Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 308 of 310
Found at i:101440137 original size:63 final size:63
Alignment explanation
Indices: 101440046--101440167 Score: 217
Period size: 63 Copynumber: 1.9 Consensus size: 63
101440036 TTACCCATCT
* *
101440046 GGGCTAAATTCTTAATGCACCCATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCCAACC
1 GGGCTAAATCCTTAATGCACACATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCCAACC
*
101440109 GGGCTAGATCCTTAATGCACACATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCC
1 GGGCTAAATCCTTAATGCACACATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCC
101440168 GTCCAGGCTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.20
Consensus pattern (63 bp):
GGGCTAAATCCTTAATGCACACATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCCAACC
Found at i:101440182 original size:63 final size:63
Alignment explanation
Indices: 101440047--101440184 Score: 213
Period size: 63 Copynumber: 2.2 Consensus size: 63
101440037 TACCCATCTG
* * * *
101440047 GGCTAAATTCTTAATGCACCCATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCCAACCG
1 GGCTAGATCCTTAATGCACACATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCCAACCA
**
101440110 GGCTAGATCCTTAATGCACACATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCCGTCCA
1 GGCTAGATCCTTAATGCACACATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCCAACCA
*
101440173 GGCTTGATCCTT
1 GGCTAGATCCTT
101440185 TCTATATTTG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.22
Consensus pattern (63 bp):
GGCTAGATCCTTAATGCACACATATTCTTCGGGAGGCTCGACCACTCAAGGAACACCCAACCA
Found at i:101441576 original size:29 final size:29
Alignment explanation
Indices: 101441530--101441636 Score: 119
Period size: 29 Copynumber: 3.7 Consensus size: 29
101441520 TTCGACTTTG
101441530 AAAGGGATGGTGACGACCATCAACTATGA
1 AAAGGGATGGTGACGACCATCAACTATGA
* * *
101441559 AAAGGGATGATGATGACCATCAACTAATCA
1 AAAGGGATGGTGACGACCATCAACT-ATGA
* **
101441589 AAACGGATGGTTCCGACCATCGAA-TATGA
1 AAAGGGATGGTGACGACCATC-AACTATGA
*
101441618 AAAGGGAT-GTTACGACCAT
1 AAAGGGATGGTGACGACCAT
101441637 ATTTAACACA
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
28 10 0.15
29 33 0.51
30 20 0.31
31 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (29 bp):
AAAGGGATGGTGACGACCATCAACTATGA
Found at i:101443517 original size:25 final size:25
Alignment explanation
Indices: 101443483--101443532 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
101443473 TTAAATTACT
101443483 GAAGTGGCTCAATTTTATCTCACAA
1 GAAGTGGCTCAATTTTATCTCACAA
101443508 GAAGTGGCTCAATTTTATCTCACAA
1 GAAGTGGCTCAATTTTATCTCACAA
101443533 TCTCAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (25 bp):
GAAGTGGCTCAATTTTATCTCACAA
Found at i:101445635 original size:27 final size:27
Alignment explanation
Indices: 101445605--101445658 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
101445595 TTAGACATAG
101445605 TCAACTATGCAACATACCTTTAAATTA
1 TCAACTATGCAACATACCTTTAAATTA
101445632 TCAACTATGCAACATACCTTTAAATTA
1 TCAACTATGCAACATACCTTTAAATTA
101445659 ATCTAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (27 bp):
TCAACTATGCAACATACCTTTAAATTA
Found at i:101446482 original size:53 final size:53
Alignment explanation
Indices: 101446402--101446507 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
101446392 ATGAGAAGAG
*
101446402 GCATTCTTGTTAACAAAGAATATCATTTTGACCTAGAGATTGATAGAACTTTA
1 GCATTCCTGTTAACAAAGAATATCATTTTGACCTAGAGATTGATAGAACTTTA
101446455 GCATTCCTGTTAACAAAGAATATCATTTTGACCTAGAGATTGATAGAACTTTA
1 GCATTCCTGTTAACAAAGAATATCATTTTGACCTAGAGATTGATAGAACTTTA
101446508 TGAAGAAGGC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (53 bp):
GCATTCCTGTTAACAAAGAATATCATTTTGACCTAGAGATTGATAGAACTTTA
Found at i:101464691 original size:18 final size:18
Alignment explanation
Indices: 101464668--101464703 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
101464658 TCCTTCAAGA
101464668 GTTTTGGGTTTTCTTTAT
1 GTTTTGGGTTTTCTTTAT
101464686 GTTTTGGGTTTTCTTTAT
1 GTTTTGGGTTTTCTTTAT
101464704 TCTTCTGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.06, C:0.06, G:0.22, T:0.67
Consensus pattern (18 bp):
GTTTTGGGTTTTCTTTAT
Found at i:101491523 original size:28 final size:28
Alignment explanation
Indices: 101491490--101491624 Score: 121
Period size: 28 Copynumber: 4.8 Consensus size: 28
101491480 TACATCCATG
*
101491490 CATATGACCCATTAGGCCCAATCTCATT
1 CATATGGCCCATTAGGCCCAATCTCATT
* *
101491518 TATATGGCCCATTCGGCCCAAT-TCACGTT
1 CATATGGCCCATTAGGCCCAATCTCA--TT
* * * *
101491547 CATATGGCCTATTAGGACCAGTTCACATT
1 CATATGGCCCATTAGGCCCA-ATCTCATT
* * *
101491576 CCTACGGCCCATTAGGCCCAATCTCCTT
1 CATATGGCCCATTAGGCCCAATCTCATT
*
101491604 TATATGGCCCATCT-GGCCCAA
1 CATATGGCCCAT-TAGGCCCAA
101491625 ATCACATTAT
Statistics
Matches: 83, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
27 3 0.04
28 40 0.48
29 37 0.45
30 1 0.01
31 2 0.02
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.28
Consensus pattern (28 bp):
CATATGGCCCATTAGGCCCAATCTCATT
Found at i:101491634 original size:28 final size:28
Alignment explanation
Indices: 101491491--101491636 Score: 109
Period size: 29 Copynumber: 5.1 Consensus size: 28
101491481 ACATCCATGC
* *
101491491 ATATGACCCATTAGGCCC-AATCTCATTT
1 ATATGGCCCATTAGGCCCAAATCACA-TT
* * *
101491519 ATATGGCCCATTCGGCCCAATTCACGTT
1 ATATGGCCCATTAGGCCCAAATCACATT
* * **
101491547 CATATGGCCTATTAGGACCAGTTCACATT
1 -ATATGGCCCATTAGGCCCAAATCACATT
* * * *
101491576 CCTACGGCCCATTAGGCCC-AATCTCCTTT
1 -ATATGGCCCATTAGGCCCAAATC-ACATT
101491605 ATATGGCCCATCT-GGCCCAAATCACATT
1 ATATGGCCCAT-TAGGCCCAAATCACATT
101491633 ATAT
1 ATAT
101491637 TCATGCTCAC
Statistics
Matches: 91, Mismatches: 22, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
28 41 0.45
29 50 0.55
ACGTcount: A:0.25, C:0.31, G:0.14, T:0.29
Consensus pattern (28 bp):
ATATGGCCCATTAGGCCCAAATCACATT
Found at i:101491726 original size:18 final size:19
Alignment explanation
Indices: 101491703--101491739 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
101491693 TATGGCCCAA
*
101491703 TAGCCCA-TCGGGCCCATT
1 TAGCCCATTCCGGCCCATT
101491721 TAGCCCATTCCGGCCCATT
1 TAGCCCATTCCGGCCCATT
101491740 AAGCTAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.16, C:0.41, G:0.19, T:0.24
Consensus pattern (19 bp):
TAGCCCATTCCGGCCCATT
Found at i:101492491 original size:27 final size:27
Alignment explanation
Indices: 101492433--101492522 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 27
101492423 AGGAAGCGTC
101492433 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
101492461 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
*
101492488 CTGGTGGTACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
101492517 CTGGTG
1 CTGGTG
101492523 ACTCTATCAC
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
27 22 0.41
28 25 0.46
29 7 0.13
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:101492541 original size:55 final size:56
Alignment explanation
Indices: 101492433--101492547 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
101492423 AGGAAGCGTC
* * *
101492433 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTACCACATATATCTGTAT
* * *
101492488 CTGGTGG-TACTGCCACAAAATATCTGTATCTGGTGACTCTATCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTACCACATATATCTGTAT
101492544 CTGG
1 CTGG
101492548 CAGCCATGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 2 0.04
55 29 0.57
56 20 0.39
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTACCACATATATCTGTAT
Found at i:101493635 original size:11 final size:10
Alignment explanation
Indices: 101493607--101493640 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
101493597 AGCCTGTAAG
101493607 TATTCTGAAT
1 TATTCTGAAT
*
101493617 TTTTCTGAAT
1 TATTCTGAAT
101493627 ATATTCTGAAT
1 -TATTCTGAAT
101493638 TAT
1 TAT
101493641 CTGTCTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:101499820 original size:28 final size:28
Alignment explanation
Indices: 101499760--101499825 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
101499750 GATTTACTAG
**
101499760 AATACCCCTATGTATGCAAAATTACCAT
1 AATACCCCTATGTATGCAAAACGACCAT
*
101499788 AATACCCCTATGTATGCAAAACGACCTT
1 AATACCCCTATGTATGCAAAACGACCAT
*
101499816 TATACCCCTA
1 AATACCCCTA
101499826 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.36, C:0.29, G:0.08, T:0.27
Consensus pattern (28 bp):
AATACCCCTATGTATGCAAAACGACCAT
Found at i:101499990 original size:27 final size:27
Alignment explanation
Indices: 101499932--101500021 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 27
101499922 AGGAAGCGTC
101499932 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
101499960 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
101499987 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
101500016 CTGGTG
1 CTGGTG
101500022 ACTCTGTCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:101501687 original size:27 final size:27
Alignment explanation
Indices: 101501657--101501763 Score: 121
Period size: 27 Copynumber: 3.9 Consensus size: 27
101501647 GGCTGCCAAA
* *
101501657 ACAGATAATGTGACAGAGTCACCAGAT
1 ACAGATAATGTGGCAGAGCCACCAGAT
* *
101501684 ACAGATAATCGTGGCCGAACCACCAGA-
1 ACAGATAAT-GTGGCAGAGCCACCAGAT
101501711 ACAGATATATGTGGCAGAGCCACCAGAT
1 ACAGATA-ATGTGGCAGAGCCACCAGAT
101501739 -CAGATAATTGTGGCATG-GCCACCAG
1 ACAGATAA-TGTGGCA-GAGCCACCAG
101501764 GACGCTTCCT
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
26 1 0.01
27 52 0.75
28 16 0.23
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (27 bp):
ACAGATAATGTGGCAGAGCCACCAGAT
Found at i:101503207 original size:24 final size:24
Alignment explanation
Indices: 101503180--101503226 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
101503170 CTGGATTTCC
**
101503180 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
101503204 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
101503227 CTCCTGACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.38, G:0.02, T:0.36
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:101509536 original size:27 final size:27
Alignment explanation
Indices: 101509506--101509612 Score: 119
Period size: 27 Copynumber: 3.9 Consensus size: 27
101509496 GGCTGCCAAA
* * *
101509506 ACAGATAATGTGACAGGGTCACCAGAT
1 ACAGATAATGTGGCAGAGCCACCAGAT
* *
101509533 ACAGATAATCGTGGCCGAACCACCAGA-
1 ACAGATAAT-GTGGCAGAGCCACCAGAT
101509560 ACAGATATATGTGGCAGAGCCACCAGAT
1 ACAGATA-ATGTGGCAGAGCCACCAGAT
*
101509588 -CAGATAATTGTGGCATAGCCACCAG
1 ACAGATAA-TGTGGCAGAGCCACCAG
101509613 GACGCTTCCT
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
26 1 0.01
27 53 0.78
28 14 0.21
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (27 bp):
ACAGATAATGTGGCAGAGCCACCAGAT
Found at i:101509610 original size:54 final size:54
Alignment explanation
Indices: 101509505--101509612 Score: 137
Period size: 54 Copynumber: 2.0 Consensus size: 54
101509495 TGGCTGCCAA
* * *
101509505 AACAGATAATGTGACAGGGTCACCAGATACAGATAATCGTGGCCGAACCACCAG
1 AACAGATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAACCACCAG
* * * *
101509559 AACAGATATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCACCAG
1 AACAGATA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAACCACCAG
101509613 GACGCTTCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
54 29 0.63
55 17 0.37
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (54 bp):
AACAGATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAACCACCAG
Found at i:101513142 original size:39 final size:41
Alignment explanation
Indices: 101513069--101513245 Score: 261
Period size: 41 Copynumber: 4.4 Consensus size: 41
101513059 CGTTTTTTAC
* * *
101513069 TAAAACGCCGCTAAAAA-TAGAGCAATAGCTGCGCTTTTGG
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
*
101513109 TAAAACACCGCT-AAAA-CAGAGCATTAGCGGCGCTTTTGG
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
101513148 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
* * *
101513189 TAAAACGCTGCTAAAAACCAGAGCACTAGTGGCGCTTTTGG
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
*
101513230 TAAAACGCTGCTAAAA
1 TAAAACGCCGCTAAAA
101513246 GTCATATAAC
Statistics
Matches: 127, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.28
40 15 0.12
41 77 0.61
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (41 bp):
TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
Found at i:101514172 original size:15 final size:15
Alignment explanation
Indices: 101514152--101514183 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
101514142 TTTAATTTAG
*
101514152 AAGATAAATGTATAT
1 AAGATAAATATATAT
101514167 AAGATAAATATATAT
1 AAGATAAATATATAT
101514182 AA
1 AA
101514184 ATTATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.31
Consensus pattern (15 bp):
AAGATAAATATATAT
Found at i:101514222 original size:24 final size:23
Alignment explanation
Indices: 101514155--101514222 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 23
101514145 AATTTAGAAG
* *
101514155 ATAAATGTATATAAGATAAATATAT
1 ATAAAT-TATATATGA-AAAAATAT
* *
101514180 ATAAATTATTATTTTAAAAAATAT
1 ATAAATTA-TATATGAAAAAATAT
101514204 ATAAATATATATATGAAAA
1 ATAAAT-TATATATGAAAA
101514223 GTGGTTTAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
24 23 0.66
25 12 0.34
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
ATAAATTATATATGAAAAAATAT
Found at i:101521443 original size:12 final size:12
Alignment explanation
Indices: 101521426--101521451 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
101521416 ACGATCGAGG
101521426 GATGAATCTGAT
1 GATGAATCTGAT
101521438 GATGAATCTGAT
1 GATGAATCTGAT
101521450 GA
1 GA
101521452 GGAGGATGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.31
Consensus pattern (12 bp):
GATGAATCTGAT
Found at i:101524514 original size:24 final size:24
Alignment explanation
Indices: 101524482--101524528 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
101524472 CTGACAGGAG
**
101524482 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGCAGATAAGGGAT
101524506 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGCAGATAAGGGA
101524529 GGAAATCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.38, T:0.23
Consensus pattern (24 bp):
AGGATTTAGGAGCAGATAAGGGAT
Found at i:101525985 original size:27 final size:26
Alignment explanation
Indices: 101525945--101526056 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
101525935 AGGAAGCGTC
*
101525945 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
101525972 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
101525999 CTAGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
101526027 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
101526053 CTGG
1 CTGG
101526057 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 7 0.09
27 51 0.69
28 16 0.22
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:101526049 original size:54 final size:54
Alignment explanation
Indices: 101525948--101526054 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 54
101525938 AAGCGTCCTG
*
101525948 GTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTCTA
1 GTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTCTA
* * *
101526002 GTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTTCT
1 GTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTTCT
101526055 GGCAGCCATG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 30 0.62
55 18 0.38
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (54 bp):
GTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTCTA
Found at i:101540456 original size:26 final size:27
Alignment explanation
Indices: 101540394--101540504 Score: 113
Period size: 27 Copynumber: 4.1 Consensus size: 27
101540384 AGGAAGCGTC
* * *
101540394 CTGGTGGCTATGCCACAATTCTCT-AAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
101540421 CTGGTGGCTCTGCCACA-TATACTGT-T
1 CTGGTGGCTCTGCCACATTAT-CTGTAT
*
101540447 CTGGTGGCTCTGCCACGATTATCTATAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
* *
101540475 CTGGTGACTCTGTCACATTATCTGT-T
1 CTGGTGGCTCTGCCACATTATCTGTAT
101540501 CTGG
1 CTGG
101540505 CAGCCATGCT
Statistics
Matches: 72, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
25 2 0.03
26 25 0.35
27 27 0.38
28 18 0.25
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.36
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATTATCTGTAT
Found at i:101540492 original size:54 final size:53
Alignment explanation
Indices: 101540394--101540504 Score: 152
Period size: 54 Copynumber: 2.1 Consensus size: 53
101540384 AGGAAGCGTC
* *
101540394 CTGGTGGCTATGCCACAATTCTCTAATCTGGTGGCTCTGCCACA-TATACTGTT
1 CTGGTGGCTATGCCACAATTATCTAATCTGGTGACTCTGCCACATTAT-CTGTT
* * *
101540447 CTGGTGGCTCTGCCACGATTATCTATATCTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTATGCCACAATTATCTA-ATCTGGTGACTCTGCCACATTATCTGTT
101540501 CTGG
1 CTGG
101540505 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
53 22 0.43
54 26 0.51
55 3 0.06
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.36
Consensus pattern (53 bp):
CTGGTGGCTATGCCACAATTATCTAATCTGGTGACTCTGCCACATTATCTGTT
Found at i:101542801 original size:43 final size:42
Alignment explanation
Indices: 101542753--101542938 Score: 203
Period size: 43 Copynumber: 4.4 Consensus size: 42
101542743 ACTGGGCAAA
* * *
101542753 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTACAGGTCT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGT-CTGGTCT
* **
101542796 GTAGCGATGTTTTTTATAAAAGCGCCGCTAAAGGTTCTGGTCT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGG-TCTGGTCT
* * * *
101542839 TTAACGGTGTTTTTT-TAGAAGCGCCGCTAAAGGTCTTGGTTT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTC-TGGTCT
* * * *
101542881 TTAGTGGCGTTTTTTATAAAAGCGCCGCTAAATGTCCTTGCCT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGT-CTGGTCT
101542924 TTAGCGGCGTTTTTT
1 TTAGCGGCGTTTTTT
101542939 CTTAAAAACG
Statistics
Matches: 119, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.02
42 34 0.29
43 81 0.68
44 2 0.02
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (42 bp):
TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCTGGTCT
Found at i:101551973 original size:35 final size:35
Alignment explanation
Indices: 101551927--101552004 Score: 149
Period size: 35 Copynumber: 2.3 Consensus size: 35
101551917 TAGTAATGTT
101551927 TGCCATGAAAACTTAGTTTCTTTTGAGATTAGACA
1 TGCCATGAAAACTTAGTTTCTTTTGAGATTAGACA
101551962 TGCCATGAAAACTTAGTTTCTTTTGAGATTAGACA
1 TGCCATGAAAACTTAGTTTCTTTTGAGATTAGACA
101551997 TG-CATGAA
1 TGCCATGAA
101552005 GGTTTATATC
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 6 0.14
35 37 0.86
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (35 bp):
TGCCATGAAAACTTAGTTTCTTTTGAGATTAGACA
Found at i:101553603 original size:40 final size:40
Alignment explanation
Indices: 101553544--101553652 Score: 121
Period size: 41 Copynumber: 2.7 Consensus size: 40
101553534 GCAAAAATTG
* *
101553544 TAAAACACAGAGCAATAGCGGCG-TTTTAACAAAAACGCCGT
1 TAAAA-ACAGAGCATTAGCGGCGCTTTT-ACAAAAACGCCGC
* ***
101553585 TAAAAACTGAGCATTAGCGGCGCTTTTGGTAAAACGCCGC
1 TAAAAACAGAGCATTAGCGGCGCTTTTACAAAAACGCCGC
*
101553625 TAAAGACCAGAGCATTAGCGGCGCTTTT
1 TAAA-AACAGAGCATTAGCGGCGCTTTT
101553653 GGTAAAATGC
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 28 0.48
41 30 0.52
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (40 bp):
TAAAAACAGAGCATTAGCGGCGCTTTTACAAAAACGCCGC
Found at i:101553646 original size:41 final size:41
Alignment explanation
Indices: 101553575--101553671 Score: 151
Period size: 41 Copynumber: 2.4 Consensus size: 41
101553565 CGTTTTAACA
* *
101553575 AAAACGCCGTTAAA-AACTGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAGAACAGAGCATTAGCGGCGCTTTTGGT
*
101553615 AAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAGAACAGAGCATTAGCGGCGCTTTTGGT
*
101553656 AAAATGCCGCTAAAGA
1 AAAACGCCGCTAAAGA
101553672 GTTATATAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 13 0.25
41 39 0.75
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.21
Consensus pattern (41 bp):
AAAACGCCGCTAAAGAACAGAGCATTAGCGGCGCTTTTGGT
Found at i:101554721 original size:18 final size:19
Alignment explanation
Indices: 101554698--101554736 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
101554688 AGATCTTTTT
101554698 TATTTTT-TATCAAAATAA
1 TATTTTTATATCAAAATAA
*
101554716 TATTTTTATATGAAAATAA
1 TATTTTTATATCAAAATAA
101554735 TA
1 TA
101554737 AATATGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (19 bp):
TATTTTTATATCAAAATAA
Found at i:101562321 original size:43 final size:43
Alignment explanation
Indices: 101562260--101562343 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
101562250 AGCTCTTAAC
*
101562260 TCTGCCATTTACTCTCTACTTAAAGCATCAGCAACTACATTCG
1 TCTGCCATTTACTCTCTACTTAAAGCATCAACAACTACATTCG
* * *
101562303 TCTGCCATTTGCTTTCTACTTAAGGCATCAACAACTACATT
1 TCTGCCATTTACTCTCTACTTAAAGCATCAACAACTACATT
101562344 TGCCTTGTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.35
Consensus pattern (43 bp):
TCTGCCATTTACTCTCTACTTAAAGCATCAACAACTACATTCG
Found at i:101575025 original size:14 final size:14
Alignment explanation
Indices: 101575006--101575034 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
101574996 CGCCATTCAT
101575006 CTTCGAGTGGGGGA
1 CTTCGAGTGGGGGA
101575020 CTTCGAGTGGGGGA
1 CTTCGAGTGGGGGA
101575034 C
1 C
101575035 AGTTTGGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.17, G:0.48, T:0.21
Consensus pattern (14 bp):
CTTCGAGTGGGGGA
Found at i:101583794 original size:57 final size:57
Alignment explanation
Indices: 101583725--101583837 Score: 208
Period size: 57 Copynumber: 2.0 Consensus size: 57
101583715 CAGCATGTTA
*
101583725 GGGCACTATTTTCCGAATTTCTAAACACCAAACATTGCCTTATTTAAGAAAAAAAAC
1 GGGCACTATTTTCCGAATTTCTAAACACCAAACATTACCTTATTTAAGAAAAAAAAC
*
101583782 GGGCACTATTTTCTGAATTTCTAAACACCAAACATTACCTTATTTAAGAAAAAAAA
1 GGGCACTATTTTCCGAATTTCTAAACACCAAACATTACCTTATTTAAGAAAAAAAA
101583838 TTTTCAATTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (57 bp):
GGGCACTATTTTCCGAATTTCTAAACACCAAACATTACCTTATTTAAGAAAAAAAAC
Found at i:101584302 original size:17 final size:17
Alignment explanation
Indices: 101584249--101584369 Score: 170
Period size: 17 Copynumber: 6.8 Consensus size: 17
101584239 AATCATATCT
101584249 TCTAAGATTGTATATCATA
1 TCTAAGATTG--TATCATA
101584268 TCTAAGATTGTAATCATA
1 TCTAAGATTGT-ATCATA
101584286 TCTAAGATTGTATCATA
1 TCTAAGATTGTATCATA
*
101584303 TCTAAGATTGCAATCATA
1 TCTAAGATTG-TATCATA
101584321 TCTAAGATTGTATCATA
1 TCTAAGATTGTATCATA
*
101584338 TCTAAGATTGCATATCACA
1 TCTAAGATTG--TATCATA
101584357 TCTAAGATTGTAT
1 TCTAAGATTGTAT
101584370 ATCATTGAAG
Statistics
Matches: 95, Mismatches: 3, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
17 36 0.38
18 33 0.35
19 26 0.27
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (17 bp):
TCTAAGATTGTATCATA
Found at i:101584307 original size:35 final size:35
Alignment explanation
Indices: 101584249--101584369 Score: 197
Period size: 35 Copynumber: 3.4 Consensus size: 35
101584239 AATCATATCT
*
101584249 TCTAAGATTGTATATCATATCTAAGATTGTAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
101584286 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
*
101584321 TCTAAGATTGTATCATATCTAAGATTGCATATCACA
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCATA
101584357 TCTAAGATTGTAT
1 TCTAAGATTGTAT
101584370 ATCATTGAAG
Statistics
Matches: 81, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
35 53 0.65
36 18 0.22
37 10 0.12
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:101584382 original size:17 final size:17
Alignment explanation
Indices: 101584251--101584397 Score: 88
Period size: 18 Copynumber: 8.2 Consensus size: 17
101584241 TCATATCTTC
101584251 TAAGATTGTATATCATA
1 TAAGATTGTATATCATA
101584268 TCTAAGATTGTA-ATCATA
1 --TAAGATTGTATATCATA
*
101584286 TCTAAGATTGTATCAT-ATC
1 --TAAGATTGTAT-ATCATA
*
101584305 TAAGATTGCA-ATCATA
1 TAAGATTGTATATCATA
*
101584321 TCTAAGATTGTATCAT-ATC
1 --TAAGATTGTAT-ATCATA
* *
101584340 TAAGATTGCATATCACATC
1 TAAGATTGTATAT--CATA
101584359 TAAGATTGTATATCAT-
1 TAAGATTGTATATCATA
* *
101584375 TGAAGATTATATTTCCATA
1 T-AAGATTGTATAT-CATA
101584394 TAAG
1 TAAG
101584398 TCAAACTTGT
Statistics
Matches: 106, Mismatches: 9, Indels: 27
0.75 0.06 0.19
Matches are distributed among these distances:
15 2 0.02
16 5 0.05
17 32 0.30
18 33 0.31
19 30 0.28
20 4 0.04
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (17 bp):
TAAGATTGTATATCATA
Found at i:101585215 original size:207 final size:207
Alignment explanation
Indices: 101584758--101585474 Score: 1220
Period size: 207 Copynumber: 3.5 Consensus size: 207
101584748 AAATCTGCTT
* * * *
101584758 CTTCAATTTGTTCCCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
* *
101584823 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* * * ** * * *
101584888 GGATC-TACTTCAGTCTAATCATCTGAAGGTTAGATCTGCTATATGTCTGTCCTCTGTCGAATAT
131 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
101584952 GGAGACGCCAAA
196 GGAGACGCCAAA
* *
101584964 CTTTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACATAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
*
101585029 GTGAAAGCCAAATTAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
101585094 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
131 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
101585159 GGAGACGCCAAA
196 GGAGACGCCAAA
101585171 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
101585236 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
101585301 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
131 GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
*
101585366 GGAGATGCCAAA
196 GGAGACGCCAAA
* ** *
101585378 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCGTCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
*
101585443 GTGAAAGCCAAATCAACTATGTCTTCGATTTG
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTG
101585475 CTCTCCGTCG
Statistics
Matches: 484, Mismatches: 26, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
206 126 0.26
207 358 0.74
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (207 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
GGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
GGAGACGCCAAA
Found at i:101585593 original size:131 final size:118
Alignment explanation
Indices: 101585289--101585593 Score: 304
Period size: 131 Copynumber: 2.4 Consensus size: 118
101585279 CACAAGGATG
* *** * *
101585289 CCAAACCATCTTGGATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCC
1 CCAAATCATCTTGGATC-TGCTTCAACGT-AACACCTGAAGGCCAGATCTACTATGTGTCTGCCC
**
101585354 TCCGTCGAATATGGAGATGCCAAACTTCGATTTGTTCTCTGACAATACAGAGATG
64 TCCGTCGAATATGGAGATGCCAAACTTCGATTTGTTCTCTGACAATACAGAGACC
* * ** * * * * *
101585409 CCAAATCATCTTAGATTTGCTTCGTCGTAAGCACGTGAAAGCCAAATCAACTATGTCTTCGATTT
1 CCAAATCATCTTGGATCTGCTTCAACGTAA-CACCTGAAGGCCAGATCTACTATG---T-G-TCT
*
101585474 GCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCTTCGATTTGTTCTCTGACAATACAGAGAC
60 GCCCTCCGTCGAATATGGAGATGCCAAA-------CTTCGATTTGTTCTCTGACAATACAGAGAC
101585539 C
118 C
101585540 CCAAATCATCTTGGATCTGCTTCAACGTGAACACCTGAAGGCCAGATCTACTAT
1 CCAAATCATCTTGGATCTGCTTCAACGT-AACACCTGAAGGCCAGATCTACTAT
101585594 ACTTTAACCT
Statistics
Matches: 146, Mismatches: 25, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
118 2 0.01
119 25 0.17
120 14 0.10
122 1 0.01
123 1 0.01
124 29 0.20
131 72 0.49
132 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (118 bp):
CCAAATCATCTTGGATCTGCTTCAACGTAACACCTGAAGGCCAGATCTACTATGTGTCTGCCCTC
CGTCGAATATGGAGATGCCAAACTTCGATTTGTTCTCTGACAATACAGAGACC
Found at i:101586692 original size:23 final size:23
Alignment explanation
Indices: 101586664--101586736 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
101586654 GGCCTCTCCA
101586664 TTTTTTCTTTTT-TCTTTTTTCTC
1 TTTTTTCTTTTTAT-TTTTTTCTC
101586687 TTTTTTCTTTTTATTTTTTTCTC
1 TTTTTTCTTTTTATTTTTTTCTC
*
101586710 --TTTTCCTTTTATTTTTTTGC-C
1 TTTTTTCTTTTTATTTTTTT-CTC
101586731 TTTTTT
1 TTTTTT
101586737 TATTTTTTGA
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
21 18 0.40
22 1 0.02
23 25 0.56
24 1 0.02
ACGTcount: A:0.03, C:0.15, G:0.01, T:0.81
Consensus pattern (23 bp):
TTTTTTCTTTTTATTTTTTTCTC
Found at i:101586726 original size:7 final size:7
Alignment explanation
Indices: 101586664--101586719 Score: 60
Period size: 7 Copynumber: 7.6 Consensus size: 7
101586654 GGCCTCTCCA
101586664 TTTTTTC
1 TTTTTTC
101586671 TTTTTTC
1 TTTTTTC
101586678 TTTTTTCTC
1 -TTTTT-TC
101586687 TTTTTTC
1 TTTTTTC
101586694 TTTTTAT-
1 TTTTT-TC
101586701 TTTTTTC
1 TTTTTTC
*
101586708 TCTTTTCC
1 T-TTTTTC
101586716 TTTT
1 TTTT
101586720 ATTTTTTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
6 1 0.02
7 23 0.53
8 17 0.40
9 2 0.05
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:101588246 original size:13 final size:13
Alignment explanation
Indices: 101588228--101588252 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
101588218 TATATTCTTT
101588228 TTTCTTTTTTTTC
1 TTTCTTTTTTTTC
101588241 TTTCTTTTTTTT
1 TTTCTTTTTTTT
101588253 GAAATGGATG
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:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTCTTTTTTTTC
Found at i:101591447 original size:13 final size:13
Alignment explanation
Indices: 101591429--101591453 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
101591419 CGTAAATAAT
101591429 AACAAACATATGC
1 AACAAACATATGC
101591442 AACAAACATATG
1 AACAAACATATG
101591454 TAAAAAAAAT
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:0.56, C:0.20, G:0.08, T:0.16
Consensus pattern (13 bp):
AACAAACATATGC
Found at i:101592716 original size:22 final size:22
Alignment explanation
Indices: 101592681--101592724 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
101592671 TAGGGTCTAG
*
101592681 GGTGTGCCGTTTTCTC-CTTTT
1 GGTGTGCCATTTTCTCTCTTTT
101592702 GGTGTAGCCATTTTCTCTCTTTT
1 GGTGT-GCCATTTTCTCTCTTTT
101592725 CTTTTCCAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 10 0.50
23 5 0.25
ACGTcount: A:0.05, C:0.23, G:0.20, T:0.52
Consensus pattern (22 bp):
GGTGTGCCATTTTCTCTCTTTT
Found at i:101593929 original size:9 final size:10
Alignment explanation
Indices: 101593917--101593973 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 10
101593907 TACGTGGGAT
101593917 ATGATAT-AC
1 ATGATATGAC
*
101593926 ATGAT-TGAT
1 ATGATATGAC
101593935 ATGATATGCAC
1 ATGATATG-AC
*
101593946 ATGATATG-T
1 ATGATATGAC
101593955 ATGATATGCAC
1 ATGATATG-AC
101593966 ATGATATG
1 ATGATATG
101593974 TATGAAATGC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 1 0.03
9 19 0.49
10 2 0.05
11 17 0.44
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (10 bp):
ATGATATGAC
Found at i:101593949 original size:20 final size:20
Alignment explanation
Indices: 101593916--101593990 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
101593906 ATACGTGGGA
101593916 TATGATAT--ACATGAT-TG
1 TATGATATGCACATGATATG
101593933 ATATGATATGCACATGATATG
1 -TATGATATGCACATGATATG
101593954 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
*
101593974 TATGAAATGCACATGAT
1 TATGATATGCACATGAT
101593991 GAATTCATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
18 8 0.15
20 43 0.81
21 2 0.04
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:101593951 original size:11 final size:11
Alignment explanation
Indices: 101593935--101593990 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
101593925 CATGATTGAT
101593935 ATGATATGCAC
1 ATGATATGCAC
*
101593946 ATGATATG--T
1 ATGATATGCAC
101593955 ATGATATGCAC
1 ATGATATGCAC
*
101593966 ATGATATG--T
1 ATGATATGCAC
*
101593975 ATGAAATGCAC
1 ATGATATGCAC
101593986 ATGAT
1 ATGAT
101593991 GAATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:101594069 original size:26 final size:26
Alignment explanation
Indices: 101594040--101594161 Score: 183
Period size: 26 Copynumber: 4.7 Consensus size: 26
101594030 GAGGAAGTGC
* *
101594040 AAAAGGGCTTATGCACTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
101594066 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
101594092 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
101594118 AAAAGGGCTT-TGCCCCAGTTTACCT
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
101594143 AAAAGGGCTTATGTCCCAG
1 AAAAGGGCTTATGCCCCAG
101594162 GGCTTTGCCC
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
25 22 0.25
26 65 0.75
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:101594102 original size:52 final size:51
Alignment explanation
Indices: 101594040--101594252 Score: 202
Period size: 51 Copynumber: 4.4 Consensus size: 51
101594030 GAGGAAGTGC
*
101594040 AAAAGGGCTTATGCACTAGTTTACCGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCACCAGTTTACCGAAAAGGGCTT-TGCCCCAGTTTACCG
* ** *
101594092 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCT
1 AAAAGGGCTTATGCACCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTACCG
* *
101594143 AAAAGGGCTTAT------G--T-CC---CAGGGCTTTGCCCCAGTTTACCT
1 AAAAGGGCTTATGCACCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTACCG
*** *
101594182 AAAAGGGCTTATGTC-CCAGTTTATTAAAAAGGGCTTTGCCCCAGTTTACAG
1 AAAAGGGCTTATG-CACCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTACCG
*
101594233 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCACCAGTT
101594253 ATTAAAGAGG
Statistics
Matches: 135, Mismatches: 13, Indels: 28
0.77 0.07 0.16
Matches are distributed among these distances:
39 34 0.25
43 1 0.01
45 2 0.01
47 1 0.01
49 1 0.01
50 8 0.06
51 56 0.41
52 32 0.24
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAAGGGCTTATGCACCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTACCG
Found at i:101594175 original size:39 final size:39
Alignment explanation
Indices: 101594121--101594200 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
101594111 TTTATTGAAA
101594121 AGGGCTTTGCCCCAGTTTACCTAAAAGGGCTTATGTCCC
1 AGGGCTTTGCCCCAGTTTACCTAAAAGGGCTTATGTCCC
101594160 AGGGCTTTGCCCCAGTTTACCTAAAAGGGCTTATGTCCC
1 AGGGCTTTGCCCCAGTTTACCTAAAAGGGCTTATGTCCC
101594199 AG
1 AG
101594201 TTTATTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.28
Consensus pattern (39 bp):
AGGGCTTTGCCCCAGTTTACCTAAAAGGGCTTATGTCCC
Found at i:101594209 original size:25 final size:25
Alignment explanation
Indices: 101594160--101594252 Score: 125
Period size: 25 Copynumber: 3.7 Consensus size: 25
101594150 CTTATGTCCC
*
101594160 AGGGCTTTGCCCCAGTTTACCTAAA
1 AGGGCTTTGCCCCAGTTTACTTAAA
*
101594185 AGGGCTTATGTCCCAGTTTA-TTAAAA
1 AGGGCTT-TGCCCCAGTTTACTT-AAA
**
101594211 AGGGCTTTGCCCCAGTTTACAGAAA
1 AGGGCTTTGCCCCAGTTTACTTAAA
101594236 AGGGCTTTGCCCCAGTT
1 AGGGCTTTGCCCCAGTT
101594253 ATTAAAGAGG
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
25 39 0.65
26 21 0.35
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (25 bp):
AGGGCTTTGCCCCAGTTTACTTAAA
Found at i:101594230 original size:90 final size:90
Alignment explanation
Indices: 101594069--101594250 Score: 294
Period size: 90 Copynumber: 2.0 Consensus size: 90
101594059 TTTACCGAAA
*
101594069 AGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCC
1 AGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTAAAAAGGGCTTTGCCCC
** *
101594134 AGTTTACCTAAAAGGGCTTATGTCCC
66 AGTTTACAGAAAAGGGCTT-TGCCCC
* *
101594160 AGGGCTT-TGCCCCAGTTTACCTAAAAGGGCTTATGTCCCAGTTTATTAAAAAGGGCTTTGCCCC
1 AGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTAAAAAGGGCTTTGCCCC
101594224 AGTTTACAGAAAAGGGCTTTGCCCC
66 AGTTTACAGAAAAGGGCTTTGCCCC
101594249 AG
1 AG
101594251 TTATTAAAGA
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
89 7 0.08
90 71 0.84
91 7 0.08
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (90 bp):
AGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTAAAAAGGGCTTTGCCCC
AGTTTACAGAAAAGGGCTTTGCCCC
Found at i:101598258 original size:31 final size:31
Alignment explanation
Indices: 101598220--101598296 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
101598210 TAACGGTTAT
101598220 TGGGCCGAAGCCTTTTCATAAATCATATCAC
1 TGGGCCGAAGCCTTTTCATAAATCATATCAC
*
101598251 TGGGCCGAAGCCTTTTCATAAATCATATCAT
1 TGGGCCGAAGCCTTTTCATAAATCATATCAC
* *
101598282 TAGGCCAAAGCCTTT
1 TGGGCCGAAGCCTTT
101598297 ACTGTAAACG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (31 bp):
TGGGCCGAAGCCTTTTCATAAATCATATCAC
Found at i:101598371 original size:42 final size:42
Alignment explanation
Indices: 101598324--101598411 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
101598314 CCTTAGGCCA
* * ** *
101598324 ATTTCAATATCACATGTAATGTCAATGGATGTATGCAAGCCC
1 ATTTCAATACCACATGAAATACCAATGAATGTATGCAAGCCC
101598366 ATTTCAATACCACATGAAATACCAATGAATGTATGCAAGCCC
1 ATTTCAATACCACATGAAATACCAATGAATGTATGCAAGCCC
101598408 ATTT
1 ATTT
101598412 GGGAAGACTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (42 bp):
ATTTCAATACCACATGAAATACCAATGAATGTATGCAAGCCC
Found at i:101598608 original size:26 final size:26
Alignment explanation
Indices: 101598556--101598679 Score: 171
Period size: 26 Copynumber: 4.8 Consensus size: 26
101598546 CCTCTTTAAT
101598556 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
* **
101598581 AACTGGGGTA-AAGCCCTTTTTCAATA
1 AACTGGGGCATAAGCCC-TTTTCGGTA
101598607 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
101598633 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
* * *
101598659 AAGTAGTGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
101598680 GCACTTCCTC
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
25 15 0.17
26 67 0.76
27 6 0.07
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGGTA
Found at i:101599551 original size:27 final size:27
Alignment explanation
Indices: 101599460--101599540 Score: 128
Period size: 27 Copynumber: 3.0 Consensus size: 27
101599450 GGGCATATTC
* *
101599460 GTCATTTTACCATACAGGGG-TATTACG
1 GTCACTTTACCCTACAGGGGCT-TTACG
101599487 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
101599514 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
101599541 ATCTTTTTAC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
27 50 0.98
28 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (27 bp):
GTCACTTTACCCTACAGGGGCTTTACG
Found at i:101599635 original size:27 final size:27
Alignment explanation
Indices: 101599582--101599900 Score: 211
Period size: 27 Copynumber: 11.8 Consensus size: 27
101599572 TTTCATCCTA
* * * * *
101599582 CAAGGGTGTTTTAGTAAATCTACAAAC
1 CAAGGGTATTTCAGTAATTTTACAAAT
** *
101599609 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTCAGTAATTTTACAAAT
* *
101599636 CAATGGTATTTTCA-TAATTTTTAGAAAGT
1 CAAGGGTA-TTTCAGTAA-TTTTACAAA-T
* **
101599665 CAAGGGTATTTCTA-TAACTTTGTAAAT
1 CAAGGGTATTTC-AGTAATTTTACAAAT
* **
101599692 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTCAGTAATTTTACAAAT
* *
101599719 TAAGGGTATTTC-GATAATTTCACAAA-
1 CAAGGGTATTTCAG-TAATTTTACAAAT
* **
101599745 CTAGTGGTATTTTGGTAATTTTACAAA-
1 CAAG-GGTATTTCAGTAATTTTACAAAT
* **
101599772 CTAGGGGTATTTTGGTAATTTTACAAAT
1 C-AAGGGTATTTCAGTAATTTTACAAAT
* *
101599800 TAAGGGTATTTC-GATAATTTTACAAAC
1 CAAGGGTATTTCAG-TAATTTTACAAAT
* *
101599827 CAGGGGTATTTTAGTAATTTTACAAA-
1 CAAGGGTATTTCAGTAATTTTACAAAT
* ** *
101599853 CTAGGGTATTTTGGTAATTTTACTAAT
1 CAAGGGTATTTCAGTAATTTTACAAAT
* *
101599880 CGAGGGTATTTTAGTAATTTT
1 CAAGGGTATTTCAGTAATTTT
101599901 GTAAATCGAG
Statistics
Matches: 236, Mismatches: 43, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
26 26 0.11
27 174 0.74
28 25 0.11
29 11 0.05
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTCAGTAATTTTACAAAT
Found at i:101599788 original size:81 final size:81
Alignment explanation
Indices: 101599693--101599890 Score: 326
Period size: 81 Copynumber: 2.5 Consensus size: 81
101599683 TTTGTAAATC
* *
101599693 AGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGATAATTTCACAAACTAGTGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGATAATTTCACAAACCAGGGGTATTTT
*
101599758 GGTAATTTTACAAACT
66 AGTAATTTTACAAACT
*
101599774 AGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGATAATTTTACAAACCAGGGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGATAATTTCACAAACCAGGGGTATTTT
101599839 AGTAATTTTACAAACT
66 AGTAATTTTACAAACT
* **
101599855 A-GGGTATTTTGGTAATTTTACTAATCGAGGGTATTT
1 AGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTT
101599891 TAGTAATTTT
Statistics
Matches: 110, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
80 32 0.29
81 78 0.71
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGATAATTTCACAAACCAGGGGTATTTT
AGTAATTTTACAAACT
Found at i:101599907 original size:27 final size:27
Alignment explanation
Indices: 101599584--101600061 Score: 186
Period size: 27 Copynumber: 17.7 Consensus size: 27
101599574 TCATCCTACA
* * * * * *
101599584 AGGGTGTTTTAGTAAATCTACAAACCA
1 AGGGTATTTTAGTAATTTTATAAATCG
* * * *
101599611 AGGGTATTTCAGTAATTTTGTAAACCA
1 AGGGTATTTTAGTAATTTTATAAATCG
* * *
101599638 ATGGTATTTTCA-TAATTTTTAGAAAGTCA
1 AGGGTATTTT-AGTAA-TTTTATAAA-TCG
* *
101599667 AGGGTATTTCTA-TAACTTTGTAAATC-
1 AGGGTATTT-TAGTAATTTTATAAATCG
* * **
101599693 AGGGGTATTTTGGTAATTTTACAAATTA
1 A-GGGTATTTTAGTAATTTTATAAATCG
* * * *
101599721 AGGGTA-TTTCGATAATTTCACAAA-CT
1 AGGGTATTTTAG-TAATTTTATAAATCG
* * *
101599747 AGTGGTATTTTGGTAATTTTACAAA-CT
1 AG-GGTATTTTAGTAATTTTATAAATCG
* * **
101599774 AGGGGTATTTTGGTAATTTTACAAATTA
1 A-GGGTATTTTAGTAATTTTATAAATCG
* * *
101599802 AGGGTA-TTTCGATAATTTTACAAA-CC
1 AGGGTATTTTAG-TAATTTTATAAATCG
* *
101599828 AGGGGTATTTTAGTAATTTTACAAA-CT
1 A-GGGTATTTTAGTAATTTTATAAATCG
*
101599855 AGGGTATTTTGGTAATTTTACT-AATCG
1 AGGGTATTTTAGTAATTTTA-TAAATCG
*
101599882 AGGGTATTTTAGTAATTTTGTAAATCG
1 AGGGTATTTTAGTAATTTTATAAATCG
*** * * *
101599909 AGGGTGA-AACAGTAATTCTGTAAATCA
1 AGGGT-ATTTTAGTAATTTTATAAATCG
*** *
101599936 AGGGTAAAATAGTAATTCTATAAATCG
1 AGGGTATTTTAGTAATTTTATAAATCG
***** *
101599963 AGGGTAAAACGGTAATTTTGTAAATCG
1 AGGGTATTTTAGTAATTTTATAAATCG
*** * *
101599990 AGGGTAAAATGGTAATTCTATAAATCG
1 AGGGTATTTTAGTAATTTTATAAATCG
* * * * *
101600017 AGGGTACTTTGGTAATTTTACAATTTG
1 AGGGTATTTTAGTAATTTTATAAATCG
* *
101600044 AGGGCATTTCAGTAATTT
1 AGGGTATTTTAGTAATTT
101600062 GGTAAACTAA
Statistics
Matches: 367, Mismatches: 64, Indels: 40
0.78 0.14 0.08
Matches are distributed among these distances:
26 35 0.10
27 291 0.79
28 26 0.07
29 14 0.04
30 1 0.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.38
Consensus pattern (27 bp):
AGGGTATTTTAGTAATTTTATAAATCG
Found at i:101600059 original size:81 final size:80
Alignment explanation
Indices: 101599855--101600067 Score: 221
Period size: 81 Copynumber: 2.6 Consensus size: 80
101599845 TTTACAAACT
* * *
101599855 AGGGTATTTTGGTAATTTTACTAATCGAGGGTATTTTAGTAATTTTGTAAATCGAGGGTGAAACA
1 AGGGTAATTTGGTAATTTTAC-AATCGAGGGTATTTCAGTAATTTTGTAAATCGAGGGTAAAACA
*
101599920 GTAATTCTGTAAATCA
65 GTAATTCTATAAATCA
** * *** * *
101599936 AGGGTAAAATAGTAATTCTATA-AATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAAT
1 AGGGTAATTTGGTAATT-T-TACAATCGAGGGTATTTCAGTAATTTTGTAAATCGAGGGTAAAAC
* *
101600000 GGTAATTCTATAAATCG
64 AGTAATTCTATAAATCA
* * * *
101600017 AGGGTACTTTGGTAATTTTACAATTTGAGGGCATTTCAGTAATTTGGTAAA
1 AGGGTAATTTGGTAATTTTACAA-TCGAGGGTATTTCAGTAATTTTGTAAA
101600068 CTAAAGTATT
Statistics
Matches: 103, Mismatches: 25, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
79 2 0.02
80 3 0.03
81 95 0.92
82 1 0.01
83 2 0.02
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (80 bp):
AGGGTAATTTGGTAATTTTACAATCGAGGGTATTTCAGTAATTTTGTAAATCGAGGGTAAAACAG
TAATTCTATAAATCA
Found at i:101601332 original size:31 final size:31
Alignment explanation
Indices: 101601294--101601372 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
101601284 TTTAACGGTT
*
101601294 ATTGGGCCGAAGCCTTTTCATAAATCATATC
1 ATTGGGCCAAAGCCTTTTCATAAATCATATC
*
101601325 ATTGGGCCAAAGCTTTTTCATAAATCATATC
1 ATTGGGCCAAAGCCTTTTCATAAATCATATC
101601356 ATTGGGCCAAAGCCTTT
1 ATTGGGCCAAAGCCTTT
101601373 ACTGTAAATG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (31 bp):
ATTGGGCCAAAGCCTTTTCATAAATCATATC
Found at i:101601443 original size:42 final size:42
Alignment explanation
Indices: 101601396--101601487 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
101601386 TGGCCCTTAG
* ** * *
101601396 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATCTATGCAA
101601438 GCCCATTTCAATATCACATGAAATACCAATGAATCTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATCTATGCAA
101601480 GCCCATTT
1 GCCCATTT
101601488 GGGGAGACTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATCTATGCAA
Found at i:101601659 original size:26 final size:26
Alignment explanation
Indices: 101601595--101601769 Score: 237
Period size: 26 Copynumber: 6.8 Consensus size: 26
101601585 CCTCTTTAAT
* **
101601595 AACTGGGGCA-AAGCCTTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
*
101601620 AACTGGGGTA-AAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
***
101601645 AACTGGGGCATAAGCCCTTTTTGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
*
101601671 AACTGGGGCATAAGCCCTTTTCAACA
1 AACTGGGGCATAAGCCCTTTTCAATA
* **
101601697 AACTGGGGCATAAGCCCTTTCCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
101601723 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
101601749 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
101601770 GCACTTCCTC
Statistics
Matches: 130, Mismatches: 19, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
25 30 0.23
26 100 0.77
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCAATA
Found at i:101601690 original size:52 final size:52
Alignment explanation
Indices: 101601595--101601769 Score: 284
Period size: 52 Copynumber: 3.4 Consensus size: 52
101601585 CCTCTTTAAT
*
101601595 AACTGGGGCA-AAG-CCTTTTTCGGTAAACTGGGGTA-AAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTT-GGTAAACTGGGGCATAAGCCCTTTTCAATA
*
101601645 AACTGGGGCATAAGCCCTTTTTGGTAAACTGGGGCATAAGCCCTTTTCAACA
1 AACTGGGGCATAAGCCCTTTTTGGTAAACTGGGGCATAAGCCCTTTTCAATA
**
101601697 AACTGGGGCATAAGCCCTTTCCGGTAAACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTTGGTAAACTGGGGCATAAGCCCTTTTCAATA
101601749 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
101601770 GCACTTCCTC
Statistics
Matches: 116, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
50 10 0.09
51 16 0.14
52 90 0.78
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (52 bp):
AACTGGGGCATAAGCCCTTTTTGGTAAACTGGGGCATAAGCCCTTTTCAATA
Found at i:101601824 original size:16 final size:16
Alignment explanation
Indices: 101601803--101601833 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
101601793 ACCCAACCCA
*
101601803 ATGCAACATGTCATGT
1 ATGCAAAATGTCATGT
101601819 ATGCAAAATGTCATG
1 ATGCAAAATGTCATG
101601834 CCAATATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (16 bp):
ATGCAAAATGTCATGT
Found at i:101605852 original size:20 final size:20
Alignment explanation
Indices: 101605827--101605893 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
101605817 GATATGATCT
101605827 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGATATGC
*
101605847 ACATGATATGTATGATATGT
1 ACATGATATGTATGATATGC
*
101605867 ACATGATATGTATGAAATGC
1 ACATGATATGTATGATATGC
101605887 ACATGAT
1 ACATGAT
101605894 GAATTCTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:101605877 original size:11 final size:11
Alignment explanation
Indices: 101605826--101605878 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
101605816 GGATATGATC
101605826 TACATGAT-TG
1 TACATGATATG
*
101605836 -ATATGATATG
1 TACATGATATG
*
101605846 CACATGATATG
1 TACATGATATG
101605857 T--ATGATATG
1 TACATGATATG
101605866 TACATGATATG
1 TACATGATATG
101605877 TA
1 TA
101605879 TGAAATGCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
9 15 0.42
10 2 0.06
11 19 0.53
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (11 bp):
TACATGATATG
Found at i:101606013 original size:25 final size:26
Alignment explanation
Indices: 101605942--101606089 Score: 212
Period size: 26 Copynumber: 5.8 Consensus size: 26
101605932 GAGGAAGTGC
101605942 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
101605968 AAAAGGGCTTATGCCCCAGTTTATCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
101605994 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* ***
101606019 AAAAGGGCTTATGTCCCAGTTTATTA
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
101606045 AAAAGGGCTT-TGCCCCAGTTTACAG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
101606070 AAAAGGGCTT-TGCCCTAGTT
1 AAAAGGGCTTATGCCCCAGTT
101606090 ATTAAAGAGG
Statistics
Matches: 110, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
25 54 0.49
26 56 0.51
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:101606013 original size:51 final size:51
Alignment explanation
Indices: 101605942--101606089 Score: 235
Period size: 51 Copynumber: 2.9 Consensus size: 51
101605932 GAGGAAGTGC
*
101605942 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATCG
1 AAAAGGGCTT-TGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATCA
* *
101605994 AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTTATGTCCCAGTTTATTA
1 AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATCA
* *
101606045 AAAAGGGCTTTGCCCCAGTTTACAGAAAAGGGCTT-TGCCCTAGTT
1 AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTT
101606090 ATTAAAGAGG
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
50 8 0.09
51 72 0.80
52 10 0.11
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (51 bp):
AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATCA
Found at i:101607359 original size:19 final size:19
Alignment explanation
Indices: 101607335--101607425 Score: 143
Period size: 19 Copynumber: 4.9 Consensus size: 19
101607325 AATCATATCT
*
101607335 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
101607354 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
101607372 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
*
101607389 TCTAAGATTGCATATCACA
1 TCTAAGATTGCATATCATA
101607408 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
101607426 TGAAGATTAT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 34 0.52
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:101607393 original size:35 final size:37
Alignment explanation
Indices: 101607335--101607425 Score: 141
Period size: 35 Copynumber: 2.5 Consensus size: 37
101607325 AATCATATCT
*
101607335 TCTAAGATTGTATATCATATCTAAGATTGCA-ATCATA
1 TCTAAGATTG-ATATCATATCTAAGATTGCATATCACA
101607372 TCTAAGATTG-TATCATATCTAAGATTGCATATCACA
1 TCTAAGATTGATATCATATCTAAGATTGCATATCACA
101607408 TCTAAGATTGCATATCAT
1 TCTAAGATTG-ATATCAT
101607426 TGAAGATTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
35 19 0.38
36 15 0.30
37 10 0.20
38 6 0.12
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (37 bp):
TCTAAGATTGATATCATATCTAAGATTGCATATCACA
Found at i:101607404 original size:14 final size:15
Alignment explanation
Indices: 101607349--101607404 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 15
101607339 AGATTGTATA
101607349 TCATATCTAAGATTG
1 TCATATCTAAGATTG
101607364 CAATCATATCTAAGATTG
1 ---TCATATCTAAGATTG
101607382 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
101607399 -CATATC
1 TCATATC
101607405 ACATCTAAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
14 6 0.16
17 16 0.43
18 15 0.41
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (15 bp):
TCATATCTAAGATTG
Found at i:101610723 original size:24 final size:24
Alignment explanation
Indices: 101610691--101610739 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
101610681 AATTCATATA
101610691 TGGAATCATCATCCTATTACAATT
1 TGGAATCATCATCCTATTACAATT
*
101610715 TGGAATCATCATCTTATTACAATT
1 TGGAATCATCATCCTATTACAATT
101610739 T
1 T
101610740 CATTCACAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (24 bp):
TGGAATCATCATCCTATTACAATT
Found at i:101611072 original size:42 final size:42
Alignment explanation
Indices: 101610993--101611093 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
101610983 ATCTCAATCA
*
101610993 CGCACACTAAGTGCCAATATATATAGCTAAAACTATCTCGGTCT
1 CGCACACTAAGTGCCAATATATATA-CTAAAACTATCTCGAT-T
* *
101611037 CGCACACTAAGTGCCAATATATAT-CTGAAATTATCTCGATT
1 CGCACACTAAGTGCCAATATATATACTAAAACTATCTCGATT
*
101611078 CTGCACACCAAGTGCC
1 C-GCACACTAAGTGCC
101611094 CATAATTAGT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
41 2 0.04
42 26 0.50
44 24 0.46
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.27
Consensus pattern (42 bp):
CGCACACTAAGTGCCAATATATATACTAAAACTATCTCGATT
Found at i:101614801 original size:67 final size:62
Alignment explanation
Indices: 101614691--101614820 Score: 163
Period size: 67 Copynumber: 2.0 Consensus size: 62
101614681 TCCAAAAATA
* *
101614691 ATATTATTTTAGTAGTTTAATATTAAATTAAATTAAATGTTTATCTTGTAGATAAACATTATATT
1 ATATTATTTTAATAGTTTAATATTAAATTAAATTAAATATTTATC-T-T-GATAAACATTATATT
* *
101614756 ATATTATTTTAATAAGATTTAATATTAAATTTAATCT-AATATTTATCTTGATAAATATTATATT
1 ATATTATTTTAAT-AG-TTTAATATTAAATTAAAT-TAAATATTTATCTTGATAAACATTATATT
101614820 A
1 A
101614821 ATTTAATATT
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
64 15 0.26
65 13 0.22
66 3 0.05
67 26 0.45
68 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (62 bp):
ATATTATTTTAATAGTTTAATATTAAATTAAATTAAATATTTATCTTGATAAACATTATATT
Found at i:101624771 original size:3 final size:3
Alignment explanation
Indices: 101624763--101624801 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
101624753 TGAATAATGA
101624763 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
101624802 GAAAGCAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:101626578 original size:44 final size:44
Alignment explanation
Indices: 101626529--101626766 Score: 146
Period size: 44 Copynumber: 5.3 Consensus size: 44
101626519 TTATTCTAAC
* *
101626529 CCACTGCAACTTTAGGGGTATAGGAATTGTAGTTTCAATCTACT
1 CCACTACAACTTTAGGGGTATAGGAATTGTAGATTCAATCTACT
* *
101626573 CCACTGCAACTTTAGGGAG-AT-GAGATTTGTAGATTCAATCTACT
1 CCACTACAACTTTAGGG-GTATAG-GAATTGTAGATTCAATCTACT
* * ** * *
101626617 TCACTACAACTTTAAGGAG-ATAAGATTTGTTGTTGTAGATTCATTCTAAT
1 CCACTACAACTTT-AGGGGTAT-AG----G-AATTGTAGATTCAATCTACT
* * * * *
101626667 GCACCACAACTTCAGGGGTATAGGAATTGTAGCTTTAATCTGA-T
1 CCACTACAACTTTAGGGGTATAGGAATTGTAGATTCAATCT-ACT
* * * *
101626711 CCACTACAACTTCAGGGATATAGGATTTGTA-ACTTC-ATCTCGCT
1 CCACTACAACTTTAGGGGTATAGGAATTGTAGA-TTCAATCT-ACT
*
101626755 CCACTGCAACTT
1 CCACTACAACTT
101626767 GAAGGAGATA
Statistics
Matches: 153, Mismatches: 28, Indels: 26
0.74 0.14 0.13
Matches are distributed among these distances:
43 5 0.03
44 106 0.69
45 6 0.04
46 1 0.01
49 7 0.05
50 28 0.18
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (44 bp):
CCACTACAACTTTAGGGGTATAGGAATTGTAGATTCAATCTACT
Found at i:101626663 original size:138 final size:136
Alignment explanation
Indices: 101626485--101626922 Score: 445
Period size: 138 Copynumber: 3.2 Consensus size: 136
101626475 TGCTCTATTG
* * * *
101626485 CAACTTCAAAGAGATAAGATTTGTTGTTGTAGCCTT-ATTCTAACCCACTGCAACTTTAGGGGTA
1 CAACTTCAAGGAGATAAGATTTGTTGTTGTAG-ATTCATTCTAACCCACTACAACTTCAGGGGTA
* *
101626549 TAGGAATTGTAG-TTTCAATCTACTCCACTGCAACTTTAGGGAGATGAGATTTGTAGATTCAATC
65 TAGGAATTGTAGCTTT-AATCTACTCCACTACAACTTCAGGGAGAT-AGATTTGTA-ATTCAATC
*
101626613 TACTTCACTA
127 TACTCCACTA
* ** *
101626623 CAACTTTAAGGAGATAAGATTTGTTGTTGTAGATTCATTCTAATGCACCACAACTTCAGGGGTAT
1 CAACTTCAAGGAGATAAGATTTGTTGTTGTAGATTCATTCTAACCCACTACAACTTCAGGGGTAT
*
101626688 AGGAATTGTAGCTTTAATCTGA-TCCACTACAACTTCAGGGATATAGGATTTGTAACTTC-ATCT
66 AGGAATTGTAGCTTTAATCT-ACTCCACTACAACTTCAGGGAGATA-GATTTGTAA-TTCAATCT
* *
101626751 CGCTCCACTG
128 -ACTCCACTA
* * ** * ** * * * *
101626761 CAACTTGAAGGAGATAAGTTTTACTATAATAAATTCAATCAAACCCACTATAACTTCAGGGGTAT
1 CAACTTCAAGGAGATAAGATTTGTTGTTGTAGATTCATTCTAACCCACTACAACTTCAGGGGTAT
* * *
101626826 AGGAATTGTAGCTTT-GTCTTACTCCACTACAACTTCAAGGAGATAAGATTTGTTATTTCAATCT
66 AGGAATTGTAGCTTTAATC-TACTCCACTACAACTTCAGGGAGAT-AGATTTG-TAATTCAATCT
* *
101626890 ACTCCATTG
128 ACTCCACTA
* * *
101626899 TAACTTCAGGGAGATGAGATTTGT
1 CAACTTCAAGGAGATAAGATTTGT
101626923 AGCTTCAGTC
Statistics
Matches: 248, Mismatches: 41, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
137 11 0.04
138 226 0.91
139 11 0.04
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (136 bp):
CAACTTCAAGGAGATAAGATTTGTTGTTGTAGATTCATTCTAACCCACTACAACTTCAGGGGTAT
AGGAATTGTAGCTTTAATCTACTCCACTACAACTTCAGGGAGATAGATTTGTAATTCAATCTACT
CCACTA
Found at i:101626893 original size:44 final size:45
Alignment explanation
Indices: 101626558--101627103 Score: 198
Period size: 44 Copynumber: 12.0 Consensus size: 45
101626548 ATAGGAATTG
* * * *
101626558 TAGTTTCAATCTACTCCACTGCAACTTTAGGGAGATGAGATTTG-
1 TAGTTTCAATCTACTCCACTACAACTTCAAGGAGATAAGATTTGT
* * *
101626602 TAGATTCAATCTACTTCACTACAACTTTAAGGAGATAAGATTTGTTGTT
1 TAGTTTCAATCTACTCCACTACAACTTCAAGGAGATAAGA--T-TTG-T
* * * * * * * *
101626651 GTAGATTCATTCTAATGCACCACAACTTC-AGGGGTATAGGAATTG-
1 -TAGTTTCAATCTACTCCACTACAACTTCAAGGAG-ATAAGATTTGT
* * *
101626696 TAGCTTT-AATCTGA-TCCACTACAACTTCAGGGATATAGGATTTG-
1 TAG-TTTCAATCT-ACTCCACTACAACTTCAAGGAGATAAGATTTGT
** * * * * *
101626740 TAACTTC-ATCTCGCTCCACTGCAACTTGAAGGAGATAAGTTTTACT
1 TAGTTTCAATCT-ACTCCACTACAACTTCAAGGAGATAAGATTT-GT
* * * * * *
101626786 ATAATAAATTCAATCAAAC-CCACTATAACTTC-AGGGGTATAGGAATTG-
1 -TAGT---TTCAATC-TACTCCACTACAACTTCAAGGAG-ATAAGATTTGT
*
101626834 TAGCTTT--GTCTTACTCCACTACAACTTCAAGGAGATAAGATTTGT
1 TAG-TTTCAATC-TACTCCACTACAACTTCAAGGAGATAAGATTTGT
* ** * *
101626879 TA-TTTCAATCTACTCCATTGTAACTTCAGGGAGATGAGATTTG-
1 TAGTTTCAATCTACTCCACTACAACTTCAAGGAGATAAGATTTGT
* *
101626922 TAGCTTCAGTCTACTCCACTACAACTTC-AGAGAGATAAGATTTGTTGTT
1 TAGTTTCAATCTACTCCACTACAACTTCAAG-GAGATAAGA--T-TTG-T
* * ** * *
101626971 GTAGCTTCATTCTAAC-CCACCCCAACTTCAGAGG-TATAAGAATTG-
1 -TAGTTTCAATCT-ACTCCACTACAACTTCA-AGGAGATAAGATTTGT
* * * * * *
101627016 TA-TCTTTAATCTAATCCACTGCAACTTCAGGGATATAGGATTTG-
1 TAGT-TTCAATCTACTCCACTACAACTTCAAGGAGATAAGATTTGT
* * * *
101627060 TAGCTTC-ATCTTGCTCCACTGCAACTTCAAAGAGATAAGATTTG
1 TAGTTTCAATC-TACTCCACTACAACTTCAAGGAGATAAGATTTG
101627104 CTATAATAAA
Statistics
Matches: 373, Mismatches: 86, Indels: 86
0.68 0.16 0.16
Matches are distributed among these distances:
43 22 0.06
44 224 0.60
45 15 0.04
46 2 0.01
47 17 0.05
48 1 0.00
49 8 0.02
50 75 0.20
51 7 0.02
52 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (45 bp):
TAGTTTCAATCTACTCCACTACAACTTCAAGGAGATAAGATTTGT
Found at i:101626997 original size:50 final size:50
Alignment explanation
Indices: 101626919--101627016 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 50
101626909 GAGATGAGAT
* *
101626919 TTGTAGCTTCAGTCTACTCCACTACAACTTCAGAGAG-ATAAGATTTGTTG
1 TTGTAGCTTCAGTCTACTCCACCACAACTTCAGAG-GTATAAGAATTGTTG
* *
101626969 TTGTAGCTTCATTCTAAC-CCACCCCAACTTCAGAGGTATAAGAATTGT
1 TTGTAGCTTCAGTCT-ACTCCACCACAACTTCAGAGGTATAAGAATTGT
101627017 ATCTTTAATC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 1 0.02
50 39 0.93
51 2 0.05
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (50 bp):
TTGTAGCTTCAGTCTACTCCACCACAACTTCAGAGGTATAAGAATTGTTG
Found at i:101627088 original size:182 final size:180
Alignment explanation
Indices: 101626663--101627103 Score: 404
Period size: 182 Copynumber: 2.4 Consensus size: 180
101626653 AGATTCATTC
* * * * * * *
101626663 TAATGCACCACAACTTCAGGGGTATAGGAATTGTAGCTTTAATCTGATCCACTACAACTTCAGGG
1 TAATCCACTACAACTTCAGGGATATAGGATTTGTAGC-TTCATCTGCTCCACTGCAACTTCAGGG
* * * * *
101626728 ATATAGGATTTGTAACTTCATCTCGCTCCACTGCAACTTGAAGGAGATAAGTTTTACTATAATAA
65 AGATA-GATTTGTAACTTCATCTCACTCCACTACAACTTCAAGGAGATAAGATTTACTATAATAA
* * * * *
101626793 ATTCAATCAAACCCACTATAACTTCAGGGGTATAGGAATTGTAGCTTTGTCT
129 ATTCAATCAAACCCACCACAACTTCAGAGGTATAAGAATTGTAGCTTTATCT
* * * * * * * *
101626845 TACTCCACTACAACTTCAAGGAGATAAGATTTGTTA-TTTCAATCTACTCCATTGTAACTTCAGG
1 TAATCCACTACAACTTCAGGGATATAGGATTTG-TAGCTTC-ATCTGCTCCACTGCAACTTCAGG
* ** * **
101626909 GAGATGAGATTTGTAGCTTCAGTCT-ACTCCACTACAACTTC-AGAGAGATAAGATTTGTTGTTG
64 GAGAT-AGATTTGTAACTTCA-TCTCACTCCACTACAACTTCAAG-GAGATAAGATTTACTATAA
** * * * *
101626972 TAGCTTCATTCTAACCCACCCCAACTTCAGAGGTATAAGAATTGTATCTTTAATC-
126 TAAATTCAATCAAACCCACCACAACTTCAGAGGTATAAGAATTGTAGCTTT-ATCT
* **
101627027 TAATCCACTGCAACTTCAGGGATATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAAAG
1 TAATCCACTACAACTTCAGGGATATAGGATTTGTAGCTTCATC-TGCTCCACTGCAACTTCAGGG
101627092 AGATAAGATTTG
65 AGAT-AGATTTG
101627104 CTATAATAAA
Statistics
Matches: 202, Mismatches: 49, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
181 9 0.04
182 185 0.92
183 8 0.04
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (180 bp):
TAATCCACTACAACTTCAGGGATATAGGATTTGTAGCTTCATCTGCTCCACTGCAACTTCAGGGA
GATAGATTTGTAACTTCATCTCACTCCACTACAACTTCAAGGAGATAAGATTTACTATAATAAAT
TCAATCAAACCCACCACAACTTCAGAGGTATAAGAATTGTAGCTTTATCT
Found at i:101627097 original size:320 final size:320
Alignment explanation
Indices: 101626561--101627154 Score: 956
Period size: 320 Copynumber: 1.9 Consensus size: 320
101626551 GGAATTGTAG
* *
101626561 TTTCAATCTACTCCACTGCAACTTTAGGGAGATGAGATTTGTAGATTCAATCTACTTCACTACAA
1 TTTCAATCTACTCCACTGCAACTTCAGGGAGATGAGATTTGTAGATTCAATCTACTCCACTACAA
* ** * *
101626626 CTTTAAGGAGATAAGATTTGTTGTTGTAGATTCATTCTAATGCACCACAACTTCAGGGGTATAGG
66 CTTCAAGGAGATAAGATTTGTTGTTGTAGATTCATTCTAACCCACCACAACTTCAGAGGTATAAG
*
101626691 AATTGTAGCTTTAATCTGATCCACTACAACTTCAGGGATATAGGATTTGTAACTTCATCTCGCTC
131 AATTGTAGCTTTAATCTAATCCACTACAACTTCAGGGATATAGGATTTGTAACTTCATCTCGCTC
* * *
101626756 CACTGCAACTTGAAGGAGATAAGTTTTACTATAATAAATTCAATCAAACCCACTATAACTTCAGG
196 CACTGCAACTTCAAAGAGATAAGATTTACTATAATAAATTCAATCAAACCCACTATAACTTCAGG
101626821 GGTATAGGAATTGTAGCTTTGTCTTACTCCACTACAACTTCAAGGAGATAAGATTTGTTA
261 GGTATAGGAATTGTAGCTTTGTCTTACTCCACTACAACTTCAAGGAGATAAGATTTGTTA
* * * *
101626881 TTTCAATCTACTCCATTGTAACTTCAGGGAGATGAGATTTGTAGCTTCAGTCTACTCCACTACAA
1 TTTCAATCTACTCCACTGCAACTTCAGGGAGATGAGATTTGTAGATTCAATCTACTCCACTACAA
* *
101626946 CTTC-AGAGAGATAAGATTTGTTGTTGTAGCTTCATTCTAACCCACCCCAACTTCAGAGGTATAA
66 CTTCAAG-GAGATAAGATTTGTTGTTGTAGATTCATTCTAACCCACCACAACTTCAGAGGTATAA
* * * *
101627010 GAATTGTATCTTTAATCTAATCCACTGCAACTTCAGGGATATAGGATTTGTAGCTTCATCTTGCT
130 GAATTGTAGCTTTAATCTAATCCACTACAACTTCAGGGATATAGGATTTGTAACTTCATCTCGCT
* * *
101627075 CCACTGCAACTTCAAAGAGATAAGATTTGCTATAATAAATTCAATCTAACCCACTGTAACTTCAG
195 CCACTGCAACTTCAAAGAGATAAGATTTACTATAATAAATTCAATCAAACCCACTATAACTTCAG
101627140 GGGTATAGGAATTGT
260 GGGTATAGGAATTGT
101627155 GGTGTCACTG
Statistics
Matches: 249, Mismatches: 24, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
319 2 0.01
320 247 0.99
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (320 bp):
TTTCAATCTACTCCACTGCAACTTCAGGGAGATGAGATTTGTAGATTCAATCTACTCCACTACAA
CTTCAAGGAGATAAGATTTGTTGTTGTAGATTCATTCTAACCCACCACAACTTCAGAGGTATAAG
AATTGTAGCTTTAATCTAATCCACTACAACTTCAGGGATATAGGATTTGTAACTTCATCTCGCTC
CACTGCAACTTCAAAGAGATAAGATTTACTATAATAAATTCAATCAAACCCACTATAACTTCAGG
GGTATAGGAATTGTAGCTTTGTCTTACTCCACTACAACTTCAAGGAGATAAGATTTGTTA
Found at i:101627123 original size:138 final size:137
Alignment explanation
Indices: 101626855--101627154 Score: 336
Period size: 138 Copynumber: 2.2 Consensus size: 137
101626845 TACTCCACTA
* * * * *
101626855 CAACTTCA-AGGAGATAAGATTTGTTATTTCAATCTACTCCATTGTAACTTCAGGGAGATGAGAT
1 CAACTTCAGAGG-TATAAGAATTG-TATTTCAATCTAATCCACTGCAACTTCAGGGAGATGAGAT
* * * ** ** *
101626919 TTGTAGCTTCAGTCTACTCCACTACAACTTCAGAGAGATAAGATTTGTTGTTGTAGCTTCATTCT
64 TTGTAGCTTCAGTCTACTCCACTACAACTTCAAAGAGATAAGATTTGCTATAATAAATTCAATCT
101626984 AACCCACCC
129 AACCCACCC
* *
101626993 CAACTTCAGAGGTATAAGAATTGTATCTTTAATCTAATCCACTGCAACTTCAGGGATAT-AGGAT
1 CAACTTCAGAGGTATAAGAATTGTAT-TTCAATCTAATCCACTGCAACTTCAGGGAGATGA-GAT
* *
101627057 TTGTAGCTTCA-TCTTGCTCCACTGCAACTTCAAAGAGATAAGATTTGCTATAATAAATTCAATC
64 TTGTAGCTTCAGTC-TACTCCACTACAACTTCAAAGAGATAAGATTTGCTATAATAAATTCAATC
**
101627121 TAACCCACTG
128 TAACCCACCC
* * *
101627131 TAACTTCAGGGGTATAGGAATTGT
1 CAACTTCAGAGGTATAAGAATTGT
101627155 GGTGTCACTG
Statistics
Matches: 136, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
137 6 0.04
138 127 0.93
139 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33
Consensus pattern (137 bp):
CAACTTCAGAGGTATAAGAATTGTATTTCAATCTAATCCACTGCAACTTCAGGGAGATGAGATTT
GTAGCTTCAGTCTACTCCACTACAACTTCAAAGAGATAAGATTTGCTATAATAAATTCAATCTAA
CCCACCC
Found at i:101644902 original size:21 final size:21
Alignment explanation
Indices: 101644878--101644917 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
101644868 TTGAGGATTA
* *
101644878 AAAATTGAAGATTGAAAATAG
1 AAAATAGAAAATTGAAAATAG
*
101644899 AAAATAGAAAATTGGAAAT
1 AAAATAGAAAATTGAAAAT
101644918 TGAGGATTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (21 bp):
AAAATAGAAAATTGAAAATAG
Found at i:101652434 original size:17 final size:17
Alignment explanation
Indices: 101652412--101652444 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
101652402 TTTCTAGTTT
101652412 TATATAA-ACACATATTA
1 TATATAATA-ACATATTA
101652429 TATATAATAACATATT
1 TATATAATAACATATT
101652445 GATGTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (17 bp):
TATATAATAACATATTA
Found at i:101660665 original size:14 final size:15
Alignment explanation
Indices: 101660646--101660709 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 15
101660636 TTTTAATATA
101660646 ATTTAATAT-AAAAT
1 ATTTAATATAAAAAT
* *
101660660 ATTTAATTTCAAATTAT
1 ATTTAATAT-AAA-AAT
101660677 AATTTAATATAAAAAT
1 -ATTTAATATAAAAAT
* *
101660693 AATT-ATATTAAAAT
1 ATTTAATATAAAAAT
101660707 ATT
1 ATT
101660710 ATTAAATTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
14 19 0.49
15 3 0.08
16 4 0.10
17 5 0.13
18 8 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTAATATAAAAAT
Found at i:101660712 original size:11 final size:11
Alignment explanation
Indices: 101660698--101660751 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
101660688 AAAATAATTA
101660698 TATTAAAATAT
1 TATTAAAATAT
*
101660709 TATTAAATTA-
1 TATTAAAATAT
101660719 TATTAAAATAT
1 TATTAAAATAT
* *
101660730 AATTAAATTAT
1 TATTAAAATAT
*
101660741 TTTTAATAATA
1 TATTAA-AATA
101660752 ATCTTATTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
10 9 0.26
11 22 0.65
12 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TATTAAAATAT
Found at i:101660722 original size:10 final size:10
Alignment explanation
Indices: 101660693--101660740 Score: 60
Period size: 11 Copynumber: 4.6 Consensus size: 10
101660683 ATATAAAAAT
101660693 AATTATATTA
1 AATTATATTA
*
101660703 AAATATTATTA
1 AATTA-TATTA
101660714 AATTATATTA
1 AATTATATTA
*
101660724 AAATATAATTA
1 AATTAT-ATTA
101660735 AATTAT
1 AATTAT
101660741 TTTTAATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 14 0.44
11 18 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
AATTATATTA
Found at i:101660753 original size:21 final size:21
Alignment explanation
Indices: 101660693--101660740 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
101660683 ATATAAAAAT
*
101660693 AATTATATTAAAATATTATTA
1 AATTATATTAAAATATAATTA
101660714 AATTATATTAAAATATAATTA
1 AATTATATTAAAATATAATTA
101660735 AATTAT
1 AATTAT
101660741 TTTTAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTATATTAAAATATAATTA
Found at i:101662176 original size:9 final size:9
Alignment explanation
Indices: 101662158--101662233 Score: 91
Period size: 9 Copynumber: 8.4 Consensus size: 9
101662148 TTTGGTTAAA
101662158 AATTAACCG
1 AATTAACCG
*
101662167 AATTACCCG
1 AATTAACCG
101662176 AATTAACCG
1 AATTAACCG
* *
101662185 GATTATCCG
1 AATTAACCG
101662194 AATTAACCG
1 AATTAACCG
101662203 AATT-ACTCG
1 AATTAAC-CG
*
101662212 AATTAATCG
1 AATTAACCG
*
101662221 AATTAATCG
1 AATTAACCG
101662230 AATT
1 AATT
101662234 GAATCACTAC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
8 2 0.03
9 55 0.95
10 1 0.02
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:101662284 original size:6 final size:6
Alignment explanation
Indices: 101662273--101662301 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
101662263 ACTTTTAGAC
101662273 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
101662302 AATTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:101662325 original size:20 final size:20
Alignment explanation
Indices: 101662257--101662314 Score: 66
Period size: 18 Copynumber: 3.0 Consensus size: 20
101662247 ATTAAATTAT
* *
101662257 TTTTAGACTTTTAGACTTTAG
1 TTTTAGAATTTTAG-TTTTAG
101662278 TTTTAG--TTTTAGTTTTAG
1 TTTTAGAATTTTAGTTTTAG
*
101662296 TTTTAGAATTTTATTTTTA
1 TTTTAGAATTTTAGTTTTA
101662315 TTTATTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 11 0.33
19 6 0.18
20 10 0.30
21 6 0.18
ACGTcount: A:0.22, C:0.03, G:0.12, T:0.62
Consensus pattern (20 bp):
TTTTAGAATTTTAGTTTTAG
Found at i:101666882 original size:32 final size:32
Alignment explanation
Indices: 101666846--101667005 Score: 239
Period size: 32 Copynumber: 5.0 Consensus size: 32
101666836 TATAACCATG
*
101666846 CTACTTTTTTATATGTAAAACTAATGTATAAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
101666878 CTACTTTTTCATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
101666910 CTACTTTTTTATATGTGAACCTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
101666942 ATACTTTTTTATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
101666974 CTACTTTTTTATAGGTAAACCTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
101667006 ATTTTTTATG
Statistics
Matches: 113, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 113 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (32 bp):
CTACTTTTTTATATGTAAAACTAATGTATGAT
Found at i:101666947 original size:64 final size:64
Alignment explanation
Indices: 101666846--101667007 Score: 270
Period size: 64 Copynumber: 2.5 Consensus size: 64
101666836 TATAACCATG
* * *
101666846 CTACTTTTTTATATGTAAAACTAATGTATAATCTACTTTTTCATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAACCTAATGTATGATATACTTTTTCATATGCAAAACTAATGTATGAT
* *
101666910 CTACTTTTTTATATGTGAACCTAATGTATGATATACTTTTTTATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAACCTAATGTATGATATACTTTTTCATATGCAAAACTAATGTATGAT
*
101666974 CTACTTTTTTATAGGTAAACCTAATGTATGATAT
1 CTACTTTTTTATATGTAAACCTAATGTATGATAT
101667008 TTTTTATGTT
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 91 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (64 bp):
CTACTTTTTTATATGTAAACCTAATGTATGATATACTTTTTCATATGCAAAACTAATGTATGAT
Found at i:101670226 original size:15 final size:15
Alignment explanation
Indices: 101670206--101670257 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
101670196 ACTACAAAAC
101670206 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
101670221 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
101670240 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
101670255 ATT
1 ATT
101670258 AATGTTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:101670321 original size:16 final size:16
Alignment explanation
Indices: 101670290--101670326 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
101670280 ATGTGAATAA
101670290 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
101670306 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
101670322 TATTA
1 TATTA
101670327 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:101672516 original size:29 final size:29
Alignment explanation
Indices: 101672474--101672530 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
101672464 GGTGTAATTG
*
101672474 AATAACTTCAGTTTATTCAATGAGGCACC
1 AATAACTTCAGTTTATCCAATGAGGCACC
* *
101672503 AATAATTTCAGTTTATCCGATGAGGCAC
1 AATAACTTCAGTTTATCCAATGAGGCAC
101672531 TGGGTGCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (29 bp):
AATAACTTCAGTTTATCCAATGAGGCACC
Found at i:101672589 original size:66 final size:66
Alignment explanation
Indices: 101672514--101672675 Score: 243
Period size: 66 Copynumber: 2.5 Consensus size: 66
101672504 ATAATTTCAG
* * * *
101672514 TTTATCCGATGAGGCACTGGGTGCCAAATACATCAATGAGTGTTGGGTGCAATTGACTTACTTCG
1 TTTATCCGATGAGGCACTGGGTGCCAAATACATCAATCAGCGTTGGGTGCAATTAAATTACTTCG
101672579 A
66 A
* *
101672580 TTTATCCGATGATGCACTTGGTGCCAAATACATCAATCAGCGTTGGGTGCAATTAAATTACTTCG
1 TTTATCCGATGAGGCACTGGGTGCCAAATACATCAATCAGCGTTGGGTGCAATTAAATTACTTCG
101672645 A
66 A
* * *
101672646 TATATCTGATGAGACACTGGGTGCCAAATA
1 TTTATCCGATGAGGCACTGGGTGCCAAATA
101672676 TATCGATAAG
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 85 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (66 bp):
TTTATCCGATGAGGCACTGGGTGCCAAATACATCAATCAGCGTTGGGTGCAATTAAATTACTTCG
A
Found at i:101673490 original size:73 final size:73
Alignment explanation
Indices: 101673403--101673545 Score: 268
Period size: 73 Copynumber: 2.0 Consensus size: 73
101673393 TCTTTTGAAT
* *
101673403 CAAAATTTGGTTGGGCATGAAATGGGCACTAAATGGAAGTTTTTGATCATTTTGGTACTAAGGTA
1 CAAAATTTGGTTGGGAATGAAATAGGCACTAAATGGAAGTTTTTGATCATTTTGGTACTAAGGTA
101673468 TCGATACC
66 TCGATACC
101673476 CAAAATTTGGTTGGGAATGAAATAGGCACTAAATGGAAGTTTTTGATCATTTTGGTACTAAGGTA
1 CAAAATTTGGTTGGGAATGAAATAGGCACTAAATGGAAGTTTTTGATCATTTTGGTACTAAGGTA
101673541 TCGAT
66 TCGAT
101673546 GCCCTGATAA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.34
Consensus pattern (73 bp):
CAAAATTTGGTTGGGAATGAAATAGGCACTAAATGGAAGTTTTTGATCATTTTGGTACTAAGGTA
TCGATACC
Found at i:101675994 original size:27 final size:27
Alignment explanation
Indices: 101675964--101676027 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
101675954 GTAACACAGT
*
101675964 AAAGCTGCCAGT-ATTAATATATGTGGC
1 AAAGCTACCAGTGA-TAATATATGTGGC
*
101675991 AAAGAC-ACCAGTGATAGTATATGTGGC
1 AAAG-CTACCAGTGATAATATATGTGGC
101676018 AAAGCTACCA
1 AAAGCTACCA
101676028 ATACAGTACC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 1 0.03
27 29 0.91
28 2 0.06
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (27 bp):
AAAGCTACCAGTGATAATATATGTGGC
Found at i:101682557 original size:52 final size:52
Alignment explanation
Indices: 101682479--101682581 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
101682469 GTGTAAATGG
101682479 TTAGTCATCACATTATGAGCAGTATGGCATTACAGAAACAAAGTTTATCATT
1 TTAGTCATCACATTATGAGCAGTATGGCATTACAGAAACAAAGTTTATCATT
*
101682531 TTAGTCATCATATTATGAGCAGTATGGCATTACAGAAACAAAGTTTATCAT
1 TTAGTCATCACATTATGAGCAGTATGGCATTACAGAAACAAAGTTTATCAT
101682582 CAATGAGAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (52 bp):
TTAGTCATCACATTATGAGCAGTATGGCATTACAGAAACAAAGTTTATCATT
Found at i:101683633 original size:23 final size:24
Alignment explanation
Indices: 101683593--101683639 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
101683583 ATTAAAATAA
**
101683593 AAAAATTTATAATTATA-TATTTT
1 AAAAATTTATAAAAATATTATTTT
*
101683616 AAAATTTTATAAAAATATTATTTT
1 AAAAATTTATAAAAATATTATTTT
101683640 TAATTTTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AAAAATTTATAAAAATATTATTTT
Found at i:101683644 original size:23 final size:23
Alignment explanation
Indices: 101683618--101683669 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
101683608 TATATTTTAA
* *
101683618 AATTTTATAAAAATATTATTTTT
1 AATTTTATAAAAATATTATATAT
* * *
101683641 AATTTTCTATAATTATTATATAT
1 AATTTTATAAAAATATTATATAT
101683664 AATTTT
1 AATTTT
101683670 TTTTACATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
AATTTTATAAAAATATTATATAT
Found at i:101684155 original size:21 final size:20
Alignment explanation
Indices: 101684131--101684177 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
101684121 TCCTAAATAT
101684131 TAAATTTCAAATCC-CAAACTC
1 TAAATTT-AAA-CCTCAAACTC
*
101684152 TAAACCTTAAACCTCAAACTC
1 TAAA-TTTAAACCTCAAACTC
101684173 TAAAT
1 TAAAT
101684178 CCAAAACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
20 2 0.09
21 18 0.82
22 2 0.09
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAATTTAAACCTCAAACTC
Found at i:101684184 original size:21 final size:21
Alignment explanation
Indices: 101684145--101684185 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
101684135 TTTCAAATCC
*
101684145 CAAACTCTAAACCTTAAACCT
1 CAAACTCTAAACCTAAAACCT
101684166 CAAACTCTAAATCC-AAAACC
1 CAAACTCTAAA-CCTAAAACC
101684186 AAAACTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (21 bp):
CAAACTCTAAACCTAAAACCT
Found at i:101688481 original size:60 final size:60
Alignment explanation
Indices: 101688388--101688688 Score: 593
Period size: 60 Copynumber: 5.0 Consensus size: 60
101688378 GATTCTGCTC
101688388 ACATAGTCTTCAGTAAAATGATCATAACTTAAGCTTTCAGACTCGAAATTGAGTGATTCA
1 ACATAGTCTTCAGTAAAATGATCATAACTTAAGCTTTCAGACTCGAAATTGAGTGATTCA
101688448 ACATAGTCTTCAGTAAAATGATCATAACTTAAGCTTTCAGACTCGAAATTGAGTGATTCA
1 ACATAGTCTTCAGTAAAATGATCATAACTTAAGCTTTCAGACTCGAAATTGAGTGATTCA
101688508 ACATAGTCTTCAGTAAAATGATCATAACTTAAGCTTTCAGACTCGAAATTGAGTGATTCA
1 ACATAGTCTTCAGTAAAATGATCATAACTTAAGCTTTCAGACTCGAAATTGAGTGATTCA
101688568 ACATAGTCTTCAGTAAAATGATCATAACTTAAGCTTTCAGACTCGAAATTGAGTGATTCA
1 ACATAGTCTTCAGTAAAATGATCATAACTTAAGCTTTCAGACTCGAAATTGAGTGATTCA
*
101688628 ACATAGTCTTCAGTAAAATGATCATAACTTAAGCTTTTAGACTCGAAATTGAGTGATTCA
1 ACATAGTCTTCAGTAAAATGATCATAACTTAAGCTTTCAGACTCGAAATTGAGTGATTCA
101688688 A
1 A
101688689 AGTGCGTTTT
Statistics
Matches: 240, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 240 1.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (60 bp):
ACATAGTCTTCAGTAAAATGATCATAACTTAAGCTTTCAGACTCGAAATTGAGTGATTCA
Found at i:101691570 original size:24 final size:24
Alignment explanation
Indices: 101691542--101691608 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
101691532 TATCTATGAT
101691542 TGCCTTTGTGGCGTATTCTGTAAA
1 TGCCTTTGTGGCGTATTCTGTAAA
* * * *
101691566 TGCCTCTGTGGTGTATTTTGTAAT
1 TGCCTTTGTGGCGTATTCTGTAAA
101691590 TGCCTTTGTGGCGTATTCT
1 TGCCTTTGTGGCGTATTCT
101691609 ATGATGTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.12, C:0.16, G:0.25, T:0.46
Consensus pattern (24 bp):
TGCCTTTGTGGCGTATTCTGTAAA
Found at i:101695655 original size:56 final size:55
Alignment explanation
Indices: 101695565--101695676 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 55
101695555 GAAATATTCT
101695565 TTCCATAAGAATCGAAACCTTTAGTAGATTATCTTTAGAGTTATTCTTATAATCC
1 TTCCATAAGAATCGAAACCTTTAGTAGATTATCTTTAGAGTTATTCTTATAATCC
* *
101695620 TTCCCTAAGAATCGAAAACCTTTAGTAGATTATCTTTGGAGTTATTCTTATAATCC
1 TTCCATAAGAATCG-AAACCTTTAGTAGATTATCTTTAGAGTTATTCTTATAATCC
101695676 T
1 T
101695677 ATATATATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
55 13 0.24
56 41 0.76
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (55 bp):
TTCCATAAGAATCGAAACCTTTAGTAGATTATCTTTAGAGTTATTCTTATAATCC
Found at i:101698015 original size:41 final size:40
Alignment explanation
Indices: 101697959--101698035 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 40
101697949 TTTGATATTC
101697959 TATCTGTATACTGTATCTGACATGGGCTAAGGCCCTAAGTTG
1 TATCTGTATACTGTATCTG--ATGGGCTAAGGCCCTAAGTTG
* *
101698001 TATCTG-ATTCTGTATCTGATGGTCTAAGGCCCTAA
1 TATCTGTATACTGTATCTGATGGGCTAAGGCCCTAA
101698036 CTAATTCTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 16 0.48
41 11 0.33
42 6 0.18
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (40 bp):
TATCTGTATACTGTATCTGATGGGCTAAGGCCCTAAGTTG
Found at i:101699851 original size:14 final size:13
Alignment explanation
Indices: 101699828--101699857 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
101699818 CGTATCTGTG
101699828 AAAAAAATAAAAT
1 AAAAAAATAAAAT
101699841 AAAATAAATAAAAT
1 AAAA-AAATAAAAT
101699855 AAA
1 AAA
101699858 GAACACACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:101704252 original size:14 final size:13
Alignment explanation
Indices: 101704229--101704258 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
101704219 CCAATTTGTG
101704229 AAAAAAATAAAAT
1 AAAAAAATAAAAT
101704242 AAAATAAATAAAAT
1 AAAA-AAATAAAAT
101704256 AAA
1 AAA
101704259 GAACACATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:101705184 original size:42 final size:42
Alignment explanation
Indices: 101705134--101705239 Score: 185
Period size: 42 Copynumber: 2.5 Consensus size: 42
101705124 CAAAAGCAAT
101705134 ATACGACACATAAAGTGCCTGAAACGACACACGAGGTGCCTG
1 ATACGACACATAAAGTGCCTGAAACGACACACGAGGTGCCTG
* *
101705176 ATGCGACACATAAAGTGCTTGAAACGACACACGAGGTGCCTG
1 ATACGACACATAAAGTGCCTGAAACGACACACGAGGTGCCTG
*
101705218 ATACGACACAGAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
101705240 TCGGCAAAGC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.36, C:0.25, G:0.25, T:0.15
Consensus pattern (42 bp):
ATACGACACATAAAGTGCCTGAAACGACACACGAGGTGCCTG
Found at i:101705240 original size:21 final size:21
Alignment explanation
Indices: 101705134--101705240 Score: 110
Period size: 21 Copynumber: 5.1 Consensus size: 21
101705124 CAAAAGCAAT
*
101705134 ATACGACACATAAAGTGCCTG
1 ATACGACACAGAAAGTGCCTG
* *
101705155 AAACGACACACG-AGGTGCCTG
1 ATACGACACA-GAAAGTGCCTG
* * *
101705176 ATGCGACACATAAAGTGCTTG
1 ATACGACACAGAAAGTGCCTG
* *
101705197 AAACGACACACG-AGGTGCCTG
1 ATACGACACA-GAAAGTGCCTG
101705218 ATACGACACAGAAAGTGCCTG
1 ATACGACACAGAAAGTGCCTG
101705239 AT
1 AT
101705241 CGGCAAAGCC
Statistics
Matches: 67, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
20 1 0.01
21 66 0.99
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (21 bp):
ATACGACACAGAAAGTGCCTG
Found at i:101706130 original size:3 final size:3
Alignment explanation
Indices: 101706122--101706161 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
101706112 ATTAGTTAAC
101706122 AAT AAT AAT AAT AAT AAT AAT AAAT AAT -AT AAT -AT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
101706162 ATATTTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 27 0.79
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:101706570 original size:5 final size:5
Alignment explanation
Indices: 101706562--101706611 Score: 57
Period size: 5 Copynumber: 10.0 Consensus size: 5
101706552 TATTTATTTC
* * *
101706562 ATAAT ATAAT ATAAT ATAATT ATAAT ATAAT -TATT ATAAT TTAAC ATAAT
1 ATAAT ATAAT ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
101706612 TAAATTTATA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
4 3 0.08
5 29 0.78
6 5 0.14
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (5 bp):
ATAAT
Found at i:101706587 original size:16 final size:16
Alignment explanation
Indices: 101706562--101706613 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
101706552 TATTTATTTC
101706562 ATAA-TATAATATAAT
1 ATAATTATAATATAAT
101706577 ATAATTATAATATAAT
1 ATAATTATAATATAAT
* *
101706593 -T-ATTATAATTTAAC
1 ATAATTATAATATAAT
101706607 ATAATTA
1 ATAATTA
101706614 AATTTATAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 11 0.34
15 6 0.19
16 15 0.47
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATTATAATATAAT
Found at i:101707008 original size:23 final size:22
Alignment explanation
Indices: 101706948--101707008 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
101706938 ATTACAGCTA
*
101706948 TGCACTTTGGTGCCTATTGCTC
1 TGCACTTCGGTGCCTATTGCTC
* * *
101706970 TGCACTTCAGTCCCTATTG-TT
1 TGCACTTCGGTGCCTATTGCTC
101706991 TAAGCACTTCGGTGCCTA
1 T--GCACTTCGGTGCCTA
101707009 ATGGTGTGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 2 0.06
22 16 0.52
23 13 0.42
ACGTcount: A:0.15, C:0.28, G:0.20, T:0.38
Consensus pattern (22 bp):
TGCACTTCGGTGCCTATTGCTC
Found at i:101708842 original size:26 final size:27
Alignment explanation
Indices: 101708813--101708868 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
101708803 TTTCCATATG
* *
101708813 ACCAATTATTGTA-AA-CATTTCATACA
1 ACCAATT-TTGTATAACCAATTCATAAA
101708839 ACC-ATTTTGTATAACCAATTCATAAA
1 ACCAATTTTGTATAACCAATTCATAAA
101708865 ACCA
1 ACCA
101708869 TTCATCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
24 5 0.20
25 5 0.20
26 15 0.60
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.32
Consensus pattern (27 bp):
ACCAATTTTGTATAACCAATTCATAAA
Done.