Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 134 of 292
Found at i:39739257 original size:80 final size:79
Alignment explanation
Indices: 39739080--39739298 Score: 214
Period size: 80 Copynumber: 2.7 Consensus size: 79
39739070 TCGAATGATG
*
39739080 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTGAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGC-GAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* *
39739145 GTGCGAGTTCCCAAA
65 GTGCGAGCTACCAAA
* ** **
39739160 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCGAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
**
39739223 TTGTGCGAGCTATTATAA
63 TTGTGCGAGCTACCA-AA
* * * *
39739241 -CCGGGCTATGTCCCGAAGGCTTTTGAGCGAGTCG-CTATATCCGGA-TAAGATCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCGAGT-GACCAAATCCGGACTAAGATCCGAAGG
39739299 TACGTGATTC
Statistics
Matches: 114, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
79 13 0.11
80 91 0.80
81 10 0.09
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCGAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTG
TGCGAGCTACCAAA
Found at i:39741477 original size:9 final size:10
Alignment explanation
Indices: 39741463--39741509 Score: 53
Period size: 9 Copynumber: 4.7 Consensus size: 10
39741453 TCTTGTAACG
39741463 AGAAAAC-AA
1 AGAAAACAAA
39741472 AGAAAACAAA
1 AGAAAACAAA
39741482 AGAAAAAGCAAA
1 AG-AAAA-CAAA
*
39741494 AGAAGA-AAA
1 AGAAAACAAA
39741503 AGAAAAC
1 AGAAAAC
39741510 GAAATAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 15 0.47
10 4 0.12
11 7 0.22
12 6 0.19
ACGTcount: A:0.77, C:0.09, G:0.15, T:0.00
Consensus pattern (10 bp):
AGAAAACAAA
Found at i:39741518 original size:16 final size:16
Alignment explanation
Indices: 39741470--39741524 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
39741460 ACGAGAAAAC
*
39741470 AAAGAAAACAAAAGAA
1 AAAGAAAACGAAAGAA
39741486 AAAGCAAAA-G-AAGAA
1 AAAG-AAAACGAAAGAA
*
39741501 AAAGAAAACGAAATAA
1 AAAGAAAACGAAAGAA
39741517 AAAGAAAA
1 AAAGAAAA
39741525 GAGAGGTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 4 0.12
15 10 0.29
16 16 0.47
17 4 0.12
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.02
Consensus pattern (16 bp):
AAAGAAAACGAAAGAA
Found at i:39741595 original size:12 final size:12
Alignment explanation
Indices: 39741578--39741605 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
39741568 GAGAACTTGG
39741578 AAAAGCCTTTGA
1 AAAAGCCTTTGA
39741590 AAAAGCCTTTGA
1 AAAAGCCTTTGA
39741602 AAAA
1 AAAA
39741606 CAAAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (12 bp):
AAAAGCCTTTGA
Found at i:39741629 original size:12 final size:12
Alignment explanation
Indices: 39741607--39741631 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39741597 TTTGAAAAAC
39741607 AAAAAGAAAATG
1 AAAAAGAAAATG
39741619 AAAAAGAAAATG
1 AAAAAGAAAATG
39741631 A
1 A
39741632 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:39741638 original size:18 final size:18
Alignment explanation
Indices: 39741598--39741651 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
39741588 GAAAAAGCCT
* *
39741598 TTGAAAAACAAAAAGAAA
1 TTGAAAAAGAAAATGAAA
* *
39741616 ATGAAAAAGAAAATGAGA
1 TTGAAAAAGAAAATGAAA
*
39741634 TTGAAAAAGAGAATGAAA
1 TTGAAAAAGAAAATGAAA
39741652 AAGAGTTTGA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.67, C:0.02, G:0.19, T:0.13
Consensus pattern (18 bp):
TTGAAAAAGAAAATGAAA
Found at i:39741663 original size:30 final size:30
Alignment explanation
Indices: 39741607--39741688 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
39741597 TTTGAAAAAC
**
39741607 AAAAAGAAAATGAAAAAGAAAATGAGATTG
1 AAAAAGAAAATGAAAAAGAAAATGAGAGAG
* ***
39741637 AAAAAGAGAATGAAAAAGAGTTTGAGAGAG
1 AAAAAGAAAATGAAAAAGAAAATGAGAGAG
** *
39741667 AAAAAGAATGTGAACAAGAAAA
1 AAAAAGAAAATGAAAAAGAAAA
39741689 AAAAGTGGAA
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.63, C:0.01, G:0.23, T:0.12
Consensus pattern (30 bp):
AAAAAGAAAATGAAAAAGAAAATGAGAGAG
Found at i:39743882 original size:30 final size:30
Alignment explanation
Indices: 39743806--39743894 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
39743796 TTCAACTCAC
*
39743806 GAGCTAAACCTTAGCTCAACTTCAGCTT-AG
1 GAGCTAAA-CTTAGCTCAACTTTAGCTTAAG
* *
39743836 GAGTTTAAACTCAGCTCAACTTTAGCTTAAG
1 GAG-CTAAACTTAGCTCAACTTTAGCTTAAG
*
39743867 G-GCTAAAGCTTAGCTC-ATTTTAGCTTAA
1 GAGCTAAA-CTTAGCTCAACTTTAGCTTAA
39743895 ACCTTGACTT
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 15 0.30
30 28 0.56
31 7 0.14
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (30 bp):
GAGCTAAACTTAGCTCAACTTTAGCTTAAG
Found at i:39749737 original size:43 final size:43
Alignment explanation
Indices: 39749689--39749859 Score: 161
Period size: 43 Copynumber: 4.0 Consensus size: 43
39749679 GATACCGAGA
* *
39749689 TGTGATTACATGTAAGACCATGTTTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* * * *
39749732 TGTGATTGCGTGTAAGACCATTTCTGAGACATTGGCATCGCTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCG-TAT
* * * *
39749776 T-CGATTTA-GTGTAAGACCTTGTCTGGGACAGTGGCATCG-AT
1 TGTGA-TTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* * * *
39749817 ATGTGATAACATGTAAGACCATATCTGGGATA-TGGCATTGTAT
1 -TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
39749860 GAGCTTTATG
Statistics
Matches: 103, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
41 2 0.02
42 10 0.10
43 85 0.83
44 6 0.06
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.34
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
Found at i:39750753 original size:21 final size:21
Alignment explanation
Indices: 39750716--39750755 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
39750706 CTGCTCAAGG
*
39750716 GAAGCCGATTGATCCATCTCA
1 GAAGCCGATTCATCCATCTCA
39750737 GAAGCCGGATTCA-CCATCT
1 GAAGCC-GATTCATCCATCT
39750756 AGACTGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.23
Consensus pattern (21 bp):
GAAGCCGATTCATCCATCTCA
Found at i:39752395 original size:23 final size:24
Alignment explanation
Indices: 39752351--39752395 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
39752341 CAAATCTTAC
*
39752351 CCATCCAGCCTCTACACACCATCT
1 CCATCCAACCTCTACACACCATCT
*
39752375 CCATCCAACC-CTACACTCCAT
1 CCATCCAACCTCTACACACCAT
39752396 GTGGGGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.27, C:0.51, G:0.02, T:0.20
Consensus pattern (24 bp):
CCATCCAACCTCTACACACCATCT
Found at i:39752756 original size:27 final size:27
Alignment explanation
Indices: 39752726--39752828 Score: 84
Period size: 27 Copynumber: 3.8 Consensus size: 27
39752716 GCAAATCAGT
*
39752726 CATTTTACCTCACAAGGGTATTACAGA
1 CATTTTACCTCATAAGGGTATTACAGA
** * *
39752753 CATTTTACC-CTATGGGGGTATTTCAGT
1 CATTTTACCTC-ATAAGGGTATTACAGA
* * * *
39752780 CATTTTACCTTATAAGGGTATTTCGGT
1 CATTTTACCTCATAAGGGTATTACAGA
*
39752807 CATTTTAACCT-ATGAGGGTATT
1 CATTTT-ACCTCATAAGGGTATT
39752829 TCGTTCATTT
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
26 1 0.02
27 58 0.92
28 4 0.06
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.39
Consensus pattern (27 bp):
CATTTTACCTCATAAGGGTATTACAGA
Found at i:39752785 original size:54 final size:53
Alignment explanation
Indices: 39752721--39752916 Score: 214
Period size: 54 Copynumber: 3.6 Consensus size: 53
39752711 GAAGGGCAAA
* * *
39752721 TCAGTCATTTTACCTCACAAGGGTATTACAGACATTTTACCCTATGGGGGTATT
1 TCAGTCATTTTACCT-ATAAGGGTATTTCAGTCATTTTACCCTATGGGGGTATT
* * *
39752775 TCAGTCATTTTACCTTATAAGGGTATTTCGGTCATTTTAACCTATGAGGGTATT
1 TCAGTCATTTTACC-TATAAGGGTATTTCAGTCATTTTACCCTATGGGGGTATT
* * * *
39752829 TC-GTTCATTTTAACCTATGAGGGTATTTTAGTCATTTTACCCTATAGAGGTATT
1 TCAG-TCATTTT-ACCTATAAGGGTATTTCAGTCATTTTACCCTATGGGGGTATT
** * *
39752883 TTGGTCATTTTACCATATAGGGGTATTTCGGTCA
1 TCAGTCATTTTACC-TATAAGGGTATTTCAGTCA
39752917 CCATTTCGGC
Statistics
Matches: 119, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
53 4 0.03
54 110 0.92
55 5 0.04
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (53 bp):
TCAGTCATTTTACCTATAAGGGTATTTCAGTCATTTTACCCTATGGGGGTATT
Found at i:39752829 original size:27 final size:27
Alignment explanation
Indices: 39752753--39752916 Score: 183
Period size: 27 Copynumber: 6.1 Consensus size: 27
39752743 GTATTACAGA
* * *
39752753 CATTTTACCCTATGGGGGTATTTCAGT
1 CATTTTAACCTATGAGGGTATTTCGGT
*
39752780 CATTTT-ACCTTATAAGGGTATTTCGGT
1 CATTTTAACC-TATGAGGGTATTTCGGT
*
39752807 CATTTTAACCTATGAGGGTATTTCGTT
1 CATTTTAACCTATGAGGGTATTTCGGT
**
39752834 CATTTTAACCTATGAGGGTATTTTAGT
1 CATTTTAACCTATGAGGGTATTTCGGT
* *
39752861 CATTTTACCCTAT-AGAGGTATTTTGGT
1 CATTTTAACCTATGAG-GGTATTTCGGT
39752888 CATTTT-ACCATAT-AGGGGTATTTCGGT
1 CATTTTAACC-TATGA-GGGTATTTCGGT
39752915 CA
1 CA
39752917 CCATTTCGGC
Statistics
Matches: 119, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
26 6 0.05
27 109 0.92
28 4 0.03
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.43
Consensus pattern (27 bp):
CATTTTAACCTATGAGGGTATTTCGGT
Found at i:39752847 original size:81 final size:81
Alignment explanation
Indices: 39752753--39752912 Score: 227
Period size: 81 Copynumber: 2.0 Consensus size: 81
39752743 GTATTACAGA
* * *
39752753 CATTTTACCCTATGGGGGTATTTCAGTCATTTTACCTTATA-AGGGTATTTCGGTCATTTTAACC
1 CATTTTAACCTATGAGGGTATTTCAGTCATTTTACCCTATAGA-GGTATTTCGGTCATTTT-ACC
39752817 -TAT-GAGGGTATTTCGTT
64 ATATAG-GGGTATTTCGTT
* *
39752834 CATTTTAACCTATGAGGGTATTTTAGTCATTTTACCCTATAGAGGTATTTTGGTCATTTTACCAT
1 CATTTTAACCTATGAGGGTATTTCAGTCATTTTACCCTATAGAGGTATTTCGGTCATTTTACCAT
39752899 ATAGGGGTATTTCG
66 ATAGGGGTATTTCG
39752913 GTCACCATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
80 3 0.04
81 66 0.93
82 2 0.03
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (81 bp):
CATTTTAACCTATGAGGGTATTTCAGTCATTTTACCCTATAGAGGTATTTCGGTCATTTTACCAT
ATAGGGGTATTTCGTT
Found at i:39755981 original size:18 final size:18
Alignment explanation
Indices: 39755954--39755990 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
39755944 TGGCCCAATT
39755954 CAGTAACAGTAAACAGTA
1 CAGTAACAGTAAACAGTA
*
39755972 CAGTATCAGTAAACAGTA
1 CAGTAACAGTAAACAGTA
39755990 C
1 C
39755991 GCAAGTCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.19
Consensus pattern (18 bp):
CAGTAACAGTAAACAGTA
Found at i:39756434 original size:26 final size:26
Alignment explanation
Indices: 39756404--39756463 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
39756394 GTATTACAGA
* **
39756404 CATTTTACCCTATGGATAATTTCGGT
1 CATTTTACCCCATGGATAATTTCAAT
* *
39756430 CATTTTACCCCATGGGTTATTTCAAT
1 CATTTTACCCCATGGATAATTTCAAT
39756456 CATTTTAC
1 CATTTTAC
39756464 TCTTTGAGGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (26 bp):
CATTTTACCCCATGGATAATTTCAAT
Found at i:39760445 original size:27 final size:25
Alignment explanation
Indices: 39760415--39760471 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 25
39760405 ACATTCAACA
* * *
39760415 CTTAAGGGTATTTTGGTCATTTTTGCC
1 CTTAAGGGCATTCTGGT-AATTTT-CC
*
39760442 CTTAGGGGCATTCTGGTAATTTTCC
1 CTTAAGGGCATTCTGGTAATTTTCC
39760467 CTTAA
1 CTTAA
39760472 TTATGGTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 14 0.56
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.44
Consensus pattern (25 bp):
CTTAAGGGCATTCTGGTAATTTTCC
Found at i:39761073 original size:16 final size:16
Alignment explanation
Indices: 39761052--39761099 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
39761042 CCAAACTTTT
*
39761052 GACTTTTCGGTATTTC
1 GACTTTTCGGCATTTC
39761068 GACTTTTCGGCATTTC
1 GACTTTTCGGCATTTC
*
39761084 G-GTATTTCGGCATTTC
1 GACT-TTTCGGCATTTC
39761100 AGCTTTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 1 0.03
16 28 0.97
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (16 bp):
GACTTTTCGGCATTTC
Found at i:39761083 original size:8 final size:8
Alignment explanation
Indices: 39761056--39761099 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
39761046 ACTTTTGACT
*
39761056 TTTCGGTA
1 TTTCGGCA
* *
39761064 TTTCGACT
1 TTTCGGCA
39761072 TTTCGGCA
1 TTTCGGCA
*
39761080 TTTCGGTA
1 TTTCGGCA
39761088 TTTCGGCA
1 TTTCGGCA
39761096 TTTC
1 TTTC
39761100 AGCTTTTTTC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (8 bp):
TTTCGGCA
Found at i:39765171 original size:29 final size:29
Alignment explanation
Indices: 39765088--39765205 Score: 150
Period size: 29 Copynumber: 4.1 Consensus size: 29
39765078 CCTGTATCTA
* * * *
39765088 GCCCATTAAG-CCTAATCATATTCATATG
1 GCCCATTAGGCCCAAATCACATTTATATG
* *
39765116 GCCCATTAAGCCC-AATCATATTTATATG
1 GCCCATTAGGCCCAAATCACATTTATATG
* *
39765144 GCCCATTAGGCCCAAATCACCTATATATG
1 GCCCATTAGGCCCAAATCACATTTATATG
39765173 GCCCATTAGGCCCAAATCACATTTATATG
1 GCCCATTAGGCCCAAATCACATTTATATG
39765202 GCCC
1 GCCC
39765206 GTTAAGCCTA
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
28 36 0.44
29 45 0.56
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.28
Consensus pattern (29 bp):
GCCCATTAGGCCCAAATCACATTTATATG
Found at i:39765447 original size:16 final size:16
Alignment explanation
Indices: 39765426--39765461 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
39765416 TTAGCCAAAC
39765426 TTTCAAATTTTCAGTA
1 TTTCAAATTTTCAGTA
*
39765442 TTTCAATTTTTCAGTA
1 TTTCAAATTTTCAGTA
39765458 TTTC
1 TTTC
39765462 GGCACTTCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.25, C:0.14, G:0.06, T:0.56
Consensus pattern (16 bp):
TTTCAAATTTTCAGTA
Found at i:39767158 original size:26 final size:27
Alignment explanation
Indices: 39767089--39767250 Score: 174
Period size: 27 Copynumber: 6.1 Consensus size: 27
39767079 GGCAAATAAA
* * *
39767089 TCATTTTACCTTA-CAGGGTATTAC-G
1 TCATTTTACCCTATGAGGGTATTTCGG
*
39767114 ACATTTTACCCTATGAGGGTATTTCGG
1 TCATTTTACCCTATGAGGGTATTTCGG
39767141 TCATTTTA-CCT-TGTAGGGGTATTTCGG
1 TCATTTTACCCTATG-A-GGGTATTTCGG
* *
39767168 TCATTTTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGAGGGTATTTCGG
*
39767195 TCATTTTACCCTATGA-GGTATTTCAG
1 TCATTTTACCCTATGAGGGTATTTCGG
* *
39767221 TTATTTTACCCTATG-GAGGTATTTCAG
1 TCATTTTACCCTATGAG-GGTATTTCGG
39767248 TCA
1 TCA
39767251 CCATTTCGGC
Statistics
Matches: 117, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
25 13 0.11
26 35 0.30
27 64 0.55
28 3 0.03
29 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (27 bp):
TCATTTTACCCTATGAGGGTATTTCGG
Found at i:39767236 original size:53 final size:54
Alignment explanation
Indices: 39767088--39767245 Score: 187
Period size: 53 Copynumber: 3.0 Consensus size: 54
39767078 CGGCAAATAA
* * * * *
39767088 ATCATTTTACCTTACAG-GGTATTAC-GACATTTTACCCTATGAGGGTATTTCG
1 ATCATTTTACCCTATAGAGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCG
* * * * *
39767140 GTCATTTTACCTTGTAGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCG
1 ATCATTTTACCCTATAGAGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCG
* *
39767194 ATCATTTTACCCTAT-GAGGTATTTCAGTTATTTTACCCTATGGAGGTATTTC
1 ATCATTTTACCCTATAGAGGTATTTCAGTCATTTTACCCTATGGGGGTATTTC
39767246 AGTCACCATT
Statistics
Matches: 91, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
52 14 0.15
53 40 0.44
54 37 0.41
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.42
Consensus pattern (54 bp):
ATCATTTTACCCTATAGAGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCG
Found at i:39775613 original size:40 final size:40
Alignment explanation
Indices: 39775555--39775707 Score: 229
Period size: 40 Copynumber: 3.9 Consensus size: 40
39775545 TTATTTGATG
*
39775555 TGGAATTGTATCCAGGCTTAAAGACCCGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
39775595 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
* *
39775635 TGGAATTGTATCCCGGCTTAAAGATCCGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
* * *
39775675 TGGAA-TGACATCCGGG-TTAAAAACCTGCAGGCT
1 TGGAATTG-TATCCGGGCTTAAAGACCCGCAGGCT
39775708 GTGCTAGATA
Statistics
Matches: 104, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
39 16 0.15
40 88 0.85
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
Found at i:39791102 original size:2 final size:2
Alignment explanation
Indices: 39791095--39791135 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
39791085 CATTTTAACT
39791095 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39791136 CACAAATCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39800069 original size:43 final size:43
Alignment explanation
Indices: 39799981--39800093 Score: 133
Period size: 43 Copynumber: 2.7 Consensus size: 43
39799971 TGTGATAACA
* **
39799981 TGTAAGACCAT-TCTGGGACATTGGCATTGTATTGTGATTACG
1 TGTAAGACCATGTCTGGGACATTGGCATCGTATTGCAATTACG
**
39800023 TGTAAGACCATGTCTGGGACATTGGCATCGTTATT-CAATTTTG
1 TGTAAGACCATGTCTGGGACATTGGCATCG-TATTGCAATTACG
* *
39800066 TGTAAGACCTTGT-TGGGACAGTGGCATC
1 TGTAAGACCATGTCTGGGACATTGGCATC
39800094 AATATGTGAT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
42 25 0.40
43 33 0.53
44 4 0.06
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.35
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGTATTGCAATTACG
Found at i:39800112 original size:42 final size:42
Alignment explanation
Indices: 39799970--39800116 Score: 111
Period size: 42 Copynumber: 3.5 Consensus size: 42
39799960 GGTTACCGAG
* **
39799970 ATGTGATAACATGTAAGACCATT-CTGGGACATTGGCAT-TGT
1 ATGTGATAACATGTAAGACC-TTGTTGGGACATTGGCATCAAT
* * * **
39800011 ATTGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTT
1 A-TGTGATAACATGTAAGACCTTGT-TGGGACATTGGCATCAAT
* **** *
39800055 AT-TCAATTTTGTGTAAGACCTTGTTGGGACAGTGGCATCAAT
1 ATGT-GATAACATGTAAGACCTTGTTGGGACATTGGCATCAAT
39800097 ATGTGATAACATGTAAGACC
1 ATGTGATAACATGTAAGACC
39800117 ATATTTGGGA
Statistics
Matches: 82, Mismatches: 18, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
41 2 0.02
42 46 0.56
43 32 0.39
44 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (42 bp):
ATGTGATAACATGTAAGACCTTGTTGGGACATTGGCATCAAT
Found at i:39806239 original size:27 final size:27
Alignment explanation
Indices: 39806209--39806264 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
39806199 ATCTCATATC
* * *
39806209 TGTAGGCTAGTATTACTGAAATGCCCT
1 TGTAGGCTAGAATTACTAAAATACCCT
*
39806236 TGTAGGGTAGAATTACTAAAATACCCT
1 TGTAGGCTAGAATTACTAAAATACCCT
39806263 TG
1 TG
39806265 GTTTACAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (27 bp):
TGTAGGCTAGAATTACTAAAATACCCT
Found at i:39806364 original size:27 final size:27
Alignment explanation
Indices: 39806281--39806615 Score: 273
Period size: 27 Copynumber: 12.4 Consensus size: 27
39806271 AAAGTTATTG
* **
39806281 AATACCCTTGGTTTACAAAATTACCAA
1 AATACCCTTGATTTGTAAAATTACCAA
* * * *
39806308 AAGACCCTCGATTAGCAAAATTACCAA
1 AATACCCTTGATTTGTAAAATTACCAA
*
39806335 AATACCCTTGATTTTTAAAATTACCAA
1 AATACCCTTGATTTGTAAAATTACCAA
*
39806362 AATA-CCTTTAGTTTGTAAAATTACCAA
1 AATACCCTTGA-TTTGTAAAATTACCAA
* * *
39806389 AATACCCTTAATTTGTGACATTACCAA
1 AATACCCTTGATTTGTAAAATTACCAA
*
39806416 AATACCCTTAATTTGTAAAATTA-CAA
1 AATACCCTTGATTTGTAAAATTACCAA
* * *
39806442 AATATCCC-TGATTTGGAAAATAACCGA
1 AATA-CCCTTGATTTGTAAAATTACCAA
* * * **
39806469 AAGACCCTTAATTTGGAAAATTATAAA
1 AATACCCTTGATTTGTAAAATTACCAA
** *
39806496 AATACCCTTGATTTACAAAATTACAAA
1 AATACCCTTGATTTGTAAAATTACCAA
**
39806523 AATACCCTTGACTTTCAAAAAATTA-CAGA
1 AATACCCTTGA-TTT-GTAAAATTACCA-A
* * * * *
39806552 AATACCATTGGTTTGCAAAATTATCGA
1 AATACCCTTGATTTGTAAAATTACCAA
* * * *
39806579 AATACCCTTGGTTTGTAGATTTACTAA
1 AATACCCTTGATTTGTAAAATTACCAA
*
39806606 AACACCCTTG
1 AATACCCTTG
39806616 TAGGGTGAAA
Statistics
Matches: 252, Mismatches: 47, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
26 27 0.11
27 194 0.77
28 13 0.05
29 18 0.07
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (27 bp):
AATACCCTTGATTTGTAAAATTACCAA
Found at i:39806498 original size:80 final size:80
Alignment explanation
Indices: 39806246--39806530 Score: 270
Period size: 80 Copynumber: 3.5 Consensus size: 80
39806236 TGTAGGGTAG
* * * * *** **
39806246 AATTACTAAAATACCCTTGGTTTACAAAGTTATTGAATACCCTTG-GTTTACAAAATTACCAAAA
1 AATTACCAAAATACCCTTGATTTATAAAATTACAAAATACCC-TGAGTTTGGAAAATTACCAAAA
** * *
39806310 GACCCTCGATTAGCAA
65 GACCCTTAATTTGGAA
* * * *
39806326 AATTACCAAAATACCCTTGATTTTTAAAATTACCAAAATACCTTTAGTTTGTAAAATTACCAAAA
1 AATTACCAAAATACCCTTGATTTATAAAATTA-CAAAATACCCTGAGTTTGGAAAATTACCAAAA
*
39806391 TACCCTTAATTTGTG-A
65 GACCCTTAATTTG-GAA
* * * * *
39806407 CATTACCAAAATACCCTTAATTTGTAAAATTACAAAATATCCCTGA-TTTGGAAAATAACCGAAA
1 AATTACCAAAATACCCTTGATTTATAAAATTACAAAATA-CCCTGAGTTTGGAAAATTACCAAAA
39806471 GACCCTTAATTTGGAA
65 GACCCTTAATTTGGAA
** *
39806487 AATTATAAAAATACCCTTGATTTACAAAATTACAAAAATACCCT
1 AATTACCAAAATACCCTTGATTTATAAAATTAC-AAAATACCCT
39806531 TGACTTTCAA
Statistics
Matches: 167, Mismatches: 32, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
79 1 0.01
80 94 0.56
81 72 0.43
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (80 bp):
AATTACCAAAATACCCTTGATTTATAAAATTACAAAATACCCTGAGTTTGGAAAATTACCAAAAG
ACCCTTAATTTGGAA
Found at i:39806554 original size:29 final size:27
Alignment explanation
Indices: 39806246--39806588 Score: 167
Period size: 27 Copynumber: 12.7 Consensus size: 27
39806236 TGTAGGGTAG
* * *
39806246 AATTACTAAAATACCCTTGGTTTACAA
1 AATTACAAAAATACCCTTGATTTAAAA
* *** * *
39806273 AGTTA-TTGAATACCCTTGGTTTACAA
1 AATTACAAAAATACCCTTGATTTAAAA
* * * *
39806299 AATTACCAAAAGACCCTCGA-TTAGCAA
1 AATTACAAAAATACCCTTGATTTA-AAA
* **
39806326 AATTACCAAAATACCCTTGATTTTTAA
1 AATTACAAAAATACCCTTGATTTAAAA
* * **
39806353 AATTACCAAAATA-CCTTTAGTTTGTAA
1 AATTACAAAAATACCCTTGA-TTTAAAA
* * ***
39806380 AATTACCAAAATACCCTTAATTTGTGA
1 AATTACAAAAATACCCTTGATTTAAAA
* * * **
39806407 CATTACCAAAATACCCTTAATTTGTAA
1 AATTACAAAAATACCCTTGATTTAAAA
**
39806434 AATTAC-AAAATATCCC-TGATTTGGAA
1 AATTACAAAAATA-CCCTTGATTTAAAA
* ** * * **
39806460 AATAACCGAAAGACCCTTAATTTGGAA
1 AATTACAAAAATACCCTTGATTTAAAA
* *
39806487 AATTATAAAAATACCCTTGATTTACAA
1 AATTACAAAAATACCCTTGATTTAAAA
39806514 AATTACAAAAATACCCTTGACTTTCAAAA
1 AATTACAAAAATACCCTTGA-TTT-AAAA
* * * **
39806543 AATTACAGAAATACCATTGGTTTGCAA
1 AATTACAAAAATACCCTTGATTTAAAA
*
39806570 AATTATC-GAAATACCCTTG
1 AATTA-CAAAAATACCCTTG
39806589 GTTTGTAGAT
Statistics
Matches: 262, Mismatches: 43, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
26 53 0.20
27 175 0.67
28 14 0.05
29 20 0.08
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (27 bp):
AATTACAAAAATACCCTTGATTTAAAA
Found at i:39806898 original size:41 final size:41
Alignment explanation
Indices: 39806853--39806975 Score: 201
Period size: 41 Copynumber: 3.0 Consensus size: 41
39806843 GGAGGAAGAA
*
39806853 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCATCG
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
*
39806894 ATTGAGGATCGCATGGTTGCTTGACGACCGTGAATCCACCG
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
* * *
39806935 ATTAAGGATCGCATGGTTGCTTGACGATCGTGGATTCACCG
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
39806976 GTGGCTTTTA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (41 bp):
ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
Found at i:39807169 original size:22 final size:22
Alignment explanation
Indices: 39807117--39807181 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
39807107 GCCAATTATT
*
39807117 CTGATTATGGCTTTGTGCCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
39807139 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* *
39807161 CTGATTATGGATGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
39807182 ACGTATTTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:39809701 original size:29 final size:29
Alignment explanation
Indices: 39809669--39809800 Score: 246
Period size: 29 Copynumber: 4.5 Consensus size: 29
39809659 ATAGTGAATC
39809669 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
39809698 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATAT-ATTTTCAGCT
39809728 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
*
39809757 CGCACACTTAGTGCTATATATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCT
39809786 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39809801 GTACAATTTT
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
29 72 0.71
30 29 0.29
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAGCT
Found at i:39809810 original size:59 final size:59
Alignment explanation
Indices: 39809669--39809800 Score: 248
Period size: 59 Copynumber: 2.3 Consensus size: 59
39809659 ATAGTGAATC
39809669 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
*
39809728 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATAT-ATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
39809786 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39809801 GTACAATTTT
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
58 24 0.33
59 48 0.67
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37
Consensus pattern (59 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:39810472 original size:143 final size:143
Alignment explanation
Indices: 39810305--39810742 Score: 858
Period size: 143 Copynumber: 3.1 Consensus size: 143
39810295 TATACCGCAT
39810305 ATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
1 ATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
39810370 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
66 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
39810435 GAAGACAACATGC
131 GAAGACAACATGC
39810448 ATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
1 ATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
*
39810513 TGTTAAACATTCGAACTCACTCATCTCCATGTTTTCATCACAACAACATCAAAACACTCACCAAG
66 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
39810578 GAAGACAACATGC
131 GAAGACAACATGC
39810591 ATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
1 ATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
39810656 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
66 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
*
39810721 GAAAACAACATGC
131 GAAGACAACATGC
39810734 ATGGCCGAA
1 ATGGCCGAA
39810743 ATTTAACTCA
Statistics
Matches: 292, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
143 292 1.00
ACGTcount: A:0.39, C:0.29, G:0.10, T:0.22
Consensus pattern (143 bp):
ATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
GAAGACAACATGC
Found at i:39817596 original size:29 final size:29
Alignment explanation
Indices: 39817564--39817694 Score: 237
Period size: 29 Copynumber: 4.5 Consensus size: 29
39817554 ATAGTGAATC
39817564 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
39817593 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATAT-ATTTTCAGCT
39817623 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
*
39817652 CGCACACTTAGTGCTATATA-TTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCT
39817680 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39817695 GTACAATTTT
Statistics
Matches: 100, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
28 22 0.22
29 49 0.49
30 29 0.29
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAGCT
Found at i:39817685 original size:57 final size:59
Alignment explanation
Indices: 39817564--39817694 Score: 239
Period size: 59 Copynumber: 2.3 Consensus size: 59
39817554 ATAGTGAATC
39817564 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
*
39817623 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATAT-A-TTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
39817680 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39817695 GTACAATTTT
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
57 22 0.31
58 1 0.01
59 48 0.68
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (59 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:39817717 original size:59 final size:59
Alignment explanation
Indices: 39817564--39817724 Score: 182
Period size: 59 Copynumber: 2.7 Consensus size: 59
39817554 ATAGTGAATC
* * * * *
39817564 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATAAATTTTAAACCCACACACTTAGTGCTATATAATTTTCAGCT
* * * * * *
39817623 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATAT-A-TTTCAGTT
1 CGCACACTTAGTGCTATAAATTTTAAACCCACACACTTAGTGCTATATAATTTTCAGCT
*
39817680 CGCACACTTAGTGCTGTACAATTTTTAAACCCACACACTTAGTGC
1 CGCACACTTAGTGCTATA-AA-TTTTAAACCCACACACTTAGTGC
39817725 CAATCTTGTC
Statistics
Matches: 93, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
57 24 0.26
58 2 0.02
59 67 0.72
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (59 bp):
CGCACACTTAGTGCTATAAATTTTAAACCCACACACTTAGTGCTATATAATTTTCAGCT
Found at i:39818366 original size:143 final size:143
Alignment explanation
Indices: 39818199--39818636 Score: 840
Period size: 143 Copynumber: 3.1 Consensus size: 143
39818189 TATACCGCAT
39818199 ATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
1 ATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
39818264 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
66 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
39818329 GAAGACAACATGC
131 GAAGACAACATGC
39818342 ATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
1 ATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
*
39818407 TGTTAAACATTCGAACTCACTCATCTCCATGTTTTCATCACAACAACATCAAAACACTCACCAAG
66 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
39818472 GAAGACAACATGC
131 GAAGACAACATGC
39818485 ATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
1 ATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
*
39818550 TGTTAAACATTCGAACTCACTCACCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
66 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
*
39818615 GAAAACAACATGC
131 GAAGACAACATGC
*
39818628 ATGTCCGAA
1 ATGGCCGAA
39818637 ATTTAACTCA
Statistics
Matches: 290, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
143 290 1.00
ACGTcount: A:0.39, C:0.29, G:0.10, T:0.22
Consensus pattern (143 bp):
ATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
GAAGACAACATGC
Found at i:39820572 original size:27 final size:27
Alignment explanation
Indices: 39820535--39820633 Score: 135
Period size: 27 Copynumber: 3.7 Consensus size: 27
39820525 ATTGGTTTAC
* *
39820535 AAAATTACCAAAATACCCTTAATTAGA
1 AAAATTACCAAAATACCCTTAATTTGT
*
39820562 AAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCCTTAATTTGT
* ** *
39820589 GAAATTACTGAAATACCCTTGATTTGT
1 AAAATTACCAAAATACCCTTAATTTGT
39820616 AAAATTACCAAAATACCC
1 AAAATTACCAAAATACCC
39820634 CTGATATGGA
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.28
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTTAATTTGT
Found at i:39820638 original size:27 final size:27
Alignment explanation
Indices: 39820535--39820649 Score: 131
Period size: 27 Copynumber: 4.3 Consensus size: 27
39820525 ATTGGTTTAC
* * *
39820535 AAAATTACCAAAATACCCTTAATTAGA
1 AAAATTACCAAAATACCCCTAATTTGT
39820562 AAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCCCTAATTTGT
* ** * *
39820589 GAAATTACTGAAATACCCTTGATTTGT
1 AAAATTACCAAAATACCCCTAATTTGT
* * *
39820616 AAAATTACCAAAATACCCCTGATATGG
1 AAAATTACCAAAATACCCCTAATTTGT
39820643 AAAATTA
1 AAAATTA
39820650 TTGAAAGACC
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 74 1.00
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTAATTTGT
Found at i:39820648 original size:54 final size:55
Alignment explanation
Indices: 39820535--39820655 Score: 156
Period size: 54 Copynumber: 2.2 Consensus size: 55
39820525 ATTGGTTTAC
** *
39820535 AAAATTACCAAAATACCCTTAATTAGAAAAATTACCAAAATACCCCTAATTTGTG
1 AAAATTACTGAAATACCCTTAATTAGAAAAATTACCAAAATACCCCTAATATGTG
* * * *
39820590 -AAATTACTGAAATACCCTTGATTTGTAAAATTACCAAAATACCCCTGATATG-G
1 AAAATTACTGAAATACCCTTAATTAGAAAAATTACCAAAATACCCCTAATATGTG
*
39820643 AAAATTATTGAAA
1 AAAATTACTGAAA
39820656 GACCTGTAAC
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
53 1 0.02
54 56 0.98
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.29
Consensus pattern (55 bp):
AAAATTACTGAAATACCCTTAATTAGAAAAATTACCAAAATACCCCTAATATGTG
Found at i:39821532 original size:27 final size:27
Alignment explanation
Indices: 39821502--39821977 Score: 598
Period size: 27 Copynumber: 17.7 Consensus size: 27
39821492 TTAGTTTACC
39821502 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
* *
39821529 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCTTGGTTTGTA
* *
39821556 AAATCACCAAAATACTCC-TAGTTTGTA
1 AAATTACCAAAATAC-CCTTGGTTTGTA
* **
39821583 AAATTACC-AAATACCCTTAGTTTAAA
1 AAATTACCAAAATACCCTTGGTTTGTA
39821609 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
* * * *
39821636 AAATTACTAGAATACCCTTGGTATATA
1 AAATTACCAAAATACCCTTGGTTTGTA
* *
39821663 AAATCACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
* **
39821690 AAATTACTAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTTGGTTTGTA
*
39821717 AAATTACCAAAATACCCTTAGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
* * *
39821744 AAATTACTAAAATACCCTTTGTTTATA
1 AAATTACCAAAATACCCTTGGTTTGTA
*
39821771 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
* *
39821798 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
*
39821825 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
* *
39821852 AAATTATCAAAATACTCC-TCGTTTGTA
1 AAATTACCAAAATAC-CCTTGGTTTGTA
*
39821879 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
* * *
39821906 AAATTATCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
* *
39821933 AAATTACCAAAATACCCTTGATTTGTG
1 AAATTACCAAAATACCCTTGGTTTGTA
* **
39821960 AATTTACTGAAATACCCT
1 AAATTACCAAAATACCCT
39821978 CGACCTGTAA
Statistics
Matches: 390, Mismatches: 54, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
25 2 0.01
26 23 0.06
27 361 0.93
28 4 0.01
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.33
Consensus pattern (27 bp):
AAATTACCAAAATACCCTTGGTTTGTA
Found at i:39822029 original size:27 final size:27
Alignment explanation
Indices: 39821502--39822030 Score: 500
Period size: 27 Copynumber: 19.6 Consensus size: 27
39821492 TTAGTTTACC
*
39821502 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTCGGTTTGTA
* * *
39821529 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCTCGGTTTGTA
* *
39821556 AAATCACCAAAATACTCCT-AGTTTGTA
1 AAATTACCAAAATAC-CCTCGGTTTGTA
** **
39821583 AAATTACC-AAATACCCTTAGTTTAAA
1 AAATTACCAAAATACCCTCGGTTTGTA
*
39821609 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTCGGTTTGTA
* * * * *
39821636 AAATTACTAGAATACCCTTGGTATATA
1 AAATTACCAAAATACCCTCGGTTTGTA
*
39821663 AAATCACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GGTTTGTA
* * **
39821690 AAATTACTAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGGTTTGTA
**
39821717 AAATTACCAAAATACCCTTAGTTTGTA
1 AAATTACCAAAATACCCTCGGTTTGTA
* ** *
39821744 AAATTACTAAAATACCCTTTGTTTATA
1 AAATTACCAAAATACCCTCGGTTTGTA
39821771 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GGTTTGTA
*
39821798 AAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTC-GGTTTGTA
39821825 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GGTTTGTA
*
39821852 AAATTATCAAAATACTCCTC-GTTTGTA
1 AAATTACCAAAATAC-CCTCGGTTTGTA
39821879 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GGTTTGTA
* *
39821906 AAATTATCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTC-GGTTTGTA
* * *
39821933 AAATTACCAAAATACCCTTGATTTGTG
1 AAATTACCAAAATACCCTCGGTTTGTA
* ** ***
39821960 AATTTACTGAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCCTCGGTTTGTA
**** **
39821987 AAATTTTTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGGTTTGTA
*
39822014 AAATTACCAAAGTACCC
1 AAATTACCAAAATACCC
39822031 CTAATTTACA
Statistics
Matches: 426, Mismatches: 65, Indels: 22
0.83 0.13 0.04
Matches are distributed among these distances:
25 4 0.01
26 22 0.05
27 394 0.92
28 5 0.01
29 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGGTTTGTA
Found at i:39822046 original size:108 final size:107
Alignment explanation
Indices: 39821493--39822048 Score: 652
Period size: 108 Copynumber: 5.2 Consensus size: 107
39821483 TAGAATACTT
* * *
39821493 TAGTTTACCAAATTACCAAAATACCCTTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATAAA
1 TAGTTTACAAAATTACCAAAATACCCTTGATTTGTAAAATTACTAAAATACCC-TCGTTTATAAA
* * * *
39821558 ATCACCAAAATACTCCTAGTTTGTAAAATTACC-AAATACCCT
65 ATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCC
* * * * *
39821600 TAGTTTAAAAAATTACCAAAATACCCTTGGTTTGTAAAATTACTAGAATACCCTTGGTATATAAA
1 TAGTTTACAAAATTACCAAAATACCCTTGATTTGTAAAATTACTAAAATACCC-TCGTTTATAAA
* * *
39821665 ATCACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCT
65 ATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCC
* *
39821708 TGGTTTACAAAATTACCAAAATACCCTT-AGTTTGTAAAATTACTAAAATACCCTTTGTTTATAA
1 TAGTTTACAAAATTACCAAAATACCCTTGA-TTTGTAAAATTACTAAAATACCC-TCGTTTATAA
39821772 AATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCC
64 AATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCC
** * * *
39821816 TAGTTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTA-TCAAAATACTCCTCGTTTGTAA
1 TAGTTTACAAAATTACCAAAATACCCTTGATTTGTAAAATTACT-AAAATAC-CCTCGTTTATAA
*
39821880 AATTACCAAAATACCCCTGGTTTGTAAAATTATCAAAATACCCC
64 AATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCC
** * * * ** *
39821924 TAGTTTGTAAAATTACCAAAATACCCTTGATTTGTGAATTTACTGAAATACCCTCGACCTGTAAA
1 TAGTTTACAAAATTACCAAAATACCCTTGATTTGTAAAATTACTAAAATACCCTCG-TTTATAAA
**** ** *
39821989 ATTTTTGAAATA-CCCTCGACTTGTAAAATTACCAAAGTACCCC
65 ATTACCAAAATACCCCT-GGTTTGTAAAATTACCAAAATACCCC
* *
39822032 TAATTTACAGAATTACC
1 TAGTTTACAAAATTACC
39822049 GTTTTACCCT
Statistics
Matches: 398, Mismatches: 43, Indels: 15
0.87 0.09 0.03
Matches are distributed among these distances:
107 101 0.25
108 294 0.74
109 3 0.01
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (107 bp):
TAGTTTACAAAATTACCAAAATACCCTTGATTTGTAAAATTACTAAAATACCCTCGTTTATAAAA
TTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCC
Found at i:39822056 original size:27 final size:28
Alignment explanation
Indices: 39822026--39822101 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 28
39822016 ATTACCAAAG
*
39822026 TACCCCT-AATTTACAGAATTACCGTTT
1 TACCCCTCAATTTACAAAATTACCGTTT
* *
39822053 TA-CCCTCGATTTACAAAATTACCTTTT
1 TACCCCTCAATTTACAAAATTACCGTTT
* *
39822080 TA-CCCTCGATTTATAAAATTAC
1 TACCCCTCAATTTACAAAATTAC
39822102 TGAAATACCC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.09
27 40 0.91
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (28 bp):
TACCCCTCAATTTACAAAATTACCGTTT
Found at i:39822132 original size:27 final size:27
Alignment explanation
Indices: 39822103--39822367 Score: 318
Period size: 27 Copynumber: 9.9 Consensus size: 27
39822093 TAAAATTACT
* **
39822103 GAAATACCCTTGTAGGGTAGAAATATT
1 GAAATACCCCTGTAGGGTAGAAATACC
* *
39822130 G-AATACCCTTGTAGAGTAGAAATACC
1 GAAATACCCCTGTAGGGTAGAAATACC
*
39822156 GAAATACCCCTGTAGGGTAGAAACACC
1 GAAATACCCCTGTAGGGTAGAAATACC
*
39822183 GAAATACCCCTGTAGGGTAGAAACACC
1 GAAATACCCCTGTAGGGTAGAAATACC
* * *
39822210 AAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAAATACC
* *
39822237 AAAATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAAATACC
*
39822264 GAAATACCCTTGTAGGGTAGAAATACC
1 GAAATACCCCTGTAGGGTAGAAATACC
* * *
39822291 GAAATACCCCTATAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAAATACC
* * *
39822318 AAAATACCCCTATAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAAATACC
* * *
39822345 GAGATACCCTTGTGGGGTA-AAAT
1 GAAATACCCCTGTAGGGTAGAAAT
39822368 TACCATTTTA
Statistics
Matches: 211, Mismatches: 26, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
26 26 0.12
27 185 0.88
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.23
Consensus pattern (27 bp):
GAAATACCCCTGTAGGGTAGAAATACC
Found at i:39822244 original size:81 final size:81
Alignment explanation
Indices: 39822096--39822372 Score: 369
Period size: 81 Copynumber: 3.4 Consensus size: 81
39822086 CGATTTATAA
* *** * * * **
39822096 AATTACTGAAATACCCTTGTAGGGTAGAAATA-TTGAATACCCTTGTAGAGTAGAAATACCGAAA
1 AATTACCGAAATACCCTTGTAGGGTAGAAATACCAAAATACCCCTGTAGGGTAGAATTACTAAAA
39822160 TACCCCTGTAGGGTAG
66 TACCCCTGTAGGGTAG
** * *
39822176 AAACACCGAAATACCCCTGTAGGGTAGAAACACCAAAATACCCCTGTAGGGTAGAATTACTAAAA
1 AATTACCGAAATACCCTTGTAGGGTAGAAATACCAAAATACCCCTGTAGGGTAGAATTACTAAAA
39822241 TACCCCTGTAGGGTAG
66 TACCCCTGTAGGGTAG
* *
39822257 AATTACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTATAGGGTAGAATTACTAAAA
1 AATTACCGAAATACCCTTGTAGGGTAGAAATACCAAAATACCCCTGTAGGGTAGAATTACTAAAA
*
39822322 TACCCCTATAGGGTAG
66 TACCCCTGTAGGGTAG
* *
39822338 AATTACCGAGATACCCTTGTGGGGTA-AAATTACCA
1 AATTACCGAAATACCCTTGTAGGGTAGAAA-TACCA
39822373 TTTTACCCCT
Statistics
Matches: 172, Mismatches: 23, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
80 30 0.17
81 142 0.83
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (81 bp):
AATTACCGAAATACCCTTGTAGGGTAGAAATACCAAAATACCCCTGTAGGGTAGAATTACTAAAA
TACCCCTGTAGGGTAG
Found at i:39822890 original size:25 final size:25
Alignment explanation
Indices: 39822829--39822895 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 25
39822819 TTGCATTCAC
* * *
39822829 ATTCTGATTCTAATTCTGTTACCTG
1 ATTCTAATTCTGATTCTATTACCTG
*
39822854 ATACTAATTCTGATTCTATTACCTG
1 ATTCTAATTCTGATTCTATTACCTG
*
39822879 ATTCTAATTCTGGTTCT
1 ATTCTAATTCTGATTCT
39822896 GATTCTAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.22, C:0.19, G:0.10, T:0.48
Consensus pattern (25 bp):
ATTCTAATTCTGATTCTATTACCTG
Found at i:39822927 original size:62 final size:62
Alignment explanation
Indices: 39822829--39822988 Score: 212
Period size: 62 Copynumber: 2.6 Consensus size: 62
39822819 TTGCATTCAC
* * *
39822829 ATTCTGATTCTAATTCTGTTACCTGATACTAATTCTGATTCTATTACCTGATTCTAATTCTG
1 ATTCTGATTCTAATTCTGTTACCTGATACTGATTCTGATTCTATTACCTAAGTCTAATTCTG
* * * *
39822891 GTTCTGATTCTAATTCTGTTACCTGATACTGATTCTGATTGTGTTACCTAAGTCTGATTCTG
1 ATTCTGATTCTAATTCTGTTACCTGATACTGATTCTGATTCTATTACCTAAGTCTAATTCTG
* * * * *
39822953 ATTTTGATTTTGATTCTGTCACCTGATTCTGATTCT
1 ATTCTGATTCTAATTCTGTTACCTGATACTGATTCT
39822989 AATTTTGATT
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 85 1.00
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.47
Consensus pattern (62 bp):
ATTCTGATTCTAATTCTGTTACCTGATACTGATTCTGATTCTATTACCTAAGTCTAATTCTG
Found at i:39822947 original size:25 final size:24
Alignment explanation
Indices: 39822893--39822955 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 24
39822883 TAATTCTGGT
* *
39822893 TCTGATTCTAATTCTGTTACCTGA
1 TCTGATTCTGATTCTGTTACCTAA
*
39822917 TACTGATTCTGATTGTGTTACCTAA
1 T-CTGATTCTGATTCTGTTACCTAA
39822942 GTCTGATTCTGATT
1 -TCTGATTCTGATT
39822956 TTGATTTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 1 0.03
25 32 0.94
26 1 0.03
ACGTcount: A:0.21, C:0.17, G:0.16, T:0.46
Consensus pattern (24 bp):
TCTGATTCTGATTCTGTTACCTAA
Found at i:39822994 original size:37 final size:37
Alignment explanation
Indices: 39822920--39823000 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
39822910 TACCTGATAC
* * *
39822920 TGATTCTGATTGTGTTACCTAAGTCTGATTCTGATTT
1 TGATTCTGATTCTGTCACCTAAGTCTGATTCTAATTT
* * *
39822957 TGATTTTGATTCTGTCACCTGATTCTGATTCTAATTT
1 TGATTCTGATTCTGTCACCTAAGTCTGATTCTAATTT
39822994 TGATTCT
1 TGATTCT
39823001 CAATTTAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.51
Consensus pattern (37 bp):
TGATTCTGATTCTGTCACCTAAGTCTGATTCTAATTT
Found at i:39824091 original size:41 final size:41
Alignment explanation
Indices: 39824046--39824125 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
39824036 CGGAGGAAGA
* *
39824046 AATTGAGGATCGCATGGTTGCTTGACTATCGTGGATCCACC
1 AATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACC
*
39824087 AATTGAGGATCGCTTGGTTGCTTGACGACCGTGGATCCA
1 AATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCA
39824126 TCGGTGGCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (41 bp):
AATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACC
Found at i:39824324 original size:22 final size:22
Alignment explanation
Indices: 39824270--39824334 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
39824260 GCCAATTATT
*
39824270 CTGATTATGGCTTTGTGCCAAC
1 CTGATTATGGCTCTGTGCCAAC
* *
39824292 CT-ACATCTGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
*
39824314 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
39824335 ACGTATTTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.32
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:39827187 original size:28 final size:29
Alignment explanation
Indices: 39827140--39827194 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
39827130 ACAGGGGTTT
39827140 TCACACAGCCAAGCACACGCCCGTGTCCC
1 TCACACAGCCAAGCACACGCCCGTGTCCC
* *
39827169 TCACACGGCCTAG-ACACGCCCGTGTC
1 TCACACAGCCAAGCACACGCCCGTGTC
39827195 ATCGCCCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.22, C:0.45, G:0.20, T:0.13
Consensus pattern (29 bp):
TCACACAGCCAAGCACACGCCCGTGTCCC
Found at i:39835006 original size:50 final size:50
Alignment explanation
Indices: 39834878--39835115 Score: 248
Period size: 50 Copynumber: 4.8 Consensus size: 50
39834868 AGCTGAAGCT
* * * *
39834878 ATCTGATACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-AACA
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACC
* * *
39834927 ATCCGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTCACC
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACC
* * * *
39834977 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTC
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAA-CC
* * * * * *
39835028 AT-TGAGTACGCATAGTAGCCTGAACTTAGTACTACACATGCGTCTTAA-C
1 ATCTGA-TACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACC
* * *
39835077 AGTATGGTACACGTAGTAGCCTGCACTTACTACTACACA
1 A-TCTGATACACGTAGTAGCCTGCACTTAGTACTACACA
39835116 TGTGTATTCA
Statistics
Matches: 158, Mismatches: 26, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
49 42 0.27
50 78 0.49
51 38 0.24
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (50 bp):
ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACC
Found at i:39842444 original size:50 final size:50
Alignment explanation
Indices: 39842316--39842553 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
39842306 AGCCGAAGTT
* * *
39842316 ATCTGATACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-AACA
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACC
* * *
39842365 ATCCGATACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTCACC
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACC
* * * * *
39842415 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTC
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAA-CC
* * *
39842466 AT-TGAGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACTTAA-C
1 ATCTGA-TACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACC
* *
39842515 AGTATGGTACACGTAGTAGCCTGCACTTAGTACTACACA
1 A-TCTGATACACGTAGTAGCCTGCACTTAGTACTACACA
39842554 CGTGTATTCA
Statistics
Matches: 162, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
49 43 0.27
50 79 0.49
51 40 0.25
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (50 bp):
ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTAACC
Found at i:39843870 original size:13 final size:13
Alignment explanation
Indices: 39843852--39843876 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39843842 CCAAGCACAC
39843852 GCCCGTGTCCCTG
1 GCCCGTGTCCCTG
39843865 GCCCGTGTCCCT
1 GCCCGTGTCCCT
39843877 CACACGACCT
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:0.00, C:0.48, G:0.28, T:0.24
Consensus pattern (13 bp):
GCCCGTGTCCCTG
Found at i:39852350 original size:18 final size:19
Alignment explanation
Indices: 39852316--39852356 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
39852306 AAAAGCACCC
*
39852316 TTAAAATAATATGATTTAT
1 TTAAAATAATATAATTTAT
*
39852335 TTAAAAT-ATATAATTTTT
1 TTAAAATAATATAATTTAT
39852353 TTAA
1 TTAA
39852357 TAATTCTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TTAAAATAATATAATTTAT
Found at i:39858748 original size:26 final size:25
Alignment explanation
Indices: 39858719--39858768 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 25
39858709 TTTTGTTAAT
39858719 GGACT-TTTGATGAAAATGTGAAATAG
1 GGACTATTTG-TG-AAATGTGAAATAG
39858745 GGACTAATTTGTGAAATGTGAAAT
1 GGACT-ATTTGTGAAATGTGAAAT
39858769 TTATGAGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 16 0.73
27 2 0.09
28 4 0.18
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (25 bp):
GGACTATTTGTGAAATGTGAAATAG
Found at i:39859315 original size:42 final size:42
Alignment explanation
Indices: 39859268--39859382 Score: 117
Period size: 42 Copynumber: 2.7 Consensus size: 42
39859258 ACTGAAATTC
*
39859268 CGTATAAGACCATATTTGGGATATGGCATTGGTATG-TGATTT
1 CGTATAAGACCATATTAGGGATATGGCATTGGTATGAT-ATTT
* * ** *
39859310 CGTATAAGACCATGTTAGGGACATGGTGTCGGTATGATATTT
1 CGTATAAGACCATATTAGGGATATGGCATTGGTATGATATTT
* * *
39859352 CATGTAAGACCATATCCA-GGATATGGCATTG
1 CGTATAAGACCATAT-TAGGGATATGGCATTG
39859383 ATACAGTACT
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
42 55 0.96
43 2 0.04
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (42 bp):
CGTATAAGACCATATTAGGGATATGGCATTGGTATGATATTT
Found at i:39867421 original size:47 final size:47
Alignment explanation
Indices: 39867349--39867490 Score: 250
Period size: 47 Copynumber: 3.0 Consensus size: 47
39867339 GTTGAATTTA
39867349 AAGCTTGTTAAA-TTGCTCTTAATATTTCCAGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCTCTTAATATTTCCAGATAAGTTACTTAGTT
39867395 AAGCTTGTTAAATTTGCTCTTAATATTTCCAGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCTCTTAATATTTCCAGATAAGTTACTTAGTT
* * *
39867442 AAGCTTGTTAAATTTGCCCTTAATATTTTCGGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCTCTTAATATTTCCAGATAAGTTACTTAGTT
39867489 AA
1 AA
39867491 AGACAATTTT
Statistics
Matches: 92, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
46 12 0.13
47 80 0.87
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (47 bp):
AAGCTTGTTAAATTTGCTCTTAATATTTCCAGATAAGTTACTTAGTT
Found at i:39868370 original size:45 final size:43
Alignment explanation
Indices: 39868300--39868426 Score: 161
Period size: 45 Copynumber: 2.9 Consensus size: 43
39868290 GCACAGTATT
*
39868300 ATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATACTG
1 ATTCGAGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA-A-A-TG
39868346 -TTCGAGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATG
1 ATTCGAGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATG
* * *
39868388 ATATC-AGGCTTCGAGCCTAGCAGGCGA-AATGCCGGTGAA
1 AT-TCGAGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAA
39868427 TGAATTTAGG
Statistics
Matches: 75, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
42 14 0.19
43 21 0.28
44 3 0.04
45 37 0.49
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (43 bp):
ATTCGAGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATG
Found at i:39878635 original size:42 final size:41
Alignment explanation
Indices: 39878528--39878651 Score: 117
Period size: 42 Copynumber: 2.9 Consensus size: 41
39878518 CGAAAAACTC
* *
39878528 ATACAATGCCAATGTCCCAGAC-GTGGTCTTACATGTAATCAA
1 ATACAATGCC-ATGTCCCAGACAG-GGTCTTACACGTAAACAA
* *
39878570 ATATCGATGCCACTGTCTCAGACAGGGTCTTACACG-AAGACAA
1 ATA-CAATGCCA-TGTCCCAGACAGGGTCTTACACGTAA-ACAA
* * *
39878613 TTACAATGCCGATGTCCCAGACATGGTCTTACACATAAA
1 ATACAATGCC-ATGTCCCAGACAGGGTCTTACACGTAAA
39878652 TCTCAAATCG
Statistics
Matches: 67, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
42 33 0.49
43 33 0.49
44 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (41 bp):
ATACAATGCCATGTCCCAGACAGGGTCTTACACGTAAACAA
Found at i:39886543 original size:11 final size:11
Alignment explanation
Indices: 39886527--39886604 Score: 87
Period size: 11 Copynumber: 7.6 Consensus size: 11
39886517 TACAATATTG
39886527 ATATGATATGC
1 ATATGATATGC
*
39886538 ACATGATATG-
1 ATATGATATGC
39886548 -TATGATATGC
1 ATATGATATGC
*
39886558 ACATGATATG-
1 ATATGATATGC
39886568 -TATGATATGC
1 ATATGATATGC
39886578 ATATGATATG-
1 ATATGATATGC
39886588 -TATGATATGC
1 ATATGATATGC
*
39886598 ACATGAT
1 ATATGAT
39886605 GTATTCATAA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
9 25 0.45
11 31 0.55
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (11 bp):
ATATGATATGC
Found at i:39886553 original size:20 final size:20
Alignment explanation
Indices: 39886528--39886604 Score: 145
Period size: 20 Copynumber: 3.9 Consensus size: 20
39886518 ACAATATTGA
39886528 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
39886548 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
*
39886568 TATGATATGCATATGATATG
1 TATGATATGCACATGATATG
39886588 TATGATATGCACATGAT
1 TATGATATGCACATGAT
39886605 GTATTCATAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.36
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:39886554 original size:9 final size:9
Alignment explanation
Indices: 39886540--39886596 Score: 69
Period size: 9 Copynumber: 5.9 Consensus size: 9
39886530 TGATATGCAC
39886540 ATGATATGT
1 ATGATATGT
*
39886549 ATGATATGCAC
1 ATGATATG--T
39886560 ATGATATGT
1 ATGATATGT
39886569 ATGATATGCAT
1 ATGATATG--T
39886580 ATGATATGT
1 ATGATATGT
39886589 ATGATATG
1 ATGATATG
39886597 CACATGATGT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 25 0.60
11 17 0.40
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (9 bp):
ATGATATGT
Found at i:39886683 original size:26 final size:26
Alignment explanation
Indices: 39886654--39886726 Score: 137
Period size: 26 Copynumber: 2.8 Consensus size: 26
39886644 GAGGAAGTGC
39886654 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
39886680 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
39886706 AAAAGGGCCTATGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
39886727 ATTAAAAGAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.22
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:39892925 original size:6 final size:6
Alignment explanation
Indices: 39892908--39893019 Score: 68
Period size: 6 Copynumber: 18.0 Consensus size: 6
39892898 TAACCCATTA
* * * *
39892908 CAGAAT AAGAAT CTGAAT CAGAAT TAG-GT GACAGAAT CAGAAT CAGAAT
1 CAGAAT CAGAAT CAGAAT CAGAAT CAGAAT --CAGAAT CAGAAT CAGAAT
* * *
39892957 CAGTAT CAGGTAA- CAGAAT CAAAAT CAGAAT CAGTAT CAGGTAA- CAGAAT
1 CAGAAT CA-G-AAT CAGAAT CAGAAT CAGAAT CAGAAT CA-G-AAT CAGAAT
*
39893007 CAAAAAT CAGAAT
1 C-AGAAT CAGAAT
39893020 GTGAATGCAA
Statistics
Matches: 80, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
5 5 0.06
6 59 0.74
7 13 0.16
8 3 0.04
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (6 bp):
CAGAAT
Found at i:39892950 original size:31 final size:31
Alignment explanation
Indices: 39892907--39893019 Score: 154
Period size: 31 Copynumber: 3.6 Consensus size: 31
39892897 TTAACCCATT
* * * * *
39892907 ACAGAATAAGAATCTGAATCAGAATTAGGTG
1 ACAGAATCAGAATCAGAATCAGTATCAGGTA
39892938 ACAGAATCAGAATCAGAATCAGTATCAGGTA
1 ACAGAATCAGAATCAGAATCAGTATCAGGTA
*
39892969 ACAGAATCAAAATCAGAATCAGTATCAGGTA
1 ACAGAATCAGAATCAGAATCAGTATCAGGTA
*
39893000 ACAGAATCAAAAATCAGAAT
1 ACAGAATC-AGAATCAGAAT
39893020 GTGAATGCAA
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
31 64 0.85
32 11 0.15
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.19
Consensus pattern (31 bp):
ACAGAATCAGAATCAGAATCAGTATCAGGTA
Found at i:39892975 original size:19 final size:19
Alignment explanation
Indices: 39892951--39893008 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
39892941 GAATCAGAAT
39892951 CAGAATCAGTATCAGGTAA
1 CAGAATCAGTATCAGGTAA
*
39892970 CAGAATCA--A--A---AT
1 CAGAATCAGTATCAGGTAA
39892982 CAGAATCAGTATCAGGTAA
1 CAGAATCAGTATCAGGTAA
39893001 CAGAATCA
1 CAGAATCA
39893009 AAAATCAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
12 9 0.30
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
19 17 0.57
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (19 bp):
CAGAATCAGTATCAGGTAA
Found at i:39893198 original size:27 final size:26
Alignment explanation
Indices: 39893156--39893257 Score: 123
Period size: 27 Copynumber: 3.8 Consensus size: 26
39893146 GTTCAGTTAT
* *
39893156 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGA-A
*
39893183 TAGATATTGTGGCAGAGCCACCAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
*
39893209 CAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCAGAGCCACCAG-AA
* *
39893237 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
39893258 TTAACAGAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 6 0.09
27 52 0.79
28 8 0.12
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.20
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:39893444 original size:22 final size:22
Alignment explanation
Indices: 39893416--39893480 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
39893406 GCAAATACGT
39893416 TTGGCACAAAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
39893438 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
39893460 TTGACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
39893481 AAGGCTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:39893953 original size:27 final size:27
Alignment explanation
Indices: 39893922--39894416 Score: 657
Period size: 27 Copynumber: 18.6 Consensus size: 27
39893912 TACCACACAA
* *
39893922 GGTATCTCGGTAATTCCACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
**
39893949 GGTATTTTAGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
39893976 GGTATTTCGGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* *
39894003 GGTATTGCGATAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* *
39894030 AGTATTTTGGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* *
39894057 GTTATTCCGGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
39894084 GGTATTTCGGTGATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
39894111 GGTATTTTGGTAATTCTACCCTACTA-G
1 GGTATTTCGGTAATTCTACCCTAC-AGG
* * * **
39894138 GGTATTCCGATAATTCTACCTTATTGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* **
39894165 GGTATTTCGTTAATTCTATTCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
39894192 GGTA-TTGGGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
39894218 GGTATTTCGGTAATTCTACCATACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
39894245 GGTATTGT-GGTAATTCTACCCTACAGG
1 GGTATT-TCGGTAATTCTACCCTACAGG
*
39894272 GGTATTTCGGTAATTCTACCCTACAAG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
39894299 GGTATTTCGATAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
39894326 GGTATTTCGGTAATTCTA---T--AGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
39894348 GGTA-TTCTGGTAATTCTATCCTACAGG
1 GGTATTTC-GGTAATTCTACCCTACAGG
*
39894375 GGTATTTCGGTAATTCTGCCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
39894402 GGTATTCCGGTAATT
1 GGTATTTCGGTAATT
39894417 TTATAAATAA
Statistics
Matches: 408, Mismatches: 48, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
21 3 0.01
22 17 0.04
24 1 0.00
25 1 0.00
26 23 0.06
27 358 0.88
28 5 0.01
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (27 bp):
GGTATTTCGGTAATTCTACCCTACAGG
Found at i:39894586 original size:27 final size:27
Alignment explanation
Indices: 39894398--39894579 Score: 229
Period size: 27 Copynumber: 6.7 Consensus size: 27
39894388 TTCTGCCCTA
** *
39894398 CAGGGGTATTCCGGTAATTTTATAAAT
1 CAGGGGTATTTTGGTAATTTTATAAAC
* * * *
39894425 AAAGGGTATTTTAGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTATAAAC
* *
39894452 TAGGGGTATTTTGGTAATTTTGTAAAC
1 CAGGGGTATTTTGGTAATTTTATAAAC
* * *
39894479 TAAGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTATAAAC
*
39894506 CAGGGGTATTTTGGTGATTTTATAAAC
1 CAGGGGTATTTTGGTAATTTTATAAAC
* *
39894533 CAAGGGTATTTTAGTAATTTTATAAAC
1 CAGGGGTATTTTGGTAATTTTATAAAC
39894560 CAGGGGTATTTTGGTAATTT
1 CAGGGGTATTTTGGTAATTT
39894580 GGTAAACTAA
Statistics
Matches: 131, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 131 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (27 bp):
CAGGGGTATTTTGGTAATTTTATAAAC
Found at i:39894586 original size:54 final size:54
Alignment explanation
Indices: 39894398--39894579 Score: 274
Period size: 54 Copynumber: 3.4 Consensus size: 54
39894388 TTCTGCCCTA
** *
39894398 CAGGGGTATTCCGGTAATTTTATAAATAAAGGGTATTTTAGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTACAAAC
* * * *
39894452 TAGGGGTATTTTGGTAATTTTGTAAACTAAGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTACAAAC
* * *
39894506 CAGGGGTATTTTGGTGATTTTATAAACCAAGGGTATTTTAGTAATTTTATAAAC
1 CAGGGGTATTTTGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTACAAAC
39894560 CAGGGGTATTTTGGTAATTT
1 CAGGGGTATTTTGGTAATTT
39894580 GGTAAACTAA
Statistics
Matches: 114, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 114 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (54 bp):
CAGGGGTATTTTGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTACAAAC
Found at i:39897354 original size:40 final size:40
Alignment explanation
Indices: 39897188--39897355 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
39897178 CATTTGAATG
* * *
39897188 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* *
39897228 ATGTCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATT
* * * **
39897268 ATATCCGGGCTAAGACCCGAAGGCAATGGTGCAAGTTACC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * * *
39897308 AAATCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
*
39897348 GTATCCGG
1 ATATCCGG
39897356 TTAAATCCCG
Statistics
Matches: 102, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
39 3 0.03
40 95 0.93
41 4 0.04
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
Found at i:39905339 original size:40 final size:40
Alignment explanation
Indices: 39905173--39905340 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
39905163 CATTTGAATG
* * *
39905173 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* *
39905213 ATGTCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATT
* * * **
39905253 ATATCCGGGCTAAGACCCGAAGGCAATGGTGCAAGTTACC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * * *
39905293 AAATCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
*
39905333 GTATCCGG
1 ATATCCGG
39905341 TTAAATCCGA
Statistics
Matches: 102, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
39 3 0.03
40 95 0.93
41 4 0.04
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
Found at i:39913584 original size:68 final size:70
Alignment explanation
Indices: 39913512--39913709 Score: 294
Period size: 71 Copynumber: 2.8 Consensus size: 70
39913502 ACACCCTGTA
* * * *
39913512 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
39913574 ATAAAT
65 ATAAAT
*
39913580 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
39913645 ATAAAT
65 ATAAAT
*
39913651 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
39913710 AGACAAATCG
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:39913623 original size:41 final size:41
Alignment explanation
Indices: 39913578--39913695 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
39913568 TGAAAGATAA
39913578 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
39913619 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
39913649 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
39913690 ATGTAG
1 ATGTAG
39913696 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:39913635 original size:71 final size:71
Alignment explanation
Indices: 39913546--39913709 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
39913536 GAGATGTATC
39913546 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
39913611 AGGACA
66 AGGACA
39913617 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
39913682 AGGACA
66 AGGACA
39913688 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
39913710 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:39917622 original size:40 final size:40
Alignment explanation
Indices: 39917563--39917770 Score: 227
Period size: 40 Copynumber: 5.2 Consensus size: 40
39917553 CAATTGAATG
* * * * *
39917563 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTATT
* * * * *
39917603 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTATT
* * * *
39917643 ACATCCAGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTATT
* * *
39917683 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTATT
* * **
39917723 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTATT
39917763 ATATCCGG
1 ATATCCGG
39917771 TTGTATTCCG
Statistics
Matches: 143, Mismatches: 25, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 143 1.00
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTATT
Found at i:39919198 original size:44 final size:44
Alignment explanation
Indices: 39919135--39919608 Score: 659
Period size: 44 Copynumber: 10.8 Consensus size: 44
39919125 GGGTGTTACA
*
39919135 GCTATCTTCGATCTGCTCTCTGGCAATACAGAGACGCCAAATCT
1 GCTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCT
* **
39919179 GCTATCTTCGATCTACTCTCTGGTAATACAGAGACGCCAAATCT
1 GCTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCT
* * * *
39919223 GCTATCTTTGA-CTGTCTCTCTAACAATACGGAGACGTCAAATCT
1 GCTATCTTCGATCTG-CTCTCTGACAATACAGAGACGCCAAATCT
* * *
39919267 GTTATCTTCGATCTGCTCTCTAACAATACAGAGATGCCAAATCT
1 GCTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCT
* *
39919311 GCTATCTTCGATCTGCTCTCTGGCAATACAGAGACGTCAAATCT
1 GCTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCT
* *
39919355 GCTATCTTCGACCTGCTCTCTGACAATACAGAGATGCCAAATCT
1 GCTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCT
* *
39919399 GTTATCTTCGATCTGCTCCCTGACAATACAGAGACGCCAAATCT
1 GCTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCT
*
39919443 GCTACCTTCGA-CTTGCTCTCTGACAATACAGAGACGCCAAATCT
1 GCTATCTTCGATC-TGCTCTCTGACAATACAGAGACGCCAAATCT
* *
39919487 GTTATCTTTGATCTGCTCTCTGACAATACAGAGACGCCAAATCT
1 GCTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCT
* * *
39919531 -ATCATCTTTGATCTGCTCTCTGTCAATACAGAGACGCCAAATCT
1 GCT-ATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCT
* *
39919575 G-TCATCTTCGGTCTGCTCTCTGTCAATACAGAGA
1 GCT-ATCTTCGATCTGCTCTCTGACAATACAGAGA
39919609 TGGCAGATGT
Statistics
Matches: 387, Mismatches: 37, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
43 4 0.01
44 379 0.98
45 4 0.01
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.30
Consensus pattern (44 bp):
GCTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCT
Found at i:39931423 original size:16 final size:16
Alignment explanation
Indices: 39931395--39931432 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
39931385 ATAAGCAAAT
*
39931395 TATAAA-CATATAAAA
1 TATAAATCAAATAAAA
39931410 TATAAATCAAATAAAA
1 TATAAATCAAATAAAA
*
39931426 TAAAAAT
1 TATAAAT
39931433 AGATATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (16 bp):
TATAAATCAAATAAAA
Found at i:39931730 original size:12 final size:11
Alignment explanation
Indices: 39931701--39931810 Score: 59
Period size: 12 Copynumber: 9.7 Consensus size: 11
39931691 AACAAAATAT
39931701 ATAATGATATAG
1 ATAAT-ATATAG
*
39931713 ACAATATGATAG
1 ATAATAT-ATAG
39931725 ATAATATATA-
1 ATAATATATAG
*
39931735 A-AATA-ATAT
1 ATAATATATAG
39931744 ATATATATATAG
1 ATA-ATATATAG
* *
39931756 TAAAATATAGGTAAT
1 -ATAATATA--T-AG
39931771 ATAATATATA-
1 ATAATATATAG
*
39931781 ATAATGTATA-
1 ATAATATATAG
*
39931791 ATAATATAATAA
1 ATAATAT-ATAG
39931803 ATAATATA
1 ATAATATA
39931811 CAAAGATAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
8 3 0.04
9 5 0.06
10 17 0.22
11 13 0.16
12 30 0.38
13 2 0.03
14 8 0.10
15 1 0.01
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.35
Consensus pattern (11 bp):
ATAATATATAG
Found at i:39934224 original size:47 final size:47
Alignment explanation
Indices: 39934121--39934300 Score: 206
Period size: 46 Copynumber: 3.9 Consensus size: 47
39934111 GGTAAGGTGC
* *
39934121 CGATGCCATGTCCCAGACATGGT-TTACACTGGCTCACATCTCAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATCTCAAGT
* * * *
39934167 CAATGCCATGTCCCAGTCATGGTCTTACATTGACTTTCATCTCATAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATCTCA-AGT
* * *
39934215 CGATG-CATGTCCCAGACAT-ATCTTACACT-AGCCCTCGTCTCAATGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGA-CTCTCATCTCAA-GT
* *
39934261 CGATGCCATGTCCCAGACATGGCCTTACACTGGCTCTCAT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCAT
39934301 AATGTGGCCG
Statistics
Matches: 109, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
45 2 0.02
46 44 0.40
47 43 0.39
48 20 0.18
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATCTCAAGT
Found at i:39934313 original size:94 final size:93
Alignment explanation
Indices: 39934119--39934345 Score: 242
Period size: 94 Copynumber: 2.4 Consensus size: 93
39934109 TGGGTAAGGT
* *
39934119 GCCGATGCCATGTCCCAGACATGGT-TTACACTGGCTCACATCTCAAGTCAATGCCATGTCCCAG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCCCACATCTCAAGTCAATGCCATGTCCCAG
* * * * *
39934183 TCATGGTCTTACATTGACTTTCATCTCATA
64 ACATGGCCTTACACTGACTCTCATATCATA
* * * * *
39934213 GTCGATGCATGTCCCAGACATATCTTACACTAGCCCTCGTCTCAATGTCGATGCCATGTCCCAGA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCCCACATCTCAA-GTCAATGCCATGTCCCAGA
* * *
39934278 CATGGCCTTACACTGGCTCTCATAAT-GTG
65 CATGGCCTTACACTGACTCTCAT-ATCATA
** *
39934307 GCCGATGTGTGTCCCAGACATGTCTTACACTAGCTCACA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCCCACA
39934346 CACGAAGGAC
Statistics
Matches: 108, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
92 1 0.01
93 31 0.29
94 75 0.69
95 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (93 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCCCACATCTCAAGTCAATGCCATGTCCCAGAC
ATGGCCTTACACTGACTCTCATATCATA
Found at i:39939328 original size:17 final size:17
Alignment explanation
Indices: 39939289--39939338 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
39939279 TATGGGAAGT
* *
39939289 AATCATAGAATATTAGC
1 AATCTTAGAATATTTGC
*
39939306 AATCTTAGAATATTTGT
1 AATCTTAGAATATTTGC
* *
39939323 AGTCTTAGAAAATTTG
1 AATCTTAGAATATTTG
39939339 ATTCTGTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (17 bp):
AATCTTAGAATATTTGC
Found at i:39941005 original size:30 final size:31
Alignment explanation
Indices: 39940969--39941037 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
39940959 TTAAATTATT
* * *
39940969 AATGATAAAATTTTATTTTAA-CTTTTAAAA
1 AATGATAAAAATTTAATTTAATCCTTTAAAA
39940999 AATGATAAAAATTTAATTTAATCCTTTAAAA
1 AATGATAAAAATTTAATTTAATCCTTTAAAA
*
39941030 TAT-ATAAA
1 AATGATAAA
39941038 GATATAGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (31 bp):
AATGATAAAAATTTAATTTAATCCTTTAAAA
Found at i:39943299 original size:3 final size:3
Alignment explanation
Indices: 39943291--39943340 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
39943281 ATACAAAGTA
* *
39943291 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
39943339 AA
1 AA
39943341 GCTTGTTCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:39947407 original size:69 final size:71
Alignment explanation
Indices: 39947325--39947459 Score: 168
Period size: 69 Copynumber: 1.9 Consensus size: 71
39947315 ATATGTGAGG
* * * * * * * *
39947325 TTATATTGAACTTGTATATTTGGTTACATGTGA-GGTTATATTGAATTTGTATA-TCGGCCATAT
1 TTATATTGAACTTGAACATTAGGTTACATGTAATGATT-TATTGAACTTATATATTCGACCATAT
39947388 GACATGT
65 GACATGT
39947395 TTAT-TTGAACTTGAACATTAGGTTACATGTAATGATTTATTGAACTTATATATTCGACCATATG
1 TTATATTGAACTTGAACATTAGGTTACATGTAATGATTTATTGAACTTATATATTCGACCATATG
39947459 A
66 A
39947460 AATAATATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
69 37 0.67
70 18 0.33
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (71 bp):
TTATATTGAACTTGAACATTAGGTTACATGTAATGATTTATTGAACTTATATATTCGACCATATG
ACATGT
Found at i:39952057 original size:45 final size:45
Alignment explanation
Indices: 39951996--39952397 Score: 572
Period size: 45 Copynumber: 8.9 Consensus size: 45
39951986 GATTATCATT
*
39951996 TCACCGGCATTATAGCCTGCTAGGCTCGAAA-GCCCGAATAGTATC
1 TCACCGGCATCATAGCCTGCTAGGCTC-AAAGGCCCGAATAGTATC
* * * *
39952041 TTACCGACATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
1 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
* *
39952086 TCACCGGCATCATAGCCTACTAGGCTCAAAGGCCCGAATAGTATT
1 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
* * * *
39952131 TCACCGACATCATAGCCTGCTAGGTTTAAAGGCCCGAATAATATC
1 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
* * * *
39952176 TCACCAGCATCATAACCTGCTAGGCTCAAAGGTCCGAATAGTATT
1 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
*
39952221 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
1 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
* * * *
39952266 TCACCGGCATCTTAGCCTGCTAGGCTCAAAAGCCCGAACAATATC
1 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
* * *
39952311 TCACCAGCATCATAGCCTACTAGGCTCAAAGGCCCGAATAGTATT
1 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
*
39952356 TCACCGGCATCATAGCCTGCTACGCTCAAAGGCCCGAATAGT
1 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGT
39952398 CAAATCAACG
Statistics
Matches: 315, Mismatches: 41, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
44 3 0.01
45 312 0.99
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (45 bp):
TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
Found at i:39954154 original size:2 final size:2
Alignment explanation
Indices: 39954147--39954190 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
39954137 ATCACTTTCA
39954147 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39954189 AT
1 AT
39954191 CGAATTCCAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39960739 original size:2 final size:2
Alignment explanation
Indices: 39960726--39960760 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
39960716 AGATGTTAAT
* *
39960726 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39960761 GTTAGCGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39965156 original size:123 final size:123
Alignment explanation
Indices: 39964937--39965275 Score: 597
Period size: 123 Copynumber: 2.8 Consensus size: 123
39964927 GAATTATGTG
*
39964937 AAATGAAATATGGATGTGTAATGATTATTGACATATGTGTGTATGAGTATTTGAATGGTACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
*
39965002 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
39965060 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
39965125 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
* * * * *
39965183 AAATGAAATATGGATGTGTAATGATTATTGATTTATGTGTGCATGAGCAATTGAATGATACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
* *
39965248 GCTAAGTCCCGAAGACATTTATGCTAGT
66 GCTAAGTCCCGAAGGCAATTATGCTAGT
39965276 AATTATATCC
Statistics
Matches: 207, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 207 1.00
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (123 bp):
AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
Found at i:39965299 original size:40 final size:40
Alignment explanation
Indices: 39965244--39965487 Score: 301
Period size: 40 Copynumber: 6.1 Consensus size: 40
39965234 TGAATGATAC
* * * * **
39965244 CCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* * * *
39965284 CCGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGACTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTG-TTATAT
*
39965324 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
*
39965364 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* *
39965404 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* * ** *
39965444 CCGGGCTAAGACCCGAGGGCATTCGTGCGTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
39965484 CCGG
1 CCGG
39965488 TTGTATTCCG
Statistics
Matches: 182, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
40 180 0.99
41 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
Found at i:39966554 original size:22 final size:22
Alignment explanation
Indices: 39966529--39966572 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
39966519 AACAAACGGC
39966529 ATCAGCATTGAAGCCTTGTACA
1 ATCAGCATTGAAGCCTTGTACA
39966551 ATCAGCATTGAAGCCTTGTACA
1 ATCAGCATTGAAGCCTTGTACA
39966573 GGGAGATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (22 bp):
ATCAGCATTGAAGCCTTGTACA
Found at i:39969172 original size:91 final size:93
Alignment explanation
Indices: 39968952--39969175 Score: 278
Period size: 91 Copynumber: 2.5 Consensus size: 93
39968942 AATACCATAG
* * * * * *
39968952 TAATACACAAATTGATAG-TTCATGTACTACATTGGA-AATTTCAAAGTATAAAATACTACATTG
1 TAATACACAAATTGATAGTTTCAGGTACCACATTAGATATTTTCAAAGTATAAAATACCACATTC
*
39969015 GACATTTTATGGAAATACAGGTACCAAA
66 GACATTTTATGAAAATACAGGTACCAAA
* * * *
39969043 TAATACACAAATTAATAGTTT-AGGTACCACTTTAGATATTTTCAAAGTA-CATATACCACATTC
1 TAATACACAAATTGATAGTTTCAGGTACCACATTAGATATTTTCAAAGTATAAAATACCACATTC
* *
39969106 GACATTTTATGAAAATACATGTTCCAAA
66 GACATTTTATGAAAATACAGGTACCAAA
* *
39969134 TATTACACATATTGATAGTTTCA-GTACCACATTAGATATTTT
1 TAATACACAAATTGATAGTTTCAGGTACCACATTAGATATTTT
39969176 TAATTATAAC
Statistics
Matches: 113, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
91 99 0.88
92 14 0.12
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (93 bp):
TAATACACAAATTGATAGTTTCAGGTACCACATTAGATATTTTCAAAGTATAAAATACCACATTC
GACATTTTATGAAAATACAGGTACCAAA
Found at i:39970513 original size:99 final size:99
Alignment explanation
Indices: 39970342--39970542 Score: 357
Period size: 99 Copynumber: 2.0 Consensus size: 99
39970332 AATTATTAAC
* *
39970342 CAGCATGCAATTACAATAAAGTAGTATAAAATGCAGAGGACAAGGCAAGAATGCATAGACACTCC
1 CAGCATGCAATTACAAAAAAGTAGTATAAAATGCAGAGGACAAGGCAAGAATGCATAGACACACC
*
39970407 TGTTTCTTGTGGGTGTTATGATTACAGAGAAAAA
66 TATTTCTTGTGGGTGTTATGATTACAGAGAAAAA
* *
39970441 CAGCATGCAATTACAAAAAAGTTGTATAAAATGCAGAGGACAAGGCAAGAATGCATAGACAGACC
1 CAGCATGCAATTACAAAAAAGTAGTATAAAATGCAGAGGACAAGGCAAGAATGCATAGACACACC
39970506 TATTTCTTGTGGGTGTTATGATTACAGAGAAAAA
66 TATTTCTTGTGGGTGTTATGATTACAGAGAAAAA
39970540 CAG
1 CAG
39970543 AAATTCAGCA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.23
Consensus pattern (99 bp):
CAGCATGCAATTACAAAAAAGTAGTATAAAATGCAGAGGACAAGGCAAGAATGCATAGACACACC
TATTTCTTGTGGGTGTTATGATTACAGAGAAAAA
Found at i:39972115 original size:45 final size:45
Alignment explanation
Indices: 39972051--39972143 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
39972041 ATAAAAGGGA
39972051 AAGAGAAAAGGAAACCTGGAAGAAGTGGATGAAGTGAAAGAAGTT
1 AAGAGAAAAGGAAACCTGGAAGAAGTGGATGAAGTGAAAGAAGTT
39972096 AAGAGAAAAGGAAACCTGGAAGAAGTGGATGAAGTGAAAGAAGTT
1 AAGAGAAAAGGAAACCTGGAAGAAGTGGATGAAGTGAAAGAAGTT
39972141 AAG
1 AAG
39972144 TGTTAAGCAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.49, C:0.04, G:0.33, T:0.13
Consensus pattern (45 bp):
AAGAGAAAAGGAAACCTGGAAGAAGTGGATGAAGTGAAAGAAGTT
Found at i:39973438 original size:27 final size:27
Alignment explanation
Indices: 39973396--39973459 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
39973386 GTGGAGAGTG
**
39973396 TCAGATAGGCGGCACCAGTTGTGCCTA
1 TCAGATAGGCAACACCAGTTGTGCCTA
39973423 TCAGATAGGCAACACCAGTTGTGCCTA
1 TCAGATAGGCAACACCAGTTGTGCCTA
*
39973450 TCTGATAGGC
1 TCAGATAGGC
39973460 GGCACACCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (27 bp):
TCAGATAGGCAACACCAGTTGTGCCTA
Found at i:39973568 original size:14 final size:14
Alignment explanation
Indices: 39973551--39973577 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39973541 GAAGAGGAGA
39973551 AAGAAAGAAAAGAG
1 AAGAAAGAAAAGAG
39973565 AAGAAAGAAAAGA
1 AAGAAAGAAAAGA
39973578 AATGTAATTT
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:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AAGAAAGAAAAGAG
Found at i:39973569 original size:18 final size:19
Alignment explanation
Indices: 39973542--39973579 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
39973532 AGAGAGGGAG
*
39973542 AAGAGGAGAAAG-AAAGAA
1 AAGAGAAGAAAGAAAAGAA
39973560 AAGAGAAGAAAGAAAAGAA
1 AAGAGAAGAAAGAAAAGAA
39973579 A
1 A
39973580 TGTAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (19 bp):
AAGAGAAGAAAGAAAAGAA
Found at i:39976413 original size:40 final size:39
Alignment explanation
Indices: 39976285--39976427 Score: 178
Period size: 39 Copynumber: 3.6 Consensus size: 39
39976275 AATGTTCGAG
*
39976285 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* *
39976324 TGATATCCGGGCTAAGCCCGAAGGCAATTGTACGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
39976363 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
39976403 CCATAACCGGGCTACGTCCCGAAGG
1 TGATATCCGGGCTAAG-CCCGAAGG
39976428 TGTTTTGAAC
Statistics
Matches: 90, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 51 0.57
40 39 0.43
ACGTcount: A:0.24, C:0.23, G:0.31, T:0.22
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:39984337 original size:40 final size:39
Alignment explanation
Indices: 39984209--39984351 Score: 187
Period size: 39 Copynumber: 3.6 Consensus size: 39
39984199 AATGTTCGAG
*
39984209 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
39984248 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
39984287 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
39984327 CCATAACCGGGCTACGTCCCGAAGG
1 TGATATCCGGGCTAAG-CCCGAAGG
39984352 TGTTTTGAAC
Statistics
Matches: 92, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 52 0.57
40 40 0.43
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.22
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:39987763 original size:64 final size:64
Alignment explanation
Indices: 39987661--39987816 Score: 262
Period size: 64 Copynumber: 2.5 Consensus size: 64
39987651 TGAGCTCATG
* * *
39987661 TAATTTATATAA-A-AAATTATATTACAAAGTTTGTTCCAATTAAATTATGGTTGTAATGTATT
1 TAATTTATATAACATAATTTATATTACAAAGTTTGCTCCAATTAAATTATGATTGTAATGTATT
*
39987723 TAATTTATATAACATAATTTATATTACAAAGTTTGCTCCAATTAGATTATGATTGTAATGTATT
1 TAATTTATATAACATAATTTATATTACAAAGTTTGCTCCAATTAAATTATGATTGTAATGTATT
39987787 TAATTTATATAACATAATTTATATTACAAA
1 TAATTTATATAACATAATTTATATTACAAA
39987817 ACTAAGTTTG
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
62 12 0.14
63 1 0.01
64 75 0.85
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (64 bp):
TAATTTATATAACATAATTTATATTACAAAGTTTGCTCCAATTAAATTATGATTGTAATGTATT
Found at i:39988221 original size:33 final size:32
Alignment explanation
Indices: 39988184--39988345 Score: 119
Period size: 33 Copynumber: 4.9 Consensus size: 32
39988174 CTTGAGCTGG
* *
39988184 GAGGAGTGCCATACTGCGGTGGATACGACCTA
1 GAGGAGTGCTATACTGCGGTGGATACGACCGA
* * * * *
39988216 TGAGGAGTG-GAGTATTACGTTGGATACGGGCCGA
1 -GAGGAGTGCTA-TACTGCGGTGGATAC-GACCGA
* * * *
39988250 GGGGAGTGCTGTACTGCGGTGGATACGAGCTGG
1 GAGGAGTGCTATACTGCGGTGGATACGA-CCGA
* * * * * *
39988283 GAGGAGTGTTGTACTACAGTGGATATAGGCCGA
1 GAGGAGTGCTATACTGCGGTGGATA-CGACCGA
39988316 GAGGAGTGCTATACTGCGGTGGATACGACC
1 GAGGAGTGCTATACTGCGGTGGATACGACC
39988346 CAAAGATATC
Statistics
Matches: 95, Mismatches: 29, Indels: 11
0.70 0.21 0.08
Matches are distributed among these distances:
32 5 0.05
33 85 0.89
34 5 0.05
ACGTcount: A:0.23, C:0.16, G:0.40, T:0.22
Consensus pattern (32 bp):
GAGGAGTGCTATACTGCGGTGGATACGACCGA
Found at i:39988306 original size:66 final size:66
Alignment explanation
Indices: 39988184--39988345 Score: 209
Period size: 66 Copynumber: 2.5 Consensus size: 66
39988174 CTTGAGCTGG
* * * *
39988184 GAGGAGTGCCATACTGCGGTGGATACGACCTATGAGGAGTGGAGTATTACGTTGGATACGGGCCG
1 GAGGAGTGCTATACTGCGGTGGATACGACCTAGGAGGAGTGGAGTACTACGTTGGATACAGGCCG
39988249 A
66 A
* * * * ** *
39988250 GGGGAGTGCTGTACTGCGGTGGATACGAGCTGGGAGGAGTGTTGTACTACAG-TGGATATAGGCC
1 GAGGAGTGCTATACTGCGGTGGATACGACCTAGGAGGAGTGGAGTACTAC-GTTGGATACAGGCC
39988314 GA
65 GA
39988316 GAGGAGTGCTATACTGCGGTGGATACGACC
1 GAGGAGTGCTATACTGCGGTGGATACGACC
39988346 CAAAGATATC
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
66 80 0.99
67 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.40, T:0.22
Consensus pattern (66 bp):
GAGGAGTGCTATACTGCGGTGGATACGACCTAGGAGGAGTGGAGTACTACGTTGGATACAGGCCG
A
Found at i:39990765 original size:16 final size:17
Alignment explanation
Indices: 39990732--39990767 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
39990722 TATAAAACAT
* *
39990732 AAAATAAGATTTTAAAA
1 AAAATAAAATCTTAAAA
39990749 AAAATAAAATCTTAAAA
1 AAAATAAAATCTTAAAA
39990766 AA
1 AA
39990768 TTAAAACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (17 bp):
AAAATAAAATCTTAAAA
Found at i:39993717 original size:42 final size:42
Alignment explanation
Indices: 39993658--39993740 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
39993648 TGTGCCAGAC
39993658 CGTGTAACTCTCTGAGTTGCCACAAATGACCATGTGACAGCT
1 CGTGTAACTCTCTGAGTTGCCACAAATGACCATGTGACAGCT
39993700 CGTGTAACTCTCTGAGTTGCCACAAATGACCATGTGACAGC
1 CGTGTAACTCTCTGAGTTGCCACAAATGACCATGTGACAGC
39993741 CTGTGTCGCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (42 bp):
CGTGTAACTCTCTGAGTTGCCACAAATGACCATGTGACAGCT
Found at i:39994188 original size:36 final size:36
Alignment explanation
Indices: 39994079--39994167 Score: 162
Period size: 36 Copynumber: 2.5 Consensus size: 36
39994069 CAAGCACTTA
*
39994079 AAAG-TCACCAAATTAACACAACTTCATAATACACT
1 AAAGTTCACCAAATCAACACAACTTCATAATACACT
39994114 AAAGTTCACCAAATCAACACAACTTCATAATACACT
1 AAAGTTCACCAAATCAACACAACTTCATAATACACT
39994150 AAAGTTCACCAAATCAAC
1 AAAGTTCACCAAATCAAC
39994168 CATAATTTCC
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
35 4 0.08
36 48 0.92
ACGTcount: A:0.48, C:0.27, G:0.03, T:0.21
Consensus pattern (36 bp):
AAAGTTCACCAAATCAACACAACTTCATAATACACT
Found at i:39999068 original size:49 final size:49
Alignment explanation
Indices: 39998986--39999100 Score: 133
Period size: 49 Copynumber: 2.3 Consensus size: 49
39998976 ATATCACACC
* * * *
39998986 AATAATATGGTCAAGCCACCTGATAGTGCAGACAAGCTGCCAAATAC-A
1 AATATTATGGTCAAGCCACCAGATAATGCAGACAAGCTACCAAATACTA
* * * *
39999034 GAATATTGTGGTCAAGCCCCCAGATAATGTAGACAAGCTACCAGATACTA
1 -AATATTATGGTCAAGCCACCAGATAATGCAGACAAGCTACCAAATACTA
*
39999084 AATATTATAGTCAAGCC
1 AATATTATGGTCAAGCC
39999101 TCTAGATTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 54 0.98
50 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (49 bp):
AATATTATGGTCAAGCCACCAGATAATGCAGACAAGCTACCAAATACTA
Found at i:40002383 original size:66 final size:66
Alignment explanation
Indices: 40002311--40002441 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 66
40002301 CTAATAACAT
*
40002311 GACCTAAGAATGATATATTTAATAAATGAACAGTTTTAAAAAATAACAAAGATAAACCACGATTT
1 GACCTAAGAATGATAGATTTAATAAATGAACAGTTTTAAAAAATAACAAAGATAAACCACGATTT
40002376 A
66 A
* *
40002377 GACCTAAGAATGATAGATTTAATAAATGATCAGTTTTAAAAAATAACAAAGATAAACCATGATTT
1 GACCTAAGAATGATAGATTTAATAAATGAACAGTTTTAAAAAATAACAAAGATAAACCACGATTT
40002442 TTAATAAAAG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.50, C:0.10, G:0.11, T:0.28
Consensus pattern (66 bp):
GACCTAAGAATGATAGATTTAATAAATGAACAGTTTTAAAAAATAACAAAGATAAACCACGATTT
A
Found at i:40010401 original size:40 final size:40
Alignment explanation
Indices: 40010357--40010437 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
40010347 TTATCCACGG
* *
40010357 TTATGGACTGACGGTGGGTTGACGTGAATCATAGGTGCTT
1 TTATGGACTAACGATGGGTTGACGTGAATCATAGGTGCTT
**
40010397 TTATGGACTAACGATGGGTTTTCGTGAATCATAGGTGCTT
1 TTATGGACTAACGATGGGTTGACGTGAATCATAGGTGCTT
40010437 T
1 T
40010438 GTTCTCAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.21, C:0.12, G:0.31, T:0.36
Consensus pattern (40 bp):
TTATGGACTAACGATGGGTTGACGTGAATCATAGGTGCTT
Found at i:40014455 original size:27 final size:27
Alignment explanation
Indices: 40014409--40014461 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
40014399 CTAGAACATG
* *
40014409 GGCCTGGCACATGGGTGTGTATGGCAC
1 GGCCTGGCACACGGGCGTGTATGGCAC
40014436 GGCCTGGCACACGGGCGTGTATGGCA
1 GGCCTGGCACACGGGCGTGTATGGCA
40014462 AATTTTAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.15, C:0.25, G:0.42, T:0.19
Consensus pattern (27 bp):
GGCCTGGCACACGGGCGTGTATGGCAC
Found at i:40016331 original size:40 final size:40
Alignment explanation
Indices: 40016169--40016370 Score: 148
Period size: 40 Copynumber: 5.1 Consensus size: 40
40016159 CGAATGATGT
*
40016169 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGT-GACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AAGTCG-CTATAA
* * * * ***
40016209 CCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATA-AA
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCAAGTCGCTATAA
**
40016248 TCCGGGCTAA-TCCCGAAGGC-TTTGTGCAAGTTACTA-AA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTCGCTATAA
* *
40016286 CCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTCGCTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTCGCTATAA
** * * * *
40016327 CCGGGCTTCGTCCCGAAGGCATTTGAGCGAGTCGTTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTCGCTATAA
40016367 CCGG
1 CCGG
40016371 TTAAATTCCG
Statistics
Matches: 129, Mismatches: 25, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
38 24 0.19
39 19 0.15
40 77 0.60
41 9 0.07
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTCGCTATAA
Found at i:40016333 original size:78 final size:79
Alignment explanation
Indices: 40016168--40016319 Score: 200
Period size: 78 Copynumber: 1.9 Consensus size: 79
40016158 TCGAATGATG
* * *
40016168 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAA-TCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
* *
40016233 GTGCGAGTTAATAAA
65 GTGCAAGTCAATAAA
* **
40016248 TCCGGGCTAATCCCGAAGGCTTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATTC
1 TCCGGGCTAATCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATTC
40016311 GTGCAAGTC
65 GTGCAAGTC
40016320 GCTATAACCG
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
77 1 0.02
78 35 0.56
79 17 0.27
80 10 0.16
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (79 bp):
TCCGGGCTAATCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTCG
TGCAAGTCAATAAA
Found at i:40023563 original size:40 final size:40
Alignment explanation
Indices: 40023401--40023602 Score: 148
Period size: 40 Copynumber: 5.1 Consensus size: 40
40023391 CGAATGATGT
*
40023401 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGT-GACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AAGTCG-CTATAA
* * * * ***
40023441 CCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATA-AA
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCAAGTCGCTATAA
**
40023480 TCCGGGCTAA-TCCCGAAGGC-TTTGTGCAAGTTACTA-AA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTCGCTATAA
* *
40023518 CCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTCGCTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTCGCTATAA
** * * * *
40023559 CCGGGCTTCGTCCCGAAGGCATTTGAGCGAGTCGTTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTCGCTATAA
40023599 CCGG
1 CCGG
40023603 TTAAATTCCG
Statistics
Matches: 129, Mismatches: 25, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
38 24 0.19
39 19 0.15
40 77 0.60
41 9 0.07
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTCGCTATAA
Done.