Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 183 of 190
Found at i:53975128 original size:15 final size:15
Alignment explanation
Indices: 53975084--53975129 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
53975074 TCCCAACCCT
53975084 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
*
53975098 T-TATCCATAATCCC
1 TAAATCCATAATCCC
*
53975112 TAAATCCATACTCCC
1 TAAATCCATAATCCC
53975127 TAA
1 TAA
53975130 TCCTTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 1 0.04
14 12 0.44
15 14 0.52
ACGTcount: A:0.37, C:0.35, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:53975428 original size:15 final size:15
Alignment explanation
Indices: 53975382--53975419 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
53975372 TCCCAACCCT
53975382 TAAAT-CATAATCCC
1 TAAATCCATAATCCC
53975396 T-AATCCATAATCCC
1 TAAATCCATAATCCC
53975410 TAAATCCATA
1 TAAATCCATA
53975420 CTCTCTAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 11 0.50
15 8 0.36
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:53975435 original size:298 final size:288
Alignment explanation
Indices: 53974916--53975639 Score: 1020
Period size: 298 Copynumber: 2.5 Consensus size: 288
53974906 AATATATTTG
*
53974916 ATTTATTATTATCTATTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAATAATT
1 ATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAA-T-AAAAAATAATT
* * * *
53974981 AATCTAAACTCAAAACCTTAACCCGGCCCCTGAATCCCTAAACCTTAAATCCCTAACTCTTAACC
64 AATCTAAACCCAAAACCCTAACCCGACCCCTGAATCCCTAAACCTTAAACCCCTAACTCTTAACC
*
53975046 CCTAAACCCTTAACCACTAAACCTTAAATCCCAACCCTTAAACCATAATCCCTTATCCATAATCC
129 CCTAAACCCTTAACCACTAAACCTTAAATCCCAACCCTTAAACCATAATCCCTAATCCATAATCC
* * * *
53975111 CTAAATCCATACTCCCTAATCCTTAAAATATGAGCTCCTAAATCGGCCTTAAATCTTAAATTAAT
194 CTAAATCCATACTCCCTAAACCTTAAAATATGAACTCCTAAACCGGCCTTAAATCTTAAATAAAT
*
53975176 CATATACCCTAAACTAAAAACCCTAAACAA
259 CATATACCCTAAACCAAAAACCCTAAACAA
*
53975206 ATTTATTATTATCTCTTTTACAATCATATAAGAACATATTTAAAATATAAATGAAAAAATAATTA
1 ATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAAT-AAAAAATAATTA
* * *
53975271 ATCTAAACCCAAAACCCTAACCCGACCCCTGAATCCCT-AACTTTTAACCCCTAACGTGTCTAAC
65 ATCTAAACCCAAAACCCTAACCCGACCCCTGAATCCCTAAACCTTAAACCCCTAAC-TCT-TAAC
* *
53975335 CCCTAAACCCCTAACCATCTAACCGCTAAACCTTAAATCCCAACCCTTAAATCATAATCCCTAAT
128 CCCTAAA---C---CC-T-TAACCACTAAACCTTAAATCCCAACCCTTAAACCATAATCCCTAAT
* *
53975400 CCATAATCCCTAAATCCATACTCTCTAAACCTTAAAATATGAACTCTTAAACCGGCCTTAAATCT
185 CCATAATCCCTAAATCCATACTCCCTAAACCTTAAAATATGAACTCCTAAACCGGCCTTAAATCT
53975465 TAAATAAATCATATACCCTAAACCAAAAACCCTAAACAA
250 TAAATAAATCATATACCCTAAACCAAAAACCCTAAACAA
** *
53975504 ATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTTAAAA-AGTTAA
1 ATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATAAAAAATAATTAA
* * ** * * *
53975568 TCTAAACGCCCAAAATCCTAACTCGACCTTTGAATTCCTAAACCCTAAATCCCTAACTTTCTTAA
66 TCTAAA--CCCAAAACCCTAACCCGACCCCTGAATCCCTAAACCTTAAACCCCTAAC--TCTTAA
53975633 CCCCTAA
127 CCCCTAA
53975640 CATCTAAACC
Statistics
Matches: 385, Mismatches: 35, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
288 14 0.04
289 50 0.13
290 60 0.16
293 1 0.00
296 13 0.03
297 5 0.01
298 217 0.56
299 23 0.06
300 2 0.01
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.30
Consensus pattern (288 bp):
ATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATAAAAAATAATTAA
TCTAAACCCAAAACCCTAACCCGACCCCTGAATCCCTAAACCTTAAACCCCTAACTCTTAACCCC
TAAACCCTTAACCACTAAACCTTAAATCCCAACCCTTAAACCATAATCCCTAATCCATAATCCCT
AAATCCATACTCCCTAAACCTTAAAATATGAACTCCTAAACCGGCCTTAAATCTTAAATAAATCA
TATACCCTAAACCAAAAACCCTAAACAA
Found at i:53975661 original size:22 final size:23
Alignment explanation
Indices: 53975631--53975702 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
53975621 TAACTTTCTT
53975631 AACCCCTAA-CATCTAAACCC-TA
1 AACCCCTAACCATCT-AACCCTTA
* *
53975653 AACCGCTAACCTTCTAACCCTTA
1 AACCCCTAACCATCTAACCCTTA
* *
53975676 AACCCTTAATCC-TCTAACCTTTA
1 AACCCCTAA-CCATCTAACCCTTA
53975699 AACC
1 AACC
53975703 TTAAATCTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
22 13 0.31
23 27 0.64
24 2 0.05
ACGTcount: A:0.35, C:0.39, G:0.01, T:0.25
Consensus pattern (23 bp):
AACCCCTAACCATCTAACCCTTA
Found at i:53975691 original size:23 final size:23
Alignment explanation
Indices: 53975665--53975723 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
53975655 CCGCTAACCT
53975665 TCTAACCCTTAAACCCTT-AATCC
1 TCTAACCCTTAAACCCTTAAAT-C
*
53975688 TCTAACCTTTAAA-CCTTAAATC
1 TCTAACCCTTAAACCCTTAAATC
*
53975710 TC-AATCCTTAAACC
1 TCTAACCCTTAAACC
53975724 ATAATCCCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 8 0.26
22 8 0.26
23 15 0.48
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (23 bp):
TCTAACCCTTAAACCCTTAAATC
Found at i:53976175 original size:41 final size:41
Alignment explanation
Indices: 53976114--53976395 Score: 356
Period size: 41 Copynumber: 6.9 Consensus size: 41
53976104 TAAAATGTTT
* * * *
53976114 TTAGCGGCGCTT-TTCCAAAAACGCCGCTAAAGCCCCTAGTA
1 TTAGCGGCGCTTCTT-TAAAAACGCCGCTAAAGGCCCGAGCA
* *
53976155 TTAGCGGTGCTTCTTTAAAAACACCGCTAAAGGCCCGAGCA
1 TTAGCGGCGCTTCTTTAAAAACGCCGCTAAAGGCCCGAGCA
*
53976196 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCA
1 TTAGCGGCGCTTCTTTAAAAACGCCGCTAAAGGCCCGAGCA
* * ***
53976237 TTAGCGGCGCTTCTTCAAAAACTCCGCTAAAGGCAATAGCA
1 TTAGCGGCGCTTCTTTAAAAACGCCGCTAAAGGCCCGAGCA
*
53976278 TTAGCGGCACTT-TTTCAAAAACGCCGCTAAAGGCCCGAGCA
1 TTAGCGGCGCTTCTTT-AAAAACGCCGCTAAAGGCCCGAGCA
* **
53976319 TTAGCGGCGCTTCTTGAAAAACGCCGCTAAAGGCCATAGCA
1 TTAGCGGCGCTTCTTTAAAAACGCCGCTAAAGGCCCGAGCA
53976360 TTAGCGGCG-TT-TTTGAAAAAGCGCCGCTAAAGGCCC
1 TTAGCGGCGCTTCTTT-AAAAA-CGCCGCTAAAGGCCC
53976396 CAAAAACTCA
Statistics
Matches: 211, Mismatches: 25, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
39 2 0.01
40 9 0.04
41 196 0.93
42 4 0.02
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (41 bp):
TTAGCGGCGCTTCTTTAAAAACGCCGCTAAAGGCCCGAGCA
Found at i:53976251 original size:82 final size:82
Alignment explanation
Indices: 53976114--53976395 Score: 413
Period size: 82 Copynumber: 3.4 Consensus size: 82
53976104 TAAAATGTTT
* * * * * *
53976114 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCCTAGTATTAGCGGTGCTTCTTTAAAAACAC
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTCTTCAAAAACAC
**
53976179 CGCTAAAGGCCCGAGCA
66 CGCTAAAGGCCATAGCA
* *
53976196 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTCTTCAAAAACTC
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTCTTCAAAAACAC
*
53976261 CGCTAAAGGCAATAGCA
66 CGCTAAAGGCCATAGCA
* * *
53976278 TTAGCGGCACTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTCTTGAAAAACGC
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTCTTCAAAAACAC
53976343 CGCTAAAGGCCATAGCA
66 CGCTAAAGGCCATAGCA
*
53976360 TTAGCGGCG-TTTTTGAAAAAGCGCCGCTAAAGGCCC
1 TTAGCGGCGCTTTTTCAAAAA-CGCCGCTAAAGGCCC
53976396 CAAAAACTCA
Statistics
Matches: 181, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
81 10 0.06
82 171 0.94
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (82 bp):
TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTCTTCAAAAACAC
CGCTAAAGGCCATAGCA
Found at i:53976333 original size:123 final size:122
Alignment explanation
Indices: 53976114--53976393 Score: 400
Period size: 123 Copynumber: 2.3 Consensus size: 122
53976104 TAAAATGTTT
* ** * **
53976114 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCCTAGTATTAGCGGTGCTTCTTTAAAAACAC
1 TTAGCGGCGCTTTT-CAAAAACGCCGCTAAAGGCAATAGCATTAGCGGCACTTCTTTAAAAACAC
*
53976179 CGCTAAAGGCCCGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCA
65 CGCTAAAGGCCCGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCA
* *
53976237 TTAGCGGCGCTTCTTCAAAAACTCCGCTAAAGGCAATAGCATTAGCGGCACTT-TTTCAAAAACG
1 TTAGCGGCGCTT-TTCAAAAACGCCGCTAAAGGCAATAGCATTAGCGGCACTTCTTT-AAAAACA
* *
53976301 CCGCTAAAGGCCCGAGCATTAGCGGCGCTTCTTGAAAAACGCCGCTAAAGGCCATAGCA
64 CCGCTAAAGGCCCGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCA
* *
53976360 TTAGCGGCGTTTTTGAAAAAGCGCCGCTAAAGGC
1 TTAGCGGCGCTTTTCAAAAA-CGCCGCTAAAGGC
53976394 CCCAAAAACT
Statistics
Matches: 140, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
122 10 0.07
123 128 0.91
124 2 0.01
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.21
Consensus pattern (122 bp):
TTAGCGGCGCTTTTCAAAAACGCCGCTAAAGGCAATAGCATTAGCGGCACTTCTTTAAAAACACC
GCTAAAGGCCCGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCA
Found at i:53976480 original size:39 final size:40
Alignment explanation
Indices: 53976431--53976524 Score: 113
Period size: 39 Copynumber: 2.4 Consensus size: 40
53976421 TGGCTTAGGC
* *
53976431 TTTTT-GCGGCGCTTTT-CAAAAAACGCCGCTAATG-TTTA
1 TTTTTAGCGGCG-TTTTCCAAAAAACGCAGCTAATGCTTGA
* *
53976469 TTTTTAGCGGCGTTTTCCCAAAAGCGCAGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTCCAAAAAACGCAGCTAATGCTTGA
*
53976509 TTTTTAGTGGCGTTTT
1 TTTTTAGCGGCGTTTT
53976525 TTGTCCAAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 9 0.19
39 21 0.44
40 18 0.38
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.39
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTCCAAAAAACGCAGCTAATGCTTGA
Found at i:53976548 original size:12 final size:12
Alignment explanation
Indices: 53976531--53976556 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53976521 TTTTTTGTCC
53976531 AAACGCCGCTAA
1 AAACGCCGCTAA
53976543 AAACGCCGCTAA
1 AAACGCCGCTAA
53976555 AA
1 AA
53976557 GCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:53976898 original size:26 final size:27
Alignment explanation
Indices: 53976869--53976926 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 27
53976859 CTTTTAGAAA
53976869 TATTTA-AATATATTATATATCATTCC
1 TATTTAGAATATATTATATATCATTCC
*
53976895 TATTTAGGAATATATTATATATCTTTCC
1 TATTTA-GAATATATTATATATCATTCC
53976923 TATT
1 TATT
53976927 CCTACGTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 6 0.21
28 23 0.79
ACGTcount: A:0.34, C:0.10, G:0.03, T:0.52
Consensus pattern (27 bp):
TATTTAGAATATATTATATATCATTCC
Found at i:53978315 original size:29 final size:29
Alignment explanation
Indices: 53978281--53978337 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
53978271 TTGATATATG
*
53978281 AACTTTAATTTTGGTTCAAATATATACAC
1 AACTTTAATTTTGATTCAAATATATACAC
** *
53978310 AACTTTGTTTTTGATTCAATTATATACA
1 AACTTTAATTTTGATTCAAATATATACA
53978338 TTTAAAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (29 bp):
AACTTTAATTTTGATTCAAATATATACAC
Found at i:53992634 original size:28 final size:28
Alignment explanation
Indices: 53992597--53992681 Score: 93
Period size: 28 Copynumber: 3.0 Consensus size: 28
53992587 GGATAAGTGT
53992597 ATATATATTATAAATATT-TAA-AGTTAAA
1 ATATATATTAT-AATATTATAATA-TTAAA
*
53992625 ATATATATTATAATATTATAATATTATA
1 ATATATATTATAATATTATAATATTAAA
* * *
53992653 ATTTATATTATTATATTATTATAATTAAA
1 ATATATATTATAATATTATAAT-ATTAAA
53992682 TAAAAGAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
27 6 0.12
28 37 0.76
29 6 0.12
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
ATATATATTATAATATTATAATATTAAA
Found at i:53992642 original size:8 final size:8
Alignment explanation
Indices: 53992629--53992677 Score: 73
Period size: 8 Copynumber: 6.2 Consensus size: 8
53992619 GTTAAAATAT
53992629 ATATTATA
1 ATATTATA
53992637 ATATTATA
1 ATATTATA
53992645 ATATTATA
1 ATATTATA
53992653 AT-TTATA
1 ATATTATA
*
53992660 TTATTATA
1 ATATTATA
*
53992668 TTATTATA
1 ATATTATA
53992676 AT
1 AT
53992678 TAAATAAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
7 6 0.16
8 32 0.84
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
ATATTATA
Found at i:53992652 original size:23 final size:22
Alignment explanation
Indices: 53992626--53992683 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
53992616 AAAGTTAAAA
53992626 TATATATTATAATATTATAATAT
1 TATA-ATTATAATATTATAATAT
* *
53992649 TATAATTTATATTATTATATTAT
1 TATAA-TTATAATATTATAATAT
53992672 TATAATTA-AATA
1 TATAATTATAATA
53992684 AAAGAAAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 3 0.10
22 4 0.13
23 24 0.77
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATAATTATAATATTATAATAT
Found at i:53992744 original size:11 final size:10
Alignment explanation
Indices: 53992684--53992746 Score: 54
Period size: 11 Copynumber: 5.8 Consensus size: 10
53992674 TAATTAAATA
53992684 AAAGAAAAAG
1 AAAGAAAAAG
53992694 AATAGAAAAAG
1 AA-AGAAAAAG
* *
53992705 AAAGACCATAG
1 AAAGA-AAAAG
*
53992716 AAACGAAACAG
1 AAA-GAAAAAG
53992727 AAGAGAAAAAGG
1 AA-AGAAAAA-G
53992739 AAAGAAAA
1 AAAGAAAA
53992747 GGTGAAAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
10 5 0.12
11 32 0.74
12 6 0.14
ACGTcount: A:0.70, C:0.06, G:0.21, T:0.03
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:53993440 original size:24 final size:24
Alignment explanation
Indices: 53993396--53993442 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
53993386 ATTACTATGG
53993396 ATTGATTTAGTATGTGATGAATTT
1 ATTGATTTAGTATGTGATGAATTT
53993420 ATTGAATTTA-TAT-TGATTGAATT
1 ATTG-ATTTAGTATGTGA-TGAATT
53993443 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGATTTAGTATGTGATGAATTT
Found at i:53995317 original size:22 final size:22
Alignment explanation
Indices: 53995287--53995328 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
53995277 AAAATTGAAG
*
53995287 TAATTGAAAATATTCTACTTTC
1 TAATAGAAAATATTCTACTTTC
53995309 TAATAGAAAATATTCTACTT
1 TAATAGAAAATATTCTACTT
53995329 AATTGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (22 bp):
TAATAGAAAATATTCTACTTTC
Found at i:53998640 original size:29 final size:29
Alignment explanation
Indices: 53998597--53998703 Score: 115
Period size: 29 Copynumber: 3.7 Consensus size: 29
53998587 GCTCTTTGTA
53998597 CTGTTAATGCACTTCGGTGCCACTCTGTT
1 CTGTTAATGCACTTCGGTGCCACTCTGTT
* * * * *
53998626 TTGTTAAAGCACTTCAGTGTCATTCTGTT
1 CTGTTAATGCACTTCGGTGCCACTCTGTT
* *
53998655 CTGATATTGCACTTCGGTGCCACTCTGTT
1 CTGTTAATGCACTTCGGTGCCACTCTGTT
* * * *
53998684 CTATCATTGCACTTTGGTGC
1 CTGTTAATGCACTTCGGTGC
53998704 ATCTCTTTAT
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (29 bp):
CTGTTAATGCACTTCGGTGCCACTCTGTT
Found at i:54002849 original size:3 final size:3
Alignment explanation
Indices: 54002841--54002875 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
54002831 CCTGGGATTT
54002841 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
54002876 ATTTACATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:54008458 original size:25 final size:25
Alignment explanation
Indices: 54008424--54008502 Score: 149
Period size: 25 Copynumber: 3.2 Consensus size: 25
54008414 ACTTGGATGG
54008424 ATGTTGTCTCGCCTGCATTTTGAAA
1 ATGTTGTCTCGCCTGCATTTTGAAA
54008449 ATGTTGTCTCGCCTGCATTTTGAAA
1 ATGTTGTCTCGCCTGCATTTTGAAA
*
54008474 ATGATGTCTCGCCTGCATTTTGAAA
1 ATGTTGTCTCGCCTGCATTTTGAAA
54008499 ATGT
1 ATGT
54008503 CTGGGCTTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (25 bp):
ATGTTGTCTCGCCTGCATTTTGAAA
Found at i:54017209 original size:20 final size:20
Alignment explanation
Indices: 54017184--54017223 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
54017174 AAGCCTTATG
54017184 GATAGAGGTAAAAAAACCTC
1 GATAGAGGTAAAAAAACCTC
54017204 GATAGAGGTAAAAAAACCTC
1 GATAGAGGTAAAAAAACCTC
54017224 TAGAAAGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.20, T:0.15
Consensus pattern (20 bp):
GATAGAGGTAAAAAAACCTC
Found at i:54019034 original size:20 final size:19
Alignment explanation
Indices: 54018982--54019050 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
54018972 TTATATAGAT
*
54018982 ATATTTTTATAATTTAT-A
1 ATATTTTTATAATTTTTAA
54019000 AT-TTCTTCTAT-ATTTTTAA
1 ATATT-TT-TATAATTTTTAA
54019019 ATATTTTATATAATTTTTAA
1 ATATTTT-TATAATTTTTAA
54019039 ATATTTTTATAA
1 ATATTTTTATAA
54019051 AAAATAGATT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
17 2 0.05
18 9 0.20
19 16 0.36
20 17 0.39
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATTTTTATAATTTTTAA
Found at i:54019046 original size:11 final size:10
Alignment explanation
Indices: 54019009--54019047 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
54018999 AATTTCTTCT
54019009 ATATTTTTAA
1 ATATTTTTAA
*
54019019 ATA-TTTTAT
1 ATATTTTTAA
54019028 ATAATTTTTAA
1 AT-ATTTTTAA
54019039 ATATTTTTA
1 ATATTTTTA
54019048 TAAAAAATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 7 0.28
10 11 0.44
11 7 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATATTTTTAA
Found at i:54027581 original size:22 final size:22
Alignment explanation
Indices: 54027555--54027596 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
54027545 CATCTTAATA
54027555 TTAATATTTATATTTTTAAATT
1 TTAATATTTATATTTTTAAATT
*
54027577 TTAATATTTATGTTTTTAAA
1 TTAATATTTATATTTTTAAA
54027597 CCTTGCGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTAATATTTATATTTTTAAATT
Found at i:54030277 original size:30 final size:30
Alignment explanation
Indices: 54030234--54030299 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
54030224 AAATTGGTAT
*
54030234 TTATTTATTTTATCATAAG-GGTACCAAAA
1 TTATTTATGTTATCATAAGTGGTACCAAAA
* *
54030263 TTATATTATGTTATCTTAAGTGGTACCTAAA
1 TTAT-TTATGTTATCATAAGTGGTACCAAAA
*
54030294 TGATTT
1 TTATTT
54030300 TTCGTTACCC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 4 0.13
30 15 0.48
31 12 0.39
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (30 bp):
TTATTTATGTTATCATAAGTGGTACCAAAA
Found at i:54051486 original size:20 final size:20
Alignment explanation
Indices: 54051461--54051500 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
54051451 ATATGTCTAA
54051461 TTGAATTCTAGTAGCTAAAG
1 TTGAATTCTAGTAGCTAAAG
54051481 TTGAATTCTAGTAGCTAAAG
1 TTGAATTCTAGTAGCTAAAG
54051501 GGATCAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (20 bp):
TTGAATTCTAGTAGCTAAAG
Found at i:54051552 original size:47 final size:47
Alignment explanation
Indices: 54051483--54051575 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
54051473 AGCTAAAGTT
54051483 GAATTCTAGTAGCTAAAGGGATCAAGAAGCTATGGAATTCAATATTA
1 GAATTCTAGTAGCTAAAGGGATCAAGAAGCTATGGAATTCAATATTA
54051530 GAATTCTAGTAGCTAAAGGGATCAAGAAGCTATGGAATTCAATATT
1 GAATTCTAGTAGCTAAAGGGATCAAGAAGCTATGGAATTCAATATT
54051576 TGAGGTCCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.28
Consensus pattern (47 bp):
GAATTCTAGTAGCTAAAGGGATCAAGAAGCTATGGAATTCAATATTA
Found at i:54053965 original size:14 final size:14
Alignment explanation
Indices: 54053942--54053974 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
54053932 ATAAGGAAAC
54053942 AGAG-AAGAAAAAG
1 AGAGAAAGAAAAAG
54053955 AGAGAAAGAAAAAG
1 AGAGAAAGAAAAAG
54053969 -GAGAAA
1 AGAGAAA
54053975 AAATGAAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (14 bp):
AGAGAAAGAAAAAG
Found at i:54056602 original size:25 final size:25
Alignment explanation
Indices: 54056551--54056605 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
54056541 CTTTAGCGCC
* ***
54056551 CTCTCTGATTATTAGCACGTTGGTG
1 CTCTCTGATTACTAGCACGTCAATG
54056576 CTCTCTGATTACTAGCACGTCAATG
1 CTCTCTGATTACTAGCACGTCAATG
54056601 CTCTC
1 CTCTC
54056606 CGTTTAACAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.36
Consensus pattern (25 bp):
CTCTCTGATTACTAGCACGTCAATG
Found at i:54059678 original size:42 final size:42
Alignment explanation
Indices: 54059625--54059736 Score: 116
Period size: 42 Copynumber: 2.7 Consensus size: 42
54059615 TGCTAAATAG
* * * *
54059625 AAACCCGTAAGGGTTGACCGGAAGCTCATAAGAACTGAACGA
1 AAACCCATAAGGGTTGAACAGAAGCTCAAAAGAACTGAACGA
* * * * *
54059667 AAATCGATAAGGGTTAAACAGAAGCTCAAAAGAGCTGAACGG
1 AAACCCATAAGGGTTGAACAGAAGCTCAAAAGAACTGAACGA
* * *
54059709 AAACCCATTAGGGTTGAACTGAAACTCA
1 AAACCCATAAGGGTTGAACAGAAGCTCA
54059737 TATGAGTTAA
Statistics
Matches: 55, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.16
Consensus pattern (42 bp):
AAACCCATAAGGGTTGAACAGAAGCTCAAAAGAACTGAACGA
Found at i:54080009 original size:5 final size:5
Alignment explanation
Indices: 54079999--54080034 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
54079989 TTTTTATGTT
* *
54079999 TTATA TTATA TTATA TTATA TTGTA TTATA CTATA T
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA T
54080035 AAATTAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:54081350 original size:2 final size:2
Alignment explanation
Indices: 54081343--54081375 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
54081333 TAGTATGTAA
54081343 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54081376 AATTTAAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54082468 original size:8 final size:8
Alignment explanation
Indices: 54082451--54082513 Score: 74
Period size: 8 Copynumber: 8.0 Consensus size: 8
54082441 ATGAATATAT
*
54082451 ATGTGTAA
1 ATGTGAAA
54082459 ATGTGAAA
1 ATGTGAAA
54082467 ATGTGAAA
1 ATGTGAAA
* *
54082475 ATATGATA
1 ATGTGAAA
*
54082483 AT-TGAAT
1 ATGTGAAA
*
54082490 ATGTGTAA
1 ATGTGAAA
54082498 ATGTGAAA
1 ATGTGAAA
54082506 ATGTGAAA
1 ATGTGAAA
54082514 CTGTATCGGG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
7 5 0.11
8 41 0.89
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (8 bp):
ATGTGAAA
Found at i:54104820 original size:20 final size:20
Alignment explanation
Indices: 54104795--54104834 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
54104785 AGCAATTACA
54104795 CAATTC-ACATATATAATATT
1 CAATTCAACATATA-AATATT
54104815 CAATTCAAACATATAAATAT
1 CAATTC-AACATATAAATAT
54104835 AAACAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTCAACATATAAATATT
Found at i:54110773 original size:16 final size:17
Alignment explanation
Indices: 54110752--54110784 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
54110742 GAATATTATA
54110752 AATTTTCTTA-ATTTTT
1 AATTTTCTTAGATTTTT
*
54110768 AATTTTTTTAGATTTTT
1 AATTTTCTTAGATTTTT
54110785 CAAGTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (17 bp):
AATTTTCTTAGATTTTT
Found at i:54118273 original size:92 final size:93
Alignment explanation
Indices: 54118191--54118370 Score: 213
Period size: 93 Copynumber: 1.9 Consensus size: 93
54118181 TTTGGGGCCT
* * ** *
54118191 TTGGGCTAGAGTCC-GATGCTGTAATAATATTTTTATTATTTTTT-AGAATAGCTATC-ATAATT
1 TTGGGCCAGAG-CCTGATGCTGCAATAATATAATTATTATTTTTTGAAAATAGCTA-CAATAATT
* *
54118253 AGTATATATTTTATTTCATTTCCGGAGTAC
64 AGTATATATTTTATTTCATTTTCGGAGGAC
* * * *
54118283 TTGTGCCAGAGCCTGGTGCTGCAATATTATAATTATTATTTTTTGAAAATAGTTACAATAATTAG
1 TTGGGCCAGAGCCTGATGCTGCAATAATATAATTATTATTTTTTGAAAATAGCTACAATAATTAG
*
54118348 TATTTATTTTATTTCATTTTCGG
66 TATATATTTTATTTCATTTTCGG
54118371 GCAATTTGAC
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
91 2 0.03
92 35 0.47
93 37 0.50
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (93 bp):
TTGGGCCAGAGCCTGATGCTGCAATAATATAATTATTATTTTTTGAAAATAGCTACAATAATTAG
TATATATTTTATTTCATTTTCGGAGGAC
Found at i:54118718 original size:81 final size:81
Alignment explanation
Indices: 54118611--54118790 Score: 215
Period size: 81 Copynumber: 2.2 Consensus size: 81
54118601 TTATAATAAA
* **
54118611 TATTTATTTTATTT-AATTTCTAGGGCACTTGGGCTTGAGTTAGGTGGTGCAATAAATTTTGTT-
1 TATTTATTTTATTTCATTTTCTAGGGCACTTGAACTTGAGTTAGGTGGTGCAAT-AATTTT-TTC
*
54118674 A-TTTTCTAGAATAATTAT
64 ATTTTTC-AGAACAATTAT
* * * *
54118692 TATTTATTCTATTTCATTTTC-GGGGCACTTGAACTTGAGTTTGGTGTTGCAATAATTTTTTCAT
1 TATTTATTTTATTTCATTTTCTAGGGCACTTGAACTTGAGTTAGGTGGTGCAATAATTTTTTCAT
*
54118756 TTTTCGGAACAATTAT
66 TTTTCAGAACAATTAT
*
54118772 TAGTTATTTTATTTCATTT
1 TATTTATTTTATTTCATTT
54118791 CCGAAACACT
Statistics
Matches: 85, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
79 2 0.02
80 33 0.39
81 45 0.53
82 5 0.06
ACGTcount: A:0.24, C:0.09, G:0.16, T:0.51
Consensus pattern (81 bp):
TATTTATTTTATTTCATTTTCTAGGGCACTTGAACTTGAGTTAGGTGGTGCAATAATTTTTTCAT
TTTTCAGAACAATTAT
Found at i:54118786 original size:80 final size:82
Alignment explanation
Indices: 54118614--54118790 Score: 211
Period size: 80 Copynumber: 2.2 Consensus size: 82
54118604 TAATAAATAT
* **
54118614 TTATTTTATTT-AATTTCTAGGGCACTTGGGCTTGAGTTAGGTGGTGCAATAAATTTTGTTATTT
1 TTATTTTATTTCATTTTCTAGGGCACTTGAACTTGAGTTAGGTGGTGCAATAAATTTTGTTATTT
* *
54118678 TCTAGAATAATTATTAT
66 TCTAGAACAATTATTAG
* * * *
54118695 TTATTCTATTTCATTTTC-GGGGCACTTGAACTTGAGTTTGGTGTTGCAAT-AATTTT-TTCATT
1 TTATTTTATTTCATTTTCTAGGGCACTTGAACTTGAGTTAGGTGGTGCAATAAATTTTGTT-ATT
*
54118757 TT-TCGGAACAATTATTAG
65 TTCT-AGAACAATTATTAG
54118775 TTATTTTATTTCATTT
1 TTATTTTATTTCATTT
54118791 CCGAAACACT
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
79 3 0.04
80 37 0.45
81 37 0.45
82 5 0.06
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.50
Consensus pattern (82 bp):
TTATTTTATTTCATTTTCTAGGGCACTTGAACTTGAGTTAGGTGGTGCAATAAATTTTGTTATTT
TCTAGAACAATTATTAG
Found at i:54132171 original size:13 final size:14
Alignment explanation
Indices: 54132146--54132172 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54132136 TATTAGTTCT
54132146 ATTAAATTTTTTTA
1 ATTAAATTTTTTTA
54132160 ATTAAATTTTTTT
1 ATTAAATTTTTTT
54132173 GAAGGAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTAAATTTTTTTA
Found at i:54145626 original size:3 final size:3
Alignment explanation
Indices: 54145618--54145682 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
54145608 TTGTTTCTTA
54145618 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
54145666 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
54145683 ATCTATTAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:54146994 original size:23 final size:23
Alignment explanation
Indices: 54146950--54146994 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
54146940 ATAAAAGTCA
* * *
54146950 AAATATTCTATTTTATTTATTTC
1 AAATATTATATTTTAGTAATTTC
*
54146973 AAATATTATGTTTTAGTAATTT
1 AAATATTATATTTTAGTAATTT
54146995 ATGTTTTTAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (23 bp):
AAATATTATATTTTAGTAATTTC
Found at i:54147272 original size:15 final size:15
Alignment explanation
Indices: 54147252--54147283 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
54147242 AGAAAAATTA
54147252 TTGATCTCCTTTTTC
1 TTGATCTCCTTTTTC
54147267 TTGATCTCCTTTTTC
1 TTGATCTCCTTTTTC
54147282 TT
1 TT
54147284 TTAGTTTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.25, G:0.06, T:0.62
Consensus pattern (15 bp):
TTGATCTCCTTTTTC
Found at i:54168721 original size:29 final size:30
Alignment explanation
Indices: 54168679--54168746 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
54168669 TAATAAAAAT
*
54168679 AAAATTATACTTTAATCCTTT-AAAATTATA
1 AAAATT-TAATTTAATCCTTTAAAAATTATA
*
54168709 AAAATTTAATTTAATCTTTTAAAAATTATA
1 AAAATTTAATTTAATCCTTTAAAAATTATA
54168739 AAAATTTA
1 AAAATTTA
54168747 TAATATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 12 0.34
30 23 0.66
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (30 bp):
AAAATTTAATTTAATCCTTTAAAAATTATA
Found at i:54169261 original size:19 final size:19
Alignment explanation
Indices: 54169239--54169280 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
54169229 AAAAAAATTA
54169239 AAATAATTT-TAAAAATTCC
1 AAAT-ATTTATAAAAATTCC
*
54169258 AAATATTTATGAAAATTCC
1 AAATATTTATAAAAATTCC
54169277 AAAT
1 AAAT
54169281 TTATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (19 bp):
AAATATTTATAAAAATTCC
Found at i:54175510 original size:19 final size:22
Alignment explanation
Indices: 54175474--54175515 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 22
54175464 AACTTAATTT
54175474 AATATATTTTAAATATTT-TAA
1 AATATATTTTAAATATTTATAA
*
54175495 AATATA-TTTATA-ATTTATAA
1 AATATATTTTAAATATTTATAA
54175515 A
1 A
54175516 GTAAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATATTTTAAATATTTATAA
Found at i:54178118 original size:20 final size:20
Alignment explanation
Indices: 54178093--54178133 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
54178083 AACGATGGTC
54178093 GATACCGTCTAGCTATTAGG
1 GATACCGTCTAGCTATTAGG
54178113 GATACCGTCTAGCTATTAGG
1 GATACCGTCTAGCTATTAGG
54178133 G
1 G
54178134 TTGCTCTACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (20 bp):
GATACCGTCTAGCTATTAGG
Found at i:54178455 original size:27 final size:26
Alignment explanation
Indices: 54178407--54178461 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
54178397 AATAAATTTG
* *
54178407 AAATAAAATATTTGTCTTTTTTTTATA
1 AAATAAAACATTTATCTTTTTTTT-TA
54178434 AAATAAAACATTTAT-TTATTTTTTTA
1 AAATAAAACATTTATCTT-TTTTTTTA
54178460 AA
1 AA
54178462 TCTTACTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (26 bp):
AAATAAAACATTTATCTTTTTTTTTA
Found at i:54203442 original size:2 final size:2
Alignment explanation
Indices: 54203435--54203464 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
54203425 AAAAGATGAA
54203435 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
54203465 TACTTTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54208701 original size:341 final size:341
Alignment explanation
Indices: 54208073--54208993 Score: 1496
Period size: 341 Copynumber: 2.7 Consensus size: 341
54208063 GTATACGAAT
* * ** * *
54208073 AGTGCT-AAAATTAACTTTTCCTAGTTCCTCTACCTCAGTTAGAGCAGATTGAACTTCTTCTTTA
1 AGTGCTCAAAATTAGCTTTTCCTGGTAACTCTACCTCAGTAAGAGCAGATTGAACTTCTTCTTCA
* * *
54208137 CCGAGGCCAGGACTTGTCATGTTCCCACCATCGACACAGCCTGCGGAACCATTCATTGGCCCAGT
66 ACGAGGCCAGGACTTGTCATGTTCCCACCATCGACACAGCCTGCAGAACCTTTCATTGGCCCAGT
* * * *
54208202 AG--A-A--AG-TTGCAAACGTATTCTTCTTGGAGCAATGGCTTGGTTTACAATATTCTTCTCTG
131 AGAAAGATTAGTTTGCAAGCGTATTCTTCTTGGAGCAGTGCCTTGATTTACAATATTCTTCTCTG
*
54208261 ACTCATCAGAGCTAGAAGTCTGTCCTGCAGCTTCAGCTTCTGTGACCTGCATTTAAAGTATTGGA
196 ACTCATCAGAGCTAGAAGTCTGTCCTGCAGCTTCAGCTTCTGTGACCTGCATTCAAAGTATTGGA
* *
54208326 AGATATTGTTCACTTTGAGAAATGTATGTCAGTGTACTAATATTATAATTTGGCCTTTGGCAGTA
261 AGATATTGTTCACTTTCAGAAATGTATGTCAGTGTACTAATATTATAATTTGGCCTTTAGCAGTA
54208391 AAAACAGTATATCAAC
326 AAAACAGTATATCAAC
54208407 AGTGCTCAAAATTAGCTTTTCCTGGTAACTCTACCTCAGTAAGAGCAGATTGAACTTCTTCTTCA
1 AGTGCTCAAAATTAGCTTTTCCTGGTAACTCTACCTCAGTAAGAGCAGATTGAACTTCTTCTTCA
* * * *
54208472 ACGAGACCAGGACTTGTCATGCTCCCACCATCGACGCAGCCTGCAGAACCTTTCATTGGTCCAGT
66 ACGAGGCCAGGACTTGTCATGTTCCCACCATCGACACAGCCTGCAGAACCTTTCATTGGCCCAGT
*
54208537 AGAAAGATTAGTTTGCAAGCGTATTCTTCTTGGAGCAGTGCCTTGATTTACAATATTCTTCTCTA
131 AGAAAGATTAGTTTGCAAGCGTATTCTTCTTGGAGCAGTGCCTTGATTTACAATATTCTTCTCTG
* * *
54208602 ACTCATCTGAGCTAGAAGTCAGTCCAGCAGCTTCAGCTTCTGTGACCTGCATTCAAAGTATTGGA
196 ACTCATCAGAGCTAGAAGTCTGTCCTGCAGCTTCAGCTTCTGTGACCTGCATTCAAAGTATTGGA
*
54208667 AGATATTGTTCACTTTCAGAAATGTATTTCAGTGTACTAATATTATAATTTGGCCTTTAGCAGTA
261 AGATATTGTTCACTTTCAGAAATGTATGTCAGTGTACTAATATTATAATTTGGCCTTTAGCAGTA
54208732 AAAACAGTATATCAAC
326 AAAACAGTATATCAAC
54208748 AGTGCTCAAAATTAGCTTTTCCTGGTAACTCTACCTCAGTAAGAGCAGATTGAACTTCTTCTTCA
1 AGTGCTCAAAATTAGCTTTTCCTGGTAACTCTACCTCAGTAAGAGCAGATTGAACTTCTTCTTCA
* * * *
54208813 ACGAGGCCAGGACTAGTCATGTTCCCACCATTGTCACAGCCTGCAGAACCTTTCATTGCCCCAGT
66 ACGAGGCCAGGACTTGTCATGTTCCCACCATCGACACAGCCTGCAGAACCTTTCATTGGCCCAGT
* * *
54208878 AGAAAGTTTCGTTTGCAAGCGTATTCTTCTTGGTGCAGTGCCTTGATTTACAATATTCTTCTCTG
131 AGAAAGATTAGTTTGCAAGCGTATTCTTCTTGGAGCAGTGCCTTGATTTACAATATTCTTCTCTG
*
54208943 ACTCATCAGAGCTAGAAGTCTGTTCTGCAGCTTCAGCTTCTGTGACCTGCA
196 ACTCATCAGAGCTAGAAGTCTGTCCTGCAGCTTCAGCTTCTGTGACCTGCA
54208994 AACGAAAAAG
Statistics
Matches: 539, Mismatches: 41, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
334 6 0.01
335 112 0.21
337 1 0.00
338 1 0.00
340 2 0.00
341 417 0.77
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (341 bp):
AGTGCTCAAAATTAGCTTTTCCTGGTAACTCTACCTCAGTAAGAGCAGATTGAACTTCTTCTTCA
ACGAGGCCAGGACTTGTCATGTTCCCACCATCGACACAGCCTGCAGAACCTTTCATTGGCCCAGT
AGAAAGATTAGTTTGCAAGCGTATTCTTCTTGGAGCAGTGCCTTGATTTACAATATTCTTCTCTG
ACTCATCAGAGCTAGAAGTCTGTCCTGCAGCTTCAGCTTCTGTGACCTGCATTCAAAGTATTGGA
AGATATTGTTCACTTTCAGAAATGTATGTCAGTGTACTAATATTATAATTTGGCCTTTAGCAGTA
AAAACAGTATATCAAC
Found at i:54212835 original size:27 final size:27
Alignment explanation
Indices: 54212783--54212836 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
54212773 AATTTAAATT
*
54212783 AAAAAATATAATGAAATCAAATTATAA
1 AAAAAATATAATGAAATCAAAATATAA
* *
54212810 AAAAAATCTAATTGAACT-AAAATATAA
1 AAAAAATATAA-TGAAATCAAAATATAA
54212837 CTTTTCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.26
Consensus pattern (27 bp):
AAAAAATATAATGAAATCAAAATATAA
Found at i:54217874 original size:18 final size:18
Alignment explanation
Indices: 54217821--54217867 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
54217811 GAGAGATGGG
*
54217821 GAGAATA-AAAAACAA-A
1 GAGAATATAAAAGCAATA
* *
54217837 GAAAATATGAAAGCAATA
1 GAGAATATAAAAGCAATA
54217855 GAGAATATAAAAG
1 GAGAATATAAAAG
54217868 AAGTAGATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
16 6 0.25
17 6 0.25
18 12 0.50
ACGTcount: A:0.66, C:0.04, G:0.17, T:0.13
Consensus pattern (18 bp):
GAGAATATAAAAGCAATA
Found at i:54226725 original size:21 final size:20
Alignment explanation
Indices: 54226699--54226737 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
54226689 AAAAAAGATG
54226699 CGTAGAATTGAAGCTTGGATA
1 CGTAGAATTGAAG-TTGGATA
54226720 CGTAGAATTGAAGTTGGA
1 CGTAGAATTGAAGTTGGA
54226738 ATCTATGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (20 bp):
CGTAGAATTGAAGTTGGATA
Found at i:54234251 original size:25 final size:23
Alignment explanation
Indices: 54234217--54234265 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
54234207 GTCTCGTGAC
54234217 TATATAAAAAATAAAATTTCAAAAT
1 TATAT-AAAAA-AAAATTTCAAAAT
* *
54234242 TATATTAAAAAAAATTTTAAAAT
1 TATATAAAAAAAAATTTCAAAAT
54234265 T
1 T
54234266 CTAAAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 13 0.59
24 4 0.18
25 5 0.23
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
TATATAAAAAAAAATTTCAAAAT
Found at i:54236725 original size:19 final size:19
Alignment explanation
Indices: 54236696--54236744 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
54236686 ACCCGATTCT
*
54236696 ATATAAAAATTATTTTAAAA
1 ATATAAAAATTA-CTTAAAA
*
54236716 A-ATCAAAATTACTTAAAA
1 ATATAAAAATTACTTAAAA
54236734 ATATAAAAATT
1 ATATAAAAATT
54236745 TGAAAAAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 7 0.28
19 17 0.68
20 1 0.04
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
ATATAAAAATTACTTAAAA
Found at i:54237080 original size:17 final size:18
Alignment explanation
Indices: 54237045--54237078 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
54237035 AAAACCAAGA
54237045 ATTTTGTTTAATGTTTTT
1 ATTTTGTTTAATGTTTTT
54237063 ATTTT-TTT-ATGTTTTT
1 ATTTTGTTTAATGTTTTT
54237079 TAAAGAATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (18 bp):
ATTTTGTTTAATGTTTTT
Found at i:54238980 original size:91 final size:91
Alignment explanation
Indices: 54238825--54239009 Score: 343
Period size: 91 Copynumber: 2.0 Consensus size: 91
54238815 ACGTATTACA
*
54238825 TTTGGCCTCTTTGCTTTATTTTATTTTCATTTTTTCCTTTAATTTTGTTGTTAGTTTAATTTAAT
1 TTTGGCCTCTTTGCTTTATTTTATTTTCATTTTTTCCTTTAATTTTGTTGTTAATTTAATTTAAT
54238890 CCTTACCTATTTAATATGCTTGGTTT
66 CCTTACCTATTTAATATGCTTGGTTT
54238916 TTTGGCCTCTTTGCTTTATTTTATTTTCATTTTTTCCTTTAATTTTGTTGTTAATTTAATTTAAT
1 TTTGGCCTCTTTGCTTTATTTTATTTTCATTTTTTCCTTTAATTTTGTTGTTAATTTAATTTAAT
* *
54238981 GCTTGCCTATTTAATATGCTTGGTTT
66 CCTTACCTATTTAATATGCTTGGTTT
54239007 TTT
1 TTT
54239010 TATTTATTTC
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.16, C:0.12, G:0.10, T:0.61
Consensus pattern (91 bp):
TTTGGCCTCTTTGCTTTATTTTATTTTCATTTTTTCCTTTAATTTTGTTGTTAATTTAATTTAAT
CCTTACCTATTTAATATGCTTGGTTT
Found at i:54239206 original size:25 final size:24
Alignment explanation
Indices: 54239103--54239233 Score: 115
Period size: 25 Copynumber: 5.5 Consensus size: 24
54239093 CTTAATATAT
* *
54239103 TTTTAAACTTATCATCGA-TATTA
1 TTTTAAATTTATCATCTATTATTA
* *
54239126 TTTT-AATTTATAATATATTATTA
1 TTTTAAATTTATCATCTATTATTA
* * *
54239149 TTTTAAATTTATCATTTATTTTTT
1 TTTTAAATTTATCATCTATTATTA
* *
54239173 TATTTAAATTCATCATGTATTATTA
1 T-TTTAAATTTATCATCTATTATTA
* *
54239198 TTTTAAAATTTATCGTCTATGATTA
1 TTTT-AAATTTATCATCTATTATTA
*
54239223 -TTTAGATTTAT
1 TTTTAAATTTAT
54239234 TGTGTATTTA
Statistics
Matches: 87, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
22 9 0.10
23 20 0.23
24 22 0.25
25 36 0.41
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTTAAATTTATCATCTATTATTA
Found at i:54239497 original size:24 final size:24
Alignment explanation
Indices: 54239469--54239514 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
54239459 GTTTAAATTC
*
54239469 TCTTTTAAATATGTTTATATATCT
1 TCTTTTAAATATATTTATATATCT
*
54239493 TCTTTTAAATCTATTTATATAT
1 TCTTTTAAATATATTTATATAT
54239515 ATAATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (24 bp):
TCTTTTAAATATATTTATATATCT
Found at i:54240985 original size:20 final size:20
Alignment explanation
Indices: 54240962--54241000 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
54240952 CAAATATATT
54240962 AAAATCATTAATTAAAATAA
1 AAAATCATTAATTAAAATAA
* **
54240982 AAAATTATTTTTTAAAATA
1 AAAATCATTAATTAAAATA
54241001 CTAATTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATCATTAATTAAAATAA
Found at i:54241231 original size:35 final size:36
Alignment explanation
Indices: 54241192--54241271 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
54241182 AACTAATTTA
* * *
54241192 AATATTATTT-AAATACATA-TTTATTACTTAATAAT
1 AATA-TATTTAAAATAAATATTTTATTACTCAAAAAT
*
54241227 AATATATTTAAAATAAATATTTTATTTCTCAAAAAT
1 AATATATTTAAAATAAATATTTTATTACTCAAAAAT
54241263 AATAATATT
1 AAT-ATATT
54241272 AAACAGACAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
34 5 0.13
35 12 0.32
36 16 0.42
37 5 0.13
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (36 bp):
AATATATTTAAAATAAATATTTTATTACTCAAAAAT
Found at i:54243261 original size:24 final size:24
Alignment explanation
Indices: 54243229--54243287 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
54243219 TCCAGTACTT
*
54243229 CTGCCTTCGGTG-CTGCAAGCACTC
1 CTGCCTTCGGTGTC-ACAAGCACTC
*
54243253 CTGCTTTCGGTGTCACAAGCACTC
1 CTGCCTTCGGTGTCACAAGCACTC
54243277 CTGCCTTCGGT
1 CTGCCTTCGGT
54243288 TCAACTGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 30 0.97
25 1 0.03
ACGTcount: A:0.12, C:0.36, G:0.24, T:0.29
Consensus pattern (24 bp):
CTGCCTTCGGTGTCACAAGCACTC
Found at i:54243442 original size:21 final size:21
Alignment explanation
Indices: 54243417--54243487 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
54243407 CACTCATGCA
54243417 TTTGGAGCATCAAATTCTGCT
1 TTTGGAGCATCAAATTCTGCT
* * *
54243438 TTTGGCA-CTTCCAAGACTCCTGTT
1 TTTGG-AGCAT-CAA-A-TTCTGCT
**
54243462 TTTGGAGTGTCAAATTCTGCT
1 TTTGGAGCATCAAATTCTGCT
54243483 TTTGG
1 TTTGG
54243488 CGTTTCCGAC
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
21 17 0.45
22 5 0.13
23 5 0.13
24 11 0.29
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (21 bp):
TTTGGAGCATCAAATTCTGCT
Found at i:54243502 original size:45 final size:45
Alignment explanation
Indices: 54243390--54243517 Score: 123
Period size: 45 Copynumber: 2.8 Consensus size: 45
54243380 AAGCGCACCA
* * * *
54243390 GCTTTTGGCACTTCTC-TCACTCATGCATTTGGAGCATCAAATTCT
1 GCTTTTGGCACTTC-CAACACTCCTACTTTTGGAGCATCAAATTCT
* ** **
54243435 GCTTTTGGCACTTCCAAGACTCCTGTTTTTGGAGTGTCAAATTCT
1 GCTTTTGGCACTTCCAACACTCCTACTTTTGGAGCATCAAATTCT
** * *
54243480 GCTTTTGGCGTTTCCGACACTCCTACTTTTGGATCATC
1 GCTTTTGGCACTTCCAACACTCCTACTTTTGGAGCATC
54243518 TTCTACTCCT
Statistics
Matches: 66, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
44 1 0.02
45 65 0.98
ACGTcount: A:0.17, C:0.26, G:0.18, T:0.39
Consensus pattern (45 bp):
GCTTTTGGCACTTCCAACACTCCTACTTTTGGAGCATCAAATTCT
Found at i:54277175 original size:3 final size:3
Alignment explanation
Indices: 54277167--54277208 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
54277157 AATAAGATAT
54277167 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAAA GAA -AA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA GAA GAA
54277209 AGATGGTGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:54280783 original size:34 final size:35
Alignment explanation
Indices: 54280739--54280805 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
54280729 CAGTAAAATA
*
54280739 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
54280773 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
54280806 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:54293124 original size:16 final size:16
Alignment explanation
Indices: 54293082--54293124 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
54293072 AAATTTAACC
*
54293082 ATTTTATTGAAATAAT
1 ATTTTATTTAAATAAT
*
54293098 ATTTTAATTAAGATAAT
1 ATTTTATTTAA-ATAAT
54293115 -TTTTATTTAA
1 ATTTTATTTAA
54293125 TAAATAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
ATTTTATTTAAATAAT
Found at i:54295041 original size:29 final size:29
Alignment explanation
Indices: 54294983--54295037 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
54294973 GGCTTATTAC
*
54294983 ATTTTTTTAAATTTAAACAGGAAGGAATA
1 ATTTTTTTAAATTTAAACAGGAAGAAATA
*
54295012 ATTTTCTTT-AATTTAAA-AGGGAGAAA
1 ATTTT-TTTAAATTTAAACAGGAAGAAA
54295038 ATAAATGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 7 0.30
29 13 0.57
30 3 0.13
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.38
Consensus pattern (29 bp):
ATTTTTTTAAATTTAAACAGGAAGAAATA
Found at i:54303976 original size:108 final size:108
Alignment explanation
Indices: 54303824--54304065 Score: 315
Period size: 108 Copynumber: 2.2 Consensus size: 108
54303814 ATTTTCATTG
* * * * * *
54303824 CGGCTTATCTTTTGAGGACTCTGTGTATCTTCATTCCGGTTTATATCTCGAGCTTTCTGTGCATC
1 CGGCTTCTCTTTTGAGGACTTTGTGTACCTCCATTCCAGATTATATCTCGAGCTTTCTGTGCATC
** *
54303889 TTCATTA-GGATTTATATGTTGAGGACTACTCATGTTTGCATCG
66 TTCATTATGG-TTTATACATTGAGGACTACTCATGTTTGCATCA
* * * * *
54303932 CGGTTTTTCTTTTGAGGACTTTGTGTACCTCCATTCCAGATTATATCTTGAGGTTTTTGTGCATC
1 CGGCTTCTCTTTTGAGGACTTTGTGTACCTCCATTCCAGATTATATCTCGAGCTTTCTGTGCATC
*
54303997 TTCATTATTGTTTATACATTGAGGACTACTCATGTTTGCATCA
66 TTCATTATGGTTTATACATTGAGGACTACTCATGTTTGCATCA
* *
54304040 TGGCTTCTCTTCTGAGGACTTTGTGT
1 CGGCTTCTCTTTTGAGGACTTTGTGT
54304066 GTCATCATTG
Statistics
Matches: 115, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
108 114 0.99
109 1 0.01
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (108 bp):
CGGCTTCTCTTTTGAGGACTTTGTGTACCTCCATTCCAGATTATATCTCGAGCTTTCTGTGCATC
TTCATTATGGTTTATACATTGAGGACTACTCATGTTTGCATCA
Found at i:54304194 original size:36 final size:35
Alignment explanation
Indices: 54304124--54304209 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 35
54304114 GCTAATACCT
* *
54304124 TGAGGACTTTGTGTTTTCCCCTCTGGGCTTATCTC
1 TGAGGACTTTGTGTTTTCCCCTCCGAGCTTATCTC
*
54304159 TAGAGGACTTTGTGTTTTTCCCTCCGAG-TTAATCTC
1 T-GAGGACTTTGTGTTTTCCCCTCCGAGCTT-ATCTC
*
54304195 TGAAGGACTTGGTGT
1 TG-AGGACTTTGTGT
54304210 GTTCTCACTC
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
35 4 0.09
36 40 0.91
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.41
Consensus pattern (35 bp):
TGAGGACTTTGTGTTTTCCCCTCCGAGCTTATCTC
Found at i:54311402 original size:18 final size:18
Alignment explanation
Indices: 54311381--54311418 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
54311371 ATTTTTAAAA
*
54311381 TTTTAAAGAGTTTTT-AT
1 TTTTTAAGAGTTTTTAAT
*
54311398 TTTTTAATAGTTTTTAAT
1 TTTTTAAGAGTTTTTAAT
54311416 TTT
1 TTT
54311419 AAAAAGTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (18 bp):
TTTTTAAGAGTTTTTAAT
Found at i:54311457 original size:25 final size:24
Alignment explanation
Indices: 54311408--54311467 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
54311398 TTTTTAATAG
*
54311408 TTTTTAATTTTAAAAAGTATGAAT
1 TTTTTATTTTTAAAAAGTATGAAT
*
54311432 TTATTTATTTTTAAAAAATTAT-AAT
1 TT-TTTATTTTT-AAAAAGTATGAAT
54311457 TTTTATATTTT
1 TTTT-TATTTT
54311468 ATTTAGAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 4 0.13
25 19 0.61
26 8 0.26
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (24 bp):
TTTTTATTTTTAAAAAGTATGAAT
Found at i:54327412 original size:21 final size:21
Alignment explanation
Indices: 54327388--54327431 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
54327378 ATTATTATGA
* * *
54327388 ATTTTTTATATTTTCATTTGT
1 ATTTTTCATATTTTAATGTGT
54327409 ATTTTTCATATTTTAATGTGT
1 ATTTTTCATATTTTAATGTGT
54327430 AT
1 AT
54327432 ATATATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.66
Consensus pattern (21 bp):
ATTTTTCATATTTTAATGTGT
Found at i:54336343 original size:11 final size:13
Alignment explanation
Indices: 54336313--54336339 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
54336303 TGATGGAGTG
54336313 AATTTGATATATC
1 AATTTGATATATC
54336326 AATTTGATATATC
1 AATTTGATATATC
54336339 A
1 A
54336340 TTGAAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (13 bp):
AATTTGATATATC
Found at i:54344540 original size:9 final size:9
Alignment explanation
Indices: 54344516--54344561 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
54344506 TGAGTTTTCA
*
54344516 AATTCGAAG
1 AATTCGAAT
*
54344525 AACTCGAAT
1 AATTCGAAT
54344534 AATTCGAAT
1 AATTCGAAT
54344543 AATTCGAAT
1 AATTCGAAT
54344552 AATTCGAAT
1 AATTCGAAT
54344561 A
1 A
54344562 TCAAAATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (9 bp):
AATTCGAAT
Found at i:54377727 original size:39 final size:39
Alignment explanation
Indices: 54377652--54377728 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
54377642 GTGGTCAGCT
*
54377652 AGGACATTGCCTCAGGTGTAATAAAAAAGGAGATCAACC
1 AGGACATTGCCTCAGGTGTAATAAAAAAGGAAATCAACC
* * *
54377691 AGGACATTGTCTCAGGTGTAGTCAAAGAA-GAAATCAAC
1 AGGACATTGCCTCAGGTGTAAT-AAAAAAGGAAATCAAC
54377729 ACTTTCTATC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 28 0.85
40 5 0.15
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.19
Consensus pattern (39 bp):
AGGACATTGCCTCAGGTGTAATAAAAAAGGAAATCAACC
Found at i:54382319 original size:19 final size:19
Alignment explanation
Indices: 54382304--54382340 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
54382294 AAAAAAATAA
54382304 CAACAAAATAGTAAAAAAG
1 CAACAAAATAGTAAAAAAG
*
54382323 CAAGAAAATAGTAAAAAA
1 CAACAAAATAGTAAAAAA
54382341 AAAATTTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.70, C:0.08, G:0.11, T:0.11
Consensus pattern (19 bp):
CAACAAAATAGTAAAAAAG
Found at i:54383714 original size:3 final size:3
Alignment explanation
Indices: 54383706--54383756 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
54383696 AGCACAGACA
54383706 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
54383754 AAT
1 AAT
54383757 GTTTGGGTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:54385304 original size:4 final size:4
Alignment explanation
Indices: 54385295--54385321 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
54385285 ATTTCATTTA
54385295 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
54385322 AGAGACATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:54393165 original size:31 final size:31
Alignment explanation
Indices: 54393130--54393192 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
54393120 TGTCCAGTTT
54393130 TCAATCAAACCCACTCCTGTTGTCGCTTCTC
1 TCAATCAAACCCACTCCTGTTGTCGCTTCTC
54393161 TCAATCAAACCCACTCCTGTTGTCGCTTCTC
1 TCAATCAAACCCACTCCTGTTGTCGCTTCTC
54393192 T
1 T
54393193 TAGTTTCTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.38, G:0.10, T:0.33
Consensus pattern (31 bp):
TCAATCAAACCCACTCCTGTTGTCGCTTCTC
Found at i:54395478 original size:19 final size:18
Alignment explanation
Indices: 54395426--54395478 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
54395416 TTAAATTTTA
*
54395426 TAAAAATATTC-AAAAGT
1 TAAAAAAATTCAAAAAGT
**
54395443 TAAAAAAAACCATAAAAGT
1 TAAAAAAATTCA-AAAAGT
54395462 TAATAAAAATTCAAAAA
1 TAA-AAAAATTCAAAAA
54395479 CAATAATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 8 0.29
19 13 0.46
20 7 0.25
ACGTcount: A:0.66, C:0.08, G:0.04, T:0.23
Consensus pattern (18 bp):
TAAAAAAATTCAAAAAGT
Found at i:54399297 original size:24 final size:25
Alignment explanation
Indices: 54399270--54399316 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
54399260 GGATTCTGAA
54399270 ATAGA-AGATCTTGTTTCTTTTGTG
1 ATAGATAGATCTTGTTTCTTTTGTG
* * *
54399294 ATAGATGGTTTTTGTTTCTTTTG
1 ATAGATAGATCTTGTTTCTTTTG
54399317 GTAACACCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 5 0.26
25 14 0.74
ACGTcount: A:0.17, C:0.06, G:0.21, T:0.55
Consensus pattern (25 bp):
ATAGATAGATCTTGTTTCTTTTGTG
Found at i:54400833 original size:3 final size:3
Alignment explanation
Indices: 54400819--54400859 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
54400809 TTCCTTATCA
* * *
54400819 TCG TCA TCG TCG TCG TCG TCA TCC TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
54400860 ATGTTCTTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.05, C:0.37, G:0.24, T:0.34
Consensus pattern (3 bp):
TCG
Found at i:54400840 original size:21 final size:21
Alignment explanation
Indices: 54400816--54400861 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
54400806 ATCTTCCTTA
*
54400816 TCATCGTCATCGTCGTCGTCG
1 TCATCCTCATCGTCGTCGTCG
*
54400837 TCATCCTCGTCGTCGTCGTCG
1 TCATCCTCATCGTCGTCGTCG
54400858 TCAT
1 TCAT
54400862 GTTCTTTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.35, G:0.22, T:0.35
Consensus pattern (21 bp):
TCATCCTCATCGTCGTCGTCG
Found at i:54401696 original size:24 final size:24
Alignment explanation
Indices: 54401669--54401729 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 24
54401659 AAAAGATCAT
54401669 ATATATAATATAAAAAAGTT-TAAA
1 ATATATAATATAAAAAA-TTCTAAA
* * *
54401693 ATAT-T-TTCTATAAAATTCTAAA
1 ATATATAATATAAAAAATTCTAAA
54401715 ATATATAATTATAAA
1 ATATATAA-TATAAA
54401730 TTTTAAAATG
Statistics
Matches: 27, Mismatches: 6, Indels: 7
0.68 0.15 0.17
Matches are distributed among these distances:
21 2 0.07
22 15 0.56
23 2 0.07
24 4 0.15
25 4 0.15
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (24 bp):
ATATATAATATAAAAAATTCTAAA
Found at i:54401960 original size:6 final size:6
Alignment explanation
Indices: 54401949--54401995 Score: 58
Period size: 6 Copynumber: 7.2 Consensus size: 6
54401939 TCAGTTATCA
54401949 TATTTT TATTTTTT TATATTT TATTTT TATTTT TATTTT TATATTT T
1 TATTTT TA--TTTT TAT-TTT TATTTT TATTTT TATTTT TAT-TTT T
54401996 TAACGTGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
6 21 0.57
7 10 0.27
8 6 0.16
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:54402475 original size:22 final size:22
Alignment explanation
Indices: 54402439--54402480 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
54402429 ATTTTTTTAC
54402439 TTTTTTAAATATATTCTTTAGT
1 TTTTTTAAATATATTCTTTAGT
* * *
54402461 TTTTTTTAATTTATTTTTTA
1 TTTTTTAAATATATTCTTTA
54402481 AAAAAATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTTTAAATATATTCTTTAGT
Found at i:54403006 original size:52 final size:52
Alignment explanation
Indices: 54402928--54403032 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
54402918 CTAGGGTGCT
54402928 TGTCCAGTTTCGAGATTGGTATCTCTCCATTATCCTTTTGTTCTTGACTTTG
1 TGTCCAGTTTCGAGATTGGTATCTCTCCATTATCCTTTTGTTCTTGACTTTG
54402980 TGTCCAGTTTCGAGATTGGTATCTCTCCATTATCCTTTTGTTCTTGACTTTG
1 TGTCCAGTTTCGAGATTGGTATCTCTCCATTATCCTTTTGTTCTTGACTTTG
54403032 T
1 T
54403033 TTGTTGCTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.13, C:0.21, G:0.17, T:0.49
Consensus pattern (52 bp):
TGTCCAGTTTCGAGATTGGTATCTCTCCATTATCCTTTTGTTCTTGACTTTG
Found at i:54405241 original size:3 final size:3
Alignment explanation
Indices: 54405235--54405260 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54405225 CGACAGTGAG
54405235 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
54405261 GGGCGTCCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:54418070 original size:20 final size:20
Alignment explanation
Indices: 54418035--54418072 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54418025 TAATCACGTT
54418035 GTGACAAAACGATAACATAA
1 GTGACAAAACGATAACATAA
54418055 GTGACTAAAACG-TAACAT
1 GTGAC-AAAACGATAACAT
54418073 TTCAAACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (20 bp):
GTGACAAAACGATAACATAA
Found at i:54422380 original size:25 final size:25
Alignment explanation
Indices: 54422230--54422385 Score: 85
Period size: 25 Copynumber: 6.3 Consensus size: 25
54422220 ATGAGAGTCT
*
54422230 CGTTATATGACTCTTTGTGAGCTTCC
1 CGTTATAAG-CTCTTTGTGAGCTTCC
*
54422256 CGATTA-AAGGCTCTTTGTAAGCTTCC
1 CG-TTATAA-GCTCTTTGTGAGCTTCC
** * *
54422282 CGTTAGT--GCTCGCT-TGAACTTCT
1 CGTTA-TAAGCTCTTTGTGAGCTTCC
* * *
54422305 CGTTATATGGCTATCTGAT-A-CTTCC
1 CGTTATA-AGCTCTTTG-TGAGCTTCC
* * *
54422330 CGTTA-AGTGCTTTTTG-GAGCTACC
1 CGTTATA-AGCTCTTTGTGAGCTTCC
54422354 CGTTATAAGCTCTTTGTGAGCTTCC
1 CGTTATAAGCTCTTTGTGAGCTTCC
54422379 CGTTATA
1 CGTTATA
54422386 GTGCTTGAGA
Statistics
Matches: 99, Mismatches: 18, Indels: 27
0.69 0.12 0.19
Matches are distributed among these distances:
22 1 0.01
23 12 0.12
24 28 0.28
25 32 0.32
26 21 0.21
27 5 0.05
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (25 bp):
CGTTATAAGCTCTTTGTGAGCTTCC
Found at i:54424135 original size:8 final size:8
Alignment explanation
Indices: 54424112--54424152 Score: 64
Period size: 8 Copynumber: 5.0 Consensus size: 8
54424102 AGGAAATAGG
54424112 TATTATAT
1 TATTATAT
54424120 TAATTATAT
1 T-ATTATAT
*
54424129 TATTATAA
1 TATTATAT
54424137 TATTATAT
1 TATTATAT
54424145 TATTATAT
1 TATTATAT
54424153 ATATAAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 22 0.73
9 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTATAT
Found at i:54424256 original size:30 final size:30
Alignment explanation
Indices: 54424178--54424257 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 30
54424168 AATAAAAGAG
* *
54424178 AGAAAAAGGGAATGGAAACAGAATAGCAAAA
1 AGAAAAAGGGAA-GGAAAGAGAAAAGCAAAA
* *
54424209 CGAAAACAGGGAA-GAAAGGGAAAAAG-AAAA
1 AGAAAA-AGGGAAGGAAAGAG-AAAAGCAAAA
54424239 AGAAAAAGGGAAGGAAAGA
1 AGAAAAAGGGAAGGAAAGA
54424258 AGGAAAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
29 6 0.15
30 19 0.47
31 9 0.22
32 6 0.15
ACGTcount: A:0.62, C:0.05, G:0.30, T:0.03
Consensus pattern (30 bp):
AGAAAAAGGGAAGGAAAGAGAAAAGCAAAA
Found at i:54431457 original size:28 final size:28
Alignment explanation
Indices: 54431386--54431457 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 28
54431376 ATTTTTATGA
54431386 GAATTAAATTATAAA---AATTTTAAAG
1 GAATTAAATTATAAATTTAATTTTAAAG
* ***
54431411 G-ATTAAAAGTATTTTTTTAATTTTAAAG
1 GAATT-AAATTATAAATTTAATTTTAAAG
54431439 GAATTAAATTATAAATTTA
1 GAATTAAATTATAAATTTA
54431458 CAATTTTGTA
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
24 3 0.09
25 7 0.21
28 21 0.62
29 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (28 bp):
GAATTAAATTATAAATTTAATTTTAAAG
Found at i:54437048 original size:45 final size:46
Alignment explanation
Indices: 54436994--54437104 Score: 188
Period size: 46 Copynumber: 2.4 Consensus size: 46
54436984 ATCACTTGTC
*
54436994 CTTGATCAGATAAGTGTAGCT-AGGCTACAACTTATCACTTTACCA
1 CTTGATCAGATAAGTGTAGCTGAAGCTACAACTTATCACTTTACCA
* *
54437039 CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTATCA
1 CTTGATCAGATAAGTGTAGCTGAAGCTACAACTTATCACTTTACCA
54437085 CTTGATCAGATAAGTGTAGC
1 CTTGATCAGATAAGTGTAGC
54437105 CACTTATCAC
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
45 21 0.34
46 41 0.66
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (46 bp):
CTTGATCAGATAAGTGTAGCTGAAGCTACAACTTATCACTTTACCA
Found at i:54437087 original size:46 final size:45
Alignment explanation
Indices: 54436981--54437214 Score: 234
Period size: 37 Copynumber: 5.6 Consensus size: 45
54436971 CATATGACCT
* *
54436981 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACAA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
54437024 CTTATCACTTTACCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
54437070 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
54437107 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
** *
54437144 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAACTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
54437190 CTTATCACTTTGTCACTTGATCAGA
1 CTTATCACTTTGTCACTTGATCAGA
54437215 AGTACTCAAA
Statistics
Matches: 168, Mismatches: 10, Indels: 23
0.84 0.05 0.11
Matches are distributed among these distances:
37 64 0.38
39 2 0.01
40 3 0.02
41 1 0.01
42 1 0.01
43 10 0.06
44 5 0.03
45 21 0.12
46 61 0.36
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:54439348 original size:25 final size:25
Alignment explanation
Indices: 54439320--54439414 Score: 154
Period size: 25 Copynumber: 3.8 Consensus size: 25
54439310 GAACCTTAGT
*
54439320 GTGCTCTCTAATTATTAGCACATCA
1 GTGCTCTCTGATTATTAGCACATCA
*
54439345 GTGCTCTCTGATTATTAGCACGTCA
1 GTGCTCTCTGATTATTAGCACATCA
* *
54439370 GTGCTCTCTGATTATTAGTACATCT
1 GTGCTCTCTGATTATTAGCACATCA
54439395 GTGCTCTCTGATTATTAGCA
1 GTGCTCTCTGATTATTAGCA
54439415 TGTTAGTGCT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 64 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (25 bp):
GTGCTCTCTGATTATTAGCACATCA
Found at i:54440536 original size:10 final size:10
Alignment explanation
Indices: 54440515--54440611 Score: 55
Period size: 10 Copynumber: 9.8 Consensus size: 10
54440505 CCGAATATAA
54440515 TAAATATTTTT
1 TAAAT-TTTTT
54440526 TAAATTTTTT
1 TAAATTTTTT
54440536 T-AA--TTTT
1 TAAATTTTTT
*
54440543 AAAATACTTTTAT
1 TAAAT--TTTT-T
54440556 TAAATTTTTT
1 TAAATTTTTT
54440566 TAAA---TTT
1 TAAATTTTTT
*
54440573 AAAATTTTTT
1 TAAATTTTTT
*
54440583 AAAATACTTTTT
1 TAAAT--TTTTT
54440595 T-AATTTTTT
1 TAAATTTTTT
*
54440604 TTAATTTT
1 TAAATTTT
54440612 AAAATATTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 25
0.71 0.04 0.25
Matches are distributed among these distances:
7 10 0.14
8 2 0.03
9 8 0.11
10 25 0.36
11 12 0.17
12 8 0.11
13 5 0.07
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (10 bp):
TAAATTTTTT
Found at i:54440561 original size:30 final size:28
Alignment explanation
Indices: 54440516--54440601 Score: 111
Period size: 30 Copynumber: 3.0 Consensus size: 28
54440506 CGAATATAAT
54440516 AAATATTTTTTAAATTTTTTTAATTTTA
1 AAATATTTTTTAAATTTTTTTAATTTTA
*
54440544 AAATACTTTTATTAAATTTTTTTAAATTTA
1 AAATA-TTTT-TTAAATTTTTTTAATTTTA
*
54440574 AAAT-TTTTTAAAATACTTTTTTAATTTT
1 AAATATTTTTTAAAT--TTTTTTAATTTT
54440602 TTTTAATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
27 5 0.10
28 9 0.18
29 15 0.29
30 22 0.43
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
AAATATTTTTTAAATTTTTTTAATTTTA
Found at i:54440571 original size:40 final size:39
Alignment explanation
Indices: 54440515--54440653 Score: 131
Period size: 40 Copynumber: 3.5 Consensus size: 39
54440505 CCGAATATAA
*
54440515 TAAATATTTTTTAAATTTTTTTAATTTTAAAATACTTTTAT
1 TAAAT-TTTTTTAAATTTTTATAATTTTAAAATACTTTT-T
*
54440556 TAAATTTTTTTAAA--TTTAAAATTTTTTAAAATACTTTTT
1 TAAATTTTTTTAAATTTTTATAA--TTTTAAAATACTTTTT
* * *
54440595 T-AATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTT
1 TAAATTTTTTTAAATTTT--TATAATTTTAAAATACTTTTT
* *
54440635 TAATTTTTATTTTAATTTT
1 TAAATTTT-TTTAAATTTT
54440654 GAAAATATTT
Statistics
Matches: 83, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
38 16 0.19
39 2 0.02
40 43 0.52
41 10 0.12
42 12 0.14
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (39 bp):
TAAATTTTTTTAAATTTTTATAATTTTAAAATACTTTTT
Found at i:54440603 original size:39 final size:40
Alignment explanation
Indices: 54440539--54440665 Score: 184
Period size: 40 Copynumber: 3.1 Consensus size: 40
54440529 ATTTTTTTAA
*
54440539 TTTTAAAATACTTTTATTAAATTTTTTTAAATTTAAAAT-T
1 TTTTAAAATACTTTT-TTAATTTTTTTTAAATTTAAAATAT
*
54440579 TTTTAAAATACTTTTTTAATTTTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTTTAATTTTTTTTAAATTTAAAATAT
*
54440619 TTTTAAAATACTTTTTTAATTTTTATTTTAATTTTGAAAATAT
1 TTTTAAAATACTTTTTTAA-TTTT-TTTTAAATTT-AAAATAT
54440662 TTTT
1 TTTT
54440666 TTGGTATTTA
Statistics
Matches: 81, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
39 21 0.26
40 35 0.43
41 4 0.05
42 10 0.12
43 11 0.14
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.61
Consensus pattern (40 bp):
TTTTAAAATACTTTTTTAATTTTTTTTAAATTTAAAATAT
Found at i:54440676 original size:32 final size:32
Alignment explanation
Indices: 54440617--54440678 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
54440607 ATTTTAAAAT
* *
54440617 ATTTTTAAAATACTTTTTTAATTTTTATTTTA
1 ATTTTGAAAATACTTTTTTAATATTTATTTTA
* **
54440649 ATTTTGAAAATATTTTTTTGGTATTTATTT
1 ATTTTGAAAATACTTTTTTAATATTTATTT
54440679 AAAAAAACGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.65
Consensus pattern (32 bp):
ATTTTGAAAATACTTTTTTAATATTTATTTTA
Found at i:54441453 original size:15 final size:15
Alignment explanation
Indices: 54441433--54441465 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
54441423 AATAAAAAAA
54441433 GAAAACCTAGCCATG
1 GAAAACCTAGCCATG
54441448 GAAAACCTAGCCATG
1 GAAAACCTAGCCATG
54441463 GAA
1 GAA
54441466 GCTTGAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.24, G:0.21, T:0.12
Consensus pattern (15 bp):
GAAAACCTAGCCATG
Found at i:54444080 original size:28 final size:26
Alignment explanation
Indices: 54444039--54444095 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 26
54444029 TCACGTAATT
54444039 AATAAATTATTATATATTTAATTTTACTA
1 AATAAATTATTATATA-TT-ATTTTA-TA
*
54444068 AATACATT-TTATATATTATTTTATA
1 AATAAATTATTATATATTATTTTATA
54444093 AAT
1 AAT
54444096 GTTATTTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 5 0.19
26 6 0.22
27 2 0.07
28 7 0.26
29 7 0.26
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (26 bp):
AATAAATTATTATATATTATTTTATA
Found at i:54446278 original size:17 final size:16
Alignment explanation
Indices: 54446256--54446298 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
54446246 TACTAGTTCA
54446256 ATTAATATTTTAATAT
1 ATTAATATTTTAATAT
54446272 GATTAATATTTT--TAT
1 -ATTAATATTTTAATAT
54446287 A-TAATATTTTAA
1 ATTAATATTTTAA
54446299 GGATCTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 9 0.38
14 1 0.04
15 3 0.12
17 11 0.46
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
ATTAATATTTTAATAT
Found at i:54450318 original size:6 final size:6
Alignment explanation
Indices: 54450299--54450331 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
54450289 GTCAAACAGG
*
54450299 GGCTTC GGCATC GGCTTC GGCTTC GGCTTC GGC
1 GGCTTC GGCTTC GGCTTC GGCTTC GGCTTC GGC
54450332 GTTTGGGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.33, G:0.36, T:0.27
Consensus pattern (6 bp):
GGCTTC
Found at i:54455967 original size:2 final size:2
Alignment explanation
Indices: 54455960--54455984 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54455950 TGGAACTTGA
54455960 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
54455985 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:54455989 original size:2 final size:2
Alignment explanation
Indices: 54455984--54456012 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
54455974 TCTCTCTCTC
54455984 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54456013 GTTTGTAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54468058 original size:24 final size:24
Alignment explanation
Indices: 54468027--54468074 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
54468017 GATGCCCATC
54468027 TCTCTCCCTCCACCCAAAAAAATA
1 TCTCTCCCTCCACCCAAAAAAATA
**
54468051 TCTCTCCCTCCACCCCGAAAAATA
1 TCTCTCCCTCCACCCAAAAAAATA
54468075 ATTTTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.44, G:0.02, T:0.21
Consensus pattern (24 bp):
TCTCTCCCTCCACCCAAAAAAATA
Found at i:54471070 original size:8 final size:8
Alignment explanation
Indices: 54471030--54471081 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
54471020 GGTCAGCCGA
54471030 AAGAG-AG
1 AAGAGAAG
54471037 AA-AGAAG
1 AAGAGAAG
* *
54471044 AAGAAAAT
1 AAGAGAAG
54471052 AAGAGAAG
1 AAGAGAAG
54471060 AAGAGAAG
1 AAGAGAAG
54471068 AAGGAGAAG
1 AA-GAGAAG
*
54471077 GAGAG
1 AAGAG
54471082 GGTGGGAAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
6 2 0.05
7 6 0.16
8 22 0.59
9 7 0.19
ACGTcount: A:0.62, C:0.00, G:0.37, T:0.02
Consensus pattern (8 bp):
AAGAGAAG
Found at i:54472223 original size:27 final size:27
Alignment explanation
Indices: 54472193--54472246 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
54472183 TAGGTAAAAG
*
54472193 ATGAGACCATTGA-TATGGAATTTGTGA
1 ATGAGACCATTGAGT-TGGAATTAGTGA
*
54472220 ATGAGATCATTGAGTTGGAATTAGTGA
1 ATGAGACCATTGAGTTGGAATTAGTGA
54472247 GATAAATTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (27 bp):
ATGAGACCATTGAGTTGGAATTAGTGA
Found at i:54474953 original size:64 final size:63
Alignment explanation
Indices: 54474863--54475042 Score: 210
Period size: 64 Copynumber: 2.9 Consensus size: 63
54474853 GTATTTATTT
54474863 AATTAGAATA-ATTGCAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAGATT-AAT-TG
1 AATTA-AATACATTGCAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAG-TTCAATAT-
54474925 CA
63 -A
* * *
54474927 ACATTACA-ACATTGCAACAATAAAACTTGGAACAAACATTGTAATATAAATT--TTGCAATATA
1 A-ATTAAATACATTGCAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAGTT-CAATATA
* * *
54474989 AATTAAATACATTACAATATTAAAAATTGGAACAAACTTTGTAATATAAATTAG
1 AATTAAATACATTGCAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAG
54475043 GTACATTGGA
Statistics
Matches: 99, Mismatches: 9, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
61 7 0.07
62 41 0.41
63 4 0.04
64 43 0.43
65 4 0.04
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.32
Consensus pattern (63 bp):
AATTAAATACATTGCAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAGTTCAATATA
Found at i:54477792 original size:85 final size:85
Alignment explanation
Indices: 54477696--54477975 Score: 251
Period size: 85 Copynumber: 3.2 Consensus size: 85
54477686 TATCTTAAAA
*
54477696 AAAATAAAACATAACATTCACAATAAACACATAATTAATCTAAACACAAAACTTACTAGCAAATC
1 AAAACAAAACATAACATTCACAATAAACACATAATTAATCTAAACACAAAACTTACTAGCAAATC
*
54477761 GTAATAAACAAAATAACTTT
66 ATAATAAACAAAATAACTTT
* * * * * * ** *
54477781 AAAACAAAACATAAAAATAACACTAAACAAATTATATAATACT-AACA-ATTAATTTTTAATAGT
1 AAAACAAAACATAACATTCACAATAAACACATAAT-TAAT-CTAAACACA--AA-ACTTACTAG-
* * ****
54477844 TACTAA-CATAAAAAATTTCAAATATATTAAAAA
60 --CAAATCATAATAAA---CAAA-ATA--ACTTT
*
54477877 AAAATAAAACATAACATTCACAATAAACACATAATTAATCTAAACACAAAACTTACTAGCAAATC
1 AAAACAAAACATAACATTCACAATAAACACATAATTAATCTAAACACAAAACTTACTAGCAAATC
54477942 ATAATAAACAAAATAACTTT
66 ATAATAAACAAAATAACTTT
54477962 AAAACAAAACATAA
1 AAAACAAAACATAA
54477976 AAATAACACT
Statistics
Matches: 144, Mismatches: 34, Indels: 34
0.68 0.16 0.16
Matches are distributed among these distances:
85 43 0.30
86 8 0.06
87 7 0.05
88 10 0.07
90 10 0.07
91 11 0.08
93 10 0.07
94 7 0.05
95 8 0.06
96 30 0.21
ACGTcount: A:0.59, C:0.15, G:0.01, T:0.25
Consensus pattern (85 bp):
AAAACAAAACATAACATTCACAATAAACACATAATTAATCTAAACACAAAACTTACTAGCAAATC
ATAATAAACAAAATAACTTT
Found at i:54477840 original size:180 final size:181
Alignment explanation
Indices: 54477641--54478009 Score: 713
Period size: 181 Copynumber: 2.0 Consensus size: 181
54477631 GTTATCACTA
*
54477641 ACTAACAATTAATTTTTAATAGTTACTAACATAAAAAATTTCAAATATCTT-AAAAAAAATAAAA
1 ACTAACAATTAATTTTTAATAGTTACTAACATAAAAAATTTCAAATATATTAAAAAAAAATAAAA
*
54477705 CATAACATTCACAATAAACACATAATTAATCTAAACACAAAACTTACTAGCAAATCGTAATAAAC
66 CATAACATTCACAATAAACACATAATTAATCTAAACACAAAACTTACTAGCAAATCATAATAAAC
54477770 AAAATAACTTTAAAACAAAACATAAAAATAACACTAAACAAATTATATAAT
131 AAAATAACTTTAAAACAAAACATAAAAATAACACTAAACAAATTATATAAT
54477821 ACTAACAATTAATTTTTAATAGTTACTAACATAAAAAATTTCAAATATATTAAAAAAAAATAAAA
1 ACTAACAATTAATTTTTAATAGTTACTAACATAAAAAATTTCAAATATATTAAAAAAAAATAAAA
54477886 CATAACATTCACAATAAACACATAATTAATCTAAACACAAAACTTACTAGCAAATCATAATAAAC
66 CATAACATTCACAATAAACACATAATTAATCTAAACACAAAACTTACTAGCAAATCATAATAAAC
54477951 AAAATAACTTTAAAACAAAACATAAAAATAACACTAAACAAATTATATAAT
131 AAAATAACTTTAAAACAAAACATAAAAATAACACTAAACAAATTATATAAT
54478002 ACTAACAA
1 ACTAACAA
54478010 ACTATTTTTT
Statistics
Matches: 186, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
180 50 0.27
181 136 0.73
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.26
Consensus pattern (181 bp):
ACTAACAATTAATTTTTAATAGTTACTAACATAAAAAATTTCAAATATATTAAAAAAAAATAAAA
CATAACATTCACAATAAACACATAATTAATCTAAACACAAAACTTACTAGCAAATCATAATAAAC
AAAATAACTTTAAAACAAAACATAAAAATAACACTAAACAAATTATATAAT
Found at i:54478216 original size:27 final size:27
Alignment explanation
Indices: 54478154--54478217 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
54478144 GGGGGAAGTG
* *
54478154 GGTGCCGACTATCGGGATGGCGTGACC
1 GGTGCCGCCTATCGGGAAGGCGTGACC
*
54478181 GGTGCCGCCTATGGGGAAGGCGTGACC
1 GGTGCCGCCTATCGGGAAGGCGTGACC
*
54478208 GGTGTCGCCT
1 GGTGCCGCCT
54478218 CTTCCCTAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.12, C:0.27, G:0.42, T:0.19
Consensus pattern (27 bp):
GGTGCCGCCTATCGGGAAGGCGTGACC
Found at i:54481854 original size:24 final size:24
Alignment explanation
Indices: 54481800--54481854 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
54481790 TTCCCAATAT
* * **
54481800 ATGGCTATCCGGAGCTTTCCGTTA
1 ATGGCTCTACGGAGCTACCCGTTA
54481824 ATGGCTCTACGGAGCTACCCGTTA
1 ATGGCTCTACGGAGCTACCCGTTA
*
54481848 TTGGCTC
1 ATGGCTC
54481855 GCATGAGCTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.16, C:0.27, G:0.25, T:0.31
Consensus pattern (24 bp):
ATGGCTCTACGGAGCTACCCGTTA
Found at i:54482280 original size:17 final size:17
Alignment explanation
Indices: 54482237--54482281 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 17
54482227 AAATGCATGG
54482237 AAATG-ATGATAT-ATA
1 AAATGAATGATATAATA
*
54482252 AAAT-ATTGATATAATA
1 AAATGAATGATATAATA
54482268 AAATGAATGATATA
1 AAATGAATGATATA
54482282 TGTTTATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 10 0.40
16 7 0.28
17 8 0.32
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (17 bp):
AAATGAATGATATAATA
Found at i:54487115 original size:19 final size:19
Alignment explanation
Indices: 54487075--54487117 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
54487065 AAGATAAACC
*
54487075 AAAAAAAAAAAAAAGATCT
1 AAAAAAAAAAAAAACATCT
*
54487094 AAAAGAAAAAAAAATCAT-T
1 AAAA-AAAAAAAAAACATCT
54487113 AAAAA
1 AAAAA
54487118 CATTATAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 9 0.43
20 11 0.52
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.12
Consensus pattern (19 bp):
AAAAAAAAAAAAAACATCT
Found at i:54487475 original size:60 final size:60
Alignment explanation
Indices: 54487400--54487515 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
54487390 TATATTTTTT
* * * * * *
54487400 AATTTTTAGAGTTAGAACTAAATTGATAGATGTTGTAAATGTTGAGGGCCAAATTTATTA
1 AATTTTTAGAATTAGAACTAAAATGACAAATGTTATAAATATTGAGGGCCAAATTTATTA
* *
54487460 AATTTTTAGAATTAGAACTAAAATGACAAATTTTATAAATATTGAGGGCTAAATTT
1 AATTTTTAGAATTAGAACTAAAATGACAAATGTTATAAATATTGAGGGCCAAATTT
54487516 GTTATTTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (60 bp):
AATTTTTAGAATTAGAACTAAAATGACAAATGTTATAAATATTGAGGGCCAAATTTATTA
Found at i:54487811 original size:30 final size:30
Alignment explanation
Indices: 54487777--54487872 Score: 167
Period size: 30 Copynumber: 3.2 Consensus size: 30
54487767 TAATTGAGGA
54487777 ATTAATTTGCGCGTTTTGAGATGAATAAAT
1 ATTAATTTGCGCGTTTTGAGATGAATAAAT
54487807 ATTAATTTGCGCGTTTTGAGATGAATAAAT
1 ATTAATTTGCGCGTTTTGAGATGAATAAAT
*
54487837 ATTAATTTATC-CGTTTTGAGATGAATAAAT
1 ATTAATTT-GCGCGTTTTGAGATGAATAAAT
54487867 ATTAAT
1 ATTAAT
54487873 CTGTCCTTAA
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
30 63 0.98
31 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
ATTAATTTGCGCGTTTTGAGATGAATAAAT
Done.