Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009604.1 Hibiscus syriacus cultivar Beakdansim tig00116984_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: 3548142
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 17
Found at i:3243986 original size:10 final size:10
Alignment explanation
Indices: 3243973--3244229 Score: 272
Period size: 10 Copynumber: 26.2 Consensus size: 10
3243963 TCACACACAT
3243973 TCTCTCTCTC
1 TCTCTCTCTC
3243983 TCTCTCTCTC
1 TCTCTCTCTC
3243993 TCTCTCTCTC
1 TCTCTCTCTC
3244003 TCTCTCTCTC
1 TCTCTCTCTC
3244013 TCTCTCTCTC
1 TCTCTCTCTC
3244023 TCTCTCTCTC
1 TCTCTCTCTC
3244033 TCTCTCTCTC
1 TCTCTCTCTC
3244043 TCTCTCTCTC
1 TCTCTCTCTC
3244053 TCTCTCTCTC
1 TCTCTCTCTC
*
3244063 CCTCTCTCTC
1 TCTCTCTCTC
3244073 TCTCTCTCTC
1 TCTCTCTCTC
*
3244083 CCTCTCTCTC
1 TCTCTCTCTC
3244093 TCTCTCTCTC
1 TCTCTCTCTC
3244103 -CTCTCTCTC
1 TCTCTCTCTC
*
3244112 TCTCTCCCTC
1 TCTCTCTCTC
* *
3244122 TC-CCCTCCC
1 TCTCTCTCTC
*
3244131 TCTCCCTCTC
1 TCTCTCTCTC
* *
3244141 CCTCCCTC-C
1 TCTCTCTCTC
* * *
3244150 CCTCCCCCTC
1 TCTCTCTCTC
* *
3244160 -CCCTCCCTC
1 TCTCTCTCTC
*
3244169 TC-CTCTCCC
1 TCTCTCTCTC
* * *
3244178 TCCCCCTCCC
1 TCTCTCTCTC
*
3244188 TCTCCCTCTC
1 TCTCTCTCTC
* *
3244198 CCTCTCCCTC
1 TCTCTCTCTC
* *
3244208 CCTCCCTCTC
1 TCTCTCTCTC
*
3244218 TCTCTCCCTC
1 TCTCTCTCTC
3244228 TC
1 TC
3244230 AAACTTTACC
Statistics
Matches: 216, Mismatches: 26, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
9 37 0.17
10 179 0.83
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (10 bp):
TCTCTCTCTC
Found at i:3251014 original size:10 final size:10
Alignment explanation
Indices: 3250994--3251031 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
3250984 AAGATTCATA
3250994 TCAAC-ACAT
1 TCAACTACAT
3251003 TCAACTACAT
1 TCAACTACAT
*
3251013 TCAGCTACAT
1 TCAACTACAT
*
3251023 TCACCTACA
1 TCAACTACA
3251032 CTTGATGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 5 0.19
10 21 0.81
ACGTcount: A:0.37, C:0.34, G:0.03, T:0.26
Consensus pattern (10 bp):
TCAACTACAT
Found at i:3255441 original size:5 final size:5
Alignment explanation
Indices: 3255431--3255459 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3255421 AGTGCTTCAA
3255431 CTTTT CTTTT CTTTT CTTTT -TTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
3255460 TGAGTGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
CTTTT
Found at i:3262484 original size:23 final size:25
Alignment explanation
Indices: 3262453--3262498 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
3262443 TTTTGATAAC
3262453 TTTAGCCTTGACA-ACTTTTATTTG
1 TTTAGCCTTGACATACTTTTATTTG
* *
3262477 TTTA-CCTTTACATATTTTTATT
1 TTTAGCCTTGACATACTTTTATT
3262499 GCCTCGACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.57
Consensus pattern (25 bp):
TTTAGCCTTGACATACTTTTATTTG
Found at i:3274467 original size:21 final size:21
Alignment explanation
Indices: 3274443--3274506 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
3274433 AATATGTAAA
* * *
3274443 TCGCATTGTGATTTTCGAAAT
1 TCGCATTGCGATATTCCAAAT
*
3274464 TCGCGTTGCGATATTCCAAAT
1 TCGCATTGCGATATTCCAAAT
** *
3274485 TCGCAACGCGATAGT-CAAAT
1 TCGCATTGCGATATTCCAAAT
3274505 TC
1 TC
3274507 TCAACGCGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 7 0.20
21 28 0.80
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATATTCCAAAT
Found at i:3274505 original size:20 final size:20
Alignment explanation
Indices: 3274480--3274563 Score: 107
Period size: 20 Copynumber: 4.2 Consensus size: 20
3274470 TGCGATATTC
* *
3274480 CAAATTCGCAACGCGATAGT
1 CAAATTCACAACGCGAAAGT
*
3274500 CAAATTCTCAACGCGAAAGT
1 CAAATTCACAACGCGAAAGT
* **
3274520 CAAATTCACAAC-TGAATTT
1 CAAATTCACAACGCGAAAGT
3274539 CAAATTCACAACGCGAAAGT
1 CAAATTCACAACGCGAAAGT
3274559 CAAAT
1 CAAAT
3274564 GTTTTTACGC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
19 16 0.30
20 38 0.70
ACGTcount: A:0.42, C:0.24, G:0.13, T:0.21
Consensus pattern (20 bp):
CAAATTCACAACGCGAAAGT
Found at i:3274722 original size:22 final size:22
Alignment explanation
Indices: 3274696--3274737 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3274686 GCGACATCCG
3274696 TCCCCATCTCCGACAAAATCTA
1 TCCCCATCTCCGACAAAATCTA
* *
3274718 TCCCCATTTCCGACGAAATC
1 TCCCCATCTCCGACAAAATC
3274738 CGTCTCTCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.40, G:0.07, T:0.24
Consensus pattern (22 bp):
TCCCCATCTCCGACAAAATCTA
Found at i:3274973 original size:13 final size:13
Alignment explanation
Indices: 3274955--3274986 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3274945 AGTATTTGTC
*
3274955 TTTGTTTTGTCTT
1 TTTGTTTTGTATT
3274968 TTTGTTTTGTATT
1 TTTGTTTTGTATT
3274981 TTTGTT
1 TTTGTT
3274987 AAAGAAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.03, C:0.03, G:0.16, T:0.78
Consensus pattern (13 bp):
TTTGTTTTGTATT
Found at i:3275095 original size:20 final size:20
Alignment explanation
Indices: 3275055--3275095 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3275045 AAACTAAAAG
* * *
3275055 CGCGTTGCGATTTTCATTTT
1 CGCGTTGCGAATTTAAGTTT
3275075 CGCGTTGCGAATTTAAGTTT
1 CGCGTTGCGAATTTAAGTTT
3275095 C
1 C
3275096 AGAAACTTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.44
Consensus pattern (20 bp):
CGCGTTGCGAATTTAAGTTT
Found at i:3277290 original size:42 final size:42
Alignment explanation
Indices: 3277243--3277340 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 42
3277233 CCGATGCACA
* * * *
3277243 TATCATCATTCAAG-AGGTGCCTCCTATCGTTCAAGAGGCCCC
1 TATCATCATTCAAGAAGCT-CCTCCCACCGTTCAAGAGGCCAC
3277285 TATCATCA-TCGAAGAAGCTCCTCCCACCGTTCAAGAGGCCAC
1 TATCATCATTC-AAGAAGCTCCTCCCACCGTTCAAGAGGCCAC
* *
3277327 TGTCATCGTTCAAG
1 TATCATCATTCAAG
3277341 TGGTCCTGCC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
41 2 0.04
42 40 0.85
43 5 0.11
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (42 bp):
TATCATCATTCAAGAAGCTCCTCCCACCGTTCAAGAGGCCAC
Found at i:3278753 original size:61 final size:65
Alignment explanation
Indices: 3278670--3278809 Score: 173
Period size: 65 Copynumber: 2.2 Consensus size: 65
3278660 TTTTACATTG
*
3278670 AAAGTTGATTTG-TTACAATTGATGAGGAAATAAG-ATT-TATTTT-TTGATTAATTTATTTGTA
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATATTTTCTTGATTAATTGATTTGTA
* ** * * *
3278731 AAAGTTGATTTGTTTA-ATTTGATTTGTAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATATTTT-CTTGATTAATTGATTTGT
3278795 A
65 A
3278796 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
3278810 GTTTTTAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
61 26 0.39
62 6 0.09
63 5 0.07
65 30 0.45
ACGTcount: A:0.31, C:0.01, G:0.16, T:0.51
Consensus pattern (65 bp):
AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATATTTTCTTGATTAATTGATTTGTA
Found at i:3282272 original size:19 final size:19
Alignment explanation
Indices: 3282248--3282298 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
3282238 ACTAAAACCT
3282248 GTTGCGAAATT-AAATTCA
1 GTTGCGAAATTGAAATTCA
* *
3282266 CGTTGCGAATTTGAAATTTA
1 -GTTGCGAAATTGAAATTCA
*
3282286 GTTGCGAATTTGA
1 GTTGCGAAATTGA
3282299 CTATCGCGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 23 0.79
20 6 0.21
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (19 bp):
GTTGCGAAATTGAAATTCA
Found at i:3282315 original size:20 final size:20
Alignment explanation
Indices: 3282286--3282355 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
3282276 TTGAAATTTA
*
3282286 GTTGCGAATTTGACTATCGC
1 GTTGCAAATTTGACTATCGC
*
3282306 GTTGCAAATTTGACTTTCGC
1 GTTGCAAATTTGACTATCGC
*
3282326 GTTG-AGAATTTGACTATCAC
1 GTTGCA-AATTTGACTATCGC
*
3282346 GTTGCGAATT
1 GTTGCAAATT
3282356 CCAATTTCGC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
19 1 0.02
20 42 0.98
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (20 bp):
GTTGCAAATTTGACTATCGC
Found at i:3282364 original size:40 final size:40
Alignment explanation
Indices: 3282286--3282365 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
3282276 TTGAAATTTA
* * ** *
3282286 GTTGCGAATTTGACTATCGCGTTGCAAATTTGACTTTCGC
1 GTTGAGAATTTGACTATCACGTTGCAAATTCCAATTTCGC
*
3282326 GTTGAGAATTTGACTATCACGTTGCGAATTCCAATTTCGC
1 GTTGAGAATTTGACTATCACGTTGCAAATTCCAATTTCGC
3282366 AACGCGAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (40 bp):
GTTGAGAATTTGACTATCACGTTGCAAATTCCAATTTCGC
Found at i:3282375 original size:40 final size:40
Alignment explanation
Indices: 3282289--3282377 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
3282279 AAATTTAGTT
* ** * ***
3282289 GCGAATTTGACTATCGCGTTGCAAATTTGACTTTCGCGTT
1 GCGAATTTGACTATCACGTTGCAAATTCCAATTTCGCAAC
* *
3282329 GAGAATTTGACTATCACGTTGCGAATTCCAATTTCGCAAC
1 GCGAATTTGACTATCACGTTGCAAATTCCAATTTCGCAAC
3282369 GCGAATTTG
1 GCGAATTTG
3282378 GAAAATCGCA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (40 bp):
GCGAATTTGACTATCACGTTGCAAATTCCAATTTCGCAAC
Found at i:3282424 original size:20 final size:21
Alignment explanation
Indices: 3282401--3282453 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 21
3282391 CGATTTACAT
3282401 ATTCGCGTTGCGAAATTGGA-
1 ATTCGCGTTGCGAAATTGGAG
* *
3282421 ATTCGCATTGCG-AATTTGAG
1 ATTCGCGTTGCGAAATTGGAG
3282441 A-TCGCGTTGCGAA
1 ATTCGCGTTGCGAA
3282454 TTTGTTGGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
ATTCGCGTTGCGAAATTGGAG
Found at i:3286509 original size:25 final size:25
Alignment explanation
Indices: 3286472--3286527 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
3286462 AATTGTGAAA
* *
3286472 ATTAAAATTTAAAAATTCAAGAAAAAT
1 ATTAAAATTAAAAAAGT-AAG-AAAAT
3286499 ATTAAAA-TAAAAAAGTAAGAAAAT
1 ATTAAAATTAAAAAAGTAAGAAAAT
3286523 ATTAA
1 ATTAA
3286528 TTTCTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 10 0.37
25 3 0.11
26 7 0.26
27 7 0.26
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (25 bp):
ATTAAAATTAAAAAAGTAAGAAAAT
Found at i:3289413 original size:44 final size:44
Alignment explanation
Indices: 3289311--3289471 Score: 225
Period size: 44 Copynumber: 3.6 Consensus size: 44
3289301 TCCAAAAACT
* * * * *
3289311 CGTAAGTTTATTTTAACAATATACTTACCATTAAATCCCTAAGCT
1 CGTAAGCTTATTTTACCAATATACTTACCATT-ATTCCATAAGCA
3289356 CGTAAGCTTATTTTACCAATATACTTACCATTATTCCATAAGCA
1 CGTAAGCTTATTTTACCAATATACTTACCATTATTCCATAAGCA
3289400 CGTAAGCTTATTTTACCAATATACTTACCATTATTCCATAAGCTA
1 CGTAAGCTTATTTTACCAATATACTTACCATTATTCCATAAGC-A
* * *
3289445 -ATAAGCTTATTCTACCAACATACTTAC
1 CGTAAGCTTATTTTACCAATATACTTAC
3289472 TATAATTTTA
Statistics
Matches: 107, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
44 76 0.71
45 31 0.29
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (44 bp):
CGTAAGCTTATTTTACCAATATACTTACCATTATTCCATAAGCA
Found at i:3289639 original size:59 final size:59
Alignment explanation
Indices: 3289546--3289964 Score: 322
Period size: 59 Copynumber: 7.1 Consensus size: 59
3289536 CAGGAAATTT
* * * * * * *
3289546 ATACAATTCGTATAATTTCCTTATAATATTAGCACTCTCAGTGCTCTATCTGGAATAT-C
1 ATACACTTAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCTATATGGAA-ATCC
* * * ** * * *
3289605 ATATACTTAATATGATTTCCTTCTCATTTTAGCACACGAAGTTCCCTAT-TTGAGAATCC
1 ATACACTTAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCTATATGGA-AATCC
* * * * * * *
3289664 ATAC-CATTAGCATGATTTCTTTACCATTTTTAGCACA-TGAAATGCCCTATATGAAAATCC
1 ATACAC-TTAGTATGATTTCCTTATCA-TTTTAGCACACT-CAGTGCTCTATATGGAAATCC
* * * *
3289724 ATACTA-TTAGTATGATTTCCTTATCCTTGTAGCAC-CTTAGTGCT-T-TACTAGAAATCC
1 ATAC-ACTTAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCTATA-TGGAAATCC
* * * *
3289781 ATACACTAAGTATGATTTCCTTA-CAATTTTAGCACA-TATAATGC-CTTATCTGGAAATCC
1 ATACACTTAGTATGATTTCCTTATC-ATTTTAGCACACT-CAGTGCTC-TATATGGAAATCC
* *
3289840 ATATA-TTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCTATATGGAAATTC
1 ATACACTT-AGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCTATATGGAAATCC
* * * * *
3289899 ATACACTCAGTATGATTTCTTTATTATTTTAGCACACTCGGTGCTCCATATGGAAATCC
1 ATACACTTAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCTATATGGAAATCC
3289958 ATACACT
1 ATACACT
3289965 CAATATGGAA
Statistics
Matches: 284, Mismatches: 54, Indels: 44
0.74 0.14 0.12
Matches are distributed among these distances:
56 4 0.01
57 37 0.13
58 16 0.06
59 176 0.62
60 49 0.17
61 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (59 bp):
ATACACTTAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCTATATGGAAATCC
Found at i:3289852 original size:116 final size:118
Alignment explanation
Indices: 3289615--3289934 Score: 339
Period size: 116 Copynumber: 2.7 Consensus size: 118
3289605 ATATACTTAA
* * ** * * * * *
3289615 TATGATTTCCTTCTCATTTTAGCACACGAAGTTCCCTAT-TTGAGAATCCATAC-CATTAGCATG
1 TATGATTTCCTTATCATTGTAGCACACTCAGTGCTCTATATAGA-AATCCATACAC-TAAGTATG
*
3289678 ATTTCTTTACCATTTTTAGCACATGAAATGCCCTATATGAAAATCCATACTATTAG
64 ATTTCTTTA-CAATTTTAGCACATGAAATGCCCTATATGAAAATCCATACTATTAG
* *
3289734 TATGATTTCCTTATCCTTGTAGCAC-CTTAGTGCT-T-TACTAGAAATCCATACACTAAGTATGA
1 TATGATTTCCTTATCATTGTAGCACACTCAGTGCTCTATA-TAGAAATCCATACACTAAGTATGA
* * * *
3289796 TTTCCTTACAATTTTAGCACAT-ATAATGCCTTATCTGGAAATCCATA-TATTCAG
65 TTTCTTTACAATTTTAGCACATGA-AATGCCCTATATGAAAATCCATACTATT-AG
* * * *
3289850 TATGATTTCCTTATCATTTTAGCACACTCAGTGCTCTATATGGAAATTCATACACTCAGTATGAT
1 TATGATTTCCTTATCATTGTAGCACACTCAGTGCTCTATATAGAAATCCATACACTAAGTATGAT
**
3289915 TTCTTTATTATTTTAGCACA
66 TTCTTTACAATTTTAGCACA
3289935 CTCGGTGCTC
Statistics
Matches: 169, Mismatches: 24, Indels: 17
0.80 0.11 0.08
Matches are distributed among these distances:
115 5 0.03
116 59 0.35
117 32 0.19
118 49 0.29
119 24 0.14
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.39
Consensus pattern (118 bp):
TATGATTTCCTTATCATTGTAGCACACTCAGTGCTCTATATAGAAATCCATACACTAAGTATGAT
TTCTTTACAATTTTAGCACATGAAATGCCCTATATGAAAATCCATACTATTAG
Found at i:3289972 original size:21 final size:21
Alignment explanation
Indices: 3289946--3289992 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
3289936 TCGGTGCTCC
3289946 ATATGGAAATCCATACACTCA
1 ATATGGAAATCCATACACTCA
3289967 ATATGGAAATCCATACACTCA
1 ATATGGAAATCCATACACTCA
*
3289988 GTATG
1 ATATG
3289993 ATTTCCTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (21 bp):
ATATGGAAATCCATACACTCA
Found at i:3290024 original size:80 final size:80
Alignment explanation
Indices: 3289887--3290044 Score: 271
Period size: 80 Copynumber: 2.0 Consensus size: 80
3289877 TCAGTGCTCT
* * * **
3289887 ATATGGAAATTCATACACTCAGTATGATTTCTTTATTATTTTAGCACACTCGGTGCTCCATATGG
1 ATATGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAATGCTCCATATGG
3289952 AAATCCATACACTCA
66 AAATCCATACACTCA
3289967 ATATGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAATGCTCCATATGG
1 ATATGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAATGCTCCATATGG
3290032 AAATCCATACACT
66 AAATCCATACACT
3290045 TAGTATGATT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 73 1.00
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (80 bp):
ATATGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAATGCTCCATATGG
AAATCCATACACTCA
Found at i:3290059 original size:59 final size:59
Alignment explanation
Indices: 3289967--3290250 Score: 462
Period size: 59 Copynumber: 4.8 Consensus size: 59
3289957 CATACACTCA
*
3289967 ATATGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAATGCTCC
1 ATATGGAAATTCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAATGCTCC
* * *
3290026 ATATGGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCC
1 ATATGGAAATTCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAATGCTCC
*
3290085 ATATGGAAATTCATACACTCAGTATGATTTCCTTATCATTTTAGCACACT-AAGGGCTCC
1 ATATGGAAATTCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAA-TGCTCC
* * * *
3290144 ATATGGAAATTCATACACTCAATATGATTTCCTTATCATTTTAGAACACTCAGTACTCC
1 ATATGGAAATTCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAATGCTCC
*
3290203 ATATGGAAATTCATACACTCAGTATGATTTTCTTATCATTTTAGCACA
1 ATATGGAAATTCATACACTCAGTATGATTTCCTTATCATTTTAGCACA
3290251 TATAGTGTCA
Statistics
Matches: 209, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
58 1 0.00
59 207 0.99
60 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (59 bp):
ATATGGAAATTCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAATGCTCC
Found at i:3290082 original size:139 final size:139
Alignment explanation
Indices: 3289831--3290110 Score: 461
Period size: 139 Copynumber: 2.0 Consensus size: 139
3289821 ATGCCTTATC
* * * *
3289831 TGGAAATCCATATATTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCTATATGGAAA
1 TGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAATGCTCCATATGGAAA
* * * *
3289896 TTCATACACTCAGTATGATTTCTTTATTATTTTAGCACACTCGGTGCTCCATATGGAAATCCATA
66 TCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATA
3289961 CACTCAATA
131 CACTCAATA
3289970 TGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAATGCTCCATATGGAAA
1 TGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAATGCTCCATATGGAAA
* *
3290035 TCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATTCATA
66 TCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATA
*
3290100 CACTCAGTA
131 CACTCAATA
3290109 TG
1 TG
3290111 ATTTCCTTAT
Statistics
Matches: 130, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
139 130 1.00
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.35
Consensus pattern (139 bp):
TGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAATGCTCCATATGGAAA
TCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATA
CACTCAATA
Found at i:3290112 original size:198 final size:198
Alignment explanation
Indices: 3289774--3290169 Score: 622
Period size: 198 Copynumber: 2.0 Consensus size: 198
3289764 TGCTTTACTA
* * *
3289774 GAAATCCATACACTAAGTATGATTTCCTTACAATTTTAGCACATATAATGCCTTATCTGGAAATC
1 GAAATCCATACACTAAGTATGATTTCCTTACAATTTTAGCACATACAATGCCTCATATGGAAATC
* *
3289839 CATATATTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCTATATGGAAATTCATACA
66 CATACATTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATTCATACA
* * *
3289904 CTCAGTATGATTTCTTTATTATTTTAGCACACT-CGGTGCTCCATATGGAAATCCATACACTCAA
131 CTCAGTATGATTTCCTTATCATTTTAGCACACTAAGG-GCTCCATATGGAAATCCATACACTCAA
3289968 TATG
195 TATG
*
3289972 GAAATCCATACACTCAGTATGATTTCCTTATC-ATTTTAGCACACT-CAATG-CTCCATATGGAA
1 GAAATCCATACACTAAGTATGATTTCCTTA-CAATTTTAGCACA-TACAATGCCT-CATATGGAA
3290034 ATCCATACACTT-AGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATTCA
63 ATCCATACA-TTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATTCA
*
3290098 TACACTCAGTATGATTTCCTTATCATTTTAGCACACTAAGGGCTCCATATGGAAATTCATACACT
127 TACACTCAGTATGATTTCCTTATCATTTTAGCACACTAAGGGCTCCATATGGAAATCCATACACT
3290163 CAATATG
192 CAATATG
3290170 ATTTCCTTAT
Statistics
Matches: 183, Mismatches: 10, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
197 2 0.01
198 175 0.96
199 6 0.03
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (198 bp):
GAAATCCATACACTAAGTATGATTTCCTTACAATTTTAGCACATACAATGCCTCATATGGAAATC
CATACATTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATTCATACA
CTCAGTATGATTTCCTTATCATTTTAGCACACTAAGGGCTCCATATGGAAATCCATACACTCAAT
ATG
Found at i:3294872 original size:21 final size:21
Alignment explanation
Indices: 3294846--3294885 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3294836 TAAAATGTGT
3294846 ATCGATGCACTGCTACAGTGC
1 ATCGATGCACTGCTACAGTGC
3294867 ATCGATGCACTGCTACAGT
1 ATCGATGCACTGCTACAGT
3294886 AATTTCTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (21 bp):
ATCGATGCACTGCTACAGTGC
Found at i:3295406 original size:44 final size:44
Alignment explanation
Indices: 3295284--3295452 Score: 234
Period size: 44 Copynumber: 3.8 Consensus size: 44
3295274 TCAATAAACA
* * *
3295284 TACCATTTAATCCATAAACTCGTAAG-TATATTTTAACAATATACT
1 TACCA-TTAATCCATAAGCTCGTAAGCT-TATTTTACCAATGTACT
3295329 TACCATTAAATCTC-TAAGCTCGTAAGCTTATTTTACCAATGTACT
1 TACCATT-AATC-CATAAGCTCGTAAGCTTATTTTACCAATGTACT
* *
3295374 TACCATTATTCCACAAGCTCGTAAGCTTATTTTACCAATGTACT
1 TACCATTAATCCATAAGCTCGTAAGCTTATTTTACCAATGTACT
*
3295418 TACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
1 TACCATTAATCCATAAGCTCGTAAGCTTATTTTAC
3295453 TAACATAATT
Statistics
Matches: 114, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
43 1 0.01
44 69 0.61
45 42 0.37
46 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.38
Consensus pattern (44 bp):
TACCATTAATCCATAAGCTCGTAAGCTTATTTTACCAATGTACT
Found at i:3295406 original size:89 final size:89
Alignment explanation
Indices: 3295284--3295452 Score: 236
Period size: 89 Copynumber: 1.9 Consensus size: 89
3295274 TCAATAAACA
*
3295284 TACCATTTAATCCATAAACTCGTAAGTATATTTTAACAATATACTTACCATTAAATCTC-TAAGC
1 TACCATTTAATCCACAAACTCGTAAGTATATTTTAACAATATACTTACCATT-AATC-CATAAGC
3295348 TCGTAAGCTTATTTTACCAATGTACT
64 TCGTAAGCTTATTTTACCAATGTACT
* * * * *
3295374 TACCA-TTATTCCACAAGCTCGTAAGCT-TATTTTACCAATGTACTTACCATTATTCCATAAGCT
1 TACCATTTAATCCACAAACTCGTAAG-TATATTTTAACAATATACTTACCATTAATCCATAAGCT
3295437 CGTAAGCTTATTTTAC
65 CGTAAGCTTATTTTAC
3295453 TAACATAATT
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
87 1 0.01
88 25 0.35
89 39 0.55
90 6 0.08
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.38
Consensus pattern (89 bp):
TACCATTTAATCCACAAACTCGTAAGTATATTTTAACAATATACTTACCATTAATCCATAAGCTC
GTAAGCTTATTTTACCAATGTACT
Found at i:3295672 original size:59 final size:59
Alignment explanation
Indices: 3295539--3296226 Score: 636
Period size: 59 Copynumber: 11.8 Consensus size: 59
3295529 TAGGAAATTT
* * * * * * * * * * *
3295539 ATACAATTCGTATAATTTCCATATAATATTAGCACTCTCAGTTCTCTATCTGGAATAT-C
1 ATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCCCTATATGGAA-ATCC
* * * * *
3295598 ATATACTTAATATGATTTCCTTCTCATTTTAGCACACAAAGTGCCCTAT-TTGAGAATCC
1 ATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCCCTATATGGA-AATCC
* * *
3295657 ATAC-CATTAGTATGATTTCTTTACCATTTTTAG--CAC--A-TGCCCTATATGAAAATCC
1 ATACAC-TTAGTATGATTTCCTTATCA-TTTTAGCACACTAAGTGCCCTATATGGAAATCC
* * * * * * ** * *
3295712 ATACAATTAGTATTATTTCCTTATCCTTGTAGCACCCTTAGTGCTTTTTCTGGAAATCC
1 ATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCCCTATATGGAAATCC
* * * *
3295771 ATACACTCAGTATGATTTCCTTACCATTTTAGCACA-TATAATGCCCTATCTGGAAATCC
1 ATACACTTAGTATGATTTCCTTATCATTTTAGCACACTA-AGTGCCCTATATGGAAATCC
* * *
3295830 ATATA-TTCAGTATGATTTCCTTATCATTTTAGCACACTCAA-TTCTCTATATGGAAATCC
1 ATACACTT-AGTATGATTTCCTTATCATTTTAGCACACT-AAGTGCCCTATATGGAAATCC
* * * *
3295889 ATACACTCAGTATAATTTCCTTATCATTTTAGCACACTCAGTGCTCC-ATAAGGAAATCC
1 ATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGC-CCTATATGGAAATCC
* * *
3295948 ATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCC-ATATGGAAATTC
1 ATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGC-CCTATATGGAAATCC
* * * * * *
3296007 ATACACTTAGTATGATTTCCTAATCATTTTAGCACAGTCATTGCTCTATATGGAAATTC
1 ATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCCCTATATGGAAATCC
** * * *
3296066 --ACACGCAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCTCTATATGAAAATTC
1 ATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCCCTATATGGAAATCC
* * *
3296123 ATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCC-ATATGGAAATTC
1 ATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGC-CCTATATGGAAATCC
*
3296182 ATACACTTAATATGATTTCCTTATCATTTTAGCACA-TATAGTGCC
1 ATACACTTAGTATGATTTCCTTATCATTTTAGCACACTA-AGTGCC
3296227 ATTCGGTAAT
Statistics
Matches: 525, Mismatches: 81, Indels: 47
0.80 0.12 0.07
Matches are distributed among these distances:
54 5 0.01
55 33 0.06
56 5 0.01
57 50 0.10
58 16 0.03
59 404 0.77
60 11 0.02
61 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.37
Consensus pattern (59 bp):
ATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCCCTATATGGAAATCC
Found at i:3295961 original size:177 final size:175
Alignment explanation
Indices: 3295548--3296218 Score: 715
Period size: 177 Copynumber: 3.8 Consensus size: 175
3295538 TATACAATTC
* * * * * * * * *
3295548 GTATAATTTCCATATAATATTAGCACTCTCAGTTCTCTATCTGGAATAT-CATATACTTAATATG
1 GTATAATTTCCTTATCATTTTAGCACACTCAGTGCTCTATATGGAA-ATCCATACACTCAGTATG
* *
3295612 ATTTCCTT-CTCATTTTAGCACAC-AAAGTGC-CC-TATTTGAGAATCCATAC-CATTAGTATGA
65 ATTTCCTTAC-CATTTTAGCACACTCAA-TGCTCCATA-TGGA-AATCCATACAC-TTAGTATGA
* * * * *
3295672 TTTCTTTACCATTTTTAGCACATGC---C-CTATATGAAAATCCATACAATTA
125 TTTCCTTATCA-TTTTAGCACAT-CATTCTCTATATGGAAATCCATACACTCA
* * * * * * * *
3295721 GTATTATTTCCTTATCCTTGTAGCACCCTTAGTGCTTTTTCTGGAAATCCATACACTCAGTATGA
1 GTATAATTTCCTTATCATTTTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATGA
* * *
3295786 TTTCCTTACCATTTTAGCACA-TATAATGC-CCTATCTGGAAATCCATATA-TTCAGTATGATTT
66 TTTCCTTACCATTTTAGCACACT-CAATGCTCC-ATATGGAAATCCATACACTT-AGTATGATTT
3295848 CCTTATCATTTTAGCACACTCAATTCTCTATATGGAAATCCATACACTCA
128 CCTTATCATTTTAGCACA-TC-ATTCTCTATATGGAAATCCATACACTCA
* *
3295898 GTATAATTTCCTTATCATTTTAGCACACTCAGTGCTCCATAAGGAAATCCATACACTCAGTATGA
1 GTATAATTTCCTTATCATTTTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATGA
* * *
3295963 TTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATTCATACACTTAGTATGATTTCCT
66 TTTCCTTACCATTTTAGCACACTCAATGCTCCATATGGAAATCCATACACTTAGTATGATTTCCT
* * *
3296028 AATCATTTTAGCACAGTCATTGCTCTATATGGAAATTC--ACACGCA
131 TATCATTTTAGCACA-TCATT-CTCTATATGGAAATCCATACACTCA
* * * *
3296073 GTATGATTTCCTTATCATTTTAGCACACTAAGTGCTCTATATGAAAATTCATACACTCAGTATGA
1 GTATAATTTCCTTATCATTTTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATGA
* * * *
3296138 TTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATTCATACACTTAATATGATTTCCT
66 TTTCCTTACCATTTTAGCACACTCAATGCTCCATATGGAAATCCATACACTTAGTATGATTTCCT
3296203 TATCATTTTAGCACAT
131 TATCATTTTAGCACAT
3296219 ATAGTGCCAT
Statistics
Matches: 429, Mismatches: 51, Indels: 35
0.83 0.10 0.07
Matches are distributed among these distances:
172 15 0.03
173 97 0.23
174 7 0.02
175 144 0.34
176 4 0.01
177 157 0.37
178 5 0.01
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (175 bp):
GTATAATTTCCTTATCATTTTAGCACACTCAGTGCTCTATATGGAAATCCATACACTCAGTATGA
TTTCCTTACCATTTTAGCACACTCAATGCTCCATATGGAAATCCATACACTTAGTATGATTTCCT
TATCATTTTAGCACATCATTCTCTATATGGAAATCCATACACTCA
Found at i:3297856 original size:172 final size:174
Alignment explanation
Indices: 3297570--3297917 Score: 682
Period size: 172 Copynumber: 2.0 Consensus size: 174
3297560 TACCATACAC
3297570 AAAGGATAAAACAACATACATGCACTGTTTACTCATAAGTAAAAGTAGGTTCATTATTCCTTATT
1 AAAGGATAAAACAACATACATGCACTGTTTACTCATAAGTAAAAGTAGGTTCATTATTCCTTATT
3297635 TTCCAAGAAATTAATTGCCTTTTGTTCTTTTGATCCAAAAATGGTTGCCTGCAGAACATCAAT-A
66 TTCCAAGAAATTAATTGCCTTTTGTTCTTTTGATCCAAAAATGGTTGCCTGCAGAACATCAATAA
3297699 AAAAATTCATTCTAGATGCATAATAC-AACCCTAAATTTACTAA
131 AAAAATTCATTCTAGATGCATAATACAAACCCTAAATTTACTAA
3297742 AAAGGATAAAACAACATACATGCACTGTTTACTCATAAGTAAAAGTAGGTTCATTATTCCTTATT
1 AAAGGATAAAACAACATACATGCACTGTTTACTCATAAGTAAAAGTAGGTTCATTATTCCTTATT
3297807 TTCCAAGAAATTAATTGCCTTTTGTTCTTTTGATCCAAAAATGGTTGCCTGCAGAACATCAATAA
66 TTCCAAGAAATTAATTGCCTTTTGTTCTTTTGATCCAAAAATGGTTGCCTGCAGAACATCAATAA
3297872 AAAAATTCATTCTAGATGCATAATACAAACCCTAAATTTACTAA
131 AAAAATTCATTCTAGATGCATAATACAAACCCTAAATTTACTAA
3297916 AA
1 AA
3297918 TTTAACCAAA
Statistics
Matches: 174, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
172 128 0.74
173 27 0.16
174 19 0.11
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (174 bp):
AAAGGATAAAACAACATACATGCACTGTTTACTCATAAGTAAAAGTAGGTTCATTATTCCTTATT
TTCCAAGAAATTAATTGCCTTTTGTTCTTTTGATCCAAAAATGGTTGCCTGCAGAACATCAATAA
AAAAATTCATTCTAGATGCATAATACAAACCCTAAATTTACTAA
Found at i:3304487 original size:13 final size:14
Alignment explanation
Indices: 3304459--3304494 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
3304449 ATGTAGCGAT
3304459 TGAAGAAGGTTCTGA
1 TGAAG-AGGTTCTGA
3304474 TGAAGAGG-TCTGA
1 TGAAGAGGTTCTGA
3304487 TGAAGAGG
1 TGAAGAGG
3304495 AACAAGAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.62
14 3 0.14
15 5 0.24
ACGTcount: A:0.33, C:0.06, G:0.39, T:0.22
Consensus pattern (14 bp):
TGAAGAGGTTCTGA
Found at i:3311441 original size:16 final size:16
Alignment explanation
Indices: 3311420--3311468 Score: 98
Period size: 16 Copynumber: 3.1 Consensus size: 16
3311410 AGGGAGAAGT
3311420 GTAAAATGTTTTAAAG
1 GTAAAATGTTTTAAAG
3311436 GTAAAATGTTTTAAAG
1 GTAAAATGTTTTAAAG
3311452 GTAAAATGTTTTAAAG
1 GTAAAATGTTTTAAAG
3311468 G
1 G
3311469 GGGAGAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (16 bp):
GTAAAATGTTTTAAAG
Found at i:3311887 original size:46 final size:47
Alignment explanation
Indices: 3311831--3311929 Score: 141
Period size: 46 Copynumber: 2.1 Consensus size: 47
3311821 TTTCAAGGGC
3311831 ATGCACCGATGCACCA-ATCCATGCATCGATGCACTC-AGTGCATTTG
1 ATGCACCGATGCACCAGA-CCATGCATCGATGCACTCTAGTGCATTTG
* *
3311877 ATGCATCGATGCACCAGACCATGCATCGATGCACTCTTAGTGCA-TCG
1 ATGCACCGATGCACCAGACCATGCATCGATGCACTC-TAGTGCATTTG
3311924 ATGCAC
1 ATGCAC
3311930 TCTTAGTGCA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
46 33 0.70
47 8 0.17
48 6 0.13
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.23
Consensus pattern (47 bp):
ATGCACCGATGCACCAGACCATGCATCGATGCACTCTAGTGCATTTG
Found at i:3311922 original size:19 final size:19
Alignment explanation
Indices: 3311898--3311949 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
3311888 CACCAGACCA
3311898 TGCATCGATGCACTCTTAG
1 TGCATCGATGCACTCTTAG
3311917 TGCATCGATGCACTCTTAG
1 TGCATCGATGCACTCTTAG
*
3311936 TGCACCGATGCACT
1 TGCATCGATGCACT
3311950 GAGAGTCCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (19 bp):
TGCATCGATGCACTCTTAG
Found at i:3315508 original size:6 final size:6
Alignment explanation
Indices: 3315497--3315525 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3315487 CATTCTTACT
3315497 TCTTCC TCTTCC TCTTCC TCTTCC TCTTC
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTC
3315526 TAAGGTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCC
Found at i:3316219 original size:20 final size:20
Alignment explanation
Indices: 3316170--3316222 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
3316160 GACCGCTCAA
* **
3316170 TCTCCATACAGAAGGATTGG
1 TCTCCATACTGAAAAATTGG
*
3316190 TCTCTATACTGAAAAATTGG
1 TCTCCATACTGAAAAATTGG
3316210 TCTCCATACTGAA
1 TCTCCATACTGAA
3316223 TAAACGAGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (20 bp):
TCTCCATACTGAAAAATTGG
Found at i:3336864 original size:19 final size:20
Alignment explanation
Indices: 3336802--3336874 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
3336792 GAATGTTAGC
*
3336802 AGGGTATCTATACCATAGGC
1 AGGGTATCTATACCATAGGT
*
3336822 AGGGTATCTATACCATATGT
1 AGGGTATCTATACCATAGGT
3336842 AGGGTATCTATACCATA-GT
1 AGGGTATCTATACCATAGGT
3336861 AGGGTATCTATACC
1 AGGGTATCTATACC
3336875 TCAGTTAGGG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 16 0.31
20 35 0.69
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (20 bp):
AGGGTATCTATACCATAGGT
Found at i:3338483 original size:523 final size:522
Alignment explanation
Indices: 3337484--3338539 Score: 1760
Period size: 523 Copynumber: 2.0 Consensus size: 522
3337474 AGCTGTGGTG
*
3337484 ACAACATTAGTGCACAACCTCAATGTACTCATGTACCTCTATTCTCAATAATGTACAAGGGCAAT
1 ACAACATTAGTGCACAACCTCAATGTACTCATCTACCTCTATTCTCAATAATGTACAAGGGCAAT
*
3337549 TGAAAGATAAATTAAAGTGAAAGTGATACAAGGAGGTAAGTTTCATATGTGCATGACATGATTAT
66 TGAAAGATAAATTAAAGTGAAAGCGATACAAGGAGGTAAGTTTCATATGTGCATGACATGATTAT
*
3337614 ATTATAGTGAAATATATGCATGCATATTGAAATGTCATGATCAAATGGTAAGAATGCATATTCAT
131 ATTATAGTGAAATATATACATGCATATTGAAATGTCATGATCAAATGGTAAGAATGCATATTCAT
* * * *
3337679 GAATTTATTGTTACATGTTTATTTATTGCCTCACTAAGTCTATGACTTAGCGTGTACGTAATTTA
196 GAATCTATTGCTACATGTTTATTTATTGCCTCACTAAGTCTATGACTTAGCATGTAAGTAATTTA
3337744 CAAGTAGGTACCAAGAAACAAGAAGAGCAGTAATAGAAGTGGCAAGGACAACATCACTACTAAGA
261 CAAGTAGGTACCAAGAAACAAGAAGAGCAGTAATAGAAGT----AGG-----A-CACTACTAAGA
*
3337809 GATCATATCAGAAGTAATTGACAAAGTAGGTATTTTGGTTGTGTATATAGTGTTGGCATGTAATA
316 GATCAAATCAGAAGTAATTGACAAAGTAGGTATTTTGGTTGTGTATATAGTGTTGGCATGTAATA
3337874 AGTTGTTAATTATGAATGTTCTGATCGATTTTGGATTTTATGGTCTCTTTTATGTAAATGAACGT
381 AGTTGTTAATTATGAATGTTCTGATCGATTTTGGATTTTATGGTCTCTTTTATGTAAATGAACGT
* *
3337939 ATTTTGTTTTAATGAAAGTTTAAAA-TTCCCTATTTTTCTTTAAGTGTCAAAGTTTGAAAAGTCA
446 ATTTTGTTTTAACGAAAGTTTAAAATTTCCCTATTTTTCTTTAAGTGTCAAAGTTTAAAAAGTCA
3338003 ATGTGACACCTC
511 ATGTGACACCTC
* * *
3338015 ACAACTTTAGTGCACAACCTCAATGTACTCATCTACCTCTGTTCTCAATAATGTACATGGGCAAT
1 ACAACATTAGTGCACAACCTCAATGTACTCATCTACCTCTATTCTCAATAATGTACAAGGGCAAT
* *
3338080 TGAAAGATAAATTAAAGTGAAAGCGATACAATGAGGTAAGTTTCATATGTGTATGACATGATTAT
66 TGAAAGATAAATTAAAGTGAAAGCGATACAAGGAGGTAAGTTTCATATGTGCATGACATGA-T-T
3338145 ATATGTTATAGTGAAATATATACATGCATATTGAAATGTCATGATCAAATGGTAAGAATGCATAT
129 ATA--TTATAGTGAAATATATACATGCATATTGAAATGTCATGATCAAATGGTAAGAATGCATAT
* *
3338210 TCATGAATCTATTGCTACATGTTTATTTATTGCCTCACTAAGTCTATGACTTAGTATGTAAGTGA
192 TCATGAATCTATTGCTACATGTTTATTTATTGCCTCACTAAGTCTATGACTTAGCATGTAAGTAA
*
3338275 TTTACACA-TAGGTACCAAGAAACAAGAAGAGCATTAATAGAAGT-GG-CACTACTAAGAGATCA
257 TTTACA-AGTAGGTACCAAGAAACAAGAAGAGCAGTAATAGAAGTAGGACACTACTAAGAGATCA
3338337 AATCAGAAGTAATTGACAAAGTAGGTATTTTGGTTGTGTATATAGTGTTGGCATGTAATAAGTTG
321 AATCAGAAGTAATTGACAAAGTAGGTATTTTGGTTGTGTATATAGTGTTGGCATGTAATAAGTTG
* *
3338402 TTAATTATGAATGTTCTGATCGATTTTGGATTTTGTGGTCTCTTTTATGTAAATTAACGTATTTT
386 TTAATTATGAATGTTCTGATCGATTTTGGATTTTATGGTCTCTTTTATGTAAATGAACGTATTTT
*
3338467 GTTTTAACGAAAGTTTAAAATTTCCCTGTTTTTCTTTAAGTGTCAAAGTTTAAAAAGTCAATGTG
451 GTTTTAACGAAAGTTTAAAATTTCCCTATTTTTCTTTAAGTGTCAAAGTTTAAAAAGTCAATGTG
3338532 ACACCTC
516 ACACCTC
3338539 A
1 A
3338540 TACTCATATT
Statistics
Matches: 498, Mismatches: 21, Indels: 19
0.93 0.04 0.04
Matches are distributed among these distances:
523 162 0.33
524 50 0.10
530 2 0.00
531 119 0.24
532 1 0.00
533 4 0.01
535 159 0.32
536 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (522 bp):
ACAACATTAGTGCACAACCTCAATGTACTCATCTACCTCTATTCTCAATAATGTACAAGGGCAAT
TGAAAGATAAATTAAAGTGAAAGCGATACAAGGAGGTAAGTTTCATATGTGCATGACATGATTAT
ATTATAGTGAAATATATACATGCATATTGAAATGTCATGATCAAATGGTAAGAATGCATATTCAT
GAATCTATTGCTACATGTTTATTTATTGCCTCACTAAGTCTATGACTTAGCATGTAAGTAATTTA
CAAGTAGGTACCAAGAAACAAGAAGAGCAGTAATAGAAGTAGGACACTACTAAGAGATCAAATCA
GAAGTAATTGACAAAGTAGGTATTTTGGTTGTGTATATAGTGTTGGCATGTAATAAGTTGTTAAT
TATGAATGTTCTGATCGATTTTGGATTTTATGGTCTCTTTTATGTAAATGAACGTATTTTGTTTT
AACGAAAGTTTAAAATTTCCCTATTTTTCTTTAAGTGTCAAAGTTTAAAAAGTCAATGTGACACC
TC
Found at i:3344011 original size:21 final size:21
Alignment explanation
Indices: 3343987--3344041 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
3343977 TCTGGTCATA
3343987 GGGTATCGATACCATATAAAG
1 GGGTATCGATACCATATAAAG
* *
3344008 GGGTATCAATACCATATGAAG
1 GGGTATCGATACCATATAAAG
3344029 GGGTATCGATACC
1 GGGTATCGATACC
3344042 CCTTTTGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (21 bp):
GGGTATCGATACCATATAAAG
Found at i:3344220 original size:40 final size:40
Alignment explanation
Indices: 3344137--3344230 Score: 143
Period size: 40 Copynumber: 2.4 Consensus size: 40
3344127 GAATGTTGGC
* **
3344137 AGGGTATCTATACCATATGTAGGGTATCTATACCATAGGT
1 AGGGTATCTATACCATATGCAGGGTATCTATACCATAAAT
3344177 AGGGTATCTATACCATATGCAGGGTATCTATACCATAAAT
1 AGGGTATCTATACCATATGCAGGGTATCTATACCATAAAT
* *
3344217 AGGGTGTTTATACC
1 AGGGTATCTATACC
3344231 TCAGTTAGGA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (40 bp):
AGGGTATCTATACCATATGCAGGGTATCTATACCATAAAT
Found at i:3344230 original size:20 final size:20
Alignment explanation
Indices: 3344137--3344213 Score: 136
Period size: 20 Copynumber: 3.9 Consensus size: 20
3344127 GAATGTTGGC
3344137 AGGGTATCTATACCATATGT
1 AGGGTATCTATACCATATGT
*
3344157 AGGGTATCTATACCATAGGT
1 AGGGTATCTATACCATATGT
*
3344177 AGGGTATCTATACCATATGC
1 AGGGTATCTATACCATATGT
3344197 AGGGTATCTATACCATA
1 AGGGTATCTATACCATA
3344214 AATAGGGTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (20 bp):
AGGGTATCTATACCATATGT
Found at i:3344788 original size:22 final size:22
Alignment explanation
Indices: 3344760--3344814 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
3344750 TCGAGGGTAT
* *
3344760 AGTGGTCCTTCGGGATATATCC
1 AGTGGTCCTTCGGAACATATCC
*
3344782 AGTGGTCCTTCGGAACGTATCC
1 AGTGGTCCTTCGGAACATATCC
3344804 AGTGGTCCTTC
1 AGTGGTCCTTC
3344815 AGGACAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.31
Consensus pattern (22 bp):
AGTGGTCCTTCGGAACATATCC
Found at i:3346116 original size:267 final size:267
Alignment explanation
Indices: 3345641--3346173 Score: 1048
Period size: 267 Copynumber: 2.0 Consensus size: 267
3345631 ATATAACAAA
3345641 TTAAGTATAAATGAATTTTAAGATTTTACAAATTATTTTCTTAGTATATTCAATTTAATTACTCG
1 TTAAGTATAAATGAATTTTAAGATTTTACAAATTATTTTCTTAGTATATTCAATTTAATTACTCG
3345706 AATATCAAAATATTACTCCAATTCTTTCAAAGATCAATTTCAATCCTTACTAAAGTGTAAAATTG
66 AATATCAAAATATTACTCCAATTCTTTCAAAGATCAATTTCAATCCTTACTAAAGTGTAAAATTG
3345771 TGTTTTAATCTTAAAATATTTTTGAAACAATTTTCACAAAGTATTTCAAACCAAAAAACGAGCCT
131 TGTTTTAATCTTAAAATATTTTTGAAACAATTTTCACAAAGTATTTCAAACCAAAAAACGAGCCT
3345836 AAAATCAATTTTTCAAAAGAGTGTACCGATGCACCAATCCATGCATCGATGCACCATTGAATAAA
196 AAAATCAATTTTTCAAAAGAGTGTACCGATGCACCAATCCATGCATCGATGCACCATTGAATAAA
3345901 TTAAAAT
261 TTAAAAT
*
3345908 TTAAGTATAAATGAATTTTAAGATTTTACAAATTATTTTCTTAGTATATTCGATTTAATTACTCG
1 TTAAGTATAAATGAATTTTAAGATTTTACAAATTATTTTCTTAGTATATTCAATTTAATTACTCG
3345973 AATATCAAAATATTACTCCAATTCTTTCAAAGATCAATTTCAATCCTTACTAAAGTGTAAAATTG
66 AATATCAAAATATTACTCCAATTCTTTCAAAGATCAATTTCAATCCTTACTAAAGTGTAAAATTG
*
3346038 TGTTTTAATCTTAAAATATTTTTGAAACAATTTTCACAAAGTATTTCGAACCAAAAAACGAGCCT
131 TGTTTTAATCTTAAAATATTTTTGAAACAATTTTCACAAAGTATTTCAAACCAAAAAACGAGCCT
3346103 AAAATCAATTTTTCAAAAGAGTGTACCGATGCACCAATCCATGCATCGATGCACCATTGAATAAA
196 AAAATCAATTTTTCAAAAGAGTGTACCGATGCACCAATCCATGCATCGATGCACCATTGAATAAA
3346168 TTAAAA
261 TTAAAA
3346174 ATCGAATGCA
Statistics
Matches: 264, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
267 264 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (267 bp):
TTAAGTATAAATGAATTTTAAGATTTTACAAATTATTTTCTTAGTATATTCAATTTAATTACTCG
AATATCAAAATATTACTCCAATTCTTTCAAAGATCAATTTCAATCCTTACTAAAGTGTAAAATTG
TGTTTTAATCTTAAAATATTTTTGAAACAATTTTCACAAAGTATTTCAAACCAAAAAACGAGCCT
AAAATCAATTTTTCAAAAGAGTGTACCGATGCACCAATCCATGCATCGATGCACCATTGAATAAA
TTAAAAT
Found at i:3346217 original size:64 final size:64
Alignment explanation
Indices: 3346141--3346273 Score: 153
Period size: 64 Copynumber: 2.1 Consensus size: 64
3346131 ATGCACCAAT
* * *
3346141 CCATGCATCGATGCAC-CATTGAATAAATTAAAA-ATCGAATGCATTTTATGAATCGATGCACAT
1 CCATGCAACGATGCACTCA--GAATAAATGAAAACATCGAATGCATTTTATGAATCGATGCACAG
3346204 A
64 A
** ** * *
3346205 CCATGCAACGATGCACTCAGGTTTTATGAAAACATTGAATGCATTTTATGCATCGATGCACAGA
1 CCATGCAACGATGCACTCAGAATAAATGAAAACATCGAATGCATTTTATGAATCGATGCACAGA
3346269 CCATG
1 CCATG
3346274 TATCGATTCA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
63 8 0.14
64 48 0.83
65 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (64 bp):
CCATGCAACGATGCACTCAGAATAAATGAAAACATCGAATGCATTTTATGAATCGATGCACAGA
Found at i:3346309 original size:64 final size:61
Alignment explanation
Indices: 3346168--3346316 Score: 172
Period size: 64 Copynumber: 2.3 Consensus size: 61
3346158 ATTGAATAAA
* *
3346168 TTAAAAATCGAATGCATTTTATGAATCGATGCACATACCATGCAACGATGCACTCAGGTTT
1 TTAAAAATCGAATGCATTTTATGAATCGATGCACAGACCATGCAACGATGCACTCAGCTTT
* * * * *
3346229 TATGAAAACATTGAATGCATTTTATGCATCGATGCACAGACCATGTATCGATTCACTCGAGCTTG
1 T-T-AAAA-ATCGAATGCATTTTATGAATCGATGCACAGACCATGCAACGATGCACTC-AGCTT-
3346294 T
61 T
*
3346295 TTAAAATATCGAATGCACTTTA
1 TTAAAA-ATCGAATGCATTTTA
3346317 CACATCAATG
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
63 4 0.05
64 60 0.82
65 5 0.07
66 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Consensus pattern (61 bp):
TTAAAAATCGAATGCATTTTATGAATCGATGCACAGACCATGCAACGATGCACTCAGCTTT
Found at i:3367530 original size:33 final size:33
Alignment explanation
Indices: 3367465--3367531 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
3367455 AACGAGTAAG
* **
3367465 TCCCAAGAAACTCCAAACTTCTAAGATGTTCTT
1 TCCCAAGAAACTCCAAACTTATAAGACATTCTT
3367498 TCCCAAGAAACTCCAAACTTATAAGACATTCTT
1 TCCCAAGAAACTCCAAACTTATAAGACATTCTT
3367531 T
1 T
3367532 GGGGGTTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (33 bp):
TCCCAAGAAACTCCAAACTTATAAGACATTCTT
Found at i:3369739 original size:4 final size:4
Alignment explanation
Indices: 3369685--3369731 Score: 85
Period size: 4 Copynumber: 11.8 Consensus size: 4
3369675 CATTCTTTAA
*
3369685 ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
3369732 TATATATAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:3373322 original size:16 final size:15
Alignment explanation
Indices: 3373299--3373347 Score: 73
Period size: 16 Copynumber: 3.3 Consensus size: 15
3373289 TGGCACCATC
*
3373299 TAAAAAATATAAAAA
1 TAAAAAATAGAAAAA
3373314 TAGAAAAATAGAAAAA
1 TA-AAAAATAGAAAAA
3373330 TAAAAAATAG-AAAA
1 TAAAAAATAGAAAAA
3373344 TAAA
1 TAAA
3373348 TTGAAAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
14 8 0.25
15 10 0.31
16 14 0.44
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (15 bp):
TAAAAAATAGAAAAA
Found at i:3373345 original size:7 final size:8
Alignment explanation
Indices: 3373301--3373343 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
3373291 GCACCATCTA
*
3373301 AAAAATAT
1 AAAAATAG
3373309 AAAAATAG
1 AAAAATAG
3373317 AAAAATAG
1 AAAAATAG
3373325 AAAAATA-
1 AAAAATAG
3373332 AAAAATAG
1 AAAAATAG
3373340 AAAA
1 AAAA
3373344 TAAATTGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
7 7 0.21
8 26 0.79
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (8 bp):
AAAAATAG
Found at i:3375020 original size:17 final size:17
Alignment explanation
Indices: 3374994--3375027 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3374984 TATGATGGAA
3374994 ATATGATTTAGT-TTAT
1 ATATGATTTAGTATTAT
3375010 ATATCGATTTAGTATTAT
1 ATAT-GATTTAGTATTAT
3375028 TTACTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 8 0.50
18 4 0.25
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (17 bp):
ATATGATTTAGTATTAT
Found at i:3379194 original size:35 final size:35
Alignment explanation
Indices: 3379148--3379224 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
3379138 AATTCAAATT
* * *
3379148 CAATATTAAAAATTCCATCCTTGAAATAATATAAC
1 CAATACTAAAAATTACAGCCTTGAAATAATATAAC
* *
3379183 CAATACTAAAAATTATAGCCTTGAAATAATATAAT
1 CAATACTAAAAATTACAGCCTTGAAATAATATAAC
3379218 CAA-ACTA
1 CAATACTA
3379225 GTACATTCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 4 0.11
35 33 0.89
ACGTcount: A:0.51, C:0.16, G:0.04, T:0.30
Consensus pattern (35 bp):
CAATACTAAAAATTACAGCCTTGAAATAATATAAC
Found at i:3379343 original size:19 final size:20
Alignment explanation
Indices: 3379319--3379362 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3379309 CAATGATCCA
*
3379319 AATTTCA-CATTCTAACATC
1 AATTTCACCACTCTAACATC
*
3379338 AATTTCACCACTCTAACATT
1 AATTTCACCACTCTAACATC
3379358 AATTT
1 AATTT
3379363 ACAGCATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTTCACCACTCTAACATC
Found at i:3381073 original size:19 final size:20
Alignment explanation
Indices: 3381051--3381143 Score: 61
Period size: 20 Copynumber: 4.8 Consensus size: 20
3381041 GTGGTAACTG
3381051 AAAATATGGTTTCCAA-ATAA
1 AAAATATGGTTTCCAACAT-A
* * *
3381071 AAAATCTGGTTGCTAA-A-A
1 AAAATATGGTTTCCAACATA
* *
3381089 CAAAATATAGG-TTGCAACCTA
1 -AAAATAT-GGTTTCCAACATA
* *
3381110 AAAATATGGTCTCCAACCT-
1 AAAATATGGTTTCCAACATA
3381129 AAAATATGGTTTCCA
1 AAAATATGGTTTCCA
3381144 TATGAAAATT
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
18 1 0.02
19 25 0.44
20 30 0.53
21 1 0.02
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (20 bp):
AAAATATGGTTTCCAACATA
Found at i:3381113 original size:20 final size:20
Alignment explanation
Indices: 3381090--3381143 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
3381080 TTGCTAAAAC
*
3381090 AAAATATAGGT-TGCAACCTA
1 AAAATAT-GGTCTCCAACCTA
3381110 AAAATATGGTCTCCAACCT-
1 AAAATATGGTCTCCAACCTA
*
3381129 AAAATATGGTTTCCA
1 AAAATATGGTCTCCA
3381144 TATGAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.28
Consensus pattern (20 bp):
AAAATATGGTCTCCAACCTA
Found at i:3381177 original size:19 final size:20
Alignment explanation
Indices: 3381137--3381178 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3381127 CTAAAATATG
3381137 GTTTCCATATGAAAATTCAA
1 GTTTCCATATGAAAATTCAA
*
3381157 GTTTCCATATGAAGA-TCAA
1 GTTTCCATATGAAAATTCAA
3381176 GTT
1 GTT
3381179 CCAACGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (20 bp):
GTTTCCATATGAAAATTCAA
Found at i:3381210 original size:20 final size:20
Alignment explanation
Indices: 3381177--3381330 Score: 104
Period size: 19 Copynumber: 7.8 Consensus size: 20
3381167 GAAGATCAAG
*
3381177 TTCCAACGTAAAAAATCAGGT
1 TTCCAACCT-AAAAATCAGGT
* **
3381198 TTCCAACTTAAAACGCAGG-
1 TTCCAACCTAAAAATCAGGT
* *
3381217 TTCCCACCTAAAATTCAGG-
1 TTCCAACCTAAAAATCAGGT
*
3381236 TTCCAACCTAAAAATTCATGT
1 TTCCAACCTAAAAA-TCAGGT
3381257 TT-CAACCTAAAAA-CTAGGT
1 TTCCAACCTAAAAATC-AGGT
*
3381276 TT-CAACGTAAAAATTCAGGT
1 TTCCAACCTAAAAA-TCAGGT
* ** *
3381296 TTACAAGTTAATAATTCAGG-
1 TTCCAACCTAA-AAATCAGGT
*
3381316 TTGCAACCTAAAAAT
1 TTCCAACCTAAAAAT
3381331 TGGGTTGCAA
Statistics
Matches: 107, Mismatches: 19, Indels: 16
0.75 0.13 0.11
Matches are distributed among these distances:
18 1 0.01
19 45 0.42
20 37 0.35
21 22 0.21
22 2 0.02
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (20 bp):
TTCCAACCTAAAAATCAGGT
Found at i:3381277 original size:19 final size:20
Alignment explanation
Indices: 3381180--3381347 Score: 137
Period size: 20 Copynumber: 8.5 Consensus size: 20
3381170 GATCAAGTTC
* *
3381180 CAACGTAAAAAATCAGGTTT
1 CAACCTAAAAATTCAGGTTT
* ** *
3381200 CCAA-CTTAAAACGCAGGTTC
1 -CAACCTAAAAATTCAGGTTT
* *
3381220 CCACCT-AAAATTCAGGTTC
1 CAACCTAAAAATTCAGGTTT
*
3381239 CAACCTAAAAATTCATGTTT
1 CAACCTAAAAATTCAGGTTT
*
3381259 CAACCTAAAAACT-AGGTTT
1 CAACCTAAAAATTCAGGTTT
*
3381278 CAACGTAAAAATTCAGGTTT
1 CAACCTAAAAATTCAGGTTT
** * *
3381298 ACAAGTTAATAATTCAGGTTG
1 -CAACCTAAAAATTCAGGTTT
* *
3381319 CAACCTAAAAATT-GGGTTG
1 CAACCTAAAAATTCAGGTTT
3381338 CAACCTAAAA
1 CAACCTAAAA
3381348 TTTGTTTCCT
Statistics
Matches: 120, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
19 49 0.41
20 52 0.43
21 19 0.16
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (20 bp):
CAACCTAAAAATTCAGGTTT
Found at i:3381783 original size:10 final size:9
Alignment explanation
Indices: 3381752--3381833 Score: 51
Period size: 10 Copynumber: 9.0 Consensus size: 9
3381742 TATTTTGAGT
*
3381752 TTTTATTTA
1 TTTTATATA
3381761 TTTTATATA
1 TTTTATATA
*
3381770 TTTTAGTATG
1 TTTTA-TATA
*
3381780 TTTTTTATA
1 TTTTATATA
*
3381789 -TATATATA
1 TTTTATATA
*
3381797 -TATATATA
1 TTTTATATA
*
3381805 TATATATATA
1 T-TTTATATA
*
3381815 TATATATATA
1 T-TTTATATA
*
3381825 TATTATATA
1 TTTTATATA
3381834 AAATATATAT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
8 14 0.23
9 22 0.35
10 26 0.42
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (9 bp):
TTTTATATA
Found at i:3381862 original size:2 final size:2
Alignment explanation
Indices: 3381785--3381844 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
3381775 GTATGTTTTT
3381785 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
*
3381827 T- TA TA TA -A AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
3381845 GCCTTTAAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
1 2 0.04
2 53 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3383349 original size:19 final size:19
Alignment explanation
Indices: 3383308--3383351 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
3383298 TTGTACCCAA
* *
3383308 ATTTA-TTTCTTTTATAGT
1 ATTTATTTTCTTTTAAAAT
3383326 ATTTATTTTCTTTTAAAAT
1 ATTTATTTTCTTTTAAAAT
*
3383345 TTTTATT
1 ATTTATT
3383352 GTTTTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTTATTTTCTTTTAAAAT
Found at i:3389413 original size:30 final size:30
Alignment explanation
Indices: 3389356--3389413 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
3389346 ATGTTTTTTT
* *
3389356 AATATATATAGTATATTATATATTATATAA
1 AATATATATAGCATATTAAATATTATATAA
*
3389386 AATATATATAGCATTTTCAAATA-TATAT
1 AATATATATAGCATATT-AAATATTATAT
3389414 TACATAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (30 bp):
AATATATATAGCATATTAAATATTATATAA
Found at i:3389442 original size:16 final size:16
Alignment explanation
Indices: 3389421--3389451 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3389411 TATTACATAA
*
3389421 TTTTAAAAATATATAG
1 TTTTAAAAACATATAG
3389437 TTTTAAAAACATATA
1 TTTTAAAAACATATA
3389452 TGATATATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (16 bp):
TTTTAAAAACATATAG
Found at i:3389452 original size:2 final size:2
Alignment explanation
Indices: 3389447--3389495 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
3389437 TTTTAAAAAC
3389447 AT AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3389490 AT AT AT
1 AT AT AT
3389496 TTTTGAAAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3393242 original size:3 final size:3
Alignment explanation
Indices: 3393234--3393258 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3393224 TCATATGGGG
3393234 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
3393259 AAAACCCTAT
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:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:3393439 original size:13 final size:14
Alignment explanation
Indices: 3393421--3393450 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3393411 GTTAAAACAA
3393421 TCTTCATATGCA-G
1 TCTTCATATGCACG
3393434 TCTTCATATGCACG
1 TCTTCATATGCACG
3393448 TCT
1 TCT
3393451 GTAATAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (14 bp):
TCTTCATATGCACG
Found at i:3399582 original size:21 final size:21
Alignment explanation
Indices: 3399558--3399611 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 21
3399548 ACCCTCTCTA
3399558 TGTATCGATACA-CTATGAATG
1 TGTATCGATACATCT-TGAATG
*
3399579 TGTACCGATACATTCCTTGAATG
1 TGTATCGATACA-T-CTTGAATG
3399602 TGTATCGATA
1 TGTATCGATA
3399612 TACTCAGGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 11 0.39
23 15 0.54
24 2 0.07
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (21 bp):
TGTATCGATACATCTTGAATG
Found at i:3400136 original size:12 final size:13
Alignment explanation
Indices: 3400107--3400139 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3400097 ATCTTATGAT
*
3400107 TTTTCAAACATCG
1 TTTTCAAACATAG
3400120 TTTTCAAA-ATAG
1 TTTTCAAACATAG
3400132 TTTTCAAA
1 TTTTCAAA
3400140 TTTTTCCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.42
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:3401495 original size:23 final size:24
Alignment explanation
Indices: 3401437--3401495 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
3401427 TGTTAAAACA
*
3401437 TTTTGAATGTTTTGGATTTGTGTG
1 TTTTGAATGGTTTGGATTTGTGTG
* *
3401461 TTTTGGAT-GTTTGGATATT-TTTG
1 TTTTGAATGGTTTGGAT-TTGTGTG
3401484 -TTTGAATGGTTT
1 TTTTGAATGGTTT
3401496 AAATATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
22 6 0.21
23 14 0.48
24 9 0.31
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (24 bp):
TTTTGAATGGTTTGGATTTGTGTG
Found at i:3401928 original size:17 final size:18
Alignment explanation
Indices: 3401895--3401931 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
3401885 TTTAAGATTT
3401895 TATATTCGATTCAAAATTA
1 TATATTCGATT-AAAATTA
3401914 TATATTCGATT-AAATTA
1 TATATTCGATTAAAATTA
3401931 T
1 T
3401932 TCGAATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATTCGATTAAAATTA
Found at i:3402114 original size:20 final size:20
Alignment explanation
Indices: 3402083--3402138 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
3402073 TTATAAAGGG
*
3402083 ATGTACCAATACACTCATGT
1 ATGTACCGATACACTCATGT
*
3402103 ATGTATCGATACACTCATGT
1 ATGTACCGATACACTCATGT
3402123 ATGTACCGATACACTC
1 ATGTACCGATACACTC
3402139 CATATTTCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.30
Consensus pattern (20 bp):
ATGTACCGATACACTCATGT
Found at i:3409079 original size:14 final size:12
Alignment explanation
Indices: 3409012--3409078 Score: 55
Period size: 12 Copynumber: 5.2 Consensus size: 12
3409002 TTTGGTATCC
3409012 TTATTTATTTATT
1 TTATTTATTT-TT
*
3409025 TTATAGTATTTTT
1 TTAT-TTATTTTT
*
3409038 TTCTTTTAAATTTTT
1 TT-ATTT--ATTTTT
3409053 TTATTTATTTTT
1 TTATTTATTTTT
3409065 TTA-TTATTATTT
1 TTATTTATT-TTT
3409077 TT
1 TT
3409079 TAAATATCTA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
11 5 0.11
12 14 0.31
13 9 0.20
14 9 0.20
15 8 0.18
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.76
Consensus pattern (12 bp):
TTATTTATTTTT
Found at i:3410364 original size:60 final size:60
Alignment explanation
Indices: 3410258--3410425 Score: 187
Period size: 60 Copynumber: 2.8 Consensus size: 60
3410248 TATCTTGGTG
* * * * *
3410258 TACCAAGTAGCATAGTTTAGCATTAGCTCCTTAT-AGTTCAAATAGTTTCTTAACTTGGCA
1 TACCAAGTAACATAGATGAGCCTTAGCTCCTTATCA-TTCACATAGTTTCTTAACTTGGCA
* * * **
3410318 TA-CAATGTAATATAGATGAGCCTTAGCTCCATATCATTCACATAGTTTCTTATCTTGGTG
1 TACCAA-GTAACATAGATGAGCCTTAGCTCCTTATCATTCACATAGTTTCTTAACTTGGCA
* * *
3410378 TACCAAGTAACATAGTTTAGCCTTAGCTCCTTGTCATTCACATAGTTT
1 TACCAAGTAACATAGATGAGCCTTAGCTCCTTATCATTCACATAGTTT
3410426 TCATTCATAT
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
59 3 0.03
60 83 0.92
61 4 0.04
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (60 bp):
TACCAAGTAACATAGATGAGCCTTAGCTCCTTATCATTCACATAGTTTCTTAACTTGGCA
Found at i:3435298 original size:4 final size:4
Alignment explanation
Indices: 3435289--3435313 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3435279 TATCATAACA
3435289 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
3435314 GGTAAGAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:3436534 original size:68 final size:68
Alignment explanation
Indices: 3436420--3436557 Score: 267
Period size: 68 Copynumber: 2.0 Consensus size: 68
3436410 GATAGAGAAT
*
3436420 TTCATGTAGATTAATTCTCTATCTAATACCTTAATCCAAAAATCAATCGAATAAGCTTAAAAATG
1 TTCAAGTAGATTAATTCTCTATCTAATACCTTAATCCAAAAATCAATCGAATAAGCTTAAAAATG
3436485 GAA
66 GAA
3436488 TTCAAGTAGATTAATTCTCTATCTAATACCTTAATCCAAAAATCAATCGAATAAGCTTAAAAATG
1 TTCAAGTAGATTAATTCTCTATCTAATACCTTAATCCAAAAATCAATCGAATAAGCTTAAAAATG
3436553 GAA
66 GAA
3436556 TT
1 TT
3436558 GAAAACCTAT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.33
Consensus pattern (68 bp):
TTCAAGTAGATTAATTCTCTATCTAATACCTTAATCCAAAAATCAATCGAATAAGCTTAAAAATG
GAA
Found at i:3437207 original size:29 final size:29
Alignment explanation
Indices: 3437120--3437208 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 29
3437110 CAAATTTTAT
*
3437120 AACTTTTAAAAATTATATTTTTGGTCCCTA
1 AACTTTTAAAAATTATA-TTTTGGTCACTA
* * *
3437150 AAC-TTTACAAAGTTTATACTTTGGCCACTA
1 AACTTTTA-AAA-ATTATATTTTGGTCACTA
*
3437180 AACTTTTAAAACTTATATTTTGGTCACTA
1 AACTTTTAAAAATTATATTTTGGTCACTA
3437209 GGTAAAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
29 19 0.39
30 21 0.43
31 9 0.18
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.43
Consensus pattern (29 bp):
AACTTTTAAAAATTATATTTTGGTCACTA
Found at i:3448435 original size:20 final size:20
Alignment explanation
Indices: 3448410--3448478 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
3448400 TCGAAGTTCG
3448410 CGTTGCGATTCATTCCAATT
1 CGTTGCGATTCATTCCAATT
** *
3448430 CGTTGCGA--CAGGCGAAGTT
1 CGTTGCGATTCATTCCAA-TT
3448449 CGCGTTGCGATTCATTCCAATT
1 --CGTTGCGATTCATTCCAATT
3448471 CGTTGCGA
1 CGTTGCGA
3448479 CAGGCGAAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
18 5 0.13
19 2 0.05
20 16 0.42
21 8 0.21
22 2 0.05
23 5 0.13
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.32
Consensus pattern (20 bp):
CGTTGCGATTCATTCCAATT
Found at i:3448446 original size:41 final size:41
Alignment explanation
Indices: 3448401--3448488 Score: 176
Period size: 41 Copynumber: 2.1 Consensus size: 41
3448391 ACGCGGTAGT
3448401 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
3448442 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
3448483 CGAAGT
1 CGAAGT
3448489 ATTGCATTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.28
Consensus pattern (41 bp):
CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
Found at i:3448626 original size:20 final size:20
Alignment explanation
Indices: 3448601--3448669 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
3448591 TCGAAGTTCG
3448601 CGTTGCGATTCATTCCAATT
1 CGTTGCGATTCATTCCAATT
** *
3448621 CGTTGCGA--CAGGCGAAGTT
1 CGTTGCGATTCATTCCAA-TT
3448640 CGCGTTGCGATTCATTCCAATT
1 --CGTTGCGATTCATTCCAATT
3448662 CGTTGCGA
1 CGTTGCGA
3448670 CAGGCGAAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
18 5 0.13
19 2 0.05
20 16 0.42
21 8 0.21
22 2 0.05
23 5 0.13
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.32
Consensus pattern (20 bp):
CGTTGCGATTCATTCCAATT
Found at i:3448637 original size:41 final size:41
Alignment explanation
Indices: 3448592--3448679 Score: 176
Period size: 41 Copynumber: 2.1 Consensus size: 41
3448582 ACGCGGTAGT
3448592 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
3448633 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
3448674 CGAAGT
1 CGAAGT
3448680 ATTGCATTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.28
Consensus pattern (41 bp):
CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
Found at i:3448678 original size:191 final size:191
Alignment explanation
Indices: 3448354--3448738 Score: 770
Period size: 191 Copynumber: 2.0 Consensus size: 191
3448344 ATTCGCAACG
3448354 CGATCTCCGGTATCGCAAATCAGTTTCCAGATTCGCAACGCGGTAGTCGAAGTTCGCGTTGCGAT
1 CGATCTCCGGTATCGCAAATCAGTTTCCAGATTCGCAACGCGGTAGTCGAAGTTCGCGTTGCGAT
3448419 TCATTCCAATTCGTTGCGACAGGCGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGGC
66 TCATTCCAATTCGTTGCGACAGGCGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGGC
3448484 GAAGTATTGCATTTGTTTCTTAAGAATTTTCTCTAAAAAGATAGAATTCGCGCGGACGTGT
131 GAAGTATTGCATTTGTTTCTTAAGAATTTTCTCTAAAAAGATAGAATTCGCGCGGACGTGT
3448545 CGATCTCCGGTATCGCAAATCAGTTTCCAGATTCGCAACGCGGTAGTCGAAGTTCGCGTTGCGAT
1 CGATCTCCGGTATCGCAAATCAGTTTCCAGATTCGCAACGCGGTAGTCGAAGTTCGCGTTGCGAT
3448610 TCATTCCAATTCGTTGCGACAGGCGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGGC
66 TCATTCCAATTCGTTGCGACAGGCGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGGC
3448675 GAAGTATTGCATTTGTTTCTTAAGAATTTTCTCTAAAAAGATAGAATTCGCGCGGACGTGT
131 GAAGTATTGCATTTGTTTCTTAAGAATTTTCTCTAAAAAGATAGAATTCGCGCGGACGTGT
3448736 CGA
1 CGA
3448739 AGACACGTAT
Statistics
Matches: 194, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
191 194 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (191 bp):
CGATCTCCGGTATCGCAAATCAGTTTCCAGATTCGCAACGCGGTAGTCGAAGTTCGCGTTGCGAT
TCATTCCAATTCGTTGCGACAGGCGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGGC
GAAGTATTGCATTTGTTTCTTAAGAATTTTCTCTAAAAAGATAGAATTCGCGCGGACGTGT
Found at i:3449463 original size:6 final size:6
Alignment explanation
Indices: 3449442--3449478 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
3449432 TCCCGTCTCG
3449442 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
3449479 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:3449617 original size:41 final size:41
Alignment explanation
Indices: 3449556--3449689 Score: 252
Period size: 41 Copynumber: 3.3 Consensus size: 41
3449546 AATATTTGGA
3449556 CTATCGCAACG-ATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTT-GAATGAATCGCAACGCGAACTTCGC
3449597 CTATCGCAACGAATTTGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGAATGAATCGCAACGCGAACTTCGC
3449638 CTATCGCAACGAATTTGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGAATGAATCGCAACGCGAACTTCGC
3449679 CTATCGCAACG
1 CTATCGCAACG
3449690 CAAACTTCGC
Statistics
Matches: 92, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
41 88 0.96
42 4 0.04
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.22
Consensus pattern (41 bp):
CTATCGCAACGAATTTGAATGAATCGCAACGCGAACTTCGC
Found at i:3449750 original size:145 final size:144
Alignment explanation
Indices: 3449556--3449834 Score: 522
Period size: 145 Copynumber: 1.9 Consensus size: 144
3449546 AATATTTGGA
*
3449556 CTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGAATGAAT
1 CTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAAT
*
3449621 CGCAACGCGAACTTCGCCTATCGCAACGAATTTGAATGAATCGCAACGCGAACTTCGCCTATCGC
66 CGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCTATCGC
3449686 AACGCAAACTTCGC
131 AACGCAAACTTCGC
3449700 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAA
1 CTATCGCAACG-ATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAA
*
3449765 TCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAATCGCAACGCGAATTTCGCCTATCG
65 TCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCTATCG
3449830 CAACG
130 CAACG
3449835 AATTGGAATG
Statistics
Matches: 131, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
144 11 0.08
145 120 0.92
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (144 bp):
CTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAAT
CGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCTATCGC
AACGCAAACTTCGC
Found at i:3449762 original size:104 final size:103
Alignment explanation
Indices: 3449578--3449793 Score: 405
Period size: 104 Copynumber: 2.1 Consensus size: 103
3449568 TTTGGAATGA
*
3449578 ATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGAATGAATCGCAACGCGAACTTCGCCTATC
1 ATCGCAACGCAAACTTCGCCTATCGCAACGAATTTGAATGAATCGCAACGCGAACTTCGCCTATC
*
3449643 GCAACGAATTTGAATGAATCGCAACGCGAACTTCGCCT
66 GCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCT
3449681 ATCGCAACGCAAACTTCGCCTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTAT
1 ATCGCAACGCAAACTTCGCCTATCGCAACGAATTT-GAATGAATCGCAACGCGAACTTCGCCTAT
3449746 CGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCT
65 CGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCT
3449785 ATCGCAACG
1 ATCGCAACG
3449794 AATTGGAATG
Statistics
Matches: 110, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
103 34 0.31
104 76 0.69
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (103 bp):
ATCGCAACGCAAACTTCGCCTATCGCAACGAATTTGAATGAATCGCAACGCGAACTTCGCCTATC
GCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCT
Found at i:3449771 original size:41 final size:41
Alignment explanation
Indices: 3449681--3449954 Score: 467
Period size: 41 Copynumber: 6.6 Consensus size: 41
3449671 AACTTCGCCT
*
3449681 ATCGCAACGCAAACTTCGCCTATCGCAACGAATTTGGAATGA
1 ATCGCAACGCGAACTTCGCCTATCGCAACGAA-TTGGAATGA
3449723 ATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGA
1 ATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGA
3449764 ATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGA
1 ATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGA
*
3449805 ATCGCAACGCGAATTTCGCCTATCGCAACGAATTGGAATGA
1 ATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGA
* *
3449846 ATCGCAACGCGAACTTCGACTATCGCAACGATTTGGAATGA
1 ATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGA
*
3449887 ATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGGAATAA
1 ATCGCAACGCGAACTTCGCCTATCGCAACGAA-TTGGAATGA
* *
3449929 ATCGCAAAGCGAACTTCGACTATCGC
1 ATCGCAACGCGAACTTCGCCTATCGC
3449955 GTTGCGAATC
Statistics
Matches: 221, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
41 158 0.71
42 63 0.29
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGA
Found at i:3451487 original size:2 final size:2
Alignment explanation
Indices: 3451480--3451513 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3451470 TTCCTTTTTG
3451480 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3451514 TATTGTGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3451696 original size:14 final size:15
Alignment explanation
Indices: 3451677--3451705 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3451667 CTTTTGGAGG
3451677 ATTAAATT-TAATAA
1 ATTAAATTATAATAA
3451691 ATTAAATTATAATAA
1 ATTAAATTATAATAA
3451706 TGACTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTAAATTATAATAA
Found at i:3459979 original size:19 final size:19
Alignment explanation
Indices: 3459955--3459991 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3459945 ATACGATAAG
3459955 AAACTTCAAATCCGACAAC
1 AAACTTCAAATCCGACAAC
3459974 AAACTTCAAATCCGACAA
1 AAACTTCAAATCCGACAA
3459992 TATTGAGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.30, G:0.05, T:0.16
Consensus pattern (19 bp):
AAACTTCAAATCCGACAAC
Found at i:3462513 original size:21 final size:21
Alignment explanation
Indices: 3462470--3462513 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3462460 TAAAATCAAT
*
3462470 AATACAAAACATGATATATCA
1 AATACAAAACATGATATAACA
3462491 AATACAAAACATGAT-TCAACA
1 AATACAAAACATGATAT-AACA
3462512 AA
1 AA
3462514 AATATAGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.59, C:0.16, G:0.05, T:0.20
Consensus pattern (21 bp):
AATACAAAACATGATATAACA
Found at i:3464432 original size:3 final size:3
Alignment explanation
Indices: 3464426--3464476 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
3464416 TTATTTTGTT
* *
3464426 TTA TTA TTA TTA TTA TTA TTA ATA TTA GTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3464474 TTA
1 TTA
3464477 AATAAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:3464643 original size:30 final size:30
Alignment explanation
Indices: 3464598--3464698 Score: 157
Period size: 30 Copynumber: 3.4 Consensus size: 30
3464588 AACCCTAGCT
*
3464598 TCCAGCCGCCACCTCAAGCTTCCAGTGAGC
1 TCCAGCCGCCGCCTCAAGCTTCCAGTGAGC
*
3464628 TCCAGCTGCCGCCTCAAGCTTCCAGTGAGC
1 TCCAGCCGCCGCCTCAAGCTTCCAGTGAGC
* * *
3464658 TCCAGCTGCTGCCTCAAGCTTCCAGTGAGT
1 TCCAGCCGCCGCCTCAAGCTTCCAGTGAGC
3464688 TCCAGCCGCCG
1 TCCAGCCGCCG
3464699 TTGGGAAGAT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.17, C:0.41, G:0.23, T:0.20
Consensus pattern (30 bp):
TCCAGCCGCCGCCTCAAGCTTCCAGTGAGC
Found at i:3466117 original size:19 final size:19
Alignment explanation
Indices: 3466093--3466129 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3466083 TATATGTTTA
*
3466093 ATTTATATTTTAGATATTT
1 ATTTATATTTTAAATATTT
*
3466112 ATTTATTTTTTAAATATT
1 ATTTATATTTTAAATATT
3466130 GAAGGAAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTTATATTTTAAATATTT
Found at i:3466802 original size:20 final size:21
Alignment explanation
Indices: 3466779--3466819 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3466769 AGAAATTAAA
3466779 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTCAATTTTT
* *
3466799 AATTCTTTTCTTTCAATTTTT
1 AATTCATTTATTTCAATTTTT
3466820 TTATTACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (21 bp):
AATTCATTTATTTCAATTTTT
Found at i:3466836 original size:2 final size:2
Alignment explanation
Indices: 3466831--3466857 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3466821 TATTACTTAT
3466831 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3466858 TTATTTATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3468930 original size:7 final size:7
Alignment explanation
Indices: 3468895--3468935 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
3468885 TTTTCATATA
3468895 TGCATTT
1 TGCATTT
3468902 T-CATTT
1 TGCATTT
3468908 TGCATCTT
1 TGCAT-TT
3468916 TGCATTT
1 TGCATTT
*
3468923 TTCATTT
1 TGCATTT
3468930 TGCATT
1 TGCATT
3468936 CATACTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.20
7 17 0.57
8 7 0.23
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:3475404 original size:54 final size:54
Alignment explanation
Indices: 3475338--3475493 Score: 240
Period size: 54 Copynumber: 2.9 Consensus size: 54
3475328 AAAAATCTTG
*
3475338 GCAGAAGCCACAAAAAAGGATGAATATGTTGTCAAATGTTTTACGAACATATGA
1 GCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATATGA
* *
3475392 GCAGAAGTCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATATGA
** ***
3475446 GCAGAAGCCACATGAAAGGATGAATGCACTGTCAAATGTTTTACGAAC
1 GCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
3475494 CTGCTATTCT
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 93 1.00
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.24
Consensus pattern (54 bp):
GCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATATGA
Found at i:3476286 original size:20 final size:22
Alignment explanation
Indices: 3476261--3476300 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3476251 AGTCGTATAT
3476261 AGCCG-TTGGGGATG-TTTTAG
1 AGCCGTTTGGGGATGATTTTAG
3476281 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
3476301 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTAG
Found at i:3476354 original size:21 final size:21
Alignment explanation
Indices: 3476329--3476370 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3476319 CCAGAATGGG
3476329 GGGAATCGGTACCCCTTCATA
1 GGGAATCGGTACCCCTTCATA
3476350 GGGAATCGGTACCCCTTCATA
1 GGGAATCGGTACCCCTTCATA
3476371 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (21 bp):
GGGAATCGGTACCCCTTCATA
Found at i:3476503 original size:20 final size:20
Alignment explanation
Indices: 3476478--3476524 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
3476468 TTAAAAGAAC
3476478 TTTGAATTATTTTTATAAAT
1 TTTGAATTATTTTTATAAAT
3476498 TTTGAATTATTTTTATAAAT
1 TTTGAATTATTTTTATAAAT
3476518 TTTGAAT
1 TTTGAAT
3476525 AAATTCAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (20 bp):
TTTGAATTATTTTTATAAAT
Found at i:3476556 original size:29 final size:31
Alignment explanation
Indices: 3476524--3476583 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
3476514 AAATTTTGAA
* *
3476524 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAAATCAATTCAAGTCCAAAAATCATTTTG
3476553 TAAAATCAATTCAAGTCCAAAAATCATTTTG
1 TAAAATCAATTCAAGTCCAAAAATCATTTTG
3476584 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 10 0.37
31 7 0.26
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAAATCAATTCAAGTCCAAAAATCATTTTG
Found at i:3477312 original size:29 final size:31
Alignment explanation
Indices: 3477280--3477339 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
3477270 AAATTTTGAA
* *
3477280 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAAATCAATTCAAGTCCAAAAATCATTTTG
3477309 TAAAATCAATTCAAGTCCAAAAATCATTTTG
1 TAAAATCAATTCAAGTCCAAAAATCATTTTG
3477340 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 10 0.37
31 7 0.26
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAAATCAATTCAAGTCCAAAAATCATTTTG
Found at i:3477510 original size:22 final size:22
Alignment explanation
Indices: 3477481--3477535 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
3477471 ATCTACACTC
*
3477481 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAAATTCTCTT
*
3477503 TTTAAAGATGATAAATTCTCTT
1 TTCAAAGATGATAAATTCTCTT
3477525 TTCAAAGATGA
1 TTCAAAGATGA
3477536 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAAATTCTCTT
Found at i:3478302 original size:45 final size:45
Alignment explanation
Indices: 3478249--3478729 Score: 452
Period size: 45 Copynumber: 10.3 Consensus size: 45
3478239 GGGAGCTTTT
* *
3478249 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
3478294 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
3478339 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
3478384 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* * * * * * *** *
3478429 TGATGTTTCCAAAAAGCCTTCGGG-AACTTTTTGATGT-TTTCAAAACC
1 TGATGTTTTC-AAAA-CCTTCGGGTCA-TCTGT-AAGTCCTTCAGTGCA
* * ** * * * ***
3478476 TTAGGGTCATCTGT-AAGTCCTAC-AGTGCATGATGTTTCCAAAAAG-CCTTCGGGAGCTTTT
1 TGA-TGT--T-T-TCAAAACCTTCGGGT-CAT-CTG--T-----AAGTCCTTC---AG-TGCA
* *
3478536 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
3478581 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
3478626 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
3478671 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTAT-AGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCT-TCAGTGCA
*
3478716 TGATGTTTCCAAAA
1 TGATGTTTTCAAAA
3478730 AGTCTTCGGA
Statistics
Matches: 358, Mismatches: 51, Indels: 54
0.77 0.11 0.12
Matches are distributed among these distances:
45 281 0.78
46 8 0.02
47 17 0.05
48 9 0.03
49 10 0.03
50 5 0.01
51 1 0.00
52 1 0.00
53 1 0.00
55 3 0.01
56 14 0.04
57 3 0.01
59 3 0.01
60 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:3478677 original size:211 final size:196
Alignment explanation
Indices: 3478625--3480793 Score: 2199
Period size: 211 Copynumber: 10.6 Consensus size: 196
3478615 CCTTCAGTGC
*
3478625 ATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTA
1 ATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
* * *
3478690 GGGTCATCTGTAAGTCCTATAGTGCATGATGTTTCCAAAAAGTCTTCGGAAGCTTTTTGATGTTT
66 GGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTT
*
3478755 TCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAA-CCTTCGGGTCATC
131 TCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTC-GG-----
3478819 TGTAAGTCCTTCAGT
190 -G--AG--CTT---T
*
3478834 GCATGATGTTTTCAAAACCTTCGGGTTATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCT
1 --ATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCT
3478899 TCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGT
64 TCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGT
* * *
3478964 TTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCTTTCGGGAG
129 TTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAG
3479029 CTTT
193 CTTT
* * * * *
3479033 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAACCTTC
1 ATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
* *
3479098 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCC-AAAA-CCTTCGGGTCATCTGTAAGCCCT
66 GGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC-GG------G--AG--CT
* *
3479161 TTAGTGCATGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAA
120 TT--T---TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC--
3479226 AAAAGCCTTCGGGAGCTTT
178 AAAAGCCTTCGGGAGCTTT
*
3479245 TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCTGTTTTCAA
1 ATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGA-------TGTTTTCAA
3479310 AACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
59 AACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* * *
3479375 GATGTTTTCAAAACCTTAGGGACATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
124 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTC
3479440 GGGAGCTTT
188 GGGAGCTTT
* * * * *
3479449 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAACCTTC
1 ATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
* * * * * * * *
3479514 GAGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCC-AAAA-CCTTCGGG-TC-ATCTGTAAGCC
66 GGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG-ATG-T
* ** * * * ** *** *** *
3479575 CTTCAGTGCATGA-TGTTTTCAAAAAAG-CCTTCGGGAGCTTTTTGATGTTTTCAAAA-CCTTCG
129 TTTCAAAGCCTTAGGGTCATC-TGTAAGTCCTTC---AG-TGCATGATGTTTCCAAAAGCCTTCG
* *
3479637 GGTCATCTGT
189 GG--AGCTTT
** *** * * * *** ** ** *
3479647 A--A-GCCCTTC-AGTGCAT-GATGT-TTCCAAAAAGCATTTGGGAT-CTTTTTGATGTTTTCAA
1 ATGATG-TTTTCAAAACCTTCG-GGTCAT-CTGTAAGCCCTTCAG-TGC---ATGATGTTTTCAA
* *
3479705 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
59 AACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
3479770 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAA-CCTTCG
124 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTC-
3479834 GGTCATCTGTAAGTCCTTCAGT
188 GG------G--AG--CTT---T
3479856 GCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCT
1 --ATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCT
* * * *
3479921 TAGGGTCATCTGTAAGTCCTATAGTGCATGATGTTTCCAAAAAGTCTTCGGAAGCTTTTTGATGT
64 TCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGT
*
3479986 TTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAA-CCTTCGGGTCA
129 TTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTC-GG---
3480050 TCTGTAAGTCCTTCAGT
190 ---G--AG--CTT---T
*
3480067 GCATGATGTTTTCAAAACCTTCGGGTTATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAACCT
1 --ATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCT
3480131 TCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGT
64 TCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGT
* * *
3480196 TTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCTTTCGGGAG
129 TTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAG
3480261 CTTT
193 CTTT
* * * * *
3480265 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAACCTTC
1 ATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
* *
3480330 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCC-AAAA-CCTTCGGGTCATCTGTAAGCCCT
66 GGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC-GG------G--AG--CT
* *
3480393 TTAGTGCATGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAA
120 TT--T---TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC--
3480458 AAAAGCCTTCGGGAGCTTT
178 AAAAGCCTTCGGGAGCTTT
*
3480477 TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCTGTTTTCAA
1 ATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGA-------TGTTTTCAA
3480542 AACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
59 AACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* * *
3480607 GATGTTTTCAAAACCTTAGGGACATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
124 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTC
3480672 GGGAGCTTT
188 GGGAGCTTT
* * * * *
3480681 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAACCTTC
1 ATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
* * *
3480746 GAGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCC-AAAA-CCTTCGGG
66 GGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGG
3480794 TCATCTGTAA
Statistics
Matches: 1687, Mismatches: 171, Indels: 216
0.81 0.08 0.10
Matches are distributed among these distances:
193 3 0.00
194 12 0.01
195 50 0.03
196 83 0.05
197 257 0.15
198 68 0.04
199 5 0.00
200 19 0.01
201 15 0.01
202 8 0.00
203 2 0.00
204 141 0.08
205 101 0.06
206 11 0.01
208 4 0.00
209 1 0.00
210 121 0.07
211 494 0.29
212 144 0.09
213 9 0.01
214 17 0.01
215 2 0.00
219 98 0.06
220 12 0.01
221 10 0.01
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (196 bp):
ATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC
GGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTT
TCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGGGAGCTT
T
Found at i:3478798 original size:45 final size:45
Alignment explanation
Indices: 3478747--3478950 Score: 336
Period size: 45 Copynumber: 4.5 Consensus size: 45
3478737 GGAAGCTTTT
* *
3478747 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
3478792 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* *
3478837 TGATGTTTTCAAAACCTTCGGGTTATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
3478882 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
3478927 TGATGTTTCCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
3478951 AGCTTTTTGA
Statistics
Matches: 149, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
45 137 0.92
46 4 0.03
47 8 0.05
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:3478900 original size:90 final size:90
Alignment explanation
Indices: 3478747--3479227 Score: 351
Period size: 90 Copynumber: 5.2 Consensus size: 90
3478737 GGAAGCTTTT
* * *
3478747 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
*
3478812 GGTCATCTGTAAGTCCTTCAGTGCA
66 GGTCATCTGTAAGTCCTACAGTGCA
*
3478837 TGATGTTTTCAAAACCTTCGGGTTATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
3478902 GGTCATCTGTAAGTCCTACAGTGCA
66 GGTCATCTGTAAGTCCTACAGTGCA
* * * * * ** *** * * *
3478927 TGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATG-TTTTCAAAACCTTAGGGTCATCTGT-A
1 TGATGTTTTC-AAAA-CCTTCGGG-TCATCTGT-AAGCCCTTCAGTGCATGA-TGT--T-T-TCA
** * * * * * * * *
3478989 AGTCCTAC-AGTGCATGATGTTTCCAAAAAG-CTTTCGGGAGCT
57 AAACCTTCGGGT-CAT-CTG--T-----AAGTCCTAC-AGTGCA
** * * * *
3479031 TTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAACCT
1 TGA---TGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCT
* *
3479096 TCGGGTCATCTGTAAGCCCTTCAGTGCA
63 TCGGGTCATCTGTAAGTCCTACAGTGCA
* * *
3479124 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAGCCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* *
3479189 GGTCATCTGTAAGCCCTTCAGTGCA
66 GGTCATCTGTAAGTCCTACAGTGCA
*
3479214 TGATGTTTCCAAAA
1 TGATGTTTTCAAAA
3479228 AAGCCTTCGG
Statistics
Matches: 299, Mismatches: 65, Indels: 54
0.72 0.16 0.13
Matches are distributed among these distances:
90 188 0.63
91 4 0.01
92 18 0.06
93 11 0.04
94 4 0.01
95 3 0.01
96 10 0.03
97 3 0.01
98 1 0.00
99 1 0.00
100 2 0.01
101 10 0.03
102 3 0.01
103 3 0.01
104 12 0.04
105 17 0.06
106 3 0.01
107 6 0.02
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.35
Consensus pattern (90 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
GGTCATCTGTAAGTCCTACAGTGCA
Found at i:3479102 original size:45 final size:45
Alignment explanation
Indices: 3479034--3479227 Score: 325
Period size: 45 Copynumber: 4.3 Consensus size: 45
3479024 GGGAGCTTTT
* * * *
3479034 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
3479079 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
3479124 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCA
1 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
3479169 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
3479214 TGATGTTTCCAAAA
1 TGATGTTTCCAAAA
3479228 AAGCCTTCGG
Statistics
Matches: 139, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 139 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.34
Consensus pattern (45 bp):
TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:3479295 original size:45 final size:45
Alignment explanation
Indices: 3479246--3479366 Score: 134
Period size: 52 Copynumber: 2.5 Consensus size: 45
3479236 GGGAGCTTTT
*
3479246 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
*
3479291 TGATGTTTCCTGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCA
1 TGA-------TGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
*
3479343 TGATGTTTCCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
3479367 AGCTTTTTGA
Statistics
Matches: 64, Mismatches: 3, Indels: 16
0.77 0.04 0.19
Matches are distributed among these distances:
45 9 0.14
46 4 0.06
47 8 0.12
52 43 0.67
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
Found at i:3479306 original size:52 final size:52
Alignment explanation
Indices: 3479249--3479352 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
3479239 AGCTTTTTGA
*
3479249 TGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCC
1 TGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTCC
*
3479301 TGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC
1 TGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTCC
3479353 AAAAAGCCTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (52 bp):
TGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTCC
Found at i:3479385 original size:76 final size:76
Alignment explanation
Indices: 3479301--3479508 Score: 380
Period size: 76 Copynumber: 2.7 Consensus size: 76
3479291 TGATGTTTCC
*
3479301 TGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGG
1 TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGG
3479366 GAGCTTTTTGA
66 GAGCTTTTTGA
*
3479377 TGTTTTCAAAACCTTAGGGACATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGG
1 TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGG
3479442 GAGCTTTTTGA
66 GAGCTTTTTGA
* *
3479453 TGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAA
1 TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAA
3479509 CCTTCGAGTC
Statistics
Matches: 127, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 127 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (76 bp):
TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGG
GAGCTTTTTGA
Found at i:3479416 original size:128 final size:129
Alignment explanation
Indices: 3479124--3479671 Score: 461
Period size: 122 Copynumber: 4.4 Consensus size: 129
3479114 CTTCAGTGCA
* * * **
3479124 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCATGA-------TGTTTTCAAA
1 TGATGTTTTCAAAACCTTAGGGACATCTGTAAGCCCTACAGTGCATGATGTTTCCTGTTTTCAAA
* *
3479182 GCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
66 ACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
* * *
3479246 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCTGTTTTCAAA
1 TGATGTTTTCAAAACCTTAGGGACATCTGTAAGCCCTACAGTGCATGATGTTTCCTGTTTTCAAA
*
3479311 ACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTT
66 ACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
* *
3479374 TGATGTTTTCAAAACCTTAGGGACATCTGTAAGTCCTACAGTGCATGATGTTTCC------AAAA
1 TGATGTTTTCAAAACCTTAGGGACATCTGTAAGCCCTACAGTGCATGATGTTTCCTGTTTTCAAA
* * * * ** * ** * * ** ***
3479433 AGCCTTCGGGAGC-TTTTTGATG-TTTTCAAAGCCTTA-GGGT-CATCTGTAAGTCCTTC---AG
66 A-CCTTCGGG-TCATCTGT-AAGCCCTACAGTGCATGATGTTTCCA--AAAAAG-CCTTCGGGAG
***
3479491 -TGCA
125 CTTTT
* * * * *
3479495 TGATGTTTCCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCATGATGTTT-C------CAAA
1 TGATGTTTTCAAAACCTTAGGGACATCTGTAAGCCCTACAGTGCATGATGTTTCCTGTTTTCAAA
* *
3479553 ACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAAGCCTTCGGGAGCTTTT
66 ACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
* * *
3479617 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCC
1 TGATGTTTTCAAAACCTTAGGGACATCTGTAAGCCCTACAGTGCATGATGTTTCC
3479672 AAAAAGCATT
Statistics
Matches: 347, Mismatches: 56, Indels: 45
0.77 0.12 0.10
Matches are distributed among these distances:
118 8 0.02
119 22 0.06
120 7 0.02
121 53 0.15
122 106 0.31
123 19 0.05
124 6 0.02
125 5 0.01
128 72 0.21
129 49 0.14
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (129 bp):
TGATGTTTTCAAAACCTTAGGGACATCTGTAAGCCCTACAGTGCATGATGTTTCCTGTTTTCAAA
ACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
Found at i:3479520 original size:45 final size:45
Alignment explanation
Indices: 3479450--3479598 Score: 244
Period size: 45 Copynumber: 3.3 Consensus size: 45
3479440 GGGAGCTTTT
* * * *
3479450 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
3479495 TGATGTTTCCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
3479540 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
3479585 TGATGTTTTCAAAA
1 TGATGTTTCCAAAA
3479599 AAGCCTTCGG
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 97 1.00
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (45 bp):
TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:3479722 original size:76 final size:76
Alignment explanation
Indices: 3479540--3480332 Score: 483
Period size: 76 Copynumber: 10.9 Consensus size: 76
3479530 CTTCAGTGCA
* * *
3479540 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAAGCCT
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATG-TTTCCAAAAAGCCT
3479605 TCGGGAGCTTTT
65 TCGGGAGCTTTT
* *
3479617 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCATT
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
* *
3479682 TGGGATCTTTT
66 CGGGAGCTTTT
* * *
3479693 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
3479758 CGGGAGCTTTT
66 CGGGAGCTTTT
* * *
3479769 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAA-CCTT
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
* * *
3479832 CGGG-TC-ATC
66 CGGGAGCTTTT
* * *** * * * ** * *
3479841 TGTAAGTCCTTCAGTGCATGA-TGT--T-T-TCAAAACCTTC-GGGTCAT-CTG--T-----AAG
1 TG-ATGT-TTTCAAAACCTTAGGGTCATCTGT-AAGCCCTTCAGTG-CATGATGTTTCCAAAAAG
* * * **
3479892 CCCTTC-AGTGCATGA
62 -CCTTCGGGAGCTTTT
* * * * *
3479907 TGTTTTC---AAAACCTTAGGGTCATCTGTAAGTCCTAT-AGTGCATGATGTTTCCAAAAAGTCT
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCCT-TCAGTGCATGATGTTTCCAAAAAGCCT
*
3479968 TCGGAAGCTTTT
65 TCGGGAGCTTTT
* * *
3479980 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAA-CCTT
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
* * *
3480043 CGGG-TC-ATC
66 CGGGAGCTTTT
* * *** * * * ** * ***
3480052 TGTAAGTCCTTCAGTGCATGA-TGT--T-T-TCAAAACCTTC-G-G---G-T-TAT-CTGTAAGC
1 TG-ATGT-TTTCAAAACCTTAGGGTCATCTGT-AAGCCCTTCAGTGCATGATGTTTCCAAAAAG-
* * * **
3480104 CCTTC-AGTGCATGA
62 CCTTCGGGAGCTTTT
* * * * * *
3480118 TGTTTTC----AAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
3480179 CGGGAGCTTTT
66 CGGGAGCTTTT
* * *
3480190 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCTTT
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
3480255 CGGGAGCTTTT
66 CGGGAGCTTTT
* *
3480266 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAA-CCTT
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
3480329 CGGG
66 CGGG
3480333 TCATCTGTAA
Statistics
Matches: 552, Mismatches: 110, Indels: 111
0.71 0.14 0.14
Matches are distributed among these distances:
60 2 0.00
61 6 0.01
62 3 0.01
63 7 0.01
64 13 0.02
65 26 0.05
66 11 0.02
67 1 0.00
68 2 0.00
69 8 0.01
70 20 0.04
71 9 0.02
72 22 0.04
73 22 0.04
74 37 0.07
75 13 0.02
76 301 0.55
77 49 0.09
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (76 bp):
TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTT
Found at i:3479818 original size:319 final size:316
Alignment explanation
Indices: 3479301--3481085 Score: 1470
Period size: 319 Copynumber: 5.5 Consensus size: 316
3479291 TGATGTTTCC
* *
3479301 TGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGG
1 TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGG
* *
3479366 GAGCTTTTTGATGTTTTCAAAACCTTAGGGACATCTGTAAGTCCTACAGTGCATGATGTTTCCAA
66 GAGCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-A
3479431 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCAT
130 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCAT
* *
3479496 GATGTTTCCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCGG
195 GATGTTTTCAAAACCTTCGAGTCATCTGTAAG-CCTTCAGTGCATGATGTTTTCAAAACCTTCGG
*
3479561 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAAGCCTTCGGGAGCTTTTTGA
259 GTCATCTGTAAGCCCTTCAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTTTTGA
* * * *
3479620 TGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCATTTGG
1 TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGG
* * *
3479685 GATCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAA
66 GAGCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-A
3479750 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCAT
130 AAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCAT
*
3479815 GATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
195 GATGTTTTCAAAACCTTCGAGTCATCTGTAAG-CCTTCAGTGCATGATGTTTTCAAAACCTTCGG
* * *
3479880 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTAGGGTCATCTGTAAGTCCTAT
259 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG--AGC--T---T--T-T
3479943 AGTGCA
314 --TG-A
* * * * * * ** * * ** ***
3479949 TGATGTTTCCAAAAAGTCTTCGGAAG-C-TTTTTGATGT-TTTCAAAGCCTTA-GGGTCATCTGT
1 TG-T-TTT-C-AAAA-CCTTAGG--GTCATCTGT-AAGTCCTTCAGTGCATGATGTTTC--CAAA
*** *
3480010 AAGTCCTTC---AG-TGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCAT
56 AAG-CCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCAT
* * *
3480071 GATGTTTTCAAAA-CCTTCGGGTTATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA-CCTTCG
120 GATGTTTCCAAAAGCCTTC-GG------G--AG--CTT---T--TTGATGTTTTCAAAGCCTTAG
* *
3480134 GGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCG-G------G--AG-CTT-
169 GGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGAGTCATCTGTAAGCCTTC
* * * *
3480188 --T--TTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAA
232 AGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAA
*
3480249 AGCTTTCGGGAGCTTTTTGA
297 AGCCTTCGGGAGCTTTTTGA
*
3480269 TGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAA-CCTTCGG
1 TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGG
* * * *
3480332 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTTAG
66 G--AGCT-T------TT---TG-ATG-T-TTT-CAAAACCTTAGGGTCATCTGTAAGTCCTTCAG
* * * * * ** ** * * * *
3480397 TGCATGATGTTTTC-AAAGCCTTCGGG-TC-ATCTGTAAGCCCTTCAGTGCATGA-TGT-TTCCA
115 TGCATGATGTTTCCAAAAGCCTTCGGGAGCTTTTTG-ATG-TTTTCAAAGCCTTAGGGTCAT-C-
*** *** *
3480457 AAAAAG-CCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
176 TGTAAGTCCTTC---AG-TGCATGATGTTTTCAAAACCTTCGAGTCATCTGTAAG-CCTTCAGTG
* *
3480521 CATGATGTTTCCTGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCA
236 CATGA-------TGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCA
3480586 AAAAGCCTTCGGGAGCTTTTTGA
294 AAAAGCCTTCGGGAGCTTTTTGA
* *
3480609 TGTTTTCAAAACCTTAGGGACATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGG
1 TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGG
*
3480674 GAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAA
66 GAGCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAA
* * * *
3480739 AA-CCTTCGAGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCGGGTCATCTGTA
131 AAGCCTTCG-G------G--AG--CTT---T--TTGATGTTTTCAAAGCCTTAGGGTCATCTGTA
* * * * ** *
3480803 AGCCCTTCAGTGCATGATGTTTTCAAAA-----AAGCCTTC-GGGAG-CTT---T--TTGATGTT
180 AGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGAGTCATCTGTAAGCCTTCAGTGCATGATGTT
* * *
3480856 TTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCATTTGGGATC
245 TTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC
3480921 TTTTTGA
310 TTTTTGA
*
3480928 TGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGG
1 TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGG
* * * * *
3480993 GAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATTTGTAAGCCCTTTAATGCATGATGTTTCCAA
66 GAGCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-A
* * *
3481058 AAAGCCTTCTGGATCTTTTCGATGTTTT
130 AAAGCCTTCGGGAGCTTTTTGATGTTTT
3481086 TAAACTCTCG
Statistics
Matches: 1188, Mismatches: 151, Indels: 268
0.74 0.09 0.17
Matches are distributed among these distances:
305 7 0.01
307 1 0.00
310 3 0.00
311 5 0.00
312 1 0.00
313 5 0.00
314 9 0.01
315 28 0.02
316 19 0.02
317 12 0.01
318 15 0.01
319 482 0.41
320 9 0.01
321 7 0.01
323 2 0.00
324 3 0.00
325 1 0.00
326 54 0.05
327 9 0.01
328 10 0.01
329 8 0.01
330 16 0.01
331 115 0.10
332 57 0.05
333 24 0.02
334 21 0.02
335 7 0.01
336 7 0.01
337 1 0.00
338 3 0.00
339 18 0.02
340 129 0.11
341 7 0.01
342 17 0.01
343 10 0.01
344 4 0.00
345 38 0.03
346 18 0.02
347 6 0.01
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (316 bp):
TGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGG
GAGCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAA
AAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATG
ATGTTTTCAAAACCTTCGAGTCATCTGTAAGCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGA
Found at i:3479822 original size:45 final size:45
Alignment explanation
Indices: 3479769--3479962 Score: 327
Period size: 45 Copynumber: 4.3 Consensus size: 45
3479759 GGGAGCTTTT
*
3479769 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
*
3479814 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
* *
3479859 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
3479904 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTAT-AGTGCA
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCT-TCAGTGCA
*
3479949 TGATGTTTCCAAAA
1 TGATGTTTTCAAAA
3479963 AGTCTTCGGA
Statistics
Matches: 142, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
45 141 0.99
46 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:3480031 original size:45 final size:45
Alignment explanation
Indices: 3479980--3480182 Score: 327
Period size: 45 Copynumber: 4.5 Consensus size: 45
3479970 GGAAGCTTTT
* *
3479980 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
3480025 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* *
3480070 TGATGTTTTCAAAACCTTCGGGTTATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
3480115 TGATGTTTTC-AAACCTTCGGGTCATCTGTAAGTCCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
3480159 TGATGTTTCCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
3480183 AGCTTTTTGA
Statistics
Matches: 147, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
44 40 0.27
45 96 0.65
46 3 0.02
47 8 0.05
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:3480172 original size:89 final size:90
Alignment explanation
Indices: 3479980--3480459 Score: 342
Period size: 90 Copynumber: 5.2 Consensus size: 90
3479970 GGAAGCTTTT
* * *
3479980 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
*
3480045 GGTCATCTGTAAGTCCTTCAGTGCA
66 GGTCATCTGTAAGTCCTACAGTGCA
*
3480070 TGATGTTTTCAAAACCTTCGGGTTATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
3480134 GGTCATCTGTAAGTCCTACAGTGCA
66 GGTCATCTGTAAGTCCTACAGTGCA
* * * * * ** *** * * *
3480159 TGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATG-TTTTCAAAACCTTAGGGTCATCTGT-A
1 TGATGTTTTC-AAAA-CCTTCGGG-TCATCTGT-AAGCCCTTCAGTGCATGA-TGT--T-T-TCA
** * * * * * * * *
3480221 AGTCCTAC-AGTGCATGATGTTTCCAAAAAG-CTTTCGGGAGCT
57 AAACCTTCGGGT-CAT-CTG--T-----AAGTCCTAC-AGTGCA
** * * * *
3480263 TTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAACCT
1 TGA---TGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCT
* *
3480328 TCGGGTCATCTGTAAGCCCTTCAGTGCA
63 TCGGGTCATCTGTAAGTCCTACAGTGCA
* * *
3480356 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAGCCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* *
3480421 GGTCATCTGTAAGCCCTTCAGTGCA
66 GGTCATCTGTAAGTCCTACAGTGCA
*
3480446 TGATGTTTCCAAAA
1 TGATGTTTTCAAAA
3480460 AAGCCTTCGG
Statistics
Matches: 297, Mismatches: 65, Indels: 56
0.71 0.16 0.13
Matches are distributed among these distances:
89 42 0.14
90 149 0.50
91 18 0.06
92 4 0.01
93 7 0.02
94 5 0.02
95 3 0.01
96 9 0.03
97 2 0.01
98 1 0.00
99 1 0.00
100 2 0.01
101 10 0.03
102 3 0.01
103 3 0.01
104 12 0.04
105 17 0.06
106 3 0.01
107 6 0.02
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.35
Consensus pattern (90 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
GGTCATCTGTAAGTCCTACAGTGCA
Found at i:3480334 original size:45 final size:45
Alignment explanation
Indices: 3480266--3480459 Score: 325
Period size: 45 Copynumber: 4.3 Consensus size: 45
3480256 GGGAGCTTTT
* * * *
3480266 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
3480311 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
3480356 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCA
1 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
3480401 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
3480446 TGATGTTTCCAAAA
1 TGATGTTTCCAAAA
3480460 AAGCCTTCGG
Statistics
Matches: 139, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 139 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.34
Consensus pattern (45 bp):
TGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:3480527 original size:45 final size:45
Alignment explanation
Indices: 3480478--3480598 Score: 134
Period size: 52 Copynumber: 2.5 Consensus size: 45
3480468 GGGAGCTTTT
*
3480478 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
*
3480523 TGATGTTTCCTGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCA
1 TGA-------TGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
*
3480575 TGATGTTTCCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
3480599 AGCTTTTTGA
Statistics
Matches: 64, Mismatches: 3, Indels: 16
0.77 0.04 0.19
Matches are distributed among these distances:
45 9 0.14
46 4 0.06
47 8 0.12
52 43 0.67
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
Done.