Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 132 of 167
Found at i:44177548 original size:14 final size:15
Alignment explanation
Indices: 44177524--44177555 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
44177514 GGAGAATTGC
44177524 TTTTGGAAAAATCGA
1 TTTTGGAAAAATCGA
44177539 TTTTGGAAAAATCGA
1 TTTTGGAAAAATCGA
44177554 TT
1 TT
44177556 GAATGAAGAT
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:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (15 bp):
TTTTGGAAAAATCGA
Found at i:44182380 original size:55 final size:55
Alignment explanation
Indices: 44182320--44182425 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 55
44182310 TGCAAGCCCC
* * *
44182320 ACGCCCGTGTTAATTTAACAGCTTCAACCACGGGTGTTCCACACGGGCGTGTCGA
1 ACGCCCATGCTAATTTAACAGCTTCAACCACGGGTCTTCCACACGGGCGTGTCGA
* ** * * *
44182375 ACGCCCATGCTATTTTGGCAGGTTCGACCACGGTTCTTCCACACGGGCGTG
1 ACGCCCATGCTAATTTAACAGCTTCAACCACGGGTCTTCCACACGGGCGTG
44182426 CGATGCTTTG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 42 1.00
ACGTcount: A:0.19, C:0.30, G:0.26, T:0.25
Consensus pattern (55 bp):
ACGCCCATGCTAATTTAACAGCTTCAACCACGGGTCTTCCACACGGGCGTGTCGA
Found at i:44189678 original size:6 final size:6
Alignment explanation
Indices: 44189667--44190486 Score: 1588
Period size: 6 Copynumber: 136.8 Consensus size: 6
44189657 TGGTTTATCT
44189667 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
1 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
44189715 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
1 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
44189763 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
1 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
44189811 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
1 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
44189859 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
1 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
44189907 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
1 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
44189955 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
1 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
44190003 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
1 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
44190051 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
1 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
44190099 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
1 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
44190147 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
1 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
44190195 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
1 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
44190243 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
1 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
44190291 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
1 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
44190339 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
1 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
44190387 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
1 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
* * * * *
44190435 TATTTC TATTTC TATTTT TATTTT TATTTT TATTTT TATTTT TATTT-
1 TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC TATTTC
44190482 TATTT
1 TATTT
44190487 ATCTTTTATG
Statistics
Matches: 813, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
5 5 0.01
6 808 0.99
ACGTcount: A:0.17, C:0.16, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTC
Found at i:44197244 original size:28 final size:28
Alignment explanation
Indices: 44197181--44197303 Score: 158
Period size: 28 Copynumber: 4.4 Consensus size: 28
44197171 ATATTAAGTC
*
44197181 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
44197208 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
44197236 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * * *
44197264 TGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
44197293 CGCACACTTAG
1 CGCACACTTAG
44197304 CGCCAATCTC
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
27 21 0.25
28 47 0.57
29 15 0.18
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:44197251 original size:55 final size:57
Alignment explanation
Indices: 44197180--44197303 Score: 180
Period size: 56 Copynumber: 2.2 Consensus size: 57
44197170 TATATTAAGT
* * *
44197180 CCGCACACTCAGTGCTATATAATC-AACTTGCACACTTAGTGCTATATAA-TCAAAC
1 CCGCACACTTAGTGCTACATAATCAAACTTGCACACTTAGTGCTATACAATTCAAAC
* * *
44197235 TCGCACACTTAGTGCTACATAATCAAACTTGCACACTTAGTGCTGTACAATTTAAAC
1 CCGCACACTTAGTGCTACATAATCAAACTTGCACACTTAGTGCTATACAATTCAAAC
44197292 CCGCACACTTAG
1 CCGCACACTTAG
44197304 CGCCAATCTC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 21 0.35
56 23 0.38
57 16 0.27
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (57 bp):
CCGCACACTTAGTGCTACATAATCAAACTTGCACACTTAGTGCTATACAATTCAAAC
Found at i:44204819 original size:28 final size:28
Alignment explanation
Indices: 44204756--44204878 Score: 167
Period size: 28 Copynumber: 4.4 Consensus size: 28
44204746 ATATTAAGTC
*
44204756 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
44204783 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
44204811 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
44204839 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
44204868 CGCACACTTAG
1 CGCACACTTAG
44204879 CGCCAATCTC
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
27 21 0.25
28 48 0.56
29 16 0.19
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:44209625 original size:3 final size:3
Alignment explanation
Indices: 44209617--44209652 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
44209607 ATCTAGTTTT
* *
44209617 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA GAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
44209653 AATTAAATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:44212982 original size:31 final size:31
Alignment explanation
Indices: 44212907--44212968 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
44212897 CATGGTAAAA
44212907 GTATGAAGAATTTTCTTCATCTTTCTTTCTC
1 GTATGAAGAATTTTCTTCATCTTTCTTTCTC
44212938 GTATGAAGAATTTTCTTCATCTTTCTTTCTC
1 GTATGAAGAATTTTCTTCATCTTTCTTTCTC
44212969 TTTATACTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.52
Consensus pattern (31 bp):
GTATGAAGAATTTTCTTCATCTTTCTTTCTC
Found at i:44218429 original size:27 final size:27
Alignment explanation
Indices: 44218399--44218576 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
44218389 ATATTGAGTC
* * * *
44218399 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
44218426 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
44218453 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
44218481 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
44218508 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
44218535 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
44218562 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
44218577 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:44218538 original size:82 final size:81
Alignment explanation
Indices: 44218420--44218575 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
44218410 TGCTATATAA
* *
44218420 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
44218485 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
44218502 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
44218566 CACTTAGTGC
65 CACTTAGTGC
44218576 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:44226621 original size:27 final size:27
Alignment explanation
Indices: 44226591--44226766 Score: 201
Period size: 27 Copynumber: 6.5 Consensus size: 27
44226581 ATATTGAGTC
* * * *
44226591 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
44226618 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
44226645 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
44226673 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
44226700 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
44226727 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
44226754 CGCACACTTAGTG
1 CGCACACTTAGTG
44226767 ATGTACAATT
Statistics
Matches: 129, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:44226730 original size:82 final size:81
Alignment explanation
Indices: 44226612--44226766 Score: 231
Period size: 82 Copynumber: 1.9 Consensus size: 81
44226602 TGCTATATAA
* *
44226612 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
44226677 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
44226694 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
44226758 CACTTAGTG
65 CACTTAGTG
44226767 ATGTACAATT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.23
82 51 0.77
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:44243343 original size:43 final size:43
Alignment explanation
Indices: 44243242--44243354 Score: 147
Period size: 43 Copynumber: 2.6 Consensus size: 43
44243232 GATTACCGAG
44243242 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCATT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCATT
* * * * *
44243285 ATATGATTTCGTGTAAGACCATGTTTGGGACATTGGTATCGA-T
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATC-ATT
* *
44243328 ATGTGATAACATGTAAGACCATATCTG
1 ATGTGATTACATGTAAGACCATGTCTG
44243355 TGATATGGCA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 57 0.98
44 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (43 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCATT
Found at i:44249060 original size:48 final size:47
Alignment explanation
Indices: 44249000--44249130 Score: 165
Period size: 47 Copynumber: 2.8 Consensus size: 47
44248990 GTGCGGTCGA
* * * * *
44249000 TACCGTGATTTGGCAACGGGCCAAGGTATAGGTATTTCAAGGAGGAA-T
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCAA-GA-GAAGT
* *
44249048 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCGAGATAAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCAAGAGAAGT
*
44249095 TACCTTGGTTTGGCTACGGGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
44249131 TATTGATTGT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
46 2 0.03
47 38 0.51
48 34 0.46
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.29
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCAAGAGAAGT
Found at i:44250580 original size:23 final size:23
Alignment explanation
Indices: 44250534--44250575 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
44250524 GGTATTTGAG
44250534 TATAAATGTATAAATGTATGTAT
1 TATAAATGTATAAATGTATGTAT
*
44250557 TATATATG-ATAAATG-ATGT
1 TATAAATGTATAAATGTATGT
44250576 GTATTTATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 7 0.39
23 7 0.39
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (23 bp):
TATAAATGTATAAATGTATGTAT
Found at i:44258380 original size:22 final size:23
Alignment explanation
Indices: 44258355--44258400 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
44258345 CAACCAAATC
44258355 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
44258377 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
44258400 A
1 A
44258401 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:44258406 original size:23 final size:23
Alignment explanation
Indices: 44258362--44258406 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
44258352 ATCAATTCAA
*
44258362 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
44258385 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
44258407 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:44261845 original size:39 final size:39
Alignment explanation
Indices: 44261703--44261859 Score: 188
Period size: 39 Copynumber: 4.0 Consensus size: 39
44261693 ATAAACATGT
* * *
44261703 TATGCGTATTATGATATATGCTTGAATGTAATGTGATTA
1 TATGAGTATTGTGATATATGCTTAAATGTAATGTGATTA
* * *
44261742 TATGAGTATTGTGATATATGCTTAGATGTCATGTGACTA
1 TATGAGTATTGTGATATATGCTTAAATGTAATGTGATTA
* * *
44261781 TATAAGTATTCTGATATATGCTTAAATGTTATGTGATTA
1 TATGAGTATTGTGATATATGCTTAAATGTAATGTGATTA
* * * *
44261820 TATGTGTAATGTGATATATGCTTAAAAGTGAATATGATTA
1 TATGAGTATTGTGATATATGCTTAAATGT-AATGTGATTA
44261860 CCATGTAAAT
Statistics
Matches: 99, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
39 91 0.92
40 8 0.08
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (39 bp):
TATGAGTATTGTGATATATGCTTAAATGTAATGTGATTA
Found at i:44279207 original size:6 final size:6
Alignment explanation
Indices: 44279196--44279376 Score: 194
Period size: 6 Copynumber: 29.8 Consensus size: 6
44279186 AACCAAAATG
*
44279196 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC A-ATATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGA-ATC
* *
44279244 AGTAA-C AGAATC AGAATC AGAATC AGAATT AG-GTGAC AGAATC AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
*
44279293 AGAATC AAAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC
* *
44279341 AGAATC AGAATT ACGTGA-C AGAATC AGAATC AGAAT
1 AGAATC AGAATC A-G-AATC AGAATC AGAATC AGAAT
44279377 GTGAATGCAA
Statistics
Matches: 149, Mismatches: 12, Indels: 28
0.79 0.06 0.15
Matches are distributed among these distances:
5 9 0.06
6 128 0.86
7 9 0.06
8 3 0.02
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:44279211 original size:30 final size:30
Alignment explanation
Indices: 44279175--44279351 Score: 184
Period size: 30 Copynumber: 5.9 Consensus size: 30
44279165 AAGAAACATT
* *
44279175 ATCAGAATT-GGAACCAAAATGAGAATCAGA
1 ATCAGAATTAGGAA-CAGAATCAGAATCAGA
* *
44279205 ATCAGAATCAGTAACAGAATCAGAATCAGA
1 ATCAGAATTAGGAACAGAATCAGAATCAGA
*
44279235 ATCA-ATATTAGTAACAGAATCAGAATCAGA
1 ATCAGA-ATTAGGAACAGAATCAGAATCAGA
*
44279265 ATCAGAATTAGGTGACAGAATCAGAATCAGA
1 ATCAGAATTAGG-AACAGAATCAGAATCAGA
* *
44279296 ATCAAAATCA-GAATCAGTAA-CAGAATCAGA
1 ATCAGAATTAGGAA-CAG-AATCAGAATCAGA
*
44279326 ATCAGAATCA-GAATCAGAATCAGAAT
1 ATCAGAATTAGGAA-CAGAATCAGAAT
44279352 TACGTGACAG
Statistics
Matches: 129, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
29 4 0.03
30 94 0.73
31 31 0.24
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.19
Consensus pattern (30 bp):
ATCAGAATTAGGAACAGAATCAGAATCAGA
Found at i:44279287 original size:79 final size:79
Alignment explanation
Indices: 44279201--44279376 Score: 261
Period size: 79 Copynumber: 2.2 Consensus size: 79
44279191 AAATGAGAAT
* *
44279201 CAGAATCAGAATCAGTAA-CAGAATCAGAATCAG-AATCA-ATATTAGTAA-CAGAATCAGAATC
1 CAGAATCAGAATCAG-AATCAAAATCAGAATCAGTAA-CAGA-ATCAG-AATCAGAATCAGAATC
*
44279262 AGAATCAGAATTAGGTGA
62 AGAATCAGAATTACGTGA
44279280 CAGAATCAGAATCAGAATCAAAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGAATCAGAA
1 CAGAATCAGAATCAGAATCAAAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGAATCAGAA
44279345 TCAGAATTACGTGA
66 TCAGAATTACGTGA
44279359 CAGAATCAGAATCAGAAT
1 CAGAATCAGAATCAGAAT
44279377 GTGAATGCAA
Statistics
Matches: 90, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
78 4 0.04
79 83 0.92
80 3 0.03
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (79 bp):
CAGAATCAGAATCAGAATCAAAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGAATCAGAA
TCAGAATTACGTGA
Found at i:44279565 original size:27 final size:27
Alignment explanation
Indices: 44279494--44279567 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
44279484 AGCATGGCTG
* *
44279494 CCAGAA-CAGAT-ATCGTGACAGAGTCA
1 CCAGAATCAGATAAT-GTGGCAGAGCCA
*
44279520 CCAG-ATACAGATACTGTGGCAGAGCCA
1 CCAGAAT-CAGATAATGTGGCAGAGCCA
44279547 CCAGAATCAGATAATGTGGCA
1 CCAGAATCAGATAATGTGGCA
44279568 AACCCACCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 1 0.03
26 4 0.10
27 32 0.80
28 3 0.08
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.16
Consensus pattern (27 bp):
CCAGAATCAGATAATGTGGCAGAGCCA
Found at i:44279574 original size:27 final size:27
Alignment explanation
Indices: 44279518--44279575 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
44279508 GTGACAGAGT
* * *
44279518 CACCAGATACAGATACTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAACC
44279545 CACCAGA-ATCAGATAATGTGGCAAACC
1 CACCAGATA-CAGATAATGTGGCAAACC
44279572 CACC
1 CACC
44279576 TAACAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.36, C:0.29, G:0.21, T:0.14
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAACC
Found at i:44279957 original size:27 final size:26
Alignment explanation
Indices: 44279878--44279960 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
44279868 TCGATCGGTC
* * *
44279878 AACAGATATTGTGACAGAGTCACCAA
1 AACAGATATTGTGGCAGAGCCACCAG
44279904 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
44279931 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
44279958 AAC
1 AAC
44279961 GCTTCCTCCG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 8 0.16
27 43 0.84
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:44280221 original size:27 final size:27
Alignment explanation
Indices: 44280160--44280354 Score: 194
Period size: 27 Copynumber: 7.2 Consensus size: 27
44280150 GGGCAAAATG
* * * * * *
44280160 GTAATTTTACCCCACAAGCGTATCTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
44280187 GTAATTCTACCCTATAGGGGTTTTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* * *
44280214 GTATTTCTACCCTACAAGGGTATTT-T
1 GTAATTCTACCCTACAGGGGTATTTCA
**
44280240 GATAATTCTACCCTACAGGGGTATTTTG
1 G-TAATTCTACCCTACAGGGGTATTTCA
* * *
44280268 GTAATTCTATCCTATAAGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
44280295 GTGATTCTACCCTATAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
44280322 GAAATTCTACCCAACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
44280349 GTAATT
1 GTAATT
44280355 TCACAATCAA
Statistics
Matches: 137, Mismatches: 29, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
26 1 0.01
27 135 0.99
28 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.36
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCA
Found at i:44280296 original size:81 final size:81
Alignment explanation
Indices: 44280186--44280346 Score: 227
Period size: 81 Copynumber: 2.0 Consensus size: 81
44280176 AGCGTATCTC
* * *
44280186 GGTAATTCTACCCTATAGGGGTTTTTCAGT-ATTTCTACCCTACAAGGGTATTT-TGATAATTCT
1 GGTAATTCTACCCTATAAGGGTATTTCAGTGA-TTCTACCCTACAAGGGTATTTCAGA-AATTCT
*
44280249 ACCCTACAGGGGTATTTT
64 ACCCAACAGGGGTATTTT
* * *
44280267 GGTAATTCTATCCTATAAGGGTATTTCAGTGATTCTACCCTATAGGGGTATTTCAGAAATTCTAC
1 GGTAATTCTACCCTATAAGGGTATTTCAGTGATTCTACCCTACAAGGGTATTTCAGAAATTCTAC
44280332 CCAACAGGGGTATTT
66 CCAACAGGGGTATTT
44280347 CAGTAATTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
81 68 0.96
82 3 0.04
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.37
Consensus pattern (81 bp):
GGTAATTCTACCCTATAAGGGTATTTCAGTGATTCTACCCTACAAGGGTATTTCAGAAATTCTAC
CCAACAGGGGTATTTT
Found at i:44280396 original size:27 final size:27
Alignment explanation
Indices: 44280366--44280883 Score: 596
Period size: 27 Copynumber: 18.9 Consensus size: 27
44280356 CACAATCAAT
*
44280366 GGTAAAACGGTAATTCTGTAAATCAAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
** * *
44280393 GGTAAAACAATAATTTTGTAAA-CTGAA
1 GGTAAAACGGTAATTCTGTAAATC-GAG
* * * *
44280420 GGTAAACCAGTAATTCTATAAATCAAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
* **
44280447 GGTAAAACGGTAATTTTACAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
*
44280474 GGTAAAACGATAATTCTGTAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
**
44280501 GGTAAAATAGTAATTCTGTAAA-CTGAG
1 GGTAAAACGGTAATTCTGTAAATC-GAG
* *
44280528 GGTAAAACGGTAATTCTATAAATCAAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
44280555 GGTAAAACGGTAATTCTGTAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
* **
44280582 GGTAAAACGGTAATTTTACAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
*
44280609 GGTAAAACGGTGATTCTGTAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
** *
44280636 GGTAAAATAGTAATTCTATAAA-CTGAG
1 GGTAAAACGGTAATTCTGTAAATC-GAG
*
44280663 GGTAAAATGGTAATTCTGTAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
* *
44280690 GGTAAAACGGTAATTTTAAAAATTTACAAATCGAG
1 GGTAAAACGGTAA--TT----CTGT--AAATCGAG
44280725 GGTAAAACGGTAATTCTGTAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
*
44280752 GGTAAAACAGTAATTCTGTAAA-CG-G
1 GGTAAAACGGTAATTCTGTAAATCGAG
*
44280777 AGGTAAAACGGTAATTATGTAAATCGAG
1 -GGTAAAACGGTAATTCTGTAAATCGAG
* * **
44280805 GGTAAAATGGTAATTTTAAAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
44280832 GGTAAAACGGTAATTCTGTAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
44280859 GGTAAAACGGTAATTCTGTAAATCG
1 GGTAAAACGGTAATTCTGTAAATCG
44280884 GGAGTACTTT
Statistics
Matches: 416, Mismatches: 58, Indels: 34
0.82 0.11 0.07
Matches are distributed among these distances:
25 1 0.00
26 25 0.06
27 357 0.86
28 4 0.01
29 4 0.01
33 4 0.01
35 21 0.05
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (27 bp):
GGTAAAACGGTAATTCTGTAAATCGAG
Found at i:44280899 original size:81 final size:80
Alignment explanation
Indices: 44280717--44280914 Score: 256
Period size: 80 Copynumber: 2.5 Consensus size: 80
44280707 AAAAATTTAC
* * **
44280717 AAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTAAACGGAGGTA
1 AAATCGAGGGTAAAATGGTAATTTTAAAAATCGAGGGTAAAACAGTAATTCTGTAAACGGAGGTA
44280782 AAACGGTAATTATGT
66 AAACGGTAATTATGT
*
44280797 AAATCGAGGGTAAAATGGTAATTTTAAAAATCGAGGGTAAAACGGTAATTCTGTAAATC-GAGGG
1 AAATCGAGGGTAAAATGGTAATTTTAAAAATCGAGGGTAAAACAGTAATTCTGTAAA-CGGA-GG
*
44280861 TAAAACGGTAATTCTGT
64 TAAAACGGTAATTATGT
*** * *
44280878 AAATCG-GGAGTACTTTGGTAATTTTACAAGTCGAGGG
1 AAATCGAGG-GTAAAATGGTAATTTTAAAAATCGAGGG
44280915 CATTTTAGTA
Statistics
Matches: 104, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
80 56 0.54
81 48 0.46
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.27
Consensus pattern (80 bp):
AAATCGAGGGTAAAATGGTAATTTTAAAAATCGAGGGTAAAACAGTAATTCTGTAAACGGAGGTA
AAACGGTAATTATGT
Found at i:44286182 original size:39 final size:38
Alignment explanation
Indices: 44286139--44286215 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 38
44286129 TGTTATAAAA
*
44286139 CTCACAAATTGCTCTAGGGGTGACAAGCACCTCTTTCCC
1 CTCACAAATTGCTCTAAGGGTGACAAGCACC-CTTTCCC
*
44286178 CTCACAAATTGCTTTAAGGGTGACAAGCACCCTTTCCC
1 CTCACAAATTGCTCTAAGGGTGACAAGCACCCTTTCCC
44286216 TCTGACTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 7 0.19
39 29 0.81
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (38 bp):
CTCACAAATTGCTCTAAGGGTGACAAGCACCCTTTCCC
Found at i:44290601 original size:19 final size:18
Alignment explanation
Indices: 44290578--44290616 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
44290568 ATAGTGTAAT
44290578 AATATAT-TA-ATAATATA
1 AATATATATATATAATA-A
44290595 AATATATATATATAATAA
1 AATATATATATATAATAA
44290613 AATA
1 AATA
44290617 ACATATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 7 0.35
19 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATATATATATATAATAA
Found at i:44290622 original size:17 final size:19
Alignment explanation
Indices: 44290587--44290628 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
44290577 TAATATATTA
*
44290587 ATAATATAAATATATATAT
1 ATAATATAAATATACATAT
44290606 ATAATA-AAATA-ACATAT
1 ATAATATAAATATACATAT
*
44290623 AAAATA
1 ATAATA
44290629 CAAAAGAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 10 0.48
18 5 0.24
19 6 0.29
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAATATAAATATACATAT
Found at i:44290784 original size:10 final size:10
Alignment explanation
Indices: 44290771--44290925 Score: 81
Period size: 10 Copynumber: 14.8 Consensus size: 10
44290761 TATATGATAA
44290771 AATATAAAAT
1 AATATAAAAT
*
44290781 AATATAATAT
1 AATATAAAAT
*
44290791 AATATATAAT
1 AATATAAAAT
*
44290801 GTATATTAAAACAT
1 -AATA-T-AAA-AT
* *
44290815 AAGATAATAT
1 AATATAAAAT
44290825 AATATATATAAT
1 AATATA-A-AAT
44290837 AATAT-AAA-
1 AATATAAAAT
44290845 AATATAAAAT
1 AATATAAAAT
44290855 AATATATATTAAT
1 AATATA-A--AAT
*
44290868 AA-ATAATAT
1 AATATAAAAT
44290877 AATATATAAAT
1 AATATA-AAAT
44290888 -ATACTTGAAAAT
1 AATA--T-AAAAT
44290900 AA-A-AAAAT
1 AATATAAAAT
44290908 AATATACAAAT
1 AATATA-AAAT
44290919 AA-ATAAA
1 AATATAAA
44290926 TTTTTATATG
Statistics
Matches: 113, Mismatches: 12, Indels: 41
0.68 0.07 0.25
Matches are distributed among these distances:
8 12 0.11
9 12 0.11
10 41 0.36
11 17 0.15
12 18 0.16
13 11 0.10
14 2 0.02
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (10 bp):
AATATAAAAT
Found at i:44290787 original size:5 final size:5
Alignment explanation
Indices: 44290754--44290890 Score: 80
Period size: 5 Copynumber: 29.0 Consensus size: 5
44290744 ATGTAATAAG
* * *
44290754 ATATA A-AT- ATATG ATAAA ATATA AAATA ATATA ATATA ATAT- ATA-A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * * * *
44290800 TGTATA TTAAA ACATA AGATA ATATA ATATA TATAATA ATATA A-A-A
1 -ATATA ATATA ATATA ATATA ATATA ATATA -AT-ATA ATATA ATATA
* *
44290846 ATATA AAATA ATAT- ATATT A-ATA A-ATA ATATA ATAT- ATA-A ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
44290891 CTTGAAAATA
Statistics
Matches: 103, Mismatches: 16, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
3 3 0.03
4 26 0.25
5 66 0.64
6 5 0.05
7 3 0.03
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (5 bp):
ATATA
Found at i:44290792 original size:22 final size:22
Alignment explanation
Indices: 44290759--44290886 Score: 74
Period size: 22 Copynumber: 5.9 Consensus size: 22
44290749 ATAAGATATA
44290759 AATAT-ATGATAAAATATAAAAT
1 AATATAAT-ATAAAATATAAAAT
*
44290781 AATATAATAT--AATATATAAT
1 AATATAATATAAAATATAAAAT
* * *
44290801 -GTAT-AT-TAAAACATAAGAT
1 AATATAATATAAAATATAAAAT
44290820 AATATAATATATATAATAATATAAA-
1 AATATAATATA-A-AAT-ATA-AAAT
* * *
44290845 AATATAAAATAATATATATTAAT
1 AATATAATATAAAATATA-AAAT
*
44290868 AA-ATAATATAATATATAAA
1 AATATAATATAAAATATAAA
44290887 TATACTTGAA
Statistics
Matches: 82, Mismatches: 13, Indels: 23
0.69 0.11 0.19
Matches are distributed among these distances:
17 1 0.01
18 2 0.02
19 10 0.12
20 12 0.15
21 3 0.04
22 29 0.35
23 7 0.09
24 3 0.04
25 13 0.16
26 2 0.02
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (22 bp):
AATATAATATAAAATATAAAAT
Found at i:44290832 original size:27 final size:25
Alignment explanation
Indices: 44290786--44290967 Score: 80
Period size: 27 Copynumber: 7.2 Consensus size: 25
44290776 AAAATAATAT
*
44290786 AATATAAT-ATATAATGTATATTAAA
1 AATA-AATAATATAATATATATTAAA
44290811 ACATAAGATAATATAATATATATAATAATA
1 A-ATAA-ATAATATAATATATAT--TAA-A
* *
44290841 TAAAAATATAAAATAATATATATTAATA
1 -AATAA-ATAATATAATATATATTAA-A
* *
44290869 AATAATATAATATATAAATATACTTGAA
1 AATAA-ATAATATA-ATATATA-TTAAA
*
44290897 AAT-AA-AA-A-AATA-ATA-TACA
1 AATAAATAATATAATATATATTAAA
* * *
44290916 AATAAATAA-AT-TTTTATATGTATA
1 AATAAATAATATAATATATAT-TAAA
*
44290940 AATAAATAATA-AATA-ATATTTAA
1 AATAAATAATATAATATATATTAAA
44290963 AATAA
1 AATAA
44290968 CTAAATTTAA
Statistics
Matches: 122, Mismatches: 18, Indels: 36
0.69 0.10 0.20
Matches are distributed among these distances:
19 5 0.04
20 2 0.02
21 7 0.06
22 5 0.04
23 8 0.07
24 17 0.14
25 6 0.05
26 6 0.05
27 25 0.20
28 15 0.12
29 6 0.05
30 19 0.16
31 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (25 bp):
AATAAATAATATAATATATATTAAA
Found at i:44292895 original size:44 final size:44
Alignment explanation
Indices: 44292398--44292870 Score: 680
Period size: 44 Copynumber: 10.8 Consensus size: 44
44292388 GATGTCCTTG
* * *
44292398 AGAGACGCCAAATATGCTATCTTCGATCTGCTTTTTGACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* *
44292442 AGAGATGCCAAATCTACTATCTTCGATCTGCTCTCTGACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
** * * *
44292486 AGAGACGGTAAATCTGTTATCTTCGATCTACTCTCTGTCAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* * * *
44292530 AGAGATGCCAAATCCGTTATCTTCAATCTGCTCTCTGACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
*
44292574 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGATAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* *
44292618 AGAAACGCCAAATCTGCTATCTTCGATCTGCTTTCTGACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
44292662 AGAGACGCCAAATCTG-TCATCTTCGATCTGCTCTCTGACAATAC
1 AGAGACGCCAAATCTGCT-ATCTTCGATCTGCTCTCTGACAATAC
* * *
44292706 AGAGACGCCAAATCTACTATCTTTGATCTGCTCTCTAACAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
* * *
44292750 AAAGACGCCAAATCT-ATCATCTTCGATCTGCTCTCTGACAATGC
1 AGAGACGCCAAATCTGCT-ATCTTCGATCTGCTCTCTGACAATAC
* * *
44292794 AGAGATGCCAAATCTACTATCTTCGATCTGCTCTCTGTCAATAC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
44292838 AGAGACGCCAAATCTGCTATCTTCGATCTGCTC
1 AGAGACGCCAAATCTGCTATCTTCGATCTGCTC
44292871 ATTGTAAACA
Statistics
Matches: 381, Mismatches: 44, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
43 2 0.01
44 377 0.99
45 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.30
Consensus pattern (44 bp):
AGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATAC
Found at i:44293328 original size:20 final size:21
Alignment explanation
Indices: 44293277--44293329 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
44293267 ACGTCACCAC
*
44293277 TCATTCCTTC-GTCGAAGTTTA
1 TCATTCCTTCTCTCGAAG-TTA
**
44293298 TCATTATTTCTCTCGAAG-TA
1 TCATTCCTTCTCTCGAAGTTA
44293318 TCATTCCTTCTC
1 TCATTCCTTCTC
44293330 AGCCTGTGGG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 12 0.46
21 8 0.31
22 6 0.23
ACGTcount: A:0.19, C:0.26, G:0.09, T:0.45
Consensus pattern (21 bp):
TCATTCCTTCTCTCGAAGTTA
Found at i:44297339 original size:29 final size:26
Alignment explanation
Indices: 44297280--44297331 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
44297270 TTTTCACCTC
44297280 TTTCCCTTCCTCTAGGGCTACATTCT
1 TTTCCCTTCCTCTAGGGCTACATTCT
*
44297306 TTTCCCTTCTTCTAGGGCTACATTCT
1 TTTCCCTTCCTCTAGGGCTACATTCT
44297332 CTATTTCCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.12, C:0.33, G:0.12, T:0.44
Consensus pattern (26 bp):
TTTCCCTTCCTCTAGGGCTACATTCT
Found at i:44305043 original size:19 final size:19
Alignment explanation
Indices: 44305012--44305066 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 19
44305002 ATAGTGTAAT
44305012 AATATAT-TA-ATAATATA
1 AATATATATATATAATATA
44305029 AATATATATATATAATA-A
1 AATATATATATATAATATA
* * *
44305047 AGTA-ACATATAAAATATA
1 AATATATATATATAATATA
44305065 AA
1 AA
44305067 AGAATAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 17 0.55
18 8 0.26
19 6 0.19
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
AATATATATATATAATATA
Found at i:44305226 original size:5 final size:5
Alignment explanation
Indices: 44305187--44305323 Score: 71
Period size: 5 Copynumber: 29.0 Consensus size: 5
44305177 ATGTAATAAG
* * * *
44305187 ATATA A-AT- ATATG ATAAA ATATA AAATA ACATA ATATA ATAT- ATA-A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * * * *
44305233 TGTATA TTAAA ACATA AGATA ATATA ATATA TATAATA ATATA A-A-A
1 -ATATA ATATA ATATA ATATA ATATA ATATA -AT-ATA ATATA ATATA
* *
44305279 ATATA AAATA ATAT- ATATT A-ATA A-ATA ATATA ATAT- ATA-A ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
44305324 CTTGAAAATA
Statistics
Matches: 102, Mismatches: 17, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
3 3 0.03
4 26 0.25
5 65 0.64
6 5 0.05
7 3 0.03
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.35
Consensus pattern (5 bp):
ATATA
Found at i:44305244 original size:32 final size:30
Alignment explanation
Indices: 44305195--44305353 Score: 108
Period size: 32 Copynumber: 5.4 Consensus size: 30
44305185 AGATATAAAT
44305195 ATATGATAAA-ATA-TAAAATAACATAATATA
1 ATAT-ATAAATATATTAAAATAA-ATAATATA
*
44305225 ATATATAATGTATATTAAAACATAAGATAATATA
1 ATATATAA-ATATATT-AAA-ATAA-ATAATATA
*
44305259 ATATAT--ATA-A-TAATATAAA-AATATA
1 ATATATAAATATATTAAAATAAATAATATA
44305284 A-A-ATAATATATATT--AATAAATAATATA
1 ATATATAA-ATATATTAAAATAAATAATATA
*
44305311 ATATATAAATATACTTGAAAATAACA-AAAATA
1 ATATATAAATATA-TT-AAAATAA-ATAATATA
*
44305343 ATATACAAATA
1 ATATATAAATA
44305354 AATAAATTTT
Statistics
Matches: 104, Mismatches: 7, Indels: 34
0.72 0.05 0.23
Matches are distributed among these distances:
23 2 0.02
24 1 0.01
25 7 0.07
26 9 0.09
27 12 0.12
28 9 0.09
29 11 0.11
30 5 0.05
31 5 0.05
32 21 0.20
33 4 0.04
34 18 0.17
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (30 bp):
ATATATAAATATATTAAAATAAATAATATA
Found at i:44305265 original size:27 final size:25
Alignment explanation
Indices: 44305219--44305401 Score: 80
Period size: 27 Copynumber: 7.2 Consensus size: 25
44305209 AAAATAACAT
*
44305219 AATATAAT-ATATAATGTATATTAAA
1 AATA-AATAATATAATATATATTAAA
44305244 ACATAAGATAATATAATATATATAATAATA
1 A-ATAA-ATAATATAATATATAT--TAA-A
* *
44305274 TAAAAATATAAAATAATATATATTAATA
1 -AATAA-ATAATATAATATATATTAA-A
* *
44305302 AATAATATAATATATAAATATACTTGAA
1 AATAA-ATAATATA-ATATATA-TTAAA
* *
44305330 AAT-AACAA-A-AATA-ATA-TACA
1 AATAAATAATATAATATATATTAAA
* * *
44305350 AATAAATAA-AT-TTTTATATGTATA
1 AATAAATAATATAATATATAT-TAAA
*
44305374 AATAAATAATA-AATA-ATATTTAA
1 AATAAATAATATAATATATATTAAA
44305397 AATAA
1 AATAA
44305402 CTAAATTTAA
Statistics
Matches: 122, Mismatches: 20, Indels: 34
0.69 0.11 0.19
Matches are distributed among these distances:
20 5 0.04
21 6 0.05
22 6 0.05
23 9 0.07
24 17 0.14
25 5 0.04
26 8 0.07
27 25 0.20
28 15 0.12
29 6 0.05
30 19 0.16
31 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (25 bp):
AATAAATAATATAATATATATTAAA
Found at i:44305292 original size:30 final size:32
Alignment explanation
Indices: 44305210--44305321 Score: 96
Period size: 28 Copynumber: 3.6 Consensus size: 32
44305200 ATAAAATATA
* *
44305210 AAATAACATAATATAATATATAATGTATATTAA-
1 AAATAATATAATATAA-A-ATAATATATATTAAT
* *
44305243 AACATAAGATAATAT--AAT-ATATATAATAAT
1 AA-ATAATATAATATAAAATAATATATATTAAT
44305273 --ATAA-A-AATATAAAATAATATATATTAAT
1 AAATAATATAATATAAAATAATATATATTAAT
44305301 AAATAATATAATATATAAATA
1 AAATAATATAATATA-AAATA
44305322 TACTTGAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
25 5 0.08
26 1 0.02
27 7 0.11
28 11 0.17
29 9 0.14
30 6 0.09
31 2 0.03
32 6 0.09
33 7 0.11
34 11 0.17
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (32 bp):
AAATAATATAATATAAAATAATATATATTAAT
Found at i:44305332 original size:52 final size:55
Alignment explanation
Indices: 44305246--44305347 Score: 133
Period size: 52 Copynumber: 1.9 Consensus size: 55
44305236 ATATTAAAAC
*
44305246 ATAAGATAATATAATATATATAATAATATAAAAAT-A-TAAAATAATATATATTA
1 ATAAGATAATATAATATATATAATAATATAAAAATAACAAAAATAATATATATTA
*
44305299 ATAA-ATAATATAATATATA-AAT-ATACTTGAAAATAACAAAAATAATATA
1 ATAAGATAATATAATATATATAATAATA--TAAAAATAACAAAAATAATATA
44305348 CAAATAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
50 3 0.07
51 3 0.07
52 21 0.49
53 5 0.12
54 11 0.26
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (55 bp):
ATAAGATAATATAATATATATAATAATATAAAAATAACAAAAATAATATATATTA
Found at i:44305622 original size:30 final size:29
Alignment explanation
Indices: 44305578--44305638 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
44305568 TCAAAGGAGC
*
44305578 TGTTAGGACTAAATTGA-AATAAAATCAAAA
1 TGTTAGGACCAAATT-ATAATAAAAT-AAAA
* *
44305608 TGTTAGGGCCAAATTATATTAAAATAAAA
1 TGTTAGGACCAAATTATAATAAAATAAAA
44305637 TG
1 TG
44305639 AAATTGCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.30
Consensus pattern (29 bp):
TGTTAGGACCAAATTATAATAAAATAAAA
Found at i:44319761 original size:15 final size:15
Alignment explanation
Indices: 44319741--44319773 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
44319731 GTGAATGATG
44319741 TGTGGATGTCTTGGT
1 TGTGGATGTCTTGGT
*
44319756 TGTGGATGTTTTGGT
1 TGTGGATGTCTTGGT
44319771 TGT
1 TGT
44319774 ATGAAAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.03, G:0.39, T:0.52
Consensus pattern (15 bp):
TGTGGATGTCTTGGT
Found at i:44322405 original size:16 final size:17
Alignment explanation
Indices: 44322380--44322418 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
44322370 ATCATTCGCC
*
44322380 TATTTGTAACATAA-AA
1 TATTTATAACATAATAA
44322396 TATTTATAACATAATAA
1 TATTTATAACATAATAA
44322413 TATTTA
1 TATTTA
44322419 GATTTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (17 bp):
TATTTATAACATAATAA
Found at i:44323696 original size:25 final size:23
Alignment explanation
Indices: 44323655--44323706 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
44323645 CCTTGTTTAT
*
44323655 TTTATTTTATTTTAATTTGACCC
1 TTTATTTTATTTTAATTTGACAC
* *
44323678 TTTATTTTTTTTTTAAATTTTACAC
1 TTTA-TTTTATTTT-AATTTGACAC
44323703 TTTA
1 TTTA
44323707 AATTTCATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.17
24 8 0.33
25 12 0.50
ACGTcount: A:0.23, C:0.10, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTATTTTATTTTAATTTGACAC
Found at i:44324158 original size:18 final size:17
Alignment explanation
Indices: 44324124--44324187 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 17
44324114 TCGAATATTT
44324124 TATTATTTATTTCATTA
1 TATTATTTATTTCATTA
* *
44324141 TTTTATTTGTTCTCATTA
1 TATTATTTATT-TCATTA
*
44324159 TATTATTGTCATTTTATTA
1 TATTATT-T-ATTTCATTA
44324178 TATTATTTAT
1 TATTATTTAT
44324188 GTTGTTTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 11 0.28
18 13 0.33
19 13 0.33
20 2 0.05
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (17 bp):
TATTATTTATTTCATTA
Found at i:44327639 original size:16 final size:17
Alignment explanation
Indices: 44327612--44327648 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
44327602 ATAAAATACG
44327612 ATATTATTTAAA-AAATA
1 ATATTATTTAAATAAA-A
44327629 ATATT-TTTAAATAAAA
1 ATATTATTTAAATAAAA
44327645 ATAT
1 ATAT
44327649 AAATTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATTATTTAAATAAAA
Found at i:44351275 original size:48 final size:48
Alignment explanation
Indices: 44351204--44351295 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
44351194 TCTTGCATTA
*
44351204 ATACACAACTAAGACCATTCAATGACGCATCAG-TGAAAATCACAAACT
1 ATACACAACCAAGACCATTCAATGACGCAT-AGCTGAAAATCACAAACT
* *
44351252 ATACACAACCAAGGCCATTCAATGACGCATTGCTGAAAATCACA
1 ATACACAACCAAGACCATTCAATGACGCATAGCTGAAAATCACA
44351296 CTCTTTTCTC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 1 0.03
48 39 0.98
ACGTcount: A:0.43, C:0.26, G:0.12, T:0.18
Consensus pattern (48 bp):
ATACACAACCAAGACCATTCAATGACGCATAGCTGAAAATCACAAACT
Found at i:44355791 original size:38 final size:39
Alignment explanation
Indices: 44355741--44355834 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 39
44355731 CCATCTCCAA
* * *
44355741 CCAACCCAACACACCA-TGTGAGGATAAAATCGACCCA-
1 CCAACCCTACACACCAGTATGAGGATAAAATCAACCCAT
* *
44355778 CTCAGCCCTACACACCAAGTATGGGGATAAAATCAACCCAT
1 C-CAACCCTACACACC-AGTATGAGGATAAAATCAACCCAT
*
44355819 CCAACCCTACAAACCA
1 CCAACCCTACACACCA
44355835 AATGGTACCG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
37 1 0.02
38 12 0.26
39 2 0.04
40 30 0.65
41 1 0.02
ACGTcount: A:0.39, C:0.36, G:0.12, T:0.13
Consensus pattern (39 bp):
CCAACCCTACACACCAGTATGAGGATAAAATCAACCCAT
Found at i:44358144 original size:27 final size:27
Alignment explanation
Indices: 44358114--44358178 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
44358104 ATTACCAAAG
* * *
44358114 TACCCTCGATTTGTAGAATCACTGTTT
1 TACCCTCGATTTGCAAAATCACCGTTT
* * *
44358141 TACCCTTGACTTGCAAAATTACCGTTT
1 TACCCTCGATTTGCAAAATCACCGTTT
44358168 TACCCTCGATT
1 TACCCTCGATT
44358179 ATGAAATTAC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.38
Consensus pattern (27 bp):
TACCCTCGATTTGCAAAATCACCGTTT
Found at i:44358240 original size:27 final size:27
Alignment explanation
Indices: 44358210--44358333 Score: 133
Period size: 27 Copynumber: 4.6 Consensus size: 27
44358200 TATAGGGTAG
*
44358210 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAATTTGTAA
* ** *
44358237 AATTACCAAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTAATTTGTAA
* *
44358264 AATTACCGAAATA-CCCTCAATTTGGAA
1 AATTACCAAAATACCCCT-AATTTGTAA
* *
44358291 AATTACCAAAATACCCCTAATTTATGA
1 AATTACCAAAATACCCCTAATTTGTAA
**
44358318 AATTATAAAAATACCC
1 AATTACCAAAATACCC
44358334 TTGACTTTCT
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
26 3 0.04
27 73 0.91
28 4 0.05
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAATTTGTAA
Found at i:44358251 original size:54 final size:53
Alignment explanation
Indices: 44358182--44358309 Score: 125
Period size: 54 Copynumber: 2.4 Consensus size: 53
44358172 CTCGATTATG
** * *
44358182 AAATTACTGAAATACCCCTATAGGGT-AGAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCCTAT-GGGTGA-AATTACCAAAATACCCTC-AATTTGGA
* * ** *
44358236 AAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAATACCCTCAATTTGGA
1 AAATTACCAAAATACCCCT-ATGGGTGAAATTACCAAAATACCCTCAATTTGGA
44358290 AAATTACCAAAATACCCCTA
1 AAATTACCAAAATACCCCTA
44358310 ATTTATGAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
54 57 0.95
55 3 0.05
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.27
Consensus pattern (53 bp):
AAATTACCAAAATACCCCTATGGGTGAAATTACCAAAATACCCTCAATTTGGA
Found at i:44358319 original size:54 final size:54
Alignment explanation
Indices: 44358210--44358333 Score: 151
Period size: 54 Copynumber: 2.3 Consensus size: 54
44358200 TATAGGGTAG
* * ** *
44358210 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTAATTTGGAAAATTACCAAAATACCACTAATTTATGA
* *
44358264 AATTACCGAAATA-CCCTCAATTTGGAAAATTACCAAAATACCCCTAATTTATGA
1 AATTACCAAAATACCCCT-AATTTGGAAAATTACCAAAATACCACTAATTTATGA
**
44358318 AATTATAAAAATACCC
1 AATTACCAAAATACCC
44358334 TTGACTTTCT
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
53 4 0.07
54 52 0.90
55 2 0.03
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (54 bp):
AATTACCAAAATACCCCTAATTTGGAAAATTACCAAAATACCACTAATTTATGA
Found at i:44358384 original size:27 final size:27
Alignment explanation
Indices: 44358345--44358396 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
44358335 TGACTTTCTA
44358345 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
44358372 AAAATTACT-GAAATACCCTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
44358397 GTAGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:44358514 original size:27 final size:27
Alignment explanation
Indices: 44358437--44358514 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
44358427 AAATGACTAA
* *
44358437 AATACCCCT-AATAGGTAAAAAGACCGT
1 AATACCCCTGTAT-GGTAAAATGACCGT
* **
44358464 AA-AGCCCCTGTAGGGTAATGTGACCGT
1 AATA-CCCCTGTATGGTAAAATGACCGT
44358491 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTGTATGGTAAAATGAC
44358515 AAATATGCCC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
26 1 0.03
27 37 0.93
28 2 0.05
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTATGGTAAAATGACCGT
Found at i:44359353 original size:25 final size:25
Alignment explanation
Indices: 44359315--44359384 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
44359305 AGGAAGTGCT
* *
44359315 AAAAGGGCTATGCCCCAGTTTA-CTG
1 AAAAGGGCTTTGCCCCAGTTTATC-A
*
44359340 AAAAGGGCTTTGCCCCAATTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
44359365 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
44359385 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 39 0.98
26 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:44359397 original size:24 final size:23
Alignment explanation
Indices: 44359314--44359411 Score: 88
Period size: 25 Copynumber: 4.0 Consensus size: 23
44359304 GAGGAAGTGC
44359314 TAAAAGGGCTATGCCCCAGTTTACT
1 TAAAAGGGCTATGCCCCAG-TTA-T
* * *
44359339 GAAAAGGGCTTTGCCCCAATTTAT
1 TAAAAGGGCTATGCCCC-AGTTAT
* *
44359363 CAAAAAGGGCTTTGCCCCAGTTAT
1 -TAAAAGGGCTATGCCCCAGTTAT
*
44359387 TAAAAGAGGCTAGGCCTCCAGTTAT
1 TAAAAG-GGCTATGCC-CCAGTTAT
44359412 ATAATAAAGC
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
23 5 0.08
24 13 0.21
25 42 0.69
26 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (23 bp):
TAAAAGGGCTATGCCCCAGTTAT
Found at i:44359656 original size:31 final size:30
Alignment explanation
Indices: 44359604--44359686 Score: 123
Period size: 31 Copynumber: 2.7 Consensus size: 30
44359594 CGCTTATAGT
*
44359604 AAAGGCTTCGGCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCAGTTATATGATTTATGA
*
44359634 AAAGGCTTTGGCCCAGTTATATGATTTATGA
1 AAAGGCTTCGG-CCAGTTATATGATTTATGA
44359665 AAAGGCTTCGGACCAG-TATATG
1 AAAGGCTTCGG-CCAGTTATATG
44359687 TCGAGACTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 16 0.33
31 32 0.67
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (30 bp):
AAAGGCTTCGGCCAGTTATATGATTTATGA
Found at i:44359742 original size:29 final size:28
Alignment explanation
Indices: 44359700--44359754 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
44359690 AGACTGAATT
* *
44359700 AGGGCTTAGGCCCATACTGCTATTGTTTA
1 AGGGCTAAAGCCCATACTG-TATTGTTTA
44359729 AGGGCTAAAGCCCATACTGTATTGTT
1 AGGGCTAAAGCCCATACTGTATTGTT
44359755 ACTGAACAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (28 bp):
AGGGCTAAAGCCCATACTGTATTGTTTA
Found at i:44364837 original size:40 final size:39
Alignment explanation
Indices: 44364779--44364909 Score: 140
Period size: 40 Copynumber: 3.3 Consensus size: 39
44364769 ATTTGAATGA
* *
44364779 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTG-TTT
*
44364819 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGT-TTCT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGTT-T
* * * * *
44364858 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTA
1 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGT-GTTT
44364899 TATCC-GGCTAA
1 TATCCGGGCTAA
44364910 ATTCCGAAGA
Statistics
Matches: 76, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
38 2 0.03
39 6 0.08
40 66 0.87
42 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (39 bp):
TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGTTT
Found at i:44369464 original size:40 final size:40
Alignment explanation
Indices: 44369388--44369464 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
44369378 ACACACCATG
** * *
44369388 TGGGGATAAAATCGGCCCACCCAGCCGTACACACCAAGTA
1 TGGGGATAAAATCAACCCACCCAACCGTACAAACCAAGTA
* *
44369428 TGGGGATAAAATCAACCCATCCAACCTTACAAACCAA
1 TGGGGATAAAATCAACCCACCCAACCGTACAAACCAA
44369465 ATGGTACCGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.38, C:0.31, G:0.17, T:0.14
Consensus pattern (40 bp):
TGGGGATAAAATCAACCCACCCAACCGTACAAACCAAGTA
Found at i:44371567 original size:20 final size:21
Alignment explanation
Indices: 44371531--44371571 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
44371521 CCACTTTTTT
44371531 CATTTATTTACACTTTTCTACA
1 CATTTATTTACACTTTT-TACA
44371553 CATTT-TTTA-ACTTTTTACA
1 CATTTATTTACACTTTTTACA
44371572 AATAAGTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 4 0.21
22 5 0.26
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.54
Consensus pattern (21 bp):
CATTTATTTACACTTTTTACA
Found at i:44393833 original size:501 final size:494
Alignment explanation
Indices: 44392886--44393890 Score: 1647
Period size: 501 Copynumber: 2.0 Consensus size: 494
44392876 GTGACCCTTG
* * *
44392886 TATATAAGAAAATTTTGAAATTTTGCGAAATATTCTCTTAGATCCCGATTTAGTCCCGACTTGTT
1 TATATAAGAAAATTTTGAAATTTTGAGAAATATTCTCTGAGATCCCAATTTAGTCCCGACTTGTT
*
44392951 TCTAATGCTTAGATTGCGCGTTGAGGGTTCATTCAAGGGACGATATGATTAATTTCGAACATGAA
66 TCTAATGCTTAAATTGCGCGTTGAGGGTTCATTCAAGGGACGATATGATTAATTTCGAACATG--
*
44393016 TAATAATTGATATGAATTATCTATAATTGTTCTAAAAACTTTGGTAATACTTTATAACCCTGTTC
129 -AATAATTGACATGAATTATCTATAATTGTTCTAAAAACTTTGGTAATACTTTATAACCCTGTTC
44393081 TGGTGACAAATACAGGTGTTACATGTAAAGCTATACAGCTGTGTGACCATGTTTCCAAAATTTTC
193 TGGTGACAAATACAGGTGTTACATGTAAAGCTATACAGCTGTGTGACCATGTTTCCAAAATTTTC
*
44393146 AAATTTTTGCATGTTTTTTTTATTTTGATTCAAATTAGTCCCTGATTGTTCCCAAACCATTTTTA
258 AAATTTTTGCATGTTTTTTTTATTTTGATTCAAATTAGCCCCTGATTGTTCCCAAACCATTTTTA
*
44393211 GAGCCCCGTAAACTCAGTTTAAGTCTCATAAGTTTATTTTATCATGATTTTTATAAGCTATTGAT
323 GAGCCCCGTAAACTCAGTTTAAGGCTCATAAGTTTATTTTATCATGATTTTTATAAGCTATTGAT
44393276 TATTATCATTTATTTTATATTTTTACTTCTATTTGATGATAAATACCCTGATTTGTACTGTAACA
388 TATTATCATTTATTTTATATTTTTACTTCTATTTGATGATAAATACCCTGATTTGTACTGTAAC-
44393341 GCTTTGTAACCCCAATTCGACGACGGAGATGGGTTAGGGGTGT
452 GCTTTGTAACCCCAATTCGACGACGGAGATGGGTTAGGGGTGT
44393384 TATATAAGAAAATTTTGAAATTTTGAGAAATATTCTCTGAGATCCCAATTTAGTCCCGACTTGTT
1 TATATAAGAAAATTTTGAAATTTTGAGAAATATTCTCTGAGATCCCAATTTAGTCCCGACTTGTT
* *
44393449 TCTAATGCTTAAATTGGGTGTTGAGGG-TCTATTCAAGGGACGATATGATTAATTTCGAACATG-
66 TCTAATGCTTAAATTGCGCGTTGAGGGTTC-ATTCAAGGGACGATATGATTAATTTCGAACATGA
* * *
44393512 ATAATTGACATGAATTATCTATAATTGTTTTGAAAACTTTGGTAATACTTTGTAACCCTGTTCTG
130 ATAATTGACATGAATTATCTATAATTGTTCTAAAAACTTTGGTAATACTTTATAACCCTGTTCTG
44393577 GTGACAAATACAGGTTGGTGGGTGTTACATGTAAAGCTATACAGCTGTGTGACCATGTTTCCAAA
195 GTGACAAATACA--------GGTGTTACATGTAAAGCTATACAGCTGTGTGACCATGTTTCCAAA
* *
44393642 ATTTTCAAATTTTTGCATG-TTTTTTTGTTTTGATTCAAGTTAGCCCCTGATTGTTCCCAAACCA
252 ATTTTCAAATTTTTGCATGTTTTTTTTATTTTGATTCAAATTAGCCCCTGATTGTTCCCAAACCA
* * * *
44393706 TTTTTAGGGCCCTGTAAACTCTGTTTAAGGCTCGTAAGTTTATTTTATCATGATTTTTATAAGCT
317 TTTTTAGAGCCCCGTAAACTCAGTTTAAGGCTCATAAGTTTATTTTATCATGATTTTTATAAGCT
* * * *
44393771 ATTGATTATTATCATTTATTTTATATTTTTACTTCTGTTTGATTATAAATATCCTTATTTGTACT
382 ATTGATTATTATCATTTATTTTATATTTTTACTTCTATTTGATGATAAATACCCTGATTTGTACT
* *
44393836 GTAACGCTTTGTAACCCCAATTTGACGATGGAGATGGGTTAGGGGTGT
447 GTAACGCTTTGTAACCCCAATTCGACGACGGAGATGGGTTAGGGGTGT
*
44393884 TACATAA
1 TATATAA
44393891 AGTCTAAAAC
Statistics
Matches: 473, Mismatches: 25, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
494 73 0.15
497 2 0.00
498 119 0.25
500 47 0.10
501 168 0.36
502 64 0.14
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (494 bp):
TATATAAGAAAATTTTGAAATTTTGAGAAATATTCTCTGAGATCCCAATTTAGTCCCGACTTGTT
TCTAATGCTTAAATTGCGCGTTGAGGGTTCATTCAAGGGACGATATGATTAATTTCGAACATGAA
TAATTGACATGAATTATCTATAATTGTTCTAAAAACTTTGGTAATACTTTATAACCCTGTTCTGG
TGACAAATACAGGTGTTACATGTAAAGCTATACAGCTGTGTGACCATGTTTCCAAAATTTTCAAA
TTTTTGCATGTTTTTTTTATTTTGATTCAAATTAGCCCCTGATTGTTCCCAAACCATTTTTAGAG
CCCCGTAAACTCAGTTTAAGGCTCATAAGTTTATTTTATCATGATTTTTATAAGCTATTGATTAT
TATCATTTATTTTATATTTTTACTTCTATTTGATGATAAATACCCTGATTTGTACTGTAACGCTT
TGTAACCCCAATTCGACGACGGAGATGGGTTAGGGGTGT
Found at i:44397061 original size:40 final size:40
Alignment explanation
Indices: 44397006--44397087 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
44396996 TTTTCCTACT
*
44397006 AATTCTTGATAGAAGTTCATTAAGTTTGGCACTCCTGCTG
1 AATTCTTGATAGAAGTTCATTAAGTTTGACACTCCTGCTG
*
44397046 AATTCTTGATAGAAGTTCATTAAGTTTGACACTCCTGTTG
1 AATTCTTGATAGAAGTTCATTAAGTTTGACACTCCTGCTG
44397086 AA
1 AA
44397088 AGTCAATTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (40 bp):
AATTCTTGATAGAAGTTCATTAAGTTTGACACTCCTGCTG
Found at i:44402412 original size:53 final size:53
Alignment explanation
Indices: 44402353--44402460 Score: 180
Period size: 53 Copynumber: 2.0 Consensus size: 53
44402343 ACATATATTT
*
44402353 TTTATTTAAATTTTAATTATTTTAAAATTTTAATATAACTATTTTTTATTATA
1 TTTATTTAAATTTTAATCATTTTAAAATTTTAATATAACTATTTTTTATTATA
* * *
44402406 TTTATTTTATTTTTAATCATTTTAAATTTTTAATATAACTATTTTTTATTATA
1 TTTATTTAAATTTTAATCATTTTAAAATTTTAATATAACTATTTTTTATTATA
44402459 TT
1 TT
44402461 GTCAATTTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (53 bp):
TTTATTTAAATTTTAATCATTTTAAAATTTTAATATAACTATTTTTTATTATA
Found at i:44402518 original size:20 final size:21
Alignment explanation
Indices: 44402497--44402566 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 21
44402487 TGCTTTAGTA
*
44402497 TTATTTTTATTTTTTTAATAT
1 TTATTTTTATATTTTTAATAT
*
44402518 TTGTTTTTATATTTTTAAATATAT
1 TTATTTTTATATTTTT--A-ATAT
*
44402542 TTGATTTATTATATTTTTAAAAT
1 TT-ATTT-TTATATTTTTAATAT
44402565 TT
1 TT
44402567 TTATTTAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
21 14 0.35
23 6 0.15
24 7 0.17
25 3 0.08
26 10 0.25
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (21 bp):
TTATTTTTATATTTTTAATAT
Found at i:44402541 original size:24 final size:26
Alignment explanation
Indices: 44402514--44402562 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
44402504 TATTTTTTTA
44402514 ATATTTG-TTT-TTATATTTTTAAAT
1 ATATTTGATTTATTATATTTTTAAAT
44402538 ATATTTGATTTATTATATTTTTAAA
1 ATATTTGATTTATTATATTTTTAAA
44402563 ATTTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (26 bp):
ATATTTGATTTATTATATTTTTAAAT
Found at i:44410725 original size:37 final size:37
Alignment explanation
Indices: 44410677--44410751 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
44410667 TGCGTGAAGA
44410677 AAGTTTCAAATAAACAGAAGTGAATCCAAGGGGATTG
1 AAGTTTCAAATAAACAGAAGTGAATCCAAGGGGATTG
44410714 AAGTTTCAAATAAACAGAAGTGAATCCAAGGGGATTG
1 AAGTTTCAAATAAACAGAAGTGAATCCAAGGGGATTG
44410751 A
1 A
44410752 TAGGGCTGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.21
Consensus pattern (37 bp):
AAGTTTCAAATAAACAGAAGTGAATCCAAGGGGATTG
Found at i:44423848 original size:21 final size:19
Alignment explanation
Indices: 44423822--44423862 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
44423812 CAAGATAAAT
*
44423822 TTAATTGCTTGCATTTATATA
1 TTAATTGCATG-ATTTA-ATA
44423843 TTAATTGCATGATTTAATA
1 TTAATTGCATGATTTAATA
44423862 T
1 T
44423863 CAAAGTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
21 10 0.53
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (19 bp):
TTAATTGCATGATTTAATA
Found at i:44424417 original size:30 final size:29
Alignment explanation
Indices: 44424383--44424450 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
44424373 TCAGACGAGT
* *
44424383 AACCTAATATAAATTTTAGGTTATGTGAGC
1 AACCTAATAT-AATGTTAGCTTATGTGAGC
* *
44424413 AACCTTGATATAATGTTAGCTTGTGTGAGC
1 AACC-TAATATAATGTTAGCTTATGTGAGC
*
44424443 AACTTAAT
1 AACCTAAT
44424451 TCACCCGTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
29 3 0.10
30 23 0.74
31 5 0.16
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (29 bp):
AACCTAATATAATGTTAGCTTATGTGAGC
Found at i:44428250 original size:27 final size:26
Alignment explanation
Indices: 44428189--44428251 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
44428179 ACTCCATTTT
44428189 ATTTATATTAGGATACTTAATATTAAG
1 ATTT-TATTAGGATACTTAATATTAAG
* * * *
44428216 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGA-TACTTAATATTAAG
44428244 ATTTTATT
1 ATTTTATT
44428252 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.51
Consensus pattern (26 bp):
ATTTTATTAGGATACTTAATATTAAG
Found at i:44428266 original size:10 final size:10
Alignment explanation
Indices: 44428247--44428278 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
44428237 TTTTAGGATT
44428247 TTAT-TTTAA
1 TTATCTTTAA
44428256 TTATCTTTAA
1 TTATCTTTAA
44428266 TTATCTTTAA
1 TTATCTTTAA
44428276 TTA
1 TTA
44428279 AATGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:44431987 original size:6 final size:6
Alignment explanation
Indices: 44431976--44432013 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
44431966 AGGTAACCCA
*
44431976 ATTTTT ATTTTT A-TTTT A-TTTT ATTTTT CTTTTT ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTT
44432014 ATTTTATCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
ATTTTT
Found at i:44431992 original size:5 final size:5
Alignment explanation
Indices: 44431978--44432039 Score: 58
Period size: 5 Copynumber: 12.4 Consensus size: 5
44431968 GTAACCCAAT
* *
44431978 TTTTA TTTTTA TTTTA TTTTA TTTT- TCTTTT TATTTA TTTTA TCTTA
1 TTTTA -TTTTA TTTTA TTTTA TTTTA T-TTTA T-TTTA TTTTA TTTTA
44432025 --TTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TT
44432040 CAGATATTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
3 3 0.06
4 1 0.02
5 35 0.71
6 10 0.20
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:44432003 original size:17 final size:17
Alignment explanation
Indices: 44431978--44432036 Score: 77
Period size: 16 Copynumber: 3.5 Consensus size: 17
44431968 GTAACCCAAT
*
44431978 TTTTATTTTT-ATTTTA
1 TTTTATTTTTCTTTTTA
44431994 TTTTATTTTTCTTTTTA
1 TTTTATTTTTCTTTTTA
*
44432011 -TTTATTTTATCTTATTA
1 TTTTATTTT-TCTTTTTA
44432028 TTTTATTTT
1 TTTTATTTT
44432037 ATTCAGATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
16 18 0.47
17 12 0.32
18 8 0.21
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTATTTTTCTTTTTA
Found at i:44432008 original size:22 final size:21
Alignment explanation
Indices: 44431976--44432039 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 21
44431966 AGGTAACCCA
44431976 ATTTTTATTTTTATTTTATTTT
1 ATTTTT-TTTTTATTTTATTTT
44431998 ATTTTTCTTTTTA-TTTATTTT
1 ATTTTT-TTTTTATTTTATTTT
*
44432019 ATCTTATTATTTTATTTTATT
1 AT-TT-TTTTTTTATTTTATT
44432040 CAGATATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
21 10 0.27
22 19 0.51
23 8 0.22
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (21 bp):
ATTTTTTTTTTATTTTATTTT
Found at i:44432019 original size:26 final size:27
Alignment explanation
Indices: 44431985--44432039 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
44431975 AATTTTTATT
*
44431985 TTTATTTTATTTTATT-TTTCT-TTTTA
1 TTTATTTTATCTTATTATTT-TATTTTA
44432011 TTTATTTTATCTTATTATTTTATTTTA
1 TTTATTTTATCTTATTATTTTATTTTA
44432038 TT
1 TT
44432040 CAGATATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (27 bp):
TTTATTTTATCTTATTATTTTATTTTA
Found at i:44432976 original size:96 final size:96
Alignment explanation
Indices: 44432812--44433171 Score: 675
Period size: 96 Copynumber: 3.8 Consensus size: 96
44432802 TAATTTCTAA
44432812 GAATGTGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCACGTCAAAAGGT
1 GAATGTGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCACGTCAAAAGGT
44432877 TCGATATGTTCTTAGGAAAAATAAAAATTAG
66 TCGATATGTTCTTAGGAAAAATAAAAATTAG
44432908 GAATGTGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCACGTCAAAAGGT
1 GAATGTGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCACGTCAAAAGGT
44432973 TCGATATGTTCTTAGGAAAAATAAAAATTAG
66 TCGATATGTTCTTAGGAAAAATAAAAATTAG
44433004 GAATGTGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCACGTCAAAAGGT
1 GAATGTGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCACGTCAAAAGGT
44433069 TCGATATGTTCTTAGGAAAAATAAAAATTAG
66 TCGATATGTTCTTAGGAAAAATAAAAATTAG
* * * *
44433100 GAATGTGTTGGGCTGAGTAACCGGGGTGGGGTGTTTGGCTGTCATCTCTCTTCGCATCAAAAGGT
1 GAATGTGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCACGTCAAAAGGT
*
44433165 TCAATAT
66 TCGATAT
44433172 TTTTCCTAAG
Statistics
Matches: 259, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 259 1.00
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.31
Consensus pattern (96 bp):
GAATGTGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCACGTCAAAAGGT
TCGATATGTTCTTAGGAAAAATAAAAATTAG
Found at i:44433830 original size:15 final size:15
Alignment explanation
Indices: 44433810--44433839 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44433800 CATTTTATTT
*
44433810 ATATTAGGATAATTA
1 ATATTAAGATAATTA
44433825 ATATTAAGATAATTA
1 ATATTAAGATAATTA
44433840 TTAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:44433883 original size:10 final size:10
Alignment explanation
Indices: 44433864--44433895 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
44433854 TTTTGGGATT
44433864 TTAT-TTTAA
1 TTATCTTTAA
44433873 TTATCTTTAA
1 TTATCTTTAA
44433883 TTATCTTTAA
1 TTATCTTTAA
44433893 TTA
1 TTA
44433896 AATGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:44438077 original size:14 final size:13
Alignment explanation
Indices: 44438058--44438087 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
44438048 TAATTACCAT
44438058 AAAAAAAAGAAAAG
1 AAAAAAAAG-AAAG
44438072 AAAAAAAAGAAAG
1 AAAAAAAAGAAAG
44438085 AAA
1 AAA
44438088 CAATGTAGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAG
Found at i:44443447 original size:14 final size:16
Alignment explanation
Indices: 44443418--44443456 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
44443408 GACAGATTTA
44443418 AATAATTTTAAATTAT
1 AATAATTTTAAATTAT
44443434 AA-AATTTT-AATTAT
1 AATAATTTTAAATTAT
44443448 AATAATTTT
1 AATAATTTT
44443457 TTTATATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.36
15 12 0.55
16 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AATAATTTTAAATTAT
Found at i:44446048 original size:2 final size:2
Alignment explanation
Indices: 44446041--44446075 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
44446031 ATATGAGAAT
*
44446041 TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44446076 GATACCTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:44446620 original size:28 final size:27
Alignment explanation
Indices: 44446559--44446640 Score: 101
Period size: 28 Copynumber: 3.0 Consensus size: 27
44446549 GAGATCTAAC
* * *
44446559 GCTTTATGCGTGTTATATGGATCCAAT
1 GCTTTATGTGTGTTATATTGATTCAAT
* *
44446586 GCTTTATGTGTATTATATTTGATTCAGT
1 GCTTTATGTGTGTTATA-TTGATTCAAT
44446614 GCTTTATGTGTGTTATACTTGATTCAA
1 GCTTTATGTGTGTTATA-TTGATTCAA
44446641 CTCAATTCCC
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
27 15 0.33
28 31 0.67
ACGTcount: A:0.22, C:0.11, G:0.20, T:0.48
Consensus pattern (27 bp):
GCTTTATGTGTGTTATATTGATTCAAT
Found at i:44450874 original size:21 final size:21
Alignment explanation
Indices: 44450848--44450887 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44450838 AAAAAAAAAA
44450848 ACTATTTTCTAGCTATTTTTT
1 ACTATTTTCTAGCTATTTTTT
* *
44450869 ACTATTTTGTTGCTATTTT
1 ACTATTTTCTAGCTATTTT
44450888 CTTGTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.62
Consensus pattern (21 bp):
ACTATTTTCTAGCTATTTTTT
Found at i:44451152 original size:13 final size:13
Alignment explanation
Indices: 44451134--44451171 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
44451124 TAGTTTTTTT
*
44451134 TTAAAAAATTATA
1 TTAAAAAATAATA
44451147 TT-AAAAATAATA
1 TTAAAAAATAATA
*
44451159 TAAAAAAATAATA
1 TTAAAAAATAATA
44451172 CGGGCAGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAAAAATAATA
Found at i:44466026 original size:13 final size:14
Alignment explanation
Indices: 44466010--44466045 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
44466000 CAATCTCATA
44466010 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
44466023 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
44466036 TCTC-ATTTCA
1 TCTCAATTTCA
44466046 TTCCGATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:44466035 original size:18 final size:19
Alignment explanation
Indices: 44465997--44466037 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
44465987 TGGTTCTTGT
44465997 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
44466016 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
44466034 TTTC
1 TTTC
44466038 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:44466227 original size:39 final size:38
Alignment explanation
Indices: 44466160--44466294 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
44466150 ACCAATATGG
* * *
44466160 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
44466199 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
44466237 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
44466278 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
44466295 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:44466561 original size:18 final size:19
Alignment explanation
Indices: 44466535--44466573 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
44466525 TTTCAATTCA
44466535 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
44466554 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
44466572 AT
1 AT
44466574 ATATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:44467901 original size:5 final size:5
Alignment explanation
Indices: 44467891--44467947 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
44467881 TTACTTATTT
* *
44467891 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
44467939 ATAT- ATATA
1 ATATA ATATA
44467948 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:44467907 original size:12 final size:12
Alignment explanation
Indices: 44467890--44467945 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
44467880 TTTACTTATT
44467890 TATATAATATAA
1 TATATAATATAA
44467902 TATATAATATAATA
1 TATATAATAT-A-A
44467916 TACTATAATATAA
1 TA-TATAATATAA
*
44467929 TA-ATAATTTAA
1 TATATAATATAA
44467940 TATATA
1 TATATA
44467946 TATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:44467960 original size:26 final size:26
Alignment explanation
Indices: 44467892--44467947 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
44467882 TACTTATTTA
*
44467892 TATAATATAATATATAATATAATATAC
1 TATAATATAACA-ATAATATAATATAC
* *
44467919 TATAATATAATAATAATTTAATATA-
1 TATAATATAACAATAATATAATATAC
44467944 TATA
1 TATA
44467948 TTTTAACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATATAACAATAATATAATATAC
Found at i:44469751 original size:12 final size:12
Alignment explanation
Indices: 44469734--44469779 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
44469724 ATTACTTCAT
44469734 TTTTTTATTTTA
1 TTTTTTATTTTA
44469746 TTTTTTATTTTA
1 TTTTTTATTTTA
*
44469758 -TTTTCATTTTA
1 TTTTTTATTTTA
44469769 TTTTTTATTTT
1 TTTTTTATTTT
44469780 TTGCATCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTATTTTA
Found at i:44469766 original size:23 final size:23
Alignment explanation
Indices: 44469735--44469779 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
44469725 TTACTTCATT
*
44469735 TTTTTATTTTATTTTTTATTTTA
1 TTTTCATTTTATTTTTTATTTTA
44469758 TTTTCATTTTATTTTTTATTTT
1 TTTTCATTTTATTTTTTATTTT
44469780 TTGCATCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTCATTTTATTTTTTATTTTA
Found at i:44472501 original size:13 final size:14
Alignment explanation
Indices: 44472485--44472520 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
44472475 CAATCTCATA
44472485 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
44472498 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
44472511 TCTC-ATTTCA
1 TCTCAATTTCA
44472521 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:44472510 original size:18 final size:19
Alignment explanation
Indices: 44472472--44472512 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
44472462 TGGTTCATGT
44472472 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
44472491 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
44472509 TTTC
1 TTTC
44472513 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:44473834 original size:5 final size:5
Alignment explanation
Indices: 44473824--44473880 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
44473814 TTACTTATTT
* *
44473824 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
44473872 ATAT- ATATA
1 ATATA ATATA
44473881 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:44473840 original size:12 final size:12
Alignment explanation
Indices: 44473823--44473878 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
44473813 TTTACTTATT
44473823 TATATAATATAA
1 TATATAATATAA
44473835 TATATAATATAATA
1 TATATAATAT-A-A
44473849 TACTATAATATAA
1 TA-TATAATATAA
*
44473862 TA-ATAATTTAA
1 TATATAATATAA
44473873 TATATA
1 TATATA
44473879 TATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:44473893 original size:26 final size:26
Alignment explanation
Indices: 44473825--44473880 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
44473815 TACTTATTTA
*
44473825 TATAATATAATATATAATATAATATAC
1 TATAATATAACA-ATAATATAATATAC
* *
44473852 TATAATATAATAATAATTTAATATA-
1 TATAATATAACAATAATATAATATAC
44473877 TATA
1 TATA
44473881 TTTTAACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATATAACAATAATATAATATAC
Found at i:44480644 original size:39 final size:39
Alignment explanation
Indices: 44480590--44480669 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
44480580 ATAGGTCAAA
44480590 GGCTCGTTCACACTATCCGAAGACCTAAATTGGTAAAAT
1 GGCTCGTTCACACTATCCGAAGACCTAAATTGGTAAAAT
*
44480629 GGCTCGTTCACACTATCTGAAGACCTAAATTGGTAAAAT
1 GGCTCGTTCACACTATCCGAAGACCTAAATTGGTAAAAT
44480668 GG
1 GG
44480670 GTTTGTAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (39 bp):
GGCTCGTTCACACTATCCGAAGACCTAAATTGGTAAAAT
Found at i:44497753 original size:30 final size:30
Alignment explanation
Indices: 44497718--44497775 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
44497708 CACGGCCATG
44497718 ACACACGGGCGTGTGG-TCTACCCGTGTGTC
1 ACACACGGGCGTGTGGATC-ACCCGTGTGTC
44497748 ACACACGGGCGTGTGGATCACCCGTGTG
1 ACACACGGGCGTGTGGATCACCCGTGTG
44497776 GAAGTGCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.16, C:0.29, G:0.34, T:0.21
Consensus pattern (30 bp):
ACACACGGGCGTGTGGATCACCCGTGTGTC
Found at i:44501551 original size:20 final size:20
Alignment explanation
Indices: 44501522--44501574 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
44501512 CCAGGTCAAG
44501522 GTATCTATACTTTGCA-CAGA
1 GTATCTATACTTTGCACCA-A
*
44501542 GTATCGATACTTTGCACCAA
1 GTATCTATACTTTGCACCAA
44501562 GTATCTATACTTT
1 GTATCTATACTTT
44501575 TTACAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (20 bp):
GTATCTATACTTTGCACCAA
Found at i:44504332 original size:13 final size:13
Alignment explanation
Indices: 44504316--44504341 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44504306 TTATCCCTCC
44504316 AACATGTCCCAGG
1 AACATGTCCCAGG
44504329 AACATGTCCCAGG
1 AACATGTCCCAGG
44504342 GCCTCAACGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.23, T:0.15
Consensus pattern (13 bp):
AACATGTCCCAGG
Found at i:44533498 original size:16 final size:16
Alignment explanation
Indices: 44533477--44533510 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
44533467 CATTTCATTA
*
44533477 TTATGTCTTTTGTATT
1 TTATGTCTTTTATATT
44533493 TTATGTCTTTTATATT
1 TTATGTCTTTTATATT
44533509 TT
1 TT
44533511 GCATATATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.06, G:0.09, T:0.71
Consensus pattern (16 bp):
TTATGTCTTTTATATT
Found at i:44540614 original size:20 final size:20
Alignment explanation
Indices: 44540571--44540618 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
44540561 GCTGTTTTGT
44540571 TATGGGCCAACTGTATTGAA
1 TATGGGCCAACTGTATTGAA
*
44540591 -ATGGGCCCAACTGTGTT-AA
1 TATGGG-CCAACTGTATTGAA
44540610 TAT-GGCCAA
1 TATGGGCCAA
44540619 GGCCCAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 4 0.16
19 9 0.36
20 12 0.48
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (20 bp):
TATGGGCCAACTGTATTGAA
Found at i:44540674 original size:60 final size:59
Alignment explanation
Indices: 44540607--44540745 Score: 138
Period size: 60 Copynumber: 2.3 Consensus size: 59
44540597 CCAACTGTGT
* *
44540607 TAATATGGCCAAGGCCCAATATA-TCTCGACT-TGTAATAGGGCTACGGCCCAGATTGATAC
1 TAATATGGCCAAGGCCCAAAATACTCT-GA-TATGTAA-AGGGCTACGGCCCAGATTAATAC
* * * * *
44540667 TAATATGGGCTAGGCCCAAAATACTCTGATACTGTAAGGGGCTATGGCCCAGATTAATAT
1 TAATATGGCCAAGGCCCAAAATACTCTGATA-TGTAAAGGGCTACGGCCCAGATTAATAC
* *
44540727 TGATATGGGCTAAGGCCCA
1 TAATAT-GGCCAAGGCCCA
44540746 GGTAACACTG
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
59 1 0.02
60 46 0.72
61 17 0.27
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (59 bp):
TAATATGGCCAAGGCCCAAAATACTCTGATATGTAAAGGGCTACGGCCCAGATTAATAC
Found at i:44542923 original size:17 final size:18
Alignment explanation
Indices: 44542884--44542923 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
44542874 TGCATTATTG
*
44542884 GTATT-TGAAATTTTTAT
1 GTATTATGAAATTATTAT
44542901 GT-TTATGAAATTATTAT
1 GTATTATGAAATTATTAT
44542918 -TATTAT
1 GTATTAT
44542924 TATTAGTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (18 bp):
GTATTATGAAATTATTAT
Found at i:44544615 original size:20 final size:20
Alignment explanation
Indices: 44544572--44544619 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
44544562 GTTATTTTGT
44544572 TATGGGCCAACTGTATTGAA
1 TATGGGCCAACTGTATTGAA
*
44544592 -ATGGGCCCAACTGTGTT-AA
1 TATGGG-CCAACTGTATTGAA
44544611 TAT-GGCCAA
1 TATGGGCCAA
44544620 GGCCTAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 4 0.16
19 9 0.36
20 12 0.48
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (20 bp):
TATGGGCCAACTGTATTGAA
Found at i:44545746 original size:45 final size:43
Alignment explanation
Indices: 44545696--44545814 Score: 150
Period size: 42 Copynumber: 2.7 Consensus size: 43
44545686 GCCTATAAAA
* **
44545696 TTAGCGGCGTTTTTCTGAAAAAAGCGCTTCTAAAGACCAGGACTT
1 TTAGCGGCG-TTTT-TGAAAAAAACGCCGCTAAAGACCAGGACTT
*
44545741 TTAGCGGCGCTTTT-AAAAAAACGCCGCTAAAGACCAGGACTT
1 TTAGCGGCGTTTTTGAAAAAAACGCCGCTAAAGACCAGGACTT
* *
44545783 TTAGCTGCGCTTTTAGAAAAAAACGCCGCTAA
1 TTAGCGGCG-TTTTTGAAAAAAACGCCGCTAA
44545815 TTTGCCCAGT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
42 33 0.51
43 4 0.06
44 19 0.29
45 9 0.14
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (43 bp):
TTAGCGGCGTTTTTGAAAAAAACGCCGCTAAAGACCAGGACTT
Found at i:44545771 original size:42 final size:43
Alignment explanation
Indices: 44545725--44545814 Score: 155
Period size: 42 Copynumber: 2.1 Consensus size: 43
44545715 AAAAGCGCTT
44545725 CTAAAGACCAGGACTTTTAGCGGCGCTTTT-AAAAAAACGCCG
1 CTAAAGACCAGGACTTTTAGCGGCGCTTTTAAAAAAAACGCCG
*
44545767 CTAAAGACCAGGACTTTTAGCTGCGCTTTTAGAAAAAAACGCCG
1 CTAAAGACCAGGACTTTTAGCGGCGCTTTTA-AAAAAAACGCCG
44545811 CTAA
1 CTAA
44545815 TTTGCCCAGT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 29 0.64
44 16 0.36
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.22
Consensus pattern (43 bp):
CTAAAGACCAGGACTTTTAGCGGCGCTTTTAAAAAAAACGCCG
Found at i:44546095 original size:21 final size:21
Alignment explanation
Indices: 44546071--44546118 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
44546061 TTTTGTTCTG
* *
44546071 CTCCGCCTCCCTCGCTGTTGC
1 CTCCGCCTCCCGCGCTGCTGC
44546092 CTCCGCCTCCCGCGCTGCTGC
1 CTCCGCCTCCCGCGCTGCTGC
44546113 CTCCGC
1 CTCCGC
44546119 TCTAAGTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.00, C:0.56, G:0.21, T:0.23
Consensus pattern (21 bp):
CTCCGCCTCCCGCGCTGCTGC
Found at i:44551564 original size:79 final size:79
Alignment explanation
Indices: 44551447--44551633 Score: 241
Period size: 79 Copynumber: 2.3 Consensus size: 79
44551437 AGTATTTTGT
** *
44551447 TTTTGCGGCGTTTTTTTTAAAACGCCGGTACTCCCCTAAAAATCCAATTAAAACGACGCCGTTTT
1 TTTTGCGGCGTTTTTTAAAAAACGCCGCTACTCCCCTAAAAATCCAATTAAAACGACGCCGTTTT
44551512 CATTAAACTGCTATG
66 CATT-AACTGCTATG
* * * * *
44551527 TTTTGTGGC-TTTTTTAAAAAATGCCGCTACTCTCCTAAATATCCAATTAAAATGACGCCGTTTT
1 TTTTGCGGCGTTTTTTAAAAAACGCCGCTACTCCCCTAAAAATCCAATTAAAACGACGCCGTTTT
**
44551591 TGTTAACTGCTATG
66 CATTAACTGCTATG
44551605 TTTTTTGCGGCGTTTTTTAAATAAACGCC
1 --TTTTGCGGCGTTTTTTAAA-AAACGCC
44551634 AGTAATCTCT
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
78 10 0.11
79 50 0.55
80 16 0.18
81 9 0.10
82 6 0.07
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (79 bp):
TTTTGCGGCGTTTTTTAAAAAACGCCGCTACTCCCCTAAAAATCCAATTAAAACGACGCCGTTTT
CATTAACTGCTATG
Found at i:44552534 original size:41 final size:41
Alignment explanation
Indices: 44552497--44552596 Score: 182
Period size: 41 Copynumber: 2.4 Consensus size: 41
44552487 TGTTTTATTG
*
44552497 AAAGCGCCGCTAATGCTCGGGTCTTTAGCGGCGTTTTACCA
1 AAAGCGCCGCTAATGCTCGAGTCTTTAGCGGCGTTTTACCA
44552538 AAAGCGCCGCTAATGCTCGAGTCTTTAGCGGCGTTTTACCA
1 AAAGCGCCGCTAATGCTCGAGTCTTTAGCGGCGTTTTACCA
*
44552579 AAAGCACCGCTAATGCTC
1 AAAGCGCCGCTAATGCTC
44552597 TGTTTTTAGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (41 bp):
AAAGCGCCGCTAATGCTCGAGTCTTTAGCGGCGTTTTACCA
Found at i:44565904 original size:109 final size:108
Alignment explanation
Indices: 44565682--44565910 Score: 320
Period size: 110 Copynumber: 2.1 Consensus size: 108
44565672 TTAATCTTGT
44565682 ATTAATCTTGAGGAGTTGAAAATGAAGATTAGCCAAAAAAAAATTACATAACGTTGTGGAAGGAC
1 ATTAATCTTGAGGAGTTGAAAATGAAGATTAGCCAAAAAAAAATTACATAACGTTGTGGAAGGAC
* * * * *
44565747 AATATGAGATTTCATGGTTTATTAGTATGATATTTAGATATAGT
66 AATATAAGATTTCATGGTTTATTACTATGAGATTTAGACATA-C
*
44565791 ATTAATCTTGAGGAGTTGAAAATGAAGATTAGCCAAAAACAAATATTGCA-ACACGTT-TGGAAG
1 ATTAATCTTGAGGAGTTGAAAATGAAGATTAGCCAAAAA-AAA-ATTACATA-ACGTTGTGGAAG
*
44565854 GACAATATAAGATTTCATGGTTTATTACTATGAGATTTCTGACAT-C
63 GACAATATAAGATTTCATGGTTTATTACTATGAGATTT-AGACATAC
44565900 ATTAAATCTTG
1 ATT-AATCTTG
44565911 TTATGATTAA
Statistics
Matches: 108, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
109 42 0.39
110 52 0.48
111 14 0.13
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (108 bp):
ATTAATCTTGAGGAGTTGAAAATGAAGATTAGCCAAAAAAAAATTACATAACGTTGTGGAAGGAC
AATATAAGATTTCATGGTTTATTACTATGAGATTTAGACATAC
Found at i:44567860 original size:8 final size:8
Alignment explanation
Indices: 44567847--44567884 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
44567837 AAAAGTACCG
44567847 AAAATAAT
1 AAAATAAT
44567855 AAAATAAT
1 AAAATAAT
44567863 AAAATAA-
1 AAAATAAT
* *
44567870 CAAATAAA
1 AAAATAAT
44567878 AAAATAA
1 AAAATAA
44567885 GTAGGCAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (8 bp):
AAAATAAT
Found at i:44572456 original size:28 final size:27
Alignment explanation
Indices: 44572416--44572542 Score: 141
Period size: 28 Copynumber: 4.6 Consensus size: 27
44572406 AAAAATTTTC
*
44572416 TCGCACACTTAGTGCTCAATAACCGATT
1 TCGCACACTTAGTGCTCAA-AACCAATT
*
44572444 TCGCACACTTAGTGCTCGGAAATCCAATT
1 TCGCACACTTAGTGCTC--AAAACCAATT
* *
44572473 T-GCACACTTAGTGCTTAAAACCAACT
1 TCGCACACTTAGTGCTCAAAACCAATT
* *
44572499 T-GCACACTTAGTGCTCAATGACCGATT
1 TCGCACACTTAGTGCTCAA-AACCAATT
*
44572526 TCACACACTTAGTGCTC
1 TCGCACACTTAGTGCTC
44572543 GGTATCAAAT
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
26 25 0.29
27 6 0.07
28 45 0.53
29 7 0.08
30 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
TCGCACACTTAGTGCTCAAAACCAATT
Done.