Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 124 of 279
Found at i:39217752 original size:6 final size:6
Alignment explanation
Indices: 39217741--39217768 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
39217731 CACTCTCTCT
39217741 TCTTCC TCTTCC TCTTCC TCTTCC TCTT
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTT
39217769 ATCTCAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (6 bp):
TCTTCC
Found at i:39225176 original size:20 final size:20
Alignment explanation
Indices: 39225151--39225189 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
39225141 AAAATGAGAT
39225151 AAACTTACA-AATTGACAGAC
1 AAACTTA-ATAATTGACAGAC
39225171 AAACTTAATAATTGACAGA
1 AAACTTAATAATTGACAGA
39225190 TCACCTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.23
Consensus pattern (20 bp):
AAACTTAATAATTGACAGAC
Found at i:39225581 original size:24 final size:24
Alignment explanation
Indices: 39225554--39225605 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
39225544 TTAGTAAGTC
*
39225554 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
39225578 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
39225602 AAAT
1 AAAT
39225606 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:39237799 original size:13 final size:14
Alignment explanation
Indices: 39237781--39237827 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
39237771 AATTAAAAGT
39237781 AATATATTAAA-AA
1 AATATATTAAATAA
*
39237794 AATATA-AAAATAA
1 AATATATTAAATAA
*
39237807 AATTTATTAAATTAA
1 AATATATTAAA-TAA
39237822 AATATA
1 AATATA
39237828 AAACGCTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 3 0.11
13 13 0.48
14 3 0.11
15 8 0.30
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AATATATTAAATAA
Found at i:39237821 original size:31 final size:31
Alignment explanation
Indices: 39237754--39237823 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
39237744 AAAATTAACC
*
39237754 AATTCAAAAAATATAAAAATTAAAAGTAATA
1 AATTAAAAAAATATAAAAATTAAAAGTAATA
* * *
39237785 TATTAAAAAAATATAAAAA-TAAAATTTATTA
1 AATTAAAAAAATATAAAAATTAAAA-GTAATA
39237816 AATTAAAA
1 AATTAAAA
39237824 TATAAAACGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (31 bp):
AATTAAAAAAATATAAAAATTAAAAGTAATA
Found at i:39254580 original size:16 final size:16
Alignment explanation
Indices: 39254561--39254591 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39254551 TTAGCGTGAG
*
39254561 CTTTTTTTCATAAATA
1 CTTTATTTCATAAATA
39254577 CTTTATTTCATAAAT
1 CTTTATTTCATAAAT
39254592 TTATTTAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (16 bp):
CTTTATTTCATAAATA
Found at i:39259225 original size:3 final size:3
Alignment explanation
Indices: 39259217--39259295 Score: 149
Period size: 3 Copynumber: 26.3 Consensus size: 3
39259207 ACACACACAA
*
39259217 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
39259265 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
39259296 GAGACATACA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39263807 original size:11 final size:11
Alignment explanation
Indices: 39263764--39263806 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
39263754 ATTTTCTTTC
39263764 TTTTCTTTTAG
1 TTTTCTTTTAG
39263775 TTTTCTTCTTTAG
1 TTTTC-T-TTTAG
39263788 TTTTCTTTTAG
1 TTTTCTTTTAG
39263799 TTTT-TTTT
1 TTTTCTTTT
39263807 TTTGAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.13
11 14 0.47
12 2 0.07
13 10 0.33
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.77
Consensus pattern (11 bp):
TTTTCTTTTAG
Found at i:39263809 original size:13 final size:13
Alignment explanation
Indices: 39263764--39263808 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
39263754 ATTTTCTTTC
39263764 TTTTCTTTTAGTT
1 TTTTCTTTTAGTT
39263777 TTCTTC-TTTAG--
1 TT-TTCTTTTAGTT
39263788 TTTTCTTTTAGTT
1 TTTTCTTTTAGTT
39263801 TTTT-TTTT
1 TTTTCTTTT
39263809 TGAAATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
10 3 0.11
11 7 0.25
12 4 0.14
13 11 0.39
14 3 0.11
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.78
Consensus pattern (13 bp):
TTTTCTTTTAGTT
Found at i:39268587 original size:1 final size:1
Alignment explanation
Indices: 39268583--39268607 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
39268573 TTTGGGTTTC
39268583 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
39268608 GTCTTGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:39274273 original size:26 final size:26
Alignment explanation
Indices: 39274237--39274293 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
39274227 CCAAGAAGTC
39274237 ATCTACAAGGGTTGAGGTATGTTTTA
1 ATCTACAAGGGTTGAGGTATGTTTTA
39274263 ATCTACAAGGGTTGAGGTATGTTTTA
1 ATCTACAAGGGTTGAGGTATGTTTTA
*
39274289 TTCTA
1 ATCTA
39274294 TCTTAACAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.26, C:0.09, G:0.25, T:0.40
Consensus pattern (26 bp):
ATCTACAAGGGTTGAGGTATGTTTTA
Found at i:39278042 original size:11 final size:11
Alignment explanation
Indices: 39278026--39278068 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
39278016 GTCATTTCGT
*
39278026 TATTATTTTAT
1 TATTATTTTAC
*
39278037 TTTTATTTTAC
1 TATTATTTTAC
*
39278048 TATTATATTAC
1 TATTATTTTAC
39278059 TATTATTTTA
1 TATTATTTTA
39278069 TTGTTATTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTATTTTAC
Found at i:39278051 original size:22 final size:22
Alignment explanation
Indices: 39278026--39278127 Score: 69
Period size: 22 Copynumber: 4.5 Consensus size: 22
39278016 GTCATTTCGT
*
39278026 TATTATTTTATTTTTATTTTAC
1 TATTATTTTATTGTTATTTTAC
* * * *
39278048 TATTATATTACTATTATTTTAT
1 TATTATTTTATTGTTATTTTAC
* * * *
39278070 TGTTATTATTTAGATGTTATATAAC
1 TATTA-T-TTTA-TTGTTATTTTAC
* *
39278095 TCTTATTTTATTGTTATTTTTTC
1 TATTATTTTATTGTTA-TTTTAC
39278118 TATTATTTTA
1 TATTATTTTA
39278128 GAGGTAGTTG
Statistics
Matches: 59, Mismatches: 17, Indels: 7
0.71 0.20 0.08
Matches are distributed among these distances:
22 27 0.46
23 17 0.29
24 4 0.07
25 11 0.19
ACGTcount: A:0.25, C:0.05, G:0.04, T:0.66
Consensus pattern (22 bp):
TATTATTTTATTGTTATTTTAC
Found at i:39278079 original size:36 final size:36
Alignment explanation
Indices: 39278026--39278123 Score: 109
Period size: 36 Copynumber: 2.9 Consensus size: 36
39278016 GTCATTTCGT
*
39278026 TATTATTTTA-T-TT-TTATTTTACTATTATATTAC
1 TATTATTTTATTGTTATTATTTTACTATTATATAAC
* *
39278059 TATTATTTTATTGTTATTA-TTTAGATGTTATATAAC
1 TATTATTTTATTGTTATTATTTTA-CTATTATATAAC
*
39278095 TCTTATTTTATTGTTATT-TTTT-CTATTAT
1 TATTATTTTATTGTTATTATTTTACTATTAT
39278124 TTTAGAGGTA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
33 10 0.19
34 6 0.11
35 6 0.11
36 32 0.59
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.65
Consensus pattern (36 bp):
TATTATTTTATTGTTATTATTTTACTATTATATAAC
Found at i:39285164 original size:9 final size:9
Alignment explanation
Indices: 39285152--39285177 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
39285142 GAGAAAAGTA
39285152 TAATAATAG
1 TAATAATAG
39285161 TAATAATAG
1 TAATAATAG
39285170 TAATAATA
1 TAATAATA
39285178 ATAAGTGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (9 bp):
TAATAATAG
Found at i:39295094 original size:27 final size:27
Alignment explanation
Indices: 39295056--39295109 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
39295046 GACCCTAAGA
*
39295056 AAAATCACCAAATTTCACAAACAAATC
1 AAAATCACCAAACTTCACAAACAAATC
39295083 AAAATCACCAAACTTCACAAACAAATC
1 AAAATCACCAAACTTCACAAACAAATC
39295110 TTCATCGCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.17
Consensus pattern (27 bp):
AAAATCACCAAACTTCACAAACAAATC
Found at i:39301734 original size:6 final size:6
Alignment explanation
Indices: 39301725--39301749 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
39301715 TGGTGTTGGG
39301725 GTTGAT GTTGAT GTTGAT GTTGAT G
1 GTTGAT GTTGAT GTTGAT GTTGAT G
39301750 AGGGTGGTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (6 bp):
GTTGAT
Found at i:39302825 original size:26 final size:26
Alignment explanation
Indices: 39302789--39302840 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
39302779 TTGTATATAG
39302789 GATAATTCTTGATGTATAATTATGCA
1 GATAATTCTTGATGTATAATTATGCA
*
39302815 GATAGTTCTTGATGTATAATTATGCA
1 GATAATTCTTGATGTATAATTATGCA
39302841 CTATGTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (26 bp):
GATAATTCTTGATGTATAATTATGCA
Found at i:39305076 original size:26 final size:26
Alignment explanation
Indices: 39305023--39305105 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
39305013 AAAAGAGTCA
* * * * *
39305023 TAATCAGGAAGTTCACAAATAACTTT
1 TAATCAAGAAGCTCACAAAGAGCCTT
*
39305049 TAATCAAGAAGCTCATAAAGAGCCTT
1 TAATCAAGAAGCTCACAAAGAGCCTT
* * * *
39305075 TAAACGAGAAGCTCACGAAGAGCCAT
1 TAATCAAGAAGCTCACAAAGAGCCTT
39305101 TAATC
1 TAATC
39305106 GGGAGCTTTG
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (26 bp):
TAATCAAGAAGCTCACAAAGAGCCTT
Found at i:39305234 original size:65 final size:65
Alignment explanation
Indices: 39305153--39305304 Score: 223
Period size: 65 Copynumber: 2.3 Consensus size: 65
39305143 AAGCTATATT
* *
39305153 AGGACGCTCACAAAGAGCTGCGTTTGTGTCTGCAACATATGCAAGATCACAACCGATCATAAAAC
1 AGGACGCTCACAAAGAGCTGCGTTTGTATCTGCAACATATGCAAGATCACAACCAATCATAAAAC
* * * * *
39305218 AGGACGCTCACAAAGAGCTGCGTTTGTATCTGCAATATGTGCAGGATCACAATCAATCATATAAC
1 AGGACGCTCACAAAGAGCTGCGTTTGTATCTGCAACATATGCAAGATCACAACCAATCATAAAAC
* *
39305283 AAGACGCTCACAAAGATCTGCG
1 AGGACGCTCACAAAGAGCTGCG
39305305 GTAGTCCACA
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 78 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (65 bp):
AGGACGCTCACAAAGAGCTGCGTTTGTATCTGCAACATATGCAAGATCACAACCAATCATAAAAC
Found at i:39306759 original size:19 final size:20
Alignment explanation
Indices: 39306735--39306773 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
39306725 GTCCCATTAT
39306735 TTATTTATTTTT-TGTTTTA
1 TTATTTATTTTTATGTTTTA
39306754 TTATTTATTTTTATGTTTTA
1 TTATTTATTTTTATGTTTTA
39306774 AATGTATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (20 bp):
TTATTTATTTTTATGTTTTA
Found at i:39306765 original size:20 final size:19
Alignment explanation
Indices: 39306735--39306773 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
39306725 GTCCCATTAT
*
39306735 TTATTTATTTTTTGTTTTA
1 TTATTTATTTTATGTTTTA
39306754 TTATTTATTTTTATGTTTTA
1 TTATTTA-TTTTATGTTTTA
39306774 AATGTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (19 bp):
TTATTTATTTTATGTTTTA
Found at i:39306792 original size:25 final size:23
Alignment explanation
Indices: 39306736--39306800 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 23
39306726 TCCCATTATT
*
39306736 TATTTATTTTT-TGTTTT--AT-
1 TATTTATTTTTATATTTTAAATG
*
39306755 TATTTATTTTTATGTTTTAAATG
1 TATTTATTTTTATATTTTAAATG
39306778 TATTTGATTTATTATATTTTAAA
1 TATTT-ATTT-TTATATTTTAAA
39306801 GTTTTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 11 0.28
20 6 0.15
22 2 0.05
23 5 0.13
24 4 0.10
25 11 0.28
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (23 bp):
TATTTATTTTTATATTTTAAATG
Found at i:39309609 original size:29 final size:29
Alignment explanation
Indices: 39309575--39309632 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
39309565 TAGAAAATAG
39309575 TATGATTTAATTGATATAAGATGATTGGT
1 TATGATTTAATTGATATAAGATGATTGGT
39309604 TATGATTTAATTGATATAAGATGATTGGT
1 TATGATTTAATTGATATAAGATGATTGGT
39309633 ATTAAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (29 bp):
TATGATTTAATTGATATAAGATGATTGGT
Found at i:39309642 original size:29 final size:29
Alignment explanation
Indices: 39309581--39309642 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
39309571 ATAGTATGAT
* *
39309581 TTAATTGATATAAGATGATTGGTTATGAT
1 TTAATTGATATAAGATGATTGGTTATAAA
39309610 TTAATTGATATAAGATGATTGG-TATTAAA
1 TTAATTGATATAAGATGATTGGTTA-TAAA
39309639 TTAA
1 TTAA
39309643 GTTAAAGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.44
Consensus pattern (29 bp):
TTAATTGATATAAGATGATTGGTTATAAA
Found at i:39346732 original size:38 final size:40
Alignment explanation
Indices: 39346660--39346735 Score: 111
Period size: 38 Copynumber: 1.9 Consensus size: 40
39346650 CTGGAATAGA
*
39346660 GTTTCGAAACATTACCGAATAAACATAATCTAATTCATTG
1 GTTTCGAAACATTACCGAATAAACATAATATAATTCATTG
* *
39346700 GTTTTGAAACATTA-CG-ATAATCATAATATAATTCAT
1 GTTTCGAAACATTACCGAATAAACATAATATAATTCAT
39346736 CCTTAAACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 18 0.55
39 2 0.06
40 13 0.39
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (40 bp):
GTTTCGAAACATTACCGAATAAACATAATATAATTCATTG
Found at i:39350216 original size:35 final size:35
Alignment explanation
Indices: 39350177--39350304 Score: 116
Period size: 35 Copynumber: 3.5 Consensus size: 35
39350167 GAAAAAGTGT
*
39350177 GAAATGTAGGTATGGTATCATCCATACTGAGTTGC
1 GAAATGTAGGTATGGTATCATCCATACTGAGTTGA
* *
39350212 GAAATGTACGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGA
* * * *
39350252 GAAATGTAGGTATCGCAT-TTCCCATACCGAGTTGTA
1 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTG-A
39350288 -AAATGTAGGTATGGTAT
1 GAAATGTAGGTATGGTAT
39350305 TTCAATAAGG
Statistics
Matches: 75, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
34 1 0.01
35 40 0.53
36 1 0.01
37 2 0.03
38 4 0.05
40 27 0.36
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATCATCCATACTGAGTTGA
Found at i:39350691 original size:25 final size:24
Alignment explanation
Indices: 39350657--39350740 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 24
39350647 TTTTTGTTTT
39350657 ATGTTTAAATGAATTGAAGTAAAG
1 ATGTTTAAATGAATTGAAGTAAAG
* * * *
39350681 ATGTTATAAATTATATGGCATGTATAG
1 ATGTT-TAAATGA-ATTG-AAGTAAAG
39350708 A-GTTTAAATGAATTGAAGTAAAG
1 ATGTTTAAATGAATTGAAGTAAAG
39350731 ATGTTATAAA
1 ATGTT-TAAA
39350741 CTAGTTAACA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
23 7 0.15
24 11 0.23
25 16 0.34
26 6 0.13
27 7 0.15
ACGTcount: A:0.44, C:0.01, G:0.19, T:0.36
Consensus pattern (24 bp):
ATGTTTAAATGAATTGAAGTAAAG
Found at i:39356053 original size:17 final size:18
Alignment explanation
Indices: 39356031--39356068 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
39356021 TATGTTTTGT
39356031 TTTAATTATT-ATTAACC
1 TTTAATTATTAATTAACC
*
39356048 TTTAATTATTAATTTACC
1 TTTAATTATTAATTAACC
39356066 TTT
1 TTT
39356069 TTAACCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTAATTATTAATTAACC
Found at i:39358055 original size:46 final size:47
Alignment explanation
Indices: 39357990--39358388 Score: 447
Period size: 46 Copynumber: 8.7 Consensus size: 47
39357980 TTATCTTTGA
* * * * *
39357990 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCATGT
**
39358036 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCATGT
* ** * *
39358082 CATGCTATCATGGTATCTTTCAACCATGATCTTAGTCA-TTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCATGT
* * **
39358128 CATGCTGCCATGTTATCTTTCAACCATGGTCTTATTCA-TTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCATGT
* * *
39358174 CATGTTTCCATGGTATCTTTCAACCACGGTCTTATTCA-TTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCATGT
** **
39358220 CACATTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCATGT
* * *
39358266 CATGTTTCCATGGTATCTTTCAACCACGGTCTTATTCA-TTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCATGT
** ** *
39358312 CACATTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCATGT
*
39358358 C-GGTTGCCATGGTATCTTTCAACCATGGTCT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCT
39358389 CACACATTTC
Statistics
Matches: 303, Mismatches: 49, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
45 32 0.11
46 271 0.89
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.41
Consensus pattern (47 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCATGT
Found at i:39358129 original size:92 final size:92
Alignment explanation
Indices: 39358005--39358404 Score: 527
Period size: 92 Copynumber: 4.4 Consensus size: 92
39357995 TGCCATAGTG
* * * * **
39358005 TCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATCTTTCAACCATGGTCTT
1 TCTTTCAACCACGGTCTTATTCA-TTTCATATCACATTGCCATGGTATCTTTCAACCATGGTCTT
*
39358069 ATTCATTTCCCGTCATGCTAT-CATGGTA
65 ATTCATTTCCCGTCATG-TTTCCATGGTA
* * * * *** *
39358097 TCTTTCAACCATGATCTTAGTCATTTCATGTCATGCTGCCATGTTATCTTTCAACCATGGTCTTA
1 TCTTTCAACCACGGTCTTATTCATTTCATATCACATTGCCATGGTATCTTTCAACCATGGTCTTA
39358162 TTCATTTCCCGTCATGTTTCCATGGTA
66 TTCATTTCCCGTCATGTTTCCATGGTA
39358189 TCTTTCAACCACGGTCTTATTCATTTCATATCACATTGCCATGGTATCTTTCAACCATGGTCTTA
1 TCTTTCAACCACGGTCTTATTCATTTCATATCACATTGCCATGGTATCTTTCAACCATGGTCTTA
39358254 TTCATTTCCCGTCATGTTTCCATGGTA
66 TTCATTTCCCGTCATGTTTCCATGGTA
39358281 TCTTTCAACCACGGTCTTATTCATTTCATATCACATTGCCATGGTATCTTTCAACCATGGTCTTA
1 TCTTTCAACCACGGTCTTATTCATTTCATATCACATTGCCATGGTATCTTTCAACCATGGTCTTA
** *** * *
39358346 CACATTTCATATC-GGTTGCCATGGTA
66 TTCATTTCCCGTCATGTTTCCATGGTA
* * **
39358372 TCTTTCAACCATGGTCTCACACATTTCATATCA
1 TCTTTCAACCACGGTCTTATTCATTTCATATCA
39358405 GAGAGCACAC
Statistics
Matches: 281, Mismatches: 25, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
91 46 0.16
92 235 0.84
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.41
Consensus pattern (92 bp):
TCTTTCAACCACGGTCTTATTCATTTCATATCACATTGCCATGGTATCTTTCAACCATGGTCTTA
TTCATTTCCCGTCATGTTTCCATGGTA
Found at i:39358243 original size:138 final size:138
Alignment explanation
Indices: 39357990--39358384 Score: 495
Period size: 138 Copynumber: 2.9 Consensus size: 138
39357980 TTATCTTTGA
* * * * * *
39357990 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTT
1 CATGCTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCTGTCATGTTGCCATGGTATCTT
*** * * **
39358055 TCAACCATGGTCTTATTCATTTCCCGTCATGCTATCATGGTATCTTTCAACCATGATCTTAGTCA
66 TCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGATCTTAGTCA
*
39358120 TTTCATGT
131 TTTCACGT
* * *
39358128 CATGCTGCCATGTTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTTCCATGGTATCTT
1 CATGCTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCTGTCATGTTGCCATGGTATCTT
* * * *
39358193 TCAACCACGGTCTTATTCATTTCATATCACATTGCCATGGTATCTTTCAACCATGGTCTTATTCA
66 TCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGATCTTAGTCA
*
39358258 TTTCCCGT
131 TTTCACGT
* * * * * **
39358266 CATGTTTCCATGGTATCTTTCAACCACGGTCTTATTCATTTCATATCACATTGCCATGGTATCTT
1 CATGCTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCTGTCATGTTGCCATGGTATCTT
** *
39358331 TCAACCATGGTCTTACACATTTCATATC-GGTTGCCATGGTATCTTTCAACCATG
66 TCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATG
39358385 GTCTCACACA
Statistics
Matches: 220, Mismatches: 37, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
137 24 0.11
138 196 0.89
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.41
Consensus pattern (138 bp):
CATGCTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCTGTCATGTTGCCATGGTATCTT
TCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGATCTTAGTCA
TTTCACGT
Found at i:39360225 original size:25 final size:23
Alignment explanation
Indices: 39360187--39360238 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
39360177 CCTTTTATAC
39360187 TAAATAACTAATAATATAATAATAA
1 TAAATAACTAATAA-A-AATAATAA
* * *
39360212 TAAATATCTCATAAAAATATTAA
1 TAAATAACTAATAAAAATAATAA
39360235 TAAA
1 TAAA
39360239 ATAATATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.46
24 1 0.04
25 12 0.50
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.33
Consensus pattern (23 bp):
TAAATAACTAATAAAAATAATAA
Found at i:39365825 original size:19 final size:19
Alignment explanation
Indices: 39365801--39365839 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
39365791 CTTGAAATGC
*
39365801 AAAGAAGTAGCTTGACTGA
1 AAAGAAGGAGCTTGACTGA
39365820 AAAGAAGGAGCTTGACTGA
1 AAAGAAGGAGCTTGACTGA
39365839 A
1 A
39365840 CTTATCTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.28, T:0.18
Consensus pattern (19 bp):
AAAGAAGGAGCTTGACTGA
Found at i:39369455 original size:25 final size:25
Alignment explanation
Indices: 39369421--39369470 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
39369411 AGTCAAGGTA
39369421 TTTATTGCAATAAAGCTATACTAAC
1 TTTATTGCAATAAAGCTATACTAAC
39369446 TTTATTGCAATAAAGCTATACTAAC
1 TTTATTGCAATAAAGCTATACTAAC
39369471 ATATCGTAGA
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (25 bp):
TTTATTGCAATAAAGCTATACTAAC
Found at i:39371977 original size:21 final size:21
Alignment explanation
Indices: 39371953--39371992 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39371943 AAGTTAAAAA
*
39371953 TTAAAAAAATTAATTTAATCT
1 TTAAAAAAATAAATTTAATCT
**
39371974 TTAATTAAATAAATTTAAT
1 TTAAAAAAATAAATTTAAT
39371993 TAGTTCAATC
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:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAAAAAAATAAATTTAATCT
Found at i:39374642 original size:544 final size:544
Alignment explanation
Indices: 39373777--39374862 Score: 2064
Period size: 544 Copynumber: 2.0 Consensus size: 544
39373767 GGGTCTTCTC
* * *
39373777 CATCTTCATGGAATGGTTTAAGCATACTCACGTGGAATACTGGATGAACTTTAAGCTTTTCAGGC
1 CATCTTCATGGAATGGCTTAAGCATACTCACATGGAATACTAGATGAACTTTAAGCTTTTCAGGC
*
39373842 AACTCGAGCTTGTAGGCCACCTTGCCTACCTTCTTCACAATTCGAAATGGCCCCTCGTACCGCCG
66 AACTCGAGCTTGTAGGCCACCTTGCCTACCTTCTTCACAATTCGAAATGGCCCCTCATACCGCCG
39373907 AACGAGTCCTTTGTGTAACCCATCATGTCGCAAAATCAGGTGTAGTTTGGCAAGAACTGGTTCAC
131 AACGAGTCCTTTGTGTAACCCATCATGTCGCAAAATCAGGTGTAGTTTGGCAAGAACTGGTTCAC
39373972 CTACCTGAAATTGTACGTCCCTTCGATTTCGATCCGCCCATTTCTTGTTGCGCTTACTTGCCTTA
196 CTACCTGAAATTGTACGTCCCTTCGATTTCGATCCGCCCATTTCTTGTTGCGCTTACTTGCCTTA
39374037 TGTAGACAAGCTCTAGCTAGATCGTTTTGCTCTTGCCAATCCCTCGCAAATCGATAAGCTGCTGG
261 TGTAGACAAGCTCTAGCTAGATCGTTTTGCTCTTGCCAATCCCTCGCAAATCGATAAGCTGCTGG
*
39374102 ATTCGGTCCCGCATAACGAGTTGCAACTGCATTGGGTGTAAGCGGCTGTTGCCCCGTCACTATCT
326 ATTCGGTCCCGCATAACGAGTTGCAACTGCATTGGGTGTAAGCGGCTATTGCCCCGTCACTATCT
* *
39374167 CAAATGGACTCTGGTTCGTTGTCCCACTTCGTTGTAAGTTGTACGAAAACTGGGCCACATCCAAT
391 CAAATGGACTCTGGTTCGTTGCCCCACTTCGTTGTAAGTTGTACGAAAACTGGGCCACATCCAAC
39374232 AACTTTGGCCAATCATTTTGTGTTGCACTTACATAGTGTCGAAGATACGTCTCCAACAATGCATT
456 AACTTTGGCCAATCATTTTGTGTTGCACTTACATAGTGTCGAAGATACGTCTCCAACAATGCATT
39374297 CACTCGTTCGGTTTGCCCATCATT
521 CACTCGTTCGGTTTGCCCATCATT
39374321 CATCTTCATGGAATGGCTTAAGCATACTCACATGGAATACTAGATGAACTTTAAGCTTTTCAGGC
1 CATCTTCATGGAATGGCTTAAGCATACTCACATGGAATACTAGATGAACTTTAAGCTTTTCAGGC
*
39374386 AACTCGAGCTTGTAGGCCACCTTTCCTACCTTCTTCACAATTCGAAATGGCCCCTCATACCGCCG
66 AACTCGAGCTTGTAGGCCACCTTGCCTACCTTCTTCACAATTCGAAATGGCCCCTCATACCGCCG
*
39374451 AACGAGTCCTTTGTGTAACCCATCATGTCGCAAAATCAGGTGTAGTTTGGTAAGAACTGGTTCAC
131 AACGAGTCCTTTGTGTAACCCATCATGTCGCAAAATCAGGTGTAGTTTGGCAAGAACTGGTTCAC
*
39374516 CTACCTGAAATTGTACGTCTCTTCGATTTCGATCCGCCCATTTCTTGTTGCGCTTACTTGCCTTA
196 CTACCTGAAATTGTACGTCCCTTCGATTTCGATCCGCCCATTTCTTGTTGCGCTTACTTGCCTTA
39374581 TGTAGACAAGCTCTAGCTAGATCGTTTTGCTCTTGCCAATCCCTCGCAAATCGATAAGCTGCTGG
261 TGTAGACAAGCTCTAGCTAGATCGTTTTGCTCTTGCCAATCCCTCGCAAATCGATAAGCTGCTGG
*
39374646 ATTCGGTCCCGTATAACGAGTTGCAACTGCATTGGGTGTAAGCGGCTATTGCCCCGTCACTATCT
326 ATTCGGTCCCGCATAACGAGTTGCAACTGCATTGGGTGTAAGCGGCTATTGCCCCGTCACTATCT
39374711 CAAATGGACTCTGGTTCGTTGCCCCACTTCGTTGTAAGTTGTACGAAAACTGGGCCACATCCAAC
391 CAAATGGACTCTGGTTCGTTGCCCCACTTCGTTGTAAGTTGTACGAAAACTGGGCCACATCCAAC
*
39374776 AACTTTGGCCAATCCTTTTGTGTTGCACTTACATAGTGTCGAAGATACGTCTCCAACAATGCATT
456 AACTTTGGCCAATCATTTTGTGTTGCACTTACATAGTGTCGAAGATACGTCTCCAACAATGCATT
39374841 CACTCGTTCGGTTTGCCCATCA
521 CACTCGTTCGGTTTGCCCATCA
39374863 GTTTGAGGAT
Statistics
Matches: 530, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
544 530 1.00
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (544 bp):
CATCTTCATGGAATGGCTTAAGCATACTCACATGGAATACTAGATGAACTTTAAGCTTTTCAGGC
AACTCGAGCTTGTAGGCCACCTTGCCTACCTTCTTCACAATTCGAAATGGCCCCTCATACCGCCG
AACGAGTCCTTTGTGTAACCCATCATGTCGCAAAATCAGGTGTAGTTTGGCAAGAACTGGTTCAC
CTACCTGAAATTGTACGTCCCTTCGATTTCGATCCGCCCATTTCTTGTTGCGCTTACTTGCCTTA
TGTAGACAAGCTCTAGCTAGATCGTTTTGCTCTTGCCAATCCCTCGCAAATCGATAAGCTGCTGG
ATTCGGTCCCGCATAACGAGTTGCAACTGCATTGGGTGTAAGCGGCTATTGCCCCGTCACTATCT
CAAATGGACTCTGGTTCGTTGCCCCACTTCGTTGTAAGTTGTACGAAAACTGGGCCACATCCAAC
AACTTTGGCCAATCATTTTGTGTTGCACTTACATAGTGTCGAAGATACGTCTCCAACAATGCATT
CACTCGTTCGGTTTGCCCATCATT
Found at i:39392169 original size:16 final size:16
Alignment explanation
Indices: 39392148--39392186 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
39392138 CGCAGTTATT
39392148 TTGATGCATAGCTCAA
1 TTGATGCATAGCTCAA
39392164 TTGATGCATAGCTCAA
1 TTGATGCATAGCTCAA
39392180 TTGATGC
1 TTGATGC
39392187 TCAAGTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (16 bp):
TTGATGCATAGCTCAA
Found at i:39394101 original size:99 final size:102
Alignment explanation
Indices: 39393966--39394162 Score: 310
Period size: 102 Copynumber: 2.0 Consensus size: 102
39393956 TGGCTGTACC
*
39393966 ATTGAATCAAGATTCTGAAGTGGCTGAAAACAAGGAGG-C-T-ATTGTCAATGATTCTCTTACAG
1 ATTGAATCAAGATTCTGAAGTGGCTGAAAACAAGGAGGCCGTCATTGTCAATGATTCTCTGACAG
** *
39394028 AATTATCTGAGCAACCGGCAGCAAAGAGGATGCAACA
66 AATTATCCCAGCAACCAGCAGCAAAGAGGATGCAACA
**
39394065 ATTGAATCAAGATTCTGAAGTGGCTGAAAACAAGGAGGCCGTCATTGTCAATGATTCTCTGGGAG
1 ATTGAATCAAGATTCTGAAGTGGCTGAAAACAAGGAGGCCGTCATTGTCAATGATTCTCTGACAG
*
39394130 AGTTATCCCAGCAACCAGCAGCAAAGAGGATGC
66 AATTATCCCAGCAACCAGCAGCAAAGAGGATGC
39394163 GGCTTACGCC
Statistics
Matches: 88, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
99 38 0.43
100 1 0.01
101 1 0.01
102 48 0.55
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (102 bp):
ATTGAATCAAGATTCTGAAGTGGCTGAAAACAAGGAGGCCGTCATTGTCAATGATTCTCTGACAG
AATTATCCCAGCAACCAGCAGCAAAGAGGATGCAACA
Found at i:39398861 original size:16 final size:16
Alignment explanation
Indices: 39398837--39398870 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
39398827 ATTAATAACA
*
39398837 TTTACATATATATTTT
1 TTTAAATATATATTTT
39398853 TTTAAATATATATTTT
1 TTTAAATATATATTTT
39398869 TT
1 TT
39398871 AATTTTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTAAATATATATTTT
Found at i:39409533 original size:20 final size:20
Alignment explanation
Indices: 39409493--39409536 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
39409483 ACACAATGTA
*
39409493 TAAATATTAACGCTAACAAT
1 TAAATATTAACACTAACAAT
* *
39409513 TAAATATTAACATTAATAAT
1 TAAATATTAACACTAACAAT
39409533 TAAA
1 TAAA
39409537 AGCAATGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (20 bp):
TAAATATTAACACTAACAAT
Found at i:39409980 original size:7 final size:7
Alignment explanation
Indices: 39409968--39409992 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39409958 AATTATTTGA
39409968 AATATGT
1 AATATGT
39409975 AATATGT
1 AATATGT
39409982 AATATGT
1 AATATGT
39409989 AATA
1 AATA
39409993 ACTAAGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (7 bp):
AATATGT
Found at i:39411037 original size:13 final size:13
Alignment explanation
Indices: 39411021--39411045 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39411011 ATCGAAAGGT
39411021 GAAAAAAAGAAAA
1 GAAAAAAAGAAAA
39411034 GAAAAAAAGAAA
1 GAAAAAAAGAAA
39411046 TCAAATCCAC
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
GAAAAAAAGAAAA
Found at i:39414017 original size:14 final size:12
Alignment explanation
Indices: 39413985--39414037 Score: 56
Period size: 11 Copynumber: 4.3 Consensus size: 12
39413975 ATAAAATAAT
39413985 AAAAAAAGTAAA-
1 AAAAAAAG-AAAC
*
39413997 ATAAAAAGAAAC
1 AAAAAAAGAAAC
39414009 AAAGTAAAAGAAAC
1 AAA--AAAAGAAAC
39414023 -AAAAAAGAAAC
1 AAAAAAAGAAAC
39414034 AAAA
1 AAAA
39414038 GAACATTCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
11 12 0.34
12 12 0.34
13 2 0.06
14 9 0.26
ACGTcount: A:0.79, C:0.06, G:0.09, T:0.06
Consensus pattern (12 bp):
AAAAAAAGAAAC
Found at i:39422064 original size:6 final size:5
Alignment explanation
Indices: 39422023--39422057 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
39422013 TAGGCTGTCT
*
39422023 TTTTC TGTTC TTTTC TTTTC TTTTC TTTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTT
39422058 TCGTTTTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:39425416 original size:13 final size:13
Alignment explanation
Indices: 39425398--39425423 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39425388 AATAACCCAA
39425398 CATACATTAAAAT
1 CATACATTAAAAT
39425411 CATACATTAAAAT
1 CATACATTAAAAT
39425424 AAGCACAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
CATACATTAAAAT
Found at i:39427327 original size:19 final size:19
Alignment explanation
Indices: 39427303--39427339 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39427293 GTGAGAATTA
*
39427303 AATTAATTAGTATTTTAGT
1 AATTAATTAATATTTTAGT
39427322 AATTAATTAATATTTTAG
1 AATTAATTAATATTTTAG
39427340 AAAATAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (19 bp):
AATTAATTAATATTTTAGT
Found at i:39427818 original size:70 final size:71
Alignment explanation
Indices: 39427676--39427821 Score: 161
Period size: 70 Copynumber: 2.1 Consensus size: 71
39427666 AATGAATTTT
* * * * * *
39427676 AAACCTAGAGGGGGAATATCCAGCCTTCAATGTCATGACAACAGCCATCCAATGTTGCGACAACG
1 AAACCTAGAGGGGGAACATCCAACCTTCAATGTCATGACAACAACCATCCAATGTCGCAACAACA
*
39427741 AATTTC
66 AACTTC
* * * * *
39427747 AAACCTAGA-GGGGAACATTCAACCTTCAATGTCATGATAACAACTA-CTTAATGTCGCAACATC
1 AAACCTAGAGGGGGAACATCCAACCTTCAATGTCATGACAACAACCATC-CAATGTCGCAACAAC
39427810 AAACTTC
65 AAACTTC
39427817 AAACC
1 AAACC
39427822 AAAAAAAGGG
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
69 1 0.02
70 52 0.84
71 9 0.15
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (71 bp):
AAACCTAGAGGGGGAACATCCAACCTTCAATGTCATGACAACAACCATCCAATGTCGCAACAACA
AACTTC
Found at i:39429776 original size:16 final size:16
Alignment explanation
Indices: 39429755--39429822 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
39429745 TTTGGTTCGC
*
39429755 TGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
39429771 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
39429787 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
*
39429803 TGTATTGGAATAGAGG
1 TGTATTGGATTAGAGG
39429819 TGTA
1 TGTA
39429823 ATAGCAAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:39429859 original size:45 final size:44
Alignment explanation
Indices: 39429803--39429893 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
39429793 GGATTAGAGG
* *
39429803 TGTATTGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
39429848 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
39429892 TG
1 TG
39429894 GAATAGAGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 18 0.45
45 22 0.55
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:39430100 original size:19 final size:19
Alignment explanation
Indices: 39430058--39430094 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
39430048 TTATTATTAA
39430058 ATATATTTTAATTAAAATT
1 ATATATTTTAATTAAAATT
39430077 ATATATTTTAA-TAAAATT
1 ATATATTTTAATTAAAATT
39430095 CTTATAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATATTTTAATTAAAATT
Found at i:39430145 original size:157 final size:157
Alignment explanation
Indices: 39429945--39430261 Score: 555
Period size: 157 Copynumber: 2.0 Consensus size: 157
39429935 TAGAATACCC
*
39429945 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * * *
39430010 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
*
39430075 TTATATATTTTAATAAAATTCTT-ATAA
131 -TATATAATTTAATAAAATTCTTAATAA
*
39430102 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
39430167 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
39430232 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
39430259 TTA
1 TTA
39430262 ATATTCTTAT
Statistics
Matches: 152, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
156 21 0.14
157 131 0.86
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:39430232 original size:16 final size:16
Alignment explanation
Indices: 39430195--39430236 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
39430185 TTAATCATAT
*
39430195 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
39430211 TT-AAATATATTATAA
1 TTAAAATATATTATAA
39430226 TTAAAATATAT
1 TTAAAATATAT
39430237 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:39430243 original size:14 final size:15
Alignment explanation
Indices: 39430204--39430245 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
39430194 TTTAAACATA
*
39430204 ATTATTATTAAATAT
1 ATTATAATTAAATAT
39430219 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
39430233 A-TATAATTTAATA
1 ATTATAATTAAATA
39430246 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:39430332 original size:120 final size:121
Alignment explanation
Indices: 39430198--39430490 Score: 502
Period size: 120 Copynumber: 2.4 Consensus size: 121
39430188 ATCATATTTA
39430198 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
39430263 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA-GT-
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AAATGTG
39430318 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
39430383 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATTTG
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATGTG
* * *
39430439 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
39430491 TAAAATAATT
Statistics
Matches: 165, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
119 3 0.02
120 160 0.97
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATGTG
Found at i:39430363 original size:14 final size:15
Alignment explanation
Indices: 39430324--39430365 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
39430314 AAGTAACATA
*
39430324 ATTATTATTAAATAT
1 ATTATAATTAAATAT
39430339 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
39430353 A-TATAATTTAATA
1 ATTATAATTAAATA
39430366 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:39443895 original size:35 final size:35
Alignment explanation
Indices: 39443849--39443921 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
39443839 ATTGTAAGGC
* *
39443849 TTATGATTTTGATTTTTTAAATTAACACAATTAAT
1 TTATAATTTTGATTTTTTAAATTAACACAAGTAAT
39443884 TTATAATTTTGATTTTTTAAATTAACACAAGTAAT
1 TTATAATTTTGATTTTTTAAATTAACACAAGTAAT
39443919 TTA
1 TTA
39443922 AAGAAGGTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (35 bp):
TTATAATTTTGATTTTTTAAATTAACACAAGTAAT
Found at i:39450422 original size:34 final size:34
Alignment explanation
Indices: 39450379--39450446 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
39450369 AAGAATAGCT
39450379 AATATTCTCAATGCAAGAAATTTTTTAAACAATG
1 AATATTCTCAATGCAAGAAATTTTTTAAACAATG
39450413 AATATTCTCAATGCAAGAAATTTTTTAAACAATG
1 AATATTCTCAATGCAAGAAATTTTTTAAACAATG
39450447 GCACAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (34 bp):
AATATTCTCAATGCAAGAAATTTTTTAAACAATG
Found at i:39454139 original size:16 final size:16
Alignment explanation
Indices: 39454120--39454150 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39454110 AAATTTAAAG
*
39454120 ATTAAATTATTAAAAT
1 ATTAAATTAATAAAAT
39454136 ATTAAATTAATAAAA
1 ATTAAATTAATAAAA
39454151 AACTACAAAA
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTAAATTAATAAAAT
Found at i:39454376 original size:31 final size:31
Alignment explanation
Indices: 39454338--39454474 Score: 90
Period size: 31 Copynumber: 4.5 Consensus size: 31
39454328 AAATAACATT
39454338 TTATATATTTTTATATGGTTCTTAACTAATA
1 TTATATATTTTTATATGGTTCTTAACTAATA
* * ** *
39454369 TTATATATTTTTATCACGGGATC--AACTTTTC
1 TTATATATTTTTAT-A-TGGTTCTTAACTAATA
* * * *
39454400 TTA-ACA-ATTTAT-TAGG--CTATAAATAACA
1 TTATATATTTTTATAT-GGTTCT-TAACTAATA
39454428 TTTCATATATTTTTATATGGTTCTTAACTAATA
1 -TT-ATATATTTTTATATGGTTCTTAACTAATA
39454461 TTATATATTTTTAT
1 TTATATATTTTTAT
39454475 CACGGGATCA
Statistics
Matches: 76, Mismatches: 17, Indels: 26
0.64 0.14 0.22
Matches are distributed among these distances:
25 1 0.01
27 2 0.03
28 3 0.04
29 7 0.09
30 3 0.04
31 36 0.47
32 10 0.13
33 12 0.16
34 2 0.03
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (31 bp):
TTATATATTTTTATATGGTTCTTAACTAATA
Found at i:39454470 original size:92 final size:92
Alignment explanation
Indices: 39454313--39454498 Score: 363
Period size: 92 Copynumber: 2.0 Consensus size: 92
39454303 TGATATTTTG
*
39454313 AATTTATTAGGCTATAAATAACATTTTATATATTTTTATATGGTTCTTAACTAATATTATATATT
1 AATTTATTAGGCTATAAATAACATTTCATATATTTTTATATGGTTCTTAACTAATATTATATATT
39454378 TTTATCACGGGATCAACTTTTCTTAAC
66 TTTATCACGGGATCAACTTTTCTTAAC
39454405 AATTTATTAGGCTATAAATAACATTTCATATATTTTTATATGGTTCTTAACTAATATTATATATT
1 AATTTATTAGGCTATAAATAACATTTCATATATTTTTATATGGTTCTTAACTAATATTATATATT
39454470 TTTATCACGGGATCAACTTTTCTTAAC
66 TTTATCACGGGATCAACTTTTCTTAAC
39454497 AA
1 AA
39454499 CATTTTAATC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (92 bp):
AATTTATTAGGCTATAAATAACATTTCATATATTTTTATATGGTTCTTAACTAATATTATATATT
TTTATCACGGGATCAACTTTTCTTAAC
Found at i:39456029 original size:19 final size:20
Alignment explanation
Indices: 39455996--39456035 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
39455986 AAATTATAGC
39455996 ATATCATAATCTAAAAATTA
1 ATATCATAATCTAAAAATTA
* *
39456016 ATAT-ATAATTTAAAATTTA
1 ATATCATAATCTAAAAATTA
39456035 A
1 A
39456036 AGATTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATCATAATCTAAAAATTA
Found at i:39458283 original size:17 final size:18
Alignment explanation
Indices: 39458257--39458291 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
39458247 AAATCTACTA
39458257 AAAAACTAGGCATTATTT
1 AAAAACTAGGCATTATTT
39458275 AAAAA-TAGGCATTATTT
1 AAAAACTAGGCATTATTT
39458292 CCTATCCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (18 bp):
AAAAACTAGGCATTATTT
Found at i:39472607 original size:56 final size:56
Alignment explanation
Indices: 39472539--39472646 Score: 207
Period size: 56 Copynumber: 1.9 Consensus size: 56
39472529 GAGGCCCAGT
39472539 AAGGTTAATAAAACCCAACTGCAGATGGAAAATAAAAAGAAAATTTCACTATGATC
1 AAGGTTAATAAAACCCAACTGCAGATGGAAAATAAAAAGAAAATTTCACTATGATC
*
39472595 AAGGTTAATAAAACCCAACTGCAGATGGAAAATAAAACGAAAATTTCACTAT
1 AAGGTTAATAAAACCCAACTGCAGATGGAAAATAAAAAGAAAATTTCACTAT
39472647 CTAAGCACAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.50, C:0.15, G:0.14, T:0.21
Consensus pattern (56 bp):
AAGGTTAATAAAACCCAACTGCAGATGGAAAATAAAAAGAAAATTTCACTATGATC
Found at i:39478395 original size:26 final size:26
Alignment explanation
Indices: 39478363--39478419 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
39478353 ATTAAGTGAA
39478363 TAACAACAAAAAACAAGGAAACAAAT
1 TAACAACAAAAAACAAGGAAACAAAT
39478389 TAACAACAAAAAACAAGGAAACAAAT
1 TAACAACAAAAAACAAGGAAACAAAT
*
39478415 GAACA
1 TAACA
39478420 TAGTCCAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.68, C:0.16, G:0.09, T:0.07
Consensus pattern (26 bp):
TAACAACAAAAAACAAGGAAACAAAT
Found at i:39479752 original size:11 final size:10
Alignment explanation
Indices: 39479732--39479761 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
39479722 AATTATATGG
39479732 TTTTTTTATT
1 TTTTTTTATT
39479742 TTTTATTTATT
1 TTTT-TTTATT
39479753 TTTTTTTAT
1 TTTTTTTAT
39479762 GAAGTCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:39486008 original size:58 final size:57
Alignment explanation
Indices: 39485929--39486110 Score: 197
Period size: 58 Copynumber: 3.2 Consensus size: 57
39485919 ACTTAGATAA
* * *
39485929 AAAAAAAGTTGAAGCCTCAATGTGATAATATTTGCTAAGTTCAATGCCTAACTTGGAC
1 AAAAAAATTTCAAGCCTCAATGTGAGAATATTTGCTAAGTTCAA-GCCTAACTTGGAC
* * * * **
39485987 CAAAAAATTTCAAGCCTCAATGTGGGGATATTTGCTAAATTCAAGGCCTAACTTGGGT
1 AAAAAAATTTCAAGCCTCAATGTGAGAATATTTGCTAAGTTCAA-GCCTAACTTGGAC
* * * *
39486045 AAAATAATTTCAAGCC-CAATGTAAGAATATTT-ATCAAGTTCAAGACCTAAATTGGAC
1 AAAAAAATTTCAAGCCTCAATGTGAGAATATTTGCT-AAGTTCAAG-CCTAACTTGGAC
39486102 AAAAAAATT
1 AAAAAAATT
39486111 AGACCCACTA
Statistics
Matches: 101, Mismatches: 21, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
56 2 0.02
57 37 0.37
58 62 0.61
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (57 bp):
AAAAAAATTTCAAGCCTCAATGTGAGAATATTTGCTAAGTTCAAGCCTAACTTGGAC
Found at i:39489514 original size:12 final size:13
Alignment explanation
Indices: 39489499--39489527 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39489489 AACGCACCCA
39489499 AAAAAT-AAAAAT
1 AAAAATAAAAAAT
39489511 AAAAATAAAAAAT
1 AAAAATAAAAAAT
39489524 AAAA
1 AAAA
39489528 CAAAGATTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:39495484 original size:5 final size:6
Alignment explanation
Indices: 39495467--39495497 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
39495457 GACAATTAGG
*
39495467 TATTTT TATTTT TATTTT TATTTT TGTTTT T
1 TATTTT TATTTT TATTTT TATTTT TATTTT T
39495498 TTGCATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:39504002 original size:31 final size:31
Alignment explanation
Indices: 39503964--39504034 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
39503954 ACAAAAGTGT
39503964 TCAAATAAGGGCCAAAT-ATATTCGAAAATGC
1 TCAAATAAGGG-CAAATCATATTCGAAAATGC
** * *
39503995 TCAAATAAGGGTGAATCATTTTCGAAAGTGC
1 TCAAATAAGGGCAAATCATATTCGAAAATGC
39504026 TCAAATAAG
1 TCAAATAAG
39504035 ATTTTTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 3 0.09
31 32 0.91
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.25
Consensus pattern (31 bp):
TCAAATAAGGGCAAATCATATTCGAAAATGC
Found at i:39507405 original size:24 final size:24
Alignment explanation
Indices: 39507378--39507425 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
39507368 TTTTGTATAC
39507378 AAATAAT-TAAAAATCATAAAAAAT
1 AAATAATATAAAAAT-ATAAAAAAT
*
39507402 AAATATTATAAAAATATAAAAAAT
1 AAATAATATAAAAATATAAAAAAT
39507426 CTAATAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (24 bp):
AAATAATATAAAAATATAAAAAAT
Found at i:39507443 original size:19 final size:20
Alignment explanation
Indices: 39507416--39507464 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
39507406 ATTATAAAAA
*
39507416 TATAAAAAATCTA-ATAAAC
1 TATAAAAAACCTATATAAAC
* *
39507435 TATATAAAACCTATATAAAA
1 TATAAAAAACCTATATAAAC
*
39507455 TAAAAAAAAC
1 TATAAAAAAC
39507465 TTATTAGAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.24
Consensus pattern (20 bp):
TATAAAAAACCTATATAAAC
Found at i:39507463 original size:20 final size:20
Alignment explanation
Indices: 39507408--39507464 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
39507398 AAATAAATAT
*
39507408 TATA-AAAATATAAAAAATC
1 TATATAAAATATAAAAAACC
* *
39507427 TA-ATAAACTATATAAAACC
1 TATATAAAATATAAAAAACC
*
39507446 TATATAAAATAAAAAAAAC
1 TATATAAAATATAAAAAAC
39507465 TTATTAGAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 1 0.03
19 16 0.53
20 13 0.43
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.25
Consensus pattern (20 bp):
TATATAAAATATAAAAAACC
Found at i:39508180 original size:20 final size:21
Alignment explanation
Indices: 39508104--39508177 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 21
39508094 AATAAATTTT
*
39508104 ATTTTTTGATAATTTTATCTG
1 ATTTTTTGATAATTTTATATG
*
39508125 ATTATTT-ATAATTTTATATG
1 ATTTTTTGATAATTTTATATG
*
39508145 -GTTTTTGAT--TTTT-TATG
1 ATTTTTTGATAATTTTATATG
*
39508162 ATTTTTTTATAATTTT
1 ATTTTTTGATAATTTT
39508178 TATAATTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
17 4 0.09
18 11 0.26
19 4 0.09
20 18 0.42
21 6 0.14
ACGTcount: A:0.24, C:0.01, G:0.08, T:0.66
Consensus pattern (21 bp):
ATTTTTTGATAATTTTATATG
Found at i:39517158 original size:6 final size:6
Alignment explanation
Indices: 39517126--39517157 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
39517116 TCCGGACATC
*
39517126 TCCTCA TCCTCA TCCTCA TCCTCA TCATCA TC
1 TCCTCA TCCTCA TCCTCA TCCTCA TCCTCA TC
39517158 AAGGTTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.47, G:0.00, T:0.34
Consensus pattern (6 bp):
TCCTCA
Found at i:39530071 original size:12 final size:13
Alignment explanation
Indices: 39530054--39530084 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
39530044 CGATATCTCA
39530054 ATTTCAATTCA-C
1 ATTTCAATTCATC
39530066 ATTTCAATTCATC
1 ATTTCAATTCATC
39530079 ATTTCA
1 ATTTCA
39530085 CTCTCTCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTTCAATTCATC
Found at i:39530135 original size:13 final size:13
Alignment explanation
Indices: 39530119--39530150 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
39530109 ATCAATCAAT
39530119 TCATTTGATTTTC
1 TCATTTGATTTTC
*
39530132 TCATTTGATTTTT
1 TCATTTGATTTTC
39530145 TCATTT
1 TCATTT
39530151 CAATTATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.12, G:0.06, T:0.66
Consensus pattern (13 bp):
TCATTTGATTTTC
Found at i:39530512 original size:23 final size:23
Alignment explanation
Indices: 39530431--39530516 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 23
39530421 CTTGATCAGT
39530431 ATACGACACAT-AAGTGCCT-AA
1 ATACGACACATGAAGTGCCTGAA
* *
39530452 A-ATGACACATGAGGTGCCTG--
1 ATACGACACATGAAGTGCCTGAA
* * *
39530472 ATATGACACACGAGGTGCCTGAA
1 ATACGACACATGAAGTGCCTGAA
*
39530495 ATACGACACATAAAGTGCCTGA
1 ATACGACACATGAAGTGCCTGA
39530517 TCGGCAAAGC
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
20 9 0.17
21 26 0.49
23 18 0.34
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (23 bp):
ATACGACACATGAAGTGCCTGAA
Found at i:39531080 original size:72 final size:73
Alignment explanation
Indices: 39530934--39531084 Score: 184
Period size: 72 Copynumber: 2.1 Consensus size: 73
39530924 ATCACTAATT
* * * *
39530934 ACTTTTCAATCAATATATATTTCAAATACTCACATATTTTCTTCATTCAATTCAATTTGATTCAA
1 ACTTTTCAATCAATATATAGTTCAAATACTCACATATATTCATAATTCAATTCAATTTGATTCAA
39530999 TTCAAATC
66 TTCAAATC
* *
39531007 ACTTTTCCAATCAATATA-CGTTCAAATATTCACATA-ATTCATAATTCATAATTCAA-TT-ATT
1 ACTTTT-CAATCAATATATAGTTCAAATACTCACATATATTCATAATTC--AATTCAATTTGATT
*
39531068 TAATTCAAATC
63 CAATTCAAATC
39531079 ACTTTT
1 ACTTTT
39531085 AATTTCTAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
72 27 0.40
73 23 0.34
74 18 0.26
ACGTcount: A:0.37, C:0.19, G:0.01, T:0.43
Consensus pattern (73 bp):
ACTTTTCAATCAATATATAGTTCAAATACTCACATATATTCATAATTCAATTCAATTTGATTCAA
TTCAAATC
Found at i:39531429 original size:17 final size:18
Alignment explanation
Indices: 39531399--39531432 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39531389 AATTTCTATT
39531399 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
39531417 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
39531433 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:39532394 original size:171 final size:171
Alignment explanation
Indices: 39532207--39532548 Score: 666
Period size: 171 Copynumber: 2.0 Consensus size: 171
39532197 ATAAATAATA
*
39532207 AATATATATTTACTAATTAAATATAAGTATTACAAATGTACATATATTTTTTTTTACAATTGTAC
1 AATATATATTTACTAATTAAATATAAGTATTACAAATGTACATATATATTTTTTTACAATTGTAC
39532272 ATTATCATCACCATCCATTTGACAAATTTTTTATTTATTCATATAATATAATATTTTTAATTTAT
66 ATTATCATCACCATCCATTTGACAAATTTTTTATTTATTCATATAATATAATATTTTTAATTTAT
39532337 AACTAATATAAATTACAATATAATAAAATAATTATATACAT
131 AACTAATATAAATTACAATATAATAAAATAATTATATACAT
*
39532378 AATATATATTTACTAATTAAATATAAGTATTACAAATGTACATCTATATTTTTTTACAATTGTAC
1 AATATATATTTACTAATTAAATATAAGTATTACAAATGTACATATATATTTTTTTACAATTGTAC
39532443 ATTATCATCACCATCCATTTGACAAATTTTTTATTTATTCATATAATATAATATTTTTAATTTAT
66 ATTATCATCACCATCCATTTGACAAATTTTTTATTTATTCATATAATATAATATTTTTAATTTAT
39532508 AACTAATATAAATTACAATATAATAAAATAATTATATACAT
131 AACTAATATAAATTACAATATAATAAAATAATTATATACAT
39532549 TATAATTTAA
Statistics
Matches: 169, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
171 169 1.00
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (171 bp):
AATATATATTTACTAATTAAATATAAGTATTACAAATGTACATATATATTTTTTTACAATTGTAC
ATTATCATCACCATCCATTTGACAAATTTTTTATTTATTCATATAATATAATATTTTTAATTTAT
AACTAATATAAATTACAATATAATAAAATAATTATATACAT
Found at i:39532747 original size:20 final size:19
Alignment explanation
Indices: 39532701--39532747 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
39532691 CTTTTTTTTT
*
39532701 CCTAATTTCTCTTAATTAAG
1 CCTAA-TTCACTTAATTAAG
39532721 -CTAAATTCACTTAATTAAAG
1 CCT-AATTCACTTAATT-AAG
39532741 CCTAATT
1 CCTAATT
39532748 AAACACACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 12 0.52
20 9 0.39
21 2 0.09
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.40
Consensus pattern (19 bp):
CCTAATTCACTTAATTAAG
Found at i:39535134 original size:41 final size:41
Alignment explanation
Indices: 39535107--39535260 Score: 290
Period size: 41 Copynumber: 3.8 Consensus size: 41
39535097 CTTATAGCTT
* *
39535107 GATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACCT
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
39535148 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
39535189 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
39535230 GATTCAAATCACCGGCACGTAGCCTGCTAGG
1 GATTCAAATCACCGGCACGTAGCCTGCTAGG
39535261 NNNNNNNNNN
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 111 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (41 bp):
GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
Found at i:39546337 original size:42 final size:42
Alignment explanation
Indices: 39546288--39546397 Score: 145
Period size: 42 Copynumber: 2.6 Consensus size: 42
39546278 CATAGTTCAA
** *
39546288 CTATGGTCTTACACATCTTCACATAAT-GATGTCATAGCCCAG
1 CTATGGTCTTACACAAATTCACAT-ATCGATGTCATAGACCAG
*
39546330 CTATGGTCTTACACAAATTCATATATCGATGTCATAGACCAG
1 CTATGGTCTTACACAAATTCACATATCGATGTCATAGACCAG
39546372 CTATGGTCTTACACGAAA--CACATATC
1 CTATGGTCTTACAC-AAATTCACATATC
39546398 TCACTGATGC
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
41 9 0.15
42 49 0.80
43 3 0.05
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.30
Consensus pattern (42 bp):
CTATGGTCTTACACAAATTCACATATCGATGTCATAGACCAG
Found at i:39546454 original size:47 final size:47
Alignment explanation
Indices: 39546393--39546574 Score: 337
Period size: 47 Copynumber: 3.9 Consensus size: 47
39546383 CACGAAACAC
* *
39546393 ATATCTCACTGATGCCATATCCCAGATATGGTCTTATACAGTAGCAT
1 ATATCACACCGATGCCATATCCCAGATATGGTCTTATACAGTAGCAT
39546440 ATATCACACCGATGCCATATCCCAGATATGGTCTTATACAGTAGCAT
1 ATATCACACCGATGCCATATCCCAGATATGGTCTTATACAGTAGCAT
39546487 ATATCACACCGATGCCATATCCCAGATATGGTCTTATACAGTAGCAT
1 ATATCACACCGATGCCATATCCCAGATATGGTCTTATACAGTAGCAT
*
39546534 ATATCACACCGATGCCATATCCTAGATATGGTCTTATACAG
1 ATATCACACCGATGCCATATCCCAGATATGGTCTTATACAG
39546575 AAATCACTTG
Statistics
Matches: 132, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 132 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (47 bp):
ATATCACACCGATGCCATATCCCAGATATGGTCTTATACAGTAGCAT
Found at i:39555390 original size:122 final size:122
Alignment explanation
Indices: 39555168--39555424 Score: 471
Period size: 122 Copynumber: 2.1 Consensus size: 122
39555158 TCTAATGCAG
* *
39555168 CATATAACTAAATTAACATCAAAATAATAGAAAGGACTAAACTAAAGAGGAATGTTATAACAGAA
1 CATACAACTAAATTAACATCAAAATAATAGAAAGGACTAAACTAAAGAGCAATGTTATAACAGAA
39555233 AGACTGCAGTTATTATTGACTTAAAAGATACCATATGGTCTATCTTGTTACTTAGGT
66 AGACTGCAGTTATTATTGACTTAAAAGATACCATATGGTCTATCTTGTTACTTAGGT
39555290 CATACAACTAAATTAACATCAAAATAATA-AAATGGACTAAACTAAAGAGCAATGTTATAACAGA
1 CATACAACTAAATTAACATCAAAATAATAGAAA-GGACTAAACTAAAGAGCAATGTTATAACAGA
39555354 AAGACTGCAGTTATTATTGACTTAAAAGATACCATATGGTCTATCTTGTTACTTAGGT
65 AAGACTGCAGTTATTATTGACTTAAAAGATACCATATGGTCTATCTTGTTACTTAGGT
*
39555412 CATACAAATAAAT
1 CATACAACTAAAT
39555425 AGTGATCAAT
Statistics
Matches: 131, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
121 3 0.02
122 128 0.98
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.29
Consensus pattern (122 bp):
CATACAACTAAATTAACATCAAAATAATAGAAAGGACTAAACTAAAGAGCAATGTTATAACAGAA
AGACTGCAGTTATTATTGACTTAAAAGATACCATATGGTCTATCTTGTTACTTAGGT
Found at i:39585181 original size:23 final size:22
Alignment explanation
Indices: 39585155--39585216 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
39585145 AATTAATTAA
39585155 TTAATTATTAATTTATTAATATT
1 TTAATTATTAATTTATT-ATATT
*
39585178 TTAATT-TGACATTTAATTATATT
1 TTAATTATTA-ATTT-ATTATATT
*
39585201 TT-ATTATTATTTTATT
1 TTAATTATTAATTTATT
39585217 TAGTATATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
21 3 0.09
22 8 0.24
23 19 0.58
24 3 0.09
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
TTAATTATTAATTTATTATATT
Found at i:39585959 original size:19 final size:20
Alignment explanation
Indices: 39585935--39585973 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
39585925 TCTCATTTTT
39585935 TATTTGTTTCT-TGTTTTAA
1 TATTTGTTTCTATGTTTTAA
*
39585954 TATTTGTTTTTATGTTTTAA
1 TATTTGTTTCTATGTTTTAA
39585974 AATGTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.18, C:0.03, G:0.10, T:0.69
Consensus pattern (20 bp):
TATTTGTTTCTATGTTTTAA
Found at i:39585982 original size:24 final size:26
Alignment explanation
Indices: 39585954--39586002 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
39585944 CTTGTTTTAA
*
39585954 TATTTG-TTT-TTATGTTTTAAAATG
1 TATTTGATTTATTATATTTTAAAATG
39585978 TATTTGATTTATTATATTTTAAAAT
1 TATTTGATTTATTATATTTTAAAAT
39586003 TTTTTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 3 0.14
26 13 0.59
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (26 bp):
TATTTGATTTATTATATTTTAAAATG
Found at i:39587713 original size:24 final size:24
Alignment explanation
Indices: 39587686--39587738 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
39587676 GATAATCTAA
39587686 ACAATATCGACAATAACTCAAGCC
1 ACAATATCGACAATAACTCAAGCC
39587710 ACAATATCGACAATAACTCAAGCC
1 ACAATATCGACAATAACTCAAGCC
*
39587734 TCAAT
1 ACAAT
39587739 CTCTAGTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.45, C:0.28, G:0.08, T:0.19
Consensus pattern (24 bp):
ACAATATCGACAATAACTCAAGCC
Found at i:39592367 original size:14 final size:14
Alignment explanation
Indices: 39592348--39592374 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39592338 GTCGATACAT
39592348 TAAATATTTATTTA
1 TAAATATTTATTTA
39592362 TAAATATTTATTT
1 TAAATATTTATTT
39592375 TTCTTGTAAT
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAAATATTTATTTA
Found at i:39595355 original size:3 final size:3
Alignment explanation
Indices: 39595347--39595371 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39595337 GTGGATGGAC
39595347 AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG A
39595372 AAAAATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:39602310 original size:42 final size:42
Alignment explanation
Indices: 39602243--39602362 Score: 152
Period size: 43 Copynumber: 2.8 Consensus size: 42
39602233 TGAGTTACTA
* * * *
39602243 AGACTACGTGTAAGACTATATCTGGGATATGGCATCGATATG
1 AGACTTCGTGTAAGACCATATCTGGGATATGGCATCAATACG
* *
39602285 AGACTTCGTGTAAGACCATAGCTGGGCTATTGGCATCAATACG
1 AGACTTCGTGTAAGACCATATCTGGGATA-TGGCATCAATACG
*
39602328 AGA-TTACATGTAAGACCATATCTGGGATATGGCAT
1 AGACTT-CGTGTAAGACCATATCTGGGATATGGCAT
39602363 TAGTATGGTA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 33 0.49
43 34 0.51
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.28
Consensus pattern (42 bp):
AGACTTCGTGTAAGACCATATCTGGGATATGGCATCAATACG
Found at i:39604746 original size:30 final size:30
Alignment explanation
Indices: 39604710--39604771 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
39604700 GTAAACTAAC
39604710 TTTAACGGAT-ACTGAATCAGACATTAAATG
1 TTTAAC-GATCACTGAATCAGACATTAAATG
39604740 TTTAACGATCACTGAATCAGACATTAAATG
1 TTTAACGATCACTGAATCAGACATTAAATG
39604770 TT
1 TT
39604772 AATAGTATCG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 3 0.10
30 28 0.90
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (30 bp):
TTTAACGATCACTGAATCAGACATTAAATG
Found at i:39619373 original size:6 final size:7
Alignment explanation
Indices: 39619354--39619382 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
39619344 TACTTCGTGT
39619354 TTAAAAA
1 TTAAAAA
39619361 TTAAAAA
1 TTAAAAA
39619368 TTAAAAA
1 TTAAAAA
39619375 TTAAAAA
1 TTAAAAA
39619382 T
1 T
39619383 AACCCATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
TTAAAAA
Found at i:39619784 original size:26 final size:26
Alignment explanation
Indices: 39619735--39619784 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
39619725 TATATTTTAA
* *
39619735 ATAATTAAAATATATAATTATTATTT
1 ATAATTAAAATAAATAAGTATTATTT
39619761 ATAATTAAAATAAATTAAGT-TTAT
1 ATAATTAAAATAAA-TAAGTATTAT
39619785 GATTTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
ATAATTAAAATAAATAAGTATTATTT
Found at i:39619983 original size:25 final size:23
Alignment explanation
Indices: 39619955--39620004 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
39619945 AAATTATTAG
*
39619955 TAATTATTAAACAATATTATATTTT
1 TAATAATTAAA-AAT-TTATATTTT
* *
39619980 TAATAATTTAAGATTTATATTTT
1 TAATAATTAAAAATTTATATTTT
39620003 TA
1 TA
39620005 TGATATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 11 0.50
24 2 0.09
25 9 0.41
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
TAATAATTAAAAATTTATATTTT
Found at i:39625812 original size:30 final size:31
Alignment explanation
Indices: 39625769--39625851 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 31
39625759 AAGACATCAC
* *
39625769 ATCATCTTGAATTTTTTATTA-ATTATTTA-AT
1 ATCAT-TTAAATTTTTT-TTATATTATTGATAT
*
39625800 ATCATTTAAATTTTTTTTATGTTATTGATAT
1 ATCATTTAAATTTTTTTTATATTATTGATAT
*
39625831 ATCATTTTAATAATTTTTTTA
1 ATCA-TTTAA-ATTTTTTTTA
39625852 AAATTGAACT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
29 3 0.07
30 16 0.36
31 11 0.25
32 5 0.11
33 9 0.20
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.60
Consensus pattern (31 bp):
ATCATTTAAATTTTTTTTATATTATTGATAT
Found at i:39626430 original size:18 final size:18
Alignment explanation
Indices: 39626386--39626422 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
39626376 AAATAGAACG
39626386 CCGAAATAAGTTAGTACT
1 CCGAAATAAGTTAGTACT
*
39626404 CCGAAATAAGTTGGTACT
1 CCGAAATAAGTTAGTACT
39626422 C
1 C
39626423 GTATATAACA
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:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (18 bp):
CCGAAATAAGTTAGTACT
Found at i:39627247 original size:6 final size:6
Alignment explanation
Indices: 39627236--39627263 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
39627226 AAAAGTTTTA
39627236 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
39627264 GCTCGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:39628356 original size:130 final size:128
Alignment explanation
Indices: 39628106--39628386 Score: 465
Period size: 130 Copynumber: 2.2 Consensus size: 128
39628096 TAAGTGGCAG
* * *
39628106 ACTACAAATTAACCCTTAAAAAATTAATGTTGTTAAGAAATTGAGACTGTGTGATGGAATGCAAG
1 ACTACATATTAACCCTTAAATAATTAATGTTGTTAAGAAATTGAGACTGTGTGATGGAATACAAG
*
39628171 TTTAGGTAATACAAAAAAAAAATCAAATACTAATTAATACCTTTGGATAAGTTCAAGAAATAA
66 TTTAGGTAATACAAAAAAAAAATCAAATACTAATAAATACCTTTGGATAAGTTCAAGAAATAA
* *
39628234 ACTACATATTAACCATTAAATAATTAATGTTGTTAAGAAATTGAGACTGTGTGTGGTGGAATACA
1 ACTACATATTAACCCTTAAATAATTAATGTTGTTAAGAAATTGAGAC--TGTGTGATGGAATACA
39628299 AGTTTAGGTAATAC-AAAAAAAAATCAAATACTAACTAAATACCTTTGGATAAGTTCAAGAAATA
64 AGTTTAGGTAATACAAAAAAAAAATCAAATACTAA-TAAATACCTTTGGATAAGTTCAAGAAATA
39628363 A
128 A
*
39628364 TCTACATATTAACCCTTAAATAA
1 ACTACATATTAACCCTTAAATAA
39628387 ATATTAGTAA
Statistics
Matches: 142, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
128 44 0.31
129 20 0.14
130 78 0.55
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (128 bp):
ACTACATATTAACCCTTAAATAATTAATGTTGTTAAGAAATTGAGACTGTGTGATGGAATACAAG
TTTAGGTAATACAAAAAAAAAATCAAATACTAATAAATACCTTTGGATAAGTTCAAGAAATAA
Found at i:39629250 original size:37 final size:38
Alignment explanation
Indices: 39629204--39629278 Score: 143
Period size: 37 Copynumber: 2.0 Consensus size: 38
39629194 AGAATTTAAG
39629204 CCATTCATTTAATACATATTTTAAACTT-GAAAAACAA
1 CCATTCATTTAATACATATTTTAAACTTAGAAAAACAA
39629241 CCATTCATTTAATACATATTTTAAACTTAGAAAAACAA
1 CCATTCATTTAATACATATTTTAAACTTAGAAAAACAA
39629279 TTTCATCATA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 28 0.76
38 9 0.24
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.35
Consensus pattern (38 bp):
CCATTCATTTAATACATATTTTAAACTTAGAAAAACAA
Found at i:39639887 original size:4 final size:4
Alignment explanation
Indices: 39639878--39639904 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
39639868 GTAGATGTTG
39639878 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
39639905 TGGTAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:39641809 original size:25 final size:25
Alignment explanation
Indices: 39641781--39641927 Score: 73
Period size: 25 Copynumber: 6.0 Consensus size: 25
39641771 TAAAATATTT
* * *
39641781 TTATTTATA-TGAGTTATTTCATATA
1 TTATTTATATTAAATTATTT-AAATA
39641806 TTA-TTATATTAAATTATTTAAATA
1 TTATTTATATTAAATTATTTAAATA
39641830 TTATTTATTATTATTAATT-TTTAAA-A
1 TTATTTA-TATTA--AATTATTTAAATA
*
39641856 -TATTT-TA-AAATATTATTTAAATA
1 TTATTTATATTAA-ATTATTTAAATA
**
39641879 -TATTTA-A--AAATTATATTTCATA
1 TTATTTATATTAAATTAT-TTAAATA
* * *
39641901 TATAATTATATTAAAATATTAAAATA
1 T-TATTTATATTAAATTATTTAAATA
39641927 T
1 T
39641928 CATATATCTT
Statistics
Matches: 96, Mismatches: 11, Indels: 29
0.71 0.08 0.21
Matches are distributed among these distances:
20 1 0.01
21 8 0.08
22 14 0.15
23 9 0.09
24 17 0.18
25 20 0.21
26 11 0.11
27 12 0.12
28 4 0.04
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (25 bp):
TTATTTATATTAAATTATTTAAATA
Found at i:39641833 original size:21 final size:20
Alignment explanation
Indices: 39641807--39641892 Score: 65
Period size: 21 Copynumber: 4.3 Consensus size: 20
39641797 TTTCATATAT
39641807 TATTATATTAAATTATTTAAA
1 TATTAT-TTAAATTATTTAAA
*
39641828 TATTATTT--ATTA-TT-AT
1 TATTATTTAAATTATTTAAA
*
39641844 TAATT-TTTAAAATATTTTAAAA
1 T-ATTATTTAAATTA-TTT-AAA
39641866 TATTATTTAAATATATTTAAA
1 TATTATTTAAAT-TATTTAAA
*
39641887 AATTAT
1 TATTAT
39641893 ATTTCATATA
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
16 5 0.10
17 5 0.10
18 7 0.14
20 4 0.08
21 17 0.33
22 11 0.22
23 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTATTTAAATTATTTAAA
Found at i:39641838 original size:28 final size:28
Alignment explanation
Indices: 39641764--39641859 Score: 80
Period size: 28 Copynumber: 3.6 Consensus size: 28
39641754 AGGTATTTAA
*
39641764 AAATTATTAAAATATT-TTTATT-TATAT
1 AAATTATTTAAATATTATTTATTATAT-T
* * *
39641791 GAGTTATTT-CATA-TA-TTATTATATT
1 AAATTATTTAAATATTATTTATTATATT
39641816 AAATTATTTAAATATTATTTATTATTATT
1 AAATTATTTAAATATTATTTATTA-TATT
39641845 -AATT-TTTAAAATATT
1 AAATTATTT-AAATATT
39641860 TTAAAATATT
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
25 14 0.25
26 9 0.16
27 11 0.20
28 17 0.31
29 4 0.07
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (28 bp):
AAATTATTTAAATATTATTTATTATATT
Found at i:39641859 original size:52 final size:49
Alignment explanation
Indices: 39641759--39641884 Score: 125
Period size: 52 Copynumber: 2.5 Consensus size: 49
39641749 GATTTAGGTA
* * * *
39641759 TTTAAAAATTATTAAAATATT-TTTATTTATATGAGTTATTTCATATAT
1 TTTAAAAATTATTTAAATATTATTTATTTATATGAATTATTTAAAATAT
*
39641807 TATTATATTAAATTATTTAAATATTATTTA-TTATTATTAATT-TTTAAAATAT
1 T-TTA-A--AAATTATTTAAATATTATTTATTTA-TATGAATTATTTAAAATAT
39641859 TTTAAAATATTATTTAAATA-TATTTA
1 TTTAAAA-ATTATTTAAATATTATTTA
39641885 AAAATTATAT
Statistics
Matches: 66, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
48 9 0.14
49 15 0.23
50 2 0.03
51 3 0.05
52 27 0.41
53 10 0.15
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.56
Consensus pattern (49 bp):
TTTAAAAATTATTTAAATATTATTTATTTATATGAATTATTTAAAATAT
Found at i:39641903 original size:22 final size:22
Alignment explanation
Indices: 39641853--39641892 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
39641843 TTAATTTTTA
39641853 AAATAT-TTTAAAATATTATTT
1 AAATATATTTAAAATATTATTT
39641874 AAATATATTTAAAA-ATTAT
1 AAATATATTTAAAATATTAT
39641893 ATTTCATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATATATTTAAAATATTATTT
Found at i:39641907 original size:59 final size:59
Alignment explanation
Indices: 39641807--39641932 Score: 145
Period size: 59 Copynumber: 2.1 Consensus size: 59
39641797 TTTCATATAT
* *
39641807 TATTATATTAAATTATTTAAATATTATTTATTATTATTAATT-T-TTAAAATATTTTAAAA
1 TATTATATTAAATTATTTAAAAATTATTTATCATTATTAATTATATTAAAATA--TTAAAA
39641866 TATTAT-TTAAATATATTTAAAAATTATATT-TCA-TATATAATTATATTAAAATATTAAAA
1 TATTATATTAAAT-TATTTAAAAATTAT-TTATCATTAT-TAATTATATTAAAATATTAAAA
*
39641925 TATCATAT
1 TATTATAT
39641933 ATCTTAATTA
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
58 9 0.16
59 37 0.64
60 4 0.07
61 8 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (59 bp):
TATTATATTAAATTATTTAAAAATTATTTATCATTATTAATTATATTAAAATATTAAAA
Found at i:39646305 original size:32 final size:32
Alignment explanation
Indices: 39646263--39646324 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
39646253 CAATATGTAA
39646263 GAGAATAATATCTAGAAATAAGGATTAAATAT
1 GAGAATAATATCTAGAAATAAGGATTAAATAT
*
39646295 GAGACTAATATCTAGAAATAAGGATTAAAT
1 GAGAATAATATCTAGAAATAAGGATTAAAT
39646325 TGCAAGAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.52, C:0.05, G:0.16, T:0.27
Consensus pattern (32 bp):
GAGAATAATATCTAGAAATAAGGATTAAATAT
Found at i:39647012 original size:46 final size:46
Alignment explanation
Indices: 39646960--39647279 Score: 507
Period size: 46 Copynumber: 7.0 Consensus size: 46
39646950 AGTGTGCTCT
39646960 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
39647006 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
39647052 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
39647098 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
39647144 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCGTGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * ***
39647190 GTGTTATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
39647236 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
39647280 TCATGTCAAA
Statistics
Matches: 256, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 1 0.00
46 255 1.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:39648070 original size:13 final size:14
Alignment explanation
Indices: 39648041--39648072 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
39648031 TGTTTCACTG
39648041 AAAATAATTTCCAA
1 AAAATAATTTCCAA
*
39648055 AAAATAATTTCTAA
1 AAAATAATTTCCAA
39648069 AAAA
1 AAAA
39648073 GCAAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATAATTTCCAA
Found at i:39648542 original size:15 final size:15
Alignment explanation
Indices: 39648522--39648578 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
39648512 ATTATAAAAC
39648522 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
39648537 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
39648556 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
39648571 A-TTATTAT
1 ATTTATTAT
39648579 CGAATATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
14 7 0.20
15 10 0.29
16 1 0.03
17 7 0.20
18 1 0.03
19 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:39648637 original size:16 final size:16
Alignment explanation
Indices: 39648606--39648642 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
39648596 ATATGAATAA
39648606 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
39648622 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
39648638 TATTA
1 TATTA
39648643 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:39648709 original size:16 final size:17
Alignment explanation
Indices: 39648683--39648714 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
39648673 AAAATAACAA
39648683 AATATATTTATTATATT
1 AATATATTTATTATATT
39648700 AATA-ATTTATTATAT
1 AATATATTTATTATAT
39648715 GACTAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATATATTTATTATATT
Found at i:39649697 original size:60 final size:59
Alignment explanation
Indices: 39649572--39649700 Score: 150
Period size: 60 Copynumber: 2.2 Consensus size: 59
39649562 ACAACTTTCA
* * ** *
39649572 AATAGTTCATTAACCATTTTGTAGCCTTTTGAAGTTGAGTGATTAAAGCATAAGCTTTT
1 AATAGTTCAGTAACCATTTTGTAGCCTTTTAAAGTTGAGTGATTAAAGCATAAAATTCT
* ** **
39649631 AGATAGTTTAGTAACCATTTTGTAGTTTTTTAAAGTTGAGTGATTAAAGTGTAAAATTACT
1 A-ATAGTTCAGTAACCATTTTGTAGCCTTTTAAAGTTGAGTGATTAAAGCATAAAATT-CT
39649692 AATAGTTCA
1 AATAGTTCA
39649701 ATGACCTTAG
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
59 1 0.02
60 54 0.95
61 2 0.04
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (59 bp):
AATAGTTCAGTAACCATTTTGTAGCCTTTTAAAGTTGAGTGATTAAAGCATAAAATTCT
Found at i:39651209 original size:8 final size:9
Alignment explanation
Indices: 39651187--39651221 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
39651177 TTTTTAAAAA
39651187 ATATTTTTT
1 ATATTTTTT
39651196 ATATTTTTT
1 ATATTTTTT
39651205 A-A-TTTTT
1 ATATTTTTT
39651212 ATATTTTTT
1 ATATTTTTT
39651221 A
1 A
39651222 AAATTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 6 0.25
8 2 0.08
9 16 0.67
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
ATATTTTTT
Found at i:39651212 original size:16 final size:16
Alignment explanation
Indices: 39651191--39651222 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39651181 TAAAAAATAT
39651191 TTTTTATATTTTTTAA
1 TTTTTATATTTTTTAA
39651207 TTTTTATATTTTTTAA
1 TTTTTATATTTTTTAA
39651223 AATTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTATATTTTTTAA
Found at i:39651220 original size:18 final size:18
Alignment explanation
Indices: 39651189--39651242 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
39651179 TTTAAAAAAT
**
39651189 ATTTTT-TATATTTTTTA
1 ATTTTTATATATTTTAAA
*
39651206 ATTTTTATATTTTTTAAA
1 ATTTTTATATATTTTAAA
* *
39651224 ATTTTTAAAAATTTTAAA
1 ATTTTTATATATTTTAAA
39651242 A
1 A
39651243 ATAATTAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 6 0.20
18 24 0.80
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTTATATATTTTAAA
Found at i:39663454 original size:25 final size:24
Alignment explanation
Indices: 39663426--39663481 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
39663416 TATTTAAAAC
39663426 TAAAGATATTTTGATTATACAATTT-
1 TAAAGATATTTTGATT-TA-AATTTG
**
39663451 TAAATTTATTTTGATTTAAATTTG
1 TAAAGATATTTTGATTTAAATTTG
39663475 TAAAGAT
1 TAAAGAT
39663482 CATTCTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 5 0.19
24 7 0.27
25 14 0.54
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (24 bp):
TAAAGATATTTTGATTTAAATTTG
Done.