Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000851.1 Hibiscus syriacus cultivar Beakdansim tig00001644_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: 7304151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 30 of 31
Found at i:7038559 original size:41 final size:42
Alignment explanation
Indices: 7038402--7038742 Score: 600
Period size: 41 Copynumber: 8.2 Consensus size: 42
7038392 GCAATATTTG
7038402 GCCTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTC
1 GCCTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTC
7038444 GCCTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTC
1 GCCTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTC
7038486 GCCTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTC
1 GCCTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTC
7038528 GCCTATCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTC
1 GCCTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTC
7038569 GCCTATCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTC
1 GCCTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTC
*
7038610 GCCTATCGCAAC-AATTTGGAATGAATCGCGACGCGAACTTC
1 GCCTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTC
*
7038651 GACTATCGCAACG-ATTTGGAATGAATCGCAACGCGAACTTC
1 GCCTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTC
* **
7038692 GCCTATCGCAACGAATTTGGAATAAATCGCAAATCGAACTTC
1 GCCTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTC
*
7038734 GACTATCGC
1 GCCTATCGC
7038743 GTTGCGAATC
Statistics
Matches: 288, Mismatches: 8, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
40 2 0.01
41 154 0.53
42 132 0.46
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (42 bp):
GCCTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTC
Found at i:7045968 original size:2 final size:2
Alignment explanation
Indices: 7045961--7046000 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
7045951 ATTTTACACA
7045961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7046001 GTTATATCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7049590 original size:22 final size:23
Alignment explanation
Indices: 7049565--7049625 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
7049555 TATTATGAAG
*
7049565 ATTTATGTTGAATATTTT-GGAT
1 ATTTATGTTGAATATTTTAGCAT
*
7049587 ATTTATGATGGATATATTTTAGCAT
1 ATTTATG-TTGA-ATATTTTAGCAT
*
7049612 ATCATATGTTGAAT
1 AT-TTATGTTGAAT
7049626 TATTATTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
22 7 0.23
23 3 0.10
24 9 0.29
25 8 0.26
26 4 0.13
ACGTcount: A:0.31, C:0.03, G:0.16, T:0.49
Consensus pattern (23 bp):
ATTTATGTTGAATATTTTAGCAT
Found at i:7049629 original size:25 final size:23
Alignment explanation
Indices: 7049568--7049629 Score: 54
Period size: 25 Copynumber: 2.6 Consensus size: 23
7049558 TATGAAGATT
* *
7049568 TATGTTGAA-TATTTTGGATATT
1 TATGTTGAATTATTTTGCATATA
* *
7049590 TATGATGGATATATTTTAGCATATCA
1 TATGTTGAAT-TATTTT-GCATAT-A
7049616 TATGTTGAATTATT
1 TATGTTGAATTATT
7049630 ATTATCTTGG
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
22 7 0.23
24 6 0.20
25 9 0.30
26 8 0.27
ACGTcount: A:0.31, C:0.03, G:0.16, T:0.50
Consensus pattern (23 bp):
TATGTTGAATTATTTTGCATATA
Found at i:7051149 original size:20 final size:21
Alignment explanation
Indices: 7051118--7051156 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
7051108 ACTTTACAAT
7051118 TTTGGAAAGTTTCAAAACTCC
1 TTTGGAAAGTTTCAAAACTCC
*
7051139 TTTGG-AAGTTTCGAAACT
1 TTTGGAAAGTTTCAAAACT
7051157 TCTGGTCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (21 bp):
TTTGGAAAGTTTCAAAACTCC
Found at i:7055447 original size:29 final size:30
Alignment explanation
Indices: 7055405--7055536 Score: 178
Period size: 29 Copynumber: 4.4 Consensus size: 30
7055395 CCCGAAGGAC
7055405 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCACAAAGATCCCCGGTAA
7055434 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCACAAAGATCCCCGGTAA
* *
7055463 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCCCGGTAA
* * *
7055493 CTGTCCAGAGGTCATAAAGATCCTCGGTAAA
1 CTATCCAGAGGTCACAAAGATCCCCGGT-AA
* *
7055524 CTGTCCATAGGTC
1 CTATCCAGAGGTC
7055537 CGAAGAACCT
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
29 48 0.49
30 35 0.36
31 14 0.14
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGATCCCCGGTAA
Found at i:7055506 original size:59 final size:60
Alignment explanation
Indices: 7055405--7055536 Score: 178
Period size: 59 Copynumber: 2.2 Consensus size: 60
7055395 CCCGAAGGAC
7055405 CTATCCAGAGGTCACAAAGACCCCGGTAACTATCCAGAGGTCACAAAGA-CCCCGGT-AA
1 CTATCCAGAGGTCACAAAGACCCCGGTAACTATCCAGAGGTCACAAAGATCCCCGGTAAA
* * * * *
7055463 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAAA
1 CTATCCAGAGGTCACAAAGA-CCCCGGTAACTATCCAGAGGTCACAAAGATCCCCGGTAAA
* *
7055524 CTGTCCATAGGTC
1 CTATCCAGAGGTC
7055537 CGAAGAACCT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
58 19 0.30
59 26 0.41
60 6 0.09
61 13 0.20
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (60 bp):
CTATCCAGAGGTCACAAAGACCCCGGTAACTATCCAGAGGTCACAAAGATCCCCGGTAAA
Found at i:7055554 original size:30 final size:31
Alignment explanation
Indices: 7055491--7055584 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 31
7055481 GATCCTCGGT
* ** * *
7055491 AACTGTCCAGAGGTCATAAAGATCCTCGGTA
1 AACTGTCCATAGGTCACGAAGAACCTAGGTA
7055522 AACTGTCCATAGGTC-CGAAGAACCTAGGTA
1 AACTGTCCATAGGTCACGAAGAACCTAGGTA
* * * *
7055552 AACTGTCTATATGTCTCGAAG-ACATAGGTA
1 AACTGTCCATAGGTCACGAAGAACCTAGGTA
7055582 AAC
1 AAC
7055585 CCTCGACTCT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
30 35 0.65
31 19 0.35
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (31 bp):
AACTGTCCATAGGTCACGAAGAACCTAGGTA
Found at i:7056070 original size:2 final size:2
Alignment explanation
Indices: 7056063--7056091 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
7056053 TATACAATTC
7056063 AT AT AT AT AT -T 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
7056092 CTAACTCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:7056666 original size:21 final size:21
Alignment explanation
Indices: 7056636--7056680 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
7056626 ATTCTGTCGT
* *
7056636 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
7056657 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
7056678 TTG
1 TTG
7056681 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:7059938 original size:30 final size:30
Alignment explanation
Indices: 7059879--7059981 Score: 145
Period size: 30 Copynumber: 3.4 Consensus size: 30
7059869 CCCGAAGGAC
* *
7059879 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
7059908 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
7059938 CTGTCCAGAGGTCATAAAGATCCTCGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGT-AA
* *
7059969 CTGTCCATAGGTC
1 CTATCCAGAGGTC
7059982 CCGAAGAACC
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 19 0.28
30 35 0.51
31 14 0.21
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:7059974 original size:31 final size:30
Alignment explanation
Indices: 7059882--7060004 Score: 140
Period size: 30 Copynumber: 4.1 Consensus size: 30
7059872 GAAGGACCTA
* *
7059882 TCCAGAGGTCACAAAGA-CCCCGGTAACTA
1 TCCAGAGGTCACAAAGATCCTCGGTAACTG
*
7059911 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGATCCTCGGTAACTG
*
7059941 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCACAAAGATCCTCGGT-AACTG
* * * * *
7059972 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCAGAGGTCACAAAGATCCTCGGT-AACTG
7060003 TC
1 TC
7060005 TATATGTCTC
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
29 16 0.19
30 35 0.42
31 32 0.39
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGATCCTCGGTAACTG
Found at i:7060027 original size:31 final size:31
Alignment explanation
Indices: 7059963--7060031 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
7059953 AAAGATCCTC
*
7059963 GGTAAACTGTCCATAGGTCCCGAAGAACCTA
1 GGTAAACTGTCCATAGGTCCCGAAGAACATA
* * *
7059994 GGTAAACTGTCTATATGTCTCGAA-AGACATA
1 GGTAAACTGTCCATAGGTCCCGAAGA-ACATA
7060025 GGTAAAC
1 GGTAAAC
7060032 CCCGACTTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 1 0.03
31 32 0.97
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (31 bp):
GGTAAACTGTCCATAGGTCCCGAAGAACATA
Found at i:7061111 original size:21 final size:21
Alignment explanation
Indices: 7061081--7061125 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
7061071 ATTCTGTCGT
* *
7061081 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
7061102 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
7061123 TTG
1 TTG
7061126 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:7062623 original size:11 final size:11
Alignment explanation
Indices: 7062607--7062638 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
7062597 AAATAATTAC
*
7062607 GATTCAAATTT
1 GATTCAAATAT
7062618 GATTCAAATAT
1 GATTCAAATAT
7062629 GATTCAAATA
1 GATTCAAATA
7062639 CATAACTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (11 bp):
GATTCAAATAT
Found at i:7064055 original size:63 final size:63
Alignment explanation
Indices: 7063983--7064108 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
7063973 TCTTAGTTTA
7063983 ATCCTTGTGGTTAAAGATTTTCCAACAGATGATCTAATATAATGAAATCCCAAACAGCGCATT
1 ATCCTTGTGGTTAAAGATTTTCCAACAGATGATCTAATATAATGAAATCCCAAACAGCGCATT
7064046 ATCCTTGTGGTTAAAGATTTTCCAACAGATGATCTAATATAATGAAATCCCAAACAGCGCATT
1 ATCCTTGTGGTTAAAGATTTTCCAACAGATGATCTAATATAATGAAATCCCAAACAGCGCATT
7064109 CACCTCTTAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (63 bp):
ATCCTTGTGGTTAAAGATTTTCCAACAGATGATCTAATATAATGAAATCCCAAACAGCGCATT
Found at i:7065849 original size:24 final size:24
Alignment explanation
Indices: 7065817--7065875 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
7065807 ATCAATTCAA
*
7065817 CCCTCGAAGTTGTCTTTATCCTAG
1 CCCTCGAAGTCGTCTTTATCCTAG
7065841 CCCTCGAAGTCGTCTTTATCCTAG
1 CCCTCGAAGTCGTCTTTATCCTAG
*
7065865 CACTCGAAGTC
1 CCCTCGAAGTC
7065876 CGTTAATTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.19, C:0.32, G:0.17, T:0.32
Consensus pattern (24 bp):
CCCTCGAAGTCGTCTTTATCCTAG
Found at i:7067294 original size:17 final size:17
Alignment explanation
Indices: 7067272--7067362 Score: 66
Period size: 17 Copynumber: 5.6 Consensus size: 17
7067262 CTTGTAAAAT
7067272 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
** **
7067289 AAATATAAAAAATTTATT
1 AAATAT-TTAAATTTAAA
7067307 AAATATTTAAA--T---
1 AAATATTTAAATTTAAA
7067319 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
** **
7067336 AAATATAAAAATTTATT
1 AAATATTTAAATTTAAA
7067353 AAATATTTAA
1 AAATATTTAA
7067363 TCAAATAGTG
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
12 11 0.20
14 1 0.02
15 1 0.02
17 30 0.54
18 13 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:7067310 original size:18 final size:17
Alignment explanation
Indices: 7067289--7067341 Score: 52
Period size: 20 Copynumber: 2.9 Consensus size: 17
7067279 TAAATTTAAA
*
7067289 AAATATAAAAAATTTATT
1 AAATATAAAAAATAT-TT
7067307 AAATATTTAAATAAATATTT
1 AAATA--TAAA-AAATATTT
*
7067327 AAATTTAAAAAATAT
1 AAATATAAAAAATAT
7067342 AAAAATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 6 0.20
18 9 0.30
20 10 0.33
21 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATAAAAAATATTT
Found at i:7067321 original size:12 final size:12
Alignment explanation
Indices: 7067306--7067330 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7067296 AAAAATTTAT
7067306 TAAATATTTAAA
1 TAAATATTTAAA
7067318 TAAATATTTAAA
1 TAAATATTTAAA
7067330 T
1 T
7067331 TTAAAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAATATTTAAA
Found at i:7067369 original size:46 final size:47
Alignment explanation
Indices: 7067268--7067362 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
7067258 TGGTCTTGTA
7067268 AAATAAATATTTAAATTTAAAAAATATAAAAAATTTATTAAATATTT
1 AAATAAATATTTAAATTTAAAAAATATAAAAAATTTATTAAATATTT
7067315 AAATAAATATTTAAATTTAAAAAATAT-AAAAATTTATTAAATATTT
1 AAATAAATATTTAAATTTAAAAAATATAAAAAATTTATTAAATATTT
7067361 AA
1 AA
7067363 TCAAATAGTG
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 21 0.44
47 27 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (47 bp):
AAATAAATATTTAAATTTAAAAAATATAAAAAATTTATTAAATATTT
Found at i:7068274 original size:24 final size:24
Alignment explanation
Indices: 7068247--7068377 Score: 95
Period size: 24 Copynumber: 5.9 Consensus size: 24
7068237 TTATCTTACA
7068247 TAATTTATTTATTTTAATAATAGT
1 TAATTTATTTATTTTAATAATAGT
*
7068271 TAATTTTTTTATTTTAAT-A-A--
1 TAATTTATTTATTTTAATAATAGT
*
7068291 TAATTT-TTTA--TTAATAATAAT
1 TAATTTATTTATTTTAATAATAGT
* * * *
7068312 T-ATTGAATGATTTTAAT-A-CG-
1 TAATTTATTTATTTTAATAATAGT
*
7068332 TAATTTTTTTATTTTAATAATAGT
1 TAATTTATTTATTTTAATAATAGT
* * *
7068356 TGAGTAATTTATTTTAATAATA
1 TAATTTATTTATTTTAATAATA
7068378 TTTGAGTGAT
Statistics
Matches: 81, Mismatches: 15, Indels: 22
0.69 0.13 0.19
Matches are distributed among these distances:
17 5 0.06
18 1 0.01
19 5 0.06
20 10 0.12
21 15 0.19
22 3 0.04
23 7 0.09
24 35 0.43
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.56
Consensus pattern (24 bp):
TAATTTATTTATTTTAATAATAGT
Found at i:7068291 original size:17 final size:18
Alignment explanation
Indices: 7068271--7068312 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
7068261 TAATAATAGT
7068271 TAATTTTTTTATTTTAATAA
1 TAATTTTTTTA--TTAATAA
7068291 TAA-TTTTTTATTAATAA
1 TAATTTTTTTATTAATAA
7068308 TAATT
1 TAATT
7068313 ATTGAATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 10 0.48
18 1 0.05
19 7 0.33
20 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TAATTTTTTTATTAATAA
Found at i:7068305 original size:41 final size:41
Alignment explanation
Indices: 7068246--7068377 Score: 124
Period size: 44 Copynumber: 3.1 Consensus size: 41
7068236 TTTATCTTAC
**
7068246 ATAATTTATTTATTTTAATAATAGTTAATTTTTTTATTTTAATA
1 ATAATTT-TTTA-TTTAATAATAGTT-ATTAATTTATTTTAATA
* *
7068290 ATAATTTTTTA-TTAATAATAATTATTGAA-TGATTTTAATA
1 ATAATTTTTTATTTAATAATAGTTATT-AATTTATTTTAATA
* *
7068330 CGTAATTTTTTTATTTTAATAATAGTTGAGTAATTTATTTTAATA
1 -ATAA-TTTTTTA-TTTAATAATAGTT-ATTAATTTATTTTAATA
7068375 ATA
1 ATA
7068378 TTTGAGTGAT
Statistics
Matches: 72, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
40 13 0.18
41 14 0.19
42 7 0.10
43 4 0.06
44 22 0.31
45 12 0.17
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (41 bp):
ATAATTTTTTATTTAATAATAGTTATTAATTTATTTTAATA
Found at i:7068363 original size:28 final size:28
Alignment explanation
Indices: 7068331--7068390 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 28
7068321 ATTTTAATAC
7068331 GTAATTTTTTTATTTTAATAATAGTTGA
1 GTAATTTTTTTATTTTAATAATAGTTGA
*
7068359 GTAA----TTTATTTTAATAATATTTGA
1 GTAATTTTTTTATTTTAATAATAGTTGA
*
7068383 GTGATTTT
1 GTAATTTT
7068391 AATGATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
24 22 0.85
28 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.57
Consensus pattern (28 bp):
GTAATTTTTTTATTTTAATAATAGTTGA
Found at i:7068382 original size:24 final size:24
Alignment explanation
Indices: 7068339--7068389 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
7068329 ACGTAATTTT
7068339 TTTATTTTAATAATAGTTGAGTAA
1 TTTATTTTAATAATAGTTGAGTAA
* *
7068363 TTTATTTTAATAATATTTGAGTGA
1 TTTATTTTAATAATAGTTGAGTAA
7068387 TTT
1 TTT
7068390 TAATGATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (24 bp):
TTTATTTTAATAATAGTTGAGTAA
Found at i:7074765 original size:254 final size:263
Alignment explanation
Indices: 7074450--7074967 Score: 930
Period size: 254 Copynumber: 2.0 Consensus size: 263
7074440 CTATGCTGTG
7074450 GTTAGACAGCCTTCCTGTTAGCCTTCTTTCTTTGAAATTCTTTGATGATATTGTAAAATATTTCT
1 GTTAGACAGCCTTCCTGTTAGCCTTCTTTCTTTGAAATTCTTTGATGATATTGTAAAATATTTCT
*
7074515 TACTGAAATTAGTAGATA-T-AATA-GTCAATGAAGAACAGCTTTATGCCCAAAATCTTTGCATG
66 TACTGAAATTAGTAGATACTAAATATGTCAATGAAGAACAGCTTTATGCACAAAATCTTTGCATG
7074577 AAGCTCCTAGTTTACTCTCGCTCGCTACAG-TATT-TCAGGATTATTGCTGAACTATTGAA-G-G
131 AAGCTCCTAGTTTACTCTCGCTCGCTACAGTTATTCT-AGGATTATTGCTGAACTATTGAATGAG
7074638 GGTAATCACATCTAA-GTGCTTATTGGCCTGTCAAAA-TC-TGTAGTTGGTGATTCTTGATTCCT
195 GGTAATCACATCTAAGGTGCTTATTGGCCTGTCAAAATTCTTGTAGTTGGTGATTCTTGATTCCT
7074700 CAAA
260 CAAA
7074704 GTTAGACAGCCTTCCTGTTAGCCTTCTTTCTTTGAAATTCTTTGATGATATTGTAAAATATTTCT
1 GTTAGACAGCCTTCCTGTTAGCCTTCTTTCTTTGAAATTCTTTGATGATATTGTAAAATATTTCT
7074769 TACTGAAATTAGTAGATATCTAAATATGTCAATGAAGAACAGCTTTATGCACAAAATCTTTGCAT
66 TACTGAAATTAGTAGATA-CTAAATATGTCAATGAAGAACAGCTTTATGCACAAAATCTTTGCAT
7074834 GAAGCTCCTAGTTTACTCTCGCTCGCTACAGTTATTCTAGGATTATTGCTGAACTATTGAATGAG
130 GAAGCTCCTAGTTTACTCTCGCTCGCTACAGTTATTCTAGGATTATTGCTGAACTATTGAATGAG
*
7074899 GTTAATCACATCTAAGGTGCTTATTGGCCTGTCAAAATTCTTGTAGTTGGTGATTCTTGATTCCT
195 GGTAATCACATCTAAGGTGCTTATTGGCCTGTCAAAATTCTTGTAGTTGGTGATTCTTGATTCCT
7074964 CAAA
260 CAAA
7074968 TCTCAGTGAA
Statistics
Matches: 251, Mismatches: 2, Indels: 12
0.95 0.01 0.05
Matches are distributed among these distances:
254 83 0.33
256 1 0.00
257 4 0.02
258 68 0.27
259 27 0.11
260 2 0.01
261 15 0.06
262 21 0.08
263 2 0.01
264 28 0.11
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (263 bp):
GTTAGACAGCCTTCCTGTTAGCCTTCTTTCTTTGAAATTCTTTGATGATATTGTAAAATATTTCT
TACTGAAATTAGTAGATACTAAATATGTCAATGAAGAACAGCTTTATGCACAAAATCTTTGCATG
AAGCTCCTAGTTTACTCTCGCTCGCTACAGTTATTCTAGGATTATTGCTGAACTATTGAATGAGG
GTAATCACATCTAAGGTGCTTATTGGCCTGTCAAAATTCTTGTAGTTGGTGATTCTTGATTCCTC
AAA
Found at i:7078457 original size:21 final size:21
Alignment explanation
Indices: 7078431--7078566 Score: 138
Period size: 21 Copynumber: 6.6 Consensus size: 21
7078421 GTTTCCAGAT
* *
7078431 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
7078452 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
7078473 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
7078494 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
7078514 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
7078534 TCGCAATGCGATAGTCGG-CTA
1 TCGCAATGCGA-ACTTGGACTA
7078555 TCGCAATGCGAA
1 TCGCAATGCGAA
7078567 TATGTAAATC
Statistics
Matches: 104, Mismatches: 7, Indels: 9
0.87 0.06 0.08
Matches are distributed among these distances:
20 34 0.33
21 69 0.66
22 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:7078518 original size:20 final size:20
Alignment explanation
Indices: 7078493--7078580 Score: 124
Period size: 20 Copynumber: 4.3 Consensus size: 20
7078483 AACTTGGACT
7078493 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
7078513 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
***
7078533 ATCGCAATGCG-ATAGTCGGCT
1 ATCGCAATGCGAATA-T-GTAA
7078554 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
7078574 ATCGCAA
1 ATCGCAA
7078581 CGACTGGTTG
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.05
20 40 0.68
21 13 0.22
22 3 0.05
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:7078672 original size:6 final size:6
Alignment explanation
Indices: 7078661--7078688 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
7078651 AGACACGTAT
7078661 GACCAC GACCAC GACCAC GACCAC GACC
1 GACCAC GACCAC GACCAC GACCAC GACC
7078689 CGAGACGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.50, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:7079206 original size:20 final size:22
Alignment explanation
Indices: 7079168--7079211 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
7079158 GCCGCCGCCT
7079168 GTCTCGTCGGTTCGTGGTCGTG
1 GTCTCGTCGGTTCGTGGTCGTG
7079190 GTCTCGT-GGTT-GTGGTCGTG
1 GTCTCGTCGGTTCGTGGTCGTG
7079210 GT
1 GT
7079212 AATACGTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 11 0.50
21 4 0.18
22 7 0.32
ACGTcount: A:0.00, C:0.18, G:0.43, T:0.39
Consensus pattern (22 bp):
GTCTCGTCGGTTCGTGGTCGTG
Found at i:7079352 original size:21 final size:20
Alignment explanation
Indices: 7079322--7079497 Score: 135
Period size: 21 Copynumber: 8.6 Consensus size: 20
7079312 AATATGTAAA
*
7079322 TCGCAATGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAA-T
* *
7079343 TCGCATTGCGATAGTCGACT
1 TCGCATTGCGATAGTCCAAT
* *
7079363 ATCGCATTGCGAT-TTACATAT
1 -TCGCATTGCGATAGTCCA-AT
*
7079384 TCGCATTGCGATAG-CCGACT
1 TCGCATTGCGATAGTCC-AAT
* *
7079404 ATCGCATTGCGAT-TTACATAT
1 -TCGCATTGCGATAGTCCA-AT
* *
7079425 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGTCCA-AT
7079445 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAA-T
*
7079466 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAA-T
*
7079487 TCGCGTTGCGA
1 TCGCATTGCGA
7079498 ATCTGGAAAC
Statistics
Matches: 129, Mismatches: 17, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
20 51 0.40
21 78 0.60
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (20 bp):
TCGCATTGCGATAGTCCAAT
Found at i:7079387 original size:41 final size:41
Alignment explanation
Indices: 7079342--7079483 Score: 184
Period size: 41 Copynumber: 3.5 Consensus size: 41
7079332 ATAGTCCAAG
7079342 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
*
7079383 TTCGCATTGCGATAGCCGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
* * *
7079424 TTCGCATTGCGAT--T-TACATATTCGCATTGCGATAGTCCA-A
1 TTCGCATTGCGATAGTCGAC-TA-TCGCATTGCGAT-TTACATA
7079464 GTTCGCATTGCGATAGTCGA
1 -TTCGCATTGCGATAGTCGA
7079484 AGTTCGCGTT
Statistics
Matches: 88, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
38 2 0.02
39 2 0.02
40 13 0.15
41 69 0.78
43 1 0.01
44 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (41 bp):
TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
Found at i:7079389 original size:20 final size:20
Alignment explanation
Indices: 7079364--7079456 Score: 134
Period size: 20 Copynumber: 4.6 Consensus size: 20
7079354 TAGTCGACTA
7079364 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
***
7079384 TCGCATTGCGATAGCCGACTA-
1 TCGCATTGCGATTTAC-A-TAT
7079405 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
7079425 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
7079445 TCGCATTGCGAT
1 TCGCATTGCGAT
7079457 AGTCCAAGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.03
20 46 0.72
21 14 0.22
22 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:7085677 original size:37 final size:36
Alignment explanation
Indices: 7085602--7085677 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
7085592 TTTTTATATT
*
7085602 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
7085638 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
7085675 TTT
1 TTT
7085678 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:7085859 original size:20 final size:20
Alignment explanation
Indices: 7085823--7085860 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7085813 ATCCTATTCC
**
7085823 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
7085843 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
7085861 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:7085876 original size:23 final size:23
Alignment explanation
Indices: 7085849--7085894 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
7085839 CCCACTGGTA
7085849 ATCTTACATTCCGTGAACCAAAC
1 ATCTTACATTCCGTGAACCAAAC
7085872 ATCTTACATTCCGTGAACCAAAC
1 ATCTTACATTCCGTGAACCAAAC
7085895 GCATCCTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.30, G:0.09, T:0.26
Consensus pattern (23 bp):
ATCTTACATTCCGTGAACCAAAC
Found at i:7086243 original size:4 final size:4
Alignment explanation
Indices: 7086234--7086258 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
7086224 TGATGTAAGA
7086234 TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT T
7086259 TTGTTCATCT
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:7088490 original size:23 final size:23
Alignment explanation
Indices: 7088464--7088508 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
7088454 CACCACAGCT
*
7088464 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
* *
7088487 CGTAGAATTTCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
7088509 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:7088676 original size:150 final size:149
Alignment explanation
Indices: 7088476--7088752 Score: 493
Period size: 150 Copynumber: 1.9 Consensus size: 149
7088466 TATAATTGCA
* *
7088476 CCGAAGTGCCGCGTAGAATTTCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATAAT
1 CCGAAGTGCCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
* *
7088541 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGTT
66 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTT-CAAGACCTCACACATGTT
7088606 CCACAGAATATATATATATC
130 CCACAGAATATATATATATC
7088626 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
7088690 TTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACCTCACACATG
65 TTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACCTCACACATG
7088753 ATGTGTGGCT
Statistics
Matches: 122, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
149 16 0.13
150 106 0.87
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGTGCCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACCTCACACATGTTC
CACAGAATATATATATATC
Found at i:7097171 original size:150 final size:149
Alignment explanation
Indices: 7096979--7097286 Score: 553
Period size: 150 Copynumber: 2.1 Consensus size: 149
7096969 CACCGAAATG
*
7096979 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
* * *
7097044 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGTTCCACAGAA
66 AATCATATACATATACTAAGGATCAAGTATGTGTCTTT-CAAGACCTCACACATGTTCCAAAGAA
*
7097109 TATATATATATCCCGAAGGA
130 TATACATATATCCCGAAGGA
7097129 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
7097194 AATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACCTCACACATGTTCCAAAGAAT
66 AATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACCTCACACATGTTCCAAAGAAT
*
7097259 ATACATATGTCCCGAAGGA
131 ATACATATATCCCGAAGGA
7097278 CCGCGTAGA
1 CCGCGTAGA
7097287 CCCTCTACCC
Statistics
Matches: 152, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
149 51 0.34
150 101 0.66
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
AATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACCTCACACATGTTCCAAAGAAT
ATACATATATCCCGAAGGA
Found at i:7101149 original size:13 final size:13
Alignment explanation
Indices: 7101131--7101161 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
7101121 AACCCTTTAA
7101131 TTTTATATAAAAT
1 TTTTATATAAAAT
7101144 TTTTATATAAAAT
1 TTTTATATAAAAT
7101157 TTTTA
1 TTTTA
7101162 ATTAGGGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTTATATAAAAT
Found at i:7102098 original size:25 final size:26
Alignment explanation
Indices: 7102054--7102103 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
7102044 CAGAAAATCA
*
7102054 TTAAAAGTTTAACAG-CCTTTAATAG
1 TTAAAAGTTTAACAGACTTTTAATAG
*
7102079 TTAAAAGTTTAACGGACTTTTAATA
1 TTAAAAGTTTAACAGACTTTTAATA
7102104 ACCACGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (26 bp):
TTAAAAGTTTAACAGACTTTTAATAG
Found at i:7117700 original size:2 final size:2
Alignment explanation
Indices: 7117693--7117732 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
7117683 TAAAGAAACA
7117693 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7117733 GGATAATTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7122480 original size:9 final size:9
Alignment explanation
Indices: 7122466--7122540 Score: 60
Period size: 10 Copynumber: 7.8 Consensus size: 9
7122456 GGCTGCTGGA
7122466 AACCGGTTT
1 AACCGGTTT
7122475 AACCGGTTTT
1 AACCGG-TTT
7122485 CAACCGGTTTT
1 -AACCGG-TTT
*
7122496 AACCGGTTCG
1 AACCGGTT-T
7122506 AACCGGTTT
1 AACCGGTTT
* *
7122515 GACCGGTCTG
1 AACCGGT-TT
*
7122525 AATCGGTTT
1 AACCGGTTT
*
7122534 GACCGGT
1 AACCGGT
7122541 ATGACCCGAC
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
9 20 0.38
10 23 0.43
11 10 0.19
ACGTcount: A:0.19, C:0.24, G:0.27, T:0.31
Consensus pattern (9 bp):
AACCGGTTT
Found at i:7122491 original size:20 final size:20
Alignment explanation
Indices: 7122466--7122540 Score: 75
Period size: 19 Copynumber: 3.8 Consensus size: 20
7122456 GGCTGCTGGA
7122466 AACCGGTTTAACCGGTTTTC-
1 AACCGGTTTAACCGG-TTTCG
7122486 AACCGGTTTTAACCGG-TTCG
1 AACCGG-TTTAACCGGTTTCG
* *
7122506 AACCGGTTTGACCGGTCT-G
1 AACCGGTTTAACCGGTTTCG
* *
7122525 AATCGGTTTGACCGGT
1 AACCGGTTTAACCGGT
7122541 ATGACCCGAC
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
19 27 0.55
20 13 0.27
21 9 0.18
ACGTcount: A:0.19, C:0.24, G:0.27, T:0.31
Consensus pattern (20 bp):
AACCGGTTTAACCGGTTTCG
Found at i:7122501 original size:10 final size:10
Alignment explanation
Indices: 7122466--7122514 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
7122456 GGCTGCTGGA
7122466 AACCGG-TTT
1 AACCGGTTTT
7122475 AACCGGTTTT
1 AACCGGTTTT
7122485 CAACCGGTTTT
1 -AACCGGTTTT
**
7122496 AACCGGTTCG
1 AACCGGTTTT
7122506 AACCGGTTT
1 AACCGGTTT
7122515 GACCGGTCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
9 6 0.17
10 19 0.54
11 10 0.29
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.33
Consensus pattern (10 bp):
AACCGGTTTT
Found at i:7122545 original size:9 final size:9
Alignment explanation
Indices: 7122467--7122546 Score: 52
Period size: 9 Copynumber: 8.3 Consensus size: 9
7122457 GCTGCTGGAA
*
7122467 ACCGGTTTA
1 ACCGGTTTG
*
7122476 ACCGGTTTTCA
1 ACCGG-TTT-G
*
7122487 ACCGGTTTTA
1 ACCGG-TTTG
*
7122497 ACCGGTTCG
1 ACCGGTTTG
7122506 AACCGGTTTG
1 -ACCGGTTTG
*
7122516 ACCGGTCTG
1 ACCGGTTTG
*
7122525 AATCGGTTTG
1 -ACCGGTTTG
*
7122535 ACCGGTATG
1 ACCGGTTTG
7122544 ACC
1 ACC
7122547 CGACCCGATC
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
9 25 0.42
10 24 0.41
11 10 0.17
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:7122571 original size:22 final size:21
Alignment explanation
Indices: 7122543--7122602 Score: 74
Period size: 17 Copynumber: 3.0 Consensus size: 21
7122533 TGACCGGTAT
7122543 GACCCGACCCGATCGTTGACCC
1 GACCCGACCCGA-CGTTGACCC
7122565 GACCCGA--C--CGTTGACCC
1 GACCCGACCCGACGTTGACCC
7122582 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGA-CGTTGACC
7122603 GTTGACCGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
17 16 0.48
19 1 0.03
20 1 0.03
22 15 0.45
ACGTcount: A:0.18, C:0.47, G:0.23, T:0.12
Consensus pattern (21 bp):
GACCCGACCCGACGTTGACCC
Found at i:7122602 original size:17 final size:17
Alignment explanation
Indices: 7122542--7122590 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
7122532 TTGACCGGTA
*
7122542 TGACCCGACCCGATCGT
1 TGACCCGACCCGACCGT
7122559 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
7122576 TGACCCGACCCGACC
1 TGACCCGACCCGACC
7122591 CGACCGTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:7122604 original size:7 final size:7
Alignment explanation
Indices: 7122592--7122629 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
7122582 GACCCGACCC
7122592 GACCGTT
1 GACCGTT
7122599 GACCGTT
1 GACCGTT
7122606 GACCGTT
1 GACCGTT
7122613 GACCGTT
1 GACCGTT
*
7122620 GACCATT
1 GACCGTT
7122627 GAC
1 GAC
7122630 TTTCTTTGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.18, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:7129808 original size:20 final size:21
Alignment explanation
Indices: 7129783--7129841 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
7129773 GGCTGCTGGA
7129783 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
7129803 AACCGGTTCTGACCGG-TTTC
1 AACCGGTTCTAACCGGTTTTC
*
7129823 AACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
7129842 GACCGGTCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 26 0.76
21 8 0.24
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.31
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:7129819 original size:10 final size:10
Alignment explanation
Indices: 7129804--7129873 Score: 53
Period size: 10 Copynumber: 7.3 Consensus size: 10
7129794 CCGGTTTTCA
7129804 ACCGGTTCTG
1 ACCGGTTCTG
*
7129814 ACCGGTT-TCA
1 ACCGGTTCT-G
7129824 ACCGGTTC-G
1 ACCGGTTCTG
7129833 AACCGGTT-TG
1 -ACCGGTTCTG
7129843 ACCGG-TCTG
1 ACCGGTTCTG
*
7129852 AATCGGTT-TG
1 -ACCGGTTCTG
7129862 ACCGG-TCTG
1 ACCGGTTCTG
7129871 ACC
1 ACC
7129874 CGACCCAACC
Statistics
Matches: 48, Mismatches: 4, Indels: 17
0.70 0.06 0.25
Matches are distributed among these distances:
8 2 0.04
9 17 0.35
10 28 0.58
11 1 0.02
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.27
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:7129820 original size:30 final size:29
Alignment explanation
Indices: 7129784--7129848 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
7129774 GCTGCTGGAA
7129784 ACCGGTTT-AACCGGTTTTC-AACCGGTTCTG
1 ACCGGTTTCAACCGG--TTCGAACCGGTT-TG
7129814 ACCGGTTTCAACCGGTTCGAACCGGTTTG
1 ACCGGTTTCAACCGGTTCGAACCGGTTTG
7129843 ACCGGT
1 ACCGGT
7129849 CTGAATCGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
29 11 0.33
30 16 0.48
31 6 0.18
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.29
Consensus pattern (29 bp):
ACCGGTTTCAACCGGTTCGAACCGGTTTG
Found at i:7129848 original size:19 final size:20
Alignment explanation
Indices: 7129804--7129871 Score: 81
Period size: 19 Copynumber: 3.5 Consensus size: 20
7129794 CCGGTTTTCA
*
7129804 ACCGGTTCTG-ACCGGTTTCA
1 ACCGGTTCTGAACCGGTTT-G
7129824 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
*
7129843 ACCGG-TCTGAATCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
7129862 ACCGG-TCTGA
1 ACCGGTTCTGA
7129872 CCCGACCCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
18 2 0.05
19 26 0.59
20 16 0.36
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.28
Consensus pattern (20 bp):
ACCGGTTCTGAACCGGTTTG
Found at i:7129895 original size:22 final size:21
Alignment explanation
Indices: 7129870--7129929 Score: 74
Period size: 17 Copynumber: 3.0 Consensus size: 21
7129860 TGACCGGTCT
7129870 GACCCGACCCAACCGTTGACCC
1 GACCCGACCC-ACCGTTGACCC
7129892 GACCCG----ACCGTTGACCC
1 GACCCGACCCACCGTTGACCC
7129909 GACCCGACCCGACCGTTGACC
1 GACCCGACCC-ACCGTTGACC
7129930 GTTGACCGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
17 17 0.52
22 16 0.48
ACGTcount: A:0.20, C:0.48, G:0.22, T:0.10
Consensus pattern (21 bp):
GACCCGACCCACCGTTGACCC
Found at i:7129929 original size:17 final size:17
Alignment explanation
Indices: 7129869--7129917 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
7129859 TTGACCGGTC
*
7129869 TGACCCGACCCAACCGT
1 TGACCCGACCCGACCGT
7129886 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
7129903 TGACCCGACCCGACC
1 TGACCCGACCCGACC
7129918 CGACCGTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.20, C:0.49, G:0.20, T:0.10
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:7129931 original size:7 final size:7
Alignment explanation
Indices: 7129919--7129949 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
7129909 GACCCGACCC
7129919 GACCGTT
1 GACCGTT
7129926 GACCGTT
1 GACCGTT
7129933 GACCGTT
1 GACCGTT
*
7129940 GACCATT
1 GACCGTT
7129947 GAC
1 GAC
7129950 TTTCTTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:7133140 original size:18 final size:18
Alignment explanation
Indices: 7133105--7133152 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
7133095 ATTCCCAATC
*
7133105 TCTTC-TCTCCTCGTCGT
1 TCTTCTTCTCCTCGCCGT
*
7133122 TCTTCTTCTCTTCGCCGT
1 TCTTCTTCTCCTCGCCGT
7133140 TCTTCTTCTCCTC
1 TCTTCTTCTCCTC
7133153 CGACCATAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (18 bp):
TCTTCTTCTCCTCGCCGT
Found at i:7135198 original size:26 final size:26
Alignment explanation
Indices: 7135162--7135244 Score: 148
Period size: 26 Copynumber: 3.2 Consensus size: 26
7135152 TTAATGGTGT
*
7135162 TCGTCGTTAGTGGTACTCATCGTTGC
1 TCGTCATTAGTGGTACTCATCGTTGC
7135188 TCGTCATTAGTGGTACTCATCGTTGC
1 TCGTCATTAGTGGTACTCATCGTTGC
*
7135214 TTGTCATTAGTGGTACTCATCGTTGC
1 TCGTCATTAGTGGTACTCATCGTTGC
7135240 TCGTC
1 TCGTC
7135245 GAGCATAGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.13, C:0.23, G:0.24, T:0.40
Consensus pattern (26 bp):
TCGTCATTAGTGGTACTCATCGTTGC
Found at i:7135575 original size:21 final size:21
Alignment explanation
Indices: 7135551--7135590 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
7135541 TTTTCAAAGG
7135551 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
7135572 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
7135591 GAATAAGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:7135640 original size:19 final size:19
Alignment explanation
Indices: 7135616--7135654 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
7135606 TCGAATGCAT
7135616 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
7135635 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
7135654 T
1 T
7135655 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:7135679 original size:64 final size:64
Alignment explanation
Indices: 7135551--7135780 Score: 206
Period size: 64 Copynumber: 3.5 Consensus size: 64
7135541 TTTTCAAAGG
* *
7135551 CATGCACCGATGCA-TCAATACCATGCATCGATGCA-TCAATGA-ATAAGTTGAAACATCGAATG
1 CATGCACCGATGCACTC--T-CCATGCATCGATGCACTC-ATGATTTAA-TTAAAACATCGAATG
7135613 CATT
61 CATT
7135617 CCATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATT
1 -CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCA-T
7135681 T
64 T
* * ** * *
7135682 GATGCATCGATGCACAATCCATGCATCGATGCAC-CAGGCTATTT--TTCAAACATCGAATGCAC
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATG--ATTTAATTAAAACATCGAATGCA-
7135744 TT
63 TT
* * *
7135746 CATGCATCGATGCACTCT-TAGTGCACCGATGCACT
1 CATGCACCGATGCACTCTCCA-TGCATCGATGCACT
7135781 AGGAGTCCAA
Statistics
Matches: 140, Mismatches: 14, Indels: 20
0.80 0.08 0.11
Matches are distributed among these distances:
63 2 0.01
64 95 0.68
65 20 0.14
66 7 0.05
67 14 0.10
68 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCATT
Found at i:7135760 original size:17 final size:19
Alignment explanation
Indices: 7135732--7135780 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
7135722 ATTTTTCAAA
7135732 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
7135750 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
7135769 CACCGATGCACT
1 CATCGATGCACT
7135781 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:7141597 original size:24 final size:22
Alignment explanation
Indices: 7141569--7141646 Score: 88
Period size: 24 Copynumber: 3.5 Consensus size: 22
7141559 CACTTAACAA
7141569 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCAT-CC-TTGAATG
*
7141593 TGCATCGATGCATCC--GCATG
1 TGCATCGATGCATCCTTGAATG
*
7141613 ATGCACCGATGCATGCCTTGAATG
1 -TGCATCGATGCAT-CCTTGAATG
7141637 TGCATCGATG
1 TGCATCGATG
7141647 TACAAGATCA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
20 4 0.09
21 12 0.26
22 2 0.04
23 11 0.24
24 17 0.37
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:7144186 original size:21 final size:21
Alignment explanation
Indices: 7144162--7144201 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
7144152 TTTTCAAAGG
7144162 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
7144183 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
7144202 GAATAAGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:7144251 original size:19 final size:19
Alignment explanation
Indices: 7144227--7144265 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
7144217 TCGAATGCAT
7144227 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
7144246 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
7144265 T
1 T
7144266 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:7144290 original size:64 final size:64
Alignment explanation
Indices: 7144162--7144392 Score: 190
Period size: 64 Copynumber: 3.6 Consensus size: 64
7144152 TTTTCAAAGG
* *
7144162 CATGCACCGATGCA-TCAATACCATGCATCGATGCA-TCAATGA-ATAAGTTGAAACATCGAATG
1 CATGCACCGATGCACTC--T-CCATGCATCGATGCACTC-ATGATTTAA-TTAAAACATCGAATG
7144224 CATT
61 CATT
7144228 CCATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATT
1 -CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCA-T
7144292 T
64 T
* ** ** * * *
7144293 GATGCTTCGATGCACAATCCATGCATCGATGTAC-CAGGCTATTT--TTCAAACATCGAATGCAC
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATG--ATTTAATTAAAACATCGAATGCA-
7144355 TT
63 TT
* * *
7144357 CATGCATCGATGCACTCT-TAGTGCACCGATGCACTC
1 CATGCACCGATGCACTCTCCA-TGCATCGATGCACTC
7144393 TTAGTGCACC
Statistics
Matches: 137, Mismatches: 18, Indels: 20
0.78 0.10 0.11
Matches are distributed among these distances:
63 2 0.01
64 91 0.66
65 21 0.15
66 7 0.05
67 14 0.10
68 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCATT
Found at i:7144386 original size:19 final size:19
Alignment explanation
Indices: 7144359--7144429 Score: 133
Period size: 19 Copynumber: 3.7 Consensus size: 19
7144349 ATGCACTTCA
*
7144359 TGCATCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
7144378 TGCACCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
7144397 TGCACCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
7144416 TGCACCGATGCACT
1 TGCACCGATGCACT
7144430 AGGAGTCCAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27
Consensus pattern (19 bp):
TGCACCGATGCACTCTTAG
Found at i:7145519 original size:21 final size:21
Alignment explanation
Indices: 7145486--7145525 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
7145476 TTAGGTGTCA
*
7145486 TTAATATAGTTTACCCTTTATT
1 TTAATATAATTTA-CCTTTATT
7145508 TTAA-ATAATTTACCTTTA
1 TTAATATAATTTACCTTTA
7145526 AATTTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.53
Consensus pattern (21 bp):
TTAATATAATTTACCTTTATT
Found at i:7146284 original size:30 final size:29
Alignment explanation
Indices: 7146240--7146308 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
7146230 CATTAAAAAA
* *
7146240 TATTGCTTATCGTAACTTATTAAATATATTT
1 TATT-CTTATCGTAACCTA-AAAATATATTT
*
7146271 TATTCTTTTCGTAACCTAAAAATATATTT
1 TATTCTTATCGTAACCTAAAAATATATTT
7146300 TATTCTTAT
1 TATTCTTAT
7146309 TTTAATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.53
30 12 0.35
31 4 0.12
ACGTcount: A:0.32, C:0.12, G:0.04, T:0.52
Consensus pattern (29 bp):
TATTCTTATCGTAACCTAAAAATATATTT
Found at i:7146319 original size:29 final size:29
Alignment explanation
Indices: 7146261--7146352 Score: 84
Period size: 29 Copynumber: 3.3 Consensus size: 29
7146251 GTAACTTATT
* **
7146261 AAATATATTTTATTCTT-TTCGTAACCTAA
1 AAATATATTTTATTCTTATT-TTAAATTAA
*
7146290 AAATATATTTTATTCTTATTTT-AATT-T
1 AAATATATTTTATTCTTATTTTAAATTAA
* *
7146317 AAA-ATATTTTAATCTTATATTAAATTAA
1 AAATATATTTTATTCTTATTTTAAATTAA
*
7146345 AAAAATAT
1 AAATATAT
7146353 AGTTTATTAC
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
26 16 0.31
27 7 0.13
28 5 0.10
29 22 0.42
30 2 0.04
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.50
Consensus pattern (29 bp):
AAATATATTTTATTCTTATTTTAAATTAA
Found at i:7146332 original size:26 final size:26
Alignment explanation
Indices: 7146294--7146346 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
7146284 ACCTAAAAAT
* * *
7146294 ATATTTTATTCTTATTTTAATTTAAA
1 ATATTTTAATCTTATATTAAATTAAA
7146320 ATATTTTAATCTTATATTAAATTAAA
1 ATATTTTAATCTTATATTAAATTAAA
7146346 A
1 A
7146347 AAATATAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (26 bp):
ATATTTTAATCTTATATTAAATTAAA
Found at i:7146348 original size:28 final size:27
Alignment explanation
Indices: 7146287--7146348 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
7146277 TTTCGTAACC
* *
7146287 TAAAAATATATTTTATTCTTATTTTAAT
1 TAAAAA-ATATTTTAATCTTATTTAAAT
*
7146315 T-TAAAATATTTTAATCTTATATTAAAT
1 TAAAAAATATTTTAATCTTAT-TTAAAT
7146342 TAAAAAA
1 TAAAAAA
7146349 ATATAGTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 14 0.50
27 9 0.32
28 5 0.18
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (27 bp):
TAAAAAATATTTTAATCTTATTTAAAT
Found at i:7146443 original size:30 final size:30
Alignment explanation
Indices: 7146375--7146651 Score: 159
Period size: 30 Copynumber: 9.4 Consensus size: 30
7146365 TCTTAACTTA
* *
7146375 AATATTTAAGATAAAAATATAATATATTTTT
1 AATAGTTAAGATAAAAATAAAATATA-TTTT
**
7146406 TGTAGTTAAGATAAAAATAAAATATATTTT
1 AATAGTTAAGATAAAAATAAAATATATTTT
* *
7146436 AGTAGTT-A-A-AAATA-AAAATAT-TTTT
1 AATAGTTAAGATAAAAATAAAATATATTTT
* * * *
7146461 TA-AGATAAGATAAGAATAAAAGATATGTTCT
1 AATAGTTAAGATAAAAATAAAATATAT-TT-T
* * *
7146492 -A-AGTTAAAATAAGAAT-TAATCATA-TTT
1 AATAGTTAAGATAAAAATAAAAT-ATATTTT
* *
7146519 AATAATTTAATG-TAAGAATAAAATATA-TTT
1 AAT-AGTTAA-GATAAAAATAAAATATATTTT
* * * * *
7146549 AATAATTTAAGATAAGAATATAATTTA-TGT
1 AAT-AGTTAAGATAAAAATAAAATATATTTT
*
7146579 AATAAGTTAAGATAATAATAAAATATA-TTT
1 AAT-AGTTAAGATAAAAATAAAATATATTTT
* *
7146609 AATAAGTTAATATAAAAATAAAATCTATTTT
1 AAT-AGTTAAGATAAAAATAAAATATATTTT
*
7146640 AATTGTTAAGAT
1 AATAGTTAAGAT
7146652 GTAAAATTAA
Statistics
Matches: 199, Mismatches: 32, Indels: 31
0.76 0.12 0.12
Matches are distributed among these distances:
24 3 0.02
25 5 0.03
26 8 0.04
27 8 0.04
28 10 0.05
29 5 0.03
30 128 0.64
31 32 0.16
ACGTcount: A:0.52, C:0.01, G:0.08, T:0.39
Consensus pattern (30 bp):
AATAGTTAAGATAAAAATAAAATATATTTT
Found at i:7146497 original size:54 final size:54
Alignment explanation
Indices: 7146379--7146500 Score: 140
Period size: 54 Copynumber: 2.2 Consensus size: 54
7146369 AACTTAAATA
* * * * *
7146379 TTTAAGATAAAAATATAATATATTTTTTGTAGTTAAGATAAAAATAAAATATAT
1 TTTAAGTTAAAAATATAAAATATTTTTTGAAGATAAGATAAAAATAAAAGATAT
*
7146433 TTTAGTAGTTAAAAATA-AAAATATTTTTT-AAGATAAGATAAGAATAAAAGATAT
1 TTTA--AGTTAAAAATATAAAATATTTTTTGAAGATAAGATAAAAATAAAAGATAT
7146487 GTTCTAAGTTAAAA
1 -TT-TAAGTTAAAA
7146501 TAAGAATTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
54 33 0.57
55 13 0.22
56 12 0.21
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.38
Consensus pattern (54 bp):
TTTAAGTTAAAAATATAAAATATTTTTTGAAGATAAGATAAAAATAAAAGATAT
Found at i:7146535 original size:60 final size:60
Alignment explanation
Indices: 7146409--7146628 Score: 192
Period size: 60 Copynumber: 3.8 Consensus size: 60
7146399 TATTTTTTGT
* * *
7146409 AGTTAAGATAAAAATAAAATATATTTTAGT-AGTTAAAAATAA-AA-AT-AT-T-T-T-TTA
1 AGTTAAGATAAGAATAAAATATA-TTTAATAAGTT-AAAATAAGAATATAATATATGTAATA
* * * *
7146463 AGATAAGATAAGAATAAAAGATATGTT-CTAAGTTAAAATAAGAAT-TAATCATATTTAATA
1 AGTTAAGATAAGAATAAAATATAT-TTAATAAGTTAAAATAAGAATATAAT-ATATGTAATA
* * * *
7146523 ATTTAATG-TAAGAATAAAATATATTTAATAATTTAAGATAAGAATATAATTTATGTAATA
1 AGTTAA-GATAAGAATAAAATATATTTAATAAGTTAAAATAAGAATATAATATATGTAATA
* * *
7146583 AGTTAAGATAATAATAAAATATATTTAATAAGTTAATATAAAAATA
1 AGTTAAGATAAGAATAAAATATATTTAATAAGTTAAAATAAGAATA
7146629 AAATCTATTT
Statistics
Matches: 134, Mismatches: 18, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
53 9 0.07
54 29 0.22
55 2 0.01
57 1 0.01
58 1 0.01
59 4 0.03
60 83 0.62
61 5 0.04
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (60 bp):
AGTTAAGATAAGAATAAAATATATTTAATAAGTTAAAATAAGAATATAATATATGTAATA
Found at i:7146559 original size:25 final size:26
Alignment explanation
Indices: 7146526--7146575 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
7146516 TTTAATAATT
7146526 TAATGTAAGAATAA-AATAT-ATTTAA
1 TAATGTAAG-ATAAGAATATAATTTAA
*
7146551 TAATTTAAGATAAGAATATAATTTA
1 TAATGTAAGATAAGAATATAATTTA
7146576 TGTAATAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 13 0.59
26 5 0.23
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (26 bp):
TAATGTAAGATAAGAATATAATTTAA
Found at i:7146649 original size:90 final size:89
Alignment explanation
Indices: 7146409--7146651 Score: 234
Period size: 90 Copynumber: 2.8 Consensus size: 89
7146399 TATTTTTTGT
* * *
7146409 AGTTAAGATAAAAATAAAATATATTT--T-AG-TAGTTAAAAATAAAAATATTTTTTAA--GATA
1 AGTTAAGATAAAAATAAAATATATTTAATAAGTTAATTAAAAAT-AAAATATATTTTAATTGTTA
**
7146468 AGATAAGAATAAAAGATATGTTCTA
65 AGATAAGAATAAAAGATATGTAATA
* * * * *
7146493 AGTTAAAATAAGAAT-TAATCATATTTAATAATTTAATGTAAGAATAAAATATA-TTTAATAAT-
1 AGTTAAGATAAAAATAAAAT-ATATTTAATAAGTTAAT-TAAAAATAAAATATATTTTAAT--TG
* **
7146555 TTAAGATAAGAATATAATTTATGTAATA
62 TTAAGATAAGAATAAAAGATATGTAATA
* *
7146583 AGTTAAGATAATAATAAAATATATTTAATAAGTTAATATAAAAATAAAATCTATTTTAATTGTTA
1 AGTTAAGATAAAAATAAAATATATTTAATAAGTTAAT-TAAAAATAAAATATATTTTAATTGTTA
7146648 AGAT
65 AGAT
7146652 GTAAAATTAA
Statistics
Matches: 126, Mismatches: 20, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
83 3 0.02
84 19 0.15
86 1 0.01
87 6 0.05
88 10 0.08
89 7 0.06
90 71 0.56
91 9 0.07
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (89 bp):
AGTTAAGATAAAAATAAAATATATTTAATAAGTTAATTAAAAATAAAATATATTTTAATTGTTAA
GATAAGAATAAAAGATATGTAATA
Found at i:7147068 original size:36 final size:35
Alignment explanation
Indices: 7147020--7147088 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
7147010 TTGGTTTTCC
7147020 GGAAAATAAATTACTAGAATTTGAATTACTGGAACT
1 GGAAAATAAATTACTAGAATTTGAATT-CTGGAACT
* * *
7147056 GGAAAATGAATTATTGGAATTTGAATTCTGGAA
1 GGAAAATAAATTACTAGAATTTGAATTCTGGAA
7147089 AATGAATTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 6 0.20
36 24 0.80
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (35 bp):
GGAAAATAAATTACTAGAATTTGAATTCTGGAACT
Found at i:7147094 original size:14 final size:15
Alignment explanation
Indices: 7147053--7147098 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
7147043 AATTACTGGA
7147053 ACTGGAAAATGAATT
1 ACTGGAAAATGAATT
* **
7147068 ATTGGAATTTGAATT
1 ACTGGAAAATGAATT
7147083 -CTGGAAAATGAATT
1 ACTGGAAAATGAATT
7147097 AC
1 AC
7147099 ATTTCTGGAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.33
Consensus pattern (15 bp):
ACTGGAAAATGAATT
Found at i:7147104 original size:20 final size:20
Alignment explanation
Indices: 7147081--7147130 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
7147071 GGAATTTGAA
7147081 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
7147101 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
7147121 TTCTGGAAAA
1 TTCTGGAAAA
7147131 CGTTTTCCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:7147159 original size:14 final size:14
Alignment explanation
Indices: 7147119--7147161 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
7147109 AATGAATTAC
* *
7147119 ATTTCTGGAAAACG
1 ATTTCCGGAAAATG
*
7147133 TTTTCCGGAAAATG
1 ATTTCCGGAAAATG
*
7147147 ATTTCCGTAAAATG
1 ATTTCCGGAAAATG
7147161 A
1 A
7147162 ATTACATTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (14 bp):
ATTTCCGGAAAATG
Found at i:7147374 original size:49 final size:50
Alignment explanation
Indices: 7147277--7147375 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 50
7147267 TACAAATATT
*
7147277 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * * *
7147327 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TTATTTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
7147376 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
48 9 0.21
49 25 0.60
50 8 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:7147418 original size:32 final size:30
Alignment explanation
Indices: 7147354--7147422 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
7147344 ATTTATTATT
*
7147354 AAATATT-ATTTTTATAATTTTATTAATAA
1 AAATATTAATTTTTATAATTTTATAAATAA
*
7147383 AAATATTAATTTTTTTATATTTTAGTGAAAT-A
1 AAATATTAATTTTTATA-ATTTTA-T-AAATAA
7147415 AAATATTA
1 AAATATTA
7147423 TAAATTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 7 0.21
30 8 0.24
31 6 0.18
32 10 0.29
33 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (30 bp):
AAATATTAATTTTTATAATTTTATAAATAA
Found at i:7147513 original size:23 final size:23
Alignment explanation
Indices: 7147464--7147514 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
7147454 GTGTTATATT
**
7147464 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
7147487 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
7147510 ATATT
1 ATATT
7147515 ATTTAAACAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:7161600 original size:146 final size:144
Alignment explanation
Indices: 7161106--7161633 Score: 462
Period size: 145 Copynumber: 3.6 Consensus size: 144
7161096 TCTTATCGGT
* * * * *
7161106 GATCGAAATCTCTGATCAACATTCCGAATGGTCAAAAGTTGCGCAAAACCATCACGAACAACATA
1 GATCGAGACCTCTGATCAACATTCCGAACGGTCAAAAGTTGCGC-AGACCAACACGAACAACATA
* * * * *
7161171 CTGAAAA-TTCAGGACGATCGGACGGTGGACGAAGATGGATCGAAGAAAATAAGCAGAATGGTTT
65 CT-AAAATTTCAGGACGATCGGACGGTGGACGAAGGTGAATCGAAGAAAATAACCAGAACGATTT
7161235 TTGGCCTCTTGCCGGC
129 TTGGCCTCTTGCCGGC
* * * * ** * * ** *
7161251 AATCGGGATCTCCGATCAACATTTTGAACAGTCAAAAGTTGCACCAGACCAGTACAAACAACATA
1 GATCGAGACCTCTGATCAACATTCCGAACGGTCAAAAGTTGC-GCAGACCAACACGAACAACATA
* * **
7161316 CTAAAAATTT-AGAACGATCGGACGGTGGAC-AACGACAGATCGAAGAAAATAAGCC-GAAC-AG
65 CT-AAAATTTCAGGACGATCGGACGGTGGACGAAGGTGA-ATCGAAGAAAATAA-CCAGAACGA-
* * *
7161377 TTTTTGGCTTCTTACCAGC
126 TTTTTGGCCTCTTGCCGGC
* * * * * *
7161396 GATC-AGGACTTGC-GATCAACATTCCAAATGGTGAAAAGTTGTGTCATG-TCAACACGAACAAC
1 GATCGA-GACCT-CTGATCAACATTCCGAACGGTCAAAAGTTGCG-CA-GACCAACACGAACAAC
* * ** *
7161458 ATACTAAAATTTTAGGACGATCGGACAGTGGACGGTGGTGAATCGGAGAAAATAAATCCAG-ACG
62 ATACTAAAATTTCAGGACGATCGGACGGTGGACGAAGGTGAATCGAAGAAAAT-AA-CCAGAACG
* *
7161522 ATTTTTAGCCTCTCGCCGGC
125 ATTTTTGGCCTCTTGCCGGC
* **
7161542 GATCGAGACCTCTGATCAACATTCCGAACGGTCAAAAGTTGTGCGAGGTCAACACGAACAACATA
1 GATCGAGACCTCTGATCAACATTCCGAACGGTCAAAAGTTGCGC-AGACCAACACGAACAACATA
*
7161607 CTAAAATTTCAGGTCGATCGGACGGTG
65 CTAAAATTTCAGGACGATCGGACGGTG
7161634 ATACAGTAGC
Statistics
Matches: 302, Mismatches: 63, Indels: 35
0.75 0.16 0.09
Matches are distributed among these distances:
144 9 0.03
145 185 0.61
146 105 0.35
147 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (144 bp):
GATCGAGACCTCTGATCAACATTCCGAACGGTCAAAAGTTGCGCAGACCAACACGAACAACATAC
TAAAATTTCAGGACGATCGGACGGTGGACGAAGGTGAATCGAAGAAAATAACCAGAACGATTTTT
GGCCTCTTGCCGGC
Found at i:7161900 original size:30 final size:29
Alignment explanation
Indices: 7161847--7161914 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
7161837 CATTTAAATA
* * * *
7161847 TATGTTTTAACTATTTTAGCCTTTTGAGTT
1 TATGTTTTTACCATTTAAGCC-TTTAAGTT
*
7161877 TATGTTTTTACCATTTAATCCTTTAAGTT
1 TATGTTTTTACCATTTAAGCCTTTAAGTT
*
7161906 CATGTTTTT
1 TATGTTTTT
7161915 GCAAGATCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.21, C:0.12, G:0.10, T:0.57
Consensus pattern (29 bp):
TATGTTTTTACCATTTAAGCCTTTAAGTT
Found at i:7166297 original size:32 final size:32
Alignment explanation
Indices: 7166215--7166302 Score: 115
Period size: 32 Copynumber: 2.8 Consensus size: 32
7166205 AAGCAATAGA
** *
7166215 GGGCATCTTTAAAGATTCAACATCAAATGTTG
1 GGGCATCTTTCGAGATTCAACATCAAATATTG
*
7166247 GGGCATCTTTCGAGATTCAACATCGAATATTG
1 GGGCATCTTTCGAGATTCAACATCAAATATTG
*
7166279 GGGCATCTTT-GGGAATTCAACATC
1 GGGCATCTTTCGAG-ATTCAACATC
7166303 CCGATGCGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
31 2 0.04
32 48 0.96
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (32 bp):
GGGCATCTTTCGAGATTCAACATCAAATATTG
Found at i:7166858 original size:43 final size:43
Alignment explanation
Indices: 7166809--7166919 Score: 170
Period size: 43 Copynumber: 2.6 Consensus size: 43
7166799 ACGAAGAGGC
7166809 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACGA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCAC-A
*
7166853 -ATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACA
* * *
7166895 CAACCACGGTTTCAACTTCACGACG
1 CATCCACGATTTCAACTCCACGACG
7166920 AAGGGAATCG
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
42 1 0.02
43 61 0.98
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.19
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACA
Found at i:7166930 original size:43 final size:43
Alignment explanation
Indices: 7166812--7166936 Score: 164
Period size: 43 Copynumber: 2.9 Consensus size: 43
7166802 AAGAGGCCAT
* *
7166812 CCACGATTTCAACTCCACGACGGAGGATATCGTACCCACGAAT
1 CCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACGAAA
7166855 CCACGATTTCAACTCCACGACGGAGGATATCGTGCCCAC-ACAA
1 CCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACGA-AA
* * * *
7166898 CCACGGTTTCAACTTCACGACGAAGGGA-ATCGTGTCCAC
1 CCACGATTTCAACTCCACGACGGA-GGATATCGTGCCCAC
7166937 CCGCAACACA
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
42 1 0.01
43 70 0.95
44 3 0.04
ACGTcount: A:0.29, C:0.33, G:0.20, T:0.18
Consensus pattern (43 bp):
CCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACGAAA
Found at i:7167438 original size:121 final size:121
Alignment explanation
Indices: 7167273--7167497 Score: 317
Period size: 121 Copynumber: 1.9 Consensus size: 121
7167263 ATAACACAAG
* * * *
7167273 CTTGGATTTCAACTTCAGGACGAAGGATATTCAAGTCAATGCTCAACTTCATGACGAAGGAGCTC
1 CTTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAAGCTCAACTTCACGACGAAGGAGC-C
* * *
7167338 -TCCACAATTTTAACTTCACGATGAAGGATATCGTGCCCACAAGTAGCAATGCAACC
65 ACCCACAATTTCAACTTCACGAAGAAGGATATCGTGCCCACAAGTAGCAATGCAACC
* * * *
7167394 CTTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAATTTCACGACGAATGAGCCA
1 CTTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAAGCTCAACTTCACGACGAAGGAGCCA
* *
7167459 CCCACGATTTCAACTTCACGAAGAAGGATATTGTGCCCA
66 CCCACAATTTCAACTTCACGAAGAAGGATATCGTGCCCA
7167498 ATGGATTAAC
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
120 1 0.01
121 89 0.99
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (121 bp):
CTTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAAGCTCAACTTCACGACGAAGGAGCCA
CCCACAATTTCAACTTCACGAAGAAGGATATCGTGCCCACAAGTAGCAATGCAACC
Found at i:7167599 original size:40 final size:40
Alignment explanation
Indices: 7167550--7167647 Score: 117
Period size: 40 Copynumber: 2.5 Consensus size: 40
7167540 TAACCAATCG
* * * *
7167550 TCCTTATCACGTAGGAATCGTGTCATCCCTTGACTAG-GTC
1 TCCTCATCACGTAGGAACCATGTCATCCCTCGACT-GTGTC
*
7167590 TCCTCATCACGTAGGAACCATGTCATCCCTCGACTGTGTT
1 TCCTCATCACGTAGGAACCATGTCATCCCTCGACTGTGTC
* *
7167630 TCATCATCATGTAGGAAC
1 TCCTCATCACGTAGGAAC
7167648 TGTGTTATCA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.02
40 49 0.98
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCATGTCATCCCTCGACTGTGTC
Found at i:7168656 original size:145 final size:145
Alignment explanation
Indices: 7168422--7168686 Score: 433
Period size: 145 Copynumber: 1.8 Consensus size: 145
7168412 TCGTAAAACC
* **
7168422 ATCACAAACAACATACTGAATATTCAGGACGATCGGACGGTGGACGGAGATGGATCGAAGAAAAT
1 ATCACAAACAACATACTGAAAATTCAGGACGATCGGACGGTGGACGGAGACAGATCGAAGAAAAT
*
7168487 AAGCAGAACGGTTTTTGGCCTCTTGCCGGCGATCAGGATCTCCGATTAACATTCCGAACAGTCAA
66 AAGCAGAACGGTTTTTGGCCTCTTGCCGGCGATCAGGATCTCCGATCAACATTCCGAACAGTCAA
7168552 AAGATGTACGAGACT
131 AAGATGTACGAGACT
*
7168567 ATCACAAACAACATACTGAAAATTCAGGACGATCGGACTGTGGAC-GACGACAGATCGAAGAAAA
1 ATCACAAACAACATACTGAAAATTCAGGACGATCGGACGGTGGACGGA-GACAGATCGAAGAAAA
* * * *
7168631 TAAGCCGAACTGTTTTTGGCTTCTTGCCGGCGATCGGGATCTCCGATCAACATTCC
65 TAAGCAGAACGGTTTTTGGCCTCTTGCCGGCGATCAGGATCTCCGATCAACATTCC
7168687 AAATGGTGAA
Statistics
Matches: 110, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
144 2 0.02
145 108 0.98
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (145 bp):
ATCACAAACAACATACTGAAAATTCAGGACGATCGGACGGTGGACGGAGACAGATCGAAGAAAAT
AAGCAGAACGGTTTTTGGCCTCTTGCCGGCGATCAGGATCTCCGATCAACATTCCGAACAGTCAA
AAGATGTACGAGACT
Found at i:7168774 original size:145 final size:143
Alignment explanation
Indices: 7168424--7168775 Score: 365
Period size: 145 Copynumber: 2.4 Consensus size: 143
7168414 GTAAAACCAT
* * * *
7168424 CACAAACAACATACTGAATATTCAGGACGATCGGACGGTGGACGGAGATGGATCGAAGAAAATAA
1 CACAAACAACATACTGAAAATTCAGGACGATCGGAC-TTGGACGGAGGTGAATCGAAGAAAATAA
* *
7168489 GCAGAACGGTTTTTGGCCTCTTGCCGGCGATCAGGATCTCCGATTAACATTCCGAACAGTCAAAA
65 GCAGAACGGTTTTTGGCCTCTTGCCGGCGATCAGGATCTCCGATCAACATTCCAAACAGTCAAAA
*
7168554 GATGTACGAGACTAT
130 GATGTACGAGAC-AA
* **
7168569 CACAAACAACATACTGAAAATTCAGGACGATCGGACTGTGGAC-GACGACAGATCGAAGAAAATA
1 CACAAACAACATACTGAAAATTCAGGACGATCGGACT-TGGACGGAGGTGA-ATCGAAGAAAATA
* * * * ** *
7168633 AGCCGAACTGTTTTTGGCTTCTTGCCGGCGATCGGGATCTCCGATCAACATTCCAAATGGTGAAA
64 AGCAGAACGGTTTTTGGCCTCTTGCCGGCGATCAGGATCTCCGATCAACATTCCAAACAGTCAAA
*
7168698 A-ATTGTGTC-ATGTA-AA
129 AGA-TGT-ACGA-G-ACAA
* * * *
7168714 CACGAACATCATA-TTAAAATTTCAGGACGATCGGACATTGGACGGTGGTGAATC-AGAGAAAA
1 CACAAACAACATACTGAAAA-TTCAGGACGATCGGAC-TTGGACGGAGGTGAATCGA-AGAAAA
7168776 CAAATCTGGA
Statistics
Matches: 172, Mismatches: 25, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
144 9 0.05
145 156 0.91
146 6 0.03
147 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22
Consensus pattern (143 bp):
CACAAACAACATACTGAAAATTCAGGACGATCGGACTTGGACGGAGGTGAATCGAAGAAAATAAG
CAGAACGGTTTTTGGCCTCTTGCCGGCGATCAGGATCTCCGATCAACATTCCAAACAGTCAAAAG
ATGTACGAGACAA
Found at i:7172933 original size:51 final size:51
Alignment explanation
Indices: 7172755--7172938 Score: 291
Period size: 51 Copynumber: 3.6 Consensus size: 51
7172745 TTCATACTGC
7172755 AAAAAA-TGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
*
7172805 AAACAAGTGTAGCACTTAACACATAC-TACACCGGTGTAAGTGAATAAAAT
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
* * *
7172855 AAAAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTTAGTAAACAAAAT
1 --AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
*
7172908 AAAAAAGTGTAACACTTAACACATACTTACA
1 AAAAAAGTGTAGCACTTAACACATACTTACA
7172939 TTGGTTTAAG
Statistics
Matches: 124, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
50 29 0.23
51 49 0.40
52 25 0.20
53 21 0.17
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (51 bp):
AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
Found at i:7174720 original size:3 final size:3
Alignment explanation
Indices: 7174714--7174755 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
7174704 GAGGTATTCC
7174714 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
7174756 AGCCATGAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:7180409 original size:60 final size:60
Alignment explanation
Indices: 7180293--7180446 Score: 156
Period size: 60 Copynumber: 2.6 Consensus size: 60
7180283 TCTTATAATA
* * *
7180293 CATTCTAAATTGATTCTTAAACTTTT-AGACATTCTAAATTCATTCCCAAACTATGACAAT
1 CATTCTAAATTGGTCCTTAAACTTTTGA-ACATTCCAAATTCATTCCCAAACTATGACAAT
* * **
7180353 CATTCTAAATTGGTCCTTAAGCTTTTGAACATTCCAAATTCA-TCCTTAAA-TCATGACCCT
1 CATTCTAAATTGGTCCTTAAACTTTTGAACATTCCAAATTCATTCC-CAAACT-ATGACAAT
* *
7180413 CTTTCTAAATTAGTACC-TAAACTTTTGAA-ATTCC
1 CATTCTAAATTGGT-CCTTAAACTTTTGAACATTCC
7180447 TATAATTTCC
Statistics
Matches: 80, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
59 9 0.11
60 68 0.85
61 3 0.04
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.38
Consensus pattern (60 bp):
CATTCTAAATTGGTCCTTAAACTTTTGAACATTCCAAATTCATTCCCAAACTATGACAAT
Found at i:7182708 original size:27 final size:26
Alignment explanation
Indices: 7182674--7182734 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
7182664 TATCTAAAAT
7182674 AATATTAT-TTTTATA-TATTAATAATA
1 AATATTATATTTT-TAGTATT-ATAATA
7182700 CAATATTATATTTTTAGTATTATAATA
1 -AATATTATATTTTTAGTATTATAATA
7182727 ATATATTA
1 A-ATATTA
7182735 AATTATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 1 0.03
27 22 0.71
28 8 0.26
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
AATATTATATTTTTAGTATTATAATA
Found at i:7182747 original size:23 final size:23
Alignment explanation
Indices: 7182717--7182766 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
7182707 ATATTTTTAG
7182717 TATTATAATAATATATTAAATTA
1 TATTATAATAATATATTAAATTA
* *
7182740 TATTATAATAATATTTTATATTA
1 TATTATAATAATATATTAAATTA
7182763 TATT
1 TATT
7182767 TTTATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTATAATAATATATTAAATTA
Found at i:7182770 original size:55 final size:52
Alignment explanation
Indices: 7182702--7182817 Score: 132
Period size: 52 Copynumber: 2.2 Consensus size: 52
7182692 TAATAATACA
* *
7182702 ATATTATATTTTTAGTATTATAATAATATAT-TAAATTATATTATAATAA-TATTTT
1 ATATTATATTTTTA-T-TT-TAACAATATATATAAATTAT-TAATAA-AACTATTTT
7182757 ATATTATATTTTTATTTTAACAATATATAATAAATTATTAATAAAACTATTTT
1 ATATTATATTTTTATTTTAACAATATAT-ATAAATTATTAATAAAACTATTTT
7182810 -TA-TATATT
1 ATATTATATT
7182818 AATTTCATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
51 6 0.11
52 14 0.25
53 13 0.23
54 9 0.16
55 14 0.25
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (52 bp):
ATATTATATTTTTATTTTAACAATATATATAAATTATTAATAAAACTATTTT
Found at i:7183101 original size:23 final size:23
Alignment explanation
Indices: 7183072--7183124 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
7183062 ACATGTTATT
7183072 TGCCTTTATGACACGTTTATCTC
1 TGCCTTTATGACACGTTTATCTC
* * * * *
7183095 TGTCTTTGTGGCATGTTTTTCTC
1 TGCCTTTATGACACGTTTATCTC
7183118 TGCCTTT
1 TGCCTTT
7183125 TGGTAGCTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.09, C:0.23, G:0.17, T:0.51
Consensus pattern (23 bp):
TGCCTTTATGACACGTTTATCTC
Found at i:7183708 original size:23 final size:25
Alignment explanation
Indices: 7183676--7183741 Score: 77
Period size: 24 Copynumber: 2.7 Consensus size: 25
7183666 AAAATAATAT
7183676 TAAATAAATTATT-TTAATATTT-TAA
1 TAAAT-AATTATTATT-ATATTTCTAA
7183701 -AAATAATTATTAATTATATTTCTAA
1 TAAATAATTATT-ATTATATTTCTAA
7183726 TAAATAA-TATTATTAT
1 TAAATAATTATTATTAT
7183742 TATACTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
23 7 0.19
24 15 0.41
25 9 0.24
26 6 0.16
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TAAATAATTATTATTATATTTCTAA
Found at i:7183759 original size:28 final size:29
Alignment explanation
Indices: 7183682--7183770 Score: 78
Period size: 28 Copynumber: 3.1 Consensus size: 29
7183672 ATATTAAATA
*
7183682 AATTAT-TTTAATATTTTAAAAATAATTATT
1 AATTATATTT-ATA-TTTAATAATAATTATT
* * *
7183712 AATTATATTTCTAATAAATAAT-ATTATT
1 AATTATATTTATATTTAATAATAATTATT
7183740 -ATTATACTTTATATTTAATAAATAATT-TT
1 AATTATA-TTTATATTTAAT-AATAATTATT
7183769 AA
1 AA
7183771 AAAAATTATC
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
27 6 0.13
28 15 0.32
29 11 0.23
30 12 0.26
31 3 0.06
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
AATTATATTTATATTTAATAATAATTATT
Found at i:7187752 original size:154 final size:155
Alignment explanation
Indices: 7187497--7188611 Score: 1172
Period size: 154 Copynumber: 7.3 Consensus size: 155
7187487 CAACCATCGA
* * *
7187497 GTTCGCTTCCTCTTT-TTTAGGGAGTATAGAACTCGAAC-TTCTTCTGCAAACGGGTTCGCTCCC
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACAATC-T-T-CAAACGGGTTCGCTCCC
* *
7187560 TCT-TATTAGGG-GTATACAACTCGAAAATCTTCAAACGGGTTCGTTCCCTCTTTCTCTAGGGAG
63 TCTCT-TTAGGGAGTATAGAACTCGAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAG
7187623 TATAGAACTCGGACATCTTCTTCAAACGG
127 TATAGAACTCGGACATCTTCTTCAAACGG
*
7187652 GTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACAATCTTCAAACGGGTTCGCT-CCTCT
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCT
* * ** *
7187716 CTTTAGGGAGTATGGAACTCGAACATCTTCTTACGGGTTCACTCCCTCTTTCTCTAGGGAGTATA
66 CTTTAGGGAGTATAGAACTCGAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATA
*
7187781 GAACTTGGACATCTTCTTCAAACGG
131 GAACTCGGACATCTTCTTCAAACGG
* *
7187806 GTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACAATCTTTAAACGGGTTCGCTCCCTCT
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCT
* * ** *
7187871 CTTTAGGGAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGAAGT
66 CTTTAGGGAGTATAGAACTCGAA-A--ATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGT
* *
7187936 ATAGAACTCGAACA--ATCTTCAAACGG
128 ATAGAACTCGGACATCTTCTTCAAACGG
* * * **
7187962 GTTCGCTCCCTC--TCTTTAGGGAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCT
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACA--ATCTTCAAACGGGTTCGCTCCCT
* * * *
7188025 CTTTATTA-GGAG-ATACAACTCG-AAATCTTCAAACGGGTTCGTTCCCTC--TCTTTAGGGAGT
64 CTCT-TTAGGGAGTATAGAACTCGAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGT
* * **
7188085 ATGGAACTCGAACATCTTCTTCTTACGG
128 ATAGAACTCGGACATCTTCTTCAAACGG
* * * *
7188113 GTTTGCTCCCTCTTTC-TCTAGGGAGTATAGAACTTGGACATCTTCTTCAAACGGGTTCGCTCCC
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAACA--ATCTTCAAACGGGTTCGCTCCC
* * *
7188177 TCTTTCTTCAGGAATTATAGAACTCGAATAATCTTCAAACGGGTTCGCT--CTC--T-T-TAGGG
63 TC--TCTTTAGGGAGTATAGAACTCGAA-AATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGG
* * *
7188236 AGTATGGAACTCAGACATCTTCTTCAAATGG
125 AGTATAGAACTCGGACATCTTCTTCAAACGG
* * *
7188267 GTTCGCT-CCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTCAAACGGGTTCACTCCCTCT
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCT
* * ** *
7188331 CTTTAGGGAGTATGGAATTC-AAACATCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGAAGTAT
66 CTTTAGGGAGTATAGAACTCGAAA-ATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTAT
* *
7188395 AGAACTCGAACA--ATCTTCAAACGG
130 AGAACTCGGACATCTTCTTCAAACGG
* * * *
7188419 GTTCG-T---TC--TCTTTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCT
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACA--ATCTTCAAACGGGTTCGCTCCCT
* * * * *
7188478 CTTTCTTCAAGAAGTATAGAACTCGAATAATCTTCGAACGGGTTTGCTCCCTCTTTCTCTAGGGA
64 C--TCTTTAGGGAGTATAGAACTCGAA-AATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGA
7188543 GTATAGAACTCGGACA-CTTC-T--AACGG
126 GTATAGAACTCGGACATCTTCTTCAAACGG
* * *
7188569 GTTCGCTCCCTCTAT-TT-AGGGAGTATGGAACTCGGAC-ATCTTC
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACAATCTTC
7188612 TTCTGCTTCA
Statistics
Matches: 820, Mismatches: 97, Indels: 90
0.81 0.10 0.09
Matches are distributed among these distances:
147 22 0.03
148 19 0.02
149 63 0.08
150 13 0.02
151 85 0.10
152 67 0.08
153 85 0.10
154 251 0.31
155 58 0.07
156 85 0.10
157 6 0.01
158 66 0.08
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (155 bp):
GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCT
CTTTAGGGAGTATAGAACTCGAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATA
GAACTCGGACATCTTCTTCAAACGG
Found at i:7187910 original size:52 final size:53
Alignment explanation
Indices: 7187497--7188614 Score: 1088
Period size: 52 Copynumber: 21.9 Consensus size: 53
7187487 CAACCATCGA
* * * *
7187497 GTTCGCTTCCTCTTTTTTAGGGAGTATAGAACTCGAACTTCTTCTGCAAACGG
1 GTTCGCTCCCTCTTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* * *
7187550 GTTCGCTCCCTCTT-ATTAGGG-GTATACAACTCGAA-A--ATCTTCAAACGG
1 GTTCGCTCCCTCTTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* * *
7187598 GTTCGTTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTCAAACGG
1 GTTCGCTCCCTC-TTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* * *
7187652 GTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACA--ATCTTCAAACGG
1 GTTCGCTCCCTC-TTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
*
7187704 GTTCGCT-CCTC-TCTTTAGGGAGTATGGAACTCGAACATCTTCTT---ACGG
1 GTTCGCTCCCTCTTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* * * *
7187752 GTTCACTCCCTCTTTCTCTAGGGAGTATAGAACTTGGACATCTTCTTCAAACGG
1 GTTCGCTCCCTC-TTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* *
7187806 GTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACAATC-T-TT-AAACGG
1 GTTCGCTCCCTC-TTCTTTAGGGAGTATAGAACTCGAAC-ATCTTCTTCAAACGG
* **
7187858 GTTCGCTCCCTC-TCTTTAGGGAGTATGGAACTCGAACATCTTCTTCTTACGG
1 GTTCGCTCCCTCTTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* * *
7187910 GTTCGCTCCCTCTTTCTCTAGGAAGTATAGAACTCGAACA--ATCTTCAAACGG
1 GTTCGCTCCCTC-TTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* **
7187962 GTTCGCTCCCTC-TCTTTAGGGAGTATGGAACTCGAACATCTTCTTCTTACGG
1 GTTCGCTCCCTCTTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
*
7188014 GTTCGCTCCCTCTT-TATTA-GGAG-ATACAACTCGAA-A---TCTTCAAACGG
1 GTTCGCTCCCTCTTCT-TTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* * **
7188061 GTTCGTTCCCTC-TCTTTAGGGAGTATGGAACTCGAACATCTTCTTCTTACGG
1 GTTCGCTCCCTCTTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* * * *
7188113 GTTTGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGACATCTTCTTCAAACGG
1 GTTCGCTCCCTC-TTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* * * **
7188167 GTTCGCTCCCTCTTTCTTCAGGAATTATAGAACTCG-A-ATAATCTTCAAACGG
1 GTTCGCTCCCTC-TTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* *
7188219 GTTCG----CTC-TCTTTAGGGAGTATGGAACTC-AGACATCTTCTTCAAATGG
1 GTTCGCTCCCTCTTCTTTAGGGAGTATAGAACTCGA-ACATCTTCTTCAAACGG
* * **
7188267 GTTCGCT-CCTCTTTCTTCAGGAAGTATAGAACTCG-A-ATAATCTTCAAACGG
1 GTTCGCTCCCTC-TTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* * * *
7188318 GTTCACTCCCTC-TCTTTAGGGAGTATGGAATTCAAACATCTTCTT---ACGG
1 GTTCGCTCCCTCTTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* * *
7188367 GTTCGCTCCCTCTTTCTCTAGGAAGTATAGAACTCGAACA--ATCTTCAAACGG
1 GTTCGCTCCCTC-TTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* *
7188419 GTTCG-T---TC-TCTTTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* * * ** *
7188467 GTTCGCTCCCTCTTTCTTCAAGAAGTATAGAACTCG-A-ATAATCTTCGAACGG
1 GTTCGCTCCCTC-TTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* * *
7188519 GTTTGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACA-CTTC-T--AACGG
1 GTTCGCTCCCTC-TTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* * *
7188569 GTTCGCTCCCTC-TATTTAGGGAGTATGGAACTCGGACATCTTCTTC
1 GTTCGCTCCCTCTTCTTTAGGGAGTATAGAACTCGAACATCTTCTTC
7188615 TGCTTCACTA
Statistics
Matches: 876, Mismatches: 126, Indels: 128
0.78 0.11 0.11
Matches are distributed among these distances:
46 43 0.05
47 26 0.03
48 102 0.12
49 57 0.07
50 86 0.10
51 118 0.13
52 209 0.24
53 42 0.05
54 190 0.22
55 3 0.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (53 bp):
GTTCGCTCCCTCTTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
Found at i:7189045 original size:36 final size:35
Alignment explanation
Indices: 7188975--7189197 Score: 249
Period size: 36 Copynumber: 6.4 Consensus size: 35
7188965 CACTTTCTGA
* * *
7188975 GAAGGCTTAAAATGGATCTGCTTCACT-T-T-TGGT
1 GAAGGCTTAAGATGG-TTTGCTTCACTATCTCCGGT
* * *
7189008 GAAGACTTAAGATGGTTTGCTTCGCTACTCTCTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTA-TCTCCGGT
* *
7189044 GAAGACTTATGATGGTTTGCTTCACTAT-TCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATCTCCGGT
* * *
7189078 GAAGGCTTCAGATTGATTGCTTCACTATCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATCTCCGGT
*
7189113 GAAGGCTTCAGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTA-TCTCCGGT
*
7189149 GAAGGCTTAGGATGGTTTGCTTCACT-TCTCTTCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATCTC--CGGT
7189185 GAAGGCTTAAGAT
1 GAAGGCTTAAGAT
7189198 TGACTTTGCT
Statistics
Matches: 165, Mismatches: 17, Indels: 13
0.85 0.09 0.07
Matches are distributed among these distances:
32 9 0.05
33 13 0.08
34 33 0.20
35 33 0.20
36 77 0.47
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (35 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATCTCCGGT
Found at i:7189131 original size:105 final size:106
Alignment explanation
Indices: 7188975--7189200 Score: 291
Period size: 105 Copynumber: 2.2 Consensus size: 106
7188965 CACTTTCTGA
* * * *
7188975 GAAGGCTTAAAATGGATCTGCTTCACT-T-T-TGGTGAAGACTTAAGATGGTTTGCTTCGCTACT
1 GAAGGCTTAAGATTGAT-TGCTTCACTATCTCCGGTGAAGACTTAAGATGGTTTGCTTCACTACT
* *
7189037 CTCTGGTGAAGACTTATGATGGTTTGCTTCACTAT-TC-CGGT
65 CTCCGGTGAAGACTTAGGATGGTTTGCTTCACT-TCTCTCGGT
* * * *
7189078 GAAGGCTTCAGATTGATTGCTTCACTATCTCCGGTGAAGGCTTCAGATGGTTTGCTTCACTATTC
1 GAAGGCTTAAGATTGATTGCTTCACTATCTCCGGTGAAGACTTAAGATGGTTTGCTTCACTACTC
*
7189143 TCCGGTGAAGGCTTAGGATGGTTTGCTTCACTTCTCTTCGGT
66 TCCGGTGAAGACTTAGGATGGTTTGCTTCACTTCTC-TCGGT
7189185 GAAGGCTTAAGATTGA
1 GAAGGCTTAAGATTGA
7189201 CTTTGCTCCA
Statistics
Matches: 105, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
102 9 0.09
103 15 0.14
104 2 0.02
105 60 0.57
107 19 0.18
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (106 bp):
GAAGGCTTAAGATTGATTGCTTCACTATCTCCGGTGAAGACTTAAGATGGTTTGCTTCACTACTC
TCCGGTGAAGACTTAGGATGGTTTGCTTCACTTCTCTCGGT
Found at i:7198056 original size:3 final size:3
Alignment explanation
Indices: 7198050--7198085 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
7198040 ACATTATTAT
7198050 TAA TAA TAA -AA TAA T-A TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
7198086 TCCCGGACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:7198867 original size:2 final size:2
Alignment explanation
Indices: 7198860--7198887 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7198850 ATAAAGGATA
7198860 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
7198888 GAAATAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7203800 original size:25 final size:25
Alignment explanation
Indices: 7203746--7203800 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
7203736 GAGTATATAG
* *
7203746 ACTATCAATTTTAATCTATTTTAAT
1 ACTATAAATTTTAATCTATTTTAAA
*
7203771 A-TATAAACTTTTAAT-TTTTTTAAA
1 ACTATAAA-TTTTAATCTATTTTAAA
7203795 ACTATA
1 ACTATA
7203801 TGCTAAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (25 bp):
ACTATAAATTTTAATCTATTTTAAA
Found at i:7214723 original size:24 final size:24
Alignment explanation
Indices: 7214696--7214743 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
7214686 GAATATCTCT
*
7214696 GTCTC-GTCTGCGTTCTCTATCGCG
1 GTCTCGGTCT-CGTTCCCTATCGCG
*
7214720 GTCTCGGTCTCGTTCCCTCTCGCG
1 GTCTCGGTCTCGTTCCCTATCGCG
7214744 TCGGTCTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.02, C:0.38, G:0.25, T:0.35
Consensus pattern (24 bp):
GTCTCGGTCTCGTTCCCTATCGCG
Found at i:7221432 original size:17 final size:19
Alignment explanation
Indices: 7221410--7221446 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
7221400 TATTATGATG
7221410 AATATTTTT-A-AAGTTTT
1 AATATTTTTCATAAGTTTT
7221427 AATATTTTTCATAAGTTTT
1 AATATTTTTCATAAGTTTT
7221446 A
1 A
7221447 GTTCATCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 1 0.06
19 8 0.44
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (19 bp):
AATATTTTTCATAAGTTTT
Found at i:7223526 original size:29 final size:29
Alignment explanation
Indices: 7223480--7223535 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
7223470 TATGTTAAGA
* *
7223480 GAGCGAACTTGAACTTATAAAATTTTAGT
1 GAGCGAACTTAAAATTATAAAATTTTAGT
7223509 GAGCGAACTTAAAATTATAAAATTTTA
1 GAGCGAACTTAAAATTATAAAATTTTA
7223536 ATGGGACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (29 bp):
GAGCGAACTTAAAATTATAAAATTTTAGT
Found at i:7228168 original size:2 final size:2
Alignment explanation
Indices: 7228161--7228188 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7228151 TTTTATTTAA
7228161 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
7228189 ACACAGCCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:7228394 original size:15 final size:15
Alignment explanation
Indices: 7228374--7228418 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
7228364 GAGTATTATT
7228374 AATTTAATTTATAAA
1 AATTTAATTTATAAA
7228389 AATTTAAATTT-TAAA
1 AATTT-AATTTATAAA
*
7228404 ATATTTAATATATAA
1 A-ATTTAATTTATAA
7228419 TTATAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTAATTTATAAA
Found at i:7228409 original size:16 final size:16
Alignment explanation
Indices: 7228374--7228411 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
7228364 GAGTATTATT
7228374 AATTT-AATTTATAAA
1 AATTTAAATTTATAAA
7228389 AATTTAAATTT-TAAA
1 AATTTAAATTTATAAA
7228404 ATATTTAA
1 A-ATTTAA
7228412 TATATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTAAATTTATAAA
Found at i:7228447 original size:22 final size:22
Alignment explanation
Indices: 7228422--7228471 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
7228412 TATATAATTA
7228422 TAAATTAA-TTAAAAAATAAAGG
1 TAAATTAACTTAAAAAA-AAAGG
*
7228444 TAAA-TAACTTAAAATAAAAGG
1 TAAATTAACTTAAAAAAAAAGG
7228465 TAAATTA
1 TAAATTA
7228472 TATCAATAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (22 bp):
TAAATTAACTTAAAAAAAAAGG
Found at i:7231401 original size:31 final size:31
Alignment explanation
Indices: 7231333--7231429 Score: 119
Period size: 31 Copynumber: 3.1 Consensus size: 31
7231323 AATTTAAGTG
* *
7231333 TTAAAATGAAACAAAAAGTTAAC--AACGAGTTA
1 TTAAAATGAAATAAAAAATTAACGTAAC-A--TA
7231365 TTAAAATGAAATAAAAAATTAACGATAA-ATA
1 TTAAAATGAAATAAAAAATTAACG-TAACATA
7231396 TTAAAATGAAATAAAAAATTAACGTAACATA
1 TTAAAATGAAATAAAAAATTAACGTAACATA
7231427 TTA
1 TTA
7231430 TTTTGAAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
30 3 0.05
31 32 0.54
32 21 0.36
33 1 0.02
35 2 0.03
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.26
Consensus pattern (31 bp):
TTAAAATGAAATAAAAAATTAACGTAACATA
Found at i:7234839 original size:15 final size:15
Alignment explanation
Indices: 7234819--7234849 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
7234809 GATATGCATA
7234819 GTGATAATGCACATG
1 GTGATAATGCACATG
7234834 GTGATAATGCACATG
1 GTGATAATGCACATG
7234849 G
1 G
7234850 GACCGAACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (15 bp):
GTGATAATGCACATG
Done.