Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, whole genome shotgun sequence
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: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 102 of 127
Found at i:19081818 original size:8 final size:8
Alignment explanation
Indices: 19081805--19081838 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
19081795 ATTAAACCAA
19081805 AATAATTT
1 AATAATTT
19081813 AATAATTTTT
1 AATAA--TTT
19081823 AATAATTT
1 AATAATTT
19081831 AATAATTT
1 AATAATTT
19081839 TGTAAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 16 0.67
10 8 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
AATAATTT
Found at i:19081828 original size:18 final size:19
Alignment explanation
Indices: 19081805--19081857 Score: 74
Period size: 18 Copynumber: 2.8 Consensus size: 19
19081795 ATTAAACCAA
19081805 AATAATTTAATAATTTT-T
1 AATAATTTAATAATTTTGT
19081823 AATAATTTAATAATTTTGT
1 AATAATTTAATAATTTTGT
*
19081842 AA-ATATTAAATAATTT
1 AATA-ATTTAATAATTT
19081858 AAAATTTTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 18 0.56
19 14 0.44
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
AATAATTTAATAATTTTGT
Found at i:19081834 original size:26 final size:27
Alignment explanation
Indices: 19081805--19081864 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
19081795 ATTAAACCAA
* *
19081805 AATAATTTAAT-AATTTTTAATAATTT
1 AATAATTTAATAAATATTAAATAATTT
**
19081831 AATAATTTTGTAAATATTAAATAATTT
1 AATAATTTAATAAATATTAAATAATTT
19081858 AA-AATTT
1 AATAATTT
19081865 TCATTGCATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
AATAATTTAATAAATATTAAATAATTT
Found at i:19088138 original size:2 final size:2
Alignment explanation
Indices: 19088133--19088168 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
19088123 AAAACTCAGC
19088133 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19088169 ACTGAAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19092641 original size:17 final size:17
Alignment explanation
Indices: 19092619--19092673 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
19092609 ATGATAAGAT
19092619 AATTATTTATTAATTAA
1 AATTATTTATTAATTAA
**
19092636 AATTA-TTATTTTTTAA
1 AATTATTTATTAATTAA
* *
19092652 AATT-TATA-TAATTTA
1 AATTATTTATTAATTAA
19092667 AATTATT
1 AATTATT
19092674 GATATAATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
15 8 0.28
16 16 0.55
17 5 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTATTTATTAATTAA
Found at i:19094150 original size:25 final size:24
Alignment explanation
Indices: 19094103--19094169 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 24
19094093 TCTAGATTTG
* *
19094103 ATAATATAAAACATAA-CACAATAA
1 ATAATATAAAA-ATAATAAAAATAA
19094127 TATAATATAAAAATAATAAAAATAA
1 -ATAATATAAAAATAATAAAAATAA
* *
19094152 AAAGATACAAAAATAATA
1 ATA-ATATAAAAATAATA
19094170 TTAATTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 6 0.17
25 30 0.83
ACGTcount: A:0.70, C:0.06, G:0.01, T:0.22
Consensus pattern (24 bp):
ATAATATAAAAATAATAAAAATAA
Found at i:19095238 original size:13 final size:13
Alignment explanation
Indices: 19095222--19095250 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
19095212 AATTTATTGC
19095222 TAAAAATTATTAT
1 TAAAAATTATTAT
19095235 TAAAAATTATTAT
1 TAAAAATTATTAT
19095248 TAA
1 TAA
19095251 TTTTTTTATT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAAAATTATTAT
Found at i:19095765 original size:39 final size:38
Alignment explanation
Indices: 19095722--19095800 Score: 90
Period size: 39 Copynumber: 2.0 Consensus size: 38
19095712 TAAATTTATT
19095722 TTTAA-AAAATATATTAAATCTTTT-AATAGTTTGATAAGA
1 TTTAATAAAA-ATA-TAAAT-TTTTCAATAGTTTGATAAGA
* *
19095761 TTTAATTTAAAATATAAATTTTTCGATAGTTTGATAAGA
1 TTTAA-TAAAAATATAAATTTTTCAATAGTTTGATAAGA
19095800 T
1 T
19095801 CAAAATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
38 4 0.11
39 25 0.71
40 3 0.09
41 3 0.09
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (38 bp):
TTTAATAAAAATATAAATTTTTCAATAGTTTGATAAGA
Found at i:19096055 original size:20 final size:20
Alignment explanation
Indices: 19096030--19096069 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
19096020 TAACGAGTAA
19096030 AATAATAATTAAAT-AATAAT
1 AATAATAA-TAAATAAATAAT
19096050 AATAATAATAAATAAATAAT
1 AATAATAATAAATAAATAAT
19096070 CAAAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAATAATAAATAAATAAT
Found at i:19105590 original size:24 final size:23
Alignment explanation
Indices: 19105553--19105628 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 23
19105543 GATCCCGGGC
*
19105553 CTTTGCTCTCTCCCTATCTCTTTCT
1 CTTT-CTCTGTCCCTATC-CTTTCT
* *
19105578 CTTTCTCTGTCCCTCTCCCTTTCC
1 CTTTCTCTGTCCCTAT-CCTTTCT
* * *
19105602 CTTTCCCTGTCCCTGTCCTTGCT
1 CTTTCTCTGTCCCTATCCTTTCT
19105625 CTTT
1 CTTT
19105629 TCCCCACCTG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
23 9 0.21
24 29 0.67
25 5 0.12
ACGTcount: A:0.01, C:0.43, G:0.07, T:0.49
Consensus pattern (23 bp):
CTTTCTCTGTCCCTATCCTTTCT
Found at i:19107667 original size:202 final size:202
Alignment explanation
Indices: 19107318--19107726 Score: 809
Period size: 202 Copynumber: 2.0 Consensus size: 202
19107308 TCTTATTTCT
19107318 AATTACATATCAATATCTCTGCTTCAGAAACATTACGCTTAATGTTAGATTTTTCAAATCAATGT
1 AATTACATATCAATATCTCTGCTTCAGAAACATTACGCTTAATGTTAGATTTTTCAAATCAATGT
19107383 TCCATTTGTTGTTGGATGAAATTGTTAGATTTGTTTGAAGGACTGTTATCCATCATAAGAACATA
66 TCCATTTGTTGTTGGATGAAATTGTTAGATTTGTTTGAAGGACTGTTATCCATCATAAGAACATA
*
19107448 ATTCTAAGAACAAAATCCAGTATCTACCTCCACTGAGTTACCAATTGGGAATTGAACTTGCCATC
131 ATTCTAAGAAAAAAATCCAGTATCTACCTCCACTGAGTTACCAATTGGGAATTGAACTTGCCATC
19107513 TAACCTC
196 TAACCTC
19107520 AATTACATATCAATATCTCTGCTTCAGAAACATTACGCTTAATGTTAGATTTTTCAAATCAATGT
1 AATTACATATCAATATCTCTGCTTCAGAAACATTACGCTTAATGTTAGATTTTTCAAATCAATGT
19107585 TCCATTTGTTGTTGGATGAAATTGTTAGATTTGTTTGAAGGACTGTTATCCATCATAAGAACATA
66 TCCATTTGTTGTTGGATGAAATTGTTAGATTTGTTTGAAGGACTGTTATCCATCATAAGAACATA
19107650 ATTCTAAGAAAAAAATCCAGTATCTACCTCCACTGAGTTACCAATTGGGAATTGAACTTGCCATC
131 ATTCTAAGAAAAAAATCCAGTATCTACCTCCACTGAGTTACCAATTGGGAATTGAACTTGCCATC
19107715 TAACCTC
196 TAACCTC
19107722 AATTA
1 AATTA
19107727 TAAGCTAGTC
Statistics
Matches: 206, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
202 206 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (202 bp):
AATTACATATCAATATCTCTGCTTCAGAAACATTACGCTTAATGTTAGATTTTTCAAATCAATGT
TCCATTTGTTGTTGGATGAAATTGTTAGATTTGTTTGAAGGACTGTTATCCATCATAAGAACATA
ATTCTAAGAAAAAAATCCAGTATCTACCTCCACTGAGTTACCAATTGGGAATTGAACTTGCCATC
TAACCTC
Found at i:19110400 original size:34 final size:34
Alignment explanation
Indices: 19110342--19110410 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
19110332 ATCTACCGTT
* * *
19110342 ATTTTTATCTAACAGTTAATAAAACTGAAATTAA
1 ATTTTTATCCAACAATTAACAAAACTGAAATTAA
19110376 ATTTTTATCCAACAATTAACAAAACTGAAATTAA
1 ATTTTTATCCAACAATTAACAAAACTGAAATTAA
19110410 A
1 A
19110411 GTGACAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.35
Consensus pattern (34 bp):
ATTTTTATCCAACAATTAACAAAACTGAAATTAA
Found at i:19113117 original size:14 final size:14
Alignment explanation
Indices: 19113098--19113129 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
19113088 GAGATCTAAT
19113098 AATTGATTAAAACA
1 AATTGATTAAAACA
19113112 AATTGATTAAAACA
1 AATTGATTAAAACA
19113126 AATT
1 AATT
19113130 AATAAGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.31
Consensus pattern (14 bp):
AATTGATTAAAACA
Found at i:19113462 original size:6 final size:6
Alignment explanation
Indices: 19113445--19113474 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
19113435 AATAAAATAT
*
19113445 TTCGAG TCCGAG TTCGAG TTCGAG TTCGAG
1 TTCGAG TTCGAG TTCGAG TTCGAG TTCGAG
19113475 CATAAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.20, G:0.33, T:0.30
Consensus pattern (6 bp):
TTCGAG
Found at i:19114905 original size:20 final size:20
Alignment explanation
Indices: 19114857--19114910 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
19114847 ATCGAGTTGG
* * * *
19114857 ATATAAAAAATAATATTTTA
1 ATATTAAAAATCATATATAA
19114877 ATATGTAAAAATCATATATAA
1 ATAT-TAAAAATCATATATAA
19114898 ATATTAAAGAATC
1 ATATTAAA-AATC
19114911 GAATTATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (20 bp):
ATATTAAAAATCATATATAA
Found at i:19116487 original size:14 final size:14
Alignment explanation
Indices: 19116468--19116494 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19116458 TTTTAAAACT
19116468 TTTTTAATTTTTTG
1 TTTTTAATTTTTTG
19116482 TTTTTAATTTTTT
1 TTTTTAATTTTTT
19116495 AATAAAAATA
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:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (14 bp):
TTTTTAATTTTTTG
Found at i:19116568 original size:26 final size:28
Alignment explanation
Indices: 19116533--19116585 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
19116523 AATAAATTGC
*
19116533 TCAATAAAAATAAATAAATAA-TAAAAG
1 TCAATAAAAATAAATAAAAAACTAAAAG
19116560 TCAAT-AAAATAAATAAAAAACTAAAA
1 TCAATAAAAATAAATAAAAAACTAAAA
19116586 TAAAATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.21
Consensus pattern (28 bp):
TCAATAAAAATAAATAAAAAACTAAAAG
Found at i:19116587 original size:22 final size:23
Alignment explanation
Indices: 19116539--19116591 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
19116529 TTGCTCAATA
*
19116539 AAAAT-AAATAAATAATAAAAGT
1 AAAATAAAATAAATAATAAAACT
*
19116561 -CAATAAAATAAATAA-AAAACT
1 AAAATAAAATAAATAATAAAACT
19116582 AAAATAAAAT
1 AAAATAAAAT
19116592 TAAAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21
Consensus pattern (23 bp):
AAAATAAAATAAATAATAAAACT
Found at i:19116607 original size:29 final size:26
Alignment explanation
Indices: 19116573--19116635 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 26
19116563 ATAAAATAAA
*
19116573 TAAAAAACTAAAATAAAATTAAAAAATT
1 TAAAAAAATAAAAT-AAA-TAAAAAATT
* *
19116601 TCAAAAATATAAAATAAATAAAAATTT
1 T-AAAAAAATAAAATAAATAAAAAATT
19116628 TAAAAAAA
1 TAAAAAAA
19116636 ACTTGTGATC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 6 0.20
27 9 0.30
28 4 0.13
29 11 0.37
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.25
Consensus pattern (26 bp):
TAAAAAAATAAAATAAATAAAAAATT
Found at i:19116622 original size:27 final size:29
Alignment explanation
Indices: 19116573--19116634 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
19116563 ATAAAATAAA
*
19116573 TAAAAAA-CTAAAATAAAATTAAAAAATT
1 TAAAAAATATAAAATAAAATTAAAAAATT
* *
19116601 TCAAAAATATAAAAT-AAA-TAAAAATTT
1 TAAAAAATATAAAATAAAATTAAAAAATT
19116628 TAAAAAA
1 TAAAAAA
19116635 AACTTGTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 14 0.48
28 9 0.31
29 6 0.21
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (29 bp):
TAAAAAATATAAAATAAAATTAAAAAATT
Found at i:19116697 original size:22 final size:22
Alignment explanation
Indices: 19116672--19116724 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
19116662 CGGGTGGCGC
19116672 GCGCGGATCCTAGTTGGGTTAT
1 GCGCGGATCCTAGTTGGGTTAT
*
19116694 GCGCGAATCCTAGTTGGGTTAT
1 GCGCGGATCCTAGTTGGGTTAT
*
19116716 GCACGGATC
1 GCGCGGATC
19116725 TAGGCTTGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.17, C:0.21, G:0.34, T:0.28
Consensus pattern (22 bp):
GCGCGGATCCTAGTTGGGTTAT
Found at i:19117450 original size:3 final size:3
Alignment explanation
Indices: 19117442--19117479 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
19117432 AAGGAAAGAA
19117442 AAT AAT AAT AAT AAT AAT ACA- AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AA
19117480 CATCATACAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.03
3 31 0.94
4 1 0.03
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:19117811 original size:63 final size:63
Alignment explanation
Indices: 19117738--19117892 Score: 276
Period size: 63 Copynumber: 2.5 Consensus size: 63
19117728 GCAAATCAAA
* *
19117738 AAAATGATCTGGACTGAGTTG-AGATCAAACATGTTATCGAAATTAAAGCATGAATTAAAATAT
1 AAAATGATCTGGACTGAG-AGAAGATCAAACATGTTATCGAAATTAAAGCATGAATTAAAAAAT
19117801 AAAATGATCTGGACTGAGAGAAGATCAAACATGTTATCGAAATTAAAGCATGAATTAAAAAAT
1 AAAATGATCTGGACTGAGAGAAGATCAAACATGTTATCGAAATTAAAGCATGAATTAAAAAAT
19117864 AAAATGATCTGGACTGAGAGAAGATCAAA
1 AAAATGATCTGGACTGAGAGAAGATCAAA
19117893 ATAGGTAACC
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
62 1 0.01
63 88 0.99
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.25
Consensus pattern (63 bp):
AAAATGATCTGGACTGAGAGAAGATCAAACATGTTATCGAAATTAAAGCATGAATTAAAAAAT
Found at i:19117922 original size:31 final size:31
Alignment explanation
Indices: 19117887--19117948 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
19117877 CTGAGAGAAG
* *
19117887 ATCAAAATAGGTAACCAAGACTGAATCGTAA
1 ATCAAAACAGGTAACCAAGACTAAATCGTAA
* **
19117918 ATCAAAACAGGTGACCGGGACTAAATCGTAA
1 ATCAAAACAGGTAACCAAGACTAAATCGTAA
19117949 GTTAGAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.18, G:0.19, T:0.18
Consensus pattern (31 bp):
ATCAAAACAGGTAACCAAGACTAAATCGTAA
Found at i:19118030 original size:55 final size:55
Alignment explanation
Indices: 19117955--19118168 Score: 257
Period size: 55 Copynumber: 3.9 Consensus size: 55
19117945 GTAAGTTAGA
* * * * * * *
19117955 AAAATGATTTGGACTAAGCCAAGATCAAGTGATCGGGATTGAACCACAAGTCAGG
1 AAAATAATCTGGACTAAGCCAAGATCAAATGATCGAGACTGAGCCACAAGTCAAG
* * * * * *
19118010 AAACTGATCTGGACTGAGCCAAGATGAAATGATCGAGACTGAGCCATAAGTCAAA
1 AAAATAATCTGGACTAAGCCAAGATCAAATGATCGAGACTGAGCCACAAGTCAAG
* *
19118065 AAAATAATCTGGACTAAACCAAGATCAAATAATCGAGACTGAGCCACAAGTCAAG
1 AAAATAATCTGGACTAAGCCAAGATCAAATGATCGAGACTGAGCCACAAGTCAAG
* * * *
19118120 AAAATAATATGGACTAAGCTAAGATCGAATGATCGAGATTGAGCCACAA
1 AAAATAATCTGGACTAAGCCAAGATCAAATGATCGAGACTGAGCCACAA
19118169 ATTCGAATGA
Statistics
Matches: 134, Mismatches: 25, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 134 1.00
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (55 bp):
AAAATAATCTGGACTAAGCCAAGATCAAATGATCGAGACTGAGCCACAAGTCAAG
Found at i:19118240 original size:82 final size:82
Alignment explanation
Indices: 19118096--19118249 Score: 200
Period size: 82 Copynumber: 1.9 Consensus size: 82
19118086 AGATCAAATA
* * *
19118096 ATCGAGACTGAGCCACAAGTCAAGAAAATAATATGGACTAAGCTAAGATCGAATGATCGAGATTG
1 ATCGAGACTGAGCCACAAGTCAAGAAAATAATATGGACTAAGCCAAGATCGAATCATCGAGATGG
*
19118161 AGCCACAAATTCGAATG
66 AACCACAAATTCGAATG
* * * * * * * *
19118178 ATCGAGATTGAGCCATAAGTTAAGAAAATGATATGGATTAAGCCAAGATTGGATCATTGAGATGG
1 ATCGAGACTGAGCCACAAGTCAAGAAAATAATATGGACTAAGCCAAGATCGAATCATCGAGATGG
19118243 AACCACA
66 AACCACA
19118250 CGTCTAAAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
82 60 1.00
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (82 bp):
ATCGAGACTGAGCCACAAGTCAAGAAAATAATATGGACTAAGCCAAGATCGAATCATCGAGATGG
AACCACAAATTCGAATG
Found at i:19118262 original size:55 final size:55
Alignment explanation
Indices: 19118194--19118374 Score: 177
Period size: 55 Copynumber: 3.3 Consensus size: 55
19118184 ATTGAGCCAT
* *
19118194 AAGT-TAAGAAAATGATATGGATTAAGCCAAGATTGGATCATTGAGATGGAACCAC
1 AAGTCTAA-AAAATGATATGGATTAAGCCAAGATTGGATAATTGAGATAGAACCAC
* * * * ** * * * *
19118249 ACGTCTAAAAAATGATCTAGACTAAGCCAAGATTGGATAACCGGGACAAAACCAT
1 AAGTCTAAAAAATGATATGGATTAAGCCAAGATTGGATAATTGAGATAGAACCAC
* * * * *
19118304 AAGTCTAAAAAATAATTTGGATTGAGCCAAGATTAGATGATT-AGAATAGAACCAC
1 AAGTCTAAAAAATGATATGGATTAAGCCAAGATTGGATAATTGAG-ATAGAACCAC
19118359 AAGTCTAAAAAATGAT
1 AAGTCTAAAAAATGAT
19118375 CTAGACTGAG
Statistics
Matches: 97, Mismatches: 27, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
54 1 0.01
55 93 0.96
56 3 0.03
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (55 bp):
AAGTCTAAAAAATGATATGGATTAAGCCAAGATTGGATAATTGAGATAGAACCAC
Found at i:19118325 original size:110 final size:110
Alignment explanation
Indices: 19118190--19118391 Score: 291
Period size: 110 Copynumber: 1.8 Consensus size: 110
19118180 CGAGATTGAG
* * * *
19118190 CCATAAGTTAAGAAAATGATATGGATTAAGCCAAGATTGGATCATT-GAGATGGAACCACACGTC
1 CCATAAGTTAAGAAAATAATATGGATTAAGCCAAGATTAGATCATTAGA-ATAGAACCACAAGTC
19118254 TAAAAAATGATCTAGACTAAGCCAAGATTGGATAACCGGGACAAAA
65 TAAAAAATGATCTAGACTAAGCCAAGATTGGATAACCGGGACAAAA
* * *
19118300 CCATAAGTCTAA-AAAATAATTTGGATTGAGCCAAGATTAGATGATTAGAATAGAACCACAAGTC
1 CCATAAGT-TAAGAAAATAATATGGATTAAGCCAAGATTAGATCATTAGAATAGAACCACAAGTC
* *
19118364 TAAAAAATGATCTAGACTGAGCTAAGAT
65 TAAAAAATGATCTAGACTAAGCCAAGAT
19118392 CGAATGACTA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
110 76 0.94
111 5 0.06
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (110 bp):
CCATAAGTTAAGAAAATAATATGGATTAAGCCAAGATTAGATCATTAGAATAGAACCACAAGTCT
AAAAAATGATCTAGACTAAGCCAAGATTGGATAACCGGGACAAAA
Found at i:19118411 original size:110 final size:109
Alignment explanation
Indices: 19118190--19118432 Score: 272
Period size: 110 Copynumber: 2.2 Consensus size: 109
19118180 CGAGATTGAG
* * * *
19118190 CCATAAGTTAAGAAAATGATATGGATTAAGCCAAGATTGGATCATTGAGATGGAACCACACGTCT
1 CCATAAGTTAA-AAAATGATTTGGATTAAGCCAAGATTAGATCATTGAGATAGAACCACAAGTCT
* * **
19118255 AAAAAATGATCTAGACTAAGCCAAGATTGGATAACCGGGACAAAA
65 AAAAAATGATCTAGACTAAGCCAAGATCGAATAACCAAGACAAAA
* * *
19118300 CCATAAGTCTAAAAAATAATTTGGATTGAGCCAAGATTAGATGATT-AGAATAGAACCACAAGTC
1 CCATAAGT-TAAAAAATGATTTGGATTAAGCCAAGATTAGATCATTGAG-ATAGAACCACAAGTC
* * * * **
19118364 TAAAAAATGATCTAGACTGAGCTAAGATCGAATGACTAAGATGAAA
64 TAAAAAATGATCTAGACTAAGCCAAGATCGAATAACCAAGACAAAA
* *
19118410 CCACAAGTTTGAAAAATGATTTG
1 CCATAAG-TTAAAAAATGATTTG
19118433 AACTAAGTTG
Statistics
Matches: 110, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
109 2 0.02
110 104 0.95
111 4 0.04
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (109 bp):
CCATAAGTTAAAAAATGATTTGGATTAAGCCAAGATTAGATCATTGAGATAGAACCACAAGTCTA
AAAAATGATCTAGACTAAGCCAAGATCGAATAACCAAGACAAAA
Found at i:19118412 original size:55 final size:54
Alignment explanation
Indices: 19118237--19118429 Score: 147
Period size: 55 Copynumber: 3.5 Consensus size: 54
19118227 TGGATCATTG
* * * * * **
19118237 AGATGGAACCACACGTCTAAAAAATGATCTAGACTAAGCCAAGATTGGATAACCG
1 AGATGAAACCACAAGTCTAAAAAATGATCTAGACTGAGCCAAGA-TGAATGACTA
* ** * * * * * * *
19118292 GGACAAAACCATAAGTCTAAAAAATAATTTGGATTGAGCCAAGATTAGATGA-TT
1 AGATGAAACCACAAGTCTAAAAAATGATCTAGACTGAGCCAAGATGA-ATGACTA
*
19118346 AGAAT-AGAACCACAAGTCTAAAAAATGATCTAGACTGAGCTAAGATCGAATGACTA
1 AG-ATGA-AACCACAAGTCTAAAAAATGATCTAGACTGAGCCAAGAT-GAATGACTA
* *
19118402 AGATGAAACCACAAGTTTGAAAAATGAT
1 AGATGAAACCACAAGTCTAAAAAATGAT
19118430 TTGAACTAAG
Statistics
Matches: 104, Mismatches: 28, Indels: 12
0.72 0.19 0.08
Matches are distributed among these distances:
54 3 0.03
55 96 0.92
56 5 0.05
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.21
Consensus pattern (54 bp):
AGATGAAACCACAAGTCTAAAAAATGATCTAGACTGAGCCAAGATGAATGACTA
Found at i:19124115 original size:19 final size:19
Alignment explanation
Indices: 19124063--19124108 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
19124053 AAAAAATTTT
*
19124063 AAAATATAA--AATAAATA
1 AAAATATAATCAAAAAATA
19124080 AAAATATAATCAAAAAATA
1 AAAATATAATCAAAAAATA
19124099 AAAATATAAT
1 AAAATATAAT
19124109 GGAAAAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 9 0.35
19 17 0.65
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATATAATCAAAAAATA
Found at i:19124120 original size:19 final size:19
Alignment explanation
Indices: 19124079--19124120 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
19124069 TAAAATAAAT
*
19124079 AAAAATATAATCAAAAAAT
1 AAAAATATAATCAAAAAAG
**
19124098 AAAAATATAATGGAAAAAG
1 AAAAATATAATCAAAAAAG
19124117 AAAA
1 AAAA
19124121 TCTATGATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (19 bp):
AAAAATATAATCAAAAAAG
Found at i:19124408 original size:13 final size:13
Alignment explanation
Indices: 19124390--19124415 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19124380 CCAAACTTCG
19124390 TCAAAAAATTTAA
1 TCAAAAAATTTAA
19124403 TCAAAAAATTTAA
1 TCAAAAAATTTAA
19124416 ATATTCATCC
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:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TCAAAAAATTTAA
Found at i:19124905 original size:3 final size:3
Alignment explanation
Indices: 19124899--19124945 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
19124889 AATAGAAGAA
*
19124899 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19124946 CATACAAACT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:19135240 original size:16 final size:16
Alignment explanation
Indices: 19135219--19135262 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
19135209 TATAAAAAAT
19135219 TATTTATTTAATTATA
1 TATTTATTTAATTATA
* *
19135235 TATTTATTTAATTTTT
1 TATTTATTTAATTATA
19135251 TATTTATATTAA
1 TATTTAT-TTAA
19135263 AAATAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTTATTTAATTATA
Found at i:19138015 original size:5 final size:5
Alignment explanation
Indices: 19138005--19138038 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
19137995 CATTGCAGAT
*
19138005 TAAAA TAAAA T-AAA TAAAA TAAAA TAAAA GAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
19138039 AAGGGAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
TAAAA
Found at i:19138024 original size:14 final size:14
Alignment explanation
Indices: 19138005--19138032 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19137995 CATTGCAGAT
19138005 TAAAATAAAATAAA
1 TAAAATAAAATAAA
19138019 TAAAATAAAATAAA
1 TAAAATAAAATAAA
19138033 AGAAAAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAAATAAAATAAA
Found at i:19141274 original size:14 final size:15
Alignment explanation
Indices: 19141239--19141275 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
19141229 TATATAAAAA
19141239 TATATATTTTTAGTT
1 TATATATTTTTAGTT
*
19141254 T-TTTATTTTTA-TT
1 TATATATTTTTAGTT
19141267 TATATATTT
1 TATATATTT
19141276 ATGTAACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
13 3 0.16
14 15 0.79
15 1 0.05
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (15 bp):
TATATATTTTTAGTT
Found at i:19145276 original size:46 final size:45
Alignment explanation
Indices: 19145204--19145295 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 45
19145194 AAAAAAATTG
**
19145204 AAAATTGAAAATATTAAAAATTTTAAAAATAACAAAATTTTAATAA
1 AAAATTGAAAATATTAAAAAAATTAAAAA-AACAAAATTTTAATAA
**
19145250 AAAATTGAAAA-ATTATAAAAAATTAAAAAATGAAAATTTTAATAA
1 AAAATTGAAAATATTA-AAAAAATTAAAAAAACAAAATTTTAATAA
19145295 A
1 A
19145296 TATAAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
45 19 0.46
46 22 0.54
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (45 bp):
AAAATTGAAAATATTAAAAAAATTAAAAAAACAAAATTTTAATAA
Found at i:19145279 original size:18 final size:18
Alignment explanation
Indices: 19145168--19145280 Score: 69
Period size: 18 Copynumber: 6.3 Consensus size: 18
19145158 AATTTTTTTT
*
19145168 AAAAA-TATAAAATATTTA
1 AAAAATTATAAAA-AATTA
19145186 AAAAAGTTA-AAAAAATT-
1 AAAAA-TTATAAAAAATTA
* * *
19145203 GAAAATT-GAAAATATT-
1 AAAAATTATAAAAAATTA
*
19145219 AAAAATT-TTAAAAA-TA
1 AAAAATTATAAAAAATTA
*
19145235 ACAAAATTTTAATAAAAAATTG
1 A-AAAA--TT-ATAAAAAATTA
19145257 AAAAATTATAAAAAATTA
1 AAAAATTATAAAAAATTA
19145275 AAAAAT
1 AAAAAT
19145281 GAAAATTTTA
Statistics
Matches: 75, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
15 1 0.01
16 20 0.27
17 8 0.11
18 24 0.32
19 8 0.11
20 2 0.03
21 10 0.13
22 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (18 bp):
AAAAATTATAAAAAATTA
Found at i:19145289 original size:62 final size:63
Alignment explanation
Indices: 19145220--19145359 Score: 155
Period size: 62 Copynumber: 2.2 Consensus size: 63
19145210 GAAAATATTA
*
19145220 AAAATTTTAAAAATAACAAAATTTTAATAAAAAATT-GAAAAATT-ATAA-AAAA-TTAAAAAAT
1 AAAATTTTAAAAATAACAAAATTTT-AT-AAAAATTCAAAAAATTCA-AAGAAAATTTAAAAAAT
19145281 G
63 G
* * *
19145282 AAAATTTTAATAAAT-ATAAAATTTTCTTAAAATTCAAAAAATTCAAAGAAAATTTAAAAAATG
1 AAAATTTTAA-AAATAACAAAATTTTATAAAAATTCAAAAAATTCAAAGAAAATTTAAAAAATG
**
19145345 AAAATAATAAAAATA
1 AAAATTTTAAAAATA
19145360 TAAATTTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
60 6 0.09
61 10 0.15
62 28 0.42
63 22 0.33
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (63 bp):
AAAATTTTAAAAATAACAAAATTTTATAAAAATTCAAAAAATTCAAAGAAAATTTAAAAAATG
Found at i:19145389 original size:20 final size:19
Alignment explanation
Indices: 19145353--19145394 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
19145343 TGAAAATAAT
**
19145353 AAAAATATAAATTTTTTCAA
1 AAAAATATAAAAGTTTT-AA
19145373 AAAAATATAAAAGTTTTAA
1 AAAAATATAAAAGTTTTAA
19145392 AAA
1 AAA
19145395 TTTATAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAAATATAAAAGTTTTAA
Found at i:19145640 original size:16 final size:17
Alignment explanation
Indices: 19145608--19145645 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
19145598 TATAAGAAAA
*
19145608 TTTTATTTTTATTAATT
1 TTTTATTTTTATGAATT
19145625 TTTTATTTTT-TGAATT
1 TTTTATTTTTATGAATT
*
19145641 ATTTA
1 TTTTA
19145646 AAAAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTATTTTTATGAATT
Found at i:19145676 original size:20 final size:20
Alignment explanation
Indices: 19145632--19145684 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
19145622 ATTTTTTATT
19145632 TTTTGAATTATTTAAAAAAA
1 TTTTGAATTATTTAAAAAAA
* ** *
19145652 ATTTGAATTATTTATTAAAG
1 TTTTGAATTATTTAAAAAAA
*
19145672 TTTTGAAATATTT
1 TTTTGAATTATTT
19145685 TTGAATTTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
TTTTGAATTATTTAAAAAAA
Found at i:19145710 original size:17 final size:17
Alignment explanation
Indices: 19145681--19145739 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
19145671 GTTTTGAAAT
19145681 ATTTTTGAA-TTTTAATA
1 ATTTTT-AATTTTTAATA
*
19145698 ATTTTTAATTTTTAAAA
1 ATTTTTAATTTTTAATA
19145715 ATATTTTATATATTTT--TA
1 AT-TTTTA-AT-TTTTAATA
19145733 ATTTTTA
1 ATTTTTA
19145740 TAATTTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
16 2 0.06
17 20 0.56
18 8 0.22
19 2 0.06
20 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
ATTTTTAATTTTTAATA
Found at i:19145720 original size:28 final size:28
Alignment explanation
Indices: 19145689--19145776 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 28
19145679 ATATTTTTGA
19145689 ATTTTAATAATTTTTAATTTTTAAAAAT
1 ATTTTAATAATTTTTAATTTTTAAAAAT
*
19145717 ATTTT-ATATATTTTTAATTTTT-ATAAT
1 ATTTTAATA-ATTTTTAATTTTTAAAAAT
* *
19145744 TTTTTAA-AATATTATAAGTTTTTAAAAA-
1 ATTTTAATAAT-TTTTAA-TTTTTAAAAAT
19145772 ATTTT
1 ATTTT
19145777 TATTAATGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
26 2 0.04
27 17 0.34
28 28 0.56
29 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (28 bp):
ATTTTAATAATTTTTAATTTTTAAAAAT
Found at i:19145721 original size:18 final size:18
Alignment explanation
Indices: 19145677--19145776 Score: 66
Period size: 19 Copynumber: 5.5 Consensus size: 18
19145667 TAAAGTTTTG
19145677 AAATATTTTTGAA-TTTTAA
1 AAATA-TTTT-AATTTTTAA
*
19145696 TAAT-TTTTAATTTTTAA
1 AAATATTTTAATTTTTAA
19145713 AAATATTTTATATATTTT--
1 AAATATTTTA-AT-TTTTAA
* * *
19145731 TAATTTTTATAATTTTTTA
1 AAATATTT-TAATTTTTAA
*
19145750 AAATATTATAAGTTTTTAA
1 AAATATTTTAA-TTTTTAA
19145769 AAA-ATTTT
1 AAATATTTT
19145777 TATTAATGTT
Statistics
Matches: 64, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
16 2 0.03
17 17 0.27
18 20 0.31
19 21 0.33
20 4 0.06
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
AAATATTTTAATTTTTAA
Found at i:19145759 original size:35 final size:36
Alignment explanation
Indices: 19145690--19145768 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 36
19145680 TATTTTTGAA
19145690 TTTTAATAATTTTTAATTTTTAAAAATATTTTATATA-T
1 TTTTAAT-ATTTTTAATTTTTAAAAATA-TTTATA-AGT
*
19145728 TTTTAAT-TTTTATAATTTTTTAAAATA-TTATAAGT
1 TTTTAATATTTT-TAATTTTTAAAAATATTTATAAGT
19145763 TTTTAA
1 TTTTAA
19145769 AAAATTTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
34 1 0.03
35 12 0.32
36 4 0.11
37 14 0.37
38 7 0.18
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (36 bp):
TTTTAATATTTTTAATTTTTAAAAATATTTATAAGT
Found at i:19148195 original size:71 final size:71
Alignment explanation
Indices: 19148023--19148174 Score: 304
Period size: 71 Copynumber: 2.1 Consensus size: 71
19148013 CCTAGGAGAG
19148023 AAAGGAAAGGAAAGAAAATGAGGAAACCTTTCCTTACTTTTCCTTTGTCTGGATTTCACATAAAT
1 AAAGGAAAGGAAAGAAAATGAGGAAACCTTTCCTTACTTTTCCTTTGTCTGGATTTCACATAAAT
19148088 ATAAAT
66 ATAAAT
19148094 AAAGGAAAGGAAAGAAAATGAGGAAACCTTTCCTTACTTTTCCTTTGTCTGGATTTCACATAAAT
1 AAAGGAAAGGAAAGAAAATGAGGAAACCTTTCCTTACTTTTCCTTTGTCTGGATTTCACATAAAT
19148159 ATAAAT
66 ATAAAT
19148165 AAAGGAAAGG
1 AAAGGAAAGG
19148175 GAGGGGTGCT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 81 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (71 bp):
AAAGGAAAGGAAAGAAAATGAGGAAACCTTTCCTTACTTTTCCTTTGTCTGGATTTCACATAAAT
ATAAAT
Found at i:19154260 original size:23 final size:25
Alignment explanation
Indices: 19154207--19154260 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
19154197 CAATACAAAA
19154207 AATATTTATTAAAAAAATAAAATTT
1 AATATTTATTAAAAAAATAAAATTT
*
19154232 AA-ATTTA-TAAAAAAAT-ATATTT
1 AATATTTATTAAAAAAATAAAATTT
19154254 AATATTT
1 AATATTT
19154261 TATCTTTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 7 0.26
23 13 0.48
24 5 0.19
25 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AATATTTATTAAAAAAATAAAATTT
Found at i:19158171 original size:36 final size:36
Alignment explanation
Indices: 19158111--19158198 Score: 115
Period size: 36 Copynumber: 2.4 Consensus size: 36
19158101 CAACATTGAT
* *
19158111 TGGATTTGGAGCT-GAAGTTGAAACTAGAATAAAAAC
1 TGGATTTGAAGCTAG-AGTTAAAACTAGAATAAAAAC
* *
19158147 TGGATTTGAAGCTAGAGTTAAAACTAGAATGAAAAT
1 TGGATTTGAAGCTAGAGTTAAAACTAGAATAAAAAC
*
19158183 TGGATTTGAAACTAGA
1 TGGATTTGAAGCTAGA
19158199 TTTCTTGAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 45 0.98
37 1 0.02
ACGTcount: A:0.42, C:0.07, G:0.24, T:0.27
Consensus pattern (36 bp):
TGGATTTGAAGCTAGAGTTAAAACTAGAATAAAAAC
Found at i:19160745 original size:41 final size:41
Alignment explanation
Indices: 19160638--19160745 Score: 110
Period size: 41 Copynumber: 2.6 Consensus size: 41
19160628 TTTCTATCCC
* * * *
19160638 TTCATTCTTTACTACCTCACCTACATGTTGATTTTTTACCCT
1 TTCATTC-TTACTACATTAACTACATGTTAATTTTTTACCCT
* * **
19160680 TTCATCCTTA-TCAAATTAGTTACATGTTAATTTTTTACCCT
1 TTCATTCTTACT-ACATTAACTACATGTTAATTTTTTACCCT
*
19160721 TTCATTCTTACTACTTTAACTACAT
1 TTCATTCTTACTACATTAACTACAT
19160746 CTTTTATTTC
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
40 1 0.02
41 44 0.85
42 7 0.13
ACGTcount: A:0.24, C:0.24, G:0.04, T:0.48
Consensus pattern (41 bp):
TTCATTCTTACTACATTAACTACATGTTAATTTTTTACCCT
Found at i:19161670 original size:18 final size:18
Alignment explanation
Indices: 19161647--19161704 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
19161637 ATAAAATTTA
19161647 TGTTATAAGCTTTTACTT
1 TGTTATAAGCTTTTACTT
**
19161665 TGTTATAA--AATT--TT
1 TGTTATAAGCTTTTACTT
*
19161679 TGTTATAAGCTTTTACAT
1 TGTTATAAGCTTTTACTT
19161697 TGTTATAA
1 TGTTATAA
19161705 CCAATGGTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
14 10 0.32
16 4 0.13
18 17 0.55
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.53
Consensus pattern (18 bp):
TGTTATAAGCTTTTACTT
Found at i:19161676 original size:32 final size:32
Alignment explanation
Indices: 19161627--19161704 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
19161617 TGCATGTCCC
*
19161627 TTACATTATTATAAAATTTATGTTATAAGCTT
1 TTACATTGTTATAAAATTTATGTTATAAGCTT
* *
19161659 TTACTTTGTTATAAAATTTTTGTTATAAGCTT
1 TTACATTGTTATAAAATTTATGTTATAAGCTT
19161691 TTACATTGTTATAA
1 TTACATTGTTATAA
19161705 CCAATGGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (32 bp):
TTACATTGTTATAAAATTTATGTTATAAGCTT
Found at i:19162565 original size:12 final size:12
Alignment explanation
Indices: 19162548--19162572 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19162538 AAAATGCATA
19162548 CATATTATTCAC
1 CATATTATTCAC
19162560 CATATTATTCAC
1 CATATTATTCAC
19162572 C
1 C
19162573 TTACACAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (12 bp):
CATATTATTCAC
Found at i:19163221 original size:13 final size:13
Alignment explanation
Indices: 19163195--19163228 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
19163185 ACTCTTGCTT
19163195 TTTCATTTGGTTCC
1 TTTC-TTTGGTTCC
*
19163209 TTTCTTTGTTTCC
1 TTTCTTTGGTTCC
19163222 TTTCTTT
1 TTTCTTT
19163229 TCATTTTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.03, C:0.21, G:0.09, T:0.68
Consensus pattern (13 bp):
TTTCTTTGGTTCC
Found at i:19172697 original size:19 final size:19
Alignment explanation
Indices: 19172673--19172710 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19172663 CACATTTACC
19172673 CAAAAAGAACTATACCATA
1 CAAAAAGAACTATACCATA
*
19172692 CAAAAATAACTATACCATA
1 CAAAAAGAACTATACCATA
19172711 TAAACTTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.58, C:0.21, G:0.03, T:0.18
Consensus pattern (19 bp):
CAAAAAGAACTATACCATA
Found at i:19174075 original size:14 final size:14
Alignment explanation
Indices: 19174034--19174105 Score: 56
Period size: 14 Copynumber: 4.9 Consensus size: 14
19174024 TCACTCAATA
19174034 AAAATAAATAACTAAT
1 AAAATAAATAA--AAT
* *
19174050 AAAATCAGTAAAAT
1 AAAATAAATAAAAT
*
19174064 GAAATAAATAAAAT
1 AAAATAAATAAAAT
*
19174078 CAAAATATAA-AATAT
1 -AAAATA-AATAAAAT
*
19174093 AAAATTAATAAAA
1 AAAATAAATAAAA
19174106 AATAAAATCA
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
13 2 0.05
14 22 0.50
15 9 0.20
16 11 0.25
ACGTcount: A:0.69, C:0.04, G:0.03, T:0.24
Consensus pattern (14 bp):
AAAATAAATAAAAT
Found at i:19174090 original size:18 final size:18
Alignment explanation
Indices: 19174059--19174118 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 18
19174049 TAAAATCAGT
19174059 AAAATGAAATAAATAAAATC
1 AAAAT-AAA-AAATAAAATC
19174079 AAAATATAAAATATAAAAT-
1 AAAATA-AAAA-ATAAAATC
*
19174098 -TAATAAAAAATAAAATC
1 AAAATAAAAAATAAAATC
19174115 AAAA
1 AAAA
19174119 AATGAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
16 7 0.21
17 4 0.12
18 6 0.18
19 3 0.09
20 14 0.41
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.22
Consensus pattern (18 bp):
AAAATAAAAAATAAAATC
Found at i:19174881 original size:3 final size:3
Alignment explanation
Indices: 19174875--19175163 Score: 71
Period size: 3 Copynumber: 95.7 Consensus size: 3
19174865 AGAAGAACAA
* * *
19174875 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGA- AGT AGT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
* * * * * * * *
19174920 AGT AGT AGT AGT AGT AGT AAT AGT AAT -AT GAT ATAT AGGAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT A--AT AAT AAT
* * * *
19174967 AAT GAT AA- ATAT AAT AAT AAA AAT -AT AAT AAT AAT AAC AAT ACT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * *
19175011 AGT AGGCT -AC AAT AAT AAT AAT ATAC AAT -AT AAT ATAT TAT ACT ATAC
1 AAT A--AT AAT AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT AAT A-AT
* * * * *
19175059 AAT -AT AAT -AT AAT AAT ACT ACT AGT AAT AAT AAC ACCAT ACT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A--AT AAT AAT
* * * * *
19175103 CAT AAT -AT TAT ACT -AT ATT ACT -AT AAT AAT AAT AAT AAT AAT ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
*
19175149 AAT AAC ATAT AAT AA
1 AAT AAT A-AT AAT AA
19175164 CAAAGAAAAT
Statistics
Matches: 218, Mismatches: 43, Indels: 50
0.70 0.14 0.16
Matches are distributed among these distances:
2 16 0.07
3 181 0.83
4 15 0.07
5 6 0.03
ACGTcount: A:0.55, C:0.06, G:0.07, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19174992 original size:14 final size:14
Alignment explanation
Indices: 19174962--19175000 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
19174952 ATATAGGATA
*
19174962 ATAATAATGATAAAT
1 ATAATAAT-AAAAAT
19174977 ATAATAATAAAAAT
1 ATAATAATAAAAAT
19174991 ATAATAATAA
1 ATAATAATAA
19175001 TAACAATACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
ATAATAATAAAAAT
Found at i:19175057 original size:22 final size:23
Alignment explanation
Indices: 19175022--19175078 Score: 89
Period size: 22 Copynumber: 2.5 Consensus size: 23
19175012 GTAGGCTACA
*
19175022 ATAATAATAATATACAATATAAT
1 ATAATAATACTATACAATATAAT
*
19175045 AT-ATTATACTATACAATATAAT
1 ATAATAATACTATACAATATAAT
19175067 ATAATAATACTA
1 ATAATAATACTA
19175079 CTAGTAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 20 0.67
23 10 0.33
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (23 bp):
ATAATAATACTATACAATATAAT
Found at i:19175062 original size:17 final size:17
Alignment explanation
Indices: 19175028--19175069 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
19175018 TACAATAATA
*
19175028 ATAATATACAATATAAT
1 ATAATATACAATACAAT
* *
19175045 ATATTATACTATACAAT
1 ATAATATACAATACAAT
19175062 ATAATATA
1 ATAATATA
19175070 ATAATACTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATATACAATACAAT
Found at i:19175152 original size:10 final size:10
Alignment explanation
Indices: 19175128--19175163 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
19175118 TATTACTATA
19175128 ATAATAATA-
1 ATAATAATAT
19175137 ATAATAATAT
1 ATAATAATAT
*
19175147 ATAATAACAT
1 ATAATAATAT
19175157 ATAATAA
1 ATAATAA
19175164 CAAAGAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (10 bp):
ATAATAATAT
Found at i:19175539 original size:110 final size:110
Alignment explanation
Indices: 19175334--19175600 Score: 259
Period size: 110 Copynumber: 2.4 Consensus size: 110
19175324 CGAGTCCAGA
** ** *
19175334 AAAAAATGATCTAGACAGAGCCAAAATGGAGCGACCGAGATTGAACCTTAGGTCTGGATAACTAA
1 AAAAAATGATCTAGACAGAGCCAAAATCAAGCGACCGAGATTGAACCACAGGTCTGGAGAACTAA
* * * * *
19175399 CTTGGATCCAGTCGAGGTCAAATGATCAAGATTGAATGTGGGTTT
66 CCTAGATCCAGTCAAGGTCAAACGACCAAGATTGAATGTGGGTTT
* ** *
19175444 AAAAAATGATCTAGACAGAGCCAAAATCAAGTGATTG-GAATTGAATCACAGGTCTGGAGAACTA
1 AAAAAATGATCTAGACAGAGCCAAAATCAAGCGACCGAG-ATTGAACCACAGGTCTGGAGAACTA
* ** *
19175508 ACCTAGA-CCGAGTCAAGGTTAAACGACCAAGATTGAATTGTTAGTCT
65 ACCTAGATCC-AGTCAAGGTCAAACGACCAAGATTGAA-TGTGGGTTT
** * * * * * *
19175555 GTAAAATGATTTGGACGGAGCCGAAATCAAGTGACCGTGATTGAAC
1 AAAAAATGATCTAGACAGAGCCAAAATCAAGCGACCGAGATTGAAC
19175601 TGTAGGTTTG
Statistics
Matches: 126, Mismatches: 27, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
109 3 0.02
110 81 0.64
111 41 0.33
112 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (110 bp):
AAAAAATGATCTAGACAGAGCCAAAATCAAGCGACCGAGATTGAACCACAGGTCTGGAGAACTAA
CCTAGATCCAGTCAAGGTCAAACGACCAAGATTGAATGTGGGTTT
Found at i:19175598 original size:111 final size:111
Alignment explanation
Indices: 19175336--19175652 Score: 259
Period size: 111 Copynumber: 2.9 Consensus size: 111
19175326 AGTCCAGAAA
** * * *
19175336 AAAATGATCTAGACAGAGCCAAAATGGAGCGACC-GAGATTGAACCT-TAGGTCTGGATAACTAA
1 AAAATGATCTAGACAGAGCCAAAATCAAGTGACCGGA-ATTGAA-CTACAGGTCTGGAGAACTAA
* * * * * * ** * **
19175399 CTTGGATCC-AGTCGAGGTCAAATGATCAAGATTGAA-TGTGGGTTTAA
64 CCTAGA-CCGAGTCAAGGTTAAACGACCAAGATTGAATTGTTAGTCTGT
**
19175446 AAAATGATCTAGACAGAGCCAAAATCAAGTGATTGGAATTGAA-TCACAGGTCTGGAGAACTAAC
1 AAAATGATCTAGACAGAGCCAAAATCAAGTGACCGGAATTGAACT-ACAGGTCTGGAGAACTAAC
19175510 CTAGACCGAGTCAAGGTTAAACGACCAAGATTGAATTGTTAGTCTGT
65 CTAGACCGAGTCAAGGTTAAACGACCAAGATTGAATTGTTAGTCTGT
* * * * ** * * *
19175557 AAAATGATTTGGACGGAGCCGAAATCAAGTGACCGTG-ATTGAACTGTAGGTTTGGAGAATTGAC
1 AAAATGATCTAGACAGAGCCAAAATCAAGTGACCG-GAATTGAACTACAGGTCTGGAGAACTAAC
* * ** *
19175621 CTGGAGCGAGTTGAGGTTAAATGACCAAGATT
65 CTAGACCGAGTCAAGGTTAAACGACCAAGATT
19175653 AAAATACAAG
Statistics
Matches: 166, Mismatches: 34, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
108 1 0.01
109 2 0.01
110 77 0.46
111 84 0.51
112 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (111 bp):
AAAATGATCTAGACAGAGCCAAAATCAAGTGACCGGAATTGAACTACAGGTCTGGAGAACTAACC
TAGACCGAGTCAAGGTTAAACGACCAAGATTGAATTGTTAGTCTGT
Found at i:19188758 original size:11 final size:11
Alignment explanation
Indices: 19188744--19188780 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
19188734 ATTTTTATTA
19188744 AATTTATATAT
1 AATTTATATAT
19188755 AATTTATCA-A-
1 AATTTAT-ATAT
19188765 AATTTATATAT
1 AATTTATATAT
19188776 AATTT
1 AATTT
19188781 TTCAAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 1 0.04
10 8 0.35
11 13 0.57
12 1 0.04
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
AATTTATATAT
Found at i:19188769 original size:21 final size:21
Alignment explanation
Indices: 19188743--19188798 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
19188733 TATTTTTATT
19188743 AAATTTATATATAATTTATCA
1 AAATTTATATATAATTTATCA
*
19188764 AAATTTATATATAATTTTTCA
1 AAATTTATATATAATTTATCA
*
19188785 AAATTT-TAAATAAT
1 AAATTTATATATAAT
19188799 ATCTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
20 7 0.21
21 26 0.79
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
AAATTTATATATAATTTATCA
Found at i:19190216 original size:32 final size:33
Alignment explanation
Indices: 19190170--19190251 Score: 112
Period size: 32 Copynumber: 2.5 Consensus size: 33
19190160 AAGCTTAGGT
* **
19190170 AAGCCCATTTGTTTTATTTTTTATAATA-GATA
1 AAGCTCATTTGTTTTATTACTTATAATATGATA
19190202 AAGCTCATTTGTTTTATTACTTATAATATGATA
1 AAGCTCATTTGTTTTATTACTTATAATATGATA
* *
19190235 AAACTCATTTTTTTTAT
1 AAGCTCATTTGTTTTAT
19190252 AAACAAAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 25 0.57
33 19 0.43
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.51
Consensus pattern (33 bp):
AAGCTCATTTGTTTTATTACTTATAATATGATA
Found at i:19193598 original size:22 final size:21
Alignment explanation
Indices: 19193573--19193616 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
19193563 GGCTAAAATT
19193573 TATAAAGGTAAATCATAAAAAA
1 TATAAAGGTAAAT-ATAAAAAA
* * *
19193595 TATAGATGTAAGTATAAAAAA
1 TATAAAGGTAAATATAAAAAA
19193616 T
1 T
19193617 GATATAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.27
Consensus pattern (21 bp):
TATAAAGGTAAATATAAAAAA
Found at i:19194886 original size:23 final size:22
Alignment explanation
Indices: 19194844--19194887 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
19194834 TTGGCATGAA
19194844 TTTAGAGATAGAATTGATTTTGT
1 TTTAGAGA-AGAATTGATTTTGT
19194867 TTTAGAG-AGAATATGAATTTT
1 TTTAGAGAAGAAT-TG-ATTTT
19194888 TAGAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.26
22 2 0.11
23 12 0.63
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.45
Consensus pattern (22 bp):
TTTAGAGAAGAATTGATTTTGT
Found at i:19194890 original size:19 final size:21
Alignment explanation
Indices: 19194866--19194907 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
19194856 ATTGATTTTG
*
19194866 TTTTAGAG-AGAA-TATGAAT
1 TTTTAGAGAAAAAGTATGAAT
19194885 TTTTAGAGAAAAAGTATGAAT
1 TTTTAGAGAAAAAGTATGAAT
19194906 TT
1 TT
19194908 AGATGAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 3 0.15
21 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (21 bp):
TTTTAGAGAAAAAGTATGAAT
Found at i:19195433 original size:2 final size:2
Alignment explanation
Indices: 19195426--19195456 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19195416 CATTGTTTTA
*
19195426 AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
19195457 TTCTTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19200109 original size:15 final size:16
Alignment explanation
Indices: 19200076--19200110 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
19200066 TCTTTGCATC
*
19200076 TTTCTAGCAATGTTTG
1 TTTCTAGCAATGCTTG
19200092 TTTCTAGCAAT-CTTG
1 TTTCTAGCAATGCTTG
19200107 TTTC
1 TTTC
19200111 CTTTCTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.51
Consensus pattern (16 bp):
TTTCTAGCAATGCTTG
Found at i:19204511 original size:22 final size:22
Alignment explanation
Indices: 19204483--19204535 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
19204473 TTTTAATTTT
19204483 TTTTTAAAATCA-ATATCTTAAA-
1 TTTTTAAAATCAGAT-T-TTAAAC
*
19204505 TTTTTAAAATTAGATTTTAAAC
1 TTTTTAAAATCAGATTTTAAAC
19204527 TTTTTAAAA
1 TTTTTAAAA
19204536 AATTCAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.18
22 21 0.75
23 2 0.07
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTTTAAAATCAGATTTTAAAC
Found at i:19205611 original size:20 final size:21
Alignment explanation
Indices: 19205586--19205635 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
19205576 GTAACAATCA
19205586 ATCCCTTTTTC-AGGTGATCG
1 ATCCCTTTTTCTAGGTGATCG
** *
19205606 ATCCCTTAGTCTGGGTGATCG
1 ATCCCTTTTTCTAGGTGATCG
19205627 ATCCCTTTT
1 ATCCCTTTT
19205636 CATGTTTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (21 bp):
ATCCCTTTTTCTAGGTGATCG
Found at i:19207460 original size:21 final size:20
Alignment explanation
Indices: 19207413--19207461 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
19207403 CTTGAATAAT
19207413 CAAGAAAAAAAAGAAAGAAA
1 CAAGAAAAAAAAGAAAGAAA
*
19207433 TAGAGAAAAAAAAGAAAGAAA
1 CA-AGAAAAAAAAGAAAGAAA
19207454 GCAAGAAA
1 -CAAGAAA
19207462 CATAAAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 23 0.92
22 1 0.04
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (20 bp):
CAAGAAAAAAAAGAAAGAAA
Found at i:19208232 original size:24 final size:24
Alignment explanation
Indices: 19208205--19208259 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
19208195 TTAAACAAAT
19208205 TTTTGGTTTTTGATTTAATTTTAA
1 TTTTGGTTTTTGATTTAATTTTAA
** **
19208229 TTTTAATTTTTGATTTAATTTTGT
1 TTTTGGTTTTTGATTTAATTTTAA
19208253 TTTTGGT
1 TTTTGGT
19208260 CAAAAGACAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.69
Consensus pattern (24 bp):
TTTTGGTTTTTGATTTAATTTTAA
Found at i:19208245 original size:12 final size:12
Alignment explanation
Indices: 19208211--19208250 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
19208201 AAATTTTTGG
19208211 TTTTTGATTTAA
1 TTTTTGATTTAA
*
19208223 -TTTTAATTTTAA
1 TTTTTGA-TTTAA
19208235 TTTTTGATTTAA
1 TTTTTGATTTAA
19208247 TTTT
1 TTTT
19208251 GTTTTTGGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 5 0.21
12 14 0.58
13 5 0.21
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (12 bp):
TTTTTGATTTAA
Found at i:19212383 original size:21 final size:22
Alignment explanation
Indices: 19212346--19212401 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
19212336 TTTGGTATTC
*
19212346 TTTAATTTTTTTAATTT-TAAT
1 TTTAATTTATTTAATTTATAAT
*
19212367 TTTAATTTAATTT-ATTTATTAT
1 TTTAATTT-ATTTAATTTATAAT
19212389 TTT-ATTT-TTTAAT
1 TTTAATTTATTTAAT
19212402 GATTTTCCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 3 0.10
20 2 0.07
21 16 0.53
22 9 0.30
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTAATTTATTTAATTTATAAT
Found at i:19212573 original size:116 final size:118
Alignment explanation
Indices: 19212427--19212643 Score: 318
Period size: 116 Copynumber: 1.8 Consensus size: 118
19212417 AAAATTCCAA
*
19212427 AAAAAATATTTTTAAGGAAAATTTGAAAGTATCAATTTTTCTTGAAAAT-AAAA-T-TAAAAAAA
1 AAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAAAGTATAAAAAAA
*
19212489 -ATATTTTTGAGGG-AAAGTCGAATGTATCAATTTTCTTTGAACGCAAAAAAAT
66 TATATTTTT-AGGGAAAAGTCGAAAGTATCAATTTTCTTTGAACGCAAAAAAAT
* *
19212541 AAAAAATATGATTTTAGGGGAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAAAGGTATAAAA
1 AAAAAATAT--TTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAAA-GTATAAAA
*
19212606 AAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTT
63 AAATATATTTTTAGGGAAAAGTCGAAAGTATCAATTTT
19212644 TCTTAAAAAT
Statistics
Matches: 90, Mismatches: 5, Indels: 9
0.87 0.05 0.09
Matches are distributed among these distances:
114 9 0.10
116 37 0.41
117 4 0.04
119 1 0.01
120 12 0.13
121 27 0.30
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (118 bp):
AAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAAAGTATAAAAAAA
TATATTTTTAGGGAAAAGTCGAAAGTATCAATTTTCTTTGAACGCAAAAAAAT
Found at i:19212627 original size:62 final size:59
Alignment explanation
Indices: 19212411--19212657 Score: 281
Period size: 59 Copynumber: 4.2 Consensus size: 59
19212401 TGATTTTCCT
* *
19212411 AAAATAAAAAT-TCCAAAAAAAATATTTTTAAGGAAAATTTGAAAGTATCAATTTTTCTTG
1 AAAATAAAAATAT--AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTG
* *
19212471 AAAAT-AAAAT-TAAAAAAAATATTTTTGAGGG-AAAGTCGAATGTATCAA-TTTTCTTTG
1 AAAATAAAAATATAAAAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTTC-TTG
*** * * *
19212528 AACGCAAAAAAATAAAAAATATGA-TTTTAGGGGAAAGTTGAAAGTATCAATTTTTCTTG
1 AAAATAAAAATATAAAAAAAAT-ATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTG
*
19212587 AAAATAAAAAGGTATAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTA
1 AAAATAAAAA--TATAAAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTG
19212649 AAAATAAAA
1 AAAATAAAA
19212658 TTTCTAAATA
Statistics
Matches: 158, Mismatches: 18, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
56 5 0.03
57 34 0.22
58 11 0.07
59 44 0.28
60 11 0.07
61 9 0.06
62 44 0.28
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (59 bp):
AAAATAAAAATATAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTG
Found at i:19212670 original size:15 final size:16
Alignment explanation
Indices: 19212642--19212685 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
19212632 AGTATCAATT
19212642 TTTCTTAAAAAT-AAAA
1 TTTC-TAAAAATAAAAA
*
19212658 TTTCTAAATATAAAAA
1 TTTCTAAAAATAAAAA
19212674 TTTCTAAAAATA
1 TTTCTAAAAATA
19212686 TTTTTAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 6 0.24
16 19 0.76
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (16 bp):
TTTCTAAAAATAAAAA
Found at i:19212746 original size:73 final size:75
Alignment explanation
Indices: 19212604--19212746 Score: 193
Period size: 73 Copynumber: 1.9 Consensus size: 75
19212594 AAAGGTATAA
* * * * *
19212604 AAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCTAAATAT
1 AAAAATATATTTTAAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCTAAAAAA
19212669 AAAAATTTCT
66 AAAAATTTCT
* *
19212679 AAAAATAT-TTTTAAAGAAAAAGTTGAAAGTATCAA-TTTTCTTGAAATTAAAATTTC-AGAAAA
1 AAAAATATATTTTAAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCTA-AAAA
19212741 AAAAAA
65 AAAAAA
19212747 CATTTTGAGA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
72 1 0.02
73 27 0.45
74 24 0.40
75 8 0.13
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (75 bp):
AAAAATATATTTTAAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCTAAAAAA
AAAAATTTCT
Found at i:19212835 original size:59 final size:57
Alignment explanation
Indices: 19212687--19212895 Score: 205
Period size: 59 Copynumber: 3.6 Consensus size: 57
19212677 CTAAAAATAT
* *
19212687 TTTTAAAGAAAAAGTTGAAAGTATCAA-TTTTCTTGAAATTAAAATTTCAGAAAAAAAAAACA
1 TTTT-AAGAAAAAGTTGAAAGTATCAATTTTTCTT-AAAATAAAATTTC----AAAAAAAGCA
* * *
19212749 TTTTGAGAAAAAGTTGGAAA-TACCAATTTTTCTTAAAAATAAAATTATCAAGAAAAGCA
1 TTTTAAGAAAAAGTT-GAAAGTATCAATTTTTCTT-AAAATAAAATT-TCAAAAAAAGCA
* * * *
19212808 TTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAATATAAACTTC--TAAATGC-
1 TTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAATA-AAATTTCAAAAAAAGCA
19212863 -TTTAAGAAAAAGTTGAAAGTATCAATTTTTCTT
1 TTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTT
19212896 GTACAAAAGC
Statistics
Matches: 129, Mismatches: 13, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
54 32 0.25
56 5 0.04
58 12 0.09
59 38 0.29
61 15 0.12
62 25 0.19
63 2 0.02
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (57 bp):
TTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAATAAAATTTCAAAAAAAGCA
Found at i:19213868 original size:172 final size:172
Alignment explanation
Indices: 19213582--19213929 Score: 687
Period size: 172 Copynumber: 2.0 Consensus size: 172
19213572 ATACTCGAGC
*
19213582 TTTGTCCCTCTAGAAGGGAGTAAAGTACCTATTACTTTCGTGAAGTTTTAATGCCTTCGCAGTGG
1 TTTGTCCCTCTAGAAGGGAGTAAAGTACCTATTACTTTCGTGAAGTTTTAATACCTTCGCAGTGG
19213647 CTAACGAAATACTTCCACTTAAATTGAACATTTTTCGCTTATAGCCTGTAACGGGTGAAGTTTGT
66 CTAACGAAATACTTCCACTTAAATTGAACATTTTTCGCTTATAGCCTGTAACGGGTGAAGTTTGT
19213712 GGTGCCTTACTAGTCTTTAATGGACAATGATGCAAGAAGCAA
131 GGTGCCTTACTAGTCTTTAATGGACAATGATGCAAGAAGCAA
19213754 TTTGTCCCTCTAGAAGGGAGTAAAGTACCTATTACTTTCGTGAAGTTTTAATACCTTCGCAGTGG
1 TTTGTCCCTCTAGAAGGGAGTAAAGTACCTATTACTTTCGTGAAGTTTTAATACCTTCGCAGTGG
19213819 CTAACGAAATACTTCCACTTAAATTGAACATTTTTCGCTTATAGCCTGTAACGGGTGAAGTTTGT
66 CTAACGAAATACTTCCACTTAAATTGAACATTTTTCGCTTATAGCCTGTAACGGGTGAAGTTTGT
19213884 GGTGCCTTACTAGTCTTTAATGGACAATGATGCAAGAAGCAA
131 GGTGCCTTACTAGTCTTTAATGGACAATGATGCAAGAAGCAA
19213926 TTTG
1 TTTG
19213930 GAAACCTTTA
Statistics
Matches: 175, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
172 175 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (172 bp):
TTTGTCCCTCTAGAAGGGAGTAAAGTACCTATTACTTTCGTGAAGTTTTAATACCTTCGCAGTGG
CTAACGAAATACTTCCACTTAAATTGAACATTTTTCGCTTATAGCCTGTAACGGGTGAAGTTTGT
GGTGCCTTACTAGTCTTTAATGGACAATGATGCAAGAAGCAA
Found at i:19218214 original size:23 final size:22
Alignment explanation
Indices: 19218184--19218227 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
19218174 TCTTGTCATT
19218184 TTAGGATTTCTTTTAGAGTAATG
1 TTAGGATTTCTTTTAG-GTAATG
19218207 TTAGGATTTCTTTTAGGTAAT
1 TTAGGATTTCTTTTAGGTAAT
19218228 AAGATTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (22 bp):
TTAGGATTTCTTTTAGGTAATG
Found at i:19218235 original size:19 final size:21
Alignment explanation
Indices: 19218188--19218235 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
19218178 GTCATTTTAG
*
19218188 GATTTCTTTTAGAGTAATGTTAG
1 GATTTCTTTTAGAGTAA--TTAA
19218211 GATTTCTTTTAG-GTAA-TAA
1 GATTTCTTTTAGAGTAATTAA
19218230 GATTTC
1 GATTTC
19218236 ATTTGTTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 8 0.33
22 4 0.17
23 12 0.50
ACGTcount: A:0.27, C:0.06, G:0.19, T:0.48
Consensus pattern (21 bp):
GATTTCTTTTAGAGTAATTAA
Found at i:19218764 original size:19 final size:19
Alignment explanation
Indices: 19218740--19218777 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19218730 TCTCAAAGAG
19218740 AGAAAGAAAAAAAAATGAA
1 AGAAAGAAAAAAAAATGAA
*
19218759 AGAAAGAGAAAAAAATGAA
1 AGAAAGAAAAAAAAATGAA
19218778 TGTCACACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.05
Consensus pattern (19 bp):
AGAAAGAAAAAAAAATGAA
Found at i:19219013 original size:13 final size:14
Alignment explanation
Indices: 19218988--19219022 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
19218978 TCCATTTGGA
19218988 TCAAATGTGAATGG
1 TCAAATGTGAATGG
19219002 TCAAAT-TGAATGG
1 TCAAATGTGAATGG
*
19219015 TCATATGT
1 TCAAATGT
19219023 TGGGCTAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (14 bp):
TCAAATGTGAATGG
Found at i:19219124 original size:11 final size:10
Alignment explanation
Indices: 19219109--19219177 Score: 84
Period size: 10 Copynumber: 6.5 Consensus size: 10
19219099 ATAATGGGTG
19219109 AAAGAAAAAA
1 AAAGAAAAAA
19219119 GAAAGAAAAAA
1 -AAAGAAAAAA
19219130 AAAGAAAAAA
1 AAAGAAAAAA
19219140 AAGAGAAAAAA
1 AA-AGAAAAAA
*
19219151 AAGGAAAATGAA
1 AAAGAAAA--AA
*
19219163 AAAAAAAAAA
1 AAAGAAAAAA
19219173 AAAGA
1 AAAGA
19219178 CTCAAGTTGA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
10 23 0.45
11 20 0.39
12 8 0.16
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.01
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:19219173 original size:21 final size:20
Alignment explanation
Indices: 19219115--19219173 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
19219105 GGTGAAAGAA
*
19219115 AAAAGAAAGAAAAAAAAA-G
1 AAAAGAAAAAAAAAAAAAGG
19219134 AAAA-AAAAGAGAAAAAAAAGG
1 AAAAGAAAA-A-AAAAAAAAGG
19219155 AAAATGAAAAAAAAAAAAA
1 AAAA-GAAAAAAAAAAAAA
19219174 AAGACTCAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 3 0.09
19 5 0.15
20 8 0.24
21 13 0.38
22 1 0.03
23 4 0.12
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAAGAAAAAAAAAAAAAGG
Found at i:19220322 original size:21 final size:21
Alignment explanation
Indices: 19220297--19220534 Score: 149
Period size: 21 Copynumber: 11.7 Consensus size: 21
19220287 GAATCTTTTG
19220297 ATGAGAATCTTTGAATTTCAA
1 ATGAGAATCTTTGAATTTCAA
* * *
19220318 ATGAGAATCTTTGAGTGTCGA
1 ATGAGAATCTTTGAATTTCAA
* * *
19220339 ATGTGAATCTTCGAA-CTCAA
1 ATGAGAATCTTTGAATTTCAA
* *
19220359 ATGAGAAT-TTTAAATCATCAA
1 ATGAGAATCTTTGAAT-TTCAA
*
19220380 ATGAAAATCTTT-AAGTGTT--A
1 ATGAGAATCTTTGAA-T-TTCAA
**
19220400 ATGAGAATCTTTG-AGGTC--
1 ATGAGAATCTTTGAATTTCAA
*** *
19220418 -TGA-AATC-CAAAATTTATCGA
1 ATGAGAATCTTTGAA-TT-TCAA
* *
19220438 ATGTGAATCTTTGAA-TTGAA
1 ATGAGAATCTTTGAATTTCAA
* *
19220458 ATGAGAATATTTGAATTTTAA
1 ATGAGAATCTTTGAATTTCAA
*
19220479 ATGAGAATCTTTGAATTTTAA
1 ATGAGAATCTTTGAATTTCAA
*
19220500 ATGAGAATCTTTGAATTTTAA
1 ATGAGAATCTTTGAATTTCAA
*
19220521 ATGAGAATATTTGA
1 ATGAGAATCTTTGA
19220535 GATGTGAAAC
Statistics
Matches: 168, Mismatches: 34, Indels: 30
0.72 0.15 0.13
Matches are distributed among these distances:
16 5 0.03
17 3 0.02
18 3 0.02
19 4 0.02
20 38 0.23
21 104 0.62
22 9 0.05
23 2 0.01
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (21 bp):
ATGAGAATCTTTGAATTTCAA
Found at i:19220717 original size:24 final size:23
Alignment explanation
Indices: 19220690--19220735 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
19220680 TTTAAACTTA
19220690 GATGTGAAA-CTCTAAGATTTTTGG
1 GATGT-AAATCTCTAA-ATTTTTGG
19220714 GATGTAAATCTCTAAATTTTTG
1 GATGTAAATCTCTAAATTTTTG
19220736 AGTGAGTACC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (23 bp):
GATGTAAATCTCTAAATTTTTGG
Found at i:19220726 original size:66 final size:65
Alignment explanation
Indices: 19220643--19220787 Score: 227
Period size: 66 Copynumber: 2.2 Consensus size: 65
19220633 AAAACTCAAC
*
19220643 TTTTGGATGTGAATCTCTAAATTTTTAAGTGAGAACCTTTAAACTTAGATGTGAAACTCTAAGAT
1 TTTTGGATGTAAATCTCTAAATTTTTAAGTGAGAACCTTTAAACTTAGATGTGAAACTCTAAGAT
* * *
19220708 TTTTGGGATGTAAATCTCTAAATTTTTGAGTGAGTACCTTTGAACTTAGATGTGAAACTCTAAGA
1 TTTT-GGATGTAAATCTCTAAATTTTTAAGTGAGAACCTTTAAACTTAGATGTGAAACTCTAAGA
19220773 T
65 T
*
19220774 TTCTTGAATGTAAA
1 TT-TTGGATGTAAA
19220788 CCTTTTGAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
65 4 0.05
66 67 0.92
67 2 0.03
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.39
Consensus pattern (65 bp):
TTTTGGATGTAAATCTCTAAATTTTTAAGTGAGAACCTTTAAACTTAGATGTGAAACTCTAAGAT
Found at i:19220893 original size:22 final size:23
Alignment explanation
Indices: 19220866--19220919 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
19220856 TAAATGTTGG
19220866 ATGTGAATCTTGTA-A-TTTGCAA
1 ATGTGAATCTTG-AGATTTTGCAA
19220888 ATGTGAATCTTGAGATTTTGCAA
1 ATGTGAATCTTGAGATTTTGCAA
*
19220911 ATTTGAATC
1 ATGTGAATC
19220920 CTTATGAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 1 0.03
22 13 0.45
23 15 0.52
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (23 bp):
ATGTGAATCTTGAGATTTTGCAA
Found at i:19221167 original size:42 final size:41
Alignment explanation
Indices: 19221088--19221471 Score: 322
Period size: 43 Copynumber: 9.1 Consensus size: 41
19221078 GATTATCAAT
* * *
19221088 GAGCATTTTATTTTTCAAAGTTATAGTTGCCTCTGTTTAGAG
1 GAGCAATTTATTTTTCAAAGTTGT-GGTGCCTCTGTTTAGAG
* *
19221130 GAGCAATTTACTTTTTCAAAGTTGTGGTGCCACTGTTTATAG
1 GAGCAATTTA-TTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
*
19221172 AAGC-ATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
* *
19221212 GAGC-ATTTATTTTTCAAAGTCGTGGTTGCCTTTGTTTAGAG
1 GAGCAATTTATTTTTCAAAGTTGTGG-TGCCTCTGTTTAGAG
* * ** *
19221253 GGGCAATTTATTTTTTTAAAGTCATGGTTGCCTCTGTCTAGAG
1 GAGCAATTTA-TTTTTCAAAGTTGTGG-TGCCTCTGTTTAGAG
** * * * *
19221296 GAATAATTTTTTTTTTCAAAGTTGTTGAGCCTCTATTTAGAG
1 GAGCAA-TTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
** ** * * *
19221338 GAGCTTTGTTTTATTTTTTCAAAGTCATTGAGCCTCTATTTAGAG
1 GAGC---AATTTA-TTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
* * * * *
19221383 GAGCTTTATTTATTTTTTCAAAGTTGTGGAGCCTTTGTCTAGAA
1 GAGC--AATTTA-TTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
* * * *
19221427 GAGTATTTTATTTTTCAAAGTTGTTGTGTCTCTGTTTAGAG
1 GAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
19221468 GAGC
1 GAGC
19221472 TTTGTTTATT
Statistics
Matches: 280, Mismatches: 53, Indels: 19
0.80 0.15 0.05
Matches are distributed among these distances:
40 52 0.19
41 50 0.18
42 49 0.17
43 56 0.20
44 40 0.14
45 33 0.12
ACGTcount: A:0.22, C:0.12, G:0.21, T:0.45
Consensus pattern (41 bp):
GAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
Found at i:19221397 original size:44 final size:44
Alignment explanation
Indices: 19221116--19221515 Score: 285
Period size: 45 Copynumber: 9.4 Consensus size: 44
19221106 AGTTATAGTT
* * * * *
19221116 GCCTCTGTTTAGAGGAGC--AATTTACTTTTTCAAAGTTGTGGT
1 GCCTCTGTTTAGAGGAGCTTTATTTATTTTTTCAAAGTCGTTGA
* * * * * *
19221158 GCCACTGTTTATAGAAGC---ATTTA-TTTTTCAAAGTTGTGGT
1 GCCTCTGTTTAGAGGAGCTTTATTTATTTTTTCAAAGTCGTTGA
* *
19221198 GCCTCTGTTTAGAGGAGC---ATTTA-TTTTTCAAAGTCGTGGTT
1 GCCTCTGTTTAGAGGAGCTTTATTTATTTTTTCAAAGTCGTTG-A
* * * * * * *
19221239 GCCTTTGTTTAGAGGGGC--AATTTATTTTTTTAAAGTCATGGTT
1 GCCTCTGTTTAGAGGAGCTTTATTTATTTTTTCAAAGTCGTTG-A
* * * * *
19221282 GCCTCTGTCTAGAGGA--ATAATTTTTTTTTTCAAAGTTGTTGA
1 GCCTCTGTTTAGAGGAGCTTTATTTATTTTTTCAAAGTCGTTGA
* * *
19221324 GCCTCTATTTAGAGGAGCTTTGTTTTATTTTTTCAAAGTCATTGA
1 GCCTCTGTTTAGAGGAGCTTT-ATTTATTTTTTCAAAGTCGTTGA
* * *
19221369 GCCTCTATTTAGAGGAGCTTTATTTATTTTTTCAAAGTTGTGGA
1 GCCTCTGTTTAGAGGAGCTTTATTTATTTTTTCAAAGTCGTTGA
* * * * * *
19221413 GCCTTTGTCTAGAAGAG-TAT-TTTA-TTTTTCAAAGTTGTTGT
1 GCCTCTGTTTAGAGGAGCTTTATTTATTTTTTCAAAGTCGTTGA
* *
19221454 GTCTCTGTTTAGAGGAGCTTTGTTTATTTTTTTCAAAGTCGTTGA
1 GCCTCTGTTTAGAGGAGCTTTATTTA-TTTTTTCAAAGTCGTTGA
*
19221499 GCTTCTGTTTAGAGGAG
1 GCCTCTGTTTAGAGGAG
19221516 TTTTGTTCAC
Statistics
Matches: 298, Mismatches: 48, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
40 52 0.17
41 50 0.17
42 40 0.13
43 53 0.18
44 33 0.11
45 70 0.23
ACGTcount: A:0.21, C:0.12, G:0.22, T:0.45
Consensus pattern (44 bp):
GCCTCTGTTTAGAGGAGCTTTATTTATTTTTTCAAAGTCGTTGA
Found at i:19221441 original size:130 final size:128
Alignment explanation
Indices: 19221093--19221515 Score: 448
Period size: 130 Copynumber: 3.3 Consensus size: 128
19221083 TCAATGAGCA
* * * *
19221093 TTTTATTTTTCAAAGTTATAGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTTCAAAGTTGTGGT
1 TTTTATTTTTCAAAGTCATTGTAGCCTCTGTTTAGAGGAGCAATTTATTTTTTCAAAGTTGTGGT
* * * * *
19221158 GCCACTGTTTA-TAGAAGCA-TTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGC----
66 GCCTCTGTCTAGAAG-AGTATTTTATTTTTCAAAGTTGTTGTGCCTCTGTTTAGAGGAGCTTTG
* * * * * * * **
19221216 ATTTATTTTTCAAAGTCGTGGTTGCCTTTGTTTAGAGGGGCAATTTATTTTTTTAAAGTCATGGT
1 TTTTATTTTTCAAAGTCATTGTAGCCTCTGTTTAGAGGAGCAATTTATTTTTTCAAAGTTGTGG-
* * * * *
19221281 TGCCTCTGTCTAGAGGAATAATTTTTTTTTTCAAAGTTGTTGAGCCTCTATTTAGAGGAGCTTTG
65 TGCCTCTGTCTAGAAGAGT-ATTTTATTTTTCAAAGTTGTTGTGCCTCTGTTTAGAGGAGCTTTG
* *
19221346 TTTTATTTTTTCAAAGTCATTG-AGCCTCTATTTAGAGGAGCTTTATTTATTTTTTCAAAGTTGT
1 TTTTA-TTTTTCAAAGTCATTGTAGCCTCTGTTTAGAGGAGC--AATTTATTTTTTCAAAGTTGT
* * *
19221410 GGAGCCTTTGTCTAGAAGAGTATTTTATTTTTCAAAGTTGTTGTGTCTCTGTTTAGAGGAGCTTT
63 GGTGCCTCTGTCTAGAAGAGTATTTTATTTTTCAAAGTTGTTGTGCCTCTGTTTAGAGGAGCTTT
19221475 G
128 G
* * *
19221476 TTTATTTTTTTCAAAGTCGTTG-AGCTTCTGTTTAGAGGAG
1 TTT-TATTTTTCAAAGTCATTGTAGCCTCTGTTTAGAGGAG
19221516 TTTTGTTCAC
Statistics
Matches: 245, Mismatches: 43, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
123 54 0.22
124 11 0.04
125 2 0.01
126 35 0.14
130 94 0.38
131 30 0.12
132 19 0.08
ACGTcount: A:0.22, C:0.12, G:0.21, T:0.46
Consensus pattern (128 bp):
TTTTATTTTTCAAAGTCATTGTAGCCTCTGTTTAGAGGAGCAATTTATTTTTTCAAAGTTGTGGT
GCCTCTGTCTAGAAGAGTATTTTATTTTTCAAAGTTGTTGTGCCTCTGTTTAGAGGAGCTTTG
Found at i:19222498 original size:14 final size:14
Alignment explanation
Indices: 19222479--19222515 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
19222469 AGGTTTTTAT
19222479 TTATTTATTTATTA
1 TTATTTATTTATTA
19222493 TTATTT-TATTATTA
1 TTATTTAT-TTATTA
19222507 TTA-TTATTT
1 TTATTTATTT
19222516 CTAAATTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATTTATTTATTA
Found at i:19222500 original size:11 final size:11
Alignment explanation
Indices: 19222473--19222514 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
19222463 GTTCCAAGGT
19222473 TTTTATTTATT-
1 TTTTA-TTATTA
19222484 TATTTATTATTA
1 T-TTTATTATTA
19222496 TTTTATTATTA
1 TTTTATTATTA
19222507 TTATTATT
1 TT-TTATT
19222515 TCTAAATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:19222668 original size:60 final size:58
Alignment explanation
Indices: 19222599--19222899 Score: 221
Period size: 59 Copynumber: 5.3 Consensus size: 58
19222589 TGATTTTTCT
19222599 AAAATAAAATTTTTGAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
1 AAAATAAAA-TTTT-AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
*
19222659 AAAATAAAA-TTT-AAAAAATATTTTTGAAGG-AAAGTTGAATGTATCAA-TTTCCTTTG
1 AAAATAAAATTTTAAAAAAATATTTTTG-AGGAAAAGTTGAAAGTATCAATTTTCC-TTG
* *** *
19222715 AACATAAAAAAAT-AAAAAATATGATTTTG-GGAAAAAGTTGAAAGTATCAA-TTTCTCTTA
1 AAAATAAAATTTTAAAAAAATAT--TTTTGAGG-AAAAGTTGAAAGTATCAATTTTC-CTTG
*
19222774 AAAATAAAATTTCT---AAAA-A----T---G-AAAGTTTAAAGTATCAATTTTCCTTG
1 AAAATAAAATTT-TAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
* * * * *
19222821 AAAATAAAAAGGTATAAAAAAATATTTTT-AGGAAAAAATTGAAAGTATCAA-TTTCTTTTA
1 AAAAT-AAAA-TTTTAAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTC-CTTG
19222881 AAAATAAAATTTCTAAAAA
1 AAAATAAAATTT-TAAAAA
19222900 TAGAAATTTT
Statistics
Matches: 195, Mismatches: 20, Indels: 53
0.73 0.07 0.20
Matches are distributed among these distances:
47 24 0.12
48 9 0.05
49 2 0.01
51 5 0.03
52 1 0.01
55 5 0.03
56 42 0.22
57 16 0.08
58 9 0.05
59 49 0.25
60 33 0.17
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.34
Consensus pattern (58 bp):
AAAATAAAATTTTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
Found at i:19222781 original size:59 final size:57
Alignment explanation
Indices: 19222615--19222889 Score: 197
Period size: 56 Copynumber: 4.9 Consensus size: 57
19222605 AAATTTTTGA
**
19222615 AAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTT-TCCTTGAAAAT-AAAATTT
1 AAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTCT-CTTGAAAATAAAAAAAT
* *
19222671 AAAAAATATTTTT--GAAGGAAAGTTGAATGTATCAATTTC-CTTTGAACATAAAAAAAT
1 AAAAAATATTTTTGGGAA--AAAGTTGAAAGTATCAATTTCTC-TTGAAAATAAAAAAAT
* **
19222728 AAAAAATATGATTTTGGGAAAAAGTTGAAAGTATCAATTTCTCTTAAAAAT-AAAATTT
1 AAAAAATAT--TTTTGGGAAAAAGTTGAAAGTATCAATTTCTCTTGAAAATAAAAAAAT
** * *
19222786 CTAAAA-A----T--G--AAAGTTTAAAGTATCAATTT-TCCTTGAAAATAAAAAGGTAT
1 AAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTCT-CTTGAAAATAAAAA--AAT
* * * *
19222836 AAAAAAATATTTTTAGGAAAAAATTGAAAGTATCAATTTCTTTTAAAAATAAAA
1 -AAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTCTCTTGAAAATAAAA
19222890 TTTCTAAAAA
Statistics
Matches: 173, Mismatches: 20, Indels: 48
0.72 0.08 0.20
Matches are distributed among these distances:
46 1 0.01
47 27 0.16
48 4 0.02
49 1 0.01
50 2 0.01
51 5 0.03
52 1 0.01
53 1 0.01
54 1 0.01
55 1 0.01
56 40 0.23
57 15 0.09
58 10 0.06
59 30 0.17
60 30 0.17
61 4 0.02
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (57 bp):
AAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTCTCTTGAAAATAAAAAAAT
Found at i:19222798 original size:106 final size:107
Alignment explanation
Indices: 19222688--19222905 Score: 309
Period size: 107 Copynumber: 2.0 Consensus size: 107
19222678 ATTTTTGAAG
* * *
19222688 GAAAGTTGAATGTATCAA-TTTCCTTTGAACATAAAAA-AAT-AAAAAATATGATTTTGGGAAAA
1 GAAAGTTGAAAGTATCAATTTTCC-TTGAAAATAAAAAGAATAAAAAAATAT--TTTTAGGAAAA
*
19222750 AGTTGAAAGTATCAATTTCTCTTAAAAATAAAATTTCTAAAAAT-
63 AATTGAAAGTATCAATTTCTCTTAAAAATAAAATTTCTAAAAATA
* *
19222794 GAAAGTTTAAAGTATCAATTTTCCTTGAAAATAAAAAGGTATAAAAAAATATTTTTAGGAAAAAA
1 GAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAA-GAATAAAAAAATATTTTTAGGAAAAAA
*
19222859 TTGAAAGTATCAATTTCTTTTAAAAATAAAATTTCTAAAAATA
65 TTGAAAGTATCAATTTCTCTTAAAAATAAAATTTCTAAAAATA
19222902 GAAA
1 GAAA
19222906 TTTTCAAAAA
Statistics
Matches: 100, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
106 28 0.28
107 57 0.57
108 6 0.06
109 9 0.09
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (107 bp):
GAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAAGAATAAAAAAATATTTTTAGGAAAAAAT
TGAAAGTATCAATTTCTCTTAAAAATAAAATTTCTAAAAATA
Found at i:19222899 original size:15 final size:15
Alignment explanation
Indices: 19222876--19222917 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
19222866 TATCAATTTC
19222876 TTTTAAAAATA-AAA
1 TTTTAAAAATAGAAA
19222890 TTTCTAAAAATAGAAA
1 TTT-TAAAAATAGAAA
19222906 TTTTCAAAAATA
1 TTTT-AAAAATA
19222918 TTTTTGAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.12
15 9 0.36
16 13 0.52
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (15 bp):
TTTTAAAAATAGAAA
Found at i:19222983 original size:74 final size:73
Alignment explanation
Indices: 19222838--19222983 Score: 197
Period size: 74 Copynumber: 2.0 Consensus size: 73
19222828 AAAGGTATAA
* * *
19222838 AAAAATATTTTTAGGAAAAAATTGAAAGTATCAATTTCTTTTAAAAATAAAATTTCTAAAAATAG
1 AAAAATATTTTTAGGAAAAAATTAAAAGTATCAATTTCTTTTAAAAATAAAATTTCTAAAAAAAA
19222903 AAATTTTC
66 AAATTTTC
* * *
19222911 AAAAATATTTTTGAGGAAAAAGTTAAAAGTATCAATTT-TCTTTGAAATTAAAATTTC-AAAAAA
1 AAAAATATTTTT-AGGAAAAAATTAAAAGTATCAATTTCT-TTTAAAAATAAAATTTCTAAAAAA
19222974 AAAATATTTT
64 AAAA-ATTTT
19222984 GAGGAAAAGT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
73 21 0.33
74 43 0.67
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.37
Consensus pattern (73 bp):
AAAAATATTTTTAGGAAAAAATTAAAAGTATCAATTTCTTTTAAAAATAAAATTTCTAAAAAAAA
AAATTTTC
Found at i:19225343 original size:9 final size:9
Alignment explanation
Indices: 19225331--19225356 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
19225321 TATATAAATT
19225331 ATTAATTTA
1 ATTAATTTA
19225340 ATTAATTTA
1 ATTAATTTA
19225349 ATTAATTT
1 ATTAATTT
19225357 TAATGAAAAT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTAATTTA
Found at i:19226680 original size:4 final size:4
Alignment explanation
Indices: 19226671--19226734 Score: 83
Period size: 4 Copynumber: 16.0 Consensus size: 4
19226661 TATCTTACAT
* * * * *
19226671 TATA TATA TACA TATA TACA TACA TACA TACA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
19226719 TATA TATA TATA TATA
1 TATA TATA TATA TATA
19226735 AAAGAAAAGG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (4 bp):
TATA
Found at i:19227246 original size:14 final size:16
Alignment explanation
Indices: 19227227--19227258 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
19227217 ATTTCCATTT
19227227 AAAA-TTAAAA-TAGA
1 AAAATTTAAAAGTAGA
19227241 AAAATTTAAAAGTAGA
1 AAAATTTAAAAGTAGA
19227257 AA
1 AA
19227259 GTCAGCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 6 0.38
16 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (16 bp):
AAAATTTAAAAGTAGA
Found at i:19229329 original size:28 final size:29
Alignment explanation
Indices: 19229271--19229329 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 29
19229261 TAAGTATTGA
* * *
19229271 ATTTTTTATTTTTTAAGGTTATTTTAGAT
1 ATTTTATATTTTATAAGGTTATTTTACAT
* *
19229300 ATTTTATATTTTATAA-TTTATTTTTCAT
1 ATTTTATATTTTATAAGGTTATTTTACAT
19229328 AT
1 AT
19229330 AATACCAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (29 bp):
ATTTTATATTTTATAAGGTTATTTTACAT
Found at i:19230180 original size:2 final size:2
Alignment explanation
Indices: 19230175--19230219 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
19230165 AAAAAATGCA
19230175 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19230217 AT A
1 AT A
19230220 GTCTAAAAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19231243 original size:8 final size:8
Alignment explanation
Indices: 19231230--19231259 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
19231220 TTGCATTCCC
19231230 CTCTCTGT
1 CTCTCTGT
19231238 CTCTCTGT
1 CTCTCTGT
*
19231246 CTCTCTCT
1 CTCTCTGT
19231254 CTCTCT
1 CTCTCT
19231260 ATATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.43, G:0.07, T:0.50
Consensus pattern (8 bp):
CTCTCTGT
Found at i:19232867 original size:2 final size:2
Alignment explanation
Indices: 19232860--19232896 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
19232850 AAAGTTTTAA
19232860 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
19232897 AGGAATTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19234770 original size:121 final size:121
Alignment explanation
Indices: 19234566--19234818 Score: 326
Period size: 121 Copynumber: 2.1 Consensus size: 121
19234556 ACTGAGATGG
* * * **
19234566 ACTCTTTTGATTTAGCTAATCACTTTGGTCGAGGTAGCCCAACCAAGCTTTTATGTAGGTAATTT
1 ACTCTTTTGGTCTAGCTAATCACTTTGATCGAGGTAGCCCAACCAAGCTTTTATGTAGACAATTT
* *
19234631 ATCGAAATGAACTCTTTGATTGAGGTGACCGAGATAAGCCATTTTGATTGAACTGA
66 ATCGAAATGAACTATTTGATTGAGGTGACCGAGATAAGCCATTTTGATCGAACTGA
* * * *
19234687 GCTCTTTTGGTCTAGCTAATCACTTTGATCGAGGTGGCCCAATCAAGTTTTTATGTAGACAATTT
1 ACTCTTTTGGTCTAGCTAATCACTTTGATCGAGGTAGCCCAACCAAGCTTTTATGTAGACAATTT
* * * * * * * **
19234752 ATTGAGATGAGCTATTTGATTGTGGTGATCGAGATGAGCTATTTTGATCGAGGTGA
66 ATCGAAATGAACTATTTGATTGAGGTGACCGAGATAAGCCATTTTGATCGAACTGA
19234808 ACTCTTTTGGT
1 ACTCTTTTGGT
19234819 TGAGCTGAGC
Statistics
Matches: 111, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
121 111 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (121 bp):
ACTCTTTTGGTCTAGCTAATCACTTTGATCGAGGTAGCCCAACCAAGCTTTTATGTAGACAATTT
ATCGAAATGAACTATTTGATTGAGGTGACCGAGATAAGCCATTTTGATCGAACTGA
Found at i:19234801 original size:19 final size:19
Alignment explanation
Indices: 19234777--19234838 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
19234767 TTGATTGTGG
*
19234777 TGATCGAGATGAGCTATTT
1 TGATCGAGATGAGCTCTTT
* *
19234796 TGATCGAGGTGAACTCTTT
1 TGATCGAGATGAGCTCTTT
* * *
19234815 TGGTTGAGCTGAGCTCTTT
1 TGATCGAGATGAGCTCTTT
19234834 TGATC
1 TGATC
19234839 TAGCTAATCA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.19, C:0.15, G:0.27, T:0.39
Consensus pattern (19 bp):
TGATCGAGATGAGCTCTTT
Found at i:19234806 original size:28 final size:27
Alignment explanation
Indices: 19234755--19234807 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
19234745 ACAATTTATT
* *
19234755 GAGATGAGCTATTTGATTGTGGTGATC
1 GAGATGAGCTATTTGATCGAGGTGATC
19234782 GAGATGAGCTATTTTGATCGAGGTGA
1 GAGATGAGCTA-TTTGATCGAGGTGA
19234808 ACTCTTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.25, C:0.08, G:0.34, T:0.34
Consensus pattern (27 bp):
GAGATGAGCTATTTGATCGAGGTGATC
Found at i:19234926 original size:140 final size:140
Alignment explanation
Indices: 19234672--19234957 Score: 333
Period size: 140 Copynumber: 2.0 Consensus size: 140
19234662 AGATAAGCCA
* * * * ***
19234672 TTTTGATTGAACTGAGCTCTTTTGGTCTAGCTAATCACTTTGATCGAGGTGGCCCAATCAAGTTT
1 TTTTGGTTGAACTGAGCTCTTTTGATCTAGCTAATCACTTTGATCGAAGTGGCCCAACCAAGCCA
* * * * * *
19234737 TTATGTAGACAATTTATTGAGATGAGCTATTTGATTGTGGTGATCGAGATGAGCTATTTTGATCG
66 TTATGTAGACAATTTATCGAGATGAGCTATTTAACTGAGGTAATCGAGATGACCTATTTTGATCG
**
19234802 AGGTGAACTC
131 AGAAGAACTC
* *
19234812 TTTTGGTTGAGCTGAGCTCTTTTGATCTAGCTAATCACTTTGA-CTGAAGTGGCCCAGCCAAGCC
1 TTTTGGTTGAACTGAGCTCTTTTGATCTAGCTAATCACTTTGATC-GAAGTGGCCCAACCAAGCC
* * * * *
19234876 ATTATGTAGATAGTTTATCGAGATGAGCTTTTTAACTGAGGTAA-CTGAGATTACCTCTTTTGAT
65 ATTATGTAGACAATTTATCGAGATGAGCTATTTAACTGAGGTAATC-GAGATGACCTATTTTGAT
*
19234940 CGAGAAGAGCTC
129 CGAGAAGAACTC
19234952 TTTTGG
1 TTTTGG
19234958 CCAAGCTAAT
Statistics
Matches: 121, Mismatches: 23, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
139 2 0.02
140 119 0.98
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (140 bp):
TTTTGGTTGAACTGAGCTCTTTTGATCTAGCTAATCACTTTGATCGAAGTGGCCCAACCAAGCCA
TTATGTAGACAATTTATCGAGATGAGCTATTTAACTGAGGTAATCGAGATGACCTATTTTGATCG
AGAAGAACTC
Found at i:19235082 original size:19 final size:19
Alignment explanation
Indices: 19235047--19235094 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
19235037 GAGGTTGAGA
19235047 TAAGCT-TTTTGACCGAGG
1 TAAGCTCTTTTGACCGAGG
*
19235065 TAAGCTCTTTT-ACTCGAGT
1 TAAGCTCTTTTGAC-CGAGG
*
19235084 TGAGCTCTTTT
1 TAAGCTCTTTT
19235095 TAGATGAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (19 bp):
TAAGCTCTTTTGACCGAGG
Found at i:19235639 original size:85 final size:85
Alignment explanation
Indices: 19235541--19235708 Score: 219
Period size: 85 Copynumber: 2.0 Consensus size: 85
19235531 TCATTAGCCA
* * * * * * *
19235541 AGCTATTTTGTCAAGTTGGGTCTTTATGAAGGCATTTGGTAGATCCAAGCTTTTTTGGCTAAGTT
1 AGCTATTTGGTCAAATTGGGTATTTATAAAGACATTTGATAGATCCAAGCTTTTTTGGCTAAGCT
19235606 GAATCTAAGCTTTTTGATTG
66 GAATCTAAGCTTTTTGATTG
* * *
19235626 AGCTGTTTGGTCAAATTGGGTATTTATAAAGACATTTGATAGATCCAAGTTTTTTTGGCTGAGCT
1 AGCTATTTGGTCAAATTGGGTATTTATAAAGACATTTGATAGATCCAAGCTTTTTTGGCTAAGCT
* * *
19235691 GAGTCTGAGTTTTTTGAT
66 GAATCTAAGCTTTTTGAT
19235709 CGGGTTGTTT
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
85 70 1.00
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.42
Consensus pattern (85 bp):
AGCTATTTGGTCAAATTGGGTATTTATAAAGACATTTGATAGATCCAAGCTTTTTTGGCTAAGCT
GAATCTAAGCTTTTTGATTG
Found at i:19235684 original size:170 final size:169
Alignment explanation
Indices: 19235372--19235694 Score: 357
Period size: 170 Copynumber: 1.9 Consensus size: 169
19235362 GCTGAGTCTG
* * *
19235372 AGCTATTTTGTCAAGTTGGGCTTTACGAAGGCATCTTGTAGTTCCAAACTCTTTTGGTTGAGTTG
1 AGCTATTTTGTCAAGTTGGGCTTTACGAAGGCATCTTGTAGATCCAAACTCTTTTGGCTAAGTTG
* * * * * * * **
19235437 AGTCTGAGTTTTTTTATCAAACTATTTTGTCAAATTAGTCTTTTCTAAAGGTATTTCGTAGATCC
66 AATCTAAGCTTTTTGATCAAACTATTTGGTCAAATTAGTCATTTATAAAGACATTTCGTAGATCC
*
19235502 GAACTCTTTTGGCTAAGTTGAGTTCGAGCTCATTAGCCA
131 GAACTCTTTTGGCTAAGCTGAGTTCGAGCTCATTAGCCA
* * *
19235541 AGCTATTTTGTCAAGTTGGGTCTTTATGAAGGCAT-TTGGTAGATCCAAGCTTTTTTGGCTAAGT
1 AGCTATTTTGTCAAGTTGGG-CTTTACGAAGGCATCTT-GTAGATCCAAACTCTTTTGGCTAAGT
** * * *
19235605 TGAATCTAAGCTTTTTGATTGAGCTGTTTGGTCAAATTGGGT-ATTTATAAAGACATTT-GATAG
64 TGAATCTAAGCTTTTTGATCAAACTATTTGGTCAAATT-AGTCATTTATAAAGACATTTCG-TAG
* * *
19235668 ATCC-AAGTTTTTTTGGCTGAGCTGAGT
127 ATCCGAA-CTCTTTTGGCTAAGCTGAGT
19235695 CTGAGTTTTT
Statistics
Matches: 125, Mismatches: 24, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
169 25 0.20
170 98 0.78
171 2 0.02
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.41
Consensus pattern (169 bp):
AGCTATTTTGTCAAGTTGGGCTTTACGAAGGCATCTTGTAGATCCAAACTCTTTTGGCTAAGTTG
AATCTAAGCTTTTTGATCAAACTATTTGGTCAAATTAGTCATTTATAAAGACATTTCGTAGATCC
GAACTCTTTTGGCTAAGCTGAGTTCGAGCTCATTAGCCA
Done.