCTAATGGCCGATGTG
* *
38880083 ATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGAATGTGAAAGTGTATATATGTGATAAG
38880113 TCCCGAAGGG
Statistics
Matches: 198, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
92 14 0.07
93 23 0.12
94 72 0.36
96 89 0.45
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (94 bp):
ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
ATATGTGATAAGGCCTAATGGCCGATGTG
Found at i:38880055 original size:143 final size:142
Alignment explanation
Indices: 38879799--38880112 Score: 517
Period size: 143 Copynumber: 2.2 Consensus size: 142
38879789 GGTTGTCACA
38879799 ATGAATGTGAAAGTGTATATATATGTGATAA-GCCTAATGGACGATGTGATGAATGTGAAGTGTA
1 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGACGATGTGATGAATGTGAAGTGTA
*
38879863 TATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGA
66 TATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGA
*
38879928 ATGGCCAATGTG
131 ATGGCCAACGTG
* *
38879940 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATTAATGTGAAAGTGT
1 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGACGATGTGATGAATGTG-AAGTGT
* * *
38880005 ATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCG
65 ATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCG
*
38880070 AATGGCCAACGTT
130 AATGGCCAACGTG
*
38880083 ATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 ATGAATGTGAAAGTGTATATATATGTGATAAG
38880113 TCCCGAAGGG
Statistics
Matches: 162, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
141 41 0.25
142 25 0.15
143 96 0.59
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (142 bp):
ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGACGATGTGATGAATGTGAAGTGTA
TATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGA
ATGGCCAACGTG
Found at i:38884274 original size:46 final size:46
Alignment explanation
Indices: 38884202--38884289 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
38884192 CATTGGGTGG
* *
38884202 TATGCGAGCCAGTGTAACACATGTCTGGCACATGCATGGGCCATGT
1 TATGAGAGCCAGTGTAACACATGTCTGGCACATGCATCGGCCATGT
* *
38884248 TATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCC
1 TATGAGAGCCAGTGTAACACATGTCTGGCACATGCATCGGCC
38884290 TCAGGATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (46 bp):
TATGAGAGCCAGTGTAACACATGTCTGGCACATGCATCGGCCATGT
Found at i:38902325 original size:49 final size:47
Alignment explanation
Indices: 38902204--38902333 Score: 145
Period size: 49 Copynumber: 2.7 Consensus size: 47
38902194 CAAGATATAC
*
38902204 AAGCTAGTGTAAGACCTGTCTGGGACATGGCATCAACACAATAAGTG
1 AAGCCAGTGTAAGACCTGTCTGGGACATGGCATCAACACAATAAGTG
* * * * *
38902251 AGAGCCAGTGAAAGACTTGTCTGGGACATGGCATCAACCTCGATGTA-TGG
1 A-AGCCAGTGTAAGACCTGTCTGGGACATGGCATCAA-CACAAT-AAGT-G
* *
38902301 AAGCCAGTGTAAGACCTGCCTGGGACATCGCAT
1 AAGCCAGTGTAAGACCTGTCTGGGACATGGCAT
38902334 TGACTTGCAT
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
47 1 0.01
48 32 0.46
49 33 0.48
50 3 0.04
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.21
Consensus pattern (47 bp):
AAGCCAGTGTAAGACCTGTCTGGGACATGGCATCAACACAATAAGTG
Found at i:38903527 original size:28 final size:29
Alignment explanation
Indices: 38903487--38903541 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
38903477 CACGAGCTAA
38903487 GACACAGGCGTGT-C-ATGGCCGTGTGAGG
1 GACACAGGCGTGTGCTA-GGCCGTGTGAGG
*
38903515 GACACGGGCGTGTGCTAGGCCGTGTGA
1 GACACAGGCGTGTGCTAGGCCGTGTGA
38903542 AAACCCCTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 12 0.50
29 11 0.46
30 1 0.04
ACGTcount: A:0.16, C:0.22, G:0.44, T:0.18
Consensus pattern (29 bp):
GACACAGGCGTGTGCTAGGCCGTGTGAGG
Found at i:38908027 original size:27 final size:27
Alignment explanation
Indices: 38907987--38908068 Score: 137
Period size: 27 Copynumber: 3.0 Consensus size: 27
38907977 CTTTAACATA
*
38907987 CCCTTTTGGAACTACCATCAAATCATT
1 CCCTTTTGGGACTACCATCAAATCATT
*
38908014 CCCTTTCGGGACTACCATCAAATCATT
1 CCCTTTTGGGACTACCATCAAATCATT
*
38908041 CCATTTTGGGACTACCATCAAATCATT
1 CCCTTTTGGGACTACCATCAAATCATT
38908068 C
1 C
38908069 TTTGAACTAC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (27 bp):
CCCTTTTGGGACTACCATCAAATCATT
Found at i:38911207 original size:93 final size:93
Alignment explanation
Indices: 38911048--38911219 Score: 238
Period size: 93 Copynumber: 1.8 Consensus size: 93
38911038 CGCCCCTAAG
* * *
38911048 TGAACTCGGACTCAACTCAACGAGCTCAGCCGTTCGCATAAATAAATGAGCTCGGACTCAACTCA
1 TGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATAAATAAATGAACTCGGACTCAACTCA
**
38911113 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAACTCGGATGCCTAGTTACATCTCA
* * ** *
38911141 TGAACTCGGACTCAACTCAACGAGTTC-GAACATTTGCATCCATAAGTGAACTCGGACTCAACTC
1 TGAACTCGGACTCAACTCAACGAGCTCAG-ACATTCGCATAAATAAATGAACTCGGACTCAACTC
38911205 AACGAACTCGGATGC
65 AACGAACTCGGATGC
38911220 TCAACCATCC
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
92 1 0.01
93 67 0.99
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (93 bp):
TGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATAAATAAATGAACTCGGACTCAACTCA
ACGAACTCGGATGCCTAGTTACATCTCA
Found at i:38911208 original size:46 final size:46
Alignment explanation
Indices: 38911044--38911209 Score: 169
Period size: 46 Copynumber: 3.6 Consensus size: 46
38911034 AACCCGCCCC
* * * *
38911044 TAAGTGAACTCGGACTCAACTCAACGAGCTC-AGCCGTTCGCATAAA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGAGCCATTTGCAT-CA
* * * *
38911090 TAAATGAGCTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATC-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-GA-GCC-ATTTGCATCA
* *
38911138 TCA-TGAACTCGGACTCAACTCAACGAGTTCGA-ACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGAGCCATTTGCAT-CA
38911183 TAAGTGAACTCGGACTCAACTCAACGA
1 TAAGTGAACTCGGACTCAACTCAACGA
38911210 ACTCGGATGC
Statistics
Matches: 99, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 53 0.54
47 26 0.26
48 3 0.03
49 3 0.03
50 4 0.04
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGAGCCATTTGCATCA
Found at i:38917878 original size:43 final size:43
Alignment explanation
Indices: 38917817--38917903 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
38917807 AAATTACATG
* *
38917817 TGTCACGTACATCATGAACTCAGACCAACTCAATGAGCTCAGA
1 TGTCACATACATCATGAACTCAAACCAACTCAATGAGCTCAGA
* *
38917860 TGTCACATATATCATGAACTCAAACCAACTCAATGAGTTCAGA
1 TGTCACATACATCATGAACTCAAACCAACTCAATGAGCTCAGA
38917903 T
1 T
38917904 TATATAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (43 bp):
TGTCACATACATCATGAACTCAAACCAACTCAATGAGCTCAGA
Found at i:38926494 original size:15 final size:14
Alignment explanation
Indices: 38926444--38926495 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
38926434 TAAATCGATT
38926444 TTAAATTAATATAA
1 TTAAATTAATATAA
*
38926458 -TAAGATT-TTATAA
1 TTAA-ATTAATATAA
38926471 GTTAAATTAATATAA
1 -TTAAATTAATATAA
38926486 TTAATATTAA
1 TTAA-ATTAA
38926496 AATTTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
13 8 0.26
14 10 0.32
15 13 0.42
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
TTAAATTAATATAA
Found at i:38926503 original size:28 final size:29
Alignment explanation
Indices: 38926441--38926507 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 29
38926431 ACTTAAATCG
* *
38926441 ATTTTAAATTAATATAATAAGATTTTATA
1 ATTTTAAATTAATATAATAAGATATTAAA
* *
38926470 A-GTTAAATTAATATAATTA-ATATTAAA
1 ATTTTAAATTAATATAATAAGATATTAAA
38926497 ATTTTAAATTA
1 ATTTTAAATTA
38926508 TTCACCCTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
27 7 0.22
28 24 0.75
29 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (29 bp):
ATTTTAAATTAATATAATAAGATATTAAA
Found at i:38931317 original size:27 final size:27
Alignment explanation
Indices: 38931287--38931464 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
38931277 ATATTGAGTC
* * * *
38931287 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
38931314 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38931341 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
38931369 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
38931396 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
38931423 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38931450 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38931465 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:38931426 original size:82 final size:81
Alignment explanation
Indices: 38931308--38931463 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
38931298 TGCTATATAA
* *
38931308 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
38931373 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
38931390 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
38931454 CACTTAGTGC
65 CACTTAGTGC
38931464 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:38931963 original size:12 final size:12
Alignment explanation
Indices: 38931946--38931971 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
38931936 ATGGCATACT
38931946 TATGTATATATA
1 TATGTATATATA
38931958 TATGTATATATA
1 TATGTATATATA
38931970 TA
1 TA
38931972 CTTCGGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:38939419 original size:27 final size:27
Alignment explanation
Indices: 38939389--38939565 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
38939379 ATATTGAGTC
* * *
38939389 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
38939416 CGCACACTTAGTGCTACGTAATCAA-T
1 CGCACACTTAGTGCTACATAGTCAACT
38939442 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
** * *
38939470 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
38939497 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
38939524 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
38939551 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38939566 GTACAATTTA
Statistics
Matches: 129, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
26 22 0.17
27 85 0.66
28 22 0.17
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:38939501 original size:81 final size:81
Alignment explanation
Indices: 38939410--38939564 Score: 233
Period size: 81 Copynumber: 1.9 Consensus size: 81
38939400 TGCTATATAA
* *
38939410 TCAACTCGCACACTTAGTGC-TACGTAATCA-ATCGCACACTTAGTGCTACATAGTCAAACTCGC
1 TCAACTCGCACACTTAGTGCAT-CATAATCATATCGCACACTTAGTGCAACATAGTCAAA-TCGC
38939473 ACACTTAGTGCCGCATGG
64 ACACTTAGTGCCGCATGG
* * *
38939491 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCAC
1 TCAACTCGCACACTTAGTGCATCATAATCATATCGCACACTTAGTGCAACATAGTCAAATCGCAC
38939556 ACTTAGTGC
66 ACTTAGTGC
38939565 TGTACAATTT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
81 40 0.60
82 27 0.40
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCATCATAATCATATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:38940055 original size:12 final size:12
Alignment explanation
Indices: 38940038--38940063 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
38940028 ATGGCATACT
38940038 TATGTATATATA
1 TATGTATATATA
38940050 TATGTATATATA
1 TATGTATATATA
38940062 TA
1 TA
38940064 CTTCGGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:38945374 original size:38 final size:38
Alignment explanation
Indices: 38945324--38945400 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
38945314 GATGATTAAC
38945324 ATATATTAGACTAAATGCAATGATCCTTAATGCAAATT
1 ATATATTAGACTAAATGCAATGATCCTTAATGCAAATT
38945362 ATATATTAGACTAAATGCAATGATCCTTAATGCAAATT
1 ATATATTAGACTAAATGCAATGATCCTTAATGCAAATT
38945400 A
1 A
38945401 ACCTAAGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (38 bp):
ATATATTAGACTAAATGCAATGATCCTTAATGCAAATT
Found at i:38950512 original size:40 final size:40
Alignment explanation
Indices: 38950435--38950578 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 40
38950425 TACTCGAATG
* *
38950435 ATATCC-GGCTAAGTCCCGAAAGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
38950475 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
38950515 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
38950555 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
38950579 CTTGTGCGAG
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
39 1 0.01
40 67 0.74
41 21 0.23
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:38964031 original size:36 final size:36
Alignment explanation
Indices: 38963979--38964048 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
38963969 AATTGAAGAT
* *
38963979 GTGCTAGTAAGGGTAGATAAATTTGTTTTTCCTAAC
1 GTGCTAGTAAGAGTAGATAAATTTATTTTTCCTAAC
38964015 GTGCTAGTAAGAGTAGATAAATTTATTTTTCCTA
1 GTGCTAGTAAGAGTAGATAAATTTATTTTTCCTA
38964049 TAGATTTCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (36 bp):
GTGCTAGTAAGAGTAGATAAATTTATTTTTCCTAAC
Found at i:38966329 original size:40 final size:40
Alignment explanation
Indices: 38966274--38966356 Score: 121
Period size: 40 Copynumber: 2.1 Consensus size: 40
38966264 TGATGACATA
*
38966274 TTGGCTAAAAATGGCACATAGTGTGTGGTTCGGAATAGCT
1 TTGGCTAAAAATGGCACATAGTGTGCGGTTCGGAATAGCT
** * *
38966314 TTGGCTAAATTTGGCACTTAGTGTGCGGTTCGGTATAGCT
1 TTGGCTAAAAATGGCACATAGTGTGCGGTTCGGAATAGCT
38966354 TTG
1 TTG
38966357 ACATATTAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.35
Consensus pattern (40 bp):
TTGGCTAAAAATGGCACATAGTGTGCGGTTCGGAATAGCT
Found at i:38970012 original size:27 final size:27
Alignment explanation
Indices: 38969982--38970158 Score: 176
Period size: 27 Copynumber: 6.5 Consensus size: 27
38969972 TATTGAGTCT
* *
38969982 GCACACTCAGTGCTATATAATCAACTC
1 GCACACTTAGTGCTACATAATCAACTC
* *
38970009 GCACACTTAGTGCTACGTAATCAAATC
1 GCACACTTAGTGCTACATAATCAACTC
*
38970036 GCACACTTAGTGCTACATAGTCAAACTC
1 GCACACTTAGTGCTACATAATC-AACTC
** ** *
38970064 GCACACTTAGTGCCGCATGGTCAATTC
1 GCACACTTAGTGCTACATAATCAACTC
* ***
38970091 GCACACTTAGTGC-ATCATATTCGTTTC
1 GCACACTTAGTGCTA-CATAATCAACTC
* * *
38970118 GCACACTTAGTGCAACATAGTCAAATC
1 GCACACTTAGTGCTACATAATCAACTC
38970145 GCACACTTAGTGCT
1 GCACACTTAGTGCT
38970159 GTACAATTTA
Statistics
Matches: 126, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 102 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
GCACACTTAGTGCTACATAATCAACTC
Found at i:38974144 original size:98 final size:98
Alignment explanation
Indices: 38973972--38974397 Score: 248
Period size: 98 Copynumber: 4.4 Consensus size: 98
38973962 TAAAATGCTT
* * * * *
38973972 ATGCCATGTCCCGGACATGGTCTTATACTGGCTCCCATACATCGGTGTCGATGCCATGTTCCAAA
1 ATGCCATGTCCCGAACATGGTCTTACACTGGCTCCCATACATCAGTGCCAATGCCATGTTCCAAA
*
38974037 CATGGTCTTACACTAGCTTACATGTCGAGGCCG
66 CATGATCTTACACTAGCTTACATGTCGAGGCCG
* * * * * **
38974070 ATGCCATGTCCCGAACATGGTGTTGCACTGGCTCTCATACATTAGTGCCAATTCCATG-TCCTTG
1 ATGCCATGTCCCGAACATGGTCTTACACTGGCTCCCATACATCAGTGCCAATGCCATGTTCC-AA
* * *
38974134 ACATGATCTTACACT-GAC--ACATATAACAATGCCG
65 ACATGATCTTACACTAG-CTTACATGT--CGAGGCCG
* * * * * * * *
38974168 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCGCATA-TTGAG-GTCAATGCCATGTCCCAGA
1 ATGCCATGTCCCGAACATGGTCTTACACTGGCTCCCATACATCAGTGCCAATGCCATGTTCCAAA
* * * * ** * ** *
38974231 CATGGTCTTACATTGGCTCACATAACAATACCA
66 CATGATCTTACACTAGCTTACATGTCGAGGCCG
* * * ** * * * * *
38974264 ATGCCATGTTCCAAACATGGTCTTAAACTGGCTCTTTATAC-T-GGTGTCGATTCCAAG-TCTCA
1 ATGCCATGTCCCGAACATGGTCTTACACTGGCTC-CCATACATCAGTGCCAATGCCATGTTC-CA
** * *
38974326 AACATGGCCTTACGCT-GAC--ACATATCGAGGCCG
64 AACATGATCTTACACTAG-CTTACATGTCGAGGCCG
*
38974359 ATGCCATGTCCC-AGACATGGTCTTACACTGGCTCTCATA
1 ATGCCATGTCCCGA-ACATGGTCTTACACTGGCTCCCATA
38974398 TCGCCATGGT
Statistics
Matches: 262, Mismatches: 52, Indels: 32
0.76 0.15 0.09
Matches are distributed among these distances:
94 5 0.02
95 39 0.15
96 72 0.27
97 38 0.15
98 108 0.41
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (98 bp):
ATGCCATGTCCCGAACATGGTCTTACACTGGCTCCCATACATCAGTGCCAATGCCATGTTCCAAA
CATGATCTTACACTAGCTTACATGTCGAGGCCG
Found at i:38974186 original size:48 final size:48
Alignment explanation
Indices: 38973972--38974297 Score: 224
Period size: 48 Copynumber: 6.7 Consensus size: 48
38973962 TAAAATGCTT
* ** * * ** * *
38973972 ATGCCATGTCCCGGACATGGTCTTATACTGGCTCCCATACATCGGTGTCG
1 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATA-A-CAATGCCA
* * ** * * *
38974022 ATGCCATGTTCCAAACATGGTCTTACACTAGCTTACATGTCGAGGCCG
1 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATAACAATGCCA
* * * * *
38974070 ATGCCATGTCCCGAACATGGTGTTGCACTGGCTCTCAT-ACATTAGTGCCA
1 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATAACA--A-TGCCA
* ** * * * * *
38974120 ATTCCATG-TCCTTGACATGATCTTACACTGACACATATAACAATGCCG
1 ATGCCATGTTCC-AAACATGGTCTTACACTGGCTCACATAACAATGCCA
* *** * *
38974168 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCGCATATTGAGGTCA
1 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATAACAATGCCA
* * * *
38974216 ATGCCATGTCCCAGACATGGTCTTACATTGGCTCACATAACAATACCA
1 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATAACAATGCCA
*
38974264 ATGCCATGTTCCAAACATGGTCTTAAACTGGCTC
1 ATGCCATGTTCCAAACATGGTCTTACACTGGCTC
38974298 TTTATACTGG
Statistics
Matches: 207, Mismatches: 63, Indels: 14
0.73 0.22 0.05
Matches are distributed among these distances:
47 1 0.00
48 138 0.67
49 7 0.03
50 58 0.28
51 3 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (48 bp):
ATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATAACAATGCCA
Found at i:38976202 original size:26 final size:27
Alignment explanation
Indices: 38976159--38976217 Score: 93
Period size: 26 Copynumber: 2.2 Consensus size: 27
38976149 ACATATTTTC
* *
38976159 TCAAAATTATTACTAAGGGTAAAATGA
1 TCAAAATTATTACCAAGGGTAAAATCA
38976186 TCAAAATT-TTACCAAGGGTAAAATCA
1 TCAAAATTATTACCAAGGGTAAAATCA
38976212 TCAAAA
1 TCAAAA
38976218 GGCCGAGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 22 0.73
27 8 0.27
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (27 bp):
TCAAAATTATTACCAAGGGTAAAATCA
Found at i:38978056 original size:43 final size:43
Alignment explanation
Indices: 38978009--38978097 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
38977999 CTCGATGAGA
*
38978009 TTGTCCCACGATGACTCATTTGTGATGCATGATGTAATAGGTG
1 TTGTCCCACGATGACTCATTTGTGATGCATCATGTAATAGGTG
38978052 TTGTCCCACGATGACTCATTTGTGATGCATCATGTAATAGGTG
1 TTGTCCCACGATGACTCATTTGTGATGCATCATGTAATAGGTG
38978095 TTG
1 TTG
38978098 AGTTGATGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (43 bp):
TTGTCCCACGATGACTCATTTGTGATGCATCATGTAATAGGTG
Found at i:38979690 original size:17 final size:18
Alignment explanation
Indices: 38979648--38979682 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
38979638 ATTTGGCCAT
38979648 ATGGG-CCGAATGGGCTAA
1 ATGGGCCCG-ATGGGCTAA
38979666 ATGGGCCCGATGGGCTA
1 ATGGGCCCGATGGGCTA
38979683 TTGGGCCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.23, C:0.20, G:0.40, T:0.17
Consensus pattern (18 bp):
ATGGGCCCGATGGGCTAA
Found at i:38979804 original size:29 final size:29
Alignment explanation
Indices: 38979762--38979838 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
38979752 TGAATATGGC
* * *
38979762 TGGGCCTAACGGGCCATGTAAATGTGATT
1 TGGGCCTAATGGGCCATATAAAGGTGATT
* *
38979791 TGGGACTAATGGGCCATATACAGGTGATT
1 TGGGCCTAATGGGCCATATAAAGGTGATT
38979820 TGGGCCTAATGGGCCATAT
1 TGGGCCTAATGGGCCATAT
38979839 GAATATGATT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAAGGTGATT
Found at i:38979847 original size:29 final size:29
Alignment explanation
Indices: 38979749--38979852 Score: 97
Period size: 29 Copynumber: 3.7 Consensus size: 29
38979739 GTGAGCACAA
** *
38979749 ATATGAATATG-GCTGGGCCTAACGGGCC
1 ATATGAATATGATTTGGGCCTAATGGGCC
* * * *
38979777 ATGTAAATGTGATTTGGGACTAATGGGCC
1 ATATGAATATGATTTGGGCCTAATGGGCC
**
38979806 ATAT-ACAGGTGATTTGGGCCTAATGGGCC
1 ATATGA-ATATGATTTGGGCCTAATGGGCC
38979835 ATATGAATATGA-TTGGGC
1 ATATGAATATGATTTGGGC
38979853 TTAGTGGACT
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
28 15 0.25
29 45 0.74
30 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.28
Consensus pattern (29 bp):
ATATGAATATGATTTGGGCCTAATGGGCC
Found at i:38993276 original size:16 final size:16
Alignment explanation
Indices: 38993255--38993298 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
38993245 ATGTATCAGC
*
38993255 AAAAGCCAAAATACCG
1 AAAAGCCAAAAAACCG
*
38993271 AAAAGCTAAAAAACCG
1 AAAAGCCAAAAAACCG
*
38993287 AAATGCCAAAAA
1 AAAAGCCAAAAA
38993299 GCTAAAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.61, C:0.20, G:0.11, T:0.07
Consensus pattern (16 bp):
AAAAGCCAAAAAACCG
Found at i:38995588 original size:28 final size:28
Alignment explanation
Indices: 38995557--38995713 Score: 136
Period size: 28 Copynumber: 5.5 Consensus size: 28
38995547 CTGACTGATT
*
38995557 TCGCACACATAGCGCTCAATTAAAGAAC
1 TCGCACACATAGTGCTCAATTAAAGAAC
* *
38995585 TCGCACACATAGTGACTCAATTACCA-ATC
1 TCGCACACATAGTG-CTCAATTA-AAGAAC
* *
38995614 TCGCACACATAGTGCTCGATTGAAGAAC
1 TCGCACACATAGTGCTCAATTAAAGAAC
* ** *
38995642 TCGCACACATAGTGCCTCAACTACTGATC
1 TCGCACACATAGTG-CTCAATTAAAGAAC
* * ** *
38995671 TGGCACACATAGTACTCGGTTGAAGAAC
1 TCGCACACATAGTGCTCAATTAAAGAAC
* *
38995699 TTGCACACACAGTGC
1 TCGCACACATAGTGC
38995714 CTCATAACTC
Statistics
Matches: 100, Mismatches: 25, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
27 1 0.01
28 54 0.54
29 44 0.44
30 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (28 bp):
TCGCACACATAGTGCTCAATTAAAGAAC
Found at i:38995616 original size:29 final size:28
Alignment explanation
Indices: 38995557--38995683 Score: 116
Period size: 29 Copynumber: 4.5 Consensus size: 28
38995547 CTGACTGATT
* *
38995557 TCGCACACATAGCGCTCAATTA-AAGAAC
1 TCGCACACATAGTGCTCAATTACAA-ATC
*
38995585 TCGCACACATAGTGACTCAATTACCAATC
1 TCGCACACATAGTG-CTCAATTACAAATC
*
38995614 TCGCACACATAGTGCTCGATTGA-AGAA-C
1 TCGCACACATAGTGCTCAATT-ACA-AATC
* **
38995642 TCGCACACATAGTGCCTCAACTACTGATC
1 TCGCACACATAGTG-CTCAATTACAAATC
*
38995671 TGGCACACATAGT
1 TCGCACACATAGT
38995684 ACTCGGTTGA
Statistics
Matches: 82, Mismatches: 10, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
28 36 0.44
29 45 0.55
30 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (28 bp):
TCGCACACATAGTGCTCAATTACAAATC
Done.