Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008280.1 Hibiscus syriacus cultivar Beakdansim tig00110940_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: 3557051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 17
Found at i:1291913 original size:15 final size:15
Alignment explanation
Indices: 1291893--1291935 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1291883 TTGCAAAAAG
*
1291893 TAATAAAAATTAGTA
1 TAATAAAAATTAATA
*
1291908 TAATAAAATTTAATA
1 TAATAAAAATTAATA
*
1291923 AAATAATAAATTA
1 TAATAA-AAATTA
1291936 TTAAATAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
TAATAAAAATTAATA
Found at i:1291998 original size:24 final size:24
Alignment explanation
Indices: 1291970--1292017 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1291960 AATATTTTAC
1291970 CTTCTTAATATAAACATTGATAAT
1 CTTCTTAATATAAACATTGATAAT
*
1291994 CTTCTTAATATAAAGATTGATAAT
1 CTTCTTAATATAAACATTGATAAT
1292018 ATGAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (24 bp):
CTTCTTAATATAAACATTGATAAT
Found at i:1292026 original size:24 final size:24
Alignment explanation
Indices: 1291975--1292027 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1291965 TTTACCTTCT
* ***
1291975 TAATATAAACATTGATAATCTTCT
1 TAATATAAACATTGATAATATGAA
*
1291999 TAATATAAAGATTGATAATATGAA
1 TAATATAAACATTGATAATATGAA
1292023 TAATA
1 TAATA
1292028 AGAGAATTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.38
Consensus pattern (24 bp):
TAATATAAACATTGATAATATGAA
Found at i:1293405 original size:29 final size:31
Alignment explanation
Indices: 1293372--1293439 Score: 77
Period size: 34 Copynumber: 2.2 Consensus size: 31
1293362 AAACTTTAAA
1293372 TTTATT-TA-AAAATTAATTTACCTGTAATG
1 TTTATTATACAAAATTAATTTACCTGTAATG
**
1293401 TTTATTGCATATCAACCTTAATTTACCTGTAATG
1 TTTATT--ATA-CAAAATTAATTTACCTGTAATG
1293435 TTTAT
1 TTTAT
1293440 GACATATCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 6 0.19
32 2 0.06
34 24 0.75
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (31 bp):
TTTATTATACAAAATTAATTTACCTGTAATG
Found at i:1293427 original size:34 final size:34
Alignment explanation
Indices: 1293384--1293451 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
1293374 TATTTAAAAA
1293384 TTAATTTACCTGTAATGTTTATTG-CATATCAACC
1 TTAATTTACCTGTAATGTTTA-TGACATATCAACC
1293418 TTAATTTACCTGTAATGTTTATGACATATCAACC
1 TTAATTTACCTGTAATGTTTATGACATATCAACC
1293452 AGCTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 2 0.06
34 31 0.94
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.43
Consensus pattern (34 bp):
TTAATTTACCTGTAATGTTTATGACATATCAACC
Found at i:1303943 original size:60 final size:58
Alignment explanation
Indices: 1303853--1304016 Score: 136
Period size: 57 Copynumber: 2.8 Consensus size: 58
1303843 TTATTTGTGG
* * * * *
1303853 TTTAGTCCCTTAAGTTTCTATTTTTTCTATTTAAGTCCTTTAACTTTCCGTTATTGTTAT
1 TTTAGTCCTTTAACTTTCT-GTTTTGCTATTTAAGTCCTTTAACTTT-CGTTATTGCTAT
* * *
1303913 TTTAGTCCTTTAACTTTCTGTTTTAGCTATTTTAA-TCCTTCAA-TTT-TTTTTTGCTAT
1 TTTAGTCCTTTAACTTTCTGTTTT-GCTA-TTTAAGTCCTTTAACTTTCGTTATTGCTAT
* * * * ** *
1303970 TTAAGTCCTTAAACTTTTTGTTGTGCTATTTTGGGCCTTTAACTTTC
1 TTTAGTCCTTTAACTTTCTGTTTTGCTATTTAAGTCCTTTAACTTTC
1304017 TGTTTTTTTT
Statistics
Matches: 83, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
55 3 0.04
56 10 0.12
57 31 0.37
59 7 0.08
60 27 0.33
61 5 0.06
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.56
Consensus pattern (58 bp):
TTTAGTCCTTTAACTTTCTGTTTTGCTATTTAAGTCCTTTAACTTTCGTTATTGCTAT
Found at i:1303944 original size:30 final size:29
Alignment explanation
Indices: 1303853--1304022 Score: 155
Period size: 30 Copynumber: 5.8 Consensus size: 29
1303843 TTATTTGTGG
* * * *
1303853 TTTAGTCCCTTAAGTTTCTATTTTTTCTAT
1 TTTAGTCCTTTAACTTTCT-GTTTTGCTAT
* * *
1303883 TTAAGTCCTTTAACTTTCCGTTATTGTTAT
1 TTTAGTCCTTTAACTTTCTGTT-TTGCTAT
1303913 TTTAGTCCTTTAACTTTCTGTTTTAGCTAT
1 TTTAGTCCTTTAACTTTCTGTTTT-GCTAT
* * *
1303943 TTTAATCCTTCAA-TTT-TTTTTTGCTAT
1 TTTAGTCCTTTAACTTTCTGTTTTGCTAT
* * * *
1303970 TTAAGTCCTTAAACTTTTTGTTGTGCTAT
1 TTTAGTCCTTTAACTTTCTGTTTTGCTAT
* *
1303999 TTTGGGCCTTTAACTTTCTGTTTT
1 TTTAGTCCTTTAACTTTCTGTTTT
1304023 TTTTTCAATT
Statistics
Matches: 112, Mismatches: 24, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
27 15 0.13
28 8 0.07
29 34 0.30
30 55 0.49
ACGTcount: A:0.17, C:0.16, G:0.10, T:0.57
Consensus pattern (29 bp):
TTTAGTCCTTTAACTTTCTGTTTTGCTAT
Found at i:1304404 original size:5 final size:5
Alignment explanation
Indices: 1304394--1304424 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1304384 CGCTTTTCAC
*
1304394 TTTTA TTTTA TTTTG TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1304425 CTTTGCGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:1305054 original size:59 final size:59
Alignment explanation
Indices: 1304982--1305099 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
1304972 GGCAACGGTC
1304982 TTTAGAGTATATTGGTAAAAGTTTTCTTAGTCGACATTTTCTCTCTTTATTTAGGTTGT
1 TTTAGAGTATATTGGTAAAAGTTTTCTTAGTCGACATTTTCTCTCTTTATTTAGGTTGT
1305041 TTTAGAGTATATTGGTAAAAGTTTTCTTAGTCGACATTTTCTCTCTTTATTTAGGTTGT
1 TTTAGAGTATATTGGTAAAAGTTTTCTTAGTCGACATTTTCTCTCTTTATTTAGGTTGT
1305100 GTGTTCAATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.51
Consensus pattern (59 bp):
TTTAGAGTATATTGGTAAAAGTTTTCTTAGTCGACATTTTCTCTCTTTATTTAGGTTGT
Found at i:1307204 original size:40 final size:40
Alignment explanation
Indices: 1307159--1307239 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
1307149 CCAAACATTC
*
1307159 AATCTCAGCTACTTCCATTGCAATGATGGATGCCATTACT
1 AATCTCAGCTACTTCCATTGCAATGATGAATGCCATTACT
1307199 AATCTCAGCTACTTCCATTGCAATGATGAATGCCATTACT
1 AATCTCAGCTACTTCCATTGCAATGATGAATGCCATTACT
1307239 A
1 A
1307240 CGAGTGTCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.32
Consensus pattern (40 bp):
AATCTCAGCTACTTCCATTGCAATGATGAATGCCATTACT
Found at i:1314654 original size:20 final size:20
Alignment explanation
Indices: 1314621--1314876 Score: 146
Period size: 20 Copynumber: 12.7 Consensus size: 20
1314611 GATTTTCCAG
*
1314621 AATCGCAATC-CGAATATGAA
1 AATCGCAA-CGCGAATACGAA
* *
1314641 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
1314661 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
1314681 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * * *
1314702 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATACGAA
*
1314722 AATTGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* *
1314743 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* *
1314763 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* *
1314783 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
1314803 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
1314823 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
1314844 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
1314864 AATCGCAACGCGA
1 AATCGCAACGCGA
1314877 TTTTTAAAGC
Statistics
Matches: 185, Mismatches: 37, Indels: 28
0.74 0.15 0.11
Matches are distributed among these distances:
19 4 0.02
20 127 0.69
21 54 0.29
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:1314730 original size:41 final size:40
Alignment explanation
Indices: 1314682--1314873 Score: 251
Period size: 41 Copynumber: 4.7 Consensus size: 40
1314672 GATTCTGACT
* * * *
1314682 ATCGCAACGAGTATCCGTAAAATCGCAACGTGTATCCGTAA
1 ATCGCAACGCGTATCCGT-AAATCGCAACGAGAATACGTAA
* * *
1314723 ATTGCAACGAC-AATACGTAAAATCGCAACGAGAATACGTAA
1 ATCGCAACG-CGTATCCGT-AAATCGCAACGAGAATACGTAA
*
1314764 ATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
* *
1314804 ATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-AA
1314845 ATCGCAACGCGTATCCGTAAATCGCAACG
1 ATCGCAACGCGTATCCGTAAATCGCAACG
1314874 CGATTTTTAA
Statistics
Matches: 133, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
40 58 0.44
41 75 0.56
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (40 bp):
ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
Found at i:1315458 original size:20 final size:20
Alignment explanation
Indices: 1315433--1315483 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1315423 TTCTAAACTT
* *
1315433 AAAATCGCAACATGAAAATG
1 AAAATCACAACACGAAAATG
1315453 AAAATCACAACACGAAAATG
1 AAAATCACAACACGAAAATG
**
1315473 ACTATCACAAC
1 AAAATCACAAC
1315484 GAGAGAATCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.55, C:0.22, G:0.10, T:0.14
Consensus pattern (20 bp):
AAAATCACAACACGAAAATG
Found at i:1315517 original size:33 final size:33
Alignment explanation
Indices: 1315480--1315547 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
1315470 ATGACTATCA
* **
1315480 CAACGAGAGAATCGTAACGCGAAATGAAAATCG
1 CAACGAGAGAATCGCAACGCGAAACCAAAATCG
*
1315513 CAACGAGATAATCGCAACGCGAAACCAAAATCG
1 CAACGAGAGAATCGCAACGCGAAACCAAAATCG
1315546 CA
1 CA
1315548 TTGCGATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.46, C:0.24, G:0.21, T:0.10
Consensus pattern (33 bp):
CAACGAGAGAATCGCAACGCGAAACCAAAATCG
Found at i:1315565 original size:19 final size:19
Alignment explanation
Indices: 1315543--1315593 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
1315533 GAAACCAAAA
* **
1315543 TCGCATTGCGATTTTCGTT
1 TCGCGTTGCGATTTTAATT
1315562 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTAATT
1315581 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1315594 CTCTCATTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.12, C:0.20, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTAATT
Found at i:1315653 original size:20 final size:20
Alignment explanation
Indices: 1315591--1315646 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
1315581 TCGCGTTGCG
*
1315591 ATTCTCTCATTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
*
1315611 ATT-TCCGCGTTGCGATAGTC
1 ATTCT-CTCGTTGCGATAGTC
1315631 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
1315647 TTTCATTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:1317513 original size:94 final size:94
Alignment explanation
Indices: 1317352--1317731 Score: 629
Period size: 94 Copynumber: 4.1 Consensus size: 94
1317342 TAGATTGCTT
* * *
1317352 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAATTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1317417 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
1317446 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1317511 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
1317540 AGTAAATTTGTTCAGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
1317605 ATTTGTCTTTGTTTTGCCTTTCGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
1317634 AGTAAATTTGTTCGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1317699 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1317727 AGTAA
1 AGTAA
1317732 TGCAATCCAT
Statistics
Matches: 270, Mismatches: 15, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
93 26 0.10
94 244 0.90
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1317835 original size:19 final size:19
Alignment explanation
Indices: 1317779--1317903 Score: 89
Period size: 19 Copynumber: 6.7 Consensus size: 19
1317769 TAGTTTACTT
* *
1317779 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
1317799 TCGCAACGTGAAAAATGACTA
1 TCGCAACGCG--AAATGAAAA
1317820 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1317839 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
1317853 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* ***
1317872 TCGCAATGCGAAACCTAAA
1 TCGCAACGCGAAATGAAAA
*
1317891 TCGCAACGTGAAA
1 TCGCAACGCGAAA
1317904 CTATAATCGC
Statistics
Matches: 82, Mismatches: 16, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 43 0.52
20 8 0.10
21 12 0.15
22 3 0.04
ACGTcount: A:0.45, C:0.22, G:0.19, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1317904 original size:19 final size:18
Alignment explanation
Indices: 1317851--1317913 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 18
1317841 GCAACGAGAG
1317851 AATCGCAACGCGAAA-TGAA
1 AATCGCAACGCGAAACT--A
*
1317870 AATCGCAATGCGAAACCTA
1 AATCGCAACGCGAAA-CTA
*
1317889 AATCGCAACGTGAAACTA
1 AATCGCAACGCGAAACTA
1317907 TAATCGC
1 -AATCGC
1317914 GTTGCGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.08
19 34 0.89
21 1 0.03
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.16
Consensus pattern (18 bp):
AATCGCAACGCGAAACTA
Found at i:1317932 original size:19 final size:19
Alignment explanation
Indices: 1317910--1317974 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 19
1317900 GAAACTATAA
1317910 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1317929 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1317943 TCTCTTTGCGATTTCCATT
1 TCGCGTTGCGATTTTCATT
1317962 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1317975 CTCTCGTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
14 9 0.26
16 2 0.06
17 3 0.09
19 21 0.60
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1317962 original size:33 final size:33
Alignment explanation
Indices: 1317913--1317987 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
1317903 ACTATAATCG
*
1317913 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTCCATTTCGCATTGCGATTCTCT
* *
1317946 CTTTGCGATTTCCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTCCATTTCGCATTGCGATTCTCT
1317979 CGTTGCGAT
1 CGTTGCGAT
1317988 AGTCATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTCCATTTCGCATTGCGATTCTCT
Found at i:1320106 original size:33 final size:33
Alignment explanation
Indices: 1320064--1320211 Score: 161
Period size: 33 Copynumber: 4.3 Consensus size: 33
1320054 ACTAAATTCG
*
1320064 CGTTGCGATTTTCATTTCGCTTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1320097 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CT
* * * *
1320136 CGTTGCGATATTCATATTCGCGTTGCGATTTTCA
1 CGTTGCGATTTTCAT-TTCGCATTGCGATTCTCT
* *
1320170 CGTTGCGATTTTCATTTCGCATTACAATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1320203 CGTTGCGAT
1 CGTTGCGAT
1320212 AGTAATTTCG
Statistics
Matches: 96, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
33 49 0.51
34 15 0.16
35 3 0.03
38 2 0.02
39 15 0.16
40 12 0.12
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1320143 original size:20 final size:19
Alignment explanation
Indices: 1320060--1320169 Score: 104
Period size: 20 Copynumber: 5.9 Consensus size: 19
1320050 CGAAACTAAA
*
1320060 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATATTCAT
*
1320079 TTCGCTTTGCG--ATTC--
1 TTCGCGTTGCGATATTCAT
* *
1320094 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATATTCAT
* *
1320112 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATATTCAT
1320131 TTCCGCGTTGCGATATTCAT
1 TT-CGCGTTGCGATATTCAT
*
1320151 ATTCGCGTTGCGATTTTCA
1 -TTCGCGTTGCGATATTCA
1320170 CGTTGCGATT
Statistics
Matches: 72, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
14 8 0.11
16 3 0.04
17 3 0.04
19 26 0.36
20 30 0.42
21 2 0.03
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATATTCAT
Found at i:1320175 original size:14 final size:14
Alignment explanation
Indices: 1320156--1320183 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1320146 TTCATATTCG
1320156 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
1320170 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
1320184 TTTCGCATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTTTCA
Found at i:1323683 original size:21 final size:21
Alignment explanation
Indices: 1323657--1323702 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1323647 TATTCACATT
1323657 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
1323678 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1323699 GCGA
1 GCGA
1323703 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1324185 original size:72 final size:71
Alignment explanation
Indices: 1324033--1324261 Score: 302
Period size: 72 Copynumber: 3.2 Consensus size: 71
1324023 TCTGGTCGAT
* * * * *
1324033 AAGTATCGATACTTTTCCACAAGTATTGATATTTTCAAATTT-AAAAAAAATAGAAAATGGGAAG
1 AAGTATCAATACTTTTCCACAAATATCGATATTTTCGAATTTAAAAAAAAATAGAAAATGAGAAG
*
1324097 GTTGTA
66 GTTGCA
*
1324103 AAGTATCAATACTTTTTCACAAATATCGATATTTTCGAATTTAAAAAAAAATTAGAAAATGAGAA
1 AAGTATCAATACTTTTCCACAAATATCGATATTTTCGAATTTAAAAAAAAA-TAGAAAATGAGAA
1324168 GGTTGCA
65 GGTTGCA
* * * *
1324175 AAGTTTCAATACTTTTCCACAAATATCAATACTTTT-GAATTTAAAAAAACATATAAAATGAGAA
1 AAGTATCAATACTTTTCCACAAATATCGATA-TTTTCGAATTTAAAAAAAAATAGAAAATGAGAA
1324239 -GTCTGCA
65 GGT-TGCA
*
1324246 AAGTATCAATATTTTT
1 AAGTATCAATACTTTT
1324262 GAATTTTATA
Statistics
Matches: 141, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
70 39 0.28
71 38 0.27
72 60 0.43
73 4 0.03
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (71 bp):
AAGTATCAATACTTTTCCACAAATATCGATATTTTCGAATTTAAAAAAAAATAGAAAATGAGAAG
GTTGCA
Found at i:1324405 original size:20 final size:19
Alignment explanation
Indices: 1324338--1324406 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
1324328 TTTGTTTTTT
*
1324338 TAACAAGTTTTGATCCTCG
1 TAACAAGTTTCGATCCTCG
* *
1324357 TAAAAAGTTTTGATCCTCG
1 TAACAAGTTTCGATCCTCG
* *
1324376 TAACAAGTTTCGATTCTCA
1 TAACAAGTTTCGATCCTCG
1324395 TAACAAAGTTTC
1 TAAC-AAGTTTC
1324407 AATACTTTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 37 0.84
20 7 0.16
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (19 bp):
TAACAAGTTTCGATCCTCG
Found at i:1324635 original size:54 final size:54
Alignment explanation
Indices: 1324494--1324934 Score: 399
Period size: 54 Copynumber: 8.3 Consensus size: 54
1324484 TAACATTATA
* * * *
1324494 GGTTGTGCCTTGTTATTTTTAAACTGGTTACCTTATAAGTAGGACTAACGTTT-AT
1 GGTTGTGCCTTGTTATTTTTAATC-GATTACCTTATAAGTAGGAGTAAC-TTTAAC
* * *
1324549 GGTTGT-CTCTT-TT-TTTTTAACTAGCA--ACCTTATAAATAAGAGTAACTTTAAC
1 GGTTGTGC-CTTGTTATTTTTAA-TCG-ATTACCTTATAAGTAGGAGTAACTTTAAC
* * * *
1324601 GGTTGTTCCTTGTTATTTTTAA-CAGATTACCTTATAAGTAGGACTAA-TGTTTAT
1 GGTTGTGCCTTGTTATTTTTAATC-GATTACCTTATAAGTAGGAGTAACT-TTAAC
* * ** *
1324655 GGTTGTGCC-T-TT-TTTTTAATCGGTAACCTTATAAGTAAAAGTAACTTTAAT
1 GGTTGTGCCTTGTTATTTTTAATCGATTACCTTATAAGTAGGAGTAACTTTAAC
** *
1324706 GGTTGCACCTTGTTTTTTTTAATC-ATTAACCTTATAAGTAGGAGTAACTTTAAC
1 GGTTGTGCCTTGTTATTTTTAATCGATT-ACCTTATAAGTAGGAGTAACTTTAAC
* * * * *
1324760 GGTTGCGTCTTGTTATTTTTAACCGATTACCTTATAAGTAGGATTAACGTTAAC
1 GGTTGTGCCTTGTTATTTTTAATCGATTACCTTATAAGTAGGAGTAACTTTAAC
* * * *
1324814 AG-TGACGCCTTG-TATTTTTAATCGGTTACCTTATAAGTAGGAGTAACGTTAAC
1 GGTTG-TGCCTTGTTATTTTTAATCGATTACCTTATAAGTAGGAGTAACTTTAAC
* *
1324867 GTTTATGCCTTGTTATTTTTAATCGATTACCTTATAAGTAGGAGTAACGTTT-AC
1 GGTTGTGCCTTGTTATTTTTAATCGATTACCTTATAAGTAGGAGTAAC-TTTAAC
* *
1324921 GATTGCGCCTTGTT
1 GGTTGTGCCTTGTT
1324935 TTCTTTTTCC
Statistics
Matches: 317, Mismatches: 47, Indels: 45
0.78 0.11 0.11
Matches are distributed among these distances:
51 39 0.12
52 33 0.10
53 63 0.20
54 168 0.53
55 14 0.04
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (54 bp):
GGTTGTGCCTTGTTATTTTTAATCGATTACCTTATAAGTAGGAGTAACTTTAAC
Found at i:1324718 original size:105 final size:105
Alignment explanation
Indices: 1324501--1324863 Score: 323
Period size: 105 Copynumber: 3.4 Consensus size: 105
1324491 ATAGGTTGTG
*
1324501 CCTTGTTATTTTTAAACTGGTTACCTTATAAGTAGGACTAACGTTTATGGTTGTCTCTTTTTTTT
1 CCTTGTTATTTTT-AAC-GATTACCTTATAAGTAGGACTAACGTTTATGGTTGTCTCTTTTTTTT
* **
1324566 TAACTAGCAACCTTATAAATAAGAGTAACTTTAACGGTTGTT
64 TAACTAGCAACCTTATAAATAAAAGTAACTTTAACGGTTGCA
*
1324608 CCTTGTTATTTTTAACAGATTACCTTATAAGTAGGACTAATGTTTATGGTTGTGC-C-TTTTTTT
1 CCTTGTTATTTTTAAC-GATTACCTTATAAGTAGGACTAACGTTTATGGTTGT-CTCTTTTTTTT
* * * *
1324671 TAA-TCGGTAACCTTATAAGTAAAAGTAACTTTAATGGTTGCA
64 TAACT-AGCAACCTTATAAATAAAAGTAACTTTAACGGTTGCA
* * *
1324713 CCTTGTTTTTTTTAATC-ATTAACCTTATAAGTAGGAGTAAC-TTTAACGGTTG-CGTCTTGTTA
1 CCTTGTTATTTTTAA-CGATT-ACCTTATAAGTAGGACTAACGTTT-ATGGTTGTC-TCTT-TT-
* * ** * * * *
1324775 TTTTTAAC-CG-ATTACCTTATAAGTAGGATTAACGTTAACAG-TGACG
60 TTTTTAACTAGCA--ACCTTATAAATAAAAGTAACTTTAACGGTTG-CA
* *
1324821 CCTTG-TATTTTTAATCGGTTACCTTATAAGTAGGAGTAACGTT
1 CCTTGTTATTTTTAA-CGATTACCTTATAAGTAGGACTAACGTT
1324864 AACGTTTATG
Statistics
Matches: 216, Mismatches: 24, Indels: 31
0.80 0.09 0.11
Matches are distributed among these distances:
103 1 0.00
104 7 0.03
105 79 0.37
106 41 0.19
107 49 0.23
108 39 0.18
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (105 bp):
CCTTGTTATTTTTAACGATTACCTTATAAGTAGGACTAACGTTTATGGTTGTCTCTTTTTTTTTA
ACTAGCAACCTTATAAATAAAAGTAACTTTAACGGTTGCA
Found at i:1324866 original size:107 final size:106
Alignment explanation
Indices: 1324495--1324958 Score: 374
Period size: 107 Copynumber: 4.3 Consensus size: 106
1324485 AACATTATAG
* * * *
1324495 GTTGTGCCTTGTTATTTTTAAACTGGTTACCTTATAAGTAGGACTAACGTTTATGGTTGTC-TCT
1 GTTGCGCCTTGTTATTTTTAATC-GGTTACCTTATAAGTAGGACTAACGTTAACGGTTG-CGTCT
* * * *
1324559 TTTTTTTTAACTAGCA--ACCTTATAAATAAGAGTAACTTTAACG
64 TTTTTTTTAAC-CG-ATTACCTTATAAGTAAGAGTAACGTTAACA
** * * * * * *
1324602 GTTGTTCCTTGTTATTTTTAA-CAGATTACCTTATAAGTAGGACTAATGTTTATGGTTGTG-CCT
1 GTTGCGCCTTGTTATTTTTAATC-GGTTACCTTATAAGTAGGACTAACGTTAACGGTTGCGTCTT
* * * * * **
1324665 TTTTTTTAATCGGTAACCTTATAAGTAAAAGTAACTTTAATG
65 TTTTTTTAACCGATTACCTTATAAGTAAGAGTAACGTTAACA
* * * * *
1324707 GTTGCACCTTGTTTTTTTTAATC-ATTAACCTTATAAGTAGGAGTAACTTTAACGGTTGCGTCTT
1 GTTGCGCCTTGTTATTTTTAATCGGTT-ACCTTATAAGTAGGACTAACGTTAACGGTTGCGTCTT
* *
1324771 GTTATTTTTAACCGATTACCTTATAAGTAGGATTAACGTTAACA
65 -TT-TTTTTAACCGATTACCTTATAAGTAAGAGTAACGTTAACA
* * ** *
1324815 G-TGACGCCTTG-TATTTTTAATCGGTTACCTTATAAGTAGGAGTAACGTTAACGTTTATGCCTT
1 GTTG-CGCCTTGTTATTTTTAATCGGTTACCTTATAAGTAGGACTAACGTTAACGGTTGCGTCTT
* * *
1324878 GTTATTTTTAATCGATTACCTTATAAGTAGGAGTAACGTTTAC-
65 -TT-TTTTTAACCGATTACCTTATAAGTAAGAGTAACGTTAACA
*
1324921 GATTGCGCCTTGTT-TTCTTT-TTCCGGTTACCTTATAAG
1 G-TTGCGCCTTGTTATT-TTTAAT-CGGTTACCTTATAAG
1324959 ATAGAATAAA
Statistics
Matches: 299, Mismatches: 43, Indels: 29
0.81 0.12 0.08
Matches are distributed among these distances:
104 4 0.01
105 80 0.27
106 38 0.13
107 116 0.39
108 61 0.20
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (106 bp):
GTTGCGCCTTGTTATTTTTAATCGGTTACCTTATAAGTAGGACTAACGTTAACGGTTGCGTCTTT
TTTTTTAACCGATTACCTTATAAGTAAGAGTAACGTTAACA
Found at i:1324911 original size:161 final size:159
Alignment explanation
Indices: 1324495--1324976 Score: 480
Period size: 161 Copynumber: 3.0 Consensus size: 159
1324485 AACATTATAG
* * * *
1324495 GTTGTGCCTTGTTATTTTTAAACTGGTTACCTTATAAGTAGGACTAACGTTTATGGTTGTCTCTT
1 GTTGCGCCTTG-TATTTTTAATC-GGTTACCTTATAAGTAGGAGTAACGTTAATGGTTGTC-CTT
* * * *
1324560 -TTTTTTTAACTAGCA--ACCTTATAAATAAGAGTAACTTTAACGGTTG-TTCCTTGTTATTTTT
63 GTTTTTTTAA-TCG-ATTACCTTATAAGTAGGAGTAACTTTAACGGTTGCGT-CTTGTTATTTTT
* * * * **
1324621 AACAGATTACCTTATAAGTAGGACTAATGTTTATG
125 AACCGATTACCTTATAAGTAGGATTAACGTTAACA
* * ** * *
1324656 GTTGTGCCTT-T-TTTTTAATCGGTAACCTTATAAGTAAAAGTAACTTTAATGGTTGCACCTTGT
1 GTTGCGCCTTGTATTTTTAATCGGTTACCTTATAAGTAGGAGTAACGTTAATGGTTG-TCCTTG-
1324719 TTTTTTTAATC-ATTAACCTTATAAGTAGGAGTAACTTTAACGGTTGCGTCTTGTTATTTTTAAC
64 TTTTTTTAATCGATT-ACCTTATAAGTAGGAGTAACTTTAACGGTTGCGTCTTGTTATTTTTAAC
1324783 CGATTACCTTATAAGTAGGATTAACGTTAACA
128 CGATTACCTTATAAGTAGGATTAACGTTAACA
* * *
1324815 G-TGACGCCTTGTATTTTTAATCGGTTACCTTATAAGTAGGAGTAACGTTAACGTTTATGCCTTG
1 GTTG-CGCCTTGTATTTTTAATCGGTTACCTTATAAGTAGGAGTAACGTTAATGGTTGT-CCTTG
* * *
1324879 TTATTTTTAATCGATTACCTTATAAGTAGGAGTAACGTTT-ACGATTGCGCCTTGTT-TTCTTTT
64 TT-TTTTTAATCGATTACCTTATAAGTAGGAGTAAC-TTTAACGGTTGCGTCTTGTTATT-TTTA
* * * *
1324942 TCCGGTTACCTTATAAGATAGAATAAAACGTTAAC
126 ACCGATTACCTTATAAG-TAGGAT-TAACGTTAAC
1324977 CATTACTTTA
Statistics
Matches: 270, Mismatches: 34, Indels: 32
0.80 0.10 0.10
Matches are distributed among these distances:
156 1 0.00
157 32 0.12
158 12 0.04
159 86 0.32
160 6 0.02
161 113 0.42
162 11 0.04
163 9 0.03
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (159 bp):
GTTGCGCCTTGTATTTTTAATCGGTTACCTTATAAGTAGGAGTAACGTTAATGGTTGTCCTTGTT
TTTTTAATCGATTACCTTATAAGTAGGAGTAACTTTAACGGTTGCGTCTTGTTATTTTTAACCGA
TTACCTTATAAGTAGGATTAACGTTAACA
Found at i:1325625 original size:107 final size:107
Alignment explanation
Indices: 1325433--1325699 Score: 315
Period size: 107 Copynumber: 2.5 Consensus size: 107
1325423 CATTTTAGGT
* * *
1325433 GCAACCTAATATGTTAATAATATTTATAATAAAATAAGTAATTAATCTATTTTGTTTTCGTGAGA
1 GCAACCTAATATGTTAATAATATTTATAAAAAAATAAGTAATTAACCTATTTTATTTTCGTGAGA
** * * * ** * *
1325498 TTTTAAGTATTCATCGGCTTAAATTTTGGTAATATTTTAAAC
66 TTTTAAGTACCCATCAGCTTAAACTCTCATAACATATTAAAC
* * * *
1325540 GCAACCAAATATGTTAATAGTATTTATAACAACATAAGTAATTAACCTATTTTATTATT-GTG-G
1 GCAACCTAATATGTTAATAATATTTATAAAAAAATAAGTAATTAACCTATTTTATT-TTCGTGAG
1325603 ATTTCTAAG-ACCCTATCAGCTTAAACTCTCATAACATATTAAAC
65 ATTT-TAAGTACCC-ATCAGCTTAAACTCTCATAACATATTAAAC
* * *
1325647 GCAACCTAATATGTTGATAATATTAATAAAAAAATAAGTAATTAACTTATTTT
1 GCAACCTAATATGTTAATAATATTTATAAAAAAATAAGTAATTAACCTATTTT
1325700 CTTACCTTTA
Statistics
Matches: 135, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
106 7 0.05
107 126 0.93
108 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (107 bp):
GCAACCTAATATGTTAATAATATTTATAAAAAAATAAGTAATTAACCTATTTTATTTTCGTGAGA
TTTTAAGTACCCATCAGCTTAAACTCTCATAACATATTAAAC
Found at i:1339619 original size:25 final size:25
Alignment explanation
Indices: 1339591--1339639 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1339581 TAAATTATAT
*
1339591 TAAAAATTGAAGAAATGTGAAATTA
1 TAAAAATTGAAGAAATGTAAAATTA
* *
1339616 TAAAATTTGAAGAAGTGTAAAATT
1 TAAAAATTGAAGAAATGTAAAATT
1339640 GGATCATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (25 bp):
TAAAAATTGAAGAAATGTAAAATTA
Found at i:1356320 original size:30 final size:31
Alignment explanation
Indices: 1356247--1356332 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 31
1356237 CAACTAATAT
* *
1356247 ATATATATATATATATATATTA-ATATAAAC
1 ATATATATATATATATAAACTATATATAAAC
* * *
1356277 -TATATAGTGTATATTTAAAGTATATATAAAC
1 ATATATA-TATATATATAAACTATATATAAAC
1356308 ATATATAT-TATATATAAACTATATA
1 ATATATATATATATATAAACTATATA
1356333 GTTTATATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
29 6 0.13
30 26 0.55
31 9 0.19
32 6 0.13
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (31 bp):
ATATATATATATATATAAACTATATATAAAC
Found at i:1356341 original size:11 final size:11
Alignment explanation
Indices: 1356327--1356371 Score: 69
Period size: 11 Copynumber: 4.4 Consensus size: 11
1356317 ATATATAAAC
1356327 TATATAGTTTA
1 TATATAGTTTA
1356338 TATATAG--TA
1 TATATAGTTTA
1356347 TATAT-GTTTA
1 TATATAGTTTA
1356357 TATATAGTTTA
1 TATATAGTTTA
1356368 TATA
1 TATA
1356372 CATCGGGACT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 1 0.03
9 7 0.23
10 7 0.23
11 16 0.52
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:1356362 original size:50 final size:51
Alignment explanation
Indices: 1356246--1356371 Score: 145
Period size: 50 Copynumber: 2.5 Consensus size: 51
1356236 ACAACTAATA
*
1356246 TATATATATATATATATATATTA-ATATAAACTATATAGTGTATATTTAAAG
1 TATATAT-TATATATATATATTATATATAAACTATATAGTGTATATATAAAG
* * *
1356297 TATATA-TAAACATATATATTATATATAAACTATATAGT-T-TATATATAG
1 TATATATTATATATATATATTATATATAAACTATATAGTGTATATATAAAG
*
1356345 TATATATGTTTATATATAGT-TTATATA
1 TATATAT-TATATATATA-TATTATATA
1356372 CATCGGGACT
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
48 13 0.20
49 14 0.22
50 30 0.47
51 7 0.11
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (51 bp):
TATATATTATATATATATATTATATATAAACTATATAGTGTATATATAAAG
Found at i:1356371 original size:2 final size:2
Alignment explanation
Indices: 1356243--1356362 Score: 75
Period size: 2 Copynumber: 58.5 Consensus size: 2
1356233 GAAACAACTA
*
1356243 AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AA ACT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T
* * * * * *
1356285 GT AT AT TT AA AGT AT AT AT AA AC AT AT AT AT -T AT AT AT AA ACT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * *
1356328 AT AT AGT TT AT AT AT AGT AT AT AT GT TT AT AT AT A
1 AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT A
1356363 GTTTATATAC
Statistics
Matches: 91, Mismatches: 18, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
1 3 0.03
2 81 0.89
3 7 0.08
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1356925 original size:30 final size:30
Alignment explanation
Indices: 1356889--1356947 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1356879 GTACCAAATA
*
1356889 TATATATACTACTATCTATAAACTATATAGTT
1 TATATATACTAGTA--TATAAACTATATAGTT
*
1356921 TATATATAGTAGTATATAAACTATATA
1 TATATATACTAGTATATAAACTATATA
1356948 TAAACCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 13 0.52
32 12 0.48
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (30 bp):
TATATATACTAGTATATAAACTATATAGTT
Found at i:1356947 original size:11 final size:11
Alignment explanation
Indices: 1356933--1356980 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
1356923 TATATAGTAG
1356933 TATATAAACTA
1 TATATAAACTA
*
1356944 TATATAAACCA
1 TATATAAACTA
1356955 TATAT--ACTA
1 TATATAAACTA
*
1356964 TATGTAAACTA
1 TATATAAACTA
*
1356975 TGTATA
1 TATATA
1356981 TTATATAGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
9 7 0.23
11 23 0.77
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (11 bp):
TATATAAACTA
Found at i:1356963 original size:20 final size:20
Alignment explanation
Indices: 1356934--1356987 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1356924 ATATAGTAGT
*
1356934 ATATAAACTATATATAAACC
1 ATATATACTATATATAAACC
* *
1356954 ATATATACTATATGTAAACT
1 ATATATACTATATATAAACC
* *
1356974 ATGTATATTATATA
1 ATATATACTATATA
1356988 GTTTACATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (20 bp):
ATATATACTATATATAAACC
Found at i:1357030 original size:62 final size:60
Alignment explanation
Indices: 1356934--1357053 Score: 163
Period size: 62 Copynumber: 2.0 Consensus size: 60
1356924 ATATAGTAGT
*
1356934 ATATAAACTATATATAAACCATATATACTATATGTAAACTATGT-ATATTATATAGTTTAC
1 ATATAAACTATATATAAACCATATATACTATATGTAAACTATATAATA-TATATAGTTTAC
* *
1356994 ATATGAACTATATGTATAAACTATATATA-TATTATGTAAACTATATAATATATATAGTTT
1 ATATAAACTATA--TATAAACCATATATACTA-TATGTAAACTATATAATATATATAGTTT
1357054 GGTAGTTTAC
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
60 11 0.21
61 2 0.04
62 37 0.70
63 3 0.06
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (60 bp):
ATATAAACTATATATAAACCATATATACTATATGTAAACTATATAATATATATAGTTTAC
Found at i:1357235 original size:13 final size:13
Alignment explanation
Indices: 1357126--1357223 Score: 58
Period size: 13 Copynumber: 7.5 Consensus size: 13
1357116 TATATGCTAC
*
1357126 ATATATAAATTAT
1 ATATATAAACTAT
1357139 ATATATAAACTAT
1 ATATATAAACTAT
**
1357152 ATACTAT-AGTTGAT
1 ATA-TATAAACT-AT
* *
1357166 ATTTATATACTAT
1 ATATATAAACTAT
* *
1357179 AT-T-TACATTATT
1 ATATATAAACTA-T
* *
1357191 ACATATGAACTAT
1 ATATATAAACTAT
*
1357204 ATATAAAAACTAT
1 ATATATAAACTAT
1357217 ATATATA
1 ATATATA
1357224 TATAAACTAT
Statistics
Matches: 62, Mismatches: 17, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
11 5 0.08
12 3 0.05
13 42 0.68
14 12 0.19
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (13 bp):
ATATATAAACTAT
Found at i:1357260 original size:18 final size:18
Alignment explanation
Indices: 1357203--1357312 Score: 88
Period size: 18 Copynumber: 6.3 Consensus size: 18
1357193 ATATGAACTA
*
1357203 TATATAAAAACTATATA-
1 TATATATAAACTATATAT
1357220 TATATATAAACTATAT-T
1 TATATATAAACTATATAT
*
1357237 ACATATATAAACTATATAT
1 -TATATATAAACTATATAT
* *
1357256 TATATAGT--TC-AT-TAG
1 TATATA-TAAACTATATAT
* * *
1357271 AATACATAAACTATATAG
1 TATATATAAACTATATAT
*
1357289 TATACATAAACTATATAT
1 TATATATAAACTATATAT
1357307 TATATA
1 TATATA
1357313 GTTCGTTAAT
Statistics
Matches: 74, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
14 1 0.01
15 6 0.08
16 3 0.04
17 18 0.24
18 44 0.59
19 2 0.03
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (18 bp):
TATATATAAACTATATAT
Found at i:1357335 original size:51 final size:52
Alignment explanation
Indices: 1357219--1357336 Score: 161
Period size: 51 Copynumber: 2.3 Consensus size: 52
1357209 AAAACTATAT
*
1357219 ATATATATAAACTATATTACATATATAAACTATATATTATATAGTTCATTAG
1 ATATATATAAACTATATTACATACATAAACTATATATTATATAGTTCATTAG
* * *
1357271 A-ATACATAAACTATA-TAGTATACATAAACTATATATTATATAGTTCGTTA-
1 ATATATATAAACTATATTA-CATACATAAACTATATATTATATAGTTCATTAG
*
1357321 ATATATATAGACTATA
1 ATATATATAAACTATA
1357337 CATTAATTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
50 3 0.05
51 54 0.93
52 1 0.02
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (52 bp):
ATATATATAAACTATATTACATACATAAACTATATATTATATAGTTCATTAG
Found at i:1357467 original size:61 final size:61
Alignment explanation
Indices: 1357398--1357534 Score: 220
Period size: 61 Copynumber: 2.2 Consensus size: 61
1357388 TATAAGGATC
*
1357398 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTACAACATTAAATTTGGACT
1 AAATTGAACAAATTTTAAATATAAAGCTTAAATTAATAAATTACAACATTAAATTTGGACT
* * * * *
1357459 AAATTGAACAAATTTTAAATATAAAGCTTAAATTAATACATTGCATCATTAACTTTGGATT
1 AAATTGAACAAATTTTAAATATAAAGCTTAAATTAATAAATTACAACATTAAATTTGGACT
1357520 AAATTGAACAAATTT
1 AAATTGAACAAATTT
1357535 AAAACTAAGG
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 70 1.00
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (61 bp):
AAATTGAACAAATTTTAAATATAAAGCTTAAATTAATAAATTACAACATTAAATTTGGACT
Found at i:1357925 original size:110 final size:111
Alignment explanation
Indices: 1357777--1357981 Score: 272
Period size: 114 Copynumber: 1.8 Consensus size: 111
1357767 AAAAATCCTC
*
1357777 ATTTGATATTCACAAACACCAAAACCTAAACCATTTCC-TTTTTTCAATCAATA-ACCCAAAAAT
1 ATTTGATATTCAAAAACACCAAAACCTAAACCATTTCCTTTTTTTCAATCAA-ACACCCAAAAAT
* *
1357840 TCAACCATTGCTCATCCGTGTTCATCCCAGTTCTTCCCCAAACCATT
65 TAAACCATTGCTCATCCATGTTCATCCCAGTTCTTCCCCAAACCATT
* *
1357887 ATTTGATATTCAAAAACACCAAAATCTAAACTCA-TTCCTATTTTTTTTCGATCAAACACCCAAA
1 ATTTGATATTCAAAAACACCAAAACCTAAAC-CATTTCC---TTTTTTTCAATCAAACACCCAAA
* * *
1357951 AATTAAACCCTTGTTCATCCATGTTCTTCCC
62 AATTAAACCATTGCTCATCCATGTTCATCCC
1357982 CAAACCCTTA
Statistics
Matches: 81, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
110 33 0.41
111 2 0.02
113 1 0.01
114 45 0.56
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (111 bp):
ATTTGATATTCAAAAACACCAAAACCTAAACCATTTCCTTTTTTTCAATCAAACACCCAAAAATT
AAACCATTGCTCATCCATGTTCATCCCAGTTCTTCCCCAAACCATT
Found at i:1358184 original size:6 final size:6
Alignment explanation
Indices: 1358175--1358215 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
1358165 ACCAGAATCT
* * *
1358175 AAACCC AAACTC AAACCT GAACCC AAACCC AAACCC AAACC
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACC
1358216 GAGCTTATTC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.49, C:0.44, G:0.02, T:0.05
Consensus pattern (6 bp):
AAACCC
Found at i:1358654 original size:2 final size:2
Alignment explanation
Indices: 1358647--1358689 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1358637 TCGTATATGT
1358647 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1358689 T
1 T
1358690 TTTTAATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1361306 original size:23 final size:23
Alignment explanation
Indices: 1361239--1361298 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
1361229 CATTTTATAT
1361239 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* * *
1361262 GGCACTTCAGTGTAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
1361285 GGTACTTCGGTGCA
1 GGCACTTCGGTGCA
1361299 TTTATACGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:1363836 original size:16 final size:16
Alignment explanation
Indices: 1363815--1363852 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1363805 TAAAAGATAT
*
1363815 GATTTGTGTATAAGGA
1 GATTTGTGTAAAAGGA
1363831 GATTTGTGTAAAAGGA
1 GATTTGTGTAAAAGGA
*
1363847 TATTTG
1 GATTTG
1363853 GATTTTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (16 bp):
GATTTGTGTAAAAGGA
Found at i:1366663 original size:23 final size:23
Alignment explanation
Indices: 1366595--1366655 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1366585 ACATTTTGTA
1366595 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
1366618 CGGCACTTCGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
1366641 TGGCACTTTGGTGCA
1 TGGCACTTCGGTGCA
1366656 TTTATACGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.16, C:0.25, G:0.28, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1367094 original size:12 final size:11
Alignment explanation
Indices: 1367058--1367099 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
1367048 AAATAATGTG
*
1367058 TGTTATGTATA
1 TGTTATATATA
1367069 TGTGTATA-ATA
1 TGT-TATATATA
1367080 TGTTATATATAA
1 TGTTATATAT-A
1367092 TGTTATAT
1 TGTTATAT
1367100 TGTTTTGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 4 0.15
11 11 0.41
12 12 0.44
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (11 bp):
TGTTATATATA
Found at i:1368152 original size:20 final size:20
Alignment explanation
Indices: 1368108--1368158 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1368098 CAAATTTTTT
* * *
1368108 TATGAATAGTA-TTGTATTG
1 TATGAATAGTACTGGTACTA
1368127 TATGAATAGTACTGGTACTA
1 TATGAATAGTACTGGTACTA
1368147 TATGAATAGTAC
1 TATGAATAGTAC
1368159 CGATATTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.39
Consensus pattern (20 bp):
TATGAATAGTACTGGTACTA
Found at i:1368248 original size:20 final size:20
Alignment explanation
Indices: 1368223--1368283 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
1368213 AAATGGGTAC
* *
1368223 CGATACTACTACAGTAGTAT
1 CGATACTGCTACAGTAATAT
*
1368243 CGATACTGTTACAGTAATAT
1 CGATACTGCTACAGTAATAT
*
1368263 CGATACTGCTACAATAATAT
1 CGATACTGCTACAGTAATAT
1368283 C
1 C
1368284 AAGCCCAACG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (20 bp):
CGATACTGCTACAGTAATAT
Found at i:1369585 original size:19 final size:18
Alignment explanation
Indices: 1369537--1369599 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
1369527 AAACTCAAAA
*
1369537 TTGAAAAT-AAATCGATT
1 TTGAAAATAAAATTGATT
*
1369554 TTGAAAGAAAAAATTGATT
1 TTGAAA-ATAAAATTGATT
1369573 TTGAAAATCAAAA-TGAAATT
1 TTGAAAAT-AAAATTG--ATT
1369593 TTGAAAA
1 TTGAAAA
1369600 ATGATTTAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
17 6 0.16
18 4 0.11
19 18 0.47
20 10 0.26
ACGTcount: A:0.52, C:0.03, G:0.13, T:0.32
Consensus pattern (18 bp):
TTGAAAATAAAATTGATT
Found at i:1382829 original size:11 final size:11
Alignment explanation
Indices: 1382801--1382832 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1382791 CGTTCTCAAA
*
1382801 TCGGGTGCAGG
1 TCGGGTTCAGG
1382812 TCGGGTTCAGG
1 TCGGGTTCAGG
1382823 TCGGGTTCAG
1 TCGGGTTCAG
1382833 ATCCACAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.19, G:0.47, T:0.25
Consensus pattern (11 bp):
TCGGGTTCAGG
Found at i:1384060 original size:139 final size:139
Alignment explanation
Indices: 1383815--1384364 Score: 691
Period size: 139 Copynumber: 4.0 Consensus size: 139
1383805 GATTCAAATC
* * * * * *
1383815 ATAATTGATTAAAATTAATTAGGATT-ATAATTAGAGTCTCCACTTTAGGCCTAATTT-AAACTT
1 ATAATTGGTTAAAATTGACTAGG-TTAATAATTAGAGCCTCCATTTTAGGCTTAATTTAAAACTT
* *
1383878 AGTCCTTAAA-TTAGAGGAATTTTTTAATTTGGTCATCGCTTTTGCTCAAGGTTCCATTTTAATT
65 AGTCCTTAAATTTAGGGGAA-TTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATT
1383942 ATTCGAA-ATAA
129 ATTCGAATA-AA
1383953 ATAATTGGTTAAAATTGACTAGGTTAATAATTAGAGCCTCCATTTTAGGCTTAATTTAAAACTTA
1 ATAATTGGTTAAAATTGACTAGGTTAATAATTAGAGCCTCCATTTTAGGCTTAATTTAAAACTTA
* * *
1384018 GTCCTTAAATTTAGGGGAATTTTTAATTTGGTCCTCACTTTTGCTCGAGGTTCTATTTTAATTAT
66 GTCCTTAAATTTAGGGGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATTAT
1384083 TCGAATAAA
131 TCGAATAAA
* * * *
1384092 ATATTTGGTTAAAATTGACTACGTTAATAATTAGAGCCTCCATTTTAGGCTTAATTTCAAGCTT-
1 ATAATTGGTTAAAATTGACTAGGTTAATAATTAGAGCCTCCATTTTAGGCTTAATTTAAAACTTA
*
1384156 GTCCTTAAATTTAGGGGAATTTTTAATTTGGTCATCGCATTTGCTCGAGGTTCCATTTTAAATTA
66 GTCCTTAAATTTAGGGGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTT-AATTA
*
1384221 TTCGAATCAA
130 TTCGAATAAA
* * ** * *
1384231 ATAATTGGTTAAAATTGACTATGTTATTTTTTAGAGCCTCCATTTTAGGTTTAATTTTATAAC-T
1 ATAATTGGTTAAAATTGACTAGGTTAATAATTAGAGCCTCCATTTTAGGCTTAA-TTTAAAACTT
* * * * * ** * * * *
1384295 AGTCCTT-TATTCTATGAGAATTTTTTATTTGATCCCCGCTTATGCTCGAGGTTCCACTTTGACT
65 AGTCCTTAAATT-TAGGGGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATT
1384359 ATTCGA
129 ATTCGA
1384365 TTCAATAATT
Statistics
Matches: 363, Mismatches: 41, Indels: 15
0.87 0.10 0.04
Matches are distributed among these distances:
137 2 0.01
138 103 0.28
139 199 0.55
140 59 0.16
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (139 bp):
ATAATTGGTTAAAATTGACTAGGTTAATAATTAGAGCCTCCATTTTAGGCTTAATTTAAAACTTA
GTCCTTAAATTTAGGGGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATTAT
TCGAATAAA
Found at i:1384418 original size:278 final size:277
Alignment explanation
Indices: 1383858--1384424 Score: 691
Period size: 278 Copynumber: 2.0 Consensus size: 277
1383848 GAGTCTCCAC
* *
1383858 TTTAGGCCTAATTTAAACTTAGTCCTTAAATTAGAGGAATTTTTTAATTTGGTCATCGCTTTTGC
1 TTTAGGCTTAATTTAAACTTAGTCCTTAAATTAGAGGAATTTTTTAATTTGGTCATCGCATTTGC
1383923 TCAAGGTTCCATTTTAATTATTCGAAATAAATAATTGGTTAAAATTGACTAGGTTAATAATTAGA
66 TCAAGGTTCCATTTTAATTATTCGAAATAAATAATTGGTTAAAATTGACTAGGTTAATAATTAGA
* * *
1383988 GCCTCCATTTTAGGCTTAATTTAAAACTTAGTCCTTAAATTTAGGGGAATTTTTAATTTGGTCCT
131 GCCTCCATTTTAGGCTTAATTTAAAACTTAGTCCTTAAATTTAGGAGAATTTTTAATTTGATCCC
* * * * ** *
1384053 CACTTTTGCTCGAGGTTCTATTTTAATTATTCGAATAAAATATTTGGTTAAAATTGACTACGTTA
196 CACTTATGCTCGAGGTTCCACTTTAACTATTCGAATAAAATATTTGACTAAAAATGACTACGTTA
* *
1384118 ATAATTAGAGCCTCCAT
261 ATAATCAGAGCCTACAT
* *
1384135 TTTAGGCTTAATTTCAAGCTT-GTCCTTAAATTTAGGGGAA-TTTTTAATTTGGTCATCGCATTT
1 TTTAGGCTTAATTT-AAACTTAGTCCTTAAA-TTAGAGGAATTTTTTAATTTGGTCATCGCATTT
* * * **
1384198 GCTCGAGGTTCCATTTTAAATTATTCG-AATCAAATAATTGGTTAAAATTGACTATGTTATTTTT
64 GCTCAAGGTTCCATTTT-AATTATTCGAAAT-AAATAATTGGTTAAAATTGACTAGGTTAATAAT
* * * * *
1384262 TAGAGCCTCCATTTTAGGTTTAATTTTATAAC-TAGTCCTT-TATTCTATGAGAATTTTTTATTT
127 TAGAGCCTCCATTTTAGGCTTAA-TTTAAAACTTAGTCCTTAAATT-TAGGAGAATTTTTAATTT
* * ** *
1384325 GATCCCCGCTTATGCTCGAGGTTCCACTTTGACTATTCG-ATTCAATAATTT-ACTAAAAATGAT
190 GATCCCCACTTATGCTCGAGGTTCCACTTTAACTATTCGAATAAAAT-ATTTGACTAAAAATGAC
* *
1384388 TAGGATTTAT-ATCAGAGCCTACATT
254 TACG-TTAATAATCAGAGCCTACA-T
*
1384413 TTTAGGTTTAAT
1 TTTAGGCTTAAT
1384425 CTCCTATGTT
Statistics
Matches: 247, Mismatches: 34, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
277 93 0.38
278 147 0.60
279 7 0.03
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (277 bp):
TTTAGGCTTAATTTAAACTTAGTCCTTAAATTAGAGGAATTTTTTAATTTGGTCATCGCATTTGC
TCAAGGTTCCATTTTAATTATTCGAAATAAATAATTGGTTAAAATTGACTAGGTTAATAATTAGA
GCCTCCATTTTAGGCTTAATTTAAAACTTAGTCCTTAAATTTAGGAGAATTTTTAATTTGATCCC
CACTTATGCTCGAGGTTCCACTTTAACTATTCGAATAAAATATTTGACTAAAAATGACTACGTTA
ATAATCAGAGCCTACAT
Found at i:1392879 original size:36 final size:36
Alignment explanation
Indices: 1392774--1392887 Score: 106
Period size: 36 Copynumber: 3.1 Consensus size: 36
1392764 CTTAAGATTG
* * *
1392774 TTTCTCTTGAAACAAATTTCGTCT-TATTCGAGACA-A
1 TTTC-CTTGAAACAAATTTCATCTCAATT-GAGACAGT
* * * *
1392810 TTTCCATTGAAACAAAAATTTTATATCACTTGAGATAGT
1 TTTCC-TTGAAAC--AAATTTCATCTCAATTGAGACAGT
1392849 TTTCCTTGAAACAAATTTCATCTCAATTGAGACAGT
1 TTTCCTTGAAACAAATTTCATCTCAATTGAGACAGT
1392885 TTT
1 TTT
1392888 TCTCAAAATA
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
35 1 0.02
36 34 0.55
38 20 0.32
39 7 0.11
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (36 bp):
TTTCCTTGAAACAAATTTCATCTCAATTGAGACAGT
Found at i:1392881 original size:74 final size:73
Alignment explanation
Indices: 1392768--1392933 Score: 187
Period size: 73 Copynumber: 2.3 Consensus size: 73
1392758 GTTTTCCTTA
* * * *
1392768 AGATTGTTTCTCTTGAAACAAATTTCGTCTTATTCGAGACAATTTCCAT-TGAAACA-AAAATTT
1 AGATAGTTTCTCTTGAAACAAATTTCATCTAATTCGAGACAATTT--ATCTCAAA-ATAAAATTT
1392831 TATATCACTTG
63 TATATCACTTG
* *
1392842 AGATAGTTT-TCCTTGAAACAAATTTCATCTCAATT-GAGACAGTTTTTCTCAAAATAAAATTTT
1 AGATAGTTTCT-CTTGAAACAAATTTCATCT-AATTCGAGACAATTTATCTCAAAATAAAATTTT
*
1392905 ATCTCACTTG
64 ATATCACTTG
*
1392915 AGATTGTTTCTCTTGAAAC
1 AGATAGTTTCTCTTGAAAC
1392934 TCCAATTTAT
Statistics
Matches: 79, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
72 2 0.03
73 38 0.48
74 36 0.46
75 3 0.04
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (73 bp):
AGATAGTTTCTCTTGAAACAAATTTCATCTAATTCGAGACAATTTATCTCAAAATAAAATTTTAT
ATCACTTG
Found at i:1393017 original size:53 final size:52
Alignment explanation
Indices: 1392911--1393230 Score: 266
Period size: 55 Copynumber: 6.0 Consensus size: 52
1392901 TTTTATCTCA
* * * *
1392911 CTTGAGATTGTTTCTCTTGAAACTCCAATTTATCTCCCTTGAAATAGTCTTC
1 CTTGAGATTGTTTCTCTTGAAACACAAATTTATCTCCCTTGAGATAGTTTTC
* *
1392963 CTTGAGATTGTTTCTCTTGAAACACTAAATTTATCTCACTTGAGATTGTTTTC
1 CTTGAGATTGTTTCTCTTGAAACAC-AAATTTATCTCCCTTGAGATAGTTTTC
* * * * * * * *
1393016 CTTGAAACTATTTCTCTTGAAATACCAGTTTGTCTCCCTTGAGACAGTTTTC
1 CTTGAGATTGTTTCTCTTGAAACACAAATTTATCTCCCTTGAGATAGTTTTC
* * * ** * * * *
1393068 CTTGAAAGAATTGTTTCCCTTGAAACACTAGTTTGCCTCCCTTAAGGTAGTCTCC
1 CTTG--AG-ATTGTTTCTCTTGAAACACAAATTTATCTCCCTTGAGATAGTTTTC
* * *
1393123 CTTGAGATTGTTTCTCTTGAAACACCAAATGTATCTCTCTTGATATAGTTTTC
1 CTTGAGATTGTTTCTCTTGAAACA-CAAATTTATCTCCCTTGAGATAGTTTTC
* * * *
1393176 CTTGA-AATGAAATTTCTCTTGGAACA-AAATTTTTATCTCGCTTGAGATTGTTTTC
1 CTTGAGATTG---TTTCTCTTGAAACACAAA--TTTATCTCCCTTGAGATAGTTTTC
1393231 TCTTTAAATG
Statistics
Matches: 212, Mismatches: 46, Indels: 17
0.77 0.17 0.06
Matches are distributed among these distances:
52 69 0.33
53 70 0.33
54 1 0.00
55 72 0.34
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (52 bp):
CTTGAGATTGTTTCTCTTGAAACACAAATTTATCTCCCTTGAGATAGTTTTC
Found at i:1393073 original size:52 final size:52
Alignment explanation
Indices: 1392921--1393182 Score: 184
Period size: 53 Copynumber: 4.9 Consensus size: 52
1392911 CTTGAGATTG
* * * * *
1392921 TTTCTCTTGAAACT-CCAATTTATCTCCCTTGAAATAGTCTTCCTTGAGATTG
1 TTTCTCTTGAAA-TACCAATTTATCTCCCTTGAGATAGTTTTCCTTGAAACTA
* * * *
1392973 TTTCTCTTGAAACACTAAATTTATCTCACTTGAGATTGTTTTCCTTGAAACTA
1 TTTCTCTTGAAATAC-CAATTTATCTCCCTTGAGATAGTTTTCCTTGAAACTA
* * * * *
1393026 TTTCTCTTGAAATACCAGTTTGTCTCCCTTGAGACAGTTTTCCTTGAAAGAATTG
1 TTTCTCTTGAAATACCAATTTATCTCCCTTGAGATAGTTTTCCTTG--A-AACTA
* * * * ** * * * * * * *
1393081 TTTCCCTTGAAACACTAGTTTGCCTCCCTTAAGGTAGTCTCCCTTGAGATTG
1 TTTCTCTTGAAATACCAATTTATCTCCCTTGAGATAGTTTTCCTTGAAACTA
* * * *
1393133 TTTCTCTTGAAACACCAAATGTATCTCTCTTGATATAGTTTTCCTTGAAA
1 TTTCTCTTGAAATACC-AATTTATCTCCCTTGAGATAGTTTTCCTTGAAA
1393183 TGAAATTTCT
Statistics
Matches: 163, Mismatches: 41, Indels: 11
0.76 0.19 0.05
Matches are distributed among these distances:
52 56 0.34
53 66 0.40
54 1 0.01
55 40 0.25
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (52 bp):
TTTCTCTTGAAATACCAATTTATCTCCCTTGAGATAGTTTTCCTTGAAACTA
Found at i:1393126 original size:55 final size:52
Alignment explanation
Indices: 1392906--1393149 Score: 175
Period size: 52 Copynumber: 4.6 Consensus size: 52
1392896 TAAAATTTTA
* * * ** *
1392906 TCTCACTTGAGATTGTTTCTCTTGAAACTCCAATTTATCTCCCTTGAA-ATAG
1 TCTCCCTTGAGATTGTTTCTCTTGAAACACCAGTTTGCCTCCCTT-AAGACAG
* * * ** * * **
1392958 TCTTCCTTGAGATTGTTTCTCTTGAAACACTAAATTTATCTCACTTGAGATTG
1 TCTCCCTTGAGATTGTTTCTCTTGAAACAC-CAGTTTGCCTCCCTTAAGACAG
* * * * * * * *
1393011 TTTTCCTTGAAACTATTTCTCTTGAAATACCAGTTTGTCTCCCTTGAGACAG
1 TCTCCCTTGAGATTGTTTCTCTTGAAACACCAGTTTGCCTCCCTTAAGACAG
* * * * **
1393063 TTTTCCTTGAAAGAATTGTTTCCCTTGAAACACTAGTTTGCCTCCCTTAAGGTAG
1 TCTCCCTTG--AG-ATTGTTTCTCTTGAAACACCAGTTTGCCTCCCTTAAGACAG
1393118 TCTCCCTTGAGATTGTTTCTCTTGAAACACCA
1 TCTCCCTTGAGATTGTTTCTCTTGAAACACCA
1393150 AATGTATCTC
Statistics
Matches: 155, Mismatches: 32, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
52 72 0.46
53 43 0.28
54 1 0.01
55 39 0.25
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.40
Consensus pattern (52 bp):
TCTCCCTTGAGATTGTTTCTCTTGAAACACCAGTTTGCCTCCCTTAAGACAG
Found at i:1393371 original size:35 final size:34
Alignment explanation
Indices: 1393319--1393451 Score: 117
Period size: 35 Copynumber: 3.8 Consensus size: 34
1393309 CTCAAAACAA
* *
1393319 AAATTTTATCTCGCTTGAGATAGTTTTCTCTTAAT
1 AAATTTTATCTCACTTGAGACA-TTTTCTCTTAAT
* * *
1393354 TAATTTTGTCTCACTTGAGACATTTTC-CTCATAT
1 AAATTTTATCTCACTTGAGACATTTTCTCTTA-AT
* *
1393388 GAAATTTTCATCTCACTTTAGATATTTTCTCTTGAA-
1 -AAATTTT-ATCTCACTTGAGACATTTTCTCTT-AAT
* * *
1393424 AAATTCTGTCTCACTCGAGACATTTTCT
1 AAATTTTATCTCACTTGAGACATTTTCT
1393452 TGGCACGACT
Statistics
Matches: 78, Mismatches: 15, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
33 3 0.04
34 24 0.31
35 30 0.38
36 17 0.22
37 3 0.04
38 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.46
Consensus pattern (34 bp):
AAATTTTATCTCACTTGAGACATTTTCTCTTAAT
Found at i:1393417 original size:70 final size:70
Alignment explanation
Indices: 1393319--1393450 Score: 187
Period size: 70 Copynumber: 1.9 Consensus size: 70
1393309 CTCAAAACAA
* * * *
1393319 AAATTTTATCTCGCTTGAGATAGTTTTCTCTT-AATTAATTTTGTCTCACTTGAGACATTTTCCT
1 AAATTTTATCTCACTTGAGATAGTTTTCTCTTGAA-AAATTCTGTCTCACTCGAGACATTTTCCT
1393383 CATATG
65 CATATG
*
1393389 AAATTTTCATCTCACTTTAGATA-TTTTCTCTTGAAAAATTCTGTCTCACTCGAGACATTTTC
1 AAATTTT-ATCTCACTTGAGATAGTTTTCTCTTGAAAAATTCTGTCTCACTCGAGACATTTTC
1393451 TTGGCACGAC
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
70 40 0.73
71 15 0.27
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (70 bp):
AAATTTTATCTCACTTGAGATAGTTTTCTCTTGAAAAATTCTGTCTCACTCGAGACATTTTCCTC
ATATG
Found at i:1393449 original size:34 final size:34
Alignment explanation
Indices: 1393317--1393451 Score: 103
Period size: 34 Copynumber: 3.9 Consensus size: 34
1393307 CTCTCAAAAC
* * * *
1393317 AAAAATTTTATCTCGCTTGAGATAGTTTTCTCTT-
1 AAAAATTCTGTCTCACTTGAGACA-TTTTCTCTTG
* *
1393351 AATTAATTTTGTCTCACTTGAGACATTTTCCTCATATG
1 AA-AAATTCTGTCTCACTTGAGACATTTT-CTC-T-TG
** * * *
1393389 AAATTTTC-ATCTCACTTTAGATATTTTCTCTTG
1 AAAAATTCTGTCTCACTTGAGACATTTTCTCTTG
*
1393422 AAAAATTCTGTCTCACTCGAGACATTTTCT
1 AAAAATTCTGTCTCACTTGAGACATTTTCT
1393452 TGGCACGACT
Statistics
Matches: 78, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
33 8 0.10
34 24 0.31
35 24 0.31
36 17 0.22
37 3 0.04
38 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.45
Consensus pattern (34 bp):
AAAAATTCTGTCTCACTTGAGACATTTTCTCTTG
Found at i:1395501 original size:23 final size:23
Alignment explanation
Indices: 1395475--1395566 Score: 94
Period size: 23 Copynumber: 4.0 Consensus size: 23
1395465 CACCACAACT
* *
1395475 CGTATAAATATACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* * * *
1395498 CGTAGAATTACACCAAAGTGACG
1 CGTAGAAATACACCGAAGTGCCA
* *
1395521 CGTAGAAATGCACCGAAGTGCCG
1 CGTAGAAATACACCGAAGTGCCA
* *
1395544 TGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
1395567 TATAAGATGT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:1398606 original size:12 final size:13
Alignment explanation
Indices: 1398589--1398629 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
1398579 CAATTATTTG
1398589 TTTTA-TTTTATT
1 TTTTATTTTTATT
1398601 TTTTATTTTTA-T
1 TTTTATTTTTATT
**
1398613 TTAAATTTTTATT
1 TTTTATTTTTATT
1398626 TTTT
1 TTTT
1398630 TACCGGTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 15 0.65
13 8 0.35
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:1398612 original size:18 final size:18
Alignment explanation
Indices: 1398589--1398628 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1398579 CAATTATTTG
* *
1398589 TTTTATTTTATTTTTTAT
1 TTTTATTTAAATTTTTAT
1398607 TTTTATTTAAATTTTTAT
1 TTTTATTTAAATTTTTAT
1398625 TTTT
1 TTTT
1398629 TTACCGGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTATTTAAATTTTTAT
Found at i:1400014 original size:35 final size:36
Alignment explanation
Indices: 1399878--1400015 Score: 113
Period size: 35 Copynumber: 3.9 Consensus size: 36
1399868 CTTTAGATTC
* * * * *
1399878 ATAAGAAATTATCAGC-TGATCGGTACTAAACCTAT
1 ATAAGGAATTACCAGCTTGATCAGAACTGAACCTAT
** * * * *
1399913 ATAAGGAATTATTAGCTTAATCATAATTGAACCTACA
1 ATAAGGAATTACCAGCTTGATCAGAACTGAACCTA-T
* *
1399950 ATAAGGAATTACTAG-TTGATC-GATGCTGAACCTAT
1 ATAAGGAATTACCAGCTTGATCAGA-ACTGAACCTAT
1399985 AT-AGGAATTACCAGCTTGATCAGAACTGAAC
1 ATAAGGAATTACCAGCTTGATCAGAACTGAAC
1400016 ATACAGAGAC
Statistics
Matches: 81, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
34 11 0.14
35 29 0.36
36 27 0.33
37 14 0.17
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (36 bp):
ATAAGGAATTACCAGCTTGATCAGAACTGAACCTAT
Found at i:1402494 original size:31 final size:31
Alignment explanation
Indices: 1402416--1402619 Score: 287
Period size: 31 Copynumber: 6.8 Consensus size: 31
1402406 ATAATAATAT
* *
1402416 CATATATCCCGAAGAACATAGGTAATCTGT-
1 CATATGTCCCGAAGAACATAGGTAAACTGTC
*
1402446 CATATGT-CCGAAGAACATAGGTAATCTGTC
1 CATATGTCCCGAAGAACATAGGTAAACTGTC
*
1402476 CATATGTCCCGAATAACATAGGTAAACTGTC
1 CATATGTCCCGAAGAACATAGGTAAACTGTC
*
1402507 CATATGTCCCGAATAACATAGGTAAACTGT-
1 CATATGTCCCGAAGAACATAGGTAAACTGTC
*
1402537 CAT-TGT-CCGAAGAACATAGGTAAACTGTT
1 CATATGTCCCGAAGAACATAGGTAAACTGTC
*
1402566 CATATGTCCCGAAGAACATAGGTAAATTGTC
1 CATATGTCCCGAAGAACATAGGTAAACTGTC
*
1402597 C--ATGTCCCAAAGAACATAGGTAA
1 CATATGTCCCGAAGAACATAGGTAA
1402620 CCCTCGACTC
Statistics
Matches: 162, Mismatches: 7, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
28 21 0.13
29 49 0.30
30 19 0.12
31 73 0.45
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (31 bp):
CATATGTCCCGAAGAACATAGGTAAACTGTC
Found at i:1402564 original size:59 final size:60
Alignment explanation
Indices: 1402422--1402619 Score: 287
Period size: 59 Copynumber: 3.3 Consensus size: 60
1402412 ATATCATATA
* *
1402422 TCCCGAAGAACATAGGTAATCTGTCATATGT-CCGAAGAACATAGGTAATCTGTCCATATG
1 TCCCGAAGAACATAGGTAAACTGTCATATGTCCCGAAGAACATAGGTAAACTGTCCAT-TG
* *
1402482 TCCCGAATAACATAGGTAAACTGTCCATATGTCCCGAATAACATAGGTAAACTGT-CATTG
1 TCCCGAAGAACATAGGTAAACTGT-CATATGTCCCGAAGAACATAGGTAAACTGTCCATTG
*
1402542 T-CCGAAGAACATAGGTAAACTGTTCATATGTCCCGAAGAACATAGGTAAATTGTCCA-TG
1 TCCCGAAGAACATAGGTAAACTG-TCATATGTCCCGAAGAACATAGGTAAACTGTCCATTG
*
1402601 TCCCAAAGAACATAGGTAA
1 TCCCGAAGAACATAGGTAA
1402620 CCCTCGACTC
Statistics
Matches: 125, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
59 51 0.41
60 44 0.35
61 10 0.08
62 20 0.16
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (60 bp):
TCCCGAAGAACATAGGTAAACTGTCATATGTCCCGAAGAACATAGGTAAACTGTCCATTG
Found at i:1402575 original size:90 final size:91
Alignment explanation
Indices: 1402416--1402619 Score: 315
Period size: 90 Copynumber: 2.3 Consensus size: 91
1402406 ATAATAATAT
* * *
1402416 CATATATCCCGAAGAACATAGGTAATCTGTCATATGTCCGAAGAACATAGGTAATCTGTCCATAT
1 CATATGTCCCGAAGAACATAGGTAAACTGTCATATGTCCGAAGAACATAGGTAAACTGTCCATAT
*
1402481 GTCCCGAATAACATAGGTAAACTGTC
66 GTCCCGAAGAACATAGGTAAACTGTC
* *
1402507 CATATGTCCCGAATAACATAGGTAAACTGTCAT-TGTCCGAAGAACATAGGTAAACTGTTCATAT
1 CATATGTCCCGAAGAACATAGGTAAACTGTCATATGTCCGAAGAACATAGGTAAACTGTCCATAT
*
1402571 GTCCCGAAGAACATAGGTAAATTGTC
66 GTCCCGAAGAACATAGGTAAACTGTC
*
1402597 C--ATGTCCCAAAGAACATAGGTAA
1 CATATGTCCCGAAGAACATAGGTAA
1402620 CCCTCGACTC
Statistics
Matches: 104, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
88 20 0.19
90 54 0.52
91 30 0.29
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (91 bp):
CATATGTCCCGAAGAACATAGGTAAACTGTCATATGTCCGAAGAACATAGGTAAACTGTCCATAT
GTCCCGAAGAACATAGGTAAACTGTC
Found at i:1403882 original size:32 final size:31
Alignment explanation
Indices: 1403846--1403916 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
1403836 ACAACCATTA
1403846 CAACTTTTCAAAAAAATTACA-AATTGGTCCCC
1 CAACTTTTCAAAAAAATTACAGAA-TGGT-CCC
**
1403878 CAACTTTT-TTAAAAATTACAGAATGGTCCC
1 CAACTTTTCAAAAAAATTACAGAATGGTCCC
*
1403908 CAAATTTTC
1 CAACTTTTC
1403917 TAAGGCTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 10 0.29
31 14 0.41
32 10 0.29
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.32
Consensus pattern (31 bp):
CAACTTTTCAAAAAAATTACAGAATGGTCCC
Found at i:1405746 original size:7 final size:7
Alignment explanation
Indices: 1405736--1405798 Score: 67
Period size: 7 Copynumber: 8.9 Consensus size: 7
1405726 TTTTCCTTTT
1405736 TTTCTTC
1 TTTCTTC
1405743 TTTCTTC
1 TTTCTTC
*
1405750 TTTTTTC
1 TTTCTTC
1405757 TTTCTT-
1 TTTCTTC
1405763 TTTCTT-
1 TTTCTTC
*
1405769 TTTCTTTT
1 TTTC-TTC
1405777 TTTCTTC
1 TTTCTTC
1405784 TTTCTATTC
1 TTTC--TTC
1405793 TTTCTT
1 TTTCTT
1405799 TTTTTCCCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
6 10 0.20
7 28 0.57
8 4 0.08
9 7 0.14
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTCTTC
Found at i:1405746 original size:24 final size:22
Alignment explanation
Indices: 1405731--1405804 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 22
1405721 TCATTTTTTC
1405731 CTTTTTTTCTTCTTTCTTCTTT
1 CTTTTTTTCTTCTTTCTTCTTT
*
1405753 -TTTCTTTCTT-TTTCTT-TTT
1 CTTTTTTTCTTCTTTCTTCTTT
1405772 CTTTTTTTCTTCTTTCTATTCTTT
1 CTTTTTTTCTTCTTTC--TTCTTT
1405796 CTTTTTTTC
1 CTTTTTTTC
1405805 CCTTAGCTCT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
19 3 0.07
20 15 0.33
21 13 0.29
23 2 0.04
24 12 0.27
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.78
Consensus pattern (22 bp):
CTTTTTTTCTTCTTTCTTCTTT
Found at i:1405754 original size:34 final size:34
Alignment explanation
Indices: 1405716--1405800 Score: 93
Period size: 34 Copynumber: 2.4 Consensus size: 34
1405706 AGTATCTCCA
1405716 TTTTTTCATT-TTTTCCTTTTT-TTCTTCTTTCTTC
1 TTTTTTCATTCTTTTCCTTTTTCTT-TT-TTTCTTC
* *
1405750 TTTTTTCTTTCTTTTTCTTTTTCTTTTTTTCTTC
1 TTTTTTCATTCTTTTCCTTTTTCTTTTTTTCTTC
*
1405784 TTTCTATTCTTTCTTTT
1 TTT-T-TTCATTCTTTT
1405801 TTTCCCTTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
34 19 0.42
35 13 0.29
36 13 0.29
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (34 bp):
TTTTTTCATTCTTTTCCTTTTTCTTTTTTTCTTC
Found at i:1405804 original size:17 final size:16
Alignment explanation
Indices: 1405716--1405804 Score: 78
Period size: 16 Copynumber: 5.4 Consensus size: 16
1405706 AGTATCTCCA
1405716 TTTTTTCATTT-TTTCCT
1 TTTTTTC-TTTCTTT-CT
1405733 TTTTTTC-TTCTTTCTT
1 TTTTTTCTTTCTTTC-T
1405749 CTTTTTTCTTTCTTT-T
1 -TTTTTTCTTTCTTTCT
*
1405765 TCTTTTTCTTTTTTTC-
1 T-TTTTTCTTTCTTTCT
*
1405781 TTCTTTCTATTCTTTCT
1 TTTTTTCT-TTCTTTCT
1405798 TTTTTTC
1 TTTTTTC
1405805 CCTTAGCTCT
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
15 10 0.17
16 24 0.40
17 20 0.33
18 6 0.10
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTCTTTCTTTCT
Found at i:1408293 original size:24 final size:24
Alignment explanation
Indices: 1408263--1408404 Score: 207
Period size: 24 Copynumber: 5.9 Consensus size: 24
1408253 AATATTAATT
*
1408263 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCATATCAGAATC
* *
1408287 CAGGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
*
1408311 CAAGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
1408335 CATGTC-AGATATCATATCAGAATC
1 CATGTCAAG-TATCATATCAGAATC
1408359 CATGTC-AGATATCATATCAGAATC
1 CATGTCAAG-TATCATATCAGAATC
*
1408383 CATGTCAAGTATCAGATCAGAA
1 CATGTCAAGTATCATATCAGAA
1408405 ATTAAATCGA
Statistics
Matches: 109, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
23 2 0.02
24 105 0.96
25 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.26
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:1411063 original size:156 final size:157
Alignment explanation
Indices: 1410837--1411150 Score: 596
Period size: 159 Copynumber: 2.0 Consensus size: 157
1410827 GTACACTTAT
1410837 GATTCAGTGTAAACAATAATAACATGATATCATATATAATGCAACCACTTTTGATATCTTTTATA
1 GATTCAGTGTAAACAATAATAACATGATATCATATATAATGCAACCACTTTTGATATCTTTTATA
1410902 AGCCCATACCAGAAGAGG-TTTCGCATAAGACGTGGGCACAG-TATTCATCCTAAGCTATCGCAG
66 AGCCCATACCAGAAGAGGTTTTCGCATAAGACGTGGGCACAGTTATTCATCCTAAGCTATCGCAG
1410965 AAGAGGTCTTCAGTTAAGACGTGGGCA
131 AAGAGGTCTTCAGTTAAGACGTGGGCA
1410992 GATTCAGTGTAAACAATAATAACATGATATCATATAATAATGCAACCACTTTTGATATCTTTTAT
1 GATTCAGTGTAAACAATAATAACATGATATCATAT-ATAATGCAACCACTTTTGATATCTTTTAT
1411057 AAGCCCATACCAGAAGAGGTTTTCGCATAAGACGTGGGCACAGTTTATTCATCCTAAGCTATCGC
65 AAGCCCATACCAGAAGAGGTTTTCGCATAAGACGTGGGCACAG-TTATTCATCCTAAGCTATCGC
1411122 AGAAGAGGTCTTCAGTTAAGACGTGGGCA
129 AGAAGAGGTCTTCAGTTAAGACGTGGGCA
1411151 TGCATTACCA
Statistics
Matches: 155, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
155 35 0.23
156 48 0.31
157 23 0.15
159 49 0.32
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (157 bp):
GATTCAGTGTAAACAATAATAACATGATATCATATATAATGCAACCACTTTTGATATCTTTTATA
AGCCCATACCAGAAGAGGTTTTCGCATAAGACGTGGGCACAGTTATTCATCCTAAGCTATCGCAG
AAGAGGTCTTCAGTTAAGACGTGGGCA
Found at i:1411405 original size:29 final size:30
Alignment explanation
Indices: 1411354--1411413 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
1411344 TAGTATTGAT
1411354 ATCTTTTATAAGCCCATGAACATTACTGAG
1 ATCTTTTATAAGCCCATGAACATTACTGAG
*
1411384 ATCTTTTAT-AGCCCATGTACATTACTGAG
1 ATCTTTTATAAGCCCATGAACATTACTGAG
1411413 A
1 A
1411414 ACTCAAGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (30 bp):
ATCTTTTATAAGCCCATGAACATTACTGAG
Found at i:1411510 original size:31 final size:31
Alignment explanation
Indices: 1411479--1411663 Score: 289
Period size: 31 Copynumber: 6.0 Consensus size: 31
1411469 GTATAATAAT
* *
1411479 CTGTCCATATGTCCCGAAGAACATAAGTAAT
1 CTGTCCATATGTCCCGAAGAACATAGGTAAA
* *
1411510 CTGTCTATATGTCCCGAAGAACATAGGTAAT
1 CTGTCCATATGTCCCGAAGAACATAGGTAAA
* *
1411541 TTGTCCATATGTCCCGGAGAACATAGGTAAA
1 CTGTCCATATGTCCCGAAGAACATAGGTAAA
*
1411572 CTGTTCATATGTCCCGAAGAACATAGGTAAA
1 CTGTCCATATGTCCCGAAGAACATAGGTAAA
*
1411603 CTGTCCATATGTCCCGAATAACATAGGTAAA
1 CTGTCCATATGTCCCGAAGAACATAGGTAAA
*
1411634 CTGTCTATATGTCCCGAAGAACATAGGTAA
1 CTGTCCATATGTCCCGAAGAACATAGGTAA
1411664 CCCTCGACTC
Statistics
Matches: 141, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 141 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (31 bp):
CTGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1412699 original size:18 final size:18
Alignment explanation
Indices: 1412676--1412710 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1412666 TTAAATACCA
1412676 AAATTCAACAAATTCCAT
1 AAATTCAACAAATTCCAT
*
1412694 AAATTCAAGAAATTCCA
1 AAATTCAACAAATTCCA
1412711 GTATTGGAAT
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:0.51, C:0.20, G:0.03, T:0.26
Consensus pattern (18 bp):
AAATTCAACAAATTCCAT
Found at i:1412973 original size:31 final size:32
Alignment explanation
Indices: 1412912--1412973 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
1412902 CAACCATTTA
1412912 CAACTTTTCAAAAAATTACAAATTGGTCCCCT
1 CAACTTTTCAAAAAATTACAAATTGGTCCCCT
1412944 CAACTTTTTC-AAAAATTACAAA-TGGTCCCC
1 CAAC-TTTTCAAAAAATTACAAATTGGTCCCC
1412974 AAATTTTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 8 0.28
32 16 0.55
33 5 0.17
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (32 bp):
CAACTTTTCAAAAAATTACAAATTGGTCCCCT
Found at i:1414505 original size:20 final size:20
Alignment explanation
Indices: 1414480--1414527 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
1414470 AGTAAATGGG
1414480 TCGGGTCAGATTGACACGAT
1 TCGGGTCAGATTGACACGAT
1414500 TCGGGTCAGATTGACACGAT
1 TCGGGTCAGATTGACACGAT
1414520 TCGGGTCA
1 TCGGGTCA
1414528 AACAGACCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.25
Consensus pattern (20 bp):
TCGGGTCAGATTGACACGAT
Found at i:1418597 original size:56 final size:56
Alignment explanation
Indices: 1418511--1418623 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
1418501 TGAATTCATG
1418511 CCCACGGATCGTTGGATAAATTCATTTATCGCCAAGGATGTGATACAAGTCGCCAA
1 CCCACGGATCGTTGGATAAATTCATTTATCGCCAAGGATGTGATACAAGTCGCCAA
1418567 CCCACGGATCGTTGGATAAATTCATTTATCGCCAAGGATGTGATACAAGTCGCCAA
1 CCCACGGATCGTTGGATAAATTCATTTATCGCCAAGGATGTGATACAAGTCGCCAA
1418623 C
1 C
1418624 TGGAGTGGAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (56 bp):
CCCACGGATCGTTGGATAAATTCATTTATCGCCAAGGATGTGATACAAGTCGCCAA
Found at i:1419883 original size:3 final size:3
Alignment explanation
Indices: 1419875--1419955 Score: 105
Period size: 3 Copynumber: 27.7 Consensus size: 3
1419865 TTTTTATCCA
* *
1419875 TAT TAT TAT TA- TAA TAT TAT TAT TAT TAT TATT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
*
1419920 TAT CAT TAT TAT TAT TAT TAT TAT TA- TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1419956 AATATATTAA
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
2 6 0.09
3 60 0.87
4 3 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1419995 original size:20 final size:19
Alignment explanation
Indices: 1419954--1419998 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1419944 TATATTATAT
* *
1419954 TAAATATATTAAATACATA
1 TAAATATATTAAAAACAAA
*
1419973 TAAATATTATTAAAAATAAA
1 TAAATA-TATTAAAAACAAA
1419993 TAAATA
1 TAAATA
1419999 AATAATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATATATTAAAAACAAA
Found at i:1425206 original size:24 final size:24
Alignment explanation
Indices: 1425124--1425218 Score: 84
Period size: 24 Copynumber: 4.0 Consensus size: 24
1425114 ATTTCCAACT
* * *
1425124 TGAATTCTATTCTGATACATGACC
1 TGAATTCTGTTCTGATATATGATC
* *
1425148 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATATGATC
* * *
1425172 T-AGATTATGTTATGATATATGTTC
1 TGA-ATTCTGTTCTGATATATGATC
* *
1425196 TGAATTCTGTTTTGATTTATGAT
1 TGAATTCTGTTCTGATATATGAT
1425219 ATCTCCGTTT
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
23 1 0.02
24 53 0.96
25 1 0.02
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATATGATC
Found at i:1428781 original size:18 final size:18
Alignment explanation
Indices: 1428750--1428785 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1428740 AATTTCTTTA
*
1428750 ATATCCCTCTCGTCGTCT
1 ATATCCCTCCCGTCGTCT
*
1428768 ATATCTCTCCCGTCGTCT
1 ATATCCCTCCCGTCGTCT
1428786 TCATCAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.39, G:0.11, T:0.39
Consensus pattern (18 bp):
ATATCCCTCCCGTCGTCT
Found at i:1432396 original size:16 final size:17
Alignment explanation
Indices: 1432362--1432398 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
1432352 AAATTTTAAT
1432362 TAATTAAAAACATTATA
1 TAATTAAAAACATTATA
1432379 TAATATAAAAA-A-TATA
1 TAAT-TAAAAACATTATA
1432395 TAAT
1 TAAT
1432399 CTCCTTCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 5 0.26
18 6 0.32
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATTAAAAACATTATA
Found at i:1433191 original size:13 final size:13
Alignment explanation
Indices: 1433173--1433198 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1433163 ACAACTGGCC
1433173 AAGAAGAAGAAGA
1 AAGAAGAAGAAGA
1433186 AAGAAGAAGAAGA
1 AAGAAGAAGAAGA
1433199 GATTGAGTTA
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGAAGA
Found at i:1433472 original size:3 final size:3
Alignment explanation
Indices: 1433464--1433488 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1433454 AGATCTGGCC
1433464 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
1433489 GATTGAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1433691 original size:291 final size:293
Alignment explanation
Indices: 1433167--1433751 Score: 1124
Period size: 291 Copynumber: 2.0 Consensus size: 293
1433157 TTTTCTACAA
1433167 CTGGCCAAGAAGAAGAAGAAAGAAGAAGAAGAGATTGAGTTAAGCTTGGGACTTTCGTTGAATGG
1 CTGGCCAAGAAGAAGAAGAAAGAAGAAGAAGAGATTGAGTTAAGCTTGGGACTTTCGTTGAATGG
1433232 TCGGTTTGGGGTTGACCGAGAGCCAAAAAGCTCAAGAGATCGTCTTCAATACCAGATTTCATCAA
66 TCGGTTTGGGGTTGACCGAGAGCCAAAAAGCTCAAGAGATCGTCTTCAATACCAGATTTCATCAA
1433297 CAACTCCACAAGAAAAGACAGTAATGAACATGCTTCTTCTGTGTTCCCCATGGCATGTGGTTCAC
131 CAACTCCACAAGAAAAGACAGTAATGAACATGCTTCTTCTGTGTTCCCCATGGCATGTGGTTCAC
1433362 TTCTGAGGACAGTTCTTTGCCCACAGAGACAGAGGAGGAGTGGAGGAAGAGGAAGGAGTTGCAGT
196 TTCTGAGGACAGTTCTTTGCCCACAGAGACAGAGGAGGAGTGGAGGAAGAGGAAGGAGTTGCAGT
1433427 G-TTAAGGAGAA-GGAAGCTAAGAGAAAGAGAT
261 GTTTAAGGAGAATGGAAGCTAAGAGAAAGAGAT
1433458 CTGGCCAAGAAGAAGAAG-AAGAAGAAGAAGAGATTGAGTTAAGCTTGGGACTTTCGTTGAATGG
1 CTGGCCAAGAAGAAGAAGAAAGAAGAAGAAGAGATTGAGTTAAGCTTGGGACTTTCGTTGAATGG
1433522 TCGGTTTGGGGTTGACCCGAGAGCCAAAAAGCTCAAGAGATCGTCTTCAATACCAGATTTCATCA
66 TCGGTTTGGGGTTGA-CCGAGAGCCAAAAAGCTCAAGAGATCGTCTTCAATACCAGATTTCATCA
1433587 ACAACTCCAC-AGAAAAGACAGTAATGAACATGCTTCTTCTGTGTTCCCCATGGCATGTGGTTCA
130 ACAACTCCACAAGAAAAGACAGTAATGAACATGCTTCTTCTGTGTTCCCCATGGCATGTGGTTCA
1433651 CTTCTGAGGACATGTTCTTTGCCCACAGAGACAGAGGAGGAGTGGAGGAAGAGGAAGGAGTTGCA
195 CTTCTGAGGACA-GTTCTTTGCCCACAGAGACAGAGGAGGAGTGGAGGAAGAGGAAGGAGTTGCA
1433716 GTGTTTAAGGAGAATGGAAGCTAAGAGAAAGAGAT
259 GTGTTTAAGGAGAATGGAAGCTAAGAGAAAGAGAT
1433751 C
1 C
1433752 AGAGAAACAG
Statistics
Matches: 290, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
290 127 0.44
291 132 0.46
292 10 0.03
293 21 0.07
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (293 bp):
CTGGCCAAGAAGAAGAAGAAAGAAGAAGAAGAGATTGAGTTAAGCTTGGGACTTTCGTTGAATGG
TCGGTTTGGGGTTGACCGAGAGCCAAAAAGCTCAAGAGATCGTCTTCAATACCAGATTTCATCAA
CAACTCCACAAGAAAAGACAGTAATGAACATGCTTCTTCTGTGTTCCCCATGGCATGTGGTTCAC
TTCTGAGGACAGTTCTTTGCCCACAGAGACAGAGGAGGAGTGGAGGAAGAGGAAGGAGTTGCAGT
GTTTAAGGAGAATGGAAGCTAAGAGAAAGAGAT
Found at i:1441501 original size:15 final size:16
Alignment explanation
Indices: 1441481--1441511 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1441471 GAGAGAAACA
1441481 TAAATA-AAGTAATTT
1 TAAATAGAAGTAATTT
1441496 TAAATAGAAGTAATTT
1 TAAATAGAAGTAATTT
1441512 AAAGAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (16 bp):
TAAATAGAAGTAATTT
Found at i:1443207 original size:26 final size:28
Alignment explanation
Indices: 1443145--1443207 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 28
1443135 CGAGTATTGC
*
1443145 TGAGCTCGACTCGACTCGAAAACTTTGAAA
1 TGAGCTCGACTCGACTCGAAAACTTCG--A
1443175 TGAAGCTCGACTCGACTCGAAAAC-TCG-
1 TG-AGCTCGACTCGACTCGAAAACTTCGA
1443202 TGAGCT
1 TGAGCT
1443208 TAAAATTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 4 0.13
27 2 0.06
30 4 0.13
31 21 0.68
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.22
Consensus pattern (28 bp):
TGAGCTCGACTCGACTCGAAAACTTCGA
Found at i:1445982 original size:13 final size:13
Alignment explanation
Indices: 1445964--1445996 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
1445954 GAACATGTAC
1445964 CAAGCACGAGTGT
1 CAAGCACGAGTGT
1445977 CAAGCACGAGTGT
1 CAAGCACGAGTGT
1445990 CAAGCAC
1 CAAGCAC
1445997 TTGTATTCCC
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:0.33, C:0.27, G:0.27, T:0.12
Consensus pattern (13 bp):
CAAGCACGAGTGT
Found at i:1447866 original size:37 final size:37
Alignment explanation
Indices: 1447825--1447902 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
1447815 TTCAAATTCT
*
1447825 TAAAAATAAGATAAAATTTTACTAGGATTTAAACTCC
1 TAAAAATAAGATAAAATTCTACTAGGATTTAAACTCC
* * * **
1447862 TAAAAATACGATAGAGTTCTACTATTATTTAAACTCC
1 TAAAAATAAGATAAAATTCTACTAGGATTTAAACTCC
1447899 TAAA
1 TAAA
1447903 GATAGGATCC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (37 bp):
TAAAAATAAGATAAAATTCTACTAGGATTTAAACTCC
Found at i:1448341 original size:10 final size:10
Alignment explanation
Indices: 1448328--1448427 Score: 55
Period size: 10 Copynumber: 9.7 Consensus size: 10
1448318 TATATATATA
1448328 TATATTTTAT
1 TATATTTTAT
1448338 TATATTTTAT
1 TATATTTTAT
1448348 T-TA-TTTAT
1 TATATTTTAT
1448356 TATAATTTGT-T
1 TAT-ATTT-TAT
** *
1448367 TACGTTATAT
1 TATATTTTAT
1448377 TATATTATT-T
1 TATATT-TTAT
* *
1448387 CATATTATAT
1 TATATTTTAT
*
1448397 ATATATATATAT
1 -TATAT-TTTAT
1448409 TATTATTTTAT
1 TA-TATTTTAT
1448420 CTATATTT
1 -TATATTT
1448428 ACTTATTTGT
Statistics
Matches: 69, Mismatches: 10, Indels: 21
0.69 0.10 0.21
Matches are distributed among these distances:
8 6 0.09
9 5 0.07
10 26 0.38
11 21 0.30
12 11 0.16
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (10 bp):
TATATTTTAT
Found at i:1448573 original size:22 final size:22
Alignment explanation
Indices: 1448548--1448589 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1448538 ATTTATTTTC
1448548 ATTTAGTA-TTATTATTATTACT
1 ATTTAGTATTTATTA-TATTACT
1448570 ATTTAGTATTTATTATATTA
1 ATTTAGTATTTATTATATTA
1448590 TACATACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (22 bp):
ATTTAGTATTTATTATATTACT
Found at i:1448621 original size:13 final size:12
Alignment explanation
Indices: 1448601--1448650 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 12
1448591 ACATACATTT
*
1448601 TATATTTTTATA
1 TATATTTTTTTA
1448613 TATATTTTTTT-
1 TATATTTTTTTA
1448624 TATATTTTATTTA
1 TATATTTT-TTTA
*
1448637 TACTATTTATTTA
1 TA-TATTTTTTTA
1448650 T
1 T
1448651 TTTCATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 8 0.24
12 13 0.39
13 7 0.21
14 5 0.15
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (12 bp):
TATATTTTTTTA
Found at i:1448627 original size:11 final size:11
Alignment explanation
Indices: 1448598--1448638 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
1448588 TATACATACA
1448598 TTTTATATTTT
1 TTTTATATTTT
*
1448609 TATATATATTTT
1 T-TTTATATTTT
1448621 TTTTATATTTT
1 TTTTATATTTT
*
1448632 ATTTATA
1 TTTTATA
1448639 CTATTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTATATTTT
Found at i:1448631 original size:22 final size:22
Alignment explanation
Indices: 1448598--1448665 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
1448588 TATACATACA
1448598 TTTTATATTTTTATATATATTTT
1 TTTTATA-TTTTATATATATTTT
*
1448621 TTTTATATTTTATTTATACTATTT
1 TTTTATATTTTATATATA-T-TTT
* *
1448645 ATTTAT-TTTCATA-ATATTTT
1 TTTTATATTTTATATATATTTT
1448665 T
1 T
1448666 AGTTTCTTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 3 0.08
21 1 0.03
22 13 0.34
23 13 0.34
24 8 0.21
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTATATTTTATATATATTTT
Found at i:1450245 original size:24 final size:24
Alignment explanation
Indices: 1450218--1450290 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
1450208 CGTTCATTTA
1450218 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
1450242 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * * *
1450266 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
1450290 C
1 C
1450291 ATTCATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 42 0.95
25 2 0.05
ACGTcount: A:0.11, C:0.15, G:0.25, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:1450247 original size:14 final size:14
Alignment explanation
Indices: 1450228--1450283 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
1450218 CGTTCGTGAA
1450228 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1450242 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1450256 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
1450266 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
1450280 CGTT
1 CGTT
1450284 TATGTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:1450300 original size:24 final size:23
Alignment explanation
Indices: 1450229--1450303 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
1450219 GTTCGTGAAC
* *
1450229 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
1450253 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
1450277 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCGTTCA-TTAT
1450301 GTT
1 GTT
1450304 TTAACCCAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.02
24 46 0.98
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCATTAT
Found at i:1451040 original size:16 final size:16
Alignment explanation
Indices: 1451015--1451088 Score: 98
Period size: 16 Copynumber: 4.7 Consensus size: 16
1451005 TCCAACGTTA
*
1451015 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
1451031 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
1451047 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
*
1451063 TGTTCGTTTTATGTTCG
1 TGTTC-ATTTATGTTCG
1451080 T-TT-ATTTAT
1 TGTTCATTTAT
1451089 TAAATGAACG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
14 5 0.09
16 37 0.70
17 11 0.21
ACGTcount: A:0.09, C:0.11, G:0.20, T:0.59
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:1451056 original size:32 final size:33
Alignment explanation
Indices: 1451015--1451080 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
1451005 TCCAACGTTA
1451015 TGTTCGTTTATGTTCGTGTTC-ATTTATGTTCG
1 TGTTCGTTTATGTTCGTGTTCGATTTATGTTCG
*
1451047 TGTTCGTTTATGTTCGTGTTCGTTTTATGTTCG
1 TGTTCGTTTATGTTCGTGTTCGATTTATGTTCG
1451080 T
1 T
1451081 TTATTTATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 21 0.66
33 11 0.34
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.58
Consensus pattern (33 bp):
TGTTCGTTTATGTTCGTGTTCGATTTATGTTCG
Found at i:1454779 original size:21 final size:22
Alignment explanation
Indices: 1454705--1454777 Score: 130
Period size: 22 Copynumber: 3.4 Consensus size: 22
1454695 AGCTACCCAT
1454705 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
1454727 CAAACCTTTGAGCATCAAATGT
1 CAAACCTTTGAGCATCAAATGC
1454749 CAAACC-TTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
1454770 CAAACCTT
1 CAAACCTT
1454778 GACCAAACAC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.42
22 28 0.58
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.23
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:1454891 original size:22 final size:22
Alignment explanation
Indices: 1454863--1454939 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
1454853 AGCTACCCAT
1454863 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
1454885 CAAACCTTTGAGCATCAAATGT
1 CAAACCTTTGAGCATCAAATGC
1454907 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
1454929 CAAACCTTTGA
1 CAAACCTTTGA
1454940 CCAAACACAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:1454904 original size:158 final size:163
Alignment explanation
Indices: 1454678--1454998 Score: 607
Period size: 158 Copynumber: 2.0 Consensus size: 163
1454668 AGAACACTTC
1454678 CAGTAGAGGAGCATGCAAGCTACCCATCAAACCTTTGAGCATCAAATGCCAAACCTTTGAGCATC
1 CAGTAGAGGAGCATGCAAGCTACCCATCAAACCTTTGAGCATCAAATGCCAAACCTTTGAGCATC
1454743 AAATGTCAAACC-TTGAGCATCAAATGCCAAACC-TTGACCAAACACAATAACCTGAGACC-TTT
66 AAATGTCAAACCTTTGAGCATCAAATGCCAAACCTTTGACCAAACACAATAACCTGAGACCTTTT
1454805 TATCATTTCCTTAC-TAACCA-TTCCCAAAGAT
131 TATCATTTCCTTACTTAACCATTTCCCAAAGAT
1454836 CAGTAGAGGAGCATGCAAGCTACCCATCAAACCTTTGAGCATCAAATGCCAAACCTTTGAGCATC
1 CAGTAGAGGAGCATGCAAGCTACCCATCAAACCTTTGAGCATCAAATGCCAAACCTTTGAGCATC
1454901 AAATGTCAAACCTTTGAGCATCAAATGCCAAACCTTTGACCAAACACAATAACCTGAGACCTTTT
66 AAATGTCAAACCTTTGAGCATCAAATGCCAAACCTTTGACCAAACACAATAACCTGAGACCTTTT
1454966 TATCATTTCCTTACTTAACCATTTCCCAAAGAT
131 TATCATTTCCTTACTTAACCATTTCCCAAAGAT
1454999 AGCTTTGATC
Statistics
Matches: 158, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
158 77 0.49
159 21 0.13
160 26 0.16
161 17 0.11
162 6 0.04
163 11 0.07
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.25
Consensus pattern (163 bp):
CAGTAGAGGAGCATGCAAGCTACCCATCAAACCTTTGAGCATCAAATGCCAAACCTTTGAGCATC
AAATGTCAAACCTTTGAGCATCAAATGCCAAACCTTTGACCAAACACAATAACCTGAGACCTTTT
TATCATTTCCTTACTTAACCATTTCCCAAAGAT
Found at i:1456079 original size:106 final size:106
Alignment explanation
Indices: 1455905--1456200 Score: 450
Period size: 106 Copynumber: 2.8 Consensus size: 106
1455895 GTGCCACTCG
* * *
1455905 AGACAACACAAGTTCAACTTCACAACGAAGGGA-CGGTGGTTGTCAACAAACAACTTCCCAAATT
1 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
1455969 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTAC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTAC
* * *
1456010 ATACAACACAAGTTCAACTTCACGACTAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
1456075 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTAC
* * ** * *
1456116 AGAAAACGCAAGTTCAACTTCACGACGAAGGGACTACTGGTTGTCAATAAACAATTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
1456181 CAGAGCCAATTTCAACTTCA
66 CAGAGCCAATTTCAACTTCA
1456201 TGATGAAGGG
Statistics
Matches: 172, Mismatches: 18, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
105 30 0.17
106 142 0.83
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (106 bp):
AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTAC
Found at i:1456215 original size:169 final size:169
Alignment explanation
Indices: 1456022--1456370 Score: 594
Period size: 169 Copynumber: 2.1 Consensus size: 169
1456012 ACAACACAAG
1456022 TTCAACTTCACGACTAAGGGACCGCTGGTTGTCAACAAACAACTT-CTCAATTTCAGAGCCAATT
1 TTCAACTTCACGACTAAGGGACCGCTGGTTGTCAACAAACAACTTCCT-AATTTCAGAGCCAATT
*
1456086 TCAACTTCACAACGAAGGATATTGGACTCCAGAAAACGCAAGTTCAACTTCACGACGAAGGGACT
65 TCAACTTCACAACGAAGGATATTGGACTCCAGAAAACGCAAGTTCAACTTCACGACGAAGGGACC
*
1456151 ACTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAAT
130 ACTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAAT
* *
1456191 TTCAACTTCATGA-TGAAGGGACCGCTGGTTGTCAATAAACAACTTCCTAATTTCAGAGCCAATT
1 TTCAACTTCACGACT-AAGGGACCGCTGGTTGTCAACAAACAACTTCCTAATTTCAGAGCCAATT
* *
1456255 TCAACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
65 TCAACTTCACAACGAAGGATATTGGACTCCAGAAAACGCAAGTTCAACTTCACGACGAAGGGACC
* *
1456320 GCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAAT
130 ACTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAAT
1456360 TTCAACTTCAC
1 TTCAACTTCAC
1456371 AACGAAGGAT
Statistics
Matches: 169, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
168 1 0.01
169 166 0.98
170 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (169 bp):
TTCAACTTCACGACTAAGGGACCGCTGGTTGTCAACAAACAACTTCCTAATTTCAGAGCCAATTT
CAACTTCACAACGAAGGATATTGGACTCCAGAAAACGCAAGTTCAACTTCACGACGAAGGGACCA
CTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAAT
Found at i:1456227 original size:63 final size:63
Alignment explanation
Indices: 1456128--1456272 Score: 220
Period size: 63 Copynumber: 2.3 Consensus size: 63
1456118 AAAACGCAAG
* *
1456128 TTCAACTTCACGACGAAGGGACTACTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAAT
1 TTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAAT
* * * *
1456191 TTCAACTTCATGATGAAGGGACCGCTGGTTGTCAATAAACAACTTCCTAATTTCAGAGCCAAT
1 TTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAAT
1456254 TTCAACTTCAC-ATCGAAGG
1 TTCAACTTCACGA-CGAAGG
1456273 ATATTGGACT
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
62 1 0.01
63 72 0.99
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (63 bp):
TTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAAT
Found at i:1456250 original size:275 final size:274
Alignment explanation
Indices: 1455917--1456484 Score: 929
Period size: 275 Copynumber: 2.1 Consensus size: 274
1455907 ACAACACAAG
*
1455917 TTCAACTTCACAACGAAGGGACGGTGGTTGTCAACAAACAACTTCCCAAATTCAGAGCCAATTTC
1 TTCAACTTCACAACGAAGGGACGCTGGTTGTCAACAAACAACTTCCCAAATTCAGAGCCAATTTC
* *
1455982 AACTTCACAGCGAAGGATATTGAACTACATACAACACAAGTTCAACTTCACGACTAAGGGACCGC
66 AACTTCACAGCGAAGGATATTGAACTACAGACAACACAAGTTCAACTTCACGACGAAGGGACCGC
1456047 TGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
131 TGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
* * * *
1456112 CTCCAGAAAACGCAAGTTCAACTTCACGACGAAGGGACTACTGGTTGTCAATAAACAATTTCCCA
196 CTCCAGAAAACGCAAGTTCAACTTCACGACGAAAGGACCACTGGTTGTCAACAAACAACTTCCCA
1456177 ATTTCAGAGCCAAT
261 ATTTCAGAGCCAAT
** * * * *
1456191 TTCAACTTCATGATGAAGGGACCGCTGGTTGTCAATAAACAACTTCCTAATTTCAGAGCCAATTT
1 TTCAACTTCACAACGAAGGGA-CGCTGGTTGTCAACAAACAACTTCCCAAATTCAGAGCCAATTT
* * * *
1456256 CAACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
65 CAACTTCACAGCGAAGGATATTGAACTACAGACAACACAAGTTCAACTTCACGACGAAGGGACCG
*
1456321 CTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
130 CTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1456386 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAAGGACCGCTGGTTGTCAACAAACAACTTCCC
195 ACTCCAGAAAACGCAAGTTCAACTTCACGACGAAAGGACCACTGGTTGTCAACAAACAACTTCCC
1456451 AATTTCAGAGCCAAT
260 AATTTCAGAGCCAAT
*
1456466 TTCAACTTCACAGCGAAGG
1 TTCAACTTCACAACGAAGG
1456485 ATATTGGACT
Statistics
Matches: 268, Mismatches: 25, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
274 18 0.07
275 250 0.93
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (274 bp):
TTCAACTTCACAACGAAGGGACGCTGGTTGTCAACAAACAACTTCCCAAATTCAGAGCCAATTTC
AACTTCACAGCGAAGGATATTGAACTACAGACAACACAAGTTCAACTTCACGACGAAGGGACCGC
TGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
CTCCAGAAAACGCAAGTTCAACTTCACGACGAAAGGACCACTGGTTGTCAACAAACAACTTCCCA
ATTTCAGAGCCAAT
Found at i:1456301 original size:106 final size:106
Alignment explanation
Indices: 1456191--1456918 Score: 1127
Period size: 106 Copynumber: 6.9 Consensus size: 106
1456181 CAGAGCCAAT
* * * *
1456191 TTCAACTTCATGATGAAGGGACCGCTGGTTGTCAATAAACAACTTCCTAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
1456256 CAACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
* *
1456297 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
1456362 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
* *
1456403 TTCAACTTCACGATGAAAGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
1456468 CAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
* **
1456509 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTTGGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
* *
1456574 CAACTCCACAGCGAAAGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
* *
1456615 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
1456680 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
* * * * *
1456721 TTCAACTTCACGACGAAGGGATCGTTGGTTGTCAACAAACAATTTCTCAATTTCGGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
* * * *
1456786 CAACTTCACAACAAAGGATATTGGACTCGAGACAACACAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
* * * * * *
1456827 TTCAACTTCACAATGAAGGGA-CGCTGGTTGTCAACAAACAATTTCCCGATTCCAAAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
1456891 CAACTTCAC-GACGGAGGATATTGGACTC
66 CAACTTCACAG-CGAAGGATATTGGACTC
1456919 GGAACAATGC
Statistics
Matches: 577, Mismatches: 44, Indels: 3
0.92 0.07 0.00
Matches are distributed among these distances:
105 61 0.11
106 516 0.89
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:1457527 original size:37 final size:37
Alignment explanation
Indices: 1457474--1457578 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
1457464 CCTTTTCGTC
1457474 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * * *
1457511 TTGCTAGGATTCAAACTCTTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
** * *
1457548 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
1457579 CCACAAGCAT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:1457997 original size:18 final size:18
Alignment explanation
Indices: 1457974--1458018 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
1457964 ATTTAACCTT
1457974 ATTATATATATATATTTA
1 ATTATATATATATATTTA
* *
1457992 ATTATATTTATTTATTTA
1 ATTATATATATATATTTA
*
1458010 TTTAT-TATA
1 ATTATATATA
1458019 ATTTTTTGCG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTATATATATATATTTA
Found at i:1458003 original size:14 final size:14
Alignment explanation
Indices: 1457980--1458021 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1457970 CCTTATTATA
*
1457980 TATATATATTTAAT
1 TATATTTATTTAAT
1457994 TATATTTATTT-AT
1 TATATTTATTTAAT
1458007 T-TATTTATTATAAT
1 TATATTTATT-TAAT
1458021 T
1 T
1458022 TTTTGCGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 8 0.32
13 4 0.16
14 13 0.52
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATATTTATTTAAT
Found at i:1458047 original size:22 final size:20
Alignment explanation
Indices: 1457992--1458064 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 20
1457982 TATATATTTA
*
1457992 ATTATATTTATTTAT-TTATTT
1 ATTATA-TTATTT-TCTTATAT
1458013 ATTATAATT-TTTTGCGTTATAT
1 ATTAT-ATTATTTT-C-TTATAT
*
1458035 ATTATATTATTTTCATATAT
1 ATTATATTATTTTCTTATAT
1458055 A-TATATTATT
1 ATTATATTATT
1458065 ATTTTTTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
19 10 0.22
20 9 0.20
21 11 0.24
22 15 0.33
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (20 bp):
ATTATATTATTTTCTTATAT
Done.