Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008460.1 Hibiscus syriacus cultivar Beakdansim tig00111273_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2854393
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 15
Found at i:1273920 original size:43 final size:38
Alignment explanation
Indices: 1273819--1274002 Score: 135
Period size: 38 Copynumber: 5.1 Consensus size: 38
1273809 TATAAGTTTT
* **
1273819 AAAACATTTT-GAAAA-TTATATAGTATATAGTTT-TG
1 AAAACATTTTGGAAAACTTATATAATATATAGTTTAAA
*
1273854 AAATCATTTT-G-AAA---ATATAATATATAGTTTTTTAAAA
1 AAAACATTTTGGAAAACTTATATAATATATAG---TTT-AAA
* *
1273891 AAAACATTTTTTGAAAATTTATATAATATATAGTTTAAA
1 AAAACA-TTTTGGAAAACTTATATAATATATAGTTTAAA
1273930 AAAACATTTTGGAAAACTTATATAATAT-T--TTT--A
1 AAAACATTTTGGAAAACTTATATAATATATAGTTTAAA
* * * *
1273963 AAATCATTTTTGAAAAC-TATATGATATATAGTTTTAA
1 AAAACATTTTGGAAAACTTATATAATATATAGTTTAAA
1274000 AAA
1 AAA
1274003 CGTTTTTAAT
Statistics
Matches: 123, Mismatches: 10, Indels: 30
0.75 0.06 0.18
Matches are distributed among these distances:
32 21 0.17
33 17 0.14
34 3 0.02
35 19 0.15
37 10 0.08
38 24 0.20
39 10 0.08
40 6 0.05
43 13 0.11
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (38 bp):
AAAACATTTTGGAAAACTTATATAATATATAGTTTAAA
Found at i:1274089 original size:5 final size:5
Alignment explanation
Indices: 1274078--1274115 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
1274068 TATTATTAAT
* *
1274078 ATTT- ATTTT ATTTT ATTTC ATTTC ATTTC ATTTC ATTT
1 ATTTC ATTTC ATTTC ATTTC ATTTC ATTTC ATTTC ATTT
1274116 TATTAATCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (5 bp):
ATTTC
Found at i:1274100 original size:15 final size:15
Alignment explanation
Indices: 1274077--1274154 Score: 63
Period size: 15 Copynumber: 5.3 Consensus size: 15
1274067 TTATTATTAA
1274077 TATTT-ATTTTATTT
1 TATTTCATTTTATTT
*
1274091 TATTTCATTTCATTT
1 TATTTCATTTTATTT
*
1274106 CATTTCATTTTA-TT
1 TATTTCATTTTATTT
* * * *
1274120 AATCTAATTTAATTT
1 TATTTCATTTTATTT
*
1274135 AATTTCA-TTTATTGT
1 TATTTCATTTTATT-T
1274150 TATTT
1 TATTT
1274155 TTGTTAGAGT
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
14 20 0.40
15 30 0.60
ACGTcount: A:0.26, C:0.08, G:0.01, T:0.65
Consensus pattern (15 bp):
TATTTCATTTTATTT
Found at i:1274144 original size:10 final size:10
Alignment explanation
Indices: 1274078--1274145 Score: 50
Period size: 10 Copynumber: 7.0 Consensus size: 10
1274068 TATTATTAAT
*
1274078 ATTT-ATTTT
1 ATTTCATTTA
* *
1274087 ATTTTATTTC
1 ATTTCATTTA
*
1274097 ATTTCATTTC
1 ATTTCATTTA
*
1274107 ATTTCATTTT
1 ATTTCATTTA
* *
1274117 A-TTAATCTA
1 ATTTCATTTA
*
1274126 ATTTAATTTA
1 ATTTCATTTA
1274136 ATTTCATTTA
1 ATTTCATTTA
1274146 TTGTTATTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
9 10 0.20
10 39 0.80
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (10 bp):
ATTTCATTTA
Found at i:1275575 original size:25 final size:26
Alignment explanation
Indices: 1275536--1275585 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
1275526 TTATTTTATT
**
1275536 TTATTATTATTATTATGT-TTTTTAA
1 TTATTATTAGAATTATGTATTTTTAA
*
1275561 TTATTATTAGAATTATTTATTTTTA
1 TTATTATTAGAATTATGTATTTTTA
1275586 CTTCATTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (26 bp):
TTATTATTAGAATTATGTATTTTTAA
Found at i:1275651 original size:11 final size:11
Alignment explanation
Indices: 1275637--1275667 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1275627 TTTTTTTGTT
*
1275637 TTTTTATTTAA
1 TTTTAATTTAA
1275648 TTTTAATTTAA
1 TTTTAATTTAA
1275659 TTTTAATTT
1 TTTTAATTT
1275668 CTTTGATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTAATTTAA
Found at i:1275683 original size:3 final size:3
Alignment explanation
Indices: 1275675--1275715 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1275665 TTTCTTTGAT
1275675 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1275716 TCCTTTGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1275760 original size:6 final size:5
Alignment explanation
Indices: 1275638--1275774 Score: 57
Period size: 6 Copynumber: 26.4 Consensus size: 5
1275628 TTTTTTGTTT
* * * * *
1275638 TTTTA TTTAA TTTTAA TTTAA TTTTA ATTTC TTTGA -TTTA TTATTA TTATTA
1 TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TT-TTA
** * *
1275690 TTATTA TTATTA TTATTA TTATTA TTTCC TTTGA -TTTA TTTT- CTTTA
1 TT-TTA TT-TTA TT-TTA TT-TTA TTTTA TTTTA TTTTA TTTTA TTTTA
* * *
1275737 TATTA CTATTA TTTTA TTTCTA TTCT- TTTTA TTTTA TT
1 TTTTA -TTTTA TTTTA TTT-TA TTTTA TTTTA TTTTA TT
1275775 GTTTTTTTTG
Statistics
Matches: 103, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
4 12 0.12
5 43 0.42
6 48 0.47
ACGTcount: A:0.25, C:0.05, G:0.01, T:0.69
Consensus pattern (5 bp):
TTTTA
Found at i:1275781 original size:15 final size:15
Alignment explanation
Indices: 1275730--1275780 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
1275720 TTGATTTATT
* *
1275730 TTCTTTATATTACTA
1 TTCTTTTTATTTCTA
*
1275745 TT-ATTTTATTTCTA
1 TTCTTTTTATTTCTA
1275759 TTCTTTTTATTT-TA
1 TTCTTTTTATTTCTA
*
1275773 TTGTTTTT
1 TTCTTTTT
1275781 TTTGTCTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 20 0.67
15 10 0.33
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.73
Consensus pattern (15 bp):
TTCTTTTTATTTCTA
Found at i:1277085 original size:17 final size:18
Alignment explanation
Indices: 1277063--1277100 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
1277053 TAACTTAATA
1277063 TAATTTTATAT-TATTTT
1 TAATTTTATATATATTTT
1277080 TAA-TTTATATATATTTT
1 TAATTTTATATATATTTT
1277097 TAAT
1 TAAT
1277101 CAAATTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TAATTTTATATATATTTT
Found at i:1281781 original size:2 final size:2
Alignment explanation
Indices: 1281774--1281814 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1281764 AATTGATTGT
1281774 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA T
1281815 GATCATAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1282141 original size:16 final size:15
Alignment explanation
Indices: 1282112--1282159 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
1282102 TAATTTAATG
*
1282112 ATTTTTTAACAAATT
1 ATTTTTTAATAAATT
* *
1282127 GTTTTTGTAATAAATA
1 ATTTTT-TAATAAATT
1282143 ATTTTTTTAATAAATT
1 A-TTTTTTAATAAATT
1282159 A
1 A
1282160 AAAATATATA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 5 0.19
16 16 0.62
17 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (15 bp):
ATTTTTTAATAAATT
Found at i:1284250 original size:174 final size:175
Alignment explanation
Indices: 1283953--1284299 Score: 615
Period size: 174 Copynumber: 2.0 Consensus size: 175
1283943 TACTAAACCG
* *
1283953 TTTACCTAAACTCATCATCCACCATTTTATTTTGATGAATGATGATTACCGTCCACTCTACAACA
1 TTTACCTAAACTCACCATCCACCATTTTATTTTGATGAATGATGATTACCGTCAACTCTACAACA
* * *
1284018 CTGATAAAGAGTCTAAAGATCAATACCCGGCACTCACAGGTAGTTGCTACGTTAACTCAAGCCAG
66 CTGATAAAGAGTCTAAAGATCAATACCCAGCACTCACAGGTAGTTGCAACGCTAACTCAAGCCAG
*
1284083 AAAAGCAGTTATTCCATCCCTTCAGT-CAACATTATACTTGTCGT
131 AAAAGCAGTTATTCCATCCCTTCAGTCCAACATTACACTTGTCGT
*
1284127 TTTACCTAAACTCACCATCCACCATTTTGTTTTGATGAATGATGATTACCGTCAACTCTACAACA
1 TTTACCTAAACTCACCATCCACCATTTTATTTTGATGAATGATGATTACCGTCAACTCTACAACA
*
1284192 CTGATAAAGAGTCTAAAGATCAATACCCAGCACTCGCAGGTAGTTGCAACGCTAACTCAAGCCAG
66 CTGATAAAGAGTCTAAAGATCAATACCCAGCACTCACAGGTAGTTGCAACGCTAACTCAAGCCAG
1284257 AAAAGCAGTTATTCCATCCCTTCAGTCCAACATTACACTTGTC
131 AAAAGCAGTTATTCCATCCCTTCAGTCCAACATTACACTTGTC
1284300 AATTATCCTT
Statistics
Matches: 164, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
174 149 0.91
175 15 0.09
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (175 bp):
TTTACCTAAACTCACCATCCACCATTTTATTTTGATGAATGATGATTACCGTCAACTCTACAACA
CTGATAAAGAGTCTAAAGATCAATACCCAGCACTCACAGGTAGTTGCAACGCTAACTCAAGCCAG
AAAAGCAGTTATTCCATCCCTTCAGTCCAACATTACACTTGTCGT
Found at i:1293904 original size:25 final size:28
Alignment explanation
Indices: 1293853--1293915 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
1293843 TAATATATTG
* *
1293853 ATTTATACGCATTTATCCTTTACTTTTTT
1 ATTTATATGCATTTATCCTTTA-TTTTTA
1293882 ATTTATATGCATTTAT-C-TT-TTTTTA
1 ATTTATATGCATTTATCCTTTATTTTTA
1293907 ATTCTATAT
1 ATT-TATAT
1293916 TGTAATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 8 0.26
26 5 0.16
27 2 0.06
28 1 0.03
29 15 0.48
ACGTcount: A:0.24, C:0.13, G:0.03, T:0.60
Consensus pattern (28 bp):
ATTTATATGCATTTATCCTTTATTTTTA
Found at i:1295850 original size:20 final size:21
Alignment explanation
Indices: 1295820--1295859 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1295810 AGCCGTTGGG
*
1295820 GCCTGATGGTATTGATACTAT
1 GCCTGATGGTATCGATACTAT
1295841 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCGATACTA
1295860 CTATACAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:1296389 original size:16 final size:16
Alignment explanation
Indices: 1296368--1296400 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1296358 ATATAAAAAA
1296368 TAATTCAATTTTAAAG
1 TAATTCAATTTTAAAG
1296384 TAATTCAATTTTAAAG
1 TAATTCAATTTTAAAG
1296400 T
1 T
1296401 TCAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATTCAATTTTAAAG
Found at i:1297231 original size:13 final size:13
Alignment explanation
Indices: 1297213--1297245 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
1297203 AACTTTTAAA
1297213 TCAAAACATTTTT
1 TCAAAACATTTTT
1297226 TCAAAACATTTTT
1 TCAAAACATTTTT
1297239 TCAAAAC
1 TCAAAAC
1297246 TTTCAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (13 bp):
TCAAAACATTTTT
Found at i:1297315 original size:19 final size:20
Alignment explanation
Indices: 1297279--1297326 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
1297269 TCTAAATCCT
* *
1297279 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTAG
1297299 TTTTCAAAA-TCCATTTTAG
1 TTTTCAAAATTCCATTTTAG
1297318 TTTTCAAAA
1 TTTTCAAAA
1297327 GAAAATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTAG
Found at i:1298601 original size:18 final size:18
Alignment explanation
Indices: 1298578--1298622 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1298568 ACAAAGTAGT
1298578 ATCGGTACCCCTTTGGGC
1 ATCGGTACCCCTTTGGGC
*
1298596 ATCGGTACCCCTTTGGGT
1 ATCGGTACCCCTTTGGGC
*
1298614 ATCAGTACC
1 ATCGGTACC
1298623 ATTTTTGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.31, G:0.24, T:0.29
Consensus pattern (18 bp):
ATCGGTACCCCTTTGGGC
Found at i:1303808 original size:32 final size:31
Alignment explanation
Indices: 1303772--1303848 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
1303762 CGGGGCCGTG
*
1303772 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** ** *
1303804 GGGCCTACCCGAGAATGATCTCAGGGCCGTA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
1303835 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
1303849 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:1303831 original size:63 final size:63
Alignment explanation
Indices: 1303725--1303848 Score: 162
Period size: 63 Copynumber: 2.0 Consensus size: 63
1303715 CCCTAAGGGA
* * * *
1303725 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGTAGAGCCTACCTAAGAAC
* *
1303788 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGTAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGTAGAGCCTACCTAAGA
1303849 GTCACATTAG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
62 2 0.04
63 51 0.96
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGTAGAGCCTACCTAAGAAC
Found at i:1304745 original size:7 final size:7
Alignment explanation
Indices: 1304718--1304765 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
1304708 GTCAAAGAAA
*
1304718 GTCAACA
1 GTCAACG
1304725 GTCAACG
1 GTCAACG
1304732 GTC--CG
1 GTCAACG
1304737 GTCAACG
1 GTCAACG
*
1304744 GTC--CA
1 GTCAACG
1304749 GTCAACG
1 GTCAACG
1304756 GTCAACG
1 GTCAACG
1304763 GTC
1 GTC
1304766 GGGTCGGGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
5 9 0.26
7 25 0.74
ACGTcount: A:0.25, C:0.31, G:0.27, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:1304770 original size:12 final size:12
Alignment explanation
Indices: 1304723--1304758 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1304713 AGAAAGTCAA
1304723 CAGTCAACGGTC
1 CAGTCAACGGTC
*
1304735 CGGTCAACGGTC
1 CAGTCAACGGTC
1304747 CAGTCAACGGTC
1 CAGTCAACGGTC
1304759 AACGGTCGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (12 bp):
CAGTCAACGGTC
Found at i:1304813 original size:19 final size:19
Alignment explanation
Indices: 1304789--1304841 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
1304779 AATCGGGTTG
* *
1304789 GGTCAACCCGGTTTAGACC
1 GGTCAAACCGGTTCAGACC
1304808 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
1304827 GGTCAAACCGGTTCA
1 GGTCAAACCGGTTCA
1304842 AAACTAGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.25, C:0.30, G:0.26, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:1304819 original size:9 final size:9
Alignment explanation
Indices: 1304805--1304858 Score: 54
Period size: 9 Copynumber: 5.7 Consensus size: 9
1304795 CCCGGTTTAG
1304805 ACCGGTCAA
1 ACCGGTCAA
*
1304814 ACCGGTTCAG
1 ACCGG-TCAA
1304824 ACCGGTCAA
1 ACCGGTCAA
1304833 ACCGGTTCAAA
1 ACCGG-TC-AA
**
1304844 ACTAGTCAA
1 ACCGGTCAA
1304853 ACCGGT
1 ACCGGT
1304859 TTTCCAGCAG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
9 19 0.53
10 12 0.33
11 5 0.14
ACGTcount: A:0.31, C:0.30, G:0.22, T:0.17
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:1304827 original size:10 final size:10
Alignment explanation
Indices: 1304791--1304843 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
1304781 TCGGGTTGGG
*
1304791 TCAACCCGGT
1 TCAAACCGGT
* *
1304801 TTAGACCGG-
1 TCAAACCGGT
1304810 TCAAACCGGT
1 TCAAACCGGT
*
1304820 TCAGACCGG-
1 TCAAACCGGT
1304829 TCAAACCGGT
1 TCAAACCGGT
1304839 TCAAA
1 TCAAA
1304844 ACTAGTCAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
9 15 0.44
10 19 0.56
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1304853 original size:20 final size:19
Alignment explanation
Indices: 1304790--1304859 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
1304780 ATCGGGTTGG
* * * *
1304790 GTCAACCCGGTTTAGACCG
1 GTCAAACCGGTTCAAACCA
* *
1304809 GTCAAACCGGTTCAGACCG
1 GTCAAACCGGTTCAAACCA
*
1304828 GTCAAACCGGTTCAAAACTA
1 GTCAAACCGGTTC-AAACCA
1304848 GTCAAACCGGTT
1 GTCAAACCGGTT
1304860 TTCCAGCAGC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 30 0.67
20 15 0.33
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.20
Consensus pattern (19 bp):
GTCAAACCGGTTCAAACCA
Found at i:1305626 original size:16 final size:17
Alignment explanation
Indices: 1305605--1305647 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
1305595 TTTGAAAATA
1305605 ATATTACT-AGAATATT
1 ATATTACTAAGAATATT
1305621 ATATTACCATAAGAATATT
1 ATATTA-C-TAAGAATATT
*
1305640 GTATTACT
1 ATATTACT
1305648 TTGTTTGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 6 0.26
17 2 0.09
18 2 0.09
19 13 0.57
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (17 bp):
ATATTACTAAGAATATT
Found at i:1305948 original size:17 final size:17
Alignment explanation
Indices: 1305919--1305951 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1305909 ATGTTTATTT
1305919 ATATAAAATATAATATA
1 ATATAAAATATAATATA
1305936 ATATGAAAA-ATAATAT
1 ATAT-AAAATATAATAT
1305952 TATGATTTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATAAAATATAATATA
Found at i:1306054 original size:17 final size:16
Alignment explanation
Indices: 1306023--1306063 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1306013 AAAGATAGAG
1306023 ATTA-TTTTAAATAAT
1 ATTATTTTTAAATAAT
1306038 -TATATTTTTACAATAAT
1 AT-TATTTTTA-AATAAT
1306055 ATTATTTTT
1 ATTATTTTT
1306064 TACCTCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.05
15 2 0.09
16 5 0.23
17 13 0.59
18 1 0.05
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTATTTTTAAATAAT
Found at i:1307626 original size:16 final size:16
Alignment explanation
Indices: 1307605--1307637 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1307595 TAAAAAATAA
1307605 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
*
1307621 ACGAACATAAACGAAC
1 ACGAACATAAACAAAC
1307637 A
1 A
1307638 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.24, G:0.09, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACAAAC
Found at i:1307731 original size:16 final size:16
Alignment explanation
Indices: 1307699--1307787 Score: 137
Period size: 16 Copynumber: 5.7 Consensus size: 16
1307689 CGTTCATTTA
1307699 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
*
1307713 ATAAATGAACACAAAC
1 ATAAATGAACACGAAC
*
1307729 ATAAACGAACACGAAC
1 ATAAATGAACACGAAC
1307745 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
1307761 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
*
1307777 ATAAACGAACA
1 ATAAATGAACA
1307788 TAAACGTAGA
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
14 6 0.09
15 2 0.03
16 60 0.88
ACGTcount: A:0.60, C:0.19, G:0.10, T:0.11
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:1310212 original size:23 final size:23
Alignment explanation
Indices: 1310186--1310254 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1310176 GACCACAACT
*
1310186 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
1310209 CGTAGAATTGCACCTAAGTGTCG
1 CGTAGAAATGCACCGAAGTGCCA
1310232 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1310255 TATAAGATGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1315465 original size:23 final size:23
Alignment explanation
Indices: 1315434--1315497 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
1315424 CACCTCGTAT
* *
1315434 AAATACACCAAAGTGCCACGTAG
1 AAATGCACCAAAGTGCCACATAG
* * *
1315457 AATTGCACCTAAGTGCCGCATAG
1 AAATGCACCAAAGTGCCACATAG
*
1315480 AAATGCACTAAAGTGCCA
1 AAATGCACCAAAGTGCCA
1315498 TATAAGATGT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (23 bp):
AAATGCACCAAAGTGCCACATAG
Found at i:1317581 original size:4 final size:4
Alignment explanation
Indices: 1317572--1317602 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1317562 ACGGCTGGAG
1317572 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG
1317603 CTCTGGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:1318895 original size:41 final size:41
Alignment explanation
Indices: 1318850--1318941 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 41
1318840 GCCTTGATTA
* *
1318850 AATTGAATTGGATTGTGAATAAATATATGTTACCATGATCT
1 AATTGAATTGGATTGTGAATAAATATATGTTACCATGACCG
* * *
1318891 AATTGAATTGGTTTGTGAATAAATGTATGTTGCCATGACCG
1 AATTGAATTGGATTGTGAATAAATATATGTTACCATGACCG
1318932 AATTGAATTG
1 AATTGAATTG
1318942 CATTATGGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.38
Consensus pattern (41 bp):
AATTGAATTGGATTGTGAATAAATATATGTTACCATGACCG
Found at i:1322043 original size:27 final size:27
Alignment explanation
Indices: 1322013--1322065 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1322003 AATATTTTTT
* *
1322013 AAAATAGTATAGTATAATATATTTAACA
1 AAAATA-TATAATATAATAAATTTAACA
*
1322041 AAAATATATAATATTATAAATTTAA
1 AAAATATATAATATAATAAATTTAA
1322066 TAGAATATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (27 bp):
AAAATATATAATATAATAAATTTAACA
Found at i:1323712 original size:11 final size:11
Alignment explanation
Indices: 1323696--1323720 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1323686 AGGAAAGGCG
1323696 GGTTAATATAC
1 GGTTAATATAC
1323707 GGTTAATATAC
1 GGTTAATATAC
1323718 GGT
1 GGT
1323721 AGTACCGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (11 bp):
GGTTAATATAC
Found at i:1324471 original size:228 final size:230
Alignment explanation
Indices: 1323967--1324656 Score: 1260
Period size: 229 Copynumber: 3.0 Consensus size: 230
1323957 GTTATATTGT
* * *
1323967 AAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGT-GAAAATATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
1324031 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA
* *
1324096 ATAATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTA
131 ATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTA
1324161 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
196 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
**
1324196 AAAGTATATATCATTTTTATAAAAGTGTTTATACTTATTTCACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
*
1324261 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC-AAATAATCAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA
*
1324325 ATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATCAAACACTATT-
131 ATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTA
*
1324389 AAAAAATTTGAAACATAAATTACATAACTTTAAAA
196 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
1324424 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
*
1324489 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA
1324554 ATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTA
131 ATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTA
1324619 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
196 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
1324654 AAA
1 AAA
1324657 AGTGTCGATC
Statistics
Matches: 443, Mismatches: 15, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
228 150 0.34
229 185 0.42
230 108 0.24
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (230 bp):
AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA
ATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTA
AAAAAAATTGAAACATAAATTACATAACTTTAAAA
Found at i:1324741 original size:23 final size:23
Alignment explanation
Indices: 1324710--1324770 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1324700 ATAGGTAAAA
*
1324710 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1324733 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
1324756 ATATAATGTAATAGG
1 ATATAATGTAATAGG
1324771 CAGTTGTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1325222 original size:23 final size:23
Alignment explanation
Indices: 1325191--1325254 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
1325181 ATAGGTAAAA
*
1325191 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1325214 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
1325237 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
1325255 TTGTAAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1325379 original size:481 final size:481
Alignment explanation
Indices: 1324475--1325657 Score: 2204
Period size: 481 Copynumber: 2.5 Consensus size: 481
1324465 ACTGTGGAAA
1324475 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
1 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
1324540 ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
66 ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
* *
1324605 ATAAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTGTCGATCCTT
131 ATGAAACACTATT-AAAAAAATTGAAACATAAATTACATAACTTT-AAAAAAAGTATCGATCCTT
1324670 TTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTAT
194 TTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTAT
* *
1324735 ATAATGTAATAGGTATCGTTTATATAATGTAATAGGCAGTTGTAAAGTATCTATCCTTTTTATAA
259 ATAATGTAATAGGTATCGTTTATATAATGTAATAGGCAGTTGTAAAGTATATATCATTTTTATAA
*
1324800 AAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAATGTTATCTTTTGAGTGAGTTTTAA
324 AAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
1324865 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACATTACGATATATATTATTAT
389 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACATTACGATATATATTATTAT
*
1324930 TAAATTAAAAACAATAAACATATATATT
454 TAAATTAAAAACAATAAAAATATATATT
1324958 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
1 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
*
1325023 ATCAAAACAATCAAATAAATTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
66 ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
1325088 ATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTT
131 ATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTT
1325153 TATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATAT
196 TATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATAT
*
1325218 AATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGTATATATCATTTTTATAAAA
261 AATGTAATAGGTATCGTTTATATAATGTAATAGGCAGTTGTAAAGTATATATCATTTTTATAAAA
*
1325283 GTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGA
326 GTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGA
* *
1325348 TATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTAGGATATATATTATTATTA
391 TATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACATTACGATATATATTATTATTA
*
1325413 AATTAAAAATAATAAAAATATATATT
456 AATTAAAAACAATAAAAATATATATT
*
1325439 ACATATTTATTATTATCTTTGGTTAATATTGCTAAATTTAAATTCTAAATATTATTTTATAAAAT
1 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
* *
1325504 ATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGAAAAAC
66 ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
*
1325569 ATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAATTATCGATCCTTTT
131 ATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTT
1325634 TATAAAAAGTATGGACACTTTCAA
196 TATAAAAAGTATGGACACTTTCAA
1325658 CATATTATAA
Statistics
Matches: 683, Mismatches: 17, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
481 511 0.75
482 31 0.05
483 141 0.21
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (481 bp):
ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
ATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTT
TATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATAT
AATGTAATAGGTATCGTTTATATAATGTAATAGGCAGTTGTAAAGTATATATCATTTTTATAAAA
GTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGA
TATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACATTACGATATATATTATTATTA
AATTAAAAACAATAAAAATATATATT
Found at i:1332972 original size:3 final size:3
Alignment explanation
Indices: 1332966--1333045 Score: 142
Period size: 3 Copynumber: 26.7 Consensus size: 3
1332956 TTTTTATCCA
*
1332966 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1333014 TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1333046 AATATATATT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1333553 original size:18 final size:18
Alignment explanation
Indices: 1333502--1333566 Score: 69
Period size: 18 Copynumber: 3.5 Consensus size: 18
1333492 CCGAACCTGA
1333502 AAAAAAAAAGCAGAGACA-
1 AAAAAAAAA-CAGAGACAG
* *
1333520 AAAACTAGAGACAGAGACAG
1 AAAA--AAAAACAGAGACAG
*
1333540 AAAAAAAAACAGAGAAAG
1 AAAAAAAAACAGAGACAG
1333558 AAAAAAAAA
1 AAAAAAAAA
1333567 AACAAACTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 24 0.62
19 8 0.21
20 7 0.18
ACGTcount: A:0.72, C:0.09, G:0.17, T:0.02
Consensus pattern (18 bp):
AAAAAAAAACAGAGACAG
Found at i:1333830 original size:13 final size:13
Alignment explanation
Indices: 1333812--1333837 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1333802 TTTCCGGCCA
1333812 CCGGCGGCGGTGG
1 CCGGCGGCGGTGG
1333825 CCGGCGGCGGTGG
1 CCGGCGGCGGTGG
1333838 TTGACGGCGG
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:0.00, C:0.31, G:0.62, T:0.08
Consensus pattern (13 bp):
CCGGCGGCGGTGG
Found at i:1334403 original size:19 final size:18
Alignment explanation
Indices: 1334367--1334415 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
1334357 TAGATTTTTA
*
1334367 ATTTTATT-TTTTCGTTT
1 ATTTTATTGTTTTCATTT
1334384 ATTTTATATGTTTTCATTT
1 ATTTTAT-TGTTTTCATTT
1334403 ATTTTATTGTTTT
1 ATTTTATTGTTTT
1334416 TAAATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 15 0.52
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.73
Consensus pattern (18 bp):
ATTTTATTGTTTTCATTT
Found at i:1334468 original size:12 final size:12
Alignment explanation
Indices: 1334453--1334515 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
1334443 ATTTTTTATA
1334453 TTATTAAATATT
1 TTATTAAATATT
1334465 TTATTAAATATT
1 TTATTAAATATT
*
1334477 TT-TATAAATATA
1 TTAT-TAAATATT
* *
1334489 TAATAAATAGTATT
1 TTATTAA-A-TATT
*
1334503 TTTTTAAATATT
1 TTATTAAATATT
1334515 T
1 T
1334516 ATTTTTAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 1 0.03
12 29 0.73
13 3 0.08
14 7 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
TTATTAAATATT
Found at i:1334525 original size:13 final size:12
Alignment explanation
Indices: 1334456--1334527 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
1334446 TTTTATATTA
*
1334456 TTAAATATTTTA
1 TTAAATATTTTT
1334468 TTAAATATTTTT
1 TTAAATATTTTT
* * **
1334480 ATAAATATATAA
1 TTAAATATTTTT
*
1334492 TAAATAGTATTTTT
1 TTAA-A-TATTTTT
1334506 TTAAATATTTATT
1 TTAAATATTT-TT
*
1334519 TTTAATATT
1 TTAAATATT
1334528 GAAGAAAAAG
Statistics
Matches: 45, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
12 26 0.58
13 12 0.27
14 7 0.16
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (12 bp):
TTAAATATTTTT
Found at i:1345891 original size:27 final size:28
Alignment explanation
Indices: 1345861--1345913 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
1345851 GAATTTTTTT
1345861 TAAAAAAAAAAAGAAAAAAAA-AGAAAA
1 TAAAAAAAAAAAGAAAAAAAAGAGAAAA
* *
1345888 TAAAAAAGAAAATAAAAAAAAGAGAA
1 TAAAAAAAAAAAGAAAAAAAAGAGAA
1345914 GAAAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (28 bp):
TAAAAAAAAAAAGAAAAAAAAGAGAAAA
Found at i:1345918 original size:26 final size:25
Alignment explanation
Indices: 1345875--1345923 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
1345865 AAAAAAAAGA
*
1345875 AAAAAAAAGAAAATAAAAAAGAAAAT
1 AAAAAAAAGAAAA-GAAAAAGAAAAT
*
1345901 AAAAAAAAGAGAAGAAAAAGAAA
1 AAAAAAAAGAAAAGAAAAAGAAA
1345924 GGGGGTCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (25 bp):
AAAAAAAAGAAAAGAAAAAGAAAAT
Found at i:1345919 original size:12 final size:12
Alignment explanation
Indices: 1345862--1345907 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
1345852 AATTTTTTTT
1345862 AAAAAAAAAAAG
1 AAAAAAAAAAAG
1345874 --AAAAAAAAAG
1 AAAAAAAAAAAG
*
1345884 AAAATAAAAAAG
1 AAAAAAAAAAAG
1345896 AAAATAAAAAAA
1 AAAA-AAAAAAA
1345908 AGAGAAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
10 10 0.34
12 13 0.45
13 6 0.21
ACGTcount: A:0.89, C:0.00, G:0.07, T:0.04
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:1346268 original size:16 final size:17
Alignment explanation
Indices: 1346249--1346295 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 17
1346239 CTATTTCAAG
*
1346249 TTCAATTTATTT-GAGA
1 TTCAATTTATTTGGAAA
1346265 TTCAATTTATTTTTGGAAA
1 TTCAATTTA--TTTGGAAA
1346284 TTCAATTTATTT
1 TTCAATTTATTT
1346296 TTTTTCTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 9 0.33
17 3 0.11
18 3 0.11
19 12 0.44
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (17 bp):
TTCAATTTATTTGGAAA
Found at i:1347260 original size:83 final size:84
Alignment explanation
Indices: 1347031--1347528 Score: 876
Period size: 83 Copynumber: 6.0 Consensus size: 84
1347021 TGTGATATCT
1347031 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1347096 GTTATCTGATCTGATTTGG
66 GTTATCTGATCTGATTTGG
1347115 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
* * *
1347180 GTTATCTGATCTGGTTAGA
66 GTTATCTGATCTGATTTGG
* *
1347199 CAGAA-CAATCATTGAGTTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
* *
1347263 GTTATCTGATCTGATTAGA
66 GTTATCTGATCTGATTTGG
* **
1347282 CAGAA-CAATCATTGAGTTTATAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1347346 GTTATCTGATCTGATTTGG
66 GTTATCTGATCTGATTTGG
1347365 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1347430 GTTATCTGATCTGATTTGG
66 GTTATCTGATCTGATTTGG
1347449 CAGAACCAATCATTGAATTTGGAAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGA
1 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
*
1347513 GTTATCTGATTTGATT
66 GTTATCTGATCTGATT
1347529 CAGTAGGAAC
Statistics
Matches: 400, Mismatches: 13, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
83 205 0.51
84 195 0.49
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (84 bp):
CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
GTTATCTGATCTGATTTGG
Found at i:1347377 original size:167 final size:168
Alignment explanation
Indices: 1347031--1347528 Score: 876
Period size: 167 Copynumber: 3.0 Consensus size: 168
1347021 TGTGATATCT
1347031 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1347096 GTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATC
66 GTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATC
*
1347161 TTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA
131 TTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGA
* *
1347199 CAGAA-CAATCATTGAGTTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
* * * **
1347263 GTTATCTGATCTGATTAGACAGAA-CAATCATTGAGTTTATAAGATGAATTTGCTCAATAGCATC
66 GTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATC
* *
1347327 TTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGG
131 TTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGA
1347365 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1347430 GTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTG-TCAATAGCATC
66 GTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATC
*
1347494 TTCTGGAAGTGTTCTTTGAGTTATCTGATTTGATT
131 TTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT
1347529 CAGTAGGAAC
Statistics
Matches: 310, Mismatches: 18, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
166 77 0.25
167 203 0.65
168 30 0.10
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (168 bp):
CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
GTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATC
TTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGA
Found at i:1347489 original size:250 final size:251
Alignment explanation
Indices: 1347031--1347528 Score: 892
Period size: 250 Copynumber: 2.0 Consensus size: 251
1347021 TGTGATATCT
*
1347031 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1 CAGAACCAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1347096 GTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATC
66 GTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATC
* *
1347161 TTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACAATCATTGAGTTTAGAAGATG
131 TTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAACAATCATTGAATTTAGAAGATG
1347226 AATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGA
196 AATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGA
* *
1347282 CAGAA-CAATCATTGAGTTTATAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1 CAGAACCAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1347346 GTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATC
66 GTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATC
* * *
1347411 TTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGAT
131 TTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAA-CAATCATTGAATTTAGAAGAT
*
1347476 GAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGATT
195 GAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT
1347529 CAGTAGGAAC
Statistics
Matches: 237, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
250 206 0.87
251 31 0.13
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (251 bp):
CAGAACCAATCATTGAATTTAGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
GTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATC
TTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAACAATCATTGAATTTAGAAGATG
AATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGA
Found at i:1348360 original size:113 final size:113
Alignment explanation
Indices: 1348162--1348823 Score: 1158
Period size: 113 Copynumber: 5.9 Consensus size: 113
1348152 TCAAATCCAC
* *
1348162 TTGATGGATCATTCATTGCCAGATAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCA-ACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1348226 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
65 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
1348275 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1348340 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
1348388 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1348453 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
1348501 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1348566 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
*
1348614 TTGATGGATCAACATTGCCAGAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCAACATTGCCAGAGAAGGTTCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* * * *
1348679 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCAC
65 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
**
1348728 TTGAT---T--ATTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
1348788 AGTTCATAATGAGAAGAGCTTGTTCAAC-CTTTGTTT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTT
1348824 GATACTATCA
Statistics
Matches: 534, Mismatches: 13, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
107 7 0.01
108 59 0.11
109 18 0.03
111 1 0.00
112 12 0.02
113 355 0.66
114 82 0.15
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (113 bp):
TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
Found at i:1349144 original size:3 final size:3
Alignment explanation
Indices: 1349138--1349205 Score: 109
Period size: 3 Copynumber: 22.7 Consensus size: 3
1349128 TTTTTATCCA
* *
1349138 TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAG TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1349186 TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
1349206 AATATATTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1349711 original size:18 final size:18
Alignment explanation
Indices: 1349660--1349724 Score: 69
Period size: 18 Copynumber: 3.5 Consensus size: 18
1349650 CCGAACCTGA
1349660 AAAAAAAAAGCAGAGACA-
1 AAAAAAAAA-CAGAGACAG
* *
1349678 AAAACTAGAGACAGAGACAG
1 AAAA--AAAAACAGAGACAG
*
1349698 AAAAAAAAACAGAGAAAG
1 AAAAAAAAACAGAGACAG
1349716 AAAAAAAAA
1 AAAAAAAAA
1349725 ACAAACTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 24 0.62
19 8 0.21
20 7 0.18
ACGTcount: A:0.72, C:0.09, G:0.17, T:0.02
Consensus pattern (18 bp):
AAAAAAAAACAGAGACAG
Found at i:1349986 original size:13 final size:13
Alignment explanation
Indices: 1349968--1349993 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1349958 TTTCCGGCCA
1349968 CCGGCGGCGGTGG
1 CCGGCGGCGGTGG
1349981 CCGGCGGCGGTGG
1 CCGGCGGCGGTGG
1349994 TTGACGGCGG
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:0.00, C:0.31, G:0.62, T:0.08
Consensus pattern (13 bp):
CCGGCGGCGGTGG
Found at i:1350559 original size:19 final size:18
Alignment explanation
Indices: 1350523--1350571 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
1350513 TAGATTTTTA
*
1350523 ATTTTATT-TTTTCGTTT
1 ATTTTATTGTTTTCATTT
1350540 ATTTTATATGTTTTCATTT
1 ATTTTAT-TGTTTTCATTT
1350559 ATTTTATTGTTTT
1 ATTTTATTGTTTT
1350572 TAAATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 15 0.52
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.73
Consensus pattern (18 bp):
ATTTTATTGTTTTCATTT
Found at i:1350626 original size:12 final size:12
Alignment explanation
Indices: 1350611--1350673 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
1350601 TTTTATTATA
1350611 TTATTAAATATT
1 TTATTAAATATT
1350623 TTATTAAATATT
1 TTATTAAATATT
*
1350635 TT-TATAAATATA
1 TTAT-TAAATATT
* *
1350647 TAATAAATAGTATT
1 TTATTAA-A-TATT
*
1350661 TTTTTAAATATT
1 TTATTAAATATT
1350673 T
1 T
1350674 ATTTTTAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 1 0.03
12 29 0.73
13 3 0.08
14 7 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
TTATTAAATATT
Found at i:1350683 original size:13 final size:12
Alignment explanation
Indices: 1350614--1350685 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
1350604 TATTATATTA
*
1350614 TTAAATATTTTA
1 TTAAATATTTTT
1350626 TTAAATATTTTT
1 TTAAATATTTTT
* * **
1350638 ATAAATATATAA
1 TTAAATATTTTT
*
1350650 TAAATAGTATTTTT
1 TTAA-A-TATTTTT
1350664 TTAAATATTTATT
1 TTAAATATTT-TT
*
1350677 TTTAATATT
1 TTAAATATT
1350686 GAAGAAAAAG
Statistics
Matches: 45, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
12 26 0.58
13 12 0.27
14 7 0.16
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (12 bp):
TTAAATATTTTT
Found at i:1357554 original size:457 final size:455
Alignment explanation
Indices: 1356699--1357614 Score: 1769
Period size: 457 Copynumber: 2.0 Consensus size: 455
1356689 ATTCTTAACG
1356699 AGCCAAAACAAACTACTTGATACTCGACTCGAAAAGCTAATGAGCAACTCAAAAATATAATATAT
1 AGCCAAAACAAACTACTTGATACTCGACTCGAAAAGCTAATGAGCAACTCAAAAATATAATATAT
*
1356764 TAAGATTTTATTTTAAAAAAAAATAAATTATTAATAATATTAACATTTATGTGTTGCTTTTTTTT
66 TAAGATTTTATTTTAAAAAAAAATAAATTATTAATAATATTAACATTTATGTGTTGATTTTTTTT
1356829 AAATACAGTAAGATTTTTATGTATTTAAGGTTTGAGTTTGAGGCTTCAATTTAGTTAAGTTTAAG
131 AAATACAGTAAGATTTTTATGTATTTAAGGTTTGAGTTTGAGGCTTCAATTTAGTTAAGTTTAAG
1356894 AATTTTTTTTTCATTTCGAGCCTTTTCGAGCTGATCACGAGCTTCAATTCAGGATTTTGAGTTCG
196 AATTTTTTTTTCATTTCGAGCCTTTTCGAGCTGATCACGAGCTTCAATTCAGGATTTTGAGTTCG
1356959 AGTCGAGCTTAAAAATTTTAAGCTCGCGAGTTTTCGAATCGAGTCGAACTGCATTTCAGAGTTTT
261 AGTCGAGCTTAAAAATTTTAAGCTCGCGAGTTTTCGAATCGAGTCGAACTGCATTTCAGAGTTTT
1357024 CGAGTCGAGTCGAGCTCAGCGATACTCGAGCTCGATTCGGCTCGTTTACACCTCTCAATTCCATG
326 CGAGTCGAGTCGAGCTCAGCGATACTCGAGCTCGATTCGGCTCGTTTACACCTCTCAATTCCATG
1357089 TTTACAGTCAATATATATTTTGTAATGATAATTAATCAATAAAAATTGTAATCAATCTCACACCT
391 TTTACAGTCAATATATATTTTGTAATGATAATTAATCAATAAAAATTGTAATCAATCTCACACCT
*
1357154 AGCCAAAACAAACTACTTGATACTCGACTCGAAAAGCTAGTGAGCAACTCAAAAATATAATATAT
1 AGCCAAAACAAACTACTTGATACTCGACTCGAAAAGCTAATGAGCAACTCAAAAATATAATATAT
1357219 TAAGATTTTATTTTAAAAAAAAATAAATTATTAATAATATTAACATTTATGTGTTGATTTTTTTT
66 TAAGATTTTATTTTAAAAAAAAATAAATTATTAATAATATTAACATTTATGTGTTGATTTTTTTT
1357284 AAATACAGTAAGATTTTTATGTATTTAAGGTTTGAGTTTGAGGCTTCAATTTAGTTAAGTTTAAG
131 AAATACAGTAAGATTTTTATGTATTTAAGGTTTGAGTTTGAGGCTTCAATTTAGTTAAGTTTAAG
* *
1357349 AATTTTTTTTTTTCATTTCGAGCCTTTTCGAGCTGCTCATGAGCTTCAATTCAGGATTTTGAGTT
196 AA--TTTTTTTTTCATTTCGAGCCTTTTCGAGCTGATCACGAGCTTCAATTCAGGATTTTGAGTT
1357414 CGAGTCGAGCTTAAAAATTTTAAGCTCGCGAGTTTTCGAATCGAGTCGAACTGCATTTCAGAGTT
259 CGAGTCGAGCTTAAAAATTTTAAGCTCGCGAGTTTTCGAATCGAGTCGAACTGCATTTCAGAGTT
1357479 TTCGAGTCGAGTCGAGCTCAGCGATACTCGAGCTCGATTCGGCTCGTTTACACCTCTCAATTCCA
324 TTCGAGTCGAGTCGAGCTCAGCGATACTCGAGCTCGATTCGGCTCGTTTACACCTCTCAATTCCA
*
1357544 TGTTTACAGTCAATATATATTTTGTAATGGTAATTAATCAATAAAAATTGTAATCAATCTCACAC
389 TGTTTACAGTCAATATATATTTTGTAATGATAATTAATCAATAAAAATTGTAATCAATCTCACAC
1357609 CT
454 CT
1357611 AGCC
1 AGCC
1357615 TAAATGGTTG
Statistics
Matches: 454, Mismatches: 5, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
455 195 0.43
457 259 0.57
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (455 bp):
AGCCAAAACAAACTACTTGATACTCGACTCGAAAAGCTAATGAGCAACTCAAAAATATAATATAT
TAAGATTTTATTTTAAAAAAAAATAAATTATTAATAATATTAACATTTATGTGTTGATTTTTTTT
AAATACAGTAAGATTTTTATGTATTTAAGGTTTGAGTTTGAGGCTTCAATTTAGTTAAGTTTAAG
AATTTTTTTTTCATTTCGAGCCTTTTCGAGCTGATCACGAGCTTCAATTCAGGATTTTGAGTTCG
AGTCGAGCTTAAAAATTTTAAGCTCGCGAGTTTTCGAATCGAGTCGAACTGCATTTCAGAGTTTT
CGAGTCGAGTCGAGCTCAGCGATACTCGAGCTCGATTCGGCTCGTTTACACCTCTCAATTCCATG
TTTACAGTCAATATATATTTTGTAATGATAATTAATCAATAAAAATTGTAATCAATCTCACACCT
Found at i:1361105 original size:32 final size:32
Alignment explanation
Indices: 1361068--1361133 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
1361058 GTTGATTATT
* *
1361068 GGATCAGTT-ATTTTCCAGTTCAGATCAATATC
1 GGATCAGTTGATTTT-CAGGTCAAATCAATATC
*
1361100 GGATCAGTTGATTTTTAGGTCAAATCAATATC
1 GGATCAGTTGATTTTCAGGTCAAATCAATATC
1361132 GG
1 GG
1361134 GTCGGGTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 25 0.83
33 5 0.17
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (32 bp):
GGATCAGTTGATTTTCAGGTCAAATCAATATC
Found at i:1361985 original size:16 final size:16
Alignment explanation
Indices: 1361900--1361999 Score: 53
Period size: 16 Copynumber: 6.2 Consensus size: 16
1361890 ATTTCAATAT
*
1361900 GTTCGTGTTACTTTCG
1 GTTCGGGTTACTTTCG
*
1361916 AG-TCGGGTTAAATTT-G
1 -GTTCGGGTT-ACTTTCG
*
1361932 GTTCGGGTTGCTTTC-
1 GTTCGGGTTACTTTCG
* * **
1361947 GTATCAGATTAAAATTCG
1 GT-TCGGGTT-ACTTTCG
*
1361965 ATTCGGGTTACTTTCG
1 GTTCGGGTTACTTTCG
* *
1361981 GTTCGAGTTACTTTTG
1 GTTCGGGTTACTTTCG
1361997 GTT
1 GTT
1362000 TCGATTCAGG
Statistics
Matches: 60, Mismatches: 17, Indels: 13
0.67 0.19 0.14
Matches are distributed among these distances:
15 6 0.10
16 40 0.67
17 13 0.22
18 1 0.02
ACGTcount: A:0.16, C:0.14, G:0.26, T:0.44
Consensus pattern (16 bp):
GTTCGGGTTACTTTCG
Found at i:1367363 original size:16 final size:17
Alignment explanation
Indices: 1367342--1367376 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1367332 AAATTATTTT
1367342 TAAA-TTTGATAATCGG
1 TAAATTTTGATAATCGG
*
1367358 TAAATTTTGATTATCGG
1 TAAATTTTGATAATCGG
1367375 TA
1 TA
1367377 GGTATCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (17 bp):
TAAATTTTGATAATCGG
Found at i:1368090 original size:182 final size:181
Alignment explanation
Indices: 1367719--1368209 Score: 657
Period size: 182 Copynumber: 2.7 Consensus size: 181
1367709 CATAAATTGT
* * * *
1367719 TTTTCTTTTAAATTCCAAAAGTATCTATACTTATTTGAATGAAATCGATACTTTTAACATATCTG
1 TTTTCTTTTAAATTCCAAAAGTGTCTATACTTATTTAAATGGAATCGATACTTTCAACATATCTG
* * * * * *
1367784 GTAGCGTTTTAACAGTTTTTTATAATGAAACCGATTTTGTCATATTTTTACATGTTATATTGTTA
66 GTAGCGCTTTAACGGTTTGTAATAATGAAACAG-TTTTGTCATATTTTTACCTGTTATATTGTTA
* *
1367849 TGTATCGATATATTTTTATAAAATATTAATACTTTATAGGCGCTAATACTGC
130 TGTATCGATACATTTTTATAAAATATTAATACTTTATAGGCGCTAATACTAC
* *
1367901 TTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAATCGATACTTTCAACATATATG
1 TTTTCTTTTAAATTCCAAAAGTGTCTATACTTATTTAAATGGAATCGATACTTTCAACATATCTG
* * *
1367966 ATAGCGCTTTACCGGATTTGTCATAATGAAATCAGTTTTGTCATATTTTTACCTGTTATATTGTT
66 GTAGCGCTTTAACGG-TTTGTAATAATGAAA-CAGTTTTGTCATATTTTTACCTGTTATATTGTT
* * *
1368031 ATGTATCGATACATTTTTATAAAGTA-TAGATATTTTATAGGCGCTATTACTAC
129 ATGTATCGATACATTTTTATAAAATATTA-ATACTTTATAGGCGCTAATACTAC
* * *
1368084 -TTTCTTTTAAATTCCAAAAGTGTTTATACTTATTTAAATAGAATCGATACTTTCAACATATCCG
1 TTTTCTTTTAAATTCCAAAAGTGTCTATACTTATTTAAATGGAATCGATACTTTCAACATATCTG
* *
1368148 GTAGCGCTTTATCGGTTTTGTAATTAAT-AAACCGAG-TTTATCATATTTTTACCTGTTATATT
66 GTAGCGCTTTAACGG-TTTGTAA-TAATGAAA-C-AGTTTTGTCATATTTTTACCTGTTATATT
1368210 AACAACTTTC
Statistics
Matches: 274, Mismatches: 30, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
182 179 0.65
183 93 0.34
184 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (181 bp):
TTTTCTTTTAAATTCCAAAAGTGTCTATACTTATTTAAATGGAATCGATACTTTCAACATATCTG
GTAGCGCTTTAACGGTTTGTAATAATGAAACAGTTTTGTCATATTTTTACCTGTTATATTGTTAT
GTATCGATACATTTTTATAAAATATTAATACTTTATAGGCGCTAATACTAC
Found at i:1368297 original size:74 final size:74
Alignment explanation
Indices: 1368206--1368744 Score: 731
Period size: 74 Copynumber: 7.3 Consensus size: 74
1368196 TTACCTGTTA
* * ** * * *
1368206 TATTAACAACTTTCAAAAAAATTGGTAGGTAGTTTAATGTAAAAGGTAGCGTCTATTTTTTTTAC
1 TATTAGCAACCTTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTAC
*
1368271 CGTTTAAAT
66 CGTTTACAT
*
1368280 TATTAGCAACCTTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGACTATTTTTTTTTA
1 TATTAGCAACCTTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTA-TTTTTTTTA
1368345 CCGTTTACAT
65 CCGTTTACAT
* * * * *
1368355 TATTAGCAACCTTAAAAAAAACCGGTAGATATTTTAATGTAATAGATAACACCTATTTTTTTTAC
1 TATTAGCAACCTTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTAC
1368420 CGTTTACAT
66 CGTTTACAT
* * * *
1368429 TATTAGCAACCTTCAAAAAAACCGGTAGATAGTTTAATGTAATAGGTAGCGCCTA-TTTCTTTAA
1 TATTAGCAACCTTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTAC
1368493 CGTTTACAT
66 CGTTTACAT
* * * *
1368502 TATTAGCAACCTTCAAAAAAACCGGTAGGTATTGTAATGTAATAGGTAACGCCTATTTTTTATAT
1 TATTAGCAACCTTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTAC
*
1368567 TGTTTACAT
66 CGTTTACAT
* * * * * *
1368576 TATTAGCAACTTTTAAAAAAACCGATAGGTATTTTAATGTATTAGGTAACGTCTATTTTTTTTAC
1 TATTAGCAACCTTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTAC
*
1368641 CGTTTATAT
66 CGTTTACAT
* * *
1368650 TATTACCAACCTTCAAAAAAACCGGTAGGTACTTTAATGTAATAAGTAGCGCCTA-TTTTTTTAC
1 TATTAGCAACCTTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTAC
*
1368714 AGTTTACAT
66 CGTTTACAT
* *
1368723 TATTATCAACCTTAAAAAAAAC
1 TATTAGCAACCTTCAAAAAAAC
1368745 GATATTTTTT
Statistics
Matches: 411, Mismatches: 52, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
73 103 0.25
74 241 0.59
75 67 0.16
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (74 bp):
TATTAGCAACCTTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTAC
CGTTTACAT
Found at i:1368372 original size:147 final size:146
Alignment explanation
Indices: 1368206--1368744 Score: 679
Period size: 147 Copynumber: 3.6 Consensus size: 146
1368196 TTACCTGTTA
* * ** * *
1368206 TATTAACAACTTTCAAAAAAATTGGTAGGTAGTTTAATGTAAAAGGTAGCGTCTATTTTTTTTAC
1 TATTAGCAACCTT-AAAAAAACCGGTAGGTA-TTTAATGTAAAAGGTAACGCCTATTTTTTTTAC
*
1368271 CGTTTAAATTATTAGCAACCTTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGACTAT
64 CGTTTACATTATTAGCAACCTTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGACTA-
1368336 TTTTTTTTACCGTTTACAT
128 TTTTTTTTACCGTTTACAT
* * * *
1368355 TATTAGCAACCTTAAAAAAAACCGGTAGATATTTTAATGTAATAGATAACACCTATTTTTTTTAC
1 TATTAGCAACCTT-AAAAAAACCGGTAGGTA-TTTAATGTAAAAGGTAACGCCTATTTTTTTTAC
* * *
1368420 CGTTTACATTATTAGCAACCTTCAAAAAAACCGGTAGATAGTTTAATGTAATAGGTAGCGCCTA-
64 CGTTTACATTATTAGCAACCTTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGACTAT
* *
1368484 TTTCTTTAACGTTTACAT
129 TTTTTTTACCGTTTACAT
* * *
1368502 TATTAGCAACCTTCAAAAAAACCGGTAGGTATTGTAATGTAATAGGTAACGCCTATTTTTTATAT
1 TATTAGCAACCTT-AAAAAAACCGGTAGGTATT-TAATGTAAAAGGTAACGCCTATTTTTTTTAC
* * * * * * *
1368567 TGTTTACATTATTAGCAACTTTTAAAAAAACCGATAGGTATTTTAATGTATTAGGTAACGTCTAT
64 CGTTTACATTATTAGCAACCTTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGACTAT
*
1368632 TTTTTTTACCGTTTATAT
129 TTTTTTTACCGTTTACAT
* *
1368650 TATTACCAACCTTCAAAAAAACCGGTAGGTACTTTAATGTAATAA-GTAGCGCCTA-TTTTTTTA
1 TATTAGCAACCTT-AAAAAAACCGGTAGGTA-TTTAATGTAA-AAGGTAACGCCTATTTTTTTTA
* * *
1368713 CAGTTTACATTATTATCAACCTTAAAAAAAAC
63 CCGTTTACATTATTAGCAACCTTCAAAAAAAC
1368745 GATATTTTTT
Statistics
Matches: 341, Mismatches: 45, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
146 2 0.01
147 161 0.47
148 62 0.18
149 116 0.34
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (146 bp):
TATTAGCAACCTTAAAAAAACCGGTAGGTATTTAATGTAAAAGGTAACGCCTATTTTTTTTACCG
TTTACATTATTAGCAACCTTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGACTATTT
TTTTTACCGTTTACAT
Found at i:1368663 original size:221 final size:221
Alignment explanation
Indices: 1368206--1368744 Score: 765
Period size: 221 Copynumber: 2.4 Consensus size: 221
1368196 TTACCTGTTA
* ** * * *
1368206 TATTAACAACTTTCAAAAAAATTGGTAGGTAGTTTAATGTAAAAGGTAGCGTCTATTTTTTTTAC
1 TATTAACAACCTTCAAAAAAACCGGTAGGTAGTTTAATGTAATAGGTAGCGCCTA--TTTTTTAA
* * *
1368271 CGTTTAAATTATTAGCAACCTTCAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGACTAT
64 CGTTTACATTATTAGCAACCTTCAAAAAAACCGGTAGGTATTGTAATGTAATAGGTAACGACTAT
* *
1368336 TTTTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAAACCGGTAGATATTTTAATGTAATAGA
129 TTTTTTATACCGTTTACATTATTAGCAACCTTAAAAAAAACCGATAGATATTTTAATGTAATAGA
1368401 TAACACCTATTTTTTTTACCGTTTACAT
194 TAACACCTATTTTTTTTACCGTTTACAT
* *
1368429 TATTAGCAACCTTCAAAAAAACCGGTAGATAGTTTAATGTAATAGGTAGCGCCTATTTCTTTAAC
1 TATTAACAACCTTCAAAAAAACCGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTT-TTTAAC
*
1368494 GTTTACATTATTAGCAACCTTCAAAAAAACCGGTAGGTATTGTAATGTAATAGGTAACGCCTA-T
65 GTTTACATTATTAGCAACCTTCAAAAAAACCGGTAGGTATTGTAATGTAATAGGTAACGACTATT
** * * * * *
1368558 TTTTTATATTGTTTACATTATTAGCAACTTTTAAAAAAACCGATAGGTATTTTAATGTATTAGGT
130 TTTTTATACCGTTTACATTATTAGCAACCTTAAAAAAAACCGATAGATATTTTAATGTAATAGAT
** *
1368623 AACGTCTATTTTTTTTACCGTTTATAT
195 AACACCTATTTTTTTTACCGTTTACAT
* * * *
1368650 TATTACCAACCTTCAAAAAAACCGGTAGGTACTTTAATGTAATAAGTAGCGCCTATTTTTTTACA
1 TATTAACAACCTTCAAAAAAACCGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTAAC-
* *
1368715 GTTTACATTATTATCAACCTTAAAAAAAAC
65 GTTTACATTATTAGCAACCTTCAAAAAAAC
1368745 GATATTTTTT
Statistics
Matches: 283, Mismatches: 31, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
220 5 0.02
221 166 0.59
222 64 0.23
223 48 0.17
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (221 bp):
TATTAACAACCTTCAAAAAAACCGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTAACG
TTTACATTATTAGCAACCTTCAAAAAAACCGGTAGGTATTGTAATGTAATAGGTAACGACTATTT
TTTTATACCGTTTACATTATTAGCAACCTTAAAAAAAACCGATAGATATTTTAATGTAATAGATA
ACACCTATTTTTTTTACCGTTTACAT
Found at i:1373797 original size:45 final size:45
Alignment explanation
Indices: 1373726--1373841 Score: 171
Period size: 45 Copynumber: 2.6 Consensus size: 45
1373716 TTGGGTAGAC
* * * *
1373726 CTGGGTCACACAACATCAACATCTCCCAAGTATCTCAGGCGAGGT
1 CTGGGTCACATAGCATCGACACCTCCCAAGTATCTCAGGCGAGGT
1373771 -TCGGGTCACATAGCATCGACACCTCCCAAGTATCTCAGGCGAGGT
1 CT-GGGTCACATAGCATCGACACCTCCCAAGTATCTCAGGCGAGGT
*
1373816 CTGGGTCACATAGCATTGACACCTCC
1 CTGGGTCACATAGCATCGACACCTCC
1373842 AAATACTTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
44 1 0.02
45 62 0.97
46 1 0.02
ACGTcount: A:0.26, C:0.32, G:0.22, T:0.21
Consensus pattern (45 bp):
CTGGGTCACATAGCATCGACACCTCCCAAGTATCTCAGGCGAGGT
Found at i:1375775 original size:24 final size:24
Alignment explanation
Indices: 1375689--1375776 Score: 122
Period size: 24 Copynumber: 3.7 Consensus size: 24
1375679 AGAGTCGATG
* ** *
1375689 ATTCTACGCGGTCCTTCGGGACAA
1 ATTCTACGTGGTCCTTTAGGATAA
*
1375713 ATTCTACGTGGTACTTTAGGATAA
1 ATTCTACGTGGTCCTTTAGGATAA
1375737 ATTCTACGTGGTCCTTTAGGATAA
1 ATTCTACGTGGTCCTTTAGGATAA
*
1375761 ATTCTACGTGATCCTT
1 ATTCTACGTGGTCCTT
1375777 CGAGACAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (24 bp):
ATTCTACGTGGTCCTTTAGGATAA
Found at i:1375786 original size:24 final size:24
Alignment explanation
Indices: 1375689--1375818 Score: 106
Period size: 24 Copynumber: 5.5 Consensus size: 24
1375679 AGAGTCGATG
*
1375689 ATTCTACGCGGTCCTTCG-GGACAA
1 ATTCTACGTGGTCCTT-GAGGACAA
* * *
1375713 ATTCTACGTGGTACTTTAGGATAA
1 ATTCTACGTGGTCCTTGAGGACAA
* *
1375737 ATTCTACGTGGTCCTTTAGGATAA
1 ATTCTACGTGGTCCTTGAGGACAA
*
1375761 ATTCTACGTGATCCTTCGA-GACAA
1 ATTCTACGTGGTCCTT-GAGGACAA
* * * *
1375785 A-TCTATGTGGTACTTCAGTG-CAT
1 ATTCTACGTGGTCCTTGAG-GACAA
1375808 ATTCTACGTGG
1 ATTCTACGTGG
1375819 CACTTCGGTG
Statistics
Matches: 87, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
22 1 0.01
23 14 0.16
24 71 0.82
25 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.34
Consensus pattern (24 bp):
ATTCTACGTGGTCCTTGAGGACAA
Found at i:1376674 original size:3 final size:3
Alignment explanation
Indices: 1376666--1376714 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1376656 TGCTATTATC
1376666 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1376714 T
1 T
1376715 AAGGCTCTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1377206 original size:22 final size:22
Alignment explanation
Indices: 1377181--1377234 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
1377171 AAGAGGTATG
*
1377181 ATACCCCTATGAATGCGTATCA
1 ATACCCCTATGAATGCGTACCA
* *
1377203 ATACCCCTATGAATGGGTACCG
1 ATACCCCTATGAATGCGTACCA
1377225 ATACCCCTAT
1 ATACCCCTAT
1377235 CAATACCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.26
Consensus pattern (22 bp):
ATACCCCTATGAATGCGTACCA
Found at i:1377236 original size:34 final size:35
Alignment explanation
Indices: 1377198--1377269 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
1377188 TATGAATGCG
*
1377198 TATCAATACC-CCTATGAATGGGTACCGATACCCC
1 TATCAATACCTCCTATGAACGGGTACCGATACCCC
* *
1377232 TATCAATACCTCTTATGAACGGGTACCTATACCCC
1 TATCAATACCTCCTATGAACGGGTACCGATACCCC
1377267 TAT
1 TAT
1377270 GAATGGGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 10 0.29
35 24 0.71
ACGTcount: A:0.29, C:0.31, G:0.12, T:0.28
Consensus pattern (35 bp):
TATCAATACCTCCTATGAACGGGTACCGATACCCC
Found at i:1377271 original size:22 final size:22
Alignment explanation
Indices: 1377235--1377293 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
1377225 ATACCCCTAT
*
1377235 CAATACCTCTTATGAACGGGTAC
1 CAATACC-CCTATGAACGGGTAC
* * *
1377258 CTATACCCCTATGAATGGGTAT
1 CAATACCCCTATGAACGGGTAC
1377280 CAATACCCC-ATGAA
1 CAATACCCCTATGAA
1377294 GGCTCAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 5 0.16
22 20 0.65
23 6 0.19
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.25
Consensus pattern (22 bp):
CAATACCCCTATGAACGGGTAC
Found at i:1378787 original size:16 final size:14
Alignment explanation
Indices: 1378769--1378797 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1378759 ATATTTTGGT
1378769 GTGTGAATTTAGGG
1 GTGTGAATTTAGGG
1378783 GTGTGAATTTAGGG
1 GTGTGAATTTAGGG
1378797 G
1 G
1378798 GGTTTGTTGT
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:0.21, C:0.00, G:0.45, T:0.34
Consensus pattern (14 bp):
GTGTGAATTTAGGG
Found at i:1382427 original size:19 final size:19
Alignment explanation
Indices: 1382403--1382439 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1382393 ATGACCAACA
*
1382403 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1382422 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1382440 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1382488 original size:20 final size:20
Alignment explanation
Indices: 1382465--1382536 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
1382455 GTTTCCAGAT
*
1382465 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
* * *
1382485 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTATG-ACTA
* *
1382505 TCGCAACACGATTCTGACTA
1 TCGCAACGCGATTATGACTA
1382525 TCGCAACGCGAT
1 TCGCAACGCGAT
1382537 AATACAAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 1 0.03
20 38 0.95
21 1 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:1382727 original size:22 final size:22
Alignment explanation
Indices: 1382702--1382751 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
1382692 CTACGGCGAC
1382702 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
1382724 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
1382746 ATCCGT
1 ATCCGT
1382752 TTATCTCCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.44, G:0.16, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:1383175 original size:20 final size:20
Alignment explanation
Indices: 1383126--1383248 Score: 158
Period size: 20 Copynumber: 6.2 Consensus size: 20
1383116 AAAATCGCAA
**
1383126 CGATAGTCAAATTCGCGTTG
1 CGATAGTCATTTTCGCGTTG
*
1383146 CAATAGTCATTTTCGCGTTG
1 CGATAGTCATTTTCGCGTTG
**
1383166 CGATAGTCATTTTCATGTTG
1 CGATAGTCATTTTCGCGTTG
*
1383186 CGATAGTCATTTTCGTGTTG
1 CGATAGTCATTTTCGCGTTG
**
1383206 CGATTTTCA-TTTCGCGTTG
1 CGATAGTCATTTTCGCGTTG
*
1383225 CGATAGTCATTTTCGTGTTG
1 CGATAGTCATTTTCGCGTTG
1383245 CGAT
1 CGAT
1383249 TTTAAGTTTC
Statistics
Matches: 89, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
19 16 0.18
20 73 0.82
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (20 bp):
CGATAGTCATTTTCGCGTTG
Found at i:1383236 original size:39 final size:40
Alignment explanation
Indices: 1383137--1383251 Score: 169
Period size: 39 Copynumber: 2.9 Consensus size: 40
1383127 GATAGTCAAA
* * **
1383137 TTCGCGTTGCAATAGTCATTTTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATT
**
1383177 TTCATGTTGCGATAGTCATTTTCGTGTTGCGATTTTCA-T
1 TTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATT
1383216 TTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTT
1 TTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTT
1383252 AAGTTTCAGA
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 35 0.52
40 32 0.48
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (40 bp):
TTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATT
Found at i:1385193 original size:20 final size:20
Alignment explanation
Indices: 1385168--1385216 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1385158 CGAAACTTAA
1385168 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
1385188 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1385208 ATCGCAACG
1 ATCGCAACG
1385217 GGATAATCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1385371 original size:20 final size:20
Alignment explanation
Indices: 1385346--1385432 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
1385336 CAATTATCCT
*
1385346 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAATTTCGC
1385366 GTTGCGATAGTC-ATTTCCGC
1 GTTGCGATAGTCAATTT-CGC
*
1385386 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAATTTCGC
* * *
1385406 GTTGCGAT-TTAAATTTCGT
1 GTTGCGATAGTCAATTTCGC
1385425 GTTGCGAT
1 GTTGCGAT
1385433 TTTAAGTTTC
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
19 18 0.31
20 38 0.64
21 3 0.05
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGTCAATTTCGC
Found at i:1385993 original size:42 final size:42
Alignment explanation
Indices: 1385929--1386040 Score: 127
Period size: 42 Copynumber: 2.7 Consensus size: 42
1385919 CTGTCATCGT
* * * *
1385929 TCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
* **
1385971 TCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCCTGTCATCGT
1 TCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
* *
1386013 TGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCAAGA-GTCCCCTCCCACCGTTCAAGAG
1386041 CTCGATTCAT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
42 58 0.97
43 2 0.03
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.21
Consensus pattern (42 bp):
TCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
Found at i:1386013 original size:21 final size:21
Alignment explanation
Indices: 1385918--1386025 Score: 101
Period size: 21 Copynumber: 5.1 Consensus size: 21
1385908 GCCCGACTCA
1385918 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
1385939 TCT-CCTATCGTTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* ** *
1385960 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
** *
1385981 CCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
1386002 CCTGTCATCGTTGAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
1386023 CCT
1 CCT
1386026 CCCACCATTC
Statistics
Matches: 67, Mismatches: 18, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
20 1 0.01
21 65 0.97
22 1 0.01
ACGTcount: A:0.19, C:0.37, G:0.19, T:0.24
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:1386039 original size:21 final size:21
Alignment explanation
Indices: 1385926--1386040 Score: 74
Period size: 21 Copynumber: 5.5 Consensus size: 21
1385916 CACCTGTCAT
* *
1385926 CGTTCAAGAGG-CCTCTCCTAT
1 CGTTCAAGAGGTCC-CTCCCAC
* **
1385947 CGTTCAAGAGGCCCCTATCATC
1 CGTTCAAGAGGTCCCTCCCA-C
*
1385969 C-CTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGT-CCCTCCCAC
* ** *
1385989 CGTTCAAGAGGCCCCTGTCAT
1 CGTTCAAGAGGTCCCTCCCAC
*
1386010 CGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGTCCCTCCCAC
*
1386031 CATTCAAGAG
1 CGTTCAAGAG
1386041 CTCGATTCAT
Statistics
Matches: 69, Mismatches: 20, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
20 3 0.04
21 62 0.90
22 4 0.06
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (21 bp):
CGTTCAAGAGGTCCCTCCCAC
Found at i:1387460 original size:28 final size:30
Alignment explanation
Indices: 1387426--1387488 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
1387416 TTTGCTTGTT
*
1387426 TAATTGATTTG-TAAAAATTGATTTGTAAA
1 TAATTGATTTGTTAAAAATTGATGTGTAAA
* *
1387455 -AATTGATTTGTTTAATATTGATGTGTAAA
1 TAATTGATTTGTTAAAAATTGATGTGTAAA
1387484 TAATT
1 TAATT
1387489 CTTATTTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 10 0.34
29 15 0.52
30 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (30 bp):
TAATTGATTTGTTAAAAATTGATGTGTAAA
Found at i:1387474 original size:15 final size:14
Alignment explanation
Indices: 1387427--1387488 Score: 79
Period size: 14 Copynumber: 4.3 Consensus size: 14
1387417 TTGCTTGTTT
1387427 AATTGATTTGTAAA
1 AATTGATTTGTAAA
1387441 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1387455 AATTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
1387470 TATTGATGTGTAAA
1 AATTGATTTGTAAA
1387484 TAATT
1 -AATT
1387489 CTTATTTGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
14 27 0.66
15 14 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1387518 original size:36 final size:36
Alignment explanation
Indices: 1387462--1387575 Score: 102
Period size: 36 Copynumber: 3.4 Consensus size: 36
1387452 AAAAATTGAT
1387462 TTGTTTAATATTGATGTGTAAATAATTCTTATTTGTGC
1 TTGTTT-A-ATTGATGTGTAAATAATTCTTATTTGTGC
* * *
1387500 TTGTTTAATTGATTTGT-AA-AAGT-TGA----T--
1 TTGTTTAATTGATGTGTAAATAATTCTTATTTGTGC
*
1387527 TTGTATAATTGATGTGTAAATAATTCTTATTTGTGC
1 TTGTTTAATTGATGTGTAAATAATTCTTATTTGTGC
*
1387563 TTATTTAATTGAT
1 TTGTTTAATTGAT
1387576 TGAAATGTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
27 15 0.26
28 2 0.03
29 4 0.07
30 2 0.03
33 2 0.03
34 4 0.07
35 2 0.03
36 20 0.34
37 1 0.02
38 6 0.10
ACGTcount: A:0.28, C:0.04, G:0.16, T:0.53
Consensus pattern (36 bp):
TTGTTTAATTGATGTGTAAATAATTCTTATTTGTGC
Found at i:1387527 original size:14 final size:13
Alignment explanation
Indices: 1387506--1387546 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
1387496 GTGCTTGTTT
1387506 AATTGATTTGTAA
1 AATTGATTTGTAA
*
1387519 AAGTTGATTTGTAT
1 AA-TTGATTTGTAA
*
1387533 AATTGATGTGTAA
1 AATTGATTTGTAA
1387546 A
1 A
1387547 TAATTCTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.44
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:1387544 original size:13 final size:13
Alignment explanation
Indices: 1387500--1387544 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
1387490 TTATTTGTGC
*
1387500 TTGTTTAATTGAT
1 TTGTATAATTGAT
*
1387513 TTGTAAAAGTTGAT
1 TTGTATAA-TTGAT
1387527 TTGTATAATTGAT
1 TTGTATAATTGAT
*
1387540 GTGTA
1 TTGTA
1387545 AATAATTCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (13 bp):
TTGTATAATTGAT
Found at i:1387557 original size:63 final size:65
Alignment explanation
Indices: 1387441--1387576 Score: 231
Period size: 63 Copynumber: 2.1 Consensus size: 65
1387431 GATTTGTAAA
* *
1387441 AATTGATTTGTAAAAATTGATTTGTTTAATATTGATGTGTAAATAATTCTTATTTGTGCTTGTTT
1 AATTGATTTGTAAAAATTGATTTGTATAATATTGATGTGTAAATAATTCTTATTTGTGCTTATTT
*
1387506 AATTGATTTGTAAAAGTTGATTTGTAT-A-ATTGATGTGTAAATAATTCTTATTTGTGCTTATTT
1 AATTGATTTGTAAAAATTGATTTGTATAATATTGATGTGTAAATAATTCTTATTTGTGCTTATTT
1387569 AATTGATT
1 AATTGATT
1387577 GAAATGTAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
63 42 0.62
64 1 0.01
65 25 0.37
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.51
Consensus pattern (65 bp):
AATTGATTTGTAAAAATTGATTTGTATAATATTGATGTGTAAATAATTCTTATTTGTGCTTATTT
Found at i:1387702 original size:20 final size:20
Alignment explanation
Indices: 1387666--1387703 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1387656 CGCTAAACTT
* *
1387666 AAAATCGCAATGTGAAAGCC
1 AAAATCGCAACGCGAAAGCC
1387686 AAAATCGCAACGCGAAAG
1 AAAATCGCAACGCGAAAG
1387704 TCAATTCGCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAGCC
Found at i:1387771 original size:20 final size:20
Alignment explanation
Indices: 1387746--1387990 Score: 280
Period size: 20 Copynumber: 12.8 Consensus size: 20
1387736 GCGATTTTCT
* * *
1387746 CGTTGCGATAGTTAAATACC
1 CGTTGCGATAGTCAAATTCG
* *
1387766 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
1387786 CGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1387806 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
1387826 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1387846 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
1387860 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1387880 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1387900 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1387920 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
1387934 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1387954 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1387974 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
1387991 GAATGTGTAA
Statistics
Matches: 192, Mismatches: 21, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
14 22 0.11
16 2 0.01
18 2 0.01
20 166 0.86
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1387833 original size:94 final size:92
Alignment explanation
Indices: 1387697--1387990 Score: 298
Period size: 94 Copynumber: 3.1 Consensus size: 92
1387687 AAATCGCAAC
* * *
1387697 GCGAAAGTC-AATTCGCGTTGCGATAGTC-TAATACGCTTTGCGATTTTCTCGTTGCGATAGTTA
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAT-ATTCGCGTTGCGATTTTCTCGTTGCGATA-TTA
*
1387760 AATACCCGTTGCGATAATCAAATTCACGTT
64 AATA-CCGTTGCGATAATCAAATTCGCGTT
* *
1387790 ACGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCGTTGCGAT--T----TTCTCGTTGCGAT
*
1387855 -TT--TTGA--GTTGCGATAATCAAATTCGCGTT
60 ATTAAAT-ACCGTTGCGATAATCAAATTCGCGTT
* * *
1387884 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TGAGTTGCGATAATCA
1 GCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCGTTGCGATTTTCT-CGTTGCGAT-ATTA
* *
1387948 AATTCGCGTTGCGATAGTCAAATTCGCGTT
64 AATAC-CGTTGCGATAATCAAATTCGCGTT
*
1387978 GCGATATTCAAAT
1 GCGATAGTCAAAT
1387991 GAATGTGTAA
Statistics
Matches: 168, Mismatches: 16, Indels: 33
0.77 0.07 0.15
Matches are distributed among these distances:
88 10 0.06
90 1 0.01
92 2 0.01
93 7 0.04
94 130 0.77
95 1 0.01
96 2 0.01
97 1 0.01
98 2 0.01
100 12 0.07
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (92 bp):
GCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCGTTGCGATTTTCTCGTTGCGATATTAAA
TACCGTTGCGATAATCAAATTCGCGTT
Found at i:1387879 original size:74 final size:74
Alignment explanation
Indices: 1387791--1387990 Score: 373
Period size: 74 Copynumber: 2.7 Consensus size: 74
1387781 ATTCACGTTA
* *
1387791 CGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATT
1 CGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATT
1387856 TTTGAGTTG
66 TTTGAGTTG
1387865 CGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATT
1 CGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATT
1387930 TTTGAGTTG
66 TTTGAGTTG
*
1387939 CGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAAT
1 CGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAAT
1387991 GAATGTGTAA
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
74 123 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (74 bp):
CGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATT
TTTGAGTTG
Found at i:1387939 original size:54 final size:54
Alignment explanation
Indices: 1387766--1387982 Score: 215
Period size: 54 Copynumber: 3.9 Consensus size: 54
1387756 GTTAAATACC
* *
1387766 CGTTGCGATAATCAAATTCACGTTACGATAGTCAAATTCGCGTTGCGATAGTCATATTCG
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT--T--T-TT-G
* ** ** * ** *
1387826 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTT-GCGATAAT-C-AAATTCG
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCG-T--TGCGATTTTTG
*
1387880 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
*
1387934 AGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1387983 ATTCAAATGA
Statistics
Matches: 130, Mismatches: 21, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
52 1 0.01
53 1 0.01
54 86 0.66
55 4 0.03
56 1 0.01
59 3 0.02
60 32 0.25
61 1 0.01
62 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (54 bp):
CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
Found at i:1388184 original size:18 final size:18
Alignment explanation
Indices: 1388161--1388195 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1388151 AAGCCGGTTG
*
1388161 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1388179 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1388196 ACCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1390261 original size:14 final size:14
Alignment explanation
Indices: 1390230--1390260 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1390220 TCCCGTGGCA
1390230 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
1390244 TTTTCTTCGGGGA-
1 TTTTCTTCGGGGAC
1390257 TTTT
1 TTTT
1390261 TTATTCTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.06, C:0.16, G:0.26, T:0.52
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:1390490 original size:24 final size:24
Alignment explanation
Indices: 1390456--1390509 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1390446 CTGAAACATC
*
1390456 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTAACCAAG
* *
1390480 ATCAAAGTCTGGGTATTAACCAAG
1 ATCAAAATCTGAGTATTAACCAAG
1390504 ATCAAA
1 ATCAAA
1390510 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTAACCAAG
Found at i:1391374 original size:41 final size:41
Alignment explanation
Indices: 1391329--1391600 Score: 422
Period size: 41 Copynumber: 6.7 Consensus size: 41
1391319 GAAATTCAAT
*
1391329 GTTGCGACAGTCAGAATCGCGTTGCGATTGTGTATTATCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTGTGTATTATCGC
* *
1391370 GTTGCGATAGTCAGAATCGCGTTTCGATTGTTTATTATCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTGTGTATTATCGC
1391411 GTTGCGATAGTCAGAATCGCGTTGCGATTGTGTATTATCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTGTGTATTATCGC
1391452 GTTGCGATAGTCAGAATCGCGTTGCGATTGTGTATTATCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTGTGTATTATCGC
*
1391493 GTTGCGATAGTCAGAATCGCGTTGCGATTGTGTATTATCTC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTGTGTATTATCGC
** **
1391534 GTTGCGATAGTCAGAATCATGTTGCGATT-TACA-TATTCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTGTGTATTA-TCGC
* * *
1391574 ATTGCGATAGTCAAAATCGCATTGCGA
1 GTTGCGATAGTCAGAATCGCGTTGCGA
1391601 ATCTGGAAAC
Statistics
Matches: 214, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
39 2 0.01
40 27 0.13
41 185 0.86
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (41 bp):
GTTGCGATAGTCAGAATCGCGTTGCGATTGTGTATTATCGC
Found at i:1391650 original size:19 final size:19
Alignment explanation
Indices: 1391626--1391662 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1391616 TACGATACTG
*
1391626 GAGATCACGTTGCGATTTA
1 GAGATCACATTGCGATTTA
*
1391645 GAGATCGCATTGCGATTT
1 GAGATCACATTGCGATTT
1391663 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCACATTGCGATTTA
Found at i:1396111 original size:60 final size:61
Alignment explanation
Indices: 1395992--1396128 Score: 140
Period size: 60 Copynumber: 2.3 Consensus size: 61
1395982 TAATGAATAA
* * * * *
1395992 TCGGATGACTATTTTGTAGCTTTTTATAGTTAAGAGACTCAACAAAATAACATATTATAG-
1 TCGGAGGACCATTTTATAACTTTTAATAGTTAAGAGACTCAACAAAATAACATATTATAGT
* * *
1396052 TCGGAGGACCATTTTATAACTTTTAATAG-TAAGATGAGTCAACAAAGTAATATCA-TATAGT
1 TCGGAGGACCATTTTATAACTTTTAATAGTTAAGA-GACTCAACAAAATAACAT-ATTATAGT
*
1396113 TAGG-GGACC-TTTTATA
1 TCGGAGGACCATTTTATA
1396129 TAATTTACCC
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
59 12 0.18
60 49 0.75
61 4 0.06
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (61 bp):
TCGGAGGACCATTTTATAACTTTTAATAGTTAAGAGACTCAACAAAATAACATATTATAGT
Found at i:1399106 original size:2 final size:2
Alignment explanation
Indices: 1399099--1399124 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1399089 TTGAAATAAT
1399099 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1399125 AATCTCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1399732 original size:31 final size:31
Alignment explanation
Indices: 1399694--1399753 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1399684 ATTAGTTATT
*
1399694 AACGTTATCGATTTATAATAAAATGATCATC
1 AACGTTATCGATTTATAACAAAATGATCATC
* *
1399725 AACGTTATTGATTTGTAACAAAATGATCA
1 AACGTTATCGATTTATAACAAAATGATCA
1399754 CTCCACTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (31 bp):
AACGTTATCGATTTATAACAAAATGATCATC
Found at i:1400386 original size:31 final size:30
Alignment explanation
Indices: 1400344--1400441 Score: 115
Period size: 31 Copynumber: 3.2 Consensus size: 30
1400334 ATAATGGTAG
*
1400344 AGTGGTCATTTTGTTATAAATCGATAACGTT
1 AGTGATCATTTTGTTATAAAT-GATAACGTT
* * **
1400375 AGTGATTATTTTGTTATAAAATAATAATTTT
1 AGTGATCATTTTGTTAT-AAATGATAACGTT
*
1400406 AGTGATCATTTTGTTATAGATAGATAACGTT
1 AGTGATCATTTTGTTATAAAT-GATAACGTT
1400437 AGTGA
1 AGTGA
1400442 CTAATTTATT
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
30 3 0.05
31 48 0.87
32 4 0.07
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (30 bp):
AGTGATCATTTTGTTATAAATGATAACGTT
Found at i:1407092 original size:19 final size:20
Alignment explanation
Indices: 1407065--1407110 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1407055 ATACAAATTG
1407065 ATATCAATT-AAAATAATTTT
1 ATAT-AATTCAAAATAATTTT
1407085 ATATAATTCAAAATAATTTT
1 ATATAATTCAAAATAATTTT
1407105 A-ATAAT
1 ATATAAT
1407111 GAAAGAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATAATTCAAAATAATTTT
Found at i:1407850 original size:3 final size:3
Alignment explanation
Indices: 1407842--1408059 Score: 259
Period size: 3 Copynumber: 71.7 Consensus size: 3
1407832 TAAATACATT
1407842 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1407889 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTCAA CTGA GTTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT--A -TTA -TTA
* ** *
1407938 TTGGA -AA AAA CTCTA -TA TACA TT- TTA TTA -TA TTA TTA TTA TTA
1 TT--A TTA TTA -T-TA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
1407981 TTA TTA TTA TTA TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1408028 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1408060 CAACTGAGTT
Statistics
Matches: 191, Mismatches: 10, Indels: 28
0.83 0.04 0.12
Matches are distributed among these distances:
2 11 0.06
3 173 0.91
4 4 0.02
5 2 0.01
6 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1413195 original size:20 final size:20
Alignment explanation
Indices: 1413159--1413206 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1413149 CCGGTCATCC
*
1413159 AATTTTCTAAACTCCAGACCG
1 AATTTT-TAAACCCCAGACCG
1413180 AATTTTTAAACCCCAGACCG
1 AATTTTTAAACCCCAGACCG
*
1413200 GATTTTT
1 AATTTTT
1413207 TTCTCGGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.33
Consensus pattern (20 bp):
AATTTTTAAACCCCAGACCG
Found at i:1413348 original size:19 final size:21
Alignment explanation
Indices: 1413308--1413349 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1413298 CGATTATACT
*
1413308 ATCCGGTTTTAAAAATATCCG
1 ATCCGGTTTTAAAAATAACCG
1413329 ATCCGG-TTTAAAAA-AACCG
1 ATCCGGTTTTAAAAATAACCG
1413348 AT
1 AT
1413350 TTTTCCCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 8 0.40
21 6 0.30
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (21 bp):
ATCCGGTTTTAAAAATAACCG
Found at i:1413598 original size:105 final size:105
Alignment explanation
Indices: 1413416--1413610 Score: 327
Period size: 105 Copynumber: 1.9 Consensus size: 105
1413406 TGTGCACCTC
* * * *
1413416 TACCGGTGGGTACACTAGTATATTTTTCATATATGATTGCACTTTGTGTGCATATTATGATTCCA
1 TACCGGAGGGTACACTAGTATATTTTTCAGATATAATTGCACTTTGCGTGCATATTATGATTCCA
1413481 ATGTGATAGCACTCTGTGTGCTTATGATATATTGTGGTAT
66 ATGTGATAGCACTCTGTGTGCTTATGATATATTGTGGTAT
*
1413521 TACCGGAGGGTACACTAGTATATTTTTCAGATATAATTTCACTTTGCGTGCATATTATGATTCCA
1 TACCGGAGGGTACACTAGTATATTTTTCAGATATAATTGCACTTTGCGTGCATATTATGATTCCA
* *
1413586 ATGTGATAGCACTGTGTGTGTTTAT
66 ATGTGATAGCACTCTGTGTGCTTAT
1413611 ATTGTTCAGA
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
105 83 1.00
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.41
Consensus pattern (105 bp):
TACCGGAGGGTACACTAGTATATTTTTCAGATATAATTGCACTTTGCGTGCATATTATGATTCCA
ATGTGATAGCACTCTGTGTGCTTATGATATATTGTGGTAT
Found at i:1417009 original size:71 final size:69
Alignment explanation
Indices: 1416860--1417009 Score: 160
Period size: 71 Copynumber: 2.1 Consensus size: 69
1416850 CGAAAGTATA
* ** * *
1416860 GATATTTTTCCACAAATATTGATACTTTTAAATTAAAAAAAATGAAAAATAAGAAGGATGCAAAG
1 GATATTTTTTCACAAATACCGATACTTTCAAATTAAAAAAAATGAAAAATAAGAAGGATGCAAAA
1416925 TATC
66 TATC
* * * * *
1416929 -AGTACTTTTTCACAAGTACCGATACTTTCAAATTTTAAAAAATATGAAAAATAAGAA-TACTGT
1 GA-TATTTTTTCACAAATACCGATACTTTCAAA--TTAAAAAAAATGAAAAATAAGAAGGA-TGC
1416992 AAAATATC
62 AAAATATC
1417000 GATATTTTTT
1 GATATTTTTT
1417010 AATTTTTTAT
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
68 1 0.02
69 24 0.37
70 1 0.02
71 38 0.58
72 1 0.02
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (69 bp):
GATATTTTTTCACAAATACCGATACTTTCAAATTAAAAAAAATGAAAAATAAGAAGGATGCAAAA
TATC
Found at i:1417471 original size:99 final size:98
Alignment explanation
Indices: 1417268--1417821 Score: 507
Period size: 99 Copynumber: 5.6 Consensus size: 98
1417258 TAAAGCCTAT
** * ** * * * *
1417268 TTTTTTAATGTCAATTGTTTAAGTTACAAAAATGAAACCGTTTATATTTTGCAAAAGTAAGACAA
1 TTTTTT-ATGTCAAACGTTTAAGTTATAAGTATGAAACCATTTATATTATGAAAAAGTAAGAAAA
* *
1417333 AATAGGTTTTTCATGATAACGTAGTAGGTAA-AGC
65 AATAGGTTGTTCATGATAATGTAGTAGGTAACA-C
* * * *
1417367 TTTTTTATGTTAACCATTTAAGTTATAAGTATTAAACCATTTATATTATGAAAAAGTAAGATAAA
1 TTTTTTATGTCAAACGTTTAAGTTATAAGTATGAAACCATTTATATTATGAAAAAGTAAGA-AAA
*
1417432 AATAGGTTGTTCATGATAATGTATTAGGTAACACC
65 AATAGGTTGTTCATGATAATGTAGTAGGTAACA-C
* * *
1417467 TTTTTAATGTCAAACGTTTAAGTTATAAGTATGAAACAATTTATATTA-GACAAAAGTAAGATAA
1 TTTTTTATGTCAAACGTTTAAGTTATAAGTATGAAACCATTTATATTATGA-AAAAGTAAGAAAA
* ** * * * *
1417531 AACAGGTTGTTCATGATAACATATTAGGGAGCGTC
65 AATAGGTTGTTCATGATAATGTAGTAGGTAAC-AC
* * *
1417566 TTTTTTAATGTCAAACGTTTAAGATATAAG--TGAAACCGTTTATATTATGTAAAAGTAA-AACA
1 TTTTTT-ATGTCAAACGTTTAAGTTATAAGTATGAAACCATTTATATTATGAAAAAGTAAGAA-A
* * * ****
1417628 AAATAGGTTTTTCATAATAATGAAGTAGGATGTGTC
64 AAATAGGTTGTTCATGATAATGTAGTAGG-TAACAC
* *
1417664 TTTTTTATGTC-AACAGTTTAAGTTATAAGTATGAAACTATTTATATTATGCAAAAGTAAGACAA
1 TTTTTTATGTCAAAC-GTTTAAGTTATAAGTATGAAACCATTTATATTATGAAAAAGTAAGA-AA
* * *
1417728 AACA-AGTTTCTT-ATGATAATGTAGTAGGTATCACC
64 AA-ATAGGTTGTTCATGATAATGTAGTAGGTAACA-C
* * *
1417763 TTTTTTATGTC-AACGGTTTAAGTTATATGTATAAAACC-TATTCTATTATGAAAAAGTAA
1 TTTTTTATGTCAAAC-GTTTAAGTTATAAGTATGAAACCAT-TTATATTATGAAAAAGTAA
1417822 AACTAAACAT
Statistics
Matches: 376, Mismatches: 63, Indels: 32
0.80 0.13 0.07
Matches are distributed among these distances:
96 3 0.01
97 19 0.05
98 101 0.27
99 165 0.44
100 86 0.23
101 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (98 bp):
TTTTTTATGTCAAACGTTTAAGTTATAAGTATGAAACCATTTATATTATGAAAAAGTAAGAAAAA
ATAGGTTGTTCATGATAATGTAGTAGGTAACAC
Found at i:1417830 original size:99 final size:98
Alignment explanation
Indices: 1417268--1417895 Score: 463
Period size: 99 Copynumber: 6.3 Consensus size: 98
1417258 TAAAGCCTAT
* * ** * * * *
1417268 TTTTTTAATGTCAATTGTTTAAGTTACAAAAATGAAACC-GTTTATATTTTGCAAAAGTAAGACA
1 TTTTTT-ATGTCAA-CGTTTAAGTTATAAGTATGAAACCTATTTATATTATGAAAAAGTAAGACT
* * * *
1417332 AAATAGGTTTTTCATGATAACGTAGTAGGTA-AAGC
64 AAACAAGTTTTT-ATGATAACGTAGTAGGTAGCACC
* * *
1417367 TTTTTTATGTTAACCATTTAAGTTATAAGTATTAAACC-ATTTATATTATGAAAAAGTAAGA-TA
1 TTTTTTATGTCAA-CGTTTAAGTTATAAGTATGAAACCTATTTATATTATGAAAAAGTAAGACTA
* * * * *
1417430 AAAATAGGTTGTTCATGATAATGTATTAGGTAACACC
65 AACA-A-GTT-TTTATGATAACGTAGTAGGTAGCACC
* *
1417467 TTTTTAATGTCAAACGTTTAAGTTATAAGTATGAAA-CAATTTATATTA-GACAAAAGTAAGA-T
1 TTTTTTATGTC-AACGTTTAAGTTATAAGTATGAAACCTATTTATATTATGA-AAAAGTAAGACT
* * * * * **
1417529 AAAACAGGTTGTTCATGATAACATATTAGGGAGCGTC
64 -AAACAAGTT-TTTATGATAACGTAGTAGGTAGCACC
* * * * *
1417566 TTTTTTAATGTCAAACGTTTAAGATATAAG--TGAAACC-GTTTATATTATGTAAAAGTAAAACA
1 TTTTTT-ATGTC-AACGTTTAAGTTATAAGTATGAAACCTATTTATATTATGAAAAAGTAAGACT
* * * * * ***
1417628 AAATAGGTTTTTCATAATAATGAAGTAGG-ATGTGTC
64 AAACAAGTTTTT-ATGATAACGTAGTAGGTA-GCACC
* *
1417664 TTTTTTATGTCAACAGTTTAAGTTATAAGTATGAAA-CTATTTATATTATGCAAAAGTAAGACAA
1 TTTTTTATGTCAAC-GTTTAAGTTATAAGTATGAAACCTATTTATATTATGAAAAAGTAAGACTA
* *
1417728 AACAAGTTTCTTATGATAATGTAGTAGGTATCACC
65 AACAAGTTT-TTATGATAACGTAGTAGGTAGCACC
* * * *
1417763 TTTTTTATGTCAACGGTTTAAGTTATATGTATAAAACCTA-TTCTATTATGAAAAAGTAAAACTA
1 TTTTTTATGTCAAC-GTTTAAGTTATAAGTATGAAACCTATTTATATTATGAAAAAGTAAGACTA
* * ** *
1417827 AACATGTTGCTTATGATAACGTACCAGGTAGCGTCC
65 AACAAGTT-TTTATGATAACGTAGTAGGTAGC-ACC
* *
1417863 TTTTTTATGTCAATCATTTAAGTTATACGTATG
1 TTTTTTATGTCAA-CGTTTAAGTTATAAGTATG
1417896 TAACTGTTTG
Statistics
Matches: 431, Mismatches: 74, Indels: 47
0.78 0.13 0.09
Matches are distributed among these distances:
96 3 0.01
97 25 0.06
98 97 0.23
99 187 0.43
100 112 0.26
101 7 0.02
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (98 bp):
TTTTTTATGTCAACGTTTAAGTTATAAGTATGAAACCTATTTATATTATGAAAAAGTAAGACTAA
ACAAGTTTTTATGATAACGTAGTAGGTAGCACC
Found at i:1417845 original size:296 final size:297
Alignment explanation
Indices: 1417268--1417889 Score: 753
Period size: 296 Copynumber: 2.1 Consensus size: 297
1417258 TAAAGCCTAT
* * * * *
1417268 TTTTTTAATGTCAATTGTTTAAGTTACAAAAATGAAACCGTTTATATTTTGCAAAAGTAAGACAA
1 TTTTTTAATGTCAATCGTTTAAG--ATATAAATGAAACCGTTTATATTATGCAAAAGTAAAACAA
* * *
1417333 AATAGGTTTTTCATGATAACGTAGTAGGTAAAGCTTTTTTATGTTAACCATTTAAGTTATAAGTA
64 AATAGGTTTTTCATAATAACGAAGTAGGTAAAGCTTTTTTATGTCAACCATTTAAGTTATAAGTA
* * * *
1417398 TTAAACCATTTATATTATGAAAAAGTAAGATAAAAATAGGTTGTTCATGATAATGTATTAGGTAA
129 TGAAACCATTTATATTATGAAAAAGTAAGACAAAAATAGGTTCTTCATGATAATGTAGTAGGTAA
* *
1417463 CACCTTTTTAATGTCAAACGTTTAAGTTATAAGTATGAAACAATTTATATTAGACAAAAGTAAGA
194 CACCTTTTTAATGTCAAACGTTTAAGTTATAAGTATAAAACAATTTATATTAGACAAAAGTAAAA
**
1417528 TAAAACAGGTTGTTCATGATAACATATTAGGGAGCGT-C
259 TAAAACAGGTTGTTCATGATAACATACCAGGGAGCGTCC
* * *
1417566 TTTTTTAATGTCAAACGTTTAAGATATAAGTGAAACCGTTTATATTATGTAAAAGTAAAACAAAA
1 TTTTTTAATGTCAATCGTTTAAGATATAAATGAAACCGTTTATATTATGCAAAAGTAAAACAAAA
* **
1417631 TAGGTTTTTCATAATAATGAAGTAGG-ATGTGTCTTTTTTATGTCAA-CAGTTTAAGTTATAAGT
66 TAGGTTTTTCATAATAACGAAGTAGGTA-AAG-CTTTTTTATGTCAACCA-TTTAAGTTATAAGT
* * *
1417694 ATGAAACTATTTATATTATGCAAAAGTAAGACAAAACA-AGTTTCTT-ATGATAATGTAGTAGGT
128 ATGAAACCATTTATATTATGAAAAAGTAAGACAAAA-ATAGGTTCTTCATGATAATGTAGTAGGT
* * * * *
1417757 ATCACCTTTTTTATGTC-AACGGTTTAAGTTATATGTATAAAAC-CTATTCTATTATGA-AAAAG
192 AACACCTTTTTAATGTCAAAC-GTTTAAGTTATAAGTATAAAACAAT-TTATATTA-GACAAAAG
* * *
1417819 TAAAACT-AAACATGTTGCTT-ATGATAACGTACCAGGTAGCGTCC
254 TAAAA-TAAAACAGGTTG-TTCATGATAACATACCAGGGAGCGTCC
* *
1417863 TTTTTT-ATGTCAATCATTTAAGTTATA
1 TTTTTTAATGTCAATCGTTTAAGATATA
1417890 CGTATGTAAC
Statistics
Matches: 278, Mismatches: 36, Indels: 22
0.83 0.11 0.07
Matches are distributed among these distances:
295 5 0.02
296 174 0.63
297 77 0.28
298 22 0.08
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (297 bp):
TTTTTTAATGTCAATCGTTTAAGATATAAATGAAACCGTTTATATTATGCAAAAGTAAAACAAAA
TAGGTTTTTCATAATAACGAAGTAGGTAAAGCTTTTTTATGTCAACCATTTAAGTTATAAGTATG
AAACCATTTATATTATGAAAAAGTAAGACAAAAATAGGTTCTTCATGATAATGTAGTAGGTAACA
CCTTTTTAATGTCAAACGTTTAAGTTATAAGTATAAAACAATTTATATTAGACAAAAGTAAAATA
AAACAGGTTGTTCATGATAACATACCAGGGAGCGTCC
Found at i:1418770 original size:187 final size:185
Alignment explanation
Indices: 1418258--1418758 Score: 497
Period size: 186 Copynumber: 2.7 Consensus size: 185
1418248 GTAAACAATG
* * * * * *
1418258 ACATTCTTAGGCTCAACCATATTTATTATAAATATTCATAACATTTTCGGATTTTAACTTTTTTT
1 ACATTCTTGGGCACAACCGTATTTATTATAAATATTCATAACATTTTCAGCTTTTAACTTATTTT
* * * * * * * * * *
1418323 TTTATTGTGAAAAAATATAAAGCTTCATCAGTTTAAACTCTTGTAATATTTTAGGCGTAA-CTCA
66 GTTATCGTGAGAAAATCTAAAGCTT-ATCAGCTTAAACACTAGTAACATTTTAGGAGCAACCT-A
** * * *
1418387 TTTTGTTAATAAAAATATTAACATCCAGATCGTAACATATTTTCTTAGTGAACCATA
129 TTTTGTTAATAAAAATATTAACATCCAGATCACAACATACTCTCTTAATGAACCATA
* * * *
1418444 ACATTCTTGGGCACAACCGTATTTATTATAGATATCCATAACA-TTTCAACCTTTAACTTATTTT
1 ACATTCTTGGGCACAACCGTATTTATTATAAATATTCATAACATTTTCAGCTTTTAACTTATTTT
* * * * * * *
1418508 GCTATCGTGTGAAAATCTATAA-CTCTATTAACTTAAATACTGGTAACATTTTAGGCA-CAACAT
66 GTTATCGTGAGAAAATCTA-AAGCT-TATCAGCTTAAACACTAGTAACATTTTAGG-AGCAACCT
* * * * * *
1418571 ATTTTGTTAATAAAAATGTTAGCATTCTATATCACAATATACTCTCTTAATGAACCATG
128 ATTTTGTTAATAAAAATATTAACA-TCCAGATCACAACATACTCTCTTAATGAACCATA
* ** * * *
1418630 ATATTCTTGGTTACAATCGTATTTATTATAAATATTCATAACATTTTTAGCTTTTAACTTACTTT
1 ACATTCTTGGGCACAACCGTATTTATTATAAATATTCATAACATTTTCAGCTTTTAACTTATTTT
* *
1418695 GTTATCGTGAGAAAATCTAAAGCATTGTCAGCTTAAACCCTAGTAACATTTTAGGAGCAACCTA
66 GTTATCGTGAGAAAATCTAAAGC-TTATCAGCTTAAACACTAGTAACATTTTAGGAGCAACCTA
1418759 AAATGTTAAT
Statistics
Matches: 250, Mismatches: 56, Indels: 17
0.77 0.17 0.05
Matches are distributed among these distances:
185 77 0.31
186 107 0.43
187 65 0.26
188 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (185 bp):
ACATTCTTGGGCACAACCGTATTTATTATAAATATTCATAACATTTTCAGCTTTTAACTTATTTT
GTTATCGTGAGAAAATCTAAAGCTTATCAGCTTAAACACTAGTAACATTTTAGGAGCAACCTATT
TTGTTAATAAAAATATTAACATCCAGATCACAACATACTCTCTTAATGAACCATA
Found at i:1419752 original size:42 final size:43
Alignment explanation
Indices: 1419548--1419864 Score: 235
Period size: 42 Copynumber: 7.5 Consensus size: 43
1419538 GTCTTAAAAA
* * *
1419548 GTAAAAAGTGAGATTGAAAAAATT-AGGAG-TCTCGACTATTAAG
1 GTAAAAAGTGAGATTGAAAAAATTAAGG-GCT-TCAATTATAAAG
* * *
1419591 GT-AAGAGTGAGATT-AAAAAATTAAGGGCCTAAATTATAAAG
1 GTAAAAAGTGAGATTGAAAAAATTAAGGGCTTCAATTATAAAG
* * * * * * *
1419632 GTAAAATGTAATATTGAAAAAACT-AGAGGCCTAAATTATAAAA
1 GTAAAAAGTGAGATTGAAAAAATTAAG-GGCTTCAATTATAAAG
* * *
1419675 GCAAAAAGT-ATGATTGAAAAAAGTAGGGGTCTT-AATTATAAAG
1 GTAAAAAGTGA-GATTGAAAAAATTAAGGG-CTTCAATTATAAAG
** * *
1419718 GTAAAAAGTGAGATT-AAAAAATTAATAGCTTTAATTATAAAA
1 GTAAAAAGTGAGATTGAAAAAATTAAGGGCTTCAATTATAAAG
* * * ** *
1419760 GTAAAAA-TGAGGTTGAAAAAATTAAGAGCCTCCGTTATAAAA
1 GTAAAAAGTGAGATTGAAAAAATTAAGGGCTTCAATTATAAAG
*
1419802 GTAAATAGTGAGATT-AAAAAATT-AGAGGCTTCAATTATAAAG
1 GTAAAAAGTGAGATTGAAAAAATTAAG-GGCTTCAATTATAAAG
*
1419844 GTAGAAAA-TAAGATTGAAAAA
1 GTA-AAAAGTGAGATTGAAAAA
1419865 GTTAGGTTTG
Statistics
Matches: 219, Mismatches: 40, Indels: 30
0.76 0.14 0.10
Matches are distributed among these distances:
41 30 0.14
42 106 0.48
43 79 0.36
44 4 0.02
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.26
Consensus pattern (43 bp):
GTAAAAAGTGAGATTGAAAAAATTAAGGGCTTCAATTATAAAG
Found at i:1419886 original size:22 final size:22
Alignment explanation
Indices: 1419861--1419910 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
1419851 ATAAGATTGA
1419861 AAAAGTTAGGTTTGTCAAGTAT
1 AAAAGTTAGGTTTGTCAAGTAT
1419883 AAAAGTTAGGTTTGTCAAGTAT
1 AAAAGTTAGGTTTGTCAAGTAT
1419905 AAAAGT
1 AAAAGT
1419911 AAAAAGTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.34
Consensus pattern (22 bp):
AAAAGTTAGGTTTGTCAAGTAT
Done.