Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 133 of 290
Found at i:41826655 original size:19 final size:19
Alignment explanation
Indices: 41826613--41826655 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
41826603 GCATGAACAA
*
41826613 AATGTTTAACTGAATGTTT
1 AATGATTAACTGAATGTTT
*
41826632 GATGATTAA-TGAATGTTTT
1 AATGATTAACTGAATG-TTT
41826651 AATGA
1 AATGA
41826656 GTTTTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (19 bp):
AATGATTAACTGAATGTTT
Found at i:41842610 original size:45 final size:45
Alignment explanation
Indices: 41842540--41842677 Score: 113
Period size: 45 Copynumber: 3.1 Consensus size: 45
41842530 TCGAAAGCCT
* * * *
41842540 GAATAGTATCTCACCGGCATTATAGCATGCTAGGCTCAAAGGCCC
1 GAATAGTATCTCACCAGCATCATAGCATACTAGGCACAAAGGCCC
* * *
41842585 GAATAGTAT-TCCACCAGCATCATAGCCTACTAGGCACGAAGGCTC
1 GAATAGTATCT-CACCAGCATCATAGCATACTAGGCACAAAGGCCC
* * * * *
41842630 GAATA-CA-CATCACCGGCA-CAAAGCCTACTAGGCACGAAGGCCC
1 GAATAGTATC-TCACCAGCATCATAGCATACTAGGCACAAAGGCCC
*
41842673 AAATA
1 GAATA
41842678 TAATACCAGC
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
43 27 0.35
44 9 0.12
45 42 0.54
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.17
Consensus pattern (45 bp):
GAATAGTATCTCACCAGCATCATAGCATACTAGGCACAAAGGCCC
Found at i:41848065 original size:45 final size:45
Alignment explanation
Indices: 41847962--41848108 Score: 126
Period size: 45 Copynumber: 3.3 Consensus size: 45
41847952 GGCCCGATAC
* * * *
41847962 CGAAAGCCTGAATAGTATCTCACCGGCATTATAGCATGCTAGGCT
1 CGAAAGCCCGAATAGTATCTCACCAGCATCATAGCATGCTAGGCA
*
41848007 C-AAAGGCCCGAATAGTAT-TCCACCAGCATCATAGCTTGCTAGGCA
1 CGAAA-GCCCGAATAGTATCT-CACCAGCATCATAGCATGCTAGGCA
* * * * *
41848052 CGAAAGCCGGAATA-CA-CATCACCGGCA-CGA-AGCCTGCTAAGCA
1 CGAAAGCCCGAATAGTATC-TCACCAGCATC-ATAGCATGCTAGGCA
41848095 CGAAAGCCCGAATA
1 CGAAAGCCCGAATA
41848109 CACATCACCG
Statistics
Matches: 85, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
43 25 0.29
44 13 0.15
45 44 0.52
46 3 0.04
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.17
Consensus pattern (45 bp):
CGAAAGCCCGAATAGTATCTCACCAGCATCATAGCATGCTAGGCA
Found at i:41848096 original size:43 final size:43
Alignment explanation
Indices: 41848043--41848194 Score: 232
Period size: 43 Copynumber: 3.5 Consensus size: 43
41848033 CATCATAGCT
*
41848043 TGCTAGGCACGAAAGCCGGAATACACATCACCGGCACGAAGCC
1 TGCTAGGCACGAAAGCCCGAATACACATCACCGGCACGAAGCC
*
41848086 TGCTAAGCACGAAAGCCCGAATACACATCACCGGCACGAAGCC
1 TGCTAGGCACGAAAGCCCGAATACACATCACCGGCACGAAGCC
* * * *
41848129 TGCTAGGCATGAAGGCCCGAATACACATCAACGGCACAAAGCC
1 TGCTAGGCACGAAAGCCCGAATACACATCACCGGCACGAAGCC
* *
41848172 TGCTAGGCACGAAGGCCCAAATA
1 TGCTAGGCACGAAAGCCCGAATA
41848195 TAATACCAGC
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 100 1.00
ACGTcount: A:0.34, C:0.32, G:0.24, T:0.11
Consensus pattern (43 bp):
TGCTAGGCACGAAAGCCCGAATACACATCACCGGCACGAAGCC
Found at i:41857773 original size:71 final size:71
Alignment explanation
Indices: 41857657--41857802 Score: 292
Period size: 71 Copynumber: 2.1 Consensus size: 71
41857647 CTTGAAATTG
41857657 TGTTAACCAACTTTTGCTAAGCGATTTTACGTGAAAACGAGTAAAACGACATAATCGGTAAAAAT
1 TGTTAACCAACTTTTGCTAAGCGATTTTACGTGAAAACGAGTAAAACGACATAATCGGTAAAAAT
41857722 ACCTAA
66 ACCTAA
41857728 TGTTAACCAACTTTTGCTAAGCGATTTTACGTGAAAACGAGTAAAACGACATAATCGGTAAAAAT
1 TGTTAACCAACTTTTGCTAAGCGATTTTACGTGAAAACGAGTAAAACGACATAATCGGTAAAAAT
41857793 ACCTAA
66 ACCTAA
41857799 TGTT
1 TGTT
41857803 CATAAGTACA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 75 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (71 bp):
TGTTAACCAACTTTTGCTAAGCGATTTTACGTGAAAACGAGTAAAACGACATAATCGGTAAAAAT
ACCTAA
Found at i:41858389 original size:55 final size:53
Alignment explanation
Indices: 41858302--41858556 Score: 220
Period size: 55 Copynumber: 4.8 Consensus size: 53
41858292 ATTAGGGTTT
*
41858302 AAGGATACCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAA-GTTTCTAAGGC
* * * * *
41858357 AAGGATATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTT--TCTAAGGC
* * * * *
41858412 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTAGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTTTC-TAAGGC
* * *
41858465 AAGGATACCATGTAAGACCATGTCGAGACATGGCAA-TAGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAAGTTTCTAAGGC
* * * *
41858514 ACGGATACCACGTAAGACCATGACAAGTCATGGCAA-TGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAAG
41858557 GTACCCGTGT
Statistics
Matches: 167, Mismatches: 26, Indels: 20
0.78 0.12 0.09
Matches are distributed among these distances:
49 37 0.22
52 7 0.04
53 39 0.23
54 12 0.07
55 68 0.41
56 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.22
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTTTCTAAGGC
Found at i:41858508 original size:108 final size:110
Alignment explanation
Indices: 41858309--41858509 Score: 302
Period size: 108 Copynumber: 1.8 Consensus size: 110
41858299 TTTAAGGATA
* *
41858309 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGATATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGAAATTAGTAAGGTTTCTAAGGCAAGGATACCATGTAAGA
*
41858374 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCATAGATAAGTTACTATAAGGCAAAGGTC
* *
41858419 CCATGTAAGACCATGCCAAGGCATGG-CATTAGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGAAATTAGTAAGGTTTC-TAAGGCAAGGATACCATGTAAG
*
41858481 ACCATGTCGAGACATGGCAATAG-TAAGTT
65 ACCATGTCAAGACATGGC-ATAGATAAGTT
41858510 TCAAACGGAT
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
107 3 0.04
108 45 0.54
109 9 0.11
110 26 0.31
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGAAATTAGTAAGGTTTCTAAGGCAAGGATACCATGTAAGA
CCATGTCAAGACATGGCATAGATAAGTTACTATAAGGCAAAGGTC
Found at i:41863091 original size:38 final size:38
Alignment explanation
Indices: 41863026--41863102 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
41863016 ATTGATTCAT
*
41863026 TAACGTGGTGCTAAGTGGATATACCATGGTTAAACATG
1 TAACATGGTGCTAAGTGGATATACCATGGTTAAACATG
* * *
41863064 TAACATGGTGCTAAGTGGTTATGCCATGGTTATACATG
1 TAACATGGTGCTAAGTGGATATACCATGGTTAAACATG
41863102 T
1 T
41863103 TAATTTGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (38 bp):
TAACATGGTGCTAAGTGGATATACCATGGTTAAACATG
Found at i:41871637 original size:25 final size:25
Alignment explanation
Indices: 41871609--41871656 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
41871599 TTATAATATG
* * *
41871609 AAAATGACTGTTTTGCCCCTAGGTA
1 AAAATGACTATTATACCCCTAGGTA
41871634 AAAATGACTATTATACCCCTAGG
1 AAAATGACTATTATACCCCTAGG
41871657 GTTTAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (25 bp):
AAAATGACTATTATACCCCTAGGTA
Found at i:41871717 original size:20 final size:21
Alignment explanation
Indices: 41871682--41871738 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
41871672 TGATACGTGG
41871682 GATATGATAT--ACATGAT-T
1 GATATGATATGCACATGATAT
41871700 GATATGATATGCACATGATAT
1 GATATGATATGCACATGATAT
*
41871721 G-TATGAAATGCACATGAT
1 GATATGATATGCACATGAT
41871739 GAATTCATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
18 10 0.29
20 23 0.66
21 2 0.06
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (21 bp):
GATATGATATGCACATGATAT
Found at i:41871885 original size:25 final size:26
Alignment explanation
Indices: 41871788--41871917 Score: 194
Period size: 26 Copynumber: 5.1 Consensus size: 26
41871778 GAGGAAGTGC
41871788 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
41871814 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
41871840 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
41871866 AAAAGGGCTT-TGCCCCAGTTTATCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
41871891 GAAAGGGCTT-TGCCCCAG-TTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
41871915 AAA
1 AAA
41871918 GAGGCTAGGC
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
24 7 0.07
25 30 0.32
26 57 0.61
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:41878568 original size:5 final size:5
Alignment explanation
Indices: 41878558--41878621 Score: 78
Period size: 5 Copynumber: 12.6 Consensus size: 5
41878548 AACCTAAATT
41878558 AATAA AATAA AATAAA TAATAA AATAA AAT-- AATAA AATAA AATAAA
1 AATAA AATAA AAT-AA -AATAA AATAA AATAA AATAA AATAA AAT-AA
*
41878604 AATAA AACAA AATAA AAT
1 AATAA AATAA AATAA AAT
41878622 CTTTCTATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
3 3 0.06
5 37 0.71
6 9 0.17
7 3 0.06
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:41878587 original size:13 final size:13
Alignment explanation
Indices: 41878563--41878610 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
41878553 AAATTAATAA
41878563 AATAAAAT-AAAT
1 AATAAAATAAAAT
41878575 AATAAAATAAAAT
1 AATAAAATAAAAT
41878588 AATAAAATAAAAT
1 AATAAAATAAAAT
41878601 -A-AAAATAAAA
1 AATAAAATAAAA
41878611 CAAAATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
11 9 0.26
12 9 0.26
13 17 0.49
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AATAAAATAAAAT
Found at i:41878592 original size:30 final size:29
Alignment explanation
Indices: 41878552--41878618 Score: 107
Period size: 30 Copynumber: 2.3 Consensus size: 29
41878542 TAGCTTAACC
*
41878552 TAAATTAATAAAATAAAATAAATAATAAAA
1 TAAAATAATAAAATAAAATAAA-AATAAAA
41878582 TAAAATAATAAAATAAAATAAAAATAAAA
1 TAAAATAATAAAATAAAATAAAAATAAAA
*
41878611 CAAAATAA
1 TAAAATAA
41878619 AATCTTTCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 14 0.40
30 21 0.60
ACGTcount: A:0.76, C:0.01, G:0.00, T:0.22
Consensus pattern (29 bp):
TAAAATAATAAAATAAAATAAAAATAAAA
Found at i:41881782 original size:27 final size:28
Alignment explanation
Indices: 41881704--41881819 Score: 114
Period size: 27 Copynumber: 4.2 Consensus size: 28
41881694 CAGCATGGCT
* * * *
41881704 ACCAGATACAGA-AAATGTGACAGAGTC
1 ACCAGATACAGATATATGTGGCAGTGCC
*
41881731 ACCAGATACAGATATTTTGTGGCAGTGCC
1 ACCAGATACAGATA-TATGTGGCAGTGCC
*
41881760 ACCAGA-ACAGATATATGTGGCAGGGCC
1 ACCAGATACAGATATATGTGGCAGTGCC
*
41881787 ACCAGA-ACAGATAATTTGTGGCA-TAGCC
1 ACCAGATACAGAT-ATATGTGGCAGT-GCC
41881815 ACCAG
1 ACCAG
41881820 GACGCTTGCT
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
27 36 0.47
28 25 0.33
29 15 0.20
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (28 bp):
ACCAGATACAGATATATGTGGCAGTGCC
Found at i:41881805 original size:55 final size:56
Alignment explanation
Indices: 41881704--41881819 Score: 148
Period size: 55 Copynumber: 2.1 Consensus size: 56
41881694 CAGCATGGCT
* *
41881704 ACCAGATACAGAAAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCC
1 ACCAGATACAGAAAATGTGACAGAGCCACCAGATACAGATAATTTGTGGCA-TAGCC
* * *
41881760 ACCAGA-ACAGATATATGTGGCAGGGCCACCAGA-ACAGATAATTTGTGGCATAGCC
1 ACCAGATACAGA-AAATGTGACAGAGCCACCAGATACAGATAATTTGTGGCATAGCC
41881815 ACCAG
1 ACCAG
41881820 GACGCTTGCT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.55
56 23 0.43
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (56 bp):
ACCAGATACAGAAAATGTGACAGAGCCACCAGATACAGATAATTTGTGGCATAGCC
Found at i:41884633 original size:40 final size:40
Alignment explanation
Indices: 41884571--41884775 Score: 285
Period size: 40 Copynumber: 5.2 Consensus size: 40
41884561 AAACCAAGTA
* * *
41884571 CCTTCGGGATTTA-ACCGGATATAG-CTACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTCGCACAAATG
41884610 CCTTCGGGACTTAGCCCGGATATAG-CAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCA-CTCGCACAAATG
*
41884650 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTCGCACAAATG
*
41884690 CCTTCGGGACTTAGCCCGGGAT-TAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCC-GGATATAGTCACTCGCACAAATG
*
41884730 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTCACTCGCACAAATG
41884770 CCTTCG
1 CCTTCG
41884776 TTATCATCCG
Statistics
Matches: 154, Mismatches: 6, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
39 16 0.10
40 133 0.86
41 5 0.03
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTCGCACAAATG
Found at i:41893120 original size:27 final size:28
Alignment explanation
Indices: 41893063--41893132 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
41893053 GTGACAGAGT
* * *
41893063 CACCAGATACAGATATTTTGTGGTAGTGC
1 CACCAGA-ACAGATATTATGTGGCAGGGC
41893092 CACCAGAACAGATA-TATGTGGCAGGGC
1 CACCAGAACAGATATTATGTGGCAGGGC
*
41893119 CACCAGAATAGATA
1 CACCAGAACAGATA
41893133 ATTTATGGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 23 0.62
28 7 0.19
29 7 0.19
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.21
Consensus pattern (28 bp):
CACCAGAACAGATATTATGTGGCAGGGC
Found at i:41893150 original size:28 final size:27
Alignment explanation
Indices: 41893057--41893152 Score: 75
Period size: 28 Copynumber: 3.4 Consensus size: 27
41893047 GAAAATGTGA
* * *
41893057 CAGAGTCACCAGATACAGATATTTTGTGG
1 CAGAGCCACCAGA-ACAGATA-TATATGG
* * *
41893086 TAGTGCCACCAGAACAGATATATGTGG
1 CAGAGCCACCAGAACAGATATATATGG
* * *
41893113 CAGGGCCACCAGAATAGATAATTTATGG
1 CAGAGCCACCAGAACAGAT-ATATATGG
*
41893141 CATAGCCACCAG
1 CAGAGCCACCAG
41893153 GACGCTTCCT
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
27 22 0.40
28 23 0.42
29 10 0.18
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (27 bp):
CAGAGCCACCAGAACAGATATATATGG
Found at i:41903222 original size:42 final size:43
Alignment explanation
Indices: 41903119--41903224 Score: 128
Period size: 43 Copynumber: 2.5 Consensus size: 43
41903109 CGATGTGAAC
* * *
41903119 ATCCCAGACGTGGTCTTACATGTAATCAAATATCGATGACACT
1 ATCCCAGACATGGTCTTACACGAAATCAAATATCGATGACACT
*
41903162 ATCCCAGACAGGGTCTTACACGAAATCAAATAT-GAT-AC-CT
1 ATCCCAGACATGGTCTTACACGAAATCAAATATCGATGACACT
*
41903202 ATGTCCCAGACATAGTCTTACAC
1 A--TCCCAGACATGGTCTTACAC
41903225 TTAAATCATA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
40 3 0.05
41 2 0.04
42 21 0.38
43 29 0.53
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (43 bp):
ATCCCAGACATGGTCTTACACGAAATCAAATATCGATGACACT
Found at i:41904390 original size:13 final size:13
Alignment explanation
Indices: 41904372--41904402 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
41904362 ACGATCAATT
41904372 TTTCATATGAAAG
1 TTTCATATGAAAG
*
41904385 TTTCATATGAAAT
1 TTTCATATGAAAG
41904398 TTTCA
1 TTTCA
41904403 AACATACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (13 bp):
TTTCATATGAAAG
Found at i:41906793 original size:26 final size:26
Alignment explanation
Indices: 41906756--41906830 Score: 98
Period size: 25 Copynumber: 2.9 Consensus size: 26
41906746 ACATATTTCC
*
41906756 TCAAAATTTTACCAGGGGTAAAATCA
1 TCAAAATTTTACTAGGGGTAAAATCA
* * *
41906782 TCAAAATATTACTA-TGGTAAAATCG
1 TCAAAATTTTACTAGGGGTAAAATCA
*
41906807 TTAAAATTTTACTAGGGGTAAAAT
1 TCAAAATTTTACTAGGGGTAAAAT
41906831 AGGGATGAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
25 21 0.51
26 20 0.49
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (26 bp):
TCAAAATTTTACTAGGGGTAAAATCA
Found at i:41908424 original size:80 final size:80
Alignment explanation
Indices: 41908334--41908493 Score: 302
Period size: 80 Copynumber: 2.0 Consensus size: 80
41908324 CAAACTCAAC
41908334 ATTCAAGTTAGTACAATAATTTCCATGTACCAATAATATATACTATGATTGATGAGCTCGACAAT
1 ATTCAAGTTAGTACAATAATTTCCATGTACCAATAATATATACTATGATTGATGAGCTCGACAAT
41908399 ACCATGATTTCCATT
66 ACCATGATTTCCATT
* *
41908414 ATTCAAGTTAGTACAGTAATTTCCATGTACCAATAATATATACTATGATTGATGAGCTCGTCAAT
1 ATTCAAGTTAGTACAATAATTTCCATGTACCAATAATATATACTATGATTGATGAGCTCGACAAT
41908479 ACCATGATTTCCATT
66 ACCATGATTTCCATT
41908494 TCCTTGTTAT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (80 bp):
ATTCAAGTTAGTACAATAATTTCCATGTACCAATAATATATACTATGATTGATGAGCTCGACAAT
ACCATGATTTCCATT
Found at i:41916274 original size:80 final size:79
Alignment explanation
Indices: 41916184--41916342 Score: 309
Period size: 80 Copynumber: 2.0 Consensus size: 79
41916174 CAAACTCAAC
41916184 ATTCAAGTTAGTACAATAATTTCCATGTACCAATAATATATACTATGATTGATGAGCTCGTCAAT
1 ATTCAAGTTAGTACAATAATTTCCATGTACCAATAATATATACTATGATTGATGAGCTCGTCAAT
41916249 ACCATGATTTCCATT
66 ACCATGA-TTCCATT
41916264 ATTCAAGTTAGTACAATAATTTCCATGTACCAATAATATATACTATGATTGATGAGCTCGTCAAT
1 ATTCAAGTTAGTACAATAATTTCCATGTACCAATAATATATACTATGATTGATGAGCTCGTCAAT
41916329 ACCATGATTCCATT
66 ACCATGATTCCATT
41916343 TCCTTGTTAT
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 7 0.09
80 72 0.91
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (79 bp):
ATTCAAGTTAGTACAATAATTTCCATGTACCAATAATATATACTATGATTGATGAGCTCGTCAAT
ACCATGATTCCATT
Found at i:41918210 original size:28 final size:28
Alignment explanation
Indices: 41918170--41918276 Score: 151
Period size: 28 Copynumber: 3.8 Consensus size: 28
41918160 GAATCATTCG
* *
41918170 ATATTTTGCACACTAAGTGTCACTCTCA
1 ATATTTCGCACACTAAGTGTCATTCTCA
*
41918198 ATATCTCGCACACTAAGTGTCATTCTCA
1 ATATTTCGCACACTAAGTGTCATTCTCA
* *
41918226 ATATTTCGTACACTAAGTGCCATTCTCA
1 ATATTTCGCACACTAAGTGTCATTCTCA
* *
41918254 ATATTTCGTACACTAAGTATCAT
1 ATATTTCGCACACTAAGTGTCAT
41918277 ATTTGATTGC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 71 1.00
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (28 bp):
ATATTTCGCACACTAAGTGTCATTCTCA
Found at i:41923264 original size:28 final size:28
Alignment explanation
Indices: 41923221--41923384 Score: 121
Period size: 28 Copynumber: 5.8 Consensus size: 28
41923211 TGCCCCAACA
* * *
41923221 ACCGATCTTGCACACACAGTGCTTGGTT
1 ACCGAACTCGCACACACAGTGCTCGGTT
* ****
41923249 ACGGAACTCGCACACACAGTGCATCAACA
1 ACCGAACTCGCACACACAGTGC-TCGGTT
*
41923278 ACCGATCTCGCACACACAGTGCTCGGTT
1 ACCGAACTCGCACACACAGTGCTCGGTT
* * ****
41923306 ACGGAACTCGCACATACAGTGCCTCAACA
1 ACCGAACTCGCACACACAGTG-CTCGGTT
* * *
41923335 ACCGATCTCTCACACACAGTGCTTGGTT
1 ACCGAACTCGCACACACAGTGCTCGGTT
** *
41923363 ACAAAACTCACACACACAGTGC
1 ACCGAACTCGCACACACAGTGC
41923385 CTATGTTCAC
Statistics
Matches: 100, Mismatches: 34, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
28 59 0.59
29 41 0.41
ACGTcount: A:0.30, C:0.34, G:0.18, T:0.19
Consensus pattern (28 bp):
ACCGAACTCGCACACACAGTGCTCGGTT
Found at i:41923270 original size:57 final size:57
Alignment explanation
Indices: 41923200--41923386 Score: 268
Period size: 57 Copynumber: 3.2 Consensus size: 57
41923190 GATCTCATTT
*
41923200 CACACACTTAGTGCCCCAACAACCGATCTTGCACACACAGTGCTTGGTTACGGAACTCG
1 CACACAC--AGTGCCTCAACAACCGATCTTGCACACACAGTGCTTGGTTACGGAACTCG
* * *
41923259 CACACACAGTGCATCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTTGCACACACAGTGCTTGGTTACGGAACTCG
* ** *
41923316 CACATACAGTGCCTCAACAACCGATCTCT-CACACACAGTGCTTGGTTACAAAACTCA
1 CACACACAGTGCCTCAACAACCGATCT-TGCACACACAGTGCTTGGTTACGGAACTCG
41923373 CACACACAGTGCCT
1 CACACACAGTGCCT
41923387 ATGTTCACTT
Statistics
Matches: 115, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
57 108 0.94
59 7 0.06
ACGTcount: A:0.30, C:0.35, G:0.17, T:0.19
Consensus pattern (57 bp):
CACACACAGTGCCTCAACAACCGATCTTGCACACACAGTGCTTGGTTACGGAACTCG
Found at i:41923296 original size:29 final size:28
Alignment explanation
Indices: 41923216--41923357 Score: 122
Period size: 28 Copynumber: 5.0 Consensus size: 28
41923206 CTTAGTGCCC
*
41923216 CAACAACCGATCTTGCACACACAGTGCT
1 CAACAACCGATCTCGCACACACAGTGCT
***** * *
41923244 TGGTTACGGAACTCGCACACACAGTGCAT
1 CAACAACCGATCTCGCACACACAGTGC-T
41923273 CAACAACCGATCTCGCACACACAGTGCT
1 CAACAACCGATCTCGCACACACAGTGCT
**** * * *
41923301 CGGTTACGGAACTCGCACATACAGTGCCT
1 CAACAACCGATCTCGCACACACAGTG-CT
*
41923330 CAACAACCGATCTCTCACACACAGTGCT
1 CAACAACCGATCTCGCACACACAGTGCT
41923358 TGGTTACAAA
Statistics
Matches: 82, Mismatches: 30, Indels: 4
0.71 0.26 0.03
Matches are distributed among these distances:
28 41 0.50
29 41 0.50
ACGTcount: A:0.30, C:0.35, G:0.18, T:0.18
Consensus pattern (28 bp):
CAACAACCGATCTCGCACACACAGTGCT
Found at i:41925383 original size:28 final size:28
Alignment explanation
Indices: 41925345--41925451 Score: 151
Period size: 28 Copynumber: 3.8 Consensus size: 28
41925335 GAATCATTCG
* *
41925345 ATATTTTGCACACTAAGTGTCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
*
41925373 ATATCTCGCACACTAAGTGCCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
* *
41925401 ATATTTCGTACACTAAGTGCCATTTTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
* *
41925429 ATATTTCGTACACTAAGTACCAT
1 ATATTTCGCACACTAAGTGCCAT
41925452 ATTTGATTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 72 1.00
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (28 bp):
ATATTTCGCACACTAAGTGCCATTCTCA
Found at i:41931600 original size:137 final size:137
Alignment explanation
Indices: 41931354--41931628 Score: 514
Period size: 137 Copynumber: 2.0 Consensus size: 137
41931344 GGACATCAAA
*
41931354 TCGGGTAGTAAGTTTTGGTAATATTTATTGATTAAAACATATAGCATATGTGAGTTTTGCTTTAG
1 TCGGGTAGGAAGTTTTGGTAATATTTATTGATTAAAACATATAGCATATGTGAGTTTTGCTTTAG
41931419 TCAGGTTGTGAAGTAGCATTTTTGTCATACTTGTGGGTTCTTACATCATTTTGATTATGTTATGT
66 TCAGGTTGTGAAGTAGCATTTTTGTCATACTTGTGGGTTCTTACATCATTTTGATTATGTTATGT
41931484 TCTGTTT
131 TCTGTTT
*
41931491 TCGGGTAGGAAGTTTTGGTAATATTTATTGATTAAAACATATAGCATATGTGAGTTTTGCTTTAT
1 TCGGGTAGGAAGTTTTGGTAATATTTATTGATTAAAACATATAGCATATGTGAGTTTTGCTTTAG
* *
41931556 TCAGGTTGTGAAGTAGCATTTTTGTCATACTTGTGGGTTTTTACATCATTTTGATTATGTTCTGT
66 TCAGGTTGTGAAGTAGCATTTTTGTCATACTTGTGGGTTCTTACATCATTTTGATTATGTTATGT
41931621 TCTGTTT
131 TCTGTTT
41931628 T
1 T
41931629 ATATTAGTCG
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 134 1.00
ACGTcount: A:0.23, C:0.09, G:0.21, T:0.47
Consensus pattern (137 bp):
TCGGGTAGGAAGTTTTGGTAATATTTATTGATTAAAACATATAGCATATGTGAGTTTTGCTTTAG
TCAGGTTGTGAAGTAGCATTTTTGTCATACTTGTGGGTTCTTACATCATTTTGATTATGTTATGT
TCTGTTT
Found at i:41940425 original size:21 final size:21
Alignment explanation
Indices: 41940399--41940444 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
41940389 TATAGGTTTA
41940399 TGTTTAAATTATTAAGTTCAT
1 TGTTTAAATTATTAAGTTCAT
41940420 TGTTTAAATTATTAAGTTCAT
1 TGTTTAAATTATTAAGTTCAT
41940441 TGTT
1 TGTT
41940445 GAAAATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.54
Consensus pattern (21 bp):
TGTTTAAATTATTAAGTTCAT
Found at i:41942485 original size:23 final size:22
Alignment explanation
Indices: 41942425--41942485 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
41942415 ATACTTTTGA
41942425 TATTTTATTATATATAAACAATTT
1 TATTTTA-TATA-ATAAACAATTT
* * *
41942449 TATTTCAATGTAATAATCAATTT
1 TATTT-TATATAATAAACAATTT
41942472 TACTTTTATATAAT
1 TA-TTTTATATAAT
41942486 GATAATATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
23 18 0.60
24 11 0.37
25 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTTTATATAATAAACAATTT
Found at i:41944191 original size:20 final size:20
Alignment explanation
Indices: 41944168--41944218 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
41944158 GAAACTTAAG
41944168 AATATCGATACTTT-TAGAAA
1 AATATCGATA-TTTATAGAAA
*
41944188 AATATCGATATTTATATAAA
1 AATATCGATATTTATAGAAA
*
41944208 AATATAGATAT
1 AATATCGATAT
41944219 CACTAGGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (20 bp):
AATATCGATATTTATAGAAA
Found at i:41952970 original size:40 final size:40
Alignment explanation
Indices: 41952915--41953125 Score: 230
Period size: 40 Copynumber: 5.3 Consensus size: 40
41952905 ATTTGAATGA
*
41952915 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
*
41952955 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
* * *
41952995 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * * *
41953035 TATCTGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * * * * *
41953075 TACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
41953115 TATCC-GGCTAA
1 TATCCGGGCTAA
41953126 ATTCCGAAGA
Statistics
Matches: 154, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
39 7 0.05
40 144 0.94
41 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
Found at i:41957656 original size:49 final size:49
Alignment explanation
Indices: 41957596--41957693 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 49
41957586 CATGTTGCTG
* * * * *
41957596 TATTTCGTCCGGGTAACTTACATGTGCTTTTTGTTGCAACCTTTTAACA
1 TATTTCATCCGGATAACGTACATATGCTGTTTGTTGCAACCTTTTAACA
*
41957645 TATTTCATCCGGATAACGTACATATGCTGTTTGTTGCCACCTTTTAACA
1 TATTTCATCCGGATAACGTACATATGCTGTTTGTTGCAACCTTTTAACA
41957694 AAGGTGAAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.22, C:0.21, G:0.15, T:0.41
Consensus pattern (49 bp):
TATTTCATCCGGATAACGTACATATGCTGTTTGTTGCAACCTTTTAACA
Found at i:41957976 original size:17 final size:17
Alignment explanation
Indices: 41957954--41957987 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41957944 TCTATGTAAG
*
41957954 AAAAATTTTTAAAAATT
1 AAAAATTATTAAAAATT
41957971 AAAAATTATTAAAAATT
1 AAAAATTATTAAAAATT
41957988 CAATTCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAAATTATTAAAAATT
Found at i:41958649 original size:12 final size:12
Alignment explanation
Indices: 41958632--41958670 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
41958622 CATAAAATGT
41958632 AAAAAAAGAAAA
1 AAAAAAAGAAAA
*
41958644 AAAAAAGGAAAA
1 AAAAAAAGAAAA
*
41958656 AGAAAAAGAAGAA
1 AAAAAAAGAA-AA
41958669 AA
1 AA
41958671 CATGATGTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 19 0.86
13 3 0.14
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:41959150 original size:16 final size:16
Alignment explanation
Indices: 41959129--41959170 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
41959119 CAACACGAAT
* *
41959129 TTAGAATTTTCTAAGG
1 TTAGAATTTTCGAAGC
41959145 TTAGAACTTTTCGAAGC
1 TTAGAA-TTTTCGAAGC
41959162 TTA-AATTTT
1 TTAGAATTTT
41959171 TTCGAGCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 4 0.17
16 8 0.35
17 11 0.48
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (16 bp):
TTAGAATTTTCGAAGC
Found at i:41959389 original size:2 final size:2
Alignment explanation
Indices: 41959382--41959408 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41959372 GCATAGTCAA
41959382 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
41959409 TATTCAGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:41960845 original size:17 final size:16
Alignment explanation
Indices: 41960808--41960851 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
41960798 TTTTTTTTTC
41960808 AAATAAAAA-AATAAA
1 AAATAAAAATAATAAA
*
41960823 ATATAAAAATAATTAAA
1 AAATAAAAATAA-TAAA
41960840 AAATAAAAATAA
1 AAATAAAAATAA
41960852 ATATTTAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 8 0.32
16 2 0.08
17 15 0.60
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
AAATAAAAATAATAAA
Found at i:41963452 original size:15 final size:14
Alignment explanation
Indices: 41963418--41963461 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
41963408 TTGAATGAAT
*
41963418 AATTTTGTATACAA
1 AATTTTGTATATAA
41963432 AA-TTTGTATATATA
1 AATTTTGTATATA-A
*
41963446 AATTTTGAATATAA
1 AATTTTGTATATAA
41963460 AA
1 AA
41963462 ATTATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 9 0.35
14 8 0.31
15 9 0.35
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (14 bp):
AATTTTGTATATAA
Found at i:41968275 original size:46 final size:46
Alignment explanation
Indices: 41968225--41968398 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
41968215 TGGTTGAGCA
41968225 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
41968271 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
41968316 CATCCG-ACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
41968362 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41968399 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 9, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
44 3 0.03
45 28 0.26
46 60 0.56
47 4 0.04
48 4 0.04
49 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:41968386 original size:91 final size:93
Alignment explanation
Indices: 41968222--41968390 Score: 297
Period size: 91 Copynumber: 1.8 Consensus size: 93
41968212 GGATGGTTGA
* *
41968222 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
41968287 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
41968315 GCATCCG-ACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
41968378 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
41968391 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
91 40 0.55
92 26 0.36
93 7 0.10
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:41971346 original size:15 final size:15
Alignment explanation
Indices: 41971326--41971394 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
41971316 GTATCTTGGG
41971326 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
41971341 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
41971356 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
41971371 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
41971386 TTTCTTTAT
1 TTTCTTTAT
41971395 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:41971395 original size:30 final size:30
Alignment explanation
Indices: 41971317--41971404 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
41971307 CATAATATCG
* * * *
41971317 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
41971347 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
41971377 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
41971405 TATTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:41984094 original size:36 final size:36
Alignment explanation
Indices: 41984047--41984120 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
41984037 CTACGGGAAG
41984047 TTAGTTTCCTTAGACATGTTGCATCTGCAGAGGGTA
1 TTAGTTTCCTTAGACATGTTGCATCTGCAGAGGGTA
41984083 TTAGTTTCCTTAGACATGTTGCATCTGCAGAGGGTA
1 TTAGTTTCCTTAGACATGTTGCATCTGCAGAGGGTA
41984119 TT
1 TT
41984121 CAGTATACCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (36 bp):
TTAGTTTCCTTAGACATGTTGCATCTGCAGAGGGTA
Found at i:41987761 original size:25 final size:25
Alignment explanation
Indices: 41987733--41987783 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
41987723 AAGAATAATT
**
41987733 TGAATATTTGATATTGCCTACTAAA
1 TGAATATCCGATATTGCCTACTAAA
* *
41987758 TGAATATCCGATATTGCTTAGTAAA
1 TGAATATCCGATATTGCCTACTAAA
41987783 T
1 T
41987784 TTCAAGCCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (25 bp):
TGAATATCCGATATTGCCTACTAAA
Found at i:41993500 original size:47 final size:47
Alignment explanation
Indices: 41993347--41993516 Score: 183
Period size: 47 Copynumber: 3.7 Consensus size: 47
41993337 CACATTATGA
* * * *
41993347 GAGCCAGTGTAAGACCATTTCTGGGATATGGGATCGGCATTGAGACGT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTGAGACAT
* *
41993395 AAGCCAGTGTAAGA-CATGTCTGGGACAT-GCA-CGGC-T-ACGAGAT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGA-GACAT
* * * *
41993438 GA--TAGTGTAAAACCATGTCTGGGACATGGCATCGACTTGAGATAT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGACAT
41993483 GAGCCAGTGTAAGACCATGTCTGGGACATGGCAT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCAT
41993517 TGACACTTTA
Statistics
Matches: 101, Mismatches: 13, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
41 8 0.08
42 15 0.15
43 8 0.08
44 3 0.03
45 11 0.11
46 3 0.03
47 40 0.40
48 13 0.13
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (47 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGACAT
Found at i:41999145 original size:18 final size:18
Alignment explanation
Indices: 41999101--41999146 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
41999091 AATTATGATT
41999101 CAAAAATCA-GCTAAAATA
1 CAAAAA-CATGCTAAAATA
*
41999119 CATAAAACATGCTGAAATA
1 CA-AAAACATGCTAAAATA
41999138 CAAAAACAT
1 CAAAAACAT
41999147 AATAAAGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.59, C:0.17, G:0.07, T:0.17
Consensus pattern (18 bp):
CAAAAACATGCTAAAATA
Found at i:41999506 original size:30 final size:30
Alignment explanation
Indices: 41999472--41999532 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
41999462 TCCTTAACTC
*
41999472 AAACTTTGGCAAAATTACAATTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTACCCCT
* * * *
41999502 AAACTTTTGCATATTTACACTTTTACCCCT
1 AAACTTTGGCAAAATTACAATTTTACCCCT
41999532 A
1 A
41999533 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.38
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTACCCCT
Found at i:42004133 original size:47 final size:47
Alignment explanation
Indices: 42004021--42004143 Score: 135
Period size: 47 Copynumber: 2.6 Consensus size: 47
42004011 ATTTGTGTGT
* *
42004021 GAGCTAGTGCAAGACATGTCTGGGACAT-GCATCGGCCACATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGGCATCGGCCACATTACGA
* * *
42004067 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-TA-TTGGTACGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGCCACAT--TACGA
* *
42004115 GATCTAGTGTAAGACATGTCTAGGACATG
1 GAGCTAGTGTAAGACATGTCTGGGACATG
42004144 ATTCGGCCTC
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
46 13 0.20
47 29 0.45
48 23 0.35
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (47 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGGCATCGGCCACATTACGA
Found at i:42004179 original size:46 final size:46
Alignment explanation
Indices: 42004120--42004236 Score: 157
Period size: 46 Copynumber: 2.5 Consensus size: 46
42004110 TACGAGATCT
*
42004120 AGTGTAAGACATGTCTAGGACATGATTCGGCCT-CGAGA-CATAAGCC
1 AGTGTAAGACATGTCTGGGACATGATTCGG-CTACGAGATCAT-AGCC
* * *
42004166 AGTGTAAGACATGTCTGGGATATGATTCGGCTACGAGATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGATTCGGCTACGAGATCATAGCC
42004212 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
42004237 GCATCGACTT
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
45 2 0.03
46 45 0.71
47 16 0.25
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGATTCGGCTACGAGATCATAGCC
Found at i:42004251 original size:47 final size:47
Alignment explanation
Indices: 42004071--42004291 Score: 151
Period size: 47 Copynumber: 4.7 Consensus size: 47
42004061 TTATGAGAGC
* * *
42004071 CAGTGTAAGACCATGTCTGGGACATGGCATCGGTA-TTG-GTACGAGA-T
1 CAGTGTAAGACCATGTCTGGGACATGGCATC-G-ACTCGAG-ATGATAGT
* * * *
42004118 CTAGTGTAAGA-CATGTCTAGGACAT-G-ATTCGGCCTCGAGA-CATAAGC
1 C-AGTGTAAGACCATGTCTGGGACATGGCA-TC-GACTCGAGATGAT-AGT
* *
42004165 CAGTGTAAGA-CATGTCTGGGATAT-G-ATTCGGCTACGAGATGATAGT
1 CAGTGTAAGACCATGTCTGGGACATGGCA-TCGACT-CGAGATGATAGT
*
42004211 CAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGAT-AT-GAT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGACTCGAGATGATAG-T
* *
42004257 CCAATGCAAGACCATGTCTGGGACATGGCATCGAC
1 -CAGTGTAAGACCATGTCTGGGACATGGCATCGAC
42004292 ACTTTACCCA
Statistics
Matches: 145, Mismatches: 16, Indels: 26
0.78 0.09 0.14
Matches are distributed among these distances:
45 6 0.04
46 55 0.38
47 68 0.47
48 15 0.10
49 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (47 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGACTCGAGATGATAGT
Found at i:42004283 original size:140 final size:139
Alignment explanation
Indices: 42004026--42004283 Score: 319
Period size: 140 Copynumber: 1.8 Consensus size: 139
42004016 TGTGTGAGCT
*
42004026 AGTGCAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
1 AGTGCAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTCTGG
* * *
42004091 GACATGGCATCGGTATTGGTACGAGATCTAGTGTAAGACATGTCTAGGACATGATTCGGCCTCGA
66 GACATGGCATCGGTATTGGTAC-AGATCCAATGCAAGACATGTCTAGGACATGATTCGGCCTCGA
42004156 GACATAAGCC
130 GACATAAGCC
* * * * *
42004166 AGTGTAAGACATGTCTGGGATATG-ATTCGGCTACGA-GATGATAGTCAGTGTAAGACCATGTCT
1 AGTGCAAGACATGTCTGGGACATGCA-TCGGCCAC-ATGATGAGAGCCAGTGTAAGACCATGTCT
* *
42004229 GGGACATGGCATC-G-ACTTGAGATA-TGATCCAATGCAAGACCATGTCTGGGACATG
64 GGGACATGGCATCGGTA-TTG-G-TACAGATCCAATGCAAGA-CATGTCTAGGACATG
42004284 GCATCGACAC
Statistics
Matches: 101, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
138 1 0.01
139 16 0.16
140 81 0.80
141 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (139 bp):
AGTGCAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTCTGG
GACATGGCATCGGTATTGGTACAGATCCAATGCAAGACATGTCTAGGACATGATTCGGCCTCGAG
ACATAAGCC
Found at i:42005306 original size:83 final size:83
Alignment explanation
Indices: 42005167--42005343 Score: 345
Period size: 83 Copynumber: 2.1 Consensus size: 83
42005157 GTGTGTGCCT
42005167 TGGCCGTGTGACATCTTAAGCATGCTGACGTCAGAAATAGAATGTCCATGTTTTTGCACACGGGC
1 TGGCCGTGTGACATCTTAAGCATGCTGACGTCAGAAATAGAATGTCCATGTTTTTGCACACGGGC
42005232 TAGGACACGGGCGTGTTG
66 TAGGACACGGGCGTGTTG
42005250 TGGCCGTGTGACATCTTAAGCATGCTGACGTCAGAAATAGAATGTCCATGTTTTTGCACACGGGC
1 TGGCCGTGTGACATCTTAAGCATGCTGACGTCAGAAATAGAATGTCCATGTTTTTGCACACGGGC
*
42005315 TAGGACACGGGTGTGTTG
66 TAGGACACGGGCGTGTTG
42005333 TGGCCGTGTGA
1 TGGCCGTGTGA
42005344 GGGACACGGG
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 93 1.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (83 bp):
TGGCCGTGTGACATCTTAAGCATGCTGACGTCAGAAATAGAATGTCCATGTTTTTGCACACGGGC
TAGGACACGGGCGTGTTG
Found at i:42005845 original size:6 final size:6
Alignment explanation
Indices: 42005830--42005898 Score: 93
Period size: 6 Copynumber: 11.0 Consensus size: 6
42005820 AGTTCATTTC
* *
42005830 TTTTAT TTTTAG TTTTAT TTTTAT TTTTAT CTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
42005878 TTTTAGTT GTTTTAT TTTTAT
1 TTTTA--T -TTTTAT TTTTAT
42005899 GTCCTTAAAC
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
6 49 0.88
7 1 0.02
8 1 0.02
9 5 0.09
ACGTcount: A:0.16, C:0.01, G:0.04, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:42020394 original size:16 final size:16
Alignment explanation
Indices: 42020373--42020408 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
42020363 TAATGGTAGC
42020373 GCCTAAATCAGCTAGT
1 GCCTAAATCAGCTAGT
42020389 GCCTAAATCAGCTAGT
1 GCCTAAATCAGCTAGT
42020405 GCCT
1 GCCT
42020409 TTTCAACGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (16 bp):
GCCTAAATCAGCTAGT
Found at i:42022249 original size:25 final size:25
Alignment explanation
Indices: 42022217--42022274 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
42022207 TGCCAAAAGC
* *
42022217 AAAT-AAAAGA-AAAATTAGTAATTA
1 AAATAAAAAGATAAAATT-GCAATAA
*
42022241 AAATAAAAAGATTAAATTGCAATAA
1 AAATAAAAAGATAAAATTGCAATAA
42022266 AAATAAAAA
1 AAATAAAAA
42022275 TGGCTAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 4 0.14
25 20 0.69
26 5 0.17
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (25 bp):
AAATAAAAAGATAAAATTGCAATAA
Found at i:42023506 original size:9 final size:10
Alignment explanation
Indices: 42023484--42023508 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42023474 AACAAACCTA
42023484 TTTTGTCCGT
1 TTTTGTCCGT
42023494 TTTTGTCCGT
1 TTTTGTCCGT
42023504 TTTTG
1 TTTTG
42023509 GCCTTTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.20, T:0.64
Consensus pattern (10 bp):
TTTTGTCCGT
Found at i:42023952 original size:20 final size:20
Alignment explanation
Indices: 42023927--42023966 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
42023917 AACCTAGAGT
42023927 TAGTTGTTTTTACTCTTGAA
1 TAGTTGTTTTTACTCTTGAA
42023947 TAGTTGTTTTTACTCTTGAA
1 TAGTTGTTTTTACTCTTGAA
42023967 AGGGATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.15, T:0.55
Consensus pattern (20 bp):
TAGTTGTTTTTACTCTTGAA
Found at i:42028978 original size:6 final size:6
Alignment explanation
Indices: 42028969--42029081 Score: 81
Period size: 6 Copynumber: 18.3 Consensus size: 6
42028959 TTGCATTCAC
* * *
42028969 ATTCTG ATTCTG ATTTTG -TTACCTG ATACTG ATTCTG ATTCTG -TTACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATT--CTG
* * *
42029019 ATTCTG ATTCTG ATTCT- ATCACCTG ATTCTG ATTCTG ATTCTC ATTTTG
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
42029068 ATTCT- AGTTCTG AT
1 ATTCTG A-TTCTG AT
42029082 AATGTTTCTT
Statistics
Matches: 84, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
5 7 0.08
6 65 0.77
7 7 0.08
8 5 0.06
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:42029000 original size:25 final size:25
Alignment explanation
Indices: 42028969--42029060 Score: 139
Period size: 25 Copynumber: 3.7 Consensus size: 25
42028959 TTGCATTCAC
*
42028969 ATTCTGATTCTGATTTTGTTACCTG
1 ATTCTGATTCTGATTCTGTTACCTG
* *
42028994 ATACTGATTCTGATTCTGTTACCTA
1 ATTCTGATTCTGATTCTGTTACCTG
* *
42029019 ATTCTGATTCTGATTCTATCACCTG
1 ATTCTGATTCTGATTCTGTTACCTG
42029044 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
42029061 CATTTTGATT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 60 1.00
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.48
Consensus pattern (25 bp):
ATTCTGATTCTGATTCTGTTACCTG
Found at i:42031176 original size:27 final size:27
Alignment explanation
Indices: 42031140--42031334 Score: 248
Period size: 27 Copynumber: 7.2 Consensus size: 27
42031130 AATTTACAAA
*
42031140 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
42031167 AATTACTGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
42031194 AATTACTGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * *
42031221 AAATACCGAAATACCCCTATAGGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
*
42031248 AATTACTGAAATACCCCTTTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
42031275 AATTATTGAAATACCCCTATATGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
42031302 AATTACT-AAGATACCCTTGTGGGGTAA
1 AATTACTGAA-ATACCCCTGTAGGGTAG
42031329 AATTAC
1 AATTAC
42031335 CATTTTGCCC
Statistics
Matches: 147, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 2 0.01
27 145 0.99
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:42031770 original size:22 final size:22
Alignment explanation
Indices: 42031719--42031782 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
42031709 CCAATTATTA
* *
42031719 TGATTATGGCTTTGCGCCAACC
1 TGATTATGGCTCTGTGCCAACC
* *
42031741 T-ACATATGGCTCTATGCCAACC
1 TGA-TTATGGCTCTGTGCCAACC
*
42031763 TGATTATGGCTGTGTGCCAA
1 TGATTATGGCTCTGTGCCAA
42031783 ACATATTTGC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
21 1 0.03
22 31 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (22 bp):
TGATTATGGCTCTGTGCCAACC
Found at i:42032148 original size:31 final size:31
Alignment explanation
Indices: 42032113--42032181 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
42032103 ATTCACATTT
* * *
42032113 TGATTCTGGTTCTGTTACCTGATACTAATTC
1 TGATTCTGATTCTATCACCTGATACTAATTC
* *
42032144 TGATTCTGATTCTATCACCTGATTCTGATTC
1 TGATTCTGATTCTATCACCTGATACTAATTC
42032175 TGATTCT
1 TGATTCT
42032182 CATTTTGATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.19, C:0.20, G:0.14, T:0.46
Consensus pattern (31 bp):
TGATTCTGATTCTATCACCTGATACTAATTC
Found at i:42032151 original size:6 final size:6
Alignment explanation
Indices: 42032113--42032202 Score: 60
Period size: 6 Copynumber: 14.7 Consensus size: 6
42032103 ATTCACATTT
* * * *
42032113 TGATTC TGGTTC TG-TTACC TGATAC TAATTC TGATTC TGATTC T-ATCACC
1 TGATTC TGATTC TGATT--C TGATTC TGATTC TGATTC TGATTC TGAT--TC
* *
42032163 TGATTC TGATTC TGATTC TCATTT TGATTC T-AGTTC TGAT
1 TGATTC TGATTC TGATTC TGATTC TGATTC TGA-TTC TGAT
42032203 AATGTTTCTT
Statistics
Matches: 65, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
5 5 0.08
6 51 0.78
7 6 0.09
8 3 0.05
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.48
Consensus pattern (6 bp):
TGATTC
Found at i:42038017 original size:43 final size:42
Alignment explanation
Indices: 42037914--42038030 Score: 112
Period size: 43 Copynumber: 2.7 Consensus size: 42
42037904 TTTGGGATGT
*
42037914 TGGCATCGAT-TTGTGATTTACGTGTAAGACCATGTCTATGACA
1 TGGCATCGATATT-TGATTT-CGTGTAAGACCATGTCTAGGACA
** * * *
42037957 TCCTCATCG-TATATGATTTCGTGTAAGACCCTGTCTGGGACAA
1 T-GGCATCGATATTTGATTTCGTGTAAGACCATGTCTAGGAC-A
* *
42038000 TGGCATCGATATTTGATTACATGTAAGACCA
1 TGGCATCGATATTTGATTTCGTGTAAGACCA
42038031 CATCTGGGAT
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
42 24 0.41
43 28 0.48
44 6 0.10
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (42 bp):
TGGCATCGATATTTGATTTCGTGTAAGACCATGTCTAGGACA
Found at i:42044623 original size:43 final size:43
Alignment explanation
Indices: 42044497--42044645 Score: 146
Period size: 43 Copynumber: 3.5 Consensus size: 43
42044487 ATGTGTTATT
* *
42044497 GTGTAAGACCACGTCTAGGAC-GTTGGCATCGAT-TTGTGATTTAC
1 GTGTAAGACCACGTCTGGGACAG-TGGCATCGGTATT-TGATTT-C
* * * *
42044541 GTGTAAGACCATGTCTGGGACA-TCGACATC-GTATATGATTTT
1 GTGTAAGACCACGTCTGGGACAGT-GGCATCGGTATTTGATTTC
*
42044583 GTGTAAGACC-CTGTCTGGGACAGTGGCATCGGTATTTGATTAC
1 GTGTAAGACCAC-GTCTGGGACAGTGGCATCGGTATTTGATTTC
*
42044626 ATGTAAGACCACGTCTGGGA
1 GTGTAAGACCACGTCTGGGA
42044646 TGCTGGCATT
Statistics
Matches: 86, Mismatches: 12, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
42 25 0.29
43 35 0.41
44 26 0.30
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (43 bp):
GTGTAAGACCACGTCTGGGACAGTGGCATCGGTATTTGATTTC
Found at i:42046327 original size:98 final size:98
Alignment explanation
Indices: 42046153--42046345 Score: 296
Period size: 98 Copynumber: 2.0 Consensus size: 98
42046143 CTTGGCACAC
* * *
42046153 GGCGTGTGTGGCTATTTTGAATGGTACACGGGCTAGACATACAGGCGTGTAGTTAGCTGTGTGAC
1 GGCGAGTGTGGCTATTTCGAATGGTACACGGGCTAGACACACAGGCGTGTAGTTAGCTGTGTGAC
*
42046218 CCAAGTCAGTTTCGACCACGGCCAAGGCATACG
66 CCAAGTCAGTTTCGACCACAGCCAAGGCATACG
* * * *
42046251 GGCGAGTGTGGCTATTTCGGATGGTACACGGGCTAGACACACGGGCGTGTGGTTAGTTGTGTGAC
1 GGCGAGTGTGGCTATTTCGAATGGTACACGGGCTAGACACACAGGCGTGTAGTTAGCTGTGTGAC
* *
42046316 CTAAGTTAGTTTCGACCACAGCCAAGGCAT
66 CCAAGTCAGTTTCGACCACAGCCAAGGCAT
42046346 TATGCCCTAT
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
98 85 1.00
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.25
Consensus pattern (98 bp):
GGCGAGTGTGGCTATTTCGAATGGTACACGGGCTAGACACACAGGCGTGTAGTTAGCTGTGTGAC
CCAAGTCAGTTTCGACCACAGCCAAGGCATACG
Found at i:42054087 original size:80 final size:80
Alignment explanation
Indices: 42053993--42054153 Score: 286
Period size: 80 Copynumber: 2.0 Consensus size: 80
42053983 TTTGAGACAG
* *
42053993 TTGAAAATGCAACTAGGATTTTTGGTAATCAAACTGAAAATATAGCTAGTAATGAAATTAAAACC
1 TTGAAAATACAACTAGGATTTTTGGTAATCAAACTGAAAATATAGCTACTAATGAAATTAAAACC
42054058 GAATATACAAGAGAA
66 GAATATACAAGAGAA
*
42054073 TTGAAAATACAACTAGGATTTTTGGTAATCAAACTGAAAATATTGCTACTAATGAAATTAAAACC
1 TTGAAAATACAACTAGGATTTTTGGTAATCAAACTGAAAATATAGCTACTAATGAAATTAAAACC
*
42054138 GAATATACAGGAGAA
66 GAATATACAAGAGAA
42054153 T
1 T
42054154 CTTCTAATCA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.27
Consensus pattern (80 bp):
TTGAAAATACAACTAGGATTTTTGGTAATCAAACTGAAAATATAGCTACTAATGAAATTAAAACC
GAATATACAAGAGAA
Found at i:42055012 original size:27 final size:27
Alignment explanation
Indices: 42054959--42055012 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
42054949 AAAAATATAG
42054959 AAAGAAAAATAGAAAATATAAATTAAT
1 AAAGAAAAATAGAAAATATAAATTAAT
42054986 AAAGAAAAATAGAAAATATAAATTAAT
1 AAAGAAAAATAGAAAATATAAATTAAT
42055013 TAGATGGAAA
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:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (27 bp):
AAAGAAAAATAGAAAATATAAATTAAT
Found at i:42057532 original size:15 final size:15
Alignment explanation
Indices: 42057512--42057541 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42057502 GAGTACTAAG
*
42057512 AAAATAGAATTAGAA
1 AAAATAGAAATAGAA
42057527 AAAATAGAAATAGAA
1 AAAATAGAAATAGAA
42057542 TTTTGAGGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (15 bp):
AAAATAGAAATAGAA
Found at i:42059336 original size:28 final size:28
Alignment explanation
Indices: 42059296--42059365 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
42059286 GCAATCAAAG
* *
42059296 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTACGAAATATTGAGA
* *
42059324 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTACGAAATATTGAGA
*
42059352 ATGACACTTAGTGT
1 ATGGCACTTAGTGT
42059366 GAAAAATATC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.30
Consensus pattern (28 bp):
ATGGCACTTAGTGTACGAAATATTGAGA
Found at i:42059366 original size:28 final size:28
Alignment explanation
Indices: 42059305--42059366 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
42059295 GATGGTACTC
* *
42059305 AGTGTACGAAATATTGAGAATGGCACTT
1 AGTGTGCGAAATATTGAGAATGACACTT
*
42059333 AGTGTGCGAGATATTGAGAATGACACTT
1 AGTGTGCGAAATATTGAGAATGACACTT
42059361 AGTGTG
1 AGTGTG
42059367 AAAAATATCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (28 bp):
AGTGTGCGAAATATTGAGAATGACACTT
Found at i:42059374 original size:28 final size:28
Alignment explanation
Indices: 42059313--42059374 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
42059303 TCAGTGTACG
* **
42059313 AAATATTGAGAATGGCACTTAGTGTGCG
1 AAATATTGAGAATGACACTTAGTGTGAA
*
42059341 AGATATTGAGAATGACACTTAGTGTGAA
1 AAATATTGAGAATGACACTTAGTGTGAA
42059369 AAATAT
1 AAATAT
42059375 CGAATGATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (28 bp):
AAATATTGAGAATGACACTTAGTGTGAA
Found at i:42064229 original size:56 final size:56
Alignment explanation
Indices: 42064099--42064232 Score: 205
Period size: 56 Copynumber: 2.4 Consensus size: 56
42064089 CAAACAAGGC
* * *
42064099 CTTACTCGCACACATATACCGGAATCACATATCGATGCCAACGTATTAAACGTGGT
1 CTTACTCGCACACATATATCGAAATCACATATCGATGCCAACATATTAAACGTGGT
* *
42064155 CTTACTTGCACACATATATCGAAATCACATATCGATGCCAACATATTAAATGTGGT
1 CTTACTCGCACACATATATCGAAATCACATATCGATGCCAACATATTAAACGTGGT
**
42064211 CTTACTCAAACACATATATCGA
1 CTTACTCGCACACATATATCGA
42064233 TGCCATGGTC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 70 1.00
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.28
Consensus pattern (56 bp):
CTTACTCGCACACATATATCGAAATCACATATCGATGCCAACATATTAAACGTGGT
Found at i:42068945 original size:15 final size:16
Alignment explanation
Indices: 42068925--42068958 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
42068915 AGATTTATAC
*
42068925 ATTATCACTGA-TTTG
1 ATTATCACCGATTTTG
42068940 ATTATCACCGATTTTG
1 ATTATCACCGATTTTG
42068956 ATT
1 ATT
42068959 CAATTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.47
Consensus pattern (16 bp):
ATTATCACCGATTTTG
Found at i:42076315 original size:10 final size:10
Alignment explanation
Indices: 42076300--42076441 Score: 54
Period size: 10 Copynumber: 14.6 Consensus size: 10
42076290 CATTTGTCTA
42076300 ATAAAAATAT
1 ATAAAAATAT
42076310 ATAAAAGAT-T
1 ATAAAA-ATAT
*
42076320 AT-AAAAT-C
1 ATAAAAATAT
42076328 AT-AAAATATT
1 ATAAAAATA-T
*
42076338 ACAAAAATATT
1 ATAAAAATA-T
*
42076349 ACATAAAATAT
1 ATA-AAAATAT
42076360 -TAAAAATTAT
1 ATAAAAA-TAT
* **
42076370 TTAAACTTAT
1 ATAAAAATAT
42076380 A-AAAAAT-T
1 ATAAAAATAT
*
42076388 ATTATAAAT-T
1 A-TAAAAATAT
* *
42076398 CTAAAAAAAT
1 ATAAAAATAT
*
42076408 ATAATAAT-T
1 ATAAAAATAT
42076417 ATAAAAA-ATT
1 ATAAAAATA-T
42076427 ATAAAAA-AT
1 ATAAAAATAT
42076436 ATAAAA
1 ATAAAA
42076442 TTTCTTAAAA
Statistics
Matches: 103, Mismatches: 17, Indels: 25
0.71 0.12 0.17
Matches are distributed among these distances:
8 11 0.11
9 30 0.29
10 38 0.37
11 18 0.17
12 6 0.06
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:42076346 original size:11 final size:11
Alignment explanation
Indices: 42076330--42076370 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
42076320 ATAAAATCAT
42076330 AAAATATTACA
1 AAAATATTACA
42076341 AAAATATTACA
1 AAAATATTACA
42076352 TAAAATATTA-A
1 -AAAATATTACA
*
42076363 AAATTATT
1 AAAATATT
42076371 TAAACTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 7 0.25
11 12 0.43
12 9 0.32
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAATATTACA
Found at i:42076353 original size:23 final size:22
Alignment explanation
Indices: 42076327--42076370 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
42076317 ATTATAAAAT
42076327 CATAAAATATTACAAAAATATTA
1 CATAAAATATTA-AAAAATATTA
*
42076350 CATAAAATATTAAAAATTATT
1 CATAAAATATTAAAAAATATT
42076371 TAAACTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (22 bp):
CATAAAATATTAAAAAATATTA
Found at i:42076358 original size:12 final size:12
Alignment explanation
Indices: 42076327--42076361 Score: 63
Period size: 11 Copynumber: 3.0 Consensus size: 12
42076317 ATTATAAAAT
42076327 CATAAAATATTA
1 CATAAAATATTA
42076339 CA-AAAATATTA
1 CATAAAATATTA
42076350 CATAAAATATTA
1 CATAAAATATTA
42076362 AAAATTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (12 bp):
CATAAAATATTA
Found at i:42076416 original size:19 final size:20
Alignment explanation
Indices: 42076351--42076502 Score: 95
Period size: 20 Copynumber: 7.8 Consensus size: 20
42076341 AAAATATTAC
* *
42076351 ATAAAATATTAAAAATTAT-
1 ATAAATTATAAAAAATTATA
* *
42076370 TTAAACTTATAAAAAATTATT
1 ATAAA-TTATAAAAAATTATA
* *
42076391 ATAAATTCTAAAAAAATATA
1 ATAAATTATAAAAAATTATA
42076411 AT-AATTATAAAAAATTATA
1 ATAAATTATAAAAAATTATA
* * *
42076430 A-AAAATAT-AAAATTTCTTA
1 ATAAATTATAAAAAATT-ATA
**
42076449 A-AAGCCTAT-AAAAATTATA
1 ATAA-ATTATAAAAAATTATA
*
42076468 ATTTAATTA-AAAAAA-TATA
1 A-TAAATTATAAAAAATTATA
42076487 TATAAATTATAAAAAA
1 -ATAAATTATAAAAAA
42076503 ATTTAGGGGT
Statistics
Matches: 103, Mismatches: 20, Indels: 19
0.73 0.14 0.13
Matches are distributed among these distances:
18 6 0.06
19 43 0.42
20 49 0.48
21 5 0.05
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (20 bp):
ATAAATTATAAAAAATTATA
Found at i:42076435 original size:78 final size:78
Alignment explanation
Indices: 42076335--42076502 Score: 182
Period size: 78 Copynumber: 2.1 Consensus size: 78
42076325 ATCATAAAAT
* * * * *
42076335 ATTACAAAAATATTACATAAAATATTAAAAATTATTTAAA-CTTATAAAAAATTATTA-TAAATT
1 ATTATAAAAA-ATTACAAAAAATA-TAAAAATTATTAAAAGCCTAT-AAAAATTATAATTAAA-T
42076398 CTAAAAAAATATA-AT-A
62 -TAAAAAAATATATATAA
* * * *
42076414 ATTATAAAAAATTATAAAAAATATAAAATTTCTTAAAAGCCTATAAAAATTATAATTTAATTAAA
1 ATTATAAAAAATTACAAAAAATATAAAAATTATTAAAAGCCTATAAAAATTATAATTAAATTAAA
42076479 AAAATATATATAA
66 AAAATATATATAA
42076492 ATTATAAAAAA
1 ATTATAAAAAA
42076503 ATTTAGGGGT
Statistics
Matches: 76, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
76 12 0.16
77 25 0.33
78 30 0.39
79 9 0.12
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.35
Consensus pattern (78 bp):
ATTATAAAAAATTACAAAAAATATAAAAATTATTAAAAGCCTATAAAAATTATAATTAAATTAAA
AAAATATATATAA
Found at i:42076565 original size:9 final size:9
Alignment explanation
Indices: 42076537--42076776 Score: 92
Period size: 10 Copynumber: 24.8 Consensus size: 9
42076527 AATACATGAC
42076537 TTTTTATAA
1 TTTTTATAA
* *
42076546 CTATTAT-A
1 TTTTTATAA
42076554 TTTTTATAA
1 TTTTTATAA
*
42076563 TTTTTATAG
1 TTTTTATAA
* ** *
42076572 CTAATACAA
1 TTTTTATAA
*
42076581 GTTTGTATAAA
1 -TTTTTAT-AA
*
42076592 TTTTTAAATA
1 TTTTTATA-A
42076602 TTTTTA-ATA
1 TTTTTATA-A
*
42076611 TGTTTTATATT
1 T-TTTTATA-A
*
42076622 TTTTTATTA
1 TTTTTATAA
*
42076631 TTCTTATAA
1 TTTTTATAA
42076640 TTTTTTTATAA
1 --TTTTTATAA
*
42076651 TTTAT-TAA
1 TTTTTATAA
42076659 TTTTT-TAA
1 TTTTTATAA
42076667 TTTTATATAA
1 TTTT-TATAA
42076677 GTTTTTATAA
1 -TTTTTATAA
*
42076687 TATTTATAA
1 TTTTTATAA
*
42076696 TATTTTATGAT
1 T-TTTTAT-AA
42076707 TTTCCTTATAA
1 TTT--TTATAA
*
42076718 GTTTTATAA
1 TTTTTATAA
42076727 GTTTTTTGTATAA
1 ---TTTT-TATAA
**
42076740 AATTTATAA
1 TTTTTATAA
*
42076749 CTTTATATAAA
1 -TTTTTAT-AA
42076760 TTTTTAATAA
1 TTTTT-ATAA
42076770 TTTTTAT
1 TTTTTAT
42076777 TAGAAAATTG
Statistics
Matches: 173, Mismatches: 36, Indels: 44
0.68 0.14 0.17
Matches are distributed among these distances:
8 20 0.12
9 57 0.33
10 58 0.34
11 26 0.15
12 7 0.04
13 5 0.03
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:42076665 original size:18 final size:19
Alignment explanation
Indices: 42076616--42076708 Score: 77
Period size: 19 Copynumber: 4.9 Consensus size: 19
42076606 TAATATGTTT
* *
42076616 TATATTTTTTTATTATTCT-
1 TATAATTTTTTATAATT-TA
42076635 TATAATTTTTTTATAATTTA
1 TATAA-TTTTTTATAATTTA
*
42076655 T-TAATTTTTTA-ATTTTA
1 TATAATTTTTTATAATTTA
*
42076672 TATAAGTTTTTATAATATT-
1 TATAATTTTTTATAAT-TTA
* *
42076691 TATAATATTTTATGATTT
1 TATAATTTTTTATAATTT
42076709 TCCTTATAAG
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
17 6 0.10
18 18 0.30
19 23 0.38
20 14 0.23
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.66
Consensus pattern (19 bp):
TATAATTTTTTATAATTTA
Found at i:42076681 original size:19 final size:18
Alignment explanation
Indices: 42076635--42076694 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 18
42076625 TTATTATTCT
*
42076635 TATAATTTTTTTATAATTTA
1 TATAA-TTTTTTA-ATTTTA
42076655 T-TAATTTTTTAATTTTA
1 TATAATTTTTTAATTTTA
42076672 TATAAGTTTTTATAATATTTA
1 TATAA-TTTTT-TAAT-TTTA
42076693 TA
1 TA
42076695 ATATTTTATG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
17 6 0.17
18 10 0.29
19 8 0.23
20 5 0.14
21 6 0.17
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
TATAATTTTTTAATTTTA
Found at i:42080789 original size:27 final size:27
Alignment explanation
Indices: 42080759--42081067 Score: 389
Period size: 27 Copynumber: 11.5 Consensus size: 27
42080749 TAATAAAGAG
* *
42080759 AAATTACTAAAATACCCTTGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
42080786 AAATTA-TCGAAATACCCCCGATTTGTA
1 AAATTACT-GAAATACCCTCGATTTGTA
*
42080813 AAATTACTGAAATACCCTCGA-TTGTG
1 AAATTACTGAAATACCCTCGATTTGTA
*
42080839 AAATTACTGAAATACCCTCGA-TTGTG
1 AAATTACTGAAATACCCTCGATTTGTA
**
42080865 AAATTACCAAAATACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
42080892 AAATTACTGAAACACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
42080919 AAATTACTGAAACACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* ** *
42080946 AAATTACCT-AAACACCCTTAATTTGTG
1 AAATTA-CTGAAATACCCTCGATTTGTA
42080973 AAATTAC-GAAAATACCCTCGATTTGTA
1 AAATTACTG-AAATACCCTCGATTTGTA
*
42081000 AAATTACTGAAATACCCTCAATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
42081027 AAATTACTGAAACATCCC-CGATTTGTA
1 AAATTACTGAAATA-CCCTCGATTTGTA
42081054 AAATTA-TCGAAATA
1 AAATTACT-GAAATA
42081068 ACCTTGTAGT
Statistics
Matches: 251, Mismatches: 22, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
26 52 0.21
27 192 0.76
28 7 0.03
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGATTTGTA
Found at i:42084091 original size:49 final size:49
Alignment explanation
Indices: 42083858--42084092 Score: 253
Period size: 49 Copynumber: 4.7 Consensus size: 49
42083848 GTGGGGTCAC
42083858 GTGTGTAGTACTAAGTGCAGGCTACTACT-TGTACCAGATAATTGGTTGCA
1 GTGTGTAGTACTAAGTGCAGGCTACTA-TGTGTACCAGATAATTGGTT-CA
* * * * *
42083908 -TGTGTAGTACTAAGTGCAAGCTACTATGCGTACCCGATAACTTCGATCA
1 GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAA-TTGGTTCA
* * * **
42083957 CGTGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGATGGTTAGG-TCAA
1 -GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT-GGTTC-A
** *
42084008 GTGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATTGGTTGCA
1 GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTT-CA
*
42084058 -TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCA
1 GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCA
42084093 CATAGCTTTG
Statistics
Matches: 153, Mismatches: 24, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
48 1 0.01
49 70 0.46
50 47 0.31
51 35 0.23
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (49 bp):
GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTTCA
Found at i:42086686 original size:28 final size:27
Alignment explanation
Indices: 42086627--42086689 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
42086617 TGGGAAGTAG
* *
42086627 TTGGGCCTGAGGGCCATATGAATGTGA
1 TTGGGCCTGAGGGCCATATGAACGAGA
* *
42086654 ATGGGCCTGATGGGCCATGTGAACGAGA
1 TTGGGCCTGA-GGGCCATATGAACGAGA
42086682 TTGGGCCT
1 TTGGGCCT
42086690 AAAGGGGCCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 9 0.30
28 21 0.70
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.24
Consensus pattern (27 bp):
TTGGGCCTGAGGGCCATATGAACGAGA
Found at i:42087138 original size:80 final size:81
Alignment explanation
Indices: 42087005--42087388 Score: 497
Period size: 80 Copynumber: 4.8 Consensus size: 81
42086995 ATAATAAAGA
* * *
42087005 GAAATTACTAAAATACCCTCGATTTGTAAAATTACTGAAATGCCCTCGATTTGTAAAATTACTGA
1 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTACTGA
42087070 AATACCCTCGA-TTGT
66 AATACCCTCGATTTGT
* * * **
42087085 GAAATTACTGAAATACCCTCGGTTTGTAAAATTACCAAAATACCCCCGATTTGTAAAATTACCAA
1 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTACTGA
42087150 AATACCCTCGA-TTGT
66 AATACCCTCGATTTGT
** *
42087165 GAAATTACTGAAATACCCTCGATTTGTAAAATTATTGAAATACCCTCGATTTGTGAAATTA-TCG
1 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTACT-G
* *
42087229 AAACACCCTCAATTTGT
65 AAATACCCTCGATTTGT
* * * * * * ** * *
42087246 GAAATTACCGAAACACCTTCGATTTGTGAAATTACCTAAACACCCTTAATTTGTAAATTTATTGA
1 GAAATTACTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTACTGA
*
42087311 AATAGCCTCGATTTGT
66 AATACCCTCGATTTGT
*
42087327 AAAATTA-TCGAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTAC
1 GAAATTACT-GAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTAC
42087389 CAAAACACTC
Statistics
Matches: 256, Mismatches: 44, Indels: 7
0.83 0.14 0.02
Matches are distributed among these distances:
80 137 0.54
81 118 0.46
82 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (81 bp):
GAAATTACTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTACTGA
AATACCCTCGATTTGT
Found at i:42087466 original size:27 final size:27
Alignment explanation
Indices: 42087006--42087453 Score: 481
Period size: 27 Copynumber: 16.7 Consensus size: 27
42086996 TAATAAAGAG
**
42087006 AAATTACTAAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* *
42087033 AAATTACTGAAATGCCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* *
42087060 AAATTACTGAAATACCCTCGA-TTGTG
1 AAATTACCGAAATACCCTCGATTTGTA
* *
42087086 AAATTACTGAAATACCCTCGGTTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* *
42087113 AAATTACCAAAATACCCCCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* *
42087140 AAATTACCAAAATACCCTCGA-TTGTG
1 AAATTACCGAAATACCCTCGATTTGTA
*
42087166 AAATTACTGAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
** *
42087193 AAATTATTGAAATACCCTCGATTTGTG
1 AAATTACCGAAATACCCTCGATTTGTA
* * * *
42087220 AAATTATCGAAACACCCTCAATTTGTG
1 AAATTACCGAAATACCCTCGATTTGTA
* * *
42087247 AAATTACCGAAACACCTTCGATTTGTG
1 AAATTACCGAAATACCCTCGATTTGTA
* * **
42087274 AAATTACCTAAACACCCTTAATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* ** *
42087301 AATTTATTGAAATAGCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
*
42087328 AAATTATCGAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
42087355 AAATTACCGAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* * * **
42087382 AAATTACCAAAACACTCCT-AATTTAAA
1 AAATTACCGAAATAC-CCTCGATTTGTA
* * * *
42087409 AAATTATCAAAATACCCTTG-TAGTGTA
1 AAATTACCGAAATACCCTCGAT-TTGTA
42087436 AAATTACCGAAATACCCT
1 AAATTACCGAAATACCCT
42087454 TGTAGTGTAA
Statistics
Matches: 363, Mismatches: 53, Indels: 10
0.85 0.12 0.02
Matches are distributed among these distances:
26 51 0.14
27 309 0.85
28 3 0.01
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (27 bp):
AAATTACCGAAATACCCTCGATTTGTA
Found at i:42087477 original size:27 final size:27
Alignment explanation
Indices: 42087418--42087498 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
42087408 AAAATTATCA
* *
42087418 AAATACCCTTGTAGTGTAAAATTACCG
1 AAATACCCTTGTAGTGTAAAATGACTG
42087445 AAATACCCTTGTAGTGTAAAATGACTG
1 AAATACCCTTGTAGTGTAAAATGACTG
* * *
42087472 ACATACCCCTGTAGGGTAAAATGACTG
1 AAATACCCTTGTAGTGTAAAATGACTG
42087499 TTTTGCCCTT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (27 bp):
AAATACCCTTGTAGTGTAAAATGACTG
Found at i:42088762 original size:26 final size:26
Alignment explanation
Indices: 42088679--42088813 Score: 208
Period size: 26 Copynumber: 5.3 Consensus size: 26
42088669 TTGGAGGCCT
42088679 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
*
42088703 AGCCCTTTT-GATAAACTGGGGCA-A
1 AGCCCTTTTCAATAAACTGGGGCATA
42088727 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
42088753 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
*
42088779 AGCCCTTTTCAATAAACTAGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
42088805 AGCCCTTTT
1 AGCCCTTTT
42088814 GCACTTCCTC
Statistics
Matches: 105, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
23 7 0.07
24 24 0.23
25 13 0.12
26 61 0.58
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:42088888 original size:20 final size:20
Alignment explanation
Indices: 42088863--42088957 Score: 133
Period size: 20 Copynumber: 4.8 Consensus size: 20
42088853 TTATGATTAC
*
42088863 ATCATGTGCATTTCATACAT
1 ATCATGTGCATATCATACAT
42088883 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
42088903 ATCATGTGCATTTTATACAT
1 ATCATGTGCATATCATACAT
42088923 ATCATGTGCATATCATATCA-
1 ATCATGTGCATATCATA-CAT
42088943 ATCATGT--ATATCATA
1 ATCATGTGCATATCATA
42088958 TCCCACGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
18 8 0.12
20 59 0.86
21 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:42088894 original size:11 final size:11
Alignment explanation
Indices: 42088863--42088938 Score: 56
Period size: 11 Copynumber: 7.5 Consensus size: 11
42088853 TTATGATTAC
42088863 ATCATGTGCAT
1 ATCATGTGCAT
* *
42088874 TTCA--TACAT
1 ATCATGTGCAT
42088883 ATCATGTGCAT
1 ATCATGTGCAT
*
42088894 ATCA--TACAT
1 ATCATGTGCAT
42088903 ATCATGTGCAT
1 ATCATGTGCAT
* * *
42088914 -T-TTATACAT
1 ATCATGTGCAT
42088923 ATCATGTGCAT
1 ATCATGTGCAT
42088934 ATCAT
1 ATCAT
42088939 ATCAATCATG
Statistics
Matches: 47, Mismatches: 12, Indels: 12
0.66 0.17 0.17
Matches are distributed among these distances:
9 20 0.43
10 2 0.04
11 25 0.53
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:42088907 original size:40 final size:40
Alignment explanation
Indices: 42088863--42088949 Score: 149
Period size: 40 Copynumber: 2.2 Consensus size: 40
42088853 TTATGATTAC
42088863 ATCATGTGCATTTCATACATATCATGTGCATATCATA-CA
1 ATCATGTGCATTTCATACATATCATGTGCATATCATATCA
*
42088902 TATCATGTGCATTTTATACATATCATGTGCATATCATATCA
1 -ATCATGTGCATTTCATACATATCATGTGCATATCATATCA
42088943 ATCATGT
1 ATCATGT
42088950 ATATCATATC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 43 0.96
41 2 0.04
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.39
Consensus pattern (40 bp):
ATCATGTGCATTTCATACATATCATGTGCATATCATATCA
Found at i:42088955 original size:9 final size:10
Alignment explanation
Indices: 42088880--42088956 Score: 54
Period size: 9 Copynumber: 7.8 Consensus size: 10
42088870 GCATTTCATA
42088880 CATATCATGT
1 CATATCATGT
*
42088890 GCATATCAT-A
1 -CATATCATGT
42088900 CATATCATGT
1 CATATCATGT
* * *
42088910 GCATTTTAT-A
1 -CATATCATGT
42088920 CATATCATGT
1 CATATCATGT
*
42088930 GCATATCATAT
1 -CATATCATGT
42088941 CA-ATCATGT
1 CATATCATGT
42088950 -ATATCAT
1 CATATCAT
42088957 ATCCCACGTA
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
8 1 0.02
9 25 0.49
10 2 0.04
11 23 0.45
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (10 bp):
CATATCATGT
Found at i:42096878 original size:26 final size:26
Alignment explanation
Indices: 42096800--42096955 Score: 169
Period size: 26 Copynumber: 6.2 Consensus size: 26
42096790 GGCCTAGCCT
* *
42096800 CTTTT-AAT-AACTGGGGC-GAAGCC
1 CTTTTCAATAAACTGGGGCATAAACC
* *
42096823 CTTTT-GATAAACTGGGGCA-AAACA
1 CTTTTCAATAAACTGGGGCATAAACC
*
42096847 CTTTTCAATAAACTAGGGCATAAACC
1 CTTTTCAATAAACTGGGGCATAAACC
* *
42096873 TTTTTCAATAAACTGGGGCATAAGCC
1 CTTTTCAATAAACTGGGGCATAAACC
* * *
42096899 CTTTGCAATGAACTGGGGCATAAGCC
1 CTTTTCAATAAACTGGGGCATAAACC
* *
42096925 CTTTTCAATAAACTAGGGCATAAGCC
1 CTTTTCAATAAACTGGGGCATAAACC
42096951 CTTTT
1 CTTTT
42096956 GCACTTCCTC
Statistics
Matches: 114, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
23 7 0.06
24 17 0.15
25 12 0.11
26 78 0.68
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (26 bp):
CTTTTCAATAAACTGGGGCATAAACC
Found at i:42097030 original size:20 final size:20
Alignment explanation
Indices: 42097005--42097071 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
42096995 TTATGATTAC
42097005 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
*
42097025 ATCATGTGCATATCATACAT
1 ATCATGTGCATTTCATACAT
*
42097045 ATCATGTGCATTTTATACAT
1 ATCATGTGCATTTCATACAT
42097065 ATCATGT
1 ATCATGT
42097072 ATATCATATC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.40
Consensus pattern (20 bp):
ATCATGTGCATTTCATACAT
Found at i:42097049 original size:40 final size:38
Alignment explanation
Indices: 42097005--42097079 Score: 123
Period size: 40 Copynumber: 1.9 Consensus size: 38
42096995 TTATGATTAC
42097005 ATCATGTGCATTTCATACATATCATGTGCATATCATACAT
1 ATCATGTGCATTTCATACATATCATGT--ATATCATACAT
*
42097045 ATCATGTGCATTTTATACATATCATGTATATCATA
1 ATCATGTGCATTTCATACATATCATGTATATCATA
42097080 TCCCACGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 8 0.24
40 26 0.76
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.40
Consensus pattern (38 bp):
ATCATGTGCATTTCATACATATCATGTATATCATACAT
Found at i:42100305 original size:34 final size:34
Alignment explanation
Indices: 42100267--42100334 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
42100257 AATTAAAATG
42100267 AAAAATGAAAAATAAACCCTAATCTAATTTCAGT
1 AAAAATGAAAAATAAACCCTAATCTAATTTCAGT
42100301 AAAAATGAAAAATAAACCCTAATCTAATTTCAGT
1 AAAAATGAAAAATAAACCCTAATCTAATTTCAGT
42100335 GTTAGTCTCT
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:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (34 bp):
AAAAATGAAAAATAAACCCTAATCTAATTTCAGT
Found at i:42105266 original size:42 final size:42
Alignment explanation
Indices: 42105219--42105381 Score: 193
Period size: 42 Copynumber: 3.9 Consensus size: 42
42105209 TACCGTACCA
*
42105219 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCGTATCG
* * * *
42105261 ATGCCAATAGCCCAGCTATGGTCTTACAC-AAAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGTAA-TCTCGTATCG
* * * * *
42105304 ATGCCATATCCCATATATGGTCTTAGACGTAGTCTTGTATTG
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCGTATCG
* *
42105346 ATGCCATATCCCAAATATGGTCTTACACGTAGTCTC
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTC
42105382 AGTAACCCTA
Statistics
Matches: 101, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
42 66 0.65
43 35 0.35
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGTAATCTCGTATCG
Found at i:42105349 original size:85 final size:84
Alignment explanation
Indices: 42105219--42105382 Score: 220
Period size: 85 Copynumber: 1.9 Consensus size: 84
42105209 TACCGTACCA
* **
42105219 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCGTATCGATGCCAATAGCCCAGCTATGGTC
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCGTATCGATGCC-ATAGCCCAAATATGGTC
42105284 TTACACAAAGTCTCATATCG
65 TTACACAAAGTCTCATATCG
* * * * * *
42105304 ATGCCATATCCCATATATGGTCTTAGACGTAGTCTTGTATTGATGCCATATCCCAAATATGGTCT
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCGTATCGATGCCATAGCCCAAATATGGTCT
**
42105369 TACACGTAGTCTCA
66 TACACAAAGTCTCA
42105383 GTAACCCTAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
84 27 0.40
85 41 0.60
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.32
Consensus pattern (84 bp):
ATGCCATATCCCAGATATGGTCTTACACGTAATCTCGTATCGATGCCATAGCCCAAATATGGTCT
TACACAAAGTCTCATATCG
Found at i:42105920 original size:3 final size:3
Alignment explanation
Indices: 42105912--42105946 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
42105902 AAATAAACTC
*
42105912 TCT TCT TCT TCT TCT TCT TCT TCT TCT TTT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
42105947 ACATCAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:42107050 original size:15 final size:16
Alignment explanation
Indices: 42107022--42107051 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42107012 TTTTTTGAAA
42107022 ATTTTTAAAGAAAATC
1 ATTTTTAAAGAAAATC
42107038 ATTTTTAAA-AAAAT
1 ATTTTTAAAGAAAAT
42107052 TAACTCGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (16 bp):
ATTTTTAAAGAAAATC
Found at i:42114021 original size:13 final size:13
Alignment explanation
Indices: 42114003--42114031 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
42113993 TATAGCTTGT
42114003 CCCATTGACTATG
1 CCCATTGACTATG
42114016 CCCATTGACTATG
1 CCCATTGACTATG
42114029 CCC
1 CCC
42114032 TAGATATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.38, G:0.14, T:0.28
Consensus pattern (13 bp):
CCCATTGACTATG
Found at i:42114141 original size:43 final size:43
Alignment explanation
Indices: 42114037--42114186 Score: 133
Period size: 43 Copynumber: 3.5 Consensus size: 43
42114027 TGCCCTAGAT
* * * * * *
42114037 ATGGTCTTATATGTTATCAC-ATATCGATGCCACTGTCCCAGAC
1 ATGGTCTTACACGTAATCACAATA-CAATGCCAATGTCCCAAAC
* * * * *
42114080 AGGGTCCTACGCGAAATCA-AATAACAATGCCAATGTTCCAAAC
1 ATGGTCTTACACGTAATCACAAT-ACAATGCCAATGTCCCAAAC
** *
42114123 ATGGTCTTACACGTAATCACAATACAATTTCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCACAATACAATGCCAATGTCCCAAAC
*
42114166 ATGGTCTTACATGTAATCACA
1 ATGGTCTTACACGTAATCACA
42114187 TCTCAGTAAC
Statistics
Matches: 84, Mismatches: 20, Indels: 6
0.76 0.18 0.05
Matches are distributed among these distances:
43 80 0.95
44 4 0.05
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (43 bp):
ATGGTCTTACACGTAATCACAATACAATGCCAATGTCCCAAAC
Found at i:42115884 original size:24 final size:24
Alignment explanation
Indices: 42115852--42115922 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
42115842 CTGACAGGAG
42115852 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
42115876 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
**
42115900 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
42115923 GGAAATCTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.35, C:0.01, G:0.38, T:0.25
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:42115934 original size:48 final size:48
Alignment explanation
Indices: 42115852--42115945 Score: 111
Period size: 48 Copynumber: 1.9 Consensus size: 48
42115842 CTGACAGGAG
** * *
42115852 AGGATTTAGGAGTTGATAAGGGATAGGATTTAGGAGTTGAT-AAGGGAT
1 AGGATTTAGGAGCAGATAAGGGA-AGGATCTAGGAGATGATCAAGGGAT
42115900 AGGATTTAGGAGCAGATAAGGG-AGGAAATCTAGGAGATGATCAAGG
1 AGGATTTAGGAGCAGATAAGGGAAGG--ATCTAGGAGATGATCAAGG
42115946 AAACAAGAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
46 3 0.08
48 32 0.82
49 4 0.10
ACGTcount: A:0.36, C:0.03, G:0.37, T:0.23
Consensus pattern (48 bp):
AGGATTTAGGAGCAGATAAGGGAAGGATCTAGGAGATGATCAAGGGAT
Found at i:42117394 original size:28 final size:29
Alignment explanation
Indices: 42117363--42117422 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
42117353 GTGGCTATTT
42117363 CACAAAT-TATCTGA-TCCGGTGGCTCTGC
1 CACAAATATATCT-ATTCCGGTGGCTCTGC
* *
42117391 CACATATATATCTATTCTGGTGGCTCTGC
1 CACAAATATATCTATTCCGGTGGCTCTGC
42117420 CAC
1 CAC
42117423 GATTATATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (29 bp):
CACAAATATATCTATTCCGGTGGCTCTGC
Found at i:42117412 original size:29 final size:27
Alignment explanation
Indices: 42117370--42117455 Score: 100
Period size: 29 Copynumber: 3.0 Consensus size: 27
42117360 TTTCACAAAT
*
42117370 TATCTGATCCGGTGGCTCTGCCACATATA
1 TATCT-ATCTGGTGGCTCTGCCACAT-TA
42117399 TATCTATTCTGGTGGCTCTGCCACGATTA
1 TATCTA-TCTGGTGGCTCTGCCAC-ATTA
* * *
42117428 TATGTATCTGGTGACTCTGTCACATTA
1 TATCTATCTGGTGGCTCTGCCACATTA
42117455 T
1 T
42117456 CTGTTCTGGC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
27 5 0.10
28 16 0.31
29 28 0.55
30 2 0.04
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (27 bp):
TATCTATCTGGTGGCTCTGCCACATTA
Found at i:42117446 original size:28 final size:27
Alignment explanation
Indices: 42117380--42117464 Score: 100
Period size: 29 Copynumber: 3.1 Consensus size: 27
42117370 TATCTGATCC
*
42117380 GGTGGCTCTGCCACATATATATCTATTCT
1 GGTGGCTCTGCCACAT-TATATGTA-TCT
42117409 GGTGGCTCTGCCACGATTATATGTATCT
1 GGTGGCTCTGCCAC-ATTATATGTATCT
* * *
42117437 GGTGACTCTGTCACATTATCTGT-TCT
1 GGTGGCTCTGCCACATTATATGTATCT
42117463 GG
1 GG
42117465 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
26 5 0.10
27 8 0.16
28 15 0.29
29 21 0.41
30 2 0.04
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (27 bp):
GGTGGCTCTGCCACATTATATGTATCT
Found at i:42120054 original size:77 final size:79
Alignment explanation
Indices: 42119919--42120069 Score: 186
Period size: 77 Copynumber: 1.9 Consensus size: 79
42119909 TTCAAGGATA
* * * *
42119919 CTTCGACTTCGACTCGATGAGACACTTGGTGGTCATTATTGCTTCAGATAGATTCGATGGGGCGT
1 CTTCGACTTAGACTCGATGAGACACTTGGTCGTCATTATTGCTTCAGATAGATCCGATGAGGCGT
*
42119984 TGGTTGCCACTTTG
66 TGGTCGCCACTTTG
*
42119998 CTTCGACTTAG-C-CGATGAGACA-TTGGTCGTCACTTATTTGCTTC-GA-ACTATCCGATGAGG
1 CTTCGACTTAGACTCGATGAGACACTTGGTCGTCA-TTA-TTGCTTCAGATA-GATCCGATGAGG
42120058 CGTTGGTCGCCA
63 CGTTGGTCGCCA
42120070 TTCTGGTGTG
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
76 10 0.16
77 35 0.56
78 8 0.13
79 10 0.16
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (79 bp):
CTTCGACTTAGACTCGATGAGACACTTGGTCGTCATTATTGCTTCAGATAGATCCGATGAGGCGT
TGGTCGCCACTTTG
Found at i:42122384 original size:47 final size:47
Alignment explanation
Indices: 42122314--42122519 Score: 259
Period size: 47 Copynumber: 4.4 Consensus size: 47
42122304 GATGTACAAG
* * * *
42122314 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTGTATATATGAGATAAGACCTAATGGCCAATGTGATGAATGTGAAA
* * *
42122361 GTGTATACATGAGATAAGACCTAATGTCCAACGTGATGAATGTGAAA
1 GTGTATATATGAGATAAGACCTAATGGCCAATGTGATGAATGTGAAA
* * * *
42122408 GCGTATATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAG
1 GTGTATATATGAGATAAGACCTAATGGCCAATGTGATGAATGTGAAA
* * * *
42122455 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAA
1 GTGTATATATGAGATAAGACCTAATGGCCAATGTGATGAATGTGAAA
* *
42122502 GTGTATAAATGTGATAAG
1 GTGTATATATGAGATAAG
42122520 TCTCGAAGGG
Statistics
Matches: 138, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 138 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
GTGTATATATGAGATAAGACCTAATGGCCAATGTGATGAATGTGAAA
Found at i:42122433 original size:94 final size:94
Alignment explanation
Indices: 42122319--42122519 Score: 285
Period size: 94 Copynumber: 2.1 Consensus size: 94
42122309 ACAAGGTGTG
* *
42122319 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATACATGAGATAAGACCTA
1 TATATGTGATAAGACCTAATGGCCGATGTGATGAATGTGAAAGTGTATACATGAGATAAGACCGA
*
42122384 ATGTCCAACGTGATGAATGTGAAAGCGTA
66 ATGGCCAACGTGATGAATGTGAAAGCGTA
* * * * * *
42122413 TATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAGGTGTATATATGTGATAAGGCCGA
1 TATATGTGATAAGACCTAATGGCCGATGTGATGAATGTGAAAGTGTATACATGAGATAAGACCGA
* * *
42122478 ATGGCCAATGTGATGGATGTGAAAGTGTA
66 ATGGCCAACGTGATGAATGTGAAAGCGTA
*
42122507 TAAATGTGATAAG
1 TATATGTGATAAG
42122520 TCTCGAAGGG
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
94 93 1.00
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.27
Consensus pattern (94 bp):
TATATGTGATAAGACCTAATGGCCGATGTGATGAATGTGAAAGTGTATACATGAGATAAGACCGA
ATGGCCAACGTGATGAATGTGAAAGCGTA
Found at i:42123868 original size:20 final size:20
Alignment explanation
Indices: 42123843--42123919 Score: 122
Period size: 20 Copynumber: 3.9 Consensus size: 20
42123833 TTGTCCACGA
42123843 CAGGCCACACGGGCATGTTC
1 CAGGCCACACGGGCATGTTC
42123863 CAGGCCACACGGGCATGTTC
1 CAGGCCACACGGGCATGTTC
42123883 CAGGCCACACGGGCATG-TC
1 CAGGCCACACGGGCATGTTC
*
42123902 TCAGGCCA-ACAGGCATGT
1 -CAGGCCACACGGGCATGT
42123920 GCCCCTATTC
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
19 10 0.19
20 44 0.81
ACGTcount: A:0.22, C:0.34, G:0.30, T:0.14
Consensus pattern (20 bp):
CAGGCCACACGGGCATGTTC
Found at i:42138620 original size:41 final size:41
Alignment explanation
Indices: 42138563--42138644 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
42138553 TCTTACCGAA
42138563 GCCTTATTGTTTCATAATCTCAGTAACTATAAGCTTGGCGT
1 GCCTTATTGTTTCATAATCTCAGTAACTATAAGCTTGGCGT
*
42138604 GCCTTATTTTTTCATAATCTCAGTAACTATAAGCTTGGCGT
1 GCCTTATTGTTTCATAATCTCAGTAACTATAAGCTTGGCGT
42138645 ACATCCCTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (41 bp):
GCCTTATTGTTTCATAATCTCAGTAACTATAAGCTTGGCGT
Found at i:42138844 original size:42 final size:42
Alignment explanation
Indices: 42138766--42138964 Score: 139
Period size: 42 Copynumber: 4.6 Consensus size: 42
42138756 TAAGATGCCA
* * * * **
42138766 ATGCCATGTCCCATACATGGTCTTACATGGGATCTCACATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCACATCG
* * **
42138808 ATGCCATATCCCAGATATGGTCTTATACGAATTCTCATTTCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCACATCG
* * ** *** *
42138850 ATGCCATGTTCCAGACGTGGTCTTACACGAAATCTTGTATCA
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCACATCG
* * *
42138892 ATGCCGTATCCCAGATATGGTCTCACATGATAAGTCAT-ACTGATGCTG
1 ATGCCATATCCCAGATATGGTCTTACACGA-AA-TC-TCAC--AT-C-G
42138940 ATGCCATATCCCAGATATGGTCTTA
1 ATGCCATATCCCAGATATGGTCTTA
42138965 TACGGTATCT
Statistics
Matches: 118, Mismatches: 32, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
42 87 0.74
43 2 0.02
44 2 0.02
45 1 0.01
46 2 0.02
47 1 0.01
48 23 0.19
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCACATCG
Found at i:42142642 original size:52 final size:51
Alignment explanation
Indices: 42142405--42142668 Score: 167
Period size: 52 Copynumber: 5.1 Consensus size: 51
42142395 GTAAATGTGA
* * *** *
42142405 AAGTCCATTAGGACAATCTAATTGGAAAGTCCGTCGGGACAATCTAATGTGG
1 AAGTCCGTCAGGACAATCTAATTGGAAAGTCTACCAGGACAATCTAATG-GG
* * * * * **
42142457 AAGCCCATTAGGACAATCTAATTAGG-AAGTCTGCTAGGATGATCTAATGTGG
1 AAGTCCGTCAGGACAATCTAATT-GGAAAGTCTACCAGGACAATCTAATG-GG
* * * * * * ** *
42142509 -ACTCTTGTCAAGACAATCCAATT-GAGAAGTCTACAAAGATTATATAATGTGG
1 AAGTC-CGTCAGGACAATCTAATTGGA-AAGTCTACCAGGACAATCTAATG-GG
* *
42142561 -AGTCTGTCAGGACAATCTAATTGGAAAGTCTGCCAGGACAATCTAATGAGG
1 AAGTCCGTCAGGACAATCTAATTGGAAAGTCTACCAGGACAATCTAATG-GG
* * * **
42142612 AAGTCCGTCCGGACAATCTATTTGGGAAGTCTATTAGGACAATCTAATTGGG
1 AAGTCCGTCAGGACAATCTAATTGGAAAGTCTACCAGGACAATCTAA-TGGG
42142664 AAGTC
1 AAGTC
42142669 TATAAGGTTG
Statistics
Matches: 169, Mismatches: 36, Indels: 14
0.77 0.16 0.06
Matches are distributed among these distances:
50 1 0.01
51 37 0.22
52 127 0.75
53 4 0.02
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (51 bp):
AAGTCCGTCAGGACAATCTAATTGGAAAGTCTACCAGGACAATCTAATGGG
Found at i:42142670 original size:26 final size:26
Alignment explanation
Indices: 42142405--42142671 Score: 125
Period size: 26 Copynumber: 10.3 Consensus size: 26
42142395 GTAAATGTGA
* *
42142405 AAGTCCATTAGGACAATCTAATTGGA
1 AAGTCTATTAGGACAATCTAATTGGG
** **
42142431 AAGTCCGTCGGGACAATCTAA-TGTGG
1 AAGTCTATTAGGACAATCTAATTG-GG
* * *
42142457 AAGCCCATTAGGACAATCTAATTAGG
1 AAGTCTATTAGGACAATCTAATTGGG
** **
42142483 AAGTCTGCTAGGATGATCTAA-TGTGG
1 AAGTCTATTAGGACAATCTAATTG-GG
* * * *
42142509 -ACTCT-TGTCAAGACAATCCAATTGAG
1 AAGTCTAT-T-AGGACAATCTAATTGGG
** * ** *
42142535 AAGTCTACAAAGATTATATAA-TGTGG
1 AAGTCTATTAGGACAATCTAATTG-GG
* * *
42142561 -AGTCTGTCAGGACAATCTAATTGGA
1 AAGTCTATTAGGACAATCTAATTGGG
***
42142586 AAGTCTGCCAGGACAATCTAA-TGAGG
1 AAGTCTATTAGGACAATCTAATTG-GG
** ** *
42142612 AAGTCCGTCCGGACAATCTATTTGGG
1 AAGTCTATTAGGACAATCTAATTGGG
42142638 AAGTCTATTAGGACAATCTAATTGGG
1 AAGTCTATTAGGACAATCTAATTGGG
42142664 AAGTCTAT
1 AAGTCTAT
42142672 AAGGTTGATT
Statistics
Matches: 178, Mismatches: 50, Indels: 26
0.70 0.20 0.10
Matches are distributed among these distances:
25 26 0.15
26 143 0.80
27 9 0.05
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.27
Consensus pattern (26 bp):
AAGTCTATTAGGACAATCTAATTGGG
Done.