Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold194
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: 3945165
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1023 characters in sequence are not A, C, G, or T
File 23 of 24
Found at i:3716769 original size:21 final size:20
Alignment explanation
Indices: 3716745--3716791 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
3716735 TAAAGAATCC
*
3716745 ATTTTTAAAGAGGGATTAATT
1 ATTTTTAAAGAGAGATTAA-T
*
3716766 ATTTTTTAAGAGAGATTAAT
1 ATTTTTAAAGAGAGATTAAT
3716786 ATTTTT
1 ATTTTT
3716792 GAGTGATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
ATTTTTAAAGAGAGATTAAT
Found at i:3716779 original size:23 final size:19
Alignment explanation
Indices: 3716746--3716791 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 19
3716736 AAAGAATCCA
3716746 TTTTTAAAGAGGGATTAATTAT
1 TTTTTAAAGA--GATTAA-TAT
3716768 TTTTTAAGAGAGATTAATAT
1 TTTTTAA-AGAGATTAATAT
3716788 TTTT
1 TTTT
3716792 GAGTGATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.30
21 6 0.26
22 7 0.30
23 3 0.13
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (19 bp):
TTTTTAAAGAGATTAATAT
Found at i:3721327 original size:14 final size:14
Alignment explanation
Indices: 3721308--3721336 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3721298 GGTTGAATCA
3721308 TTTTTAAGCCAATT
1 TTTTTAAGCCAATT
3721322 TTTTTAAGCCAATT
1 TTTTTAAGCCAATT
3721336 T
1 T
3721337 AACAAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTTTAAGCCAATT
Found at i:3722722 original size:13 final size:14
Alignment explanation
Indices: 3722693--3722722 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3722683 TTGAAAATTT
3722693 ATTTTACAAAGAAA
1 ATTTTACAAAGAAA
3722707 ATTTTACAAA-AAA
1 ATTTTACAAAGAAA
3722720 ATT
1 ATT
3722723 AAATTTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (14 bp):
ATTTTACAAAGAAA
Found at i:3734278 original size:14 final size:14
Alignment explanation
Indices: 3734259--3734287 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3734249 GGTTGAATCA
3734259 TTTTTAAGCCAATT
1 TTTTTAAGCCAATT
3734273 TTTTTAAGCCAATT
1 TTTTTAAGCCAATT
3734287 T
1 T
3734288 AACAAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTTTAAGCCAATT
Found at i:3734875 original size:17 final size:19
Alignment explanation
Indices: 3734848--3734885 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
3734838 CGGATTTGTA
3734848 TTTTATGATAAATAA-TTT
1 TTTTATGATAAATAAGTTT
3734866 TTTTAT-ATAAATAAGTTT
1 TTTTATGATAAATAAGTTT
3734884 TT
1 TT
3734886 GATAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTTATGATAAATAAGTTT
Found at i:3735628 original size:14 final size:15
Alignment explanation
Indices: 3735601--3735631 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3735591 TTTTTGCATG
3735601 AATAAATATATTTTT
1 AATAAATATATTTTT
3735616 AATAAAT-TATTTTT
1 AATAAATATATTTTT
3735630 AA
1 AA
3735632 ATCGGCATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATAAATATATTTTT
Found at i:3735684 original size:13 final size:14
Alignment explanation
Indices: 3735655--3735684 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3735645 TGAAAATTTT
3735655 ATTTTACAAAGAAA
1 ATTTTACAAAGAAA
3735669 ATTTTACAAA-AAA
1 ATTTTACAAAGAAA
3735682 ATT
1 ATT
3735685 AAAATTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (14 bp):
ATTTTACAAAGAAA
Found at i:3742293 original size:3 final size:3
Alignment explanation
Indices: 3742278--3742312 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
3742268 AACCATCAAA
*
3742278 GAT GAT AAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
3742313 AGTTGACTCG
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:0.37, C:0.00, G:0.31, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:3746238 original size:52 final size:52
Alignment explanation
Indices: 3746089--3746217 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
3746079 CGAAATATGA
3746089 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
3746141 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
3746193 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
3746218 AAGATCAGTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:3746315 original size:33 final size:33
Alignment explanation
Indices: 3746278--3746344 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3746268 AGTAGCTTAA
3746278 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
3746311 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
3746344 A
1 A
3746345 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3746318 original size:13 final size:13
Alignment explanation
Indices: 3746300--3746324 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3746290 CAAAAAAATA
3746300 TGTATCGATACAT
1 TGTATCGATACAT
3746313 TGTATCGATACA
1 TGTATCGATACA
3746325 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3752282 original size:24 final size:21
Alignment explanation
Indices: 3752236--3752308 Score: 62
Period size: 24 Copynumber: 3.5 Consensus size: 21
3752226 CACACCCAGA
*
3752236 TGTATCGATAC-ATATTACTT
1 TGTATCGATACAATATTACAT
3752256 TGTATCGATACAATATCGATACAT
1 TGTATCGATACAATAT---TACAT
* * *
3752280 TGTATCAATAC-ATGTT-CAC
1 TGTATCGATACAATATTACAT
3752299 TGTATCGATA
1 TGTATCGATA
3752309 TACACTAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
19 11 0.25
20 12 0.27
21 4 0.09
23 3 0.07
24 14 0.32
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (21 bp):
TGTATCGATACAATATTACAT
Found at i:3754113 original size:13 final size:13
Alignment explanation
Indices: 3754095--3754120 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3754085 CAATTTTTTG
3754095 TGTATCGATACAT
1 TGTATCGATACAT
3754108 TGTATCGATACAT
1 TGTATCGATACAT
3754121 ACTTTGGTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3754117 original size:33 final size:33
Alignment explanation
Indices: 3754075--3754139 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3754065 TACAAGCCAA
* *
3754075 TGTATCGATACA-ATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTGGTGTATCGATACAT
3754108 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
3754140 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:3756711 original size:13 final size:13
Alignment explanation
Indices: 3756693--3756731 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3756683 ATAATCCCCC
*
3756693 TGTATCGATACAG
1 TGTATCGATACAA
3756706 TGTATCGATACAA
1 TGTATCGATACAA
3756719 TGTATCGATACAA
1 TGTATCGATACAA
3756732 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3762927 original size:13 final size:13
Alignment explanation
Indices: 3762909--3762934 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3762899 CAATTTTTTG
3762909 TGTATCGATACAT
1 TGTATCGATACAT
3762922 TGTATCGATACAT
1 TGTATCGATACAT
3762935 ACTTTGGTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3762931 original size:33 final size:33
Alignment explanation
Indices: 3762889--3762953 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3762879 TACAAGCCAA
* *
3762889 TGTATCGATACA-ATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTGGTGTATCGATACAT
3762922 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
3762954 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:3765333 original size:21 final size:22
Alignment explanation
Indices: 3765291--3765346 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
3765281 AATTCATATT
3765291 TAAATTTAAATTCGATTTAATTCA
1 TAAATTTAAA-TCGATTTAATT-A
3765315 TAAATTTAAATC-A-TTAATTA
1 TAAATTTAAATCGATTTAATTA
*
3765335 AAAATATTAAAT
1 TAAAT-TTAAAT
3765347 TAATAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 5 0.17
21 12 0.40
22 1 0.03
23 2 0.07
24 10 0.33
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAATTTAAATCGATTTAATTA
Found at i:3770111 original size:2 final size:2
Alignment explanation
Indices: 3770104--3770128 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3770094 TTTCTTTCTT
3770104 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3770129 GTTATCCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3770787 original size:3 final size:3
Alignment explanation
Indices: 3770781--3770833 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
3770771 TGGAGAGAAC
3770781 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3770829 ATA AT
1 ATA AT
3770834 TCATTTGAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3772673 original size:2 final size:2
Alignment explanation
Indices: 3772668--3772692 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3772658 ATATATAGAT
3772668 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 A
3772693 AGCAATGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3772765 original size:2 final size:2
Alignment explanation
Indices: 3772760--3772784 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3772750 ATATATATAT
3772760 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 A
3772785 AGCAATGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3772808 original size:92 final size:92
Alignment explanation
Indices: 3772651--3772824 Score: 339
Period size: 92 Copynumber: 1.9 Consensus size: 92
3772641 TATATATATA
3772651 TATATATATATATAGATAGAGAGAGAGAGAGAGAGAGAGAGAAGCAATGGAAAAGGAAAGAGAGA
1 TATATATATATATAGATAGAGAGAGAGAGAGAGAGAGAGAGAAGCAATGGAAAAGGAAAGAGAGA
3772716 AGGATGTTAAAAGGTCCTTCTCACAGT
66 AGGATGTTAAAAGGTCCTTCTCACAGT
*
3772743 TATATATATATATATATAGAGAGAGAGAGAGAGAGAGAGAGAAGCAATGGAAAAGGAAAGAGAGA
1 TATATATATATATAGATAGAGAGAGAGAGAGAGAGAGAGAGAAGCAATGGAAAAGGAAAGAGAGA
3772808 AGGATGTTAAAAGGTCC
66 AGGATGTTAAAAGGTCC
3772825 CCCACTGGCC
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 81 1.00
ACGTcount: A:0.47, C:0.05, G:0.30, T:0.18
Consensus pattern (92 bp):
TATATATATATATAGATAGAGAGAGAGAGAGAGAGAGAGAGAAGCAATGGAAAAGGAAAGAGAGA
AGGATGTTAAAAGGTCCTTCTCACAGT
Found at i:3774265 original size:2 final size:2
Alignment explanation
Indices: 3774258--3774302 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3774248 GGGTGTGCAG
3774258 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3774300 GA G
1 GA G
3774303 TGAAATTTAT
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3776157 original size:29 final size:28
Alignment explanation
Indices: 3776104--3776159 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
3776094 ATATATTTAT
*
3776104 ATATTTTTATAATTAAATTTAAATAAAA
1 ATATTTTTATAATTAAATATAAATAAAA
*
3776132 ATATTTATTATTATTAAATA-ATAATAAA
1 ATATTT-TTATAATTAAATATA-AATAAA
3776160 CGGATCAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
ATATTTTTATAATTAAATATAAATAAAA
Found at i:3776960 original size:18 final size:17
Alignment explanation
Indices: 3776934--3776983 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
3776924 TTTATTCTTT
*
3776934 ATATGATATAAATTACATG
1 ATAT-ATATAAATTA-AAG
3776953 ATATATATAAATATAAAG
1 ATATATATAAAT-TAAAG
3776971 ATA-ATATAAATTA
1 ATATATATAAATTA
3776984 TATAATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 2 0.07
17 8 0.28
18 13 0.45
19 6 0.21
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (17 bp):
ATATATATAAATTAAAG
Found at i:3779919 original size:20 final size:20
Alignment explanation
Indices: 3779894--3779936 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3779884 GCTTGTTAGT
*
3779894 GTTGTGACGGATGATTAGAA
1 GTTGTGACAGATGATTAGAA
*
3779914 GTTGTGACAGATGATTCGAA
1 GTTGTGACAGATGATTAGAA
3779934 GTT
1 GTT
3779937 TGAATTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.28, C:0.07, G:0.33, T:0.33
Consensus pattern (20 bp):
GTTGTGACAGATGATTAGAA
Found at i:3783318 original size:52 final size:52
Alignment explanation
Indices: 3783224--3783411 Score: 232
Period size: 52 Copynumber: 3.6 Consensus size: 52
3783214 CGAGATCGAA
* * ** * * *
3783224 GTGACTTGGTGACACTCATAATGATAACTGCCCTTGTGGTGATTAGGATTAGG
1 GTGACTTGGTGTCACTGATGGTGATAAC-GCCATGGTGGTGATTAGGATCAGG
* *
3783277 GTGACTTGATGTCACTGATGGTGAAAACGCCATGGTGGTGATTAGGATCAGG
1 GTGACTTGGTGTCACTGATGGTGATAACGCCATGGTGGTGATTAGGATCAGG
* * * ** *
3783329 GTGACTTGGTGTCACTAATGGTGATAATGCCATTGTGGCAATTAGGATCGGG
1 GTGACTTGGTGTCACTGATGGTGATAACGCCATGGTGGTGATTAGGATCAGG
3783381 GTGACTTGGTGTCACTGATGGTGATAACGCC
1 GTGACTTGGTGTCACTGATGGTGATAACGCC
3783412 TATTATGGCG
Statistics
Matches: 116, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
52 94 0.81
53 22 0.19
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.30
Consensus pattern (52 bp):
GTGACTTGGTGTCACTGATGGTGATAACGCCATGGTGGTGATTAGGATCAGG
Found at i:3787667 original size:97 final size:97
Alignment explanation
Indices: 3787543--3787753 Score: 314
Period size: 97 Copynumber: 2.2 Consensus size: 97
3787533 ATTGAAAAAT
* * * **
3787543 GGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTGAG
1 GGGGTTGGAGTATCCCCTAGAAAGAATGGGGTTAAAGTGTCCCCGATGATGACAATTTAAGTGAG
3787608 AATAAAATTTAAACTTTAATGCGTTTAAAAGC
66 AATAAAATTTAAACTTTAATGCGTTTAAAAGC
* *
3787640 GGGGTTAGAGTATCCCCTAGAAAGAATGGGGTTAAAGTGTCCCCGATGGTGACAATTTAAGTGAG
1 GGGGTTGGAGTATCCCCTAGAAAGAATGGGGTTAAAGTGTCCCCGATGATGACAATTTAAGTGAG
* * *
3787705 AATAACATTTAAACTTTGATGTGTTTAAAAGC
66 AATAAAATTTAAACTTTAATGCGTTTAAAAGC
* *
3787737 AGAGTTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
3787754 GATAAATAAA
Statistics
Matches: 101, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
97 101 1.00
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (97 bp):
GGGGTTGGAGTATCCCCTAGAAAGAATGGGGTTAAAGTGTCCCCGATGATGACAATTTAAGTGAG
AATAAAATTTAAACTTTAATGCGTTTAAAAGC
Found at i:3790796 original size:20 final size:20
Alignment explanation
Indices: 3790744--3790809 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
3790734 GGTAGAGGAT
3790744 CATTCTTCAATGTATCGATA
1 CATTCTTCAATGTATCGATA
* **
3790764 CATGT-ATGGATGTATCGATA
1 CAT-TCTTCAATGTATCGATA
*
3790784 CATTCTTCAATGTATCAATA
1 CATTCTTCAATGTATCGATA
*
3790804 CTTTCT
1 CATTCT
3790810 ATCTTTTTAC
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 1 0.03
20 34 0.94
21 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (20 bp):
CATTCTTCAATGTATCGATA
Found at i:3790907 original size:90 final size:90
Alignment explanation
Indices: 3790744--3790947 Score: 277
Period size: 90 Copynumber: 2.2 Consensus size: 90
3790734 GGTAGAGGAT
* * *
3790744 CATTCTTCAATGTATCGATACATGTATGGATGTATCGATACATTCTTCAATGTATCAATACTTTC
1 CATT-TTCAATGTATCGATACATGTATGGATATATCGATACATTCTTCAATGTATCAATACATTA
*
3790809 TATCTTTTTACCTAGATGTATCGATA
65 TATCTTTTTACCCAGATGTATCGATA
* *
3790835 CATTTTCAATGTATCGATGCATGTAT-GATTATATCGAT-TATTCTTCAATGTATCAATACATTA
1 CATTTTCAATGTATCGATACATGTATGGA-TATATCGATACATTCTTCAATGTATCAATACATTA
* *
3790898 TGTCTTTTTTTCCCAGATGTATCGATA
65 TATC-TTTTTACCCAGATGTATCGATA
*
3790925 TATTTTTCAATGTATCGATACAT
1 CA-TTTTCAATGTATCGATACAT
3790948 CTAGTTAAAA
Statistics
Matches: 100, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
89 27 0.27
90 50 0.50
91 23 0.23
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (90 bp):
CATTTTCAATGTATCGATACATGTATGGATATATCGATACATTCTTCAATGTATCAATACATTAT
ATCTTTTTACCCAGATGTATCGATA
Found at i:3794245 original size:28 final size:28
Alignment explanation
Indices: 3794113--3795599 Score: 703
Period size: 28 Copynumber: 52.8 Consensus size: 28
3794103 CTAACTTATA
*
3794113 TGGGCTTTGAAAAGAGTTGCCA-TCGACTTGCG
1 TGGGCTTT-AAAAG-GATGCCACT-GACTT--G
* *
3794145 TGAGCTTTAAAAGGGTGCCACTGACTTG
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* *
3794173 TAGGCTTTGAAAAAAGAGTTGCCACTGACTTGTG
1 TGGGCTTT---AAAAG-GATGCCACTGAC-T-TG
*
3794207 TGGGCTTTGAAAGGATGCCACTGACTTG
1 TGGGCTTTAAAAGGATGCCACTGACTTG
*
3794235 TGGGCTTTGAAAA-GATGCCAC-CATCTTG
1 TGGGCTTT-AAAAGGATGCCACTGA-CTTG
*
3794263 TGGGCTTTGAAAAAG-TGCCACTGACTTG
1 TGGGCTTT-AAAAGGATGCCACTGACTTG
* * *
3794291 TGGGCTTTGAAAGGGTATGCCTCTAACTTG
1 TGGGCTTT-AAAAGG-ATGCCACTGACTTG
*
3794321 TGGGCTTTGAAAGGGTATGCCACTGACTTG
1 TGGGCTTT-AAAAGG-ATGCCACTGACTTG
* *
3794351 TGGGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTAAAAGGATGCCACTGACTTG
** * *
3794379 TGGGCTTTGGAAGGGTGTCACTGACTTG
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* *
3794407 TGGGCTTTGGAAAGG-TGCCACCT-ATTTGTG
1 TGGGCTTT-AAAAGGATGCCA-CTGA-CT-TG
* * *
3794437 TGGGCTTTGAAAAAAGTTGCCA-TCGAATTG
1 TGGGCTTT--AAAAGGATGCCACT-GACTTG
* * *
3794467 TGTAGACTTTGATAAGAGTTGCCACTGACTTG
1 TG--GGCTTT-AAAAG-GATGCCACTGACTTG
* * *
3794499 TGGGCTTTGAAAAGGGTGCCACTGAATTA
1 TGGGCTTT-AAAAGGATGCCACTGACTTG
*
3794528 TGGGCTTTGAAAGGATGCC-CTGACTTG
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* * * * * *
3794555 TGTGTTTTAAAAGGGTGCTAGTGACTTA
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* * *
3794583 TGAGCTTTAAAAGG-TGCCACGGACTTA
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* *
3794610 TGGGCTTTGAAAGGATGCCACCGACTTGTG
1 TGGGCTTTAAAAGGATGCCACTGAC-T-TG
* * * *
3794640 TGGGCTTTTAAATGGGTTGTCACCGACTAGTG
1 TGGGC-TTTAAA-AGGATGCCACTGACT--TG
* * *
3794672 TGGG-TTTCAAATGAGTTGCCACCGACTTGTG
1 TGGGCTTT-AAAAG-GATGCCACTGAC-T-TG
* * *
3794703 TGGGCTTTGAAATGAGTTGCCACCGACTTG
1 TGGGCTTT-AAAAG-GATGCCACTGACTTG
** * ** *
3794733 TGGGCTTCGAAATGATGCCACCAACTTA
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* *
3794761 TGGGCTTTGAAATGATGCCACTGACTTG
1 TGGGCTTTAAAAGGATGCCACTGACTTG
** ** * *
3794789 TGGGCTTTGCAATAATGCCACAGACTTA
1 TGGGCTTTAAAAGGATGCCACTGACTTG
3794817 TGGGCTTTGAAAA-GATGCCACTGACTTG
1 TGGGCTTT-AAAAGGATGCCACTGACTTG
* *
3794845 TGGGCTTTGAAATGAT-CCA-TGGACTTG
1 TGGGCTTTAAAAGGATGCCACT-GACTTG
* * *
3794872 TGGACTTTAAAAGG-TGCCACAGAGTTG
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* * * *
3794899 TGGACTTAAAAAGG-TGCCACGGAGTTG
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* ** *
3794926 TGGACTTTAAAATAATGCCACGGACTTG
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* * * * *
3794954 T-GGATTTTAAAGGGTGCCACGGAGTTG
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* * * * *
3794981 TGGAC-TTAAAA-GAGTGCTACAGAGTTA
1 TGGGCTTTAAAAGGA-TGCCACTGACTTG
* * * * *
3795008 TGGAC-TTAAAAGGGTGCCACGGAGTGG
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* *
3795035 TGGAC-TTAAAA-GAGTGCCA-TAGAGTTG
1 TGGGCTTTAAAAGGA-TGCCACT-GACTTG
* * * * *
3795062 TGGACTTT-AAAGGGTGCCACAGAGTTA
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* * * * *
3795089 TGGGCTTAAAAAAGGGTGTCACGGATTTG
1 TGGGCTT-TAAAAGGATGCCACTGACTTG
* * *
3795118 TGGGCTTAAAAAGGGGTGCCACTGACTTA
1 TGGGCTTTAAAA-GGATGCCACTGACTTG
** *
3795147 TGGGCTTTGGAAGGGTGCCACTGACTTG
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* * *
3795175 TGAGCTTAAAAAGGATGCCA-TGGAGTTG
1 TGGGCTTTAAAAGGATGCCACT-GACTTG
* * *
3795203 TGGAC-TTACAAGGATGCCA-TGGAGTTG
1 TGGGCTTTAAAAGGATGCCACT-GACTTG
* *
3795230 TGGAC-TTAAAAGGATGCCAC-GAGTTG
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* * *
3795256 TGGAC-TTAAAAGGATGCCACAGAGTTG
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* * *
3795283 TGGACTTTAAAAGGGTGCCAC-AACGTTG
1 TGGGCTTTAAAAGGATGCCACTGAC-TTG
*
3795311 TGGAC-TTAAAA-G--G--A--G--TTG
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* * *
3795329 TGGACTTTAAAAGGGTGCCA-TGGAGTTG
1 TGGGCTTTAAAAGGATGCCACT-GACTTG
* * * * *
3795357 TGGAC-TTAAAAAGATGTCACGGAGTTG
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* *
3795384 TGGAC-TTAAAAGGATGCCA-TAGAGTTG
1 TGGGCTTTAAAAGGATGCCACT-GACTTG
* * * *
3795411 TGGAC-TTAAAAGGATGCCACAGAGTTA
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* * *
3795438 TGGACTTTAAAAGGATGCCACAGAGTTG
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* *
3795466 TGGAC-TTAAAAGGATGCCA-TAGAGTTG
1 TGGGCTTTAAAAGGATGCCACT-GACTTG
* * ** *
3795493 TGGACTATAAAAGGAGTGCCACAAAGTTG
1 TGGGCTTTAAAAGGA-TGCCACTGACTTG
* * *
3795522 TGGACTTTAAAAGGATGCCACGGAGTTG
1 TGGGCTTTAAAAGGATGCCACTGACTTG
* * *
3795550 TGGAC-TTAAAAGGATGTCACGTAGAGTTG
1 TGGGCTTTAAAAGGATGCCAC-T-GACTTG
*
3795579 TGGACTTTAAAAGGATGCCAC
1 TGGGCTTTAAAAGGATGCCAC
3795600 AAAGTTATGG
Statistics
Matches: 1204, Mismatches: 172, Indels: 160
0.78 0.11 0.10
Matches are distributed among these distances:
18 8 0.01
19 6 0.00
20 1 0.00
22 2 0.00
24 2 0.00
26 32 0.03
27 375 0.31
28 385 0.32
29 121 0.10
30 127 0.11
31 51 0.04
32 83 0.07
33 2 0.00
34 9 0.01
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.28
Consensus pattern (28 bp):
TGGGCTTTAAAAGGATGCCACTGACTTG
Found at i:3794556 original size:234 final size:236
Alignment explanation
Indices: 3794250--3794873 Score: 666
Period size: 234 Copynumber: 2.7 Consensus size: 236
3794240 TTTGAAAAGA
* * * *
3794250 TGCCACC-ATCTTGTGGGCTTTGAAAAAGTGCCACTGACTTGTGGGCTTTGAAAGGGTATGCCTC
1 TGCCACCGA-CTTGTGGGCTTTGAAAAGGTGCCACTGAATTATGGGCTTTGAAA-GG-ATGCCAC
* * *
3794314 TAACTTGTGGGCTTTGAAAGGGTATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
63 TGACTTGTGGGCTTTGAAAGGGTATGCCACTGACTTATGGGCTTTGAAAAGGTGCCACTGACTTG
* * * * * * *
3794379 TGGGCTTTGGAAGGGTGTCACTGAC-T-TGTGGGCTTTGGAAA-GG-TGCCACCTATTTGTGTGG
128 TGGGCTTTGAAAGGATGCCACCGACTTGTGTGGGCTTT-GAAAGGGTTGCCACCGACTAGTGTGG
* *
3794440 GCTTTGAAAAAAGTTGCCATCGAATTGTGTAGACTTTGATAA-GAGT
192 G-TTTCAAAAAAGTTGCCACCGAATTGTGTAGACTTTGA-AATGAGT
*
3794486 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGAATTATGGGCTTTGAAAGGATGCC-CTG
1 TGCCACCGACTTGTGGGCTTTGAAAA-GGTGCCACTGAATTATGGGCTTTGAAAGGATGCCACTG
* * * * * * * *
3794550 ACTTGTGTGTTTTAAAAGGG--TGCTAGTGACTTATGAGCTTT-AAAAGGTGCCACGGACTTATG
65 ACTTGTGGGCTTTGAAAGGGTATGCCACTGACTTATGGGCTTTGAAAAGGTGCCACTGACTTGTG
* *
3794612 GGCTTTGAAAGGATGCCACCGACTTGTGTGGGCTTTTAAATGGGTTGTCACCGACTAGTGTGGGT
130 GGCTTTGAAAGGATGCCACCGACTTGTGTGGGCTTTGAAA-GGGTTGCCACCGACTAGTGTGGGT
** * * *
3794677 TTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGAGT
194 TTCAAAAAAGTTGCCACCGAATTGTGTAGACTTTGAAATGAGT
* * * * *
3794720 TGCCACCGACTTGTGGGCTTCGAAATGATGCCAC-CAACTTATGGGCTTTGAAATGATGCCACTG
1 TGCCACCGACTTGTGGGCTTTGAAAAGGTGCCACTGAA-TTATGGGCTTTGAAAGGATGCCACTG
* * *
3794784 ACTTGTGGGCTTTGCAA---TAATGCCACAGACTTATGGGCTTTGAAAAGATGCCACTGACTTGT
65 ACTTGTGGGCTTTGAAAGGGT-ATGCCACTGACTTATGGGCTTTGAAAAGGTGCCACTGACTTGT
* **
3794846 GGGCTTTGAAATGAT-CCATGGACTTGTG
129 GGGCTTTGAAAGGATGCCACCGACTTGTG
3794874 GACTTTAAAA
Statistics
Matches: 323, Mismatches: 51, Indels: 30
0.80 0.13 0.07
Matches are distributed among these distances:
231 37 0.11
232 23 0.07
233 40 0.12
234 122 0.38
235 51 0.16
236 25 0.08
237 25 0.08
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.31
Consensus pattern (236 bp):
TGCCACCGACTTGTGGGCTTTGAAAAGGTGCCACTGAATTATGGGCTTTGAAAGGATGCCACTGA
CTTGTGGGCTTTGAAAGGGTATGCCACTGACTTATGGGCTTTGAAAAGGTGCCACTGACTTGTGG
GCTTTGAAAGGATGCCACCGACTTGTGTGGGCTTTGAAAGGGTTGCCACCGACTAGTGTGGGTTT
CAAAAAAGTTGCCACCGAATTGTGTAGACTTTGAAATGAGT
Found at i:3794695 original size:31 final size:32
Alignment explanation
Indices: 3794625--3794790 Score: 172
Period size: 32 Copynumber: 5.5 Consensus size: 32
3794615 TTTGAAAGGA
* *
3794625 TGCCACCGACTTGTGTGGGCTTTTAAATGGGT
1 TGCCACCGACTTGTGTGGGCTTTCAAATGAGT
* *
3794657 TGTCACCGACTAGTGTGGG-TTTCAAATGAGT
1 TGCCACCGACTTGTGTGGGCTTTCAAATGAGT
*
3794688 TGCCACCGACTTGTGTGGGCTTTGAAATGAGT
1 TGCCACCGACTTGTGTGGGCTTTCAAATGAGT
3794720 TGCCACCGAC-T-TGTGGGC-TTCGAAATGA--
1 TGCCACCGACTTGTGTGGGCTTTC-AAATGAGT
* * *
3794748 TGCCACCAAC-T-TATGGGCTTTGAAATGA--
1 TGCCACCGACTTGTGTGGGCTTTCAAATGAGT
*
3794776 TGCCACTGACTTGTG
1 TGCCACCGACTTGTG
3794791 GGCTTTGCAA
Statistics
Matches: 115, Mismatches: 14, Indels: 12
0.82 0.10 0.09
Matches are distributed among these distances:
28 30 0.26
29 5 0.04
30 14 0.12
31 28 0.24
32 38 0.33
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.31
Consensus pattern (32 bp):
TGCCACCGACTTGTGTGGGCTTTCAAATGAGT
Found at i:3794900 original size:54 final size:55
Alignment explanation
Indices: 3794803--3795618 Score: 660
Period size: 54 Copynumber: 15.0 Consensus size: 55
3794793 CTTTGCAATA
* * * * * * * * *
3794803 ATGCCACAGACTTATGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAATG
1 ATGCCACAGAGTTGTGGACTTT-AAAAGGTGCCACAGAGTTGTGGACTTTAAAAGG
** * *
3794859 AT-CCATGGACTTGTGGACTTTAAAAGGTGCCACAGAGTTGTGGACTTAAAAAGG
1 ATGCCACAGAGTTGTGGACTTTAAAAGGTGCCACAGAGTTGTGGACTTTAAAAGG
* ** * * *
3794913 -TGCCACGGAGTTGTGGACTTTAAAATAATGCCACGGACTTGTGGA-TTTTAAAGG
1 ATGCCACAGAGTTGTGGACTTTAAAA-GGTGCCACAGAGTTGTGGACTTTAAAAGG
* * * *
3794967 GTGCCACGGAGTTGTGGAC-TTAAAAGAGTGCTACAGAGTTATGGAC-TTAAAAGG
1 ATGCCACAGAGTTGTGGACTTTAAAAG-GTGCCACAGAGTTGTGGACTTTAAAAGG
* * * *
3795021 GTGCCACGGAGTGGTGGAC-TTAAAAGAGTGCCATAGAGTTGTGGACTTT-AAAGG
1 ATGCCACAGAGTTGTGGACTTTAAAAG-GTGCCACAGAGTTGTGGACTTTAAAAGG
* * * * * * * * *
3795075 GTGCCACAGAGTTATGGGCTTAAAAAAGGGTGTCACGGATTTGTGGGCTTAAAAAGGG
1 ATGCCACAGAGTTGTGGACTT-TAAAA-GGTGCCACAGAGTTGTGGACTTTAAAA-GG
* * * * * * * * * *
3795133 GTGCCACTGACTTATGGGCTTTGGAAGGGTGCCACTGACTTGT-GAGCTTAAAAAGG
1 ATGCCACAGAGTTGTGGACTTT-AAAAGGTGCCACAGAGTTGTGGA-CTTTAAAAGG
** * **
3795189 ATGCCATGGAGTTGTGGAC-TTACAAGGATGCCATGGAGTTGTGGAC-TTAAAAGG
1 ATGCCACAGAGTTGTGGACTTTAAAAGG-TGCCACAGAGTTGTGGACTTTAAAAGG
3795243 ATGCCAC-GAGTTGTGGAC-TTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAGG
1 ATGCCACAGAGTTGTGGACTTTAAAAGG-TGCCACAGAGTTGTGGACTTTAAAAGG
*
3795297 GTGCCACA-ACGTTGTGGAC-TTAAAA---G-----GAGTTGTGGACTTTAAAAGG
1 ATGCCACAGA-GTTGTGGACTTTAAAAGGTGCCACAGAGTTGTGGACTTTAAAAGG
* ** * * * *
3795343 GTGCCATGGAGTTGTGGACTTAAAAAGATGTCACGGAGTTGTGGAC-TTAAAAGG
1 ATGCCACAGAGTTGTGGACTTTAAAAGGTGCCACAGAGTTGTGGACTTTAAAAGG
* *
3795397 ATGCCATAGAGTTGTGGAC-TTAAAAGGATGCCACAGAGTTATGGACTTTAAAAGG
1 ATGCCACAGAGTTGTGGACTTTAAAAGG-TGCCACAGAGTTGTGGACTTTAAAAGG
* *
3795452 ATGCCACAGAGTTGTGGAC-TTAAAAGGATGCCATAGAGTTGTGGACTATAAAAGG
1 ATGCCACAGAGTTGTGGACTTTAAAAGG-TGCCACAGAGTTGTGGACTTTAAAAGG
* *
3795507 AGTGCCACAAAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGG
1 A-TGCCACAGAGTTGTGGACTTTAAAAGG-TGCCACAGAGTTGTGGACTTTAAAAGG
* * *
3795563 ATGTCACGTAGAGTTGTGGACTTTAAAAGGATGCCACAAAGTTATGGAC-TTAAAAG
1 ATGCCAC--AGAGTTGTGGACTTTAAAAGG-TGCCACAGAGTTGTGGACTTTAAAAG
3795619 AGGTCATAGT
Statistics
Matches: 635, Mismatches: 91, Indels: 67
0.80 0.11 0.08
Matches are distributed among these distances:
46 35 0.06
47 6 0.01
50 1 0.00
51 1 0.00
53 42 0.07
54 213 0.34
55 156 0.25
56 65 0.10
57 93 0.15
58 23 0.04
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (55 bp):
ATGCCACAGAGTTGTGGACTTTAAAAGGTGCCACAGAGTTGTGGACTTTAAAAGG
Found at i:3795163 original size:57 final size:58
Alignment explanation
Indices: 3795073--3795188 Score: 144
Period size: 57 Copynumber: 2.0 Consensus size: 58
3795063 GGACTTTAAA
* * * *
3795073 GGGTGCCACAGAGTTATGGGCTTAAAAAAGGGTGTCACGGATTTGTGGGCTTAAAAAG
1 GGGTGCCACAGACTTATGGGCTTAAAAAAGGGTGCCACGGACTTGTGAGCTTAAAAAG
* *** *
3795131 GGGTGCCACTGACTTATGGGCTT-TGGAAGGGTGCCACTGACTTGTGAGCTTAAAAAG
1 GGGTGCCACAGACTTATGGGCTTAAAAAAGGGTGCCACGGACTTGTGAGCTTAAAAAG
3795188 G
1 G
3795189 ATGCCATGGA
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
57 28 0.57
58 21 0.43
ACGTcount: A:0.26, C:0.15, G:0.34, T:0.25
Consensus pattern (58 bp):
GGGTGCCACAGACTTATGGGCTTAAAAAAGGGTGCCACGGACTTGTGAGCTTAAAAAG
Found at i:3795330 original size:18 final size:19
Alignment explanation
Indices: 3795307--3795342 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
3795297 GTGCCACAAC
3795307 GTTGTGGAC-TTAAAAGGA
1 GTTGTGGACTTTAAAAGGA
3795325 GTTGTGGACTTTAAAAGG
1 GTTGTGGACTTTAAAAGG
3795343 GTGCCATGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.31, C:0.06, G:0.33, T:0.31
Consensus pattern (19 bp):
GTTGTGGACTTTAAAAGGA
Found at i:3795344 original size:46 final size:46
Alignment explanation
Indices: 3795277--3795424 Score: 149
Period size: 46 Copynumber: 3.0 Consensus size: 46
3795267 GGATGCCACA
3795277 GAGTTGTGGACTTTAAAAGGGTGCCA-CAACGTTGTGGACTTAAAAG
1 GAGTTGTGGACTTTAAAAGGGTGCCATCAA-GTTGTGGACTTAAAAG
**
3795323 GAGTTGTGGACTTTAAAAGGGTGCCATGGAGTTGTGGACTTAAAAAGATGTCACG
1 GAGTTGTGGACTTTAAAAGGGTGCCATCAAGTTGTGGACTT---AA-A----A-G
*
3795378 GAGTTGTGGAC-TTAAAAGGATGCCAT-AGAGTTGTGGACTTAAAAG
1 GAGTTGTGGACTTTAAAAGGGTGCCATCA-AGTTGTGGACTTAAAAG
3795423 GA
1 GA
3795425 TGCCACAGAG
Statistics
Matches: 87, Mismatches: 4, Indels: 23
0.76 0.04 0.20
Matches are distributed among these distances:
45 3 0.03
46 38 0.44
47 1 0.01
49 2 0.02
50 2 0.02
51 2 0.02
54 27 0.31
55 12 0.14
ACGTcount: A:0.31, C:0.11, G:0.32, T:0.26
Consensus pattern (46 bp):
GAGTTGTGGACTTTAAAAGGGTGCCATCAAGTTGTGGACTTAAAAG
Found at i:3795473 original size:55 final size:54
Alignment explanation
Indices: 3795323--3795618 Score: 394
Period size: 55 Copynumber: 5.3 Consensus size: 54
3795313 GACTTAAAAG
* ** * * *
3795323 GAGTTGTGGACTTTAAAAGGGTGCCATGGAGTTGTGGACTTAAAAAGATGTCACG
1 GAGTTGTGGAC-TTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCACA
*
3795378 GAGTTGTGGACTTAAAAGGATGCCATAGAGTTGTGGACTTAAAAGGATGCCACA
1 GAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCACA
* *
3795432 GAGTTATGGACTTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCATA
1 GAGTTGTGGAC-TTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCACA
* *
3795487 GAGTTGTGGACTATAAAAGGAGTGCCACAAAGTTGTGGACTTTAAAAGGATGCCACG
1 GAGTTGTGGACT-TAAAAGGA-TGCCACAGAGTTGTGGAC-TTAAAAGGATGCCACA
*
3795544 GAGTTGTGGACTTAAAAGGATGTCACGTAGAGTTGTGGACTTTAAAAGGATGCCACA
1 GAGTTGTGGACTTAAAAGGATGCCAC--AGAGTTGTGGAC-TTAAAAGGATGCCACA
* *
3795601 AAGTTATGGACTTAAAAG
1 GAGTTGTGGACTTAAAAG
3795619 AGGTCATAGT
Statistics
Matches: 218, Mismatches: 17, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
54 49 0.22
55 75 0.34
56 25 0.11
57 69 0.32
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.25
Consensus pattern (54 bp):
GAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCACA
Found at i:3802258 original size:97 final size:96
Alignment explanation
Indices: 3802007--3802247 Score: 338
Period size: 97 Copynumber: 2.5 Consensus size: 96
3801997 ATTGAAAAAT
**
3802007 GGGGTTAGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCTAATGATGACAATTTAAGTGAA
1 GGGGTTAGAGTATCCCCTC-GAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTGAA
*
3802072 AATAAAATTTAAACTTTGATGCGTTTGAAAGC
65 AATAAAATTTAAACTTTGATGCGTTTAAAAGC
* * * * *
3802104 GAGGTTAGAGTATCCCCTCGAAAGAATGGGGTTGAAGTGTCCCCGATGGTGACAATTTAAGTGAG
1 GGGGTTAGAGTATCCCCTCG-AGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTGAA
* *
3802169 AATAAGATTTAAACTTTGATGTGTTTAAAAGC
65 AATAAAATTTAAACTTTGATGCGTTTAAAAGC
* * *
3802201 GGGGTTGGAGTATCCCCTCAGAGGAATAGGGTTGGAGTATCCCCGAT
1 GGGGTTAGAGTATCCCCTC-GAGGAATGGGGTTGGAGTGTCCCCGAT
3802248 AAAAAAAATT
Statistics
Matches: 126, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
96 1 0.01
97 124 0.98
98 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (96 bp):
GGGGTTAGAGTATCCCCTCGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAAGTGAAA
ATAAAATTTAAACTTTGATGCGTTTAAAAGC
Found at i:3803458 original size:21 final size:21
Alignment explanation
Indices: 3803423--3803463 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3803413 TACATATATA
* *
3803423 AATAAAACAAGCAAATATTAT
1 AATAAAAAAAGCAAAAATTAT
*
3803444 AATAAAAAAATCAAAAATTA
1 AATAAAAAAAGCAAAAATTA
3803464 AATGCAAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.22
Consensus pattern (21 bp):
AATAAAAAAAGCAAAAATTAT
Found at i:3807492 original size:36 final size:36
Alignment explanation
Indices: 3807445--3807519 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
3807435 GCGCCAAATT
3807445 GTTGATGTCTTTTTCTGGATATTGTCCGAGTTGACA
1 GTTGATGTCTTTTTCTGGATATTGTCCGAGTTGACA
3807481 GTTGATGTCTTTTTCTGGATATTGTCCGAGTTGACA
1 GTTGATGTCTTTTTCTGGATATTGTCCGAGTTGACA
3807517 GTT
1 GTT
3807520 CTGCAAGAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.16, C:0.13, G:0.25, T:0.45
Consensus pattern (36 bp):
GTTGATGTCTTTTTCTGGATATTGTCCGAGTTGACA
Found at i:3809205 original size:101 final size:101
Alignment explanation
Indices: 3809063--3809260 Score: 281
Period size: 101 Copynumber: 2.0 Consensus size: 101
3809053 AAAATATTTC
* * * * * *
3809063 CTCTCTTTACAAAAGAGCCCTTTATATTTTGACGACTCCACTAGGGAATAA-TGATTGCTTTAAA
1 CTCTCTCTACAAAAGAACCCTCTACATTTTAACGACTCCACTAAGGAA-AAGTGATTGCTTTAAA
* *
3809127 TGAAATCTTCAACATTTATCTCACAGGAAAACACTTT
65 TAAAATCTTCAACATTTACCTCACAGGAAAACACTTT
* **
3809164 CTCTCTCTATAAAAGAACCCTCTACATTTTAACGACTCCACTAAGGAAAAGTGATTGCTTTATGT
1 CTCTCTCTACAAAAGAACCCTCTACATTTTAACGACTCCACTAAGGAAAAGTGATTGCTTTAAAT
3809229 AAAATCTTCAACATTTACCTCACAGGAAAACA
66 AAAATCTTCAACATTTACCTCACAGGAAAACA
3809261 TGGACAACTA
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
100 2 0.02
101 83 0.98
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.31
Consensus pattern (101 bp):
CTCTCTCTACAAAAGAACCCTCTACATTTTAACGACTCCACTAAGGAAAAGTGATTGCTTTAAAT
AAAATCTTCAACATTTACCTCACAGGAAAACACTTT
Found at i:3812879 original size:53 final size:52
Alignment explanation
Indices: 3812789--3812888 Score: 139
Period size: 53 Copynumber: 1.9 Consensus size: 52
3812779 ATCTTTCGTT
*
3812789 CCAATGTTGCTAACCTTGGATCAGCACATTGTCACCTTTCTTCATCTTTAAGA
1 CCAATGTTGCTAACCTTGGATCAGCACATTGTCACC-TTCATCATCTTTAAGA
* * *
3812842 CCAATGTTGCTAACCTTGGATCTGCGCGTTGGT-ACCTTCATCATCTT
1 CCAATGTTGCTAACCTTGGATCAGCACATT-GTCACCTTCATCATCTT
3812889 CAAATTCAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
52 10 0.24
53 30 0.71
54 2 0.05
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.36
Consensus pattern (52 bp):
CCAATGTTGCTAACCTTGGATCAGCACATTGTCACCTTCATCATCTTTAAGA
Found at i:3813045 original size:31 final size:31
Alignment explanation
Indices: 3812997--3813095 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 31
3812987 CACCATTGCA
* *
3812997 AAAGCCCACTTAAGTCGGTGGCAAACCTTTT
1 AAAGCCCACATAAGTCGGTGGCAAACCTTCT
* * *
3813028 AAAGTCTACATAAGTCGGTGGCAACCCTTCT
1 AAAGCCCACATAAGTCGGTGGCAAACCTTCT
* * *
3813059 AAAGCCCACACAAATCGGTGGC-AACCATTAT
1 AAAGCCCACATAAGTCGGTGGCAAACC-TTCT
3813090 AAAGCC
1 AAAGCC
3813096 TATGACTCTG
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
30 3 0.05
31 53 0.95
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.21
Consensus pattern (31 bp):
AAAGCCCACATAAGTCGGTGGCAAACCTTCT
Found at i:3813177 original size:31 final size:31
Alignment explanation
Indices: 3813149--3813237 Score: 124
Period size: 31 Copynumber: 2.9 Consensus size: 31
3813139 GAGGCAACTT
* *
3813149 TTCTAAAGTCCATACAAGTTAGTGGCAACCC
1 TTCTAAAGTCCACACAAGTTGGTGGCAACCC
* **
3813180 TTCTAAAGTCTACACAAGTTGGTACCAACCC
1 TTCTAAAGTCCACACAAGTTGGTGGCAACCC
*
3813211 TTCTAAAGTCCACACAAGTCGGTGGCA
1 TTCTAAAGTCCACACAAGTTGGTGGCA
3813238 TCTCTTTCTA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (31 bp):
TTCTAAAGTCCACACAAGTTGGTGGCAACCC
Found at i:3813525 original size:95 final size:92
Alignment explanation
Indices: 3813305--3813673 Score: 343
Period size: 95 Copynumber: 4.0 Consensus size: 92
3813295 CATATCTTTC
* * * * * **
3813305 TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCAC-ATTCATCTTTAAGACCAATGTCGC
1 TAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACTTTTCATCTTTAAGACCAATGTCAT
*
3813369 TGGCCTTGAATCAACACATTAGCAC--
66 TGGCCTTGAATCAACACATTGGCACTT
* * * * * * *
3813394 -AAGCCCAATATCGCTAGCCTTGAATTAGCATATTGGCACCTTTATCAACTTTGAGTCCAATGTC
1 TAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCA-CTTT-TCATCTTTAAGACCAATGTC
*
3813458 ATTGGCCTTGAATCAGCACATTGGCACCTT
64 ATTGGCCTTGAATCAACACATTGGCA-CTT
* *
3813488 TAAGTCCAATATCGCTGGTCTTGAATCAACATATTGGCATCTTTGTCATTTTTAAGACCAATGTC
1 TAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCA-CTTT-TCATCTTTAAGACCAATGTC
*
3813553 ATTGGCCTTGAATTAACACATTGGCATCTT
64 ATTGGCCTTGAATCAACACATTGGCA-CTT
* * * * * * * * *
3813583 TAAGTTCGATTTCGCTGGCCTTGAAT-AAGCATATTAGCATTTTTAATATTCCTAAGCCCAATTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAA-CATATTGGCACTTTTCATCTT--TAAGACCAATGT
** *
3813647 TGTTGGCATTGAATCAACACATTGGCA
63 CATTGGCCTTGAATCAACACATTGGCA
3813674 TTCTTCTTAT
Statistics
Matches: 228, Mismatches: 42, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
88 32 0.14
89 1 0.00
90 1 0.00
91 39 0.17
92 1 0.00
93 5 0.02
94 5 0.02
95 144 0.63
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (92 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACTTTTCATCTTTAAGACCAATGTCAT
TGGCCTTGAATCAACACATTGGCACTT
Found at i:3813879 original size:61 final size:61
Alignment explanation
Indices: 3813796--3813912 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 61
3813786 ATCTGCAATT
* * * * ** * *
3813796 CCAATATTGCTGGCCTTGAATCAGCATGTTGGCACCTTTATCATTTTTTTCATCTTTAGGC
1 CCAATATCGCTAGCCGTGAATCAGCATATTGAAACCTTTATCACTTTTCTCATCTTTAGGC
* *
3813857 CCAATATCGCTAGCCGTGAATCAGTATATTGAAATCTTTATCACTTTTCTCATCTT
1 CCAATATCGCTAGCCGTGAATCAGCATATTGAAACCTTTATCACTTTTCTCATCTT
3813913 CATCATCTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 46 1.00
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (61 bp):
CCAATATCGCTAGCCGTGAATCAGCATATTGAAACCTTTATCACTTTTCTCATCTTTAGGC
Found at i:3814599 original size:19 final size:21
Alignment explanation
Indices: 3814552--3814606 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
3814542 ATTTTTACAG
3814552 TTTGTATCGATACAAACAGTA
1 TTTGTATCGATACAAACAGTA
** *
3814573 CATGTATCGATACATA-AGT-
1 TTTGTATCGATACAAACAGTA
*
3814592 TTTGTATCAATACAA
1 TTTGTATCGATACAA
3814607 TATATGGATA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 11 0.41
20 3 0.11
21 13 0.48
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (21 bp):
TTTGTATCGATACAAACAGTA
Found at i:3828615 original size:10 final size:10
Alignment explanation
Indices: 3828602--3828644 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
3828592 AGAAAAACAG
3828602 CAAAAAAAAA
1 CAAAAAAAAA
*
3828612 CAAAGAAAAA
1 CAAAAAAAAA
*
3828622 CAATAAAAAA
1 CAAAAAAAAA
*
3828632 -ATAAAAAAA
1 CAAAAAAAAA
3828641 CAAA
1 CAAA
3828645 CAACAAAAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.84, C:0.09, G:0.02, T:0.05
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:3828616 original size:23 final size:23
Alignment explanation
Indices: 3828589--3828653 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
3828579 GTCCTTCGCG
*
3828589 AAAAGAAAAACAGCAAAAAAA-A
1 AAAAGAAAAACAACAAAAAAATA
*
3828611 ACAAAGAAAAACAATAAAAAAATA
1 A-AAAGAAAAACAACAAAAAAATA
3828635 AAAA-AACAAACAACAAAAA
1 AAAAGAA-AAACAACAAAAA
3828654 GGGTCCGGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 3 0.08
23 32 0.86
24 2 0.05
ACGTcount: A:0.82, C:0.11, G:0.05, T:0.03
Consensus pattern (23 bp):
AAAAGAAAAACAACAAAAAAATA
Found at i:3834854 original size:13 final size:13
Alignment explanation
Indices: 3834836--3834861 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3834826 CAATTTTTTG
3834836 TGTATCGATACAT
1 TGTATCGATACAT
3834849 TGTATCGATACAT
1 TGTATCGATACAT
3834862 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3834926 original size:21 final size:21
Alignment explanation
Indices: 3834900--3834975 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3834890 CTGCCAAGAA
*
3834900 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
3834921 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
3834941 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
3834962 ATGTATCGATACAT
1 ATGTATCGATACAT
3834976 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:3834946 original size:20 final size:20
Alignment explanation
Indices: 3834921--3834993 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3834911 CATCTTTTTT
3834921 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
3834941 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
3834962 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
3834982 ATGTATCGATAC
1 ATGTATCGATAC
3834994 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:3834957 original size:41 final size:41
Alignment explanation
Indices: 3834900--3834993 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
3834890 CTGCCAAGAA
*
3834900 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
3834941 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
3834982 ATGTATCGATAC
1 ATGTATCGATAC
3834994 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:3835649 original size:31 final size:31
Alignment explanation
Indices: 3835611--3835671 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
3835601 TCCCCCGTTT
3835611 AAAAAATCTCCCCCTTAATCAAGTAATTCAA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCAA
3835642 AAAAAATCTCCCCCTTAATCAAGTAATTCA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCA
3835672 TATCAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.26, G:0.03, T:0.26
Consensus pattern (31 bp):
AAAAAATCTCCCCCTTAATCAAGTAATTCAA
Found at i:3837483 original size:13 final size:13
Alignment explanation
Indices: 3837465--3837503 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3837455 ATAATCACCC
*
3837465 TGTATCGATACAG
1 TGTATCGATACAA
3837478 TGTATCGATACAA
1 TGTATCGATACAA
3837491 TGTATCGATACAA
1 TGTATCGATACAA
3837504 CAAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3837514 original size:20 final size:20
Alignment explanation
Indices: 3837489--3837567 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
3837479 GTATCGATAC
3837489 AATGTATCGATACAACAAAA
1 AATGTATCGATACAACAAAA
* *
3837509 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACA-ACAA----AA
*
3837534 GATGTATCGATAC-ACAAAA
1 AATGTATCGATACAACAAAA
3837553 ACATGTATCGATACA
1 A-ATGTATCGATACA
3837568 TTTTGGACAT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
19 1 0.02
20 26 0.57
21 3 0.07
23 3 0.07
25 13 0.28
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAACAAAA
Found at i:3839602 original size:15 final size:15
Alignment explanation
Indices: 3839582--3839612 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3839572 ATTTCGTTTG
*
3839582 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3839597 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3839612 G
1 G
3839613 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:3841558 original size:1 final size:1
Alignment explanation
Indices: 3841552--3841577 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
3841542 AAAGTGTTTG
3841552 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
3841578 TTTAAATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3841606 original size:21 final size:21
Alignment explanation
Indices: 3841582--3841638 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3841572 AAAAAATTTA
3841582 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
3841603 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
3841624 AATGTATCGATACAT
1 AATGTATCGATACAT
3841639 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:3841718 original size:19 final size:19
Alignment explanation
Indices: 3841694--3841761 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
3841684 AATTCAACAA
3841694 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3841713 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3841728 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
3841745 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
3841762 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3841733 original size:13 final size:13
Alignment explanation
Indices: 3841715--3841739 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3841705 ACATAAGTTT
3841715 TGTATCGATACAA
1 TGTATCGATACAA
3841728 TGTATCGATACA
1 TGTATCGATACA
3841740 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3841737 original size:32 final size:32
Alignment explanation
Indices: 3841696--3841758 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3841686 TTCAACAATT
*
3841696 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
3841728 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
3841759 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:3841819 original size:13 final size:13
Alignment explanation
Indices: 3841801--3841826 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3841791 CATTTTTCTG
3841801 TGTATCGATACAT
1 TGTATCGATACAT
3841814 TGTATCGATACAT
1 TGTATCGATACAT
3841827 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3841823 original size:33 final size:33
Alignment explanation
Indices: 3841781--3841847 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3841771 GCCAAGGAAA
***
3841781 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
3841814 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
3841847 T
1 T
3841848 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:3844363 original size:28 final size:27
Alignment explanation
Indices: 3844296--3844368 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
3844286 CTTCACAATC
* *
3844296 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
3844323 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
3844351 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
3844369 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:3844413 original size:51 final size:51
Alignment explanation
Indices: 3844351--3844521 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
3844341 TTATTTCTGA
* * *
3844351 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
3844402 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
3844455 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
3844507 GAGGATACTCCAACC
1 GGGGATACTCCAACC
3844522 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:3844540 original size:28 final size:28
Alignment explanation
Indices: 3844504--3844585 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
3844494 ATTTTTCACA
*
3844504 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
3844532 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
3844560 --CGAAGGAACACTCCAACCTCGTTATT
1 ATCG--GGGATACTCCAACCTCGTTATT
3844586 ATCTCCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.04
28 43 0.96
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:3847887 original size:13 final size:13
Alignment explanation
Indices: 3847869--3847894 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3847859 CAATTTTTTG
3847869 TGTATCGATACAT
1 TGTATCGATACAT
3847882 TGTATCGATACAT
1 TGTATCGATACAT
3847895 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3847959 original size:21 final size:21
Alignment explanation
Indices: 3847933--3848008 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3847923 CTGCCAAGAA
*
3847933 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
3847954 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
3847974 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
3847995 ATGTATCGATACAT
1 ATGTATCGATACAT
3848009 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:3847979 original size:20 final size:20
Alignment explanation
Indices: 3847954--3848026 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3847944 CATCTTTTTT
3847954 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
3847974 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
3847995 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
3848015 ATGTATCGATAC
1 ATGTATCGATAC
3848027 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:3847990 original size:41 final size:41
Alignment explanation
Indices: 3847933--3848026 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
3847923 CTGCCAAGAA
*
3847933 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
3847974 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
3848015 ATGTATCGATAC
1 ATGTATCGATAC
3848027 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:3850728 original size:37 final size:37
Alignment explanation
Indices: 3850678--3850752 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
3850668 CCACACTTGG
3850678 ATCAATCATTCCTAGCGCAACACCTCATTATCATTGC
1 ATCAATCATTCCTAGCGCAACACCTCATTATCATTGC
*
3850715 ATCAATCATTCCTAGCGTAACACCTCATTATCATTGC
1 ATCAATCATTCCTAGCGCAACACCTCATTATCATTGC
3850752 A
1 A
3850753 CCATGCATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (37 bp):
ATCAATCATTCCTAGCGCAACACCTCATTATCATTGC
Found at i:3858172 original size:8 final size:8
Alignment explanation
Indices: 3858150--3858229 Score: 71
Period size: 8 Copynumber: 10.5 Consensus size: 8
3858140 GGCGTCATCC
3858150 ACAAA-AA
1 ACAAACAA
*
3858157 AAAAACAA
1 ACAAACAA
3858165 ACAAACAA
1 ACAAACAA
3858173 ACAAA-AA
1 ACAAACAA
*
3858180 A-AAAGAA
1 ACAAACAA
*
3858187 AAAAACAA
1 ACAAACAA
3858195 A-AAA-AA
1 ACAAACAA
*
3858201 ACAAAAAAA
1 AC-AAACAA
3858210 ACAAACAA
1 ACAAACAA
*
3858218 ACAAAAAA
1 ACAAACAA
3858226 ACAA
1 ACAA
3858230 CAACAAAAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
6 6 0.10
7 13 0.21
8 39 0.63
9 4 0.06
ACGTcount: A:0.85, C:0.14, G:0.01, T:0.00
Consensus pattern (8 bp):
ACAAACAA
Found at i:3858196 original size:41 final size:42
Alignment explanation
Indices: 3858150--3858238 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 42
3858140 GGCGTCATCC
*
3858150 ACAAAAAAAAAAC-AAACAAACAAACAAA-AAAAAAGAAAAAA
1 ACAAAAAAAAAACAAAAAAAACAAACAAACAAAAAA-AAAAAA
* *
3858191 AC-AAAAAAAAACAAAAAAAACAAACAAACAAAAAAACAACA
1 ACAAAAAAAAAACAAAAAAAACAAACAAACAAAAAAAAAAAA
3858232 ACAAAAA
1 ACAAAAA
3858239 GGGTCCGAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
40 10 0.24
41 22 0.52
42 10 0.24
ACGTcount: A:0.84, C:0.15, G:0.01, T:0.00
Consensus pattern (42 bp):
ACAAAAAAAAAACAAAAAAAACAAACAAACAAAAAAAAAAAA
Found at i:3858238 original size:1 final size:1
Alignment explanation
Indices: 3858152--3858226 Score: 60
Period size: 1 Copynumber: 75.0 Consensus size: 1
3858142 CGTCATCCAC
* * * * * * * * *
3858152 AAAAAAAAAACAAACAAACAAACAAAAAAAAAGAAAAAAACAAAAAAAAACAAAAAAAACAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
3858217 AACAAAAAAA
1 AAAAAAAAAA
3858227 CAACAACAAA
Statistics
Matches: 54, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.87, C:0.12, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:3859741 original size:28 final size:27
Alignment explanation
Indices: 3859671--3860040 Score: 422
Period size: 28 Copynumber: 13.3 Consensus size: 27
3859661 TTCCTCACCT
*
3859671 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCA-AC
* *
3859699 TTTTCAAAAGCCCACAAGTCAATGTCAAC
1 -TTTC-AAAGCCCACAAGTCAGTGGCAAC
* * *
3859728 CTTCAAAAGCCCACAAGTTAGTGGCACAT
1 TTTC-AAAGCCCACAAGTCAGTGGCA-AC
*
3859757 TTTCAAAGCCCACAAGTCAGTGGCACAT
1 TTTCAAAGCCCACAAGTCAGTGGCA-AC
*
3859785 TTTCAAAGCCCACAAGTCAGTGGCACAT
1 TTTCAAAGCCCACAAGTCAGTGGCA-AC
*
3859813 TTTCAAAGCCCACAAGTCAGTGGCACAT
1 TTTCAAAGCCCACAAGTCAGTGGCA-AC
3859841 TTTCAAAGCCCACAAGTCAGTGGC-AC
1 TTTCAAAGCCCACAAGTCAGTGGCAAC
*
3859867 TTTTTCAAAGCCCACAAGTTAGTGGC-AC
1 --TTTCAAAGCCCACAAGTCAGTGGCAAC
3859895 TTTTTCAAAGCCCACAAGTCAGTGGC-AC
1 --TTTCAAAGCCCACAAGTCAGTGGCAAC
* * *
3859923 TTTTTCAAAGGCCACAAGTTAGTGGCACC
1 --TTTCAAAGCCCACAAGTCAGTGGCAAC
3859952 TTTTCAAAGCCCACAAGTCAGTGGCAAC
1 -TTTCAAAGCCCACAAGTCAGTGGCAAC
* *
3859980 CTTCAAAGCCCACAAGACAGTGGCAAC
1 TTTCAAAGCCCACAAGTCAGTGGCAAC
* *
3860007 CTTCAAAGCCCACAAGACAGTGGCAAC
1 TTTCAAAGCCCACAAGTCAGTGGCAAC
*
3860034 CTTCAAA
1 TTTCAAA
3860041 AGTACACAAG
Statistics
Matches: 315, Mismatches: 21, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
26 1 0.00
27 59 0.19
28 226 0.72
29 10 0.03
30 19 0.06
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.21
Consensus pattern (27 bp):
TTTCAAAGCCCACAAGTCAGTGGCAAC
Found at i:3859793 original size:56 final size:56
Alignment explanation
Indices: 3859670--3860031 Score: 505
Period size: 56 Copynumber: 6.5 Consensus size: 56
3859660 ATTCCTCACC
* * *
3859670 TTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAATGTCA-A
1 TTTTCAAAGCCCACAAGTCAGTGGCA-CATTTTC-AAAGCCCACAAGTCAGTGGCACA
** *
3859727 CCTTCAAAAGCCCACAAGTTAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCACA
1 TTTTC-AAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCACA
3859784 TTTTCAAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCACA
1 TTTTCAAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCACA
* * *
3859840 TTTTCAAAGCCCACAAGTCAGTGGCACTTTTTCAAAGCCCACAAGTTAGTGGCACT
1 TTTTCAAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCACA
* * * *
3859896 TTTTCAAAGCCCACAAGTCAGTGGCACTTTTTCAAAGGCCACAAGTTAGTGGCACC
1 TTTTCAAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCACA
** *
3859952 TTTTCAAAGCCCACAAGTCAGTGGCA-ACCTTCAAAGCCCACAAGACAGTGGCA-A
1 TTTTCAAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCACA
** *
3860006 CCTTCAAAGCCCACAAGACAGTGGCA
1 TTTTCAAAGCCCACAAGTCAGTGGCA
3860032 ACCTTCAAAA
Statistics
Matches: 279, Mismatches: 24, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
54 23 0.08
55 21 0.08
56 202 0.72
57 13 0.05
58 20 0.07
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (56 bp):
TTTTCAAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCACA
Found at i:3859828 original size:84 final size:83
Alignment explanation
Indices: 3859670--3860036 Score: 513
Period size: 84 Copynumber: 4.4 Consensus size: 83
3859660 ATTCCTCACC
* *
3859670 TTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAATGTCAACCTTCAAA
1 TTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTC-AAAGCCCACAAGTCAGTGGCAACCTTC-AA
*
3859735 AGCCCACAAGTTAGTGGCACA
63 AGCCCACAAGTCAGTGGCACA
* **
3859756 TTTTCAAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCACATTTTCAAAG
1 TTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCA-ACCTTCAAAG
3859821 CCCACAAGTCAGTGGCACA
65 CCCACAAGTCAGTGGCACA
* * *
3859840 TTTTCAAAGCCCACAAGTCAGTGGCACTTTTTCAAAGCCCACAAGTTAGTGGC-ACTTTTTCAAA
1 TTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAAC--CTTCAAA
*
3859904 GCCCACAAGTCAGTGGCACT
64 GCCCACAAGTCAGTGGCACA
* *
3859924 TTTTCAAAGGCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAGC
1 TTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAGC
*
3859989 CCACAAGACAGTGGCA-A
66 CCACAAGTCAGTGGCACA
** *
3860006 CCTTCAAAGCCCACAAGACAGTGGCAACCTT
1 TTTTCAAAGCCCACAAGTCAGTGGC-ACCTT
3860037 CAAAAGTACA
Statistics
Matches: 254, Mismatches: 22, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
82 21 0.08
83 28 0.11
84 167 0.66
85 12 0.05
86 26 0.10
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (83 bp):
TTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAGC
CCACAAGTCAGTGGCACA
Found at i:3860141 original size:21 final size:21
Alignment explanation
Indices: 3860117--3860184 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
3860107 ATATCGCTGG
3860117 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCATATTGGCA
* * **
3860138 CCTTTAAGTC--CAATGTTGTTA
1 CCTTGAA-TCAGC-ATATTGGCA
*
3860159 GCCTTGAATCAGCACATTGGCA
1 -CCTTGAATCAGCATATTGGCA
3860181 CCTT
1 CCTT
3860185 CATCTTTAAG
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
20 1 0.03
21 18 0.55
22 13 0.39
23 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (21 bp):
CCTTGAATCAGCATATTGGCA
Found at i:3860151 original size:43 final size:43
Alignment explanation
Indices: 3860099--3860233 Score: 135
Period size: 43 Copynumber: 3.0 Consensus size: 43
3860089 CATCTTCTTC
3860099 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
* * * * *
3860142 TAAGTCCAATGTTGTTAGCCTTGAATCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA----C--CTT
* ** *
3860191 TAAGTCTAATATCGCTGGCCTTGAATCAATATATTGGCGCCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
3860234 CATCATCTTT
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
43 37 0.51
45 1 0.01
47 1 0.01
49 33 0.46
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (43 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
Found at i:3860212 original size:49 final size:49
Alignment explanation
Indices: 3860094--3860427 Score: 227
Period size: 49 Copynumber: 6.8 Consensus size: 49
3860084 GGTGGCATCT
* *
3860094 TCTTCTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA----C-
1 TCTT-TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
3860139 -CTTTAAGTCCAATGTTGTTAGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * ** * *
3860187 TCTTTAAGTCTAATATCGCTGGCCTTGAATCAATATATTGGCGCCTTCATCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T--TCA
** * * *
3860239 TCTTTAAAACCAATGTTGCTGGCCTTGAATTAGCACATTGACACCTTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * * * *
3860288 TCTTTAAGTCCGATATCGTTGGCCTTGAATTAGCATATTGGCATCTTTA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * ** *
3860337 ACATTCCTAAGCCCAATGTCGCTAGCCTTGTCTCAGCACATTGGCA--TTCT
1 TC-TT--TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * *
3860387 TCTTCAAGTCTAAATGTCACTGGCCAT-AAGTCAGCACATTG
1 TCTTTAAGTC-CAATGTCGCTGGCCTTGAA-TCAGCACATTG
3860428 TCATTCTTCG
Statistics
Matches: 219, Mismatches: 56, Indels: 25
0.73 0.19 0.08
Matches are distributed among these distances:
43 34 0.16
44 3 0.01
47 5 0.02
48 23 0.11
49 80 0.37
50 6 0.03
51 1 0.00
52 67 0.31
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (49 bp):
TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
Found at i:3860286 original size:52 final size:52
Alignment explanation
Indices: 3860147--3860289 Score: 148
Period size: 52 Copynumber: 2.8 Consensus size: 52
3860137 ACCTTTAAGT
* * **
3860147 CCAATGTTGTTAGCCTTGAATCAGCACATTGGCACC-T--TCATCTTTAAGT
1 CCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCATCTTTAAAA
* * * ** * *
3860196 CTAATATCGCTGGCCTTGAATCAATATATTGGCGCCTTCATCATCTTTAAAA
1 CCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCATCTTTAAAA
* *
3860248 CCAATGTTGCTGGCCTTGAATTAGCACATTGACACCTTCATC
1 CCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
3860290 TTTAAGTCCG
Statistics
Matches: 71, Mismatches: 20, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
49 27 0.38
50 1 0.01
52 43 0.61
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (52 bp):
CCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCATCTTTAAAA
Found at i:3860326 original size:101 final size:101
Alignment explanation
Indices: 3860147--3860329 Score: 276
Period size: 101 Copynumber: 1.8 Consensus size: 101
3860137 ACCTTTAAGT
* * *
3860147 CCAATGTTGTTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCTAATATCGCTGGCCT
1 CCAATGTTGCTAGCCTTGAATCAGCACATTGACACCTTCATCTTTAAGTCCAATATCGCTGGCCT
*
3860212 TGAATCAATATATTGGCGCCTTCATCATCTTTAAAA
66 TGAATCAACATATTGGCGCCTTCATCATCTTTAAAA
* * * *
3860248 CCAATGTTGCTGGCCTTGAATTAGCACATTGACACCTTCATCTTTAAGTCCGATATCGTTGGCCT
1 CCAATGTTGCTAGCCTTGAATCAGCACATTGACACCTTCATCTTTAAGTCCAATATCGCTGGCCT
* *
3860313 TGAATTAGCATATTGGC
66 TGAATCAACATATTGGC
3860330 ATCTTTAACA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 72 1.00
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.34
Consensus pattern (101 bp):
CCAATGTTGCTAGCCTTGAATCAGCACATTGACACCTTCATCTTTAAGTCCAATATCGCTGGCCT
TGAATCAACATATTGGCGCCTTCATCATCTTTAAAA
Found at i:3860353 original size:101 final size:101
Alignment explanation
Indices: 3860142--3860379 Score: 271
Period size: 101 Copynumber: 2.4 Consensus size: 101
3860132 TTGGCACCTT
* * * *
3860142 TAAGTCCAATGTTGTTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCTAATATCGCT
1 TAAGACCAATGTTGCTAGCCTTGAATCAGCACATTGACACCTTCATCTTTAAGTCCAATATCGCT
* * * *
3860207 GGCCTTGAATCAATATATTGGCGCCTTCATCATCTT
66 GGCCTTGAATCAACATATTGGCACCTTCAACATCTC
* * * * *
3860243 TAAAACCAATGTTGCTGGCCTTGAATTAGCACATTGACACCTTCATCTTTAAGTCCGATATCGTT
1 TAAGACCAATGTTGCTAGCCTTGAATCAGCACATTGACACCTTCATCTTTAAGTCCAATATCGCT
* * * *
3860308 GGCCTTGAATTAGCATATTGGCATCTTTAACAT-TCC
66 GGCCTTGAATCAACATATTGGCACCTTCAACATCT-C
* * **
3860344 TAAGCCCAATGTCGCTAGCCTTGTCTCAGCACATTG
1 TAAGACCAATGTTGCTAGCCTTGAATCAGCACATTG
3860380 GCATTCTTCT
Statistics
Matches: 112, Mismatches: 24, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
100 1 0.01
101 111 0.99
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.34
Consensus pattern (101 bp):
TAAGACCAATGTTGCTAGCCTTGAATCAGCACATTGACACCTTCATCTTTAAGTCCAATATCGCT
GGCCTTGAATCAACATATTGGCACCTTCAACATCTC
Found at i:3861227 original size:19 final size:21
Alignment explanation
Indices: 3861184--3861234 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
3861174 CAACAATTTA
3861184 TATCGATACAAATAGTAACTG
1 TATCGATACAAATAGTAACTG
* *
3861205 TATCGATACATA-AGT-ATTG
1 TATCGATACAAATAGTAACTG
3861224 TATCGATACAA
1 TATCGATACAA
3861235 TGTATCGCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 13 0.48
20 3 0.11
21 11 0.41
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (21 bp):
TATCGATACAAATAGTAACTG
Found at i:3861283 original size:13 final size:13
Alignment explanation
Indices: 3861265--3861292 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3861255 ACCAAGGAAA
3861265 TGTATCGATACAT
1 TGTATCGATACAT
3861278 TGTATCGATACAT
1 TGTATCGATACAT
3861291 TG
1 TG
3861293 ATCTTGGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3862243 original size:21 final size:22
Alignment explanation
Indices: 3862209--3862249 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3862199 TCATGTTAAC
3862209 AGCTCATGATTCATGCATTTTG
1 AGCTCATGATTCATGCATTTTG
*
3862231 AGCT-ATGTTTCATGCATTT
1 AGCTCATGATTCATGCATTT
3862250 ACAGCATGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (22 bp):
AGCTCATGATTCATGCATTTTG
Found at i:3863529 original size:24 final size:26
Alignment explanation
Indices: 3863502--3863550 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
3863492 TCAAAATTTT
3863502 ATTCAT-C-GGGGACACTCCAACCCC
1 ATTCATCCAGGGGACACTCCAACCCC
*
3863526 ATTCCTCCTAGGGGACACTCCAACC
1 ATTCATCC-AGGGGACACTCCAACC
3863551 TCGTTTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 1 0.05
27 15 0.71
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.18
Consensus pattern (26 bp):
ATTCATCCAGGGGACACTCCAACCCC
Found at i:3864556 original size:53 final size:52
Alignment explanation
Indices: 3864466--3864565 Score: 121
Period size: 53 Copynumber: 1.9 Consensus size: 52
3864456 TGCGAGAGTT
* * *
3864466 CCAATATTGCTAACCTTGGATCAGCACGTTGTCACCTTTCTTCATCTTTAAGA
1 CCAATATTACTAACCTTGGATCAGCACGTGGTCACC-TTCATCATCTTTAAGA
* * *
3864519 CCAATGTTACTAACCTTGGATCAGTATGCTGGT-ACCTTCATCATCTT
1 CCAATATTACTAACCTTGGATCAGCACG-TGGTCACCTTCATCATCTT
3864566 CAAATTCAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
52 10 0.25
53 27 0.68
54 3 0.08
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (52 bp):
CCAATATTACTAACCTTGGATCAGCACGTGGTCACCTTCATCATCTTTAAGA
Found at i:3864616 original size:2 final size:2
Alignment explanation
Indices: 3864609--3864637 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3864599 AATACCCAAA
3864609 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3864638 AGACTTCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3864732 original size:31 final size:31
Alignment explanation
Indices: 3864689--3864929 Score: 172
Period size: 31 Copynumber: 7.7 Consensus size: 31
3864679 TCACTTTGCA
3864689 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
* * *
3864720 AAAGTCCACACAAGTCAGTGGCAATCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
* * ** *
3864751 AAAGCCCACACAAATCGGTCGCAACATTTTT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
* *
3864782 AAAGCCCACGAC---TCCGTGGC-ACCTTTTTCTTTT
1 AAAGCCCAC-ACAAGTCGGTGGCAACC-----CTTCT
* * *
3864815 CATAG-CC-CACAACTCTGG-GGCAACCTTTCT
1 -AAAGCCCACACAAGTC-GGTGGCAACCCTTCT
3864845 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
* * ** *
3864876 AAAGTCTACACAAGTTTGTAGCAACCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
* * *
3864907 AAAGCCCATATAAGTCGATGGCA
1 AAAGCCCACACAAGTCGGTGGCA
3864930 TCTCTTTCTA
Statistics
Matches: 160, Mismatches: 35, Indels: 30
0.71 0.16 0.13
Matches are distributed among these distances:
28 2 0.01
29 9 0.06
30 7 0.04
31 121 0.76
32 3 0.02
33 6 0.04
34 8 0.05
35 4 0.03
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (31 bp):
AAAGCCCACACAAGTCGGTGGCAACCCTTCT
Found at i:3865257 original size:95 final size:91
Alignment explanation
Indices: 3865039--3865269 Score: 275
Period size: 94 Copynumber: 2.5 Consensus size: 91
3865029 ATTGGCACCT
** * * *
3865039 TCATCTTTAAGACCAATGTTGCTGGACTTGAATCAGCACATTAGCACAAGCCCAATATTGCTAGC
1 TCATCTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTAGC
* *
3865104 CTTAAATTAGTATATTGGCACCTTTA
66 CTTAAATCAGTATATTGACACCTTTA
* * * *
3865130 TCATCTTTGAGTCC-ATGTCACTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCTATATCGC
1 TCATCTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCA-C---AAGCCCAATATCGC
* * * *
3865194 TGGCCTTGAATCAGTATATTGACGCCTTTG
62 TAGCCTTAAATCAGTATATTGACACCTTTA
*
3865224 TCATTTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCA
1 TCATCTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCA
3865270 TTCTTTTTAT
Statistics
Matches: 117, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
90 27 0.23
91 13 0.11
94 46 0.39
95 31 0.26
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.32
Consensus pattern (91 bp):
TCATCTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTAGC
CTTAAATCAGTATATTGACACCTTTA
Found at i:3865301 original size:52 final size:51
Alignment explanation
Indices: 3865236--3865478 Score: 240
Period size: 52 Copynumber: 4.7 Consensus size: 51
3865226 ATTTTTAAGA
* * **
3865236 CCAATGTCACTGGCCTTGAATCAGCACATTGGCA-TTCTTTTTATCTTCAAAT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTCTTCTT-TC-TCAAGC
* * * * *
3865288 CTAGTGTCTCTGGCCTTGAATCAACACATTGGCACCTTCTTCTTTCCCAAGC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTTCTTCTTTCTCAAGC
* *
3865340 CCAATGTCGTTGGCTTTGAATCAGCACATTGGCACTTTCTTCTTTCTCAAGC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC-TTCTTCTTTCTCAAGC
* * **
3865392 CCAATGTCGCTAGCCTTGAATCAGCACATTAGCA-TTCTT-TTCATCTACAATT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTCTTCTT--TCT-CAAGC
* **
3865444 CCAATATCGCTGGCCTTGAATCAGCATGTTGGCAC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
3865479 CATTATCATT
Statistics
Matches: 158, Mismatches: 26, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
49 2 0.01
50 5 0.03
51 4 0.03
52 138 0.87
53 2 0.01
54 7 0.04
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.34
Consensus pattern (51 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTCTTCTTTCTCAAGC
Found at i:3865513 original size:61 final size:61
Alignment explanation
Indices: 3865444--3865560 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
3865434 ATCTACAATT
* * * * *
3865444 CCAATATCGCTGGCCTTGAATCAGCATGTTGGCACCATTATCATTTTTCTCATCTTTAAGC
1 CCAATATCGCTGGCCATGAATCAGCATATTAGCACCATTATCACTCTTCTCATCTTTAAGC
* *
3865505 CCAATATCGCTGGCCATGAATCAGCATATTAGCATCTTTATCACTCTTCTCATCTT
1 CCAATATCGCTGGCCATGAATCAGCATATTAGCACCATTATCACTCTTCTCATCTT
3865561 CATCATCTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (61 bp):
CCAATATCGCTGGCCATGAATCAGCATATTAGCACCATTATCACTCTTCTCATCTTTAAGC
Found at i:3866228 original size:13 final size:13
Alignment explanation
Indices: 3866210--3866235 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3866200 ACATAAGTTT
3866210 TGTATCGATACAA
1 TGTATCGATACAA
3866223 TGTATCGATACAA
1 TGTATCGATACAA
3866236 AGCTACCCTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3871988 original size:52 final size:52
Alignment explanation
Indices: 3871921--3872181 Score: 195
Period size: 52 Copynumber: 5.0 Consensus size: 52
3871911 ATGATGCTGA
3871921 ACTTAATGATGATAAAGGTGTCAATGTGTTGATTCAAGGCCAGAAACATTAG
1 ACTTAATGATGATAAAGGTGTCAATGTGTTGATTCAAGGCCAGAAACATTAG
* * * * * ** *
3871973 ACTTAATGATTATAAAGATGCCAATATGCTGATTCAAGGCCATCAACATTGG
1 ACTTAATGATGATAAAGGTGTCAATGTGTTGATTCAAGGCCAGAAACATTAG
* * * * * *** *
3872025 ATTTAAGGATGATGAGGGTGTCAATGTGTTGATTCAAGGCTATTGACATTGG
1 ACTTAATGATGATAAAGGTGTCAATGTGTTGATTCAAGGCCAGAAACATTAG
* * * * * * * * ** *
3872077 ATTTAAAGATGACAAAGGTGTTAATATGCTGATTCAAGACTAGCGATATTAG
1 ACTTAATGATGATAAAGGTGTCAATGTGTTGATTCAAGGCCAGAAACATTAG
* * *
3872129 ACTTTAA-GATGA-CAAGAGTG-CTAATGTGCTGATTCAAGGCCAGCAACATTAG
1 AC-TTAATGATGATAAAG-GTGTC-AATGTGTTGATTCAAGGCCAGAAACATTAG
3872181 A
1 A
3872182 GTTGATAAAG
Statistics
Matches: 166, Mismatches: 40, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
51 3 0.02
52 159 0.96
53 4 0.02
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.30
Consensus pattern (52 bp):
ACTTAATGATGATAAAGGTGTCAATGTGTTGATTCAAGGCCAGAAACATTAG
Found at i:3872108 original size:104 final size:104
Alignment explanation
Indices: 3871923--3872181 Score: 254
Period size: 104 Copynumber: 2.5 Consensus size: 104
3871913 GATGCTGAAC
* * * *
3871923 TTAATGATGATAAAGGTGTCAATGTGTTGATTCAAGGCCAGAAACATTAGACTTAATGATTATAA
1 TTAAGGATGATAAAGGTGTCAATGTGTTGATTCAAGGCCAGAAACATTAGACTTAAAGATGACAA
3871988 AGATGCCAATATGCTGATTCAAGGCCATCAACATTGGAT
66 AGATGCCAATATGCTGATTCAAGGCCATCAACATTGGAT
* * * *** * *
3872027 TTAAGGATGATGAGGGTGTCAATGTGTTGATTCAAGGCTATTGACATTGGATTTAAAGATGACAA
1 TTAAGGATGATAAAGGTGTCAATGTGTTGATTCAAGGCCAGAAACATTAGACTTAAAGATGACAA
* ** * * * * * *
3872092 AGGTGTTAATATGCTGATTCAAGACTAGCGATATTAGACT
66 AGATGCCAATATGCTGATTCAAGGCCATCAACATTGGA-T
* * *
3872132 TTAA-GATGA-CAAGAGTG-CTAATGTGCTGATTCAAGGCCAGCAACATTAGA
1 TTAAGGATGATAAAG-GTGTC-AATGTGTTGATTCAAGGCCAGAAACATTAGA
3872182 GTTGATAAAG
Statistics
Matches: 123, Mismatches: 29, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
103 3 0.02
104 115 0.93
105 5 0.04
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (104 bp):
TTAAGGATGATAAAGGTGTCAATGTGTTGATTCAAGGCCAGAAACATTAGACTTAAAGATGACAA
AGATGCCAATATGCTGATTCAAGGCCATCAACATTGGAT
Found at i:3872346 original size:32 final size:32
Alignment explanation
Indices: 3872310--3872569 Score: 235
Period size: 32 Copynumber: 8.2 Consensus size: 32
3872300 TAGAATGAAA
*
3872310 TGCCATCGACTTGTGTGGGCTTTGAAAGAGGT
1 TGCCATCGACTTGTGTGGGCTTTGAAAAAGGT
* * * *
3872342 TGCCATCAACTTATGTGGCCTTTTGAAAAGGGT
1 TGCCATCGACTTGTGTGGGC-TTTGAAAAAGGT
* * **
3872375 TG-CACCAACTTGTGTGGGCTTTGAAAAAGAA
1 TGCCATCGACTTGTGTGGGCTTTGAAAAAGGT
* *
3872406 TGCCACCGACTTGTGTGGCCTTTTGAAAAAGGT
1 TGCCATCGACTTGTGTGGGC-TTTGAAAAAGGT
* * *
3872439 TG-C-TCGACTTGTGTAGTCTTTGAAAAAGGA
1 TGCCATCGACTTGTGTGGGCTTTGAAAAAGGT
3872469 TGCCA-CTGACTTGTGTGGGCTTTTG-AAAAGGAT
1 TGCCATC-GACTTGTGTGGGC-TTTGAAAAAGG-T
* *
3872502 TGCCATCGACTTGTGTGGGCTTT-AAAAATGA
1 TGCCATCGACTTGTGTGGGCTTTGAAAAAGGT
* * * ** *
3872533 TGCCACCAACTTGTGTCGATTTTGAAAAGGGT
1 TGCCATCGACTTGTGTGGGCTTTGAAAAAGGT
3872565 TGCCA
1 TGCCA
3872570 CTGACTTATG
Statistics
Matches: 185, Mismatches: 32, Indels: 22
0.77 0.13 0.09
Matches are distributed among these distances:
30 13 0.07
31 43 0.23
32 82 0.44
33 46 0.25
34 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.31
Consensus pattern (32 bp):
TGCCATCGACTTGTGTGGGCTTTGAAAAAGGT
Found at i:3872423 original size:64 final size:64
Alignment explanation
Indices: 3872313--3872567 Score: 318
Period size: 64 Copynumber: 4.0 Consensus size: 64
3872303 AATGAAATGC
* * * *
3872313 CATCGACTTGTGTGGGCTTTGAAAGAGGTTGCCATCAACTTATGTGGCCTTTTGAAAAGGGTTG
1 CATCGACTTGTGTGGGCTTTGAAAAAGGATGCCACCAACTTGTGTGGCCTTTTGAAAAGGGTTG
* * * * *
3872377 CACCAACTTGTGTGGGCTTTGAAAAAGAATGCCACCGACTTGTGTGGCCTTTTGAAAAAGGTTG
1 CATCGACTTGTGTGGGCTTTGAAAAAGGATGCCACCAACTTGTGTGGCCTTTTGAAAAGGGTTG
* * ** * *
3872441 C-TCGACTTGTGTAGTCTTTGAAAAAGGATGCCACTGACTTGTGTGGGCTTTTGAAAAGGATTG
1 CATCGACTTGTGTGGGCTTTGAAAAAGGATGCCACCAACTTGTGTGGCCTTTTGAAAAGGGTTG
* * *
3872504 CCATCGACTTGTGTGGGCTTT-AAAAATGATGCCACCAACTTGTGTCG-ATTTTGAAAAGGGTTG
1 -CATCGACTTGTGTGGGCTTTGAAAAAGGATGCCACCAACTTGTGTGGCCTTTTGAAAAGGGTTG
3872567 C
1 C
3872568 CACTGACTTA
Statistics
Matches: 163, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
62 1 0.01
63 67 0.41
64 79 0.48
65 16 0.10
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.31
Consensus pattern (64 bp):
CATCGACTTGTGTGGGCTTTGAAAAAGGATGCCACCAACTTGTGTGGCCTTTTGAAAAGGGTTG
Found at i:3872545 original size:96 final size:96
Alignment explanation
Indices: 3872308--3872576 Score: 314
Period size: 96 Copynumber: 2.8 Consensus size: 96
3872298 CTTAGAATGA
* * * *
3872308 AATGCCATCGACTTGTGTGGGCTTTGAAAGAGGTTGCCATCAACTTATGTGGCCTTTTGAAAAGG
1 AATGCCATCGACTTGTGTGGGCTTTGAAAAAGGTTGCCATCAACTTGTGTAGTC-TTTGAAAAGG
**
3872373 GTTG-CACCAACTTGTGTGGGCTTTGAAAAAG
65 GTTGCCACTGACTTGTGTGGGCTTTGAAAAAG
* * * *
3872404 AATGCCACCGACTTGTGTGGCCTTTTGAAAAAGGTTG-C-TCGACTTGTGTAGTCTTTGAAAAAG
1 AATGCCATCGACTTGTGTGGGC-TTTGAAAAAGGTTGCCATCAACTTGTGTAGTCTTTGAAAAGG
* *
3872467 GATGCCACTGACTTGTGTGGGCTTTTGAAAAGG
65 GTTGCCACTGACTTGTGTGGGC-TTTGAAAAAG
* * * * *
3872500 ATTGCCATCGACTTGTGTGGGCTTT-AAAAATGATGCCACCAACTTGTGTCGAT-TTTGAAAAGG
1 AATGCCATCGACTTGTGTGGGCTTTGAAAAAGGTTGCCATCAACTTGTGTAG-TCTTTGAAAAGG
3872563 GTTGCCACTGACTT
65 GTTGCCACTGACTT
3872577 ATGTAGGCAT
Statistics
Matches: 145, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
94 20 0.14
95 30 0.21
96 81 0.56
97 14 0.10
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (96 bp):
AATGCCATCGACTTGTGTGGGCTTTGAAAAAGGTTGCCATCAACTTGTGTAGTCTTTGAAAAGGG
TTGCCACTGACTTGTGTGGGCTTTGAAAAAG
Found at i:3872545 original size:127 final size:126
Alignment explanation
Indices: 3872315--3872567 Score: 323
Period size: 127 Copynumber: 2.0 Consensus size: 126
3872305 TGAAATGCCA
* * * *
3872315 TCGACTTGTGTGGGCTTTGAAAGAGGTTGCCATCAACTTATGTGGCCTTTTGAAAAGGGTTGCAC
1 TCGACTTGTGTAGGCTTTGAAAAAGGATGCCATCAACTTATGTGGCCTTTTGAAAAGGATTGCAC
* * *
3872380 CAACTTGTGTGGGCTTTGAAAAAGAATGCCACCGACTTGTGTGGCCTTTTGAAAAAGGTTGC
66 CAACTTGTGTGGGCTTTGAAAAAGAATGCCACCAACTTGTGTCG-ATTTTGAAAAAGGTTGC
* * * *
3872442 TCGACTTGTGTAGTCTTTGAAAAAGGATGCCA-CTGACTTGTGTGGGCTTTTGAAAAGGATTGCC
1 TCGACTTGTGTAGGCTTTGAAAAAGGATGCCATC-AACTTATGTGGCCTTTTGAAAAGGATTG-C
* * *
3872506 ATCGACTTGTGTGGGCTTT-AAAAATG-ATGCCACCAACTTGTGTCGATTTTGAAAAGGGTTGC
64 ACCAACTTGTGTGGGCTTTGAAAAA-GAATGCCACCAACTTGTGTCGATTTTGAAAAAGGTTGC
3872568 CACTGACTTA
Statistics
Matches: 109, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
126 16 0.15
127 74 0.68
128 19 0.17
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.32
Consensus pattern (126 bp):
TCGACTTGTGTAGGCTTTGAAAAAGGATGCCATCAACTTATGTGGCCTTTTGAAAAGGATTGCAC
CAACTTGTGTGGGCTTTGAAAAAGAATGCCACCAACTTGTGTCGATTTTGAAAAAGGTTGC
Found at i:3872659 original size:30 final size:29
Alignment explanation
Indices: 3872596--3872944 Score: 247
Period size: 30 Copynumber: 11.8 Consensus size: 29
3872586 TTTAAGAAAT
** *
3872596 GTGCCACCAAGTTGTGAACTTTGAGAAAGGG
1 GTGCCACGGAGTTGTGGACTTTGA-AAA-GG
* *
3872627 GTGCCATGGAGTTATGGACTTTAGAAAAGG
1 GTGCCACGGAGTTGTGGACTTT-GAAAAGG
** * *
3872657 GTGCCACAAAGTAGTGAACTTTGAAAA-G
1 GTGCCACGGAGTTGTGGACTTTGAAAAGG
** **
3872685 GTGCCATAGAGTTGTGGACTTTGAAAACT
1 GTGCCACGGAGTTGTGGACTTTGAAAAGG
* *
3872714 GTGCTACGGAGTTGTGGACTTTGAAAAAG
1 GTGCCACGGAGTTGTGGACTTTGAAAAGG
* *
3872743 GTG-CACGGAGTTGTGAACTTTTGAAAAAG
1 GTGCCACGGAGTTGTGGAC-TTTGAAAAGG
* * * * *
3872772 GTGCCATGAAGTCGTGGACATTGCGAAAGG
1 GTGCCACGGAGTTGTGGACTTTG-AAAAGG
* * *
3872802 GTGCCACGGAGCTGTAGACTCTTGAAAATG
1 GTGCCACGGAGTTGTGGACT-TTGAAAAGG
* ** *
3872832 GTGCCATGGAGTCATGGACTTTAAAAAGGG
1 GTGCCACGGAGTTGTGGACTTTGAAAA-GG
* * * *
3872862 GTGACACGAAGTTATGGACTTTAGAAAAAAG
1 GTGCCACGGAGTTGTGGACTTT-G-AAAAGG
* *
3872893 GTGCCACGAAGTTGTGGACTTT-AAGAGGG
1 GTGCCACGGAGTTGTGGACTTTGAA-AAGG
*
3872922 GATG-CATGGAGTTGTGGACTTTG
1 G-TGCCACGGAGTTGTGGACTTTG
3872945 GGAAATAGTG
Statistics
Matches: 249, Mismatches: 57, Indels: 25
0.75 0.17 0.08
Matches are distributed among these distances:
28 39 0.16
29 73 0.29
30 87 0.35
31 44 0.18
32 6 0.02
ACGTcount: A:0.30, C:0.13, G:0.32, T:0.25
Consensus pattern (29 bp):
GTGCCACGGAGTTGTGGACTTTGAAAAGG
Found at i:3872789 original size:87 final size:86
Alignment explanation
Indices: 3872626--3872835 Score: 217
Period size: 87 Copynumber: 2.4 Consensus size: 86
3872616 TTGAGAAAGG
* * *
3872626 GGTGCCATGGAGTTATGGACTTTAGAAAAGGGTGCCACAAAGTAGTGAACTTTGAAAAGGTGCCA
1 GGTGCCACGGAGTTGTGGACTTT-GAAAAAGGTG-CACAAAGTAGTGAACTTTGAAAAGGTGCCA
* *
3872691 TAGAGTTGTGGACTTTG-AAAAC
64 TAGAGTCGTGGACATTGCAAAAC
* * ** *
3872713 TGTGCTACGGAGTTGTGGACTTTGAAAAAGGTGCACGGAGTTGTGAACTTTTGAAAAAGGTGCCA
1 GGTGCCACGGAGTTGTGGACTTTGAAAAAGGTGCACAAAGTAGTGAAC-TTTG-AAAAGGTGCCA
* *
3872778 T-GAAGTCGTGGACATTGCGAAAG
64 TAG-AGTCGTGGACATTGCAAAAC
* * *
3872801 GGTGCCACGGAGCTGTAGACTCTTGAAAATGGTGC
1 GGTGCCACGGAGTTGTGGACT-TTGAAAAAGGTGC
3872836 CATGGAGTCA
Statistics
Matches: 101, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
85 12 0.12
86 14 0.14
87 43 0.43
88 20 0.20
89 12 0.12
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.25
Consensus pattern (86 bp):
GGTGCCACGGAGTTGTGGACTTTGAAAAAGGTGCACAAAGTAGTGAACTTTGAAAAGGTGCCATA
GAGTCGTGGACATTGCAAAAC
Found at i:3875949 original size:50 final size:51
Alignment explanation
Indices: 3875874--3875989 Score: 189
Period size: 51 Copynumber: 2.3 Consensus size: 51
3875864 AGAGATGGTA
*
3875874 GGGTTGGAGTATCCCCGAGATGAAAA-TTTAATATGTTGGAAGTAAAAACG
1 GGGTTGGAGTATCCCCAAGATGAAAATTTTAATATGTTGGAAGTAAAAACG
* *
3875924 GGGTTGGAGTATCCCCAAGATGAAAATTTTAATATTTTTGAAGTAAAAACG
1 GGGTTGGAGTATCCCCAAGATGAAAATTTTAATATGTTGGAAGTAAAAACG
*
3875975 GGGTTAGAGTATCCC
1 GGGTTGGAGTATCCC
3875990 TTCAAAAATA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 25 0.41
51 36 0.59
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.28
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCAAGATGAAAATTTTAATATGTTGGAAGTAAAAACG
Found at i:3876028 original size:29 final size:28
Alignment explanation
Indices: 3875974--3876046 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
3875964 AAGTAAAAAC
* *
3875974 GGGGTTAGAGTATCCCTTCAAAAATAAT
1 GGGGTTGGAGTATCCCCTCAAAAATAAT
* *
3876002 GGGGTTGGAGTAGTCCCCTCAGAAATATT
1 GGGGTTGGAGTA-TCCCCTCAAAAATAAT
*
3876031 GAGG-TGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
3876047 GTTGATGAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 5 0.13
28 18 0.46
29 16 0.41
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCTCAAAAATAAT
Found at i:3876071 original size:108 final size:106
Alignment explanation
Indices: 3875928--3876126 Score: 281
Period size: 108 Copynumber: 1.9 Consensus size: 106
3875918 AAAACGGGGT
* *
3875928 TGGAGTATCCCCAAGATGAAAATTTTAATATTTTTGAAGTAAAAACGGGGTTAGAGTATCCCTTC
1 TGGAGTATCCCCAAGATGAAAAATTCAATATTTTTGAAGTAAAAACGGGGTTAGAGTATCCCTTC
* *
3875993 AAAAATAATGGGGTTGGAGTAGTCCCCTCAGAAATATTGAGG
66 AAAAATAATAGGGTTAGAGTA-TCCCCTCAGAAATATTGAGG
** * * *
3876035 TGGAGTATCCCCGTTGATGAAAAATTCGATATTTTTGAAGTAAAAATGGGGTTAGAGTATCGCTT
1 TGGAGTATCCCC-AAGATGAAAAATTCAATATTTTTGAAGTAAAAACGGGGTTAGAGTATCCCTT
* *
3876100 CGAAAATGATAGGGTTAGAGTATCCCC
65 CAAAAATAATAGGGTTAGAGTATCCCC
3876127 GAAGGTGAAA
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
107 17 0.21
108 63 0.79
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (106 bp):
TGGAGTATCCCCAAGATGAAAAATTCAATATTTTTGAAGTAAAAACGGGGTTAGAGTATCCCTTC
AAAAATAATAGGGTTAGAGTATCCCCTCAGAAATATTGAGG
Found at i:3876085 original size:80 final size:81
Alignment explanation
Indices: 3875999--3876339 Score: 266
Period size: 81 Copynumber: 4.2 Consensus size: 81
3875989 CTTCAAAAAT
* ***
3875999 AATGGGGTTGGAGTAGTCCCCTCAGAAAT-ATTGAGG-TGGAGTATCCCCGTTGATGAAAAATTC
1 AATGGGGTTGGAGTA-TCCCCTCAGAAATGATTGGGGTTGGAGTATCCCCAAAGATGAAAAATTC
* *
3876062 GATATTTTTGAAGTAAA
65 AATATTTTAGAAGTAAA
* * * * * * * * *
3876079 AATGGGGTTAGAGTATCGCTTC-GAAAATGA-TAGGGTTAGAGTATCCCCGAAGGTGAAAATTTT
1 AATGGGGTTGGAGTATCCCCTCAG-AAATGATTGGGGTTGGAGTATCCCCAAAGATGAAAAATTC
* *
3876142 AATATTTTAAAATTAAA
65 AATATTTTAGAAGTAAA
** * * * *
3876159 AATAGGGACTGGAGTATCCTCTCAGAAAT-AATGGGGTTGAAGTATCCCCAATGATGAAAAATTC
1 AAT-GGGGTTGGAGTATCCCCTCAGAAATGATTGGGGTTGGAGTATCCCCAAAGATGAAAAATTC
*
3876223 AATATTTTGGAAGTAAAA
65 AATATTTTAGAAGT-AAA
* * * * * *
3876241 AATGAGGTTAGAGTATCCTCTAAGAAATGA-TGGGGTTGGAGTATCCCTCATAG-TG-AAAATTT
1 AATGGGGTTGGAGTATCCCCTCAGAAATGATTGGGGTTGGAGTATCCC-CAAAGATGAAAAATTC
* * *
3876303 GATGCTTTTAGAAGTTAA
65 AAT-ATTTTAGAAGTAAA
*
3876321 AATAGGGTTGGAGTATCCC
1 AATGGGGTTGGAGTATCCC
3876340 TTTAGCGATG
Statistics
Matches: 202, Mismatches: 49, Indels: 20
0.75 0.18 0.07
Matches are distributed among these distances:
78 1 0.00
79 12 0.06
80 78 0.39
81 100 0.50
82 11 0.05
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (81 bp):
AATGGGGTTGGAGTATCCCCTCAGAAATGATTGGGGTTGGAGTATCCCCAAAGATGAAAAATTCA
ATATTTTAGAAGTAAA
Found at i:3876335 original size:161 final size:159
Alignment explanation
Indices: 3876003--3876339 Score: 398
Period size: 162 Copynumber: 2.1 Consensus size: 159
3875993 AAAAATAATG
* * ** *
3876003 GGGTTGGAGTAGTCCCCTCAGAAATATTGAGGTGGAGTATCCCCGTTGATGAAAAATTCGATATT
1 GGGTTGGAGTA-TCCCCTCAGAAATAATGAGGTGAAGTATCCCCAATGATGAAAAATTCAATATT
* * *
3876068 TTTGAAGTAAAAATGGGGTTAGAGTATCGCTTCGAAAATGATAGGGTTAGAGTATCCCCGAAGGT
65 TTGGAAGTAAAAATGAGGTTAGAGTATCGCTTAGAAAATGATAGGGTTAGAGTATCCCCGAAGGT
3876133 GAAAATTTTAATATTTTAAAATTAAAAATA
130 GAAAATTTTAATATTTTAAAATTAAAAATA
* * *
3876163 GGGACTGGAGTATCCTCTCAGAAATAATGGGGTTGAAGTATCCCCAATGATGAAAAATTCAATAT
1 GGG-TTGGAGTATCCCCTCAGAAATAATGAGG-TGAAGTATCCCCAATGATGAAAAATTCAATAT
* *
3876228 TTTGGAAGTAAAAAATGAGGTTAGAGTATC-CTCTA-AGAAATGATGGGGTTGGAGTATCCCTC-
64 TTTGGAAGT-AAAAATGAGGTTAGAGTATCGCT-TAGA-AAATGATAGGGTTAGAGTATCCC-CG
* * *
3876290 ATA-GTGAAAA-TTTGATGCTTTTAGAAGTT-AAAATA
125 A-AGGTGAAAATTTTAAT-ATTTTA-AAATTAAAAATA
3876325 GGGTTGGAGTATCCC
1 GGGTTGGAGTATCCC
3876340 TTTAGCGATG
Statistics
Matches: 150, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
160 20 0.13
161 61 0.41
162 63 0.42
163 6 0.04
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.30
Consensus pattern (159 bp):
GGGTTGGAGTATCCCCTCAGAAATAATGAGGTGAAGTATCCCCAATGATGAAAAATTCAATATTT
TGGAAGTAAAAATGAGGTTAGAGTATCGCTTAGAAAATGATAGGGTTAGAGTATCCCCGAAGGTG
AAAATTTTAATATTTTAAAATTAAAAATA
Found at i:3878502 original size:51 final size:51
Alignment explanation
Indices: 3878440--3878577 Score: 181
Period size: 51 Copynumber: 2.7 Consensus size: 51
3878430 AATGGCCTGC
* *
3878440 ATGTATCGATATATTGAAGAATGTATCGATACATTTGGGT-CAAAACCCATA
1 ATGTATCGATATATT-AAGAATGTATCGATACATTTGGGTAAAAAACCCAGA
* *
3878491 ATGTATCGATATAATTAATAATGTATCGATATATTTGGGTAAAAAACCCAGA
1 ATGTATCGATAT-ATTAAGAATGTATCGATACATTTGGGTAAAAAACCCAGA
* *
3878543 ATGTATCGATACAAT-AGAAATGTATCGATACATTT
1 ATGTATCGATATATTAAG-AATGTATCGATACATTT
3878578 TCCTTTTAGA
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
50 1 0.01
51 52 0.68
52 23 0.30
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.33
Consensus pattern (51 bp):
ATGTATCGATATATTAAGAATGTATCGATACATTTGGGTAAAAAACCCAGA
Found at i:3878659 original size:20 final size:21
Alignment explanation
Indices: 3878634--3878687 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
3878624 CATTTTAGAT
* *
3878634 ATGTATCGATATATTGAC-TA
1 ATGTATCGATACATTCACTTA
*
3878654 ATGTATCAATACATTCACTTA
1 ATGTATCGATACATTCACTTA
*
3878675 TTGTATCGATACA
1 ATGTATCGATACA
3878688 AATTGTAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (21 bp):
ATGTATCGATACATTCACTTA
Found at i:3884925 original size:53 final size:52
Alignment explanation
Indices: 3884831--3884944 Score: 138
Period size: 53 Copynumber: 2.2 Consensus size: 52
3884821 AGAATGTAAA
* * * *
3884831 AATATATTTAGGTCAAAAACTCAAAATATATCGATATAATGAAAAATATATT
1 AATACATTTAGGTCAAAAACCCAAAATATATCGATACAATGAAAAATATATC
* * * * *
3884883 GATACATTTAGGGTCAAAAACCCAGAATGTATTGATACAATGAAAAATGTATC
1 AATACATTTA-GGTCAAAAACCCAAAATATATCGATACAATGAAAAATATATC
3884936 AATACATTT
1 AATACATTT
3884945 TCTTTCCAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
52 8 0.16
53 43 0.84
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (52 bp):
AATACATTTAGGTCAAAAACCCAAAATATATCGATACAATGAAAAATATATC
Found at i:3886542 original size:67 final size:68
Alignment explanation
Indices: 3886443--3886616 Score: 163
Period size: 67 Copynumber: 2.6 Consensus size: 68
3886433 TACAAATTTG
* * * * * * *
3886443 CATATAATGGAGAAGTCAACTATCGAGATCTCATGCACC-CCTTCTTTCACTCTTACA-TATAAG
1 CATATAGTAGAGAAGTCAACTATTGTGGTCTCATGCACCACCTTCATT-ACTCTTACATTACAAG
*
3886506 TTTT
65 TTCT
* * ** *
3886510 CATATAGTAGAGAAGTCAACTGTTGTGGTCTCATACACCATTTTCATTATTCTTACATTTACAAG
1 CATATAGTAGAGAAGTCAACTATTGTGGTCTCATGCACCACCTTCATTACTCTTACA-TTACAAG
3886575 TTCT
65 TTCT
* * * *
3886579 CACATAGTAGAGAAGTCAATTATTATGGTCTCGTGCAC
1 CATATAGTAGAGAAGTCAACTATTGTGGTCTCATGCAC
3886617 AAAGTACTTC
Statistics
Matches: 85, Mismatches: 19, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
67 40 0.47
68 5 0.06
69 40 0.47
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (68 bp):
CATATAGTAGAGAAGTCAACTATTGTGGTCTCATGCACCACCTTCATTACTCTTACATTACAAGT
TCT
Found at i:3888020 original size:32 final size:27
Alignment explanation
Indices: 3887984--3888045 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 27
3887974 GGTCCTGCAA
3887984 AAATATGAAAATATTAAATAACAATATAATTT
1 AAATAT-AAAA-A-TAAATAA-AAT-TAATTT
3888016 AAATATAAAAATAAATAAAATTAATTT
1 AAATATAAAAATAAATAAAATTAATTT
3888043 AAA
1 AAA
3888046 ATTATTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
27 9 0.30
28 3 0.10
29 7 0.23
30 1 0.03
31 4 0.13
32 6 0.20
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (27 bp):
AAATATAAAAATAAATAAAATTAATTT
Found at i:3888065 original size:11 final size:11
Alignment explanation
Indices: 3888032--3888066 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3888022 AAAAATAAAT
*
3888032 AAAATTAATTT
1 AAAATTAATTA
*
3888043 AAAATTATTTA
1 AAAATTAATTA
3888054 AAAATTAATTA
1 AAAATTAATTA
3888065 AA
1 AA
3888067 TCTAAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAATTAATTA
Found at i:3888078 original size:21 final size:22
Alignment explanation
Indices: 3888021--3888078 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
3888011 AATTTAAATA
*
3888021 TAAAAATAAAT-AAAATTAATT
1 TAAAATTAAATAAAAATTAATT
**
3888042 TAAAATTATTTAAAAATTAA-T
1 TAAAATTAAATAAAAATTAATT
3888063 T-AAATCTAAATAAAAA
1 TAAAAT-TAAATAAAAA
3888079 ATTCAAAGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 4 0.13
21 18 0.60
22 8 0.27
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAAATTAAATAAAAATTAATT
Found at i:3888282 original size:32 final size:33
Alignment explanation
Indices: 3888221--3888284 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
3888211 GCACTTTTCT
* *
3888221 TTTTCTCATTTTCCTTTTTTTCTTATTTTTTGA
1 TTTTCTCAATTTCCTTTTTTACTTATTTTTTGA
*
3888254 TTTTC-CAATTTCCTTTTTTACGT-TTTTTTGA
1 TTTTCTCAATTTCCTTTTTTACTTATTTTTTGA
3888285 AATAAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 8 0.29
32 15 0.54
33 5 0.18
ACGTcount: A:0.11, C:0.16, G:0.05, T:0.69
Consensus pattern (33 bp):
TTTTCTCAATTTCCTTTTTTACTTATTTTTTGA
Found at i:3888942 original size:20 final size:21
Alignment explanation
Indices: 3888904--3888943 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3888894 TTATTTTGTT
*
3888904 ATTTTTCTTTTTTAATTTTTA
1 ATTTTTCTTTTCTAATTTTTA
*
3888925 ATTTTT-TTTTCTAGTTTTT
1 ATTTTTCTTTTCTAATTTTT
3888944 GGGTTCTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.78
Consensus pattern (21 bp):
ATTTTTCTTTTCTAATTTTTA
Done.