Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 308 of 343
Found at i:100124664 original size:19 final size:19
Alignment explanation
Indices: 100124640--100124679 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
100124630 GTTCAATTGC
100124640 AAGTATTTCTTGGACTTTT
1 AAGTATTTCTTGGACTTTT
100124659 AAGTATTTCTTGGACTTTT
1 AAGTATTTCTTGGACTTTT
100124678 AA
1 AA
100124680 CCCAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (19 bp):
AAGTATTTCTTGGACTTTT
Found at i:100130995 original size:5 final size:5
Alignment explanation
Indices: 100130985--100131021 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
100130975 AATTTGTGTG
100130985 TTATT TTATT TT-TCT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTAT-T TTATT TTATT TTATT TTATT TT
100131022 TTTCATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 1 0.03
5 28 0.93
6 1 0.03
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:100135445 original size:5 final size:5
Alignment explanation
Indices: 100135435--100135474 Score: 64
Period size: 5 Copynumber: 8.0 Consensus size: 5
100135425 AATTTGTGTG
100135435 TTATT TTATT TT-TCT TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTAT-T TTATT TTATT TTATT TTATT TTATT
100135475 CACAAGATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 1 0.03
5 31 0.94
6 1 0.03
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:100139199 original size:20 final size:20
Alignment explanation
Indices: 100139163--100139200 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
100139153 ATCCTTCTAC
*
100139163 TTTATAATTACTGAATTTAA
1 TTTATAATTACTCAATTTAA
100139183 TTTATAATATA-TCAATTT
1 TTTATAAT-TACTCAATTT
100139201 TTTATAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTATAATTACTCAATTTAA
Found at i:100144067 original size:11 final size:11
Alignment explanation
Indices: 100144051--100144081 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
100144041 GAGAAGAGAT
*
100144051 GATGAATGAGG
1 GATGAACGAGG
100144062 GATGAACGAGG
1 GATGAACGAGG
100144073 GATGAACGA
1 GATGAACGA
100144082 AATGAGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.39, C:0.06, G:0.42, T:0.13
Consensus pattern (11 bp):
GATGAACGAGG
Found at i:100156384 original size:26 final size:26
Alignment explanation
Indices: 100156324--100156375 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
100156314 AGAATTCAAC
100156324 GATAATTAAACTTAATCACTCTAATA
1 GATAATTAAACTTAATCACTCTAATA
100156350 GATAATTAAACTTAATCACTCTAATA
1 GATAATTAAACTTAATCACTCTAATA
100156376 TTAAATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (26 bp):
GATAATTAAACTTAATCACTCTAATA
Found at i:100156406 original size:40 final size:39
Alignment explanation
Indices: 100156362--100156443 Score: 128
Period size: 40 Copynumber: 2.1 Consensus size: 39
100156352 TAATTAAACT
*
100156362 TAATCACTCTAATATTAAATTAATAAAATACTTATCAAGA
1 TAATCACTCTAATATTAAAGTAATAAAATA-TTATCAAGA
* *
100156402 TAATCATTTTAATATTAAAGTAATAAAATATTATCAAGA
1 TAATCACTCTAATATTAAAGTAATAAAATATTATCAAGA
100156441 TAA
1 TAA
100156444 GTATTAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 12 0.31
40 27 0.69
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (39 bp):
TAATCACTCTAATATTAAAGTAATAAAATATTATCAAGA
Found at i:100158355 original size:21 final size:22
Alignment explanation
Indices: 100158329--100158385 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
100158319 GTGAAGGGTA
100158329 GCACACGGTCGTGTGT-TAGAG
1 GCACACGGTCGTGTGTATAGAG
*
100158350 GCACACGCTCGTGTGGTATAGAG
1 GCACACGGTCGTGT-GTATAGAG
100158373 GCACA--GTCGTGTG
1 GCACACGGTCGTGTG
100158386 ATCAGGCCGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 1 0.03
21 19 0.59
22 2 0.06
23 10 0.31
ACGTcount: A:0.19, C:0.21, G:0.37, T:0.23
Consensus pattern (22 bp):
GCACACGGTCGTGTGTATAGAG
Found at i:100159032 original size:21 final size:21
Alignment explanation
Indices: 100158994--100159033 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
100158984 CCATCGATTC
*
100158994 CAAAAAGCAAAAAGAAGAACA
1 CAAAAAGCAAAAACAAGAACA
100159015 CAAAAA-CAAAAACCAAGAA
1 CAAAAAGCAAAAA-CAAGAA
100159034 GAAACAGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.72, C:0.17, G:0.10, T:0.00
Consensus pattern (21 bp):
CAAAAAGCAAAAACAAGAACA
Found at i:100166272 original size:39 final size:39
Alignment explanation
Indices: 100166218--100166297 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
100166208 GTGCTTGCAA
*
100166218 ATTGAAGCTCTAAATACAACGATTTGAGAGTCAGAAAAG
1 ATTGAAGCTCTAAATACAAAGATTTGAGAGTCAGAAAAG
100166257 ATTGAAGCTCTAAATACAAAGATTTGAGAGTCAGAAAAG
1 ATTGAAGCTCTAAATACAAAGATTTGAGAGTCAGAAAAG
100166296 AT
1 AT
100166298 ATTACAATAA
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:0.45, C:0.11, G:0.20, T:0.24
Consensus pattern (39 bp):
ATTGAAGCTCTAAATACAAAGATTTGAGAGTCAGAAAAG
Found at i:100166297 original size:18 final size:18
Alignment explanation
Indices: 100166238--100166297 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
100166228 TAAATACAAC
100166238 GATTTGAGAGTCAGAAAA
1 GATTTGAGAGTCAGAAAA
*
100166256 GA-TTGA-AGCTCTAAATACAAA
1 GATTTGAGAG-TC---AGA-AAA
100166277 GATTTGAGAGTCAGAAAA
1 GATTTGAGAGTCAGAAAA
100166295 GAT
1 GAT
100166298 ATTACAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
16 2 0.06
17 6 0.18
18 8 0.24
19 2 0.06
20 2 0.06
21 5 0.15
22 6 0.18
23 2 0.06
ACGTcount: A:0.45, C:0.08, G:0.23, T:0.23
Consensus pattern (18 bp):
GATTTGAGAGTCAGAAAA
Found at i:100170933 original size:52 final size:52
Alignment explanation
Indices: 100170855--100170982 Score: 247
Period size: 52 Copynumber: 2.5 Consensus size: 52
100170845 CTATACCCTA
*
100170855 AGGGATAGCATCAAGCTCTGTATTCCTTAATATTTGAATATTCTAAAAGAAG
1 AGGGATAGCATCATGCTCTGTATTCCTTAATATTTGAATATTCTAAAAGAAG
100170907 AGGGATAGCATCATGCTCTGTATTCCTTAATATTTGAATATTCTAAAAGAAG
1 AGGGATAGCATCATGCTCTGTATTCCTTAATATTTGAATATTCTAAAAGAAG
100170959 AGGGATAGCATCATGCTCTGTATT
1 AGGGATAGCATCATGCTCTGTATT
100170983 TATAGATAAA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (52 bp):
AGGGATAGCATCATGCTCTGTATTCCTTAATATTTGAATATTCTAAAAGAAG
Found at i:100180433 original size:6 final size:7
Alignment explanation
Indices: 100180414--100180449 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
100180404 TTGAACCTTC
100180414 GCTTTTT
1 GCTTTTT
100180421 GCTTTTT
1 GCTTTTT
100180428 GCTTTTT
1 GCTTTTT
100180435 GCTTTTT
1 GCTTTTT
*
100180442 GCCTTTT
1 GCTTTTT
100180449 G
1 G
100180450 TCTTCTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.00, C:0.17, G:0.17, T:0.67
Consensus pattern (7 bp):
GCTTTTT
Found at i:100182444 original size:121 final size:121
Alignment explanation
Indices: 100182279--100182519 Score: 464
Period size: 121 Copynumber: 2.0 Consensus size: 121
100182269 TGGAATTATT
100182279 TACTATAACGACAAATTTTTGGGAGATCTTTCACTGCCTATTTAACTGCTTCCATATAGATTGCT
1 TACTATAACGACAAATTTTTGGGAGATCTTTCACTGCCTATTTAACTGCTTCCATATAGATTGCT
*
100182344 TGCTCATAAGCAAAGGTTATATCAACTTGGTCTCCTGTGTATCATAGCCATTGTTG
66 TGCTCATAAGCAAAGGTTATATCAACTTGATCTCCTGTGTATCATAGCCATTGTTG
*
100182400 TACTATACCGACAAATTTTTGGGAGATCTTTCACTGCCTATTTAACTGCTTCCATATAGATTGCT
1 TACTATAACGACAAATTTTTGGGAGATCTTTCACTGCCTATTTAACTGCTTCCATATAGATTGCT
100182465 TGCTCATAAGCAAAGGTTATATCAACTTGATCTCCTGTGTATCATAGCCATTGTT
66 TGCTCATAAGCAAAGGTTATATCAACTTGATCTCCTGTGTATCATAGCCATTGTT
100182520 TGTTGTAATT
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 118 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (121 bp):
TACTATAACGACAAATTTTTGGGAGATCTTTCACTGCCTATTTAACTGCTTCCATATAGATTGCT
TGCTCATAAGCAAAGGTTATATCAACTTGATCTCCTGTGTATCATAGCCATTGTTG
Found at i:100186270 original size:48 final size:48
Alignment explanation
Indices: 100186160--100186295 Score: 168
Period size: 48 Copynumber: 2.8 Consensus size: 48
100186150 AGTGATAATT
* * *
100186160 TTAAATTTTCAATACTATTCGATATTTTTTTTAATTTATGCAAATTTAA
1 TTAAAATTTCAATACTATTTGATA-TTTTTTTCATTTATGCAAATTTAA
*
100186209 TT-AAATTTGCAATACTATTTGATATTTTATTCATTTATGC-AATTATAA
1 TTAAAATTT-CAATACTATTTGATATTTTTTTCATTTATGCAAATT-TAA
** *
100186257 TTAAAATTTCAATACTGCTTGATTTTTTTTTCATTTATG
1 TTAAAATTTCAATACTATTTGATATTTTTTTCATTTATG
100186296 ATGTTTGCAT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
47 4 0.05
48 50 0.66
49 22 0.29
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (48 bp):
TTAAAATTTCAATACTATTTGATATTTTTTTCATTTATGCAAATTTAA
Found at i:100187920 original size:18 final size:18
Alignment explanation
Indices: 100187897--100187939 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
100187887 TGCCAGGTGC
* *
100187897 GTATCCTAGCCTTTATAT
1 GTATCCTAACCCTTATAT
100187915 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
100187933 GTTTCCT
1 GTATCCT
100187940 TTTCCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:100191661 original size:126 final size:126
Alignment explanation
Indices: 100191434--100191814 Score: 620
Period size: 126 Copynumber: 3.0 Consensus size: 126
100191424 TTATAGCCTC
*
100191434 ATTTTTCTA-TGAACTACCGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCT
1 ATTTTTCTACT-AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCT
*
100191498 GACAGTGCATCCTACTTGAAGCGTTTTCGACACTATTTGTTCAGAAACGTTTACTCAGAATT
65 GACAGTGCATCCTGCTTGAAGCGTTTTCGACACTATTTGTTCAGAAACGTTTACTCAGAATT
* * *
100191560 ATTTTTCTACTAACTATTGTAACAAAAGAGCGTCCATGTGGGAGCTTTTTTCAGAAATTTTGCTG
1 ATTTTTCTACTAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCTG
** * *
100191625 ACAGTTTATCCTGCTTGAAGCGTTTTCGACAATATTTGTTCAGAAACGTTTATTCAGAATT
66 ACAGTGCATCCTGCTTGAAGCGTTTTCGACACTATTTGTTCAGAAACGTTTACTCAGAATT
*
100191686 ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCTG
1 ATTTTTCTACTAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCTG
* * * *
100191751 ACAGTGCATCCTGCTTCAAGCGTTTTCGACACTATTTGTTCAGAAACGTCTACTTAAAATT
66 ACAGTGCATCCTGCTTGAAGCGTTTTCGACACTATTTGTTCAGAAACGTTTACTCAGAATT
100191812 ATT
1 ATT
100191815 CTTGCAGAAA
Statistics
Matches: 233, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
126 232 1.00
127 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (126 bp):
ATTTTTCTACTAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCTG
ACAGTGCATCCTGCTTGAAGCGTTTTCGACACTATTTGTTCAGAAACGTTTACTCAGAATT
Found at i:100192361 original size:19 final size:19
Alignment explanation
Indices: 100192339--100192423 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
100192329 ACCATTATGT
100192339 ATCAATTAACCCTAAATTA
1 ATCAATTAACCCTAAATTA
* *
100192358 ATCAATTAGCCTTAAATTTA
1 ATCAATTAACCCTAAA-TTA
*
100192378 ATCAATTAACCCTAATTTA
1 ATCAATTAACCCTAAATTA
*
100192397 ATCAA-T--CCCTAATTTA
1 ATCAATTAACCCTAAATTA
100192413 ATCAATTAACC
1 ATCAATTAACC
100192424 TTAACACCCT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
16 15 0.26
17 1 0.02
18 1 0.02
19 24 0.42
20 16 0.28
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.35
Consensus pattern (19 bp):
ATCAATTAACCCTAAATTA
Found at i:100192408 original size:16 final size:17
Alignment explanation
Indices: 100192347--100192418 Score: 74
Period size: 16 Copynumber: 4.0 Consensus size: 17
100192337 GTATCAATTA
*
100192347 ACCCTAAATTAATCAATT
1 ACCCTAATTTAATCAA-T
*
100192365 AGCCTTAAATTTAATCAATT
1 A-CCCT-AATTTAATCAA-T
100192385 AACCCTAATTTAATCAAT
1 -ACCCTAATTTAATCAAT
100192403 -CCCTAATTTAATCAAT
1 ACCCTAATTTAATCAAT
100192419 TAACCTTAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
16 16 0.33
18 2 0.04
19 14 0.29
20 15 0.31
21 1 0.02
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.36
Consensus pattern (17 bp):
ACCCTAATTTAATCAAT
Found at i:100192418 original size:35 final size:38
Alignment explanation
Indices: 100192339--100192423 Score: 122
Period size: 39 Copynumber: 2.3 Consensus size: 38
100192329 ACCATTATGT
*
100192339 ATCAATTAACCCTAAATTAATCAATTAGCCTTAAATTTA
1 ATCAATTAACCCTAAATTAATCAATTA-CCCTAAATTTA
*
100192378 ATCAATTAACCCTAATTTAATCAA-T-CCCT-AATTTA
1 ATCAATTAACCCTAAATTAATCAATTACCCTAAATTTA
100192413 ATCAATTAACC
1 ATCAATTAACC
100192424 TTAACACCCT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
35 17 0.39
36 3 0.07
38 1 0.02
39 23 0.52
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.35
Consensus pattern (38 bp):
ATCAATTAACCCTAAATTAATCAATTACCCTAAATTTA
Found at i:100193504 original size:14 final size:13
Alignment explanation
Indices: 100193485--100193522 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
100193475 ATTTAATGTT
100193485 TAATTATATTAGGA
1 TAATTAT-TTAGGA
*
100193499 TAATTATTAAGGA
1 TAATTATTTAGGA
100193512 TAATTATTTAG
1 TAATTATTTAG
100193523 ATTTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (13 bp):
TAATTATTTAGGA
Found at i:100193551 original size:10 final size:10
Alignment explanation
Indices: 100193538--100193581 Score: 70
Period size: 10 Copynumber: 4.4 Consensus size: 10
100193528 AATTTAAGAT
* *
100193538 TTATTTTTAT
1 TTATCTTTAA
100193548 TTATCTTTAA
1 TTATCTTTAA
100193558 TTATCTTTAA
1 TTATCTTTAA
100193568 TTATCTTTAA
1 TTATCTTTAA
100193578 TTAT
1 TTAT
100193582 TTGTGTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:100193566 original size:20 final size:19
Alignment explanation
Indices: 100193542--100193595 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
100193532 TAAGATTTAT
100193542 TTTTATTTATCTTTAATTA
1 TTTTATTTATCTTTAATTA
*
100193561 TCTTTAATTATCTTTAATTA
1 T-TTTATTTATCTTTAATTA
*
100193581 TTTGTGTTTATCTTT
1 TTT-TATTTATCTTT
100193596 TAGAATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTTATTTATCTTTAATTA
Found at i:100200585 original size:7 final size:7
Alignment explanation
Indices: 100200575--100200626 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
100200565 TCTTTTTCTT
100200575 TTATTTA
1 TTATTTA
100200582 TTATTTA
1 TTATTTA
100200589 TTATTTTA
1 TTA-TTTA
*
100200597 TT-TTAA
1 TTATTTA
*
100200603 TTACTTA
1 TTATTTA
*
100200610 TTACTTAA
1 TTA-TTTA
100200618 TTATTTA
1 TTATTTA
100200625 TT
1 TT
100200627 TTATTTTGGA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
6 5 0.14
7 20 0.56
8 11 0.31
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (7 bp):
TTATTTA
Found at i:100203369 original size:99 final size:100
Alignment explanation
Indices: 100203196--100203382 Score: 277
Period size: 99 Copynumber: 1.9 Consensus size: 100
100203186 TTTTTAAGAA
* * *
100203196 TATGTTGGGTTGAGTAACTGGGGTGAGGTACTTGACTATCATCTCTCTTCGCGTCAAAAGGTTCG
1 TATGTTGGGTTGAGTAACCGAGGTGAGGTACTTGACTATCATCTCTCTTCGCGTCAAAAGGTTCA
*
100203261 ATATGTTCTTAAG-AAAATAAAAAAAAATTAGGAG
66 ATATATTCTTAAGAAAAATAAAAAAAAATTAGGAG
* * * * *
100203295 TATGTTGGTTTGAGTAACCGAGGTGGGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCA
1 TATGTTGGGTTGAGTAACCGAGGTGAGGTACTTGACTATCATCTCTCTTCGCGTCAAAAGGTTCA
100203360 ATATATTCTTAAGTAAAAATAAA
66 ATATATTCTTAAG-AAAAATAAA
100203383 TTAAATTAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
99 69 0.90
101 8 0.10
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (100 bp):
TATGTTGGGTTGAGTAACCGAGGTGAGGTACTTGACTATCATCTCTCTTCGCGTCAAAAGGTTCA
ATATATTCTTAAGAAAAATAAAAAAAAATTAGGAG
Found at i:100203581 original size:10 final size:10
Alignment explanation
Indices: 100203566--100203617 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
100203556 TAAATTTTGG
100203566 ATTTATTTTT
1 ATTTATTTTT
*
100203576 ATTTATCTTT
1 ATTTATTTTT
* * *
100203586 AATTATCTTA
1 ATTTATTTTT
*
100203596 ATTTATTTGT
1 ATTTATTTTT
100203606 ATTTATCTTTT
1 ATTTAT-TTTT
100203617 A
1 A
100203618 GAATTTAATT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
10 29 0.88
11 4 0.12
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:100207705 original size:14 final size:14
Alignment explanation
Indices: 100207686--100207723 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
100207676 GTTTGCCAGT
*
100207686 AAAATGTTTTCCGA
1 AAAATGATTTCCGA
*
100207700 AAAATGATTTCTGA
1 AAAATGATTTCCGA
100207714 AAAATGATTT
1 AAAATGATTT
100207724 ATTTTTCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (14 bp):
AAAATGATTTCCGA
Found at i:100210687 original size:24 final size:24
Alignment explanation
Indices: 100210645--100210694 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
100210635 ATCATCATTA
* *
100210645 TTATTATTATTGTTGTTGTTGTTG
1 TTATTATTATTATTATTGTTGTTG
*
100210669 TTATTATTTTTATTATTGTTGTTG
1 TTATTATTATTATTATTGTTGTTG
100210693 TT
1 TT
100210695 CGTTGATGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.16, T:0.70
Consensus pattern (24 bp):
TTATTATTATTATTATTGTTGTTG
Found at i:100211493 original size:22 final size:22
Alignment explanation
Indices: 100211445--100211497 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
100211435 TTTCGTAGAC
*
100211445 CAAAATCATTTTTTTAATAAAAT
1 CAAAAT-ATTTTATTAATAAAAT
100211468 -AAAATATTTTATTAA-AACAAT
1 CAAAATATTTTATTAATAA-AAT
100211489 CAAAATATT
1 CAAAATATT
100211498 AGGTGATCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.07
21 12 0.44
22 13 0.48
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.40
Consensus pattern (22 bp):
CAAAATATTTTATTAATAAAAT
Found at i:100223046 original size:22 final size:22
Alignment explanation
Indices: 100223003--100223046 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
100222993 AATTTTTAAA
* *
100223003 TTTTTAATATTTTATATTATTT
1 TTTTTAATATATTATATAATTT
* *
100223025 TTTTTTATATATTATGTAATTT
1 TTTTTAATATATTATATAATTT
100223047 AGAACACATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTTTAATATATTATATAATTT
Found at i:100223157 original size:40 final size:40
Alignment explanation
Indices: 100223081--100223163 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 40
100223071 CTAAACATTA
* **
100223081 AAAAATGTTAAAATGATTATATAAAAAAATTCAAT-AAAT
1 AAAAATGTTAAAATGATTAAATAAAAAAATAAAATAAAAT
* **
100223120 AAAAATGTATAAAATTATTAAATATTAAAATAAAATAAAAT
1 AAAAATGT-TAAAATGATTAAATAAAAAAATAAAATAAAAT
100223161 AAA
1 AAA
100223164 TATTTTTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
39 8 0.22
40 21 0.58
41 7 0.19
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (40 bp):
AAAAATGTTAAAATGATTAAATAAAAAAATAAAATAAAAT
Found at i:100224523 original size:23 final size:23
Alignment explanation
Indices: 100224496--100224544 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
100224486 ATAACTAAAG
100224496 ATTTTTATTTCTTGAATTATTCT
1 ATTTTTATTTCTTGAATTATTCT
*
100224519 ATTTTTATTTTTTGAATTATTCT
1 ATTTTTATTTCTTGAATTATTCT
100224542 ATT
1 ATT
100224545 GTAAGTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.67
Consensus pattern (23 bp):
ATTTTTATTTCTTGAATTATTCT
Found at i:100225019 original size:27 final size:28
Alignment explanation
Indices: 100224972--100225025 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
100224962 TGAAATTTTA
*
100224972 AAAAAAATAAAATATTATAAAAGTCATG
1 AAAAAAATAAAAAATTATAAAAGTCATG
* *
100225000 AAAAATATAAAAAATT-TAAAATTCAT
1 AAAAAAATAAAAAATTATAAAAGTCAT
100225026 TATCAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (28 bp):
AAAAAAATAAAAAATTATAAAAGTCATG
Found at i:100225130 original size:19 final size:21
Alignment explanation
Indices: 100225089--100225136 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
100225079 TTAAATTTTT
100225089 AACTAAAAATATTAAAATAAA
1 AACTAAAAATATTAAAATAAA
* *
100225110 AA-TAAAAAT-TTAGAATCAA
1 AACTAAAAATATTAAAATAAA
100225129 AACTAAAA
1 AACTAAAA
100225137 TAAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.23
Consensus pattern (21 bp):
AACTAAAAATATTAAAATAAA
Found at i:100225163 original size:17 final size:18
Alignment explanation
Indices: 100225127--100225164 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
100225117 ATTTAGAATC
100225127 AAAACTAAAATAAATAAT
1 AAAACTAAAATAAATAAT
* *
100225145 AAAATTAAATTAAAT-AT
1 AAAACTAAAATAAATAAT
100225162 AAA
1 AAA
100225165 GATATCAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAACTAAAATAAATAAT
Found at i:100226624 original size:17 final size:17
Alignment explanation
Indices: 100226599--100226631 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
100226589 TTATTTTTTC
*
100226599 TTTCTGAAAACCCATTG
1 TTTCAGAAAACCCATTG
100226616 TTTCAGAAAACCCATT
1 TTTCAGAAAACCCATT
100226632 TCTTCTTCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.33
Consensus pattern (17 bp):
TTTCAGAAAACCCATTG
Found at i:100227881 original size:7 final size:7
Alignment explanation
Indices: 100227861--100227934 Score: 67
Period size: 7 Copynumber: 10.0 Consensus size: 7
100227851 ATATGGACTA
*
100227861 AAATATT
1 AAATTTT
*
100227868 AATTTTT
1 AAATTTT
*
100227875 AAGTTTT
1 AAATTTT
**
100227882 TTATTTTT
1 AAATTT-T
100227890 AAATTTT
1 AAATTTT
100227897 AAATTTT
1 AAATTTT
100227904 AAATTTTT
1 AAA-TTTT
100227912 AAATTTTT
1 AAA-TTTT
100227920 AAATTTTT
1 AAA-TTTT
100227928 AAATTTT
1 AAATTTT
100227935 TATTTTTTGA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
7 29 0.51
8 28 0.49
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (7 bp):
AAATTTT
Found at i:100227895 original size:8 final size:8
Alignment explanation
Indices: 100227868--100227936 Score: 99
Period size: 8 Copynumber: 9.0 Consensus size: 8
100227858 CTAAAATATT
100227868 AATTTTTA
1 AATTTTTA
*
100227876 AGTTTTT-
1 AATTTTTA
*
100227883 TATTTTTA
1 AATTTTTA
100227891 AA-TTTTA
1 AATTTTTA
100227898 AA-TTTTA
1 AATTTTTA
100227905 AATTTTTA
1 AATTTTTA
100227913 AATTTTTA
1 AATTTTTA
100227921 AATTTTTA
1 AATTTTTA
100227929 AATTTTTA
1 AATTTTTA
100227937 TTTTTTGAGT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
7 19 0.35
8 36 0.65
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (8 bp):
AATTTTTA
Found at i:100228556 original size:7 final size:7
Alignment explanation
Indices: 100228544--100228607 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
100228534 CCCATGGCCA
100228544 TTAAACC
1 TTAAACC
100228551 TTAAACC
1 TTAAACC
*
100228558 ATAAAACC
1 -TTAAACC
*
100228566 CTAAACC
1 TTAAACC
* *
100228573 ATAGACC
1 TTAAACC
100228580 TTAAACC
1 TTAAACC
**
100228587 TTAAATA
1 TTAAACC
100228594 TTAAACC
1 TTAAACC
*
100228601 GTAAACC
1 TTAAACC
100228608 AAAAAATAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
7 38 0.86
8 6 0.14
ACGTcount: A:0.47, C:0.27, G:0.03, T:0.23
Consensus pattern (7 bp):
TTAAACC
Found at i:100228564 original size:15 final size:15
Alignment explanation
Indices: 100228541--100228591 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
100228531 ATACCCATGG
*
100228541 CCATTAAACCTTAAA
1 CCATAAAACCTTAAA
*
100228556 CCATAAAACCCTAAA
1 CCATAAAACCTTAAA
*
100228571 CCAT-AGACCTTAAA
1 CCATAAAACCTTAAA
*
100228585 CCTTAAA
1 CCATAAA
100228592 TATTAAACCG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.22
Consensus pattern (15 bp):
CCATAAAACCTTAAA
Found at i:100229074 original size:41 final size:41
Alignment explanation
Indices: 100228821--100229067 Score: 345
Period size: 41 Copynumber: 6.0 Consensus size: 41
100228811 AGGGGTTATA
* *
100228821 TGACTTTTAGCGGCGTTTTATCAAAAGCGCCGCTAATGCTC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
* *
100228862 CGACTTTTAGCGGCGTTTTACCGAAAGCGCCGCTATTGCTC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
* *
100228903 TGACTTTTAGCGGCGTTTTATCGAAAGCGCCGCTATTGCTC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
* *
100228944 CGACTTTTAGCGGCGTTTGACCAAAAGCGCCGCTATTGCTC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
* *
100228985 TG-TTTTTAGCGGCGTTTTAACAAAAAGCGCCGCTATTGCTC
1 TGACTTTTAGCGGCGTTTT-ACCAAAAGCGCCGCTATTGCTC
* * * *
100229026 TG-TTTTTAGTGGCGTTTTACCAAAAACGCCGCTATTGATC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
100229066 TG
1 TG
100229068 TGTTTTACAA
Statistics
Matches: 187, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
40 35 0.19
41 152 0.81
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (41 bp):
TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC
Found at i:100233213 original size:15 final size:14
Alignment explanation
Indices: 100233185--100233211 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
100233175 TGAATTATGT
100233185 TTTTTTAATATTTA
1 TTTTTTAATATTTA
100233199 TTTTTTAATATTT
1 TTTTTTAATATTT
100233212 TAATATATTT
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTAATATTTA
Found at i:100233215 original size:22 final size:21
Alignment explanation
Indices: 100233187--100233230 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
100233177 AATTATGTTT
100233187 TTTTAATATTTATTTTT-TAATA
1 TTTTAATA--TATTTTTATAATA
100233209 TTTTAATATATTTTTATAATA
1 TTTTAATATATTTTTATAATA
100233230 T
1 T
100233231 ATTTGTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 6 0.29
22 8 0.38
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTAATATATTTTTATAATA
Found at i:100236016 original size:31 final size:31
Alignment explanation
Indices: 100235981--100236063 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
100235971 AAATTAAAAA
* *
100235981 TATACATGAATTATAATTTAATGTGTGATTG
1 TATACATGAATTTTAATTTAATGTGTAATTG
* *
100236012 TATACATGAATTTTGATTT--TGTGTAATTT
1 TATACATGAATTTTAATTTAATGTGTAATTG
*
100236041 TATACATTAAATTTTAATTTAAT
1 TATACA-TGAATTTTAATTTAAT
100236064 CTAATTCTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 14 0.33
30 11 0.26
31 17 0.40
32 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.51
Consensus pattern (31 bp):
TATACATGAATTTTAATTTAATGTGTAATTG
Found at i:100236391 original size:14 final size:14
Alignment explanation
Indices: 100236372--100236399 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
100236362 AATTTGTTAA
100236372 ATCTATATTATTAT
1 ATCTATATTATTAT
100236386 ATCTATATTATTAT
1 ATCTATATTATTAT
100236400 CTAATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
ATCTATATTATTAT
Found at i:100237537 original size:3 final size:3
Alignment explanation
Indices: 100237531--100237556 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
100237521 ATATTAAAAA
100237531 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
100237557 AGGTTTAATG
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:100238424 original size:3 final size:3
Alignment explanation
Indices: 100238418--100238458 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
100238408 GTTTAATTTA
100238418 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
100238459 AGTAGTTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:100238751 original size:12 final size:12
Alignment explanation
Indices: 100238734--100238779 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
100238724 AAGAAGAGAA
100238734 AAGAAAGAAAAT
1 AAGAAAGAAAAT
100238746 AAGAAAGAAAAT
1 AAGAAAGAAAAT
* *
100238758 AAGAAAAAAAAG
1 AAGAAAGAAAAT
100238770 AAG-AAGAAAA
1 AAGAAAGAAAA
100238780 AGGAGAAGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
11 6 0.19
12 25 0.81
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.04
Consensus pattern (12 bp):
AAGAAAGAAAAT
Found at i:100238763 original size:24 final size:23
Alignment explanation
Indices: 100238724--100238779 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
100238714 TTTAGTGTTT
* * *
100238724 AAGAAGAGAA-AAGAAAGAAAAT
1 AAGAAGAAAATAAGAAAAAAAAG
100238746 AAGAAAGAAAATAAGAAAAAAAAG
1 AAG-AAGAAAATAAGAAAAAAAAG
100238770 AAGAAGAAAA
1 AAGAAGAAAA
100238780 AGGAGAAGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.10
23 13 0.45
24 13 0.45
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.04
Consensus pattern (23 bp):
AAGAAGAAAATAAGAAAAAAAAG
Found at i:100238780 original size:12 final size:13
Alignment explanation
Indices: 100238734--100238793 Score: 56
Period size: 12 Copynumber: 4.9 Consensus size: 13
100238724 AAGAAGAGAA
*
100238734 AAGAA-AGAAAAT
1 AAGAAGAGAAAAG
*
100238746 AAGAA-AGAAAAT
1 AAGAAGAGAAAAG
*
100238758 AAGAA-AAAAAAG
1 AAGAAGAGAAAAG
100238770 AAGAAGA-AAAAG
1 AAGAAGAGAAAAG
*
100238782 GAGAAGAGAAAA
1 AAGAAGAGAAAA
100238794 ATGGAGATAC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
12 38 0.88
13 5 0.12
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (13 bp):
AAGAAGAGAAAAG
Found at i:100238791 original size:29 final size:28
Alignment explanation
Indices: 100238725--100238794 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
100238715 TTAGTGTTTA
* *
100238725 AGAAGAGAAAAGAAAGAAAATAAGAAAG
1 AGAAGAGAAAAAAAAGAAAAGAAGAAAG
* *
100238753 AAAATAAGAAAAAAAAGAAGAAGAA-AAAGG
1 AGAA-GAGAAAAAAAAGAA-AAGAAGAAA-G
100238783 AGAAGAGAAAAA
1 AGAAGAGAAAAA
100238795 TGGAGATACC
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
28 3 0.09
29 22 0.67
30 8 0.24
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (28 bp):
AGAAGAGAAAAAAAAGAAAAGAAGAAAG
Found at i:100238799 original size:15 final size:15
Alignment explanation
Indices: 100238758--100238800 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
100238748 GAAAGAAAAT
**
100238758 AAGAAAAAAAAGAAG
1 AAGAAAAAGGAGAAG
100238773 AAGAAAAAGGAGAAG
1 AAGAAAAAGGAGAAG
100238788 -AGAAAAATGGAGA
1 AAGAAAAA-GGAGA
100238801 TACCTCCAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (15 bp):
AAGAAAAAGGAGAAG
Found at i:100239525 original size:20 final size:21
Alignment explanation
Indices: 100239495--100239536 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
100239485 ATCCAATGTG
100239495 GCAAGTTAACTGGCCACATCA
1 GCAAGTTAACTGGCCACATCA
*
100239516 GCAA-TTAACTTGCCACATCA
1 GCAAGTTAACTGGCCACATCA
100239536 G
1 G
100239537 TTGTCTCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (21 bp):
GCAAGTTAACTGGCCACATCA
Found at i:100240727 original size:17 final size:19
Alignment explanation
Indices: 100240700--100240739 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
100240690 TATTATTAAA
*
100240700 ATTGATTAATTTTATT-TT
1 ATTGATTAATTCTATTATT
100240718 ATTG-TTAATTCTATTATT
1 ATTGATTAATTCTATTATT
100240736 ATTG
1 ATTG
100240740 GTATTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (19 bp):
ATTGATTAATTCTATTATT
Found at i:100240737 original size:3 final size:3
Alignment explanation
Indices: 100240729--100241171 Score: 156
Period size: 3 Copynumber: 149.3 Consensus size: 3
100240719 TTGTTAATTC
** *
100240729 TAT TAT TAT TGG TAT TAT TAT TAT TAT TACT T-T TAT TCT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
* * ** * * *
100240773 TAC TAT TAT TGT TGC TAT T-T CTCT TAT TGT TTT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA-T TAT
* * * * *
100240819 T-T TAT TGT TAG TAT TAT TAG TAT TCCT TAG T-T TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
* * * * *
100240863 TAT TAT T-T CAT CAT TATT TAT T-T TAT TGT TAG TAT TAT TAG TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
100240907 TCCT TAG T-T TAT TAT TAT TAT TAT TAT T-T CAT CAT TAT TTT CTAT
1 T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* * * *
100240952 TAT TGT TAT TAT TAA TA- TAC TAT TAT TAT TCT TAT TAAT GTAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT -TAT TAT
* * * **
100240998 TGT TAT TAT TTT CTAC T-T TAT TAT TA- TAT TAT TAT TAT TGC TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
100241042 CA- TCT TAT TAT TA- AACT AAT TAAT T-T TA- TAT TGAT T-T TGT CA-
1 TAT TAT TAT TAT TAT TA-T TAT T-AT TAT TAT TAT T-AT TAT TAT TAT
* * * **
100241084 CAT TAT ATAT T-T TCT T-T T-T GTATT TAT T-T ACAT TAT TAT TGC TAT
1 TAT TAT -TAT TAT TAT TAT TAT -TA-T TAT TAT -TAT TAT TAT TAT TAT
* *
100241129 TAC TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
100241172 TTTGAACATA
Statistics
Matches: 328, Mismatches: 74, Indels: 76
0.69 0.15 0.16
Matches are distributed among these distances:
2 33 0.10
3 259 0.79
4 34 0.10
5 2 0.01
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:100240894 original size:65 final size:65
Alignment explanation
Indices: 100240810--100240965 Score: 278
Period size: 65 Copynumber: 2.4 Consensus size: 65
100240800 TGTTTTTATT
100240810 ATTATTTATTTTATTGTTAGTATTATTAGTATTCCTTAGTTTATTATTATTATTATTATTTCATC
1 ATTATTTATTTTATTGTTAGTATTATTAGTATTCCTTAGTTTATTATTATTATTATTATTTCATC
100240875 ATTATTTATTTTATTGTTAGTATTATTAGTATTCCTTAGTTTATTATTATTATTATTATTTCATC
1 ATTATTTATTTTATTGTTAGTATTATTAGTATTCCTTAGTTTATTATTATTATTATTATTTCATC
*
100240940 ATTATTT-TCTATTATTGTTATTATTA
1 ATTATTTAT-T-TTATTGTTAGTATTA
100240966 ATATACTATT
Statistics
Matches: 88, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
64 1 0.01
65 73 0.83
66 14 0.16
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (65 bp):
ATTATTTATTTTATTGTTAGTATTATTAGTATTCCTTAGTTTATTATTATTATTATTATTTCATC
Found at i:100241006 original size:20 final size:23
Alignment explanation
Indices: 100240948--100241007 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
100240938 TCATTATTTT
100240948 CTATTATTGTTATTATTAATATA
1 CTATTATTGTTATTATTAATATA
* *
100240971 CTATTATTATTCTTATT-A-AT-
1 CTATTATTGTTATTATTAATATA
*
100240991 GTATTATTGTTATTATT
1 CTATTATTGTTATTATT
100241008 TTCTACTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 14 0.44
21 2 0.06
22 1 0.03
23 15 0.47
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (23 bp):
CTATTATTGTTATTATTAATATA
Found at i:100241236 original size:27 final size:26
Alignment explanation
Indices: 100241205--100241294 Score: 69
Period size: 27 Copynumber: 3.3 Consensus size: 26
100241195 ATTATTATCA
100241205 ATTTTAAATATTTTACATATGTTATTT
1 ATTTTAAATATTTTACATAT-TTATTT
* * *
100241232 CTTTTAAACTATTATACGTA-TTATTT
1 ATTTTAAA-TATTTTACATATTTATTT
*
100241258 ATTTTGAAAT-TTTTATATATATCT-TTGT
1 ATTTT-AAATATTTTACATAT-T-TATT-T
100241286 ATTTTAAAT
1 ATTTTAAAT
100241295 TATTATGTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
25 6 0.12
26 11 0.22
27 17 0.34
28 16 0.32
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (26 bp):
ATTTTAAATATTTTACATATTTATTT
Found at i:100241560 original size:25 final size:27
Alignment explanation
Indices: 100241532--100241583 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
100241522 TTTATATGCA
*
100241532 ATTTTAAATTATT-TTTTTAT-TTATT
1 ATTTTAAATTATTCTATTTATATTATT
*
100241557 ATTTTAAGTTATTCTATTTATATTATT
1 ATTTTAAATTATTCTATTTATATTATT
100241584 TTGTTATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 12 0.52
26 6 0.26
27 5 0.22
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (27 bp):
ATTTTAAATTATTCTATTTATATTATT
Found at i:100245687 original size:43 final size:43
Alignment explanation
Indices: 100245586--100245671 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
100245576 TTATAGTGAG
100245586 AAAACACATTCATTTTTTAACACGACCCAATTTTTAACATCAT
1 AAAACACATTCATTTTTTAACACGACCCAATTTTTAACATCAT
*
100245629 AAAACACATTCATTTTTTAACACGACCCGATTTTTAACATCAT
1 AAAACACATTCATTTTTTAACACGACCCAATTTTTAACATCAT
100245672 CATTTCTATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.35
Consensus pattern (43 bp):
AAAACACATTCATTTTTTAACACGACCCAATTTTTAACATCAT
Found at i:100247726 original size:16 final size:16
Alignment explanation
Indices: 100247705--100247738 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
100247695 GGACGGAGTT
100247705 GGTGTGTAACAAATGG
1 GGTGTGTAACAAATGG
100247721 GGTGTGTAACAAATGG
1 GGTGTGTAACAAATGG
100247737 GG
1 GG
100247739 GTAGGAGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.41, T:0.24
Consensus pattern (16 bp):
GGTGTGTAACAAATGG
Found at i:100251590 original size:16 final size:16
Alignment explanation
Indices: 100251569--100251636 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
100251559 TTTGGTTCGC
100251569 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
100251585 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
100251601 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
100251617 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
100251633 TGTA
1 TGTA
100251637 ATAGCAAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:100251905 original size:17 final size:17
Alignment explanation
Indices: 100251864--100252004 Score: 61
Period size: 17 Copynumber: 8.6 Consensus size: 17
100251854 AACATAATTA
100251864 TTATT-AAATATAT--T
1 TTATTAAAATATATAAT
* *
100251878 TTTTTATAATATATAAT
1 TTATTAAAATATATAAT
100251895 TTGA-TAAAATATATGAAT
1 TT-ATTAAAATATAT-AAT
100251913 TTATTAAAAT-TATAAT
1 TTATTAAAATATATAAT
* * *
100251929 ATA-TAATATTATAAAAT
1 TTATTAA-AATATATAAT
* *
100251946 ATAATTTAAAATA-ATTA-
1 -TTA-TTAAAATATATAAT
100251963 TTATT--AA-ATATAAT
1 TTATTAAAATATATAAT
**
100251977 TTAACAAAAATATATAAT
1 TT-ATTAAAATATATAAT
*
100251995 TTAATAAAAT
1 TTATTAAAAT
100252005 TCTTAGTATT
Statistics
Matches: 92, Mismatches: 18, Indels: 31
0.65 0.13 0.22
Matches are distributed among these distances:
12 1 0.01
13 5 0.05
14 6 0.07
15 13 0.14
16 9 0.10
17 29 0.32
18 23 0.25
19 3 0.03
20 3 0.03
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (17 bp):
TTATTAAAATATATAAT
Found at i:100251932 original size:24 final size:22
Alignment explanation
Indices: 100251902--100251950 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 22
100251892 AATTTGATAA
100251902 AATATATGAAT-TTATTAAAATTAT
1 AATATAT-AATATTA-TAAAA-TAT
100251926 AATATATAATATTATAAAATAT
1 AATATATAATATTATAAAATAT
100251948 AAT
1 AAT
100251951 TTAAAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.25
23 8 0.33
24 10 0.42
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATATATAATATTATAAAATAT
Found at i:100251941 original size:15 final size:15
Alignment explanation
Indices: 100251921--100251976 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
100251911 ATTTATTAAA
*
100251921 ATTATAATATATAAT
1 ATTATAAAATATAAT
100251936 ATTATAAAATAT-A-
1 ATTATAAAATATAAT
*
100251949 ATT-TAAAATA-ATT
1 ATTATAAAATATAAT
*
100251962 ATTATTAAATATAAT
1 ATTATAAAATATAAT
100251977 TTAACAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
12 7 0.21
13 6 0.18
14 7 0.21
15 13 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTATAAAATATAAT
Found at i:100251971 original size:26 final size:25
Alignment explanation
Indices: 100251931--100251993 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 25
100251921 ATTATAATAT
100251931 ATAATATTATAAAATATAATTTAAA
1 ATAATATTATAAAATATAATTTAAA
*
100251956 ATAATTATTATTAAATATAATTTAACA
1 ATAA-TATTATAAAATATAATTTAA-A
*
100251983 AAAATA-TATAA
1 ATAATATTATAA
100251994 TTTAATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 8 0.24
26 21 0.64
27 4 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
ATAATATTATAAAATATAATTTAAA
Found at i:100256197 original size:26 final size:25
Alignment explanation
Indices: 100256168--100256241 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 25
100256158 AAAATTATGT
*
100256168 TAAATTATTTATATTTAAAATATTAA
1 TAAA-TATTTATATTTAAAATATAAA
* ** *
100256194 TAAAAATATTATATTGCAAATAAAAA
1 TAAATAT-TTATATTTAAAATATAAA
*
100256220 TAAATA-TTATTTTTAAAATATA
1 TAAATATTTATATTTAAAATATA
100256242 TAAAAAAAGG
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
24 12 0.32
25 2 0.05
26 23 0.62
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (25 bp):
TAAATATTTATATTTAAAATATAAA
Found at i:100257610 original size:42 final size:42
Alignment explanation
Indices: 100257490--100257612 Score: 126
Period size: 42 Copynumber: 2.9 Consensus size: 42
100257480 ATTTATATGC
* * *
100257490 CACACGACTTGGACACACACCTATGTCCTTGGCCGTGTGGCT
1 CACACGACTTGGACACACGCCCATGTCCTTGGCCGTGTGACT
* **
100257532 CACACGACTTGGACACACGCCCGTGT-CTCTACCCGTGTGACT
1 CACACGACTTGGACACACGCCCATGTCCT-TGGCCGTGTGACT
* *
100257574 CACAC-AGCTTGCG-CGCACGCGCATGTCCTTGGCCGTGTG
1 CACACGA-CTTG-GACACACGCCCATGTCCTTGGCCGTGTG
100257613 GTCCTAAGTC
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
41 3 0.05
42 60 0.91
43 3 0.05
ACGTcount: A:0.17, C:0.36, G:0.25, T:0.22
Consensus pattern (42 bp):
CACACGACTTGGACACACGCCCATGTCCTTGGCCGTGTGACT
Found at i:100261413 original size:15 final size:15
Alignment explanation
Indices: 100261393--100261424 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
100261383 AATTCTGAAC
100261393 AGACTTTCATTTCAA
1 AGACTTTCATTTCAA
100261408 AGACTTTCATTTCAA
1 AGACTTTCATTTCAA
100261423 AG
1 AG
100261425 TTAATCATCT
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:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (15 bp):
AGACTTTCATTTCAA
Found at i:100266897 original size:14 final size:16
Alignment explanation
Indices: 100266871--100266904 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
100266861 TAAAGCACGA
100266871 AAATTTCACACAT-AT
1 AAATTTCACACATAAT
100266886 AAATTT-ACACATAAT
1 AAATTTCACACATAAT
100266901 AAAT
1 AAAT
100266905 ACAGAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTTCACACATAAT
Found at i:100268195 original size:50 final size:48
Alignment explanation
Indices: 100268119--100268214 Score: 156
Period size: 50 Copynumber: 2.0 Consensus size: 48
100268109 TTCCAAAAAA
*
100268119 AATATTATTTTAATAGTTTAATATTAAATTTAATTTAATATTTATCTT
1 AATATTATTTTAATAGTTTAATATTAAATTTAATCTAATATTTATCTT
*
100268167 AATATTATTTTGATAAGATTTAATATTAAATTTAATCTAATATTTATC
1 AATATTATTTTAAT-AG-TTTAATATTAAATTTAATCTAATATTTATC
100268215 GTGATAAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
48 13 0.30
49 2 0.05
50 29 0.66
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (48 bp):
AATATTATTTTAATAGTTTAATATTAAATTTAATCTAATATTTATCTT
Found at i:100274248 original size:5 final size:5
Alignment explanation
Indices: 100274238--100274291 Score: 81
Period size: 5 Copynumber: 10.8 Consensus size: 5
100274228 TGTAAAACAA
* * *
100274238 TTGAT TTGAT TTGAT TTGAC TTGAC TTGAC TTGAC TTGAC TTGAC TTGAC
1 TTGAC TTGAC TTGAC TTGAC TTGAC TTGAC TTGAC TTGAC TTGAC TTGAC
100274288 TTGA
1 TTGA
100274292 TTTAAGATAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.46
Consensus pattern (5 bp):
TTGAC
Found at i:100279077 original size:21 final size:19
Alignment explanation
Indices: 100279052--100279103 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
100279042 GCCCTTCTTC
*
100279052 AAGAGTAGAAATCGGTAATGG
1 AAGAG-AGAAAT-GGAAATGG
*
100279073 AAGAG-GACAAAGGAAATGG
1 AAGAGAGA-AATGGAAATGG
100279092 AAGAGAGAAATG
1 AAGAGAGAAATG
100279104 AAGAAATGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
19 17 0.65
20 4 0.15
21 5 0.19
ACGTcount: A:0.50, C:0.04, G:0.35, T:0.12
Consensus pattern (19 bp):
AAGAGAGAAATGGAAATGG
Found at i:100279708 original size:22 final size:22
Alignment explanation
Indices: 100279674--100279727 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
100279664 CAGATTTGTG
* *
100279674 AAAATTTATTATAAAAATAATT
1 AAAATTCAATATAAAAATAATT
**
100279696 AAAATTCAATATATTAATAATT
1 AAAATTCAATATAAAAATAATT
*
100279718 TAAATTCAAT
1 AAAATTCAAT
100279728 TTAGTTATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATTCAATATAAAAATAATT
Found at i:100287972 original size:14 final size:14
Alignment explanation
Indices: 100287953--100287983 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
100287943 TACTTTCTTT
100287953 CTTTTTTCAATAAG
1 CTTTTTTCAATAAG
100287967 CTTTTTTCAATAAG
1 CTTTTTTCAATAAG
100287981 CTT
1 CTT
100287984 GTACATGCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (14 bp):
CTTTTTTCAATAAG
Found at i:100290900 original size:7 final size:7
Alignment explanation
Indices: 100290890--100290914 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
100290880 CTGATTTCCA
100290890 TTTTCTT
1 TTTTCTT
100290897 TTTTCTT
1 TTTTCTT
100290904 TTTTCTT
1 TTTTCTT
100290911 TTTT
1 TTTT
100290915 TTGAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:100293816 original size:60 final size:59
Alignment explanation
Indices: 100293737--100293873 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 59
100293727 AACTGTGTTA
* *
100293737 ATATGGGCAAGGCCCAATATATCTC-GACT-TGTAATAGGGCTACGGCCCAGATTAATACTG
1 ATATGGGCTAGGCCCAATAT-TCTCTGA-TATGTAAGA-GGCTACGGCCCAGATTAATACTG
* * *
100293797 ATATGGGCTAGGCCTAATATTCTCTGATACTGTAAGAGGCTATGGCCCAGATTAATATTG
1 ATATGGGCTAGGCCCAATATTCTCTGATA-TGTAAGAGGCTACGGCCCAGATTAATACTG
*
100293857 ATATAGGCTAAGGCCCA
1 ATATGGGCT-AGGCCCA
100293874 GTTAACACTG
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
59 5 0.08
60 49 0.74
61 12 0.18
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (59 bp):
ATATGGGCTAGGCCCAATATTCTCTGATATGTAAGAGGCTACGGCCCAGATTAATACTG
Found at i:100294737 original size:16 final size:17
Alignment explanation
Indices: 100294705--100294737 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
100294695 CATCAAGAAG
100294705 GGTTTTCAATGAAAACAT
1 GGTTTTCAA-GAAAACAT
100294723 GGTTTTCAA-AAAACA
1 GGTTTTCAAGAAAACA
100294738 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (17 bp):
GGTTTTCAAGAAAACAT
Found at i:100294916 original size:29 final size:29
Alignment explanation
Indices: 100294883--100294940 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
100294873 AGCTCTACCG
*
100294883 AAAAACACTAAAATCGATTTTATGGAAAT
1 AAAAACACTAAAATCAATTTTATGGAAAT
100294912 AAAAACACTAAAATCAATTTTATGGAAAT
1 AAAAACACTAAAATCAATTTTATGGAAAT
100294941 GTTAGAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.53, C:0.10, G:0.09, T:0.28
Consensus pattern (29 bp):
AAAAACACTAAAATCAATTTTATGGAAAT
Found at i:100296142 original size:8 final size:8
Alignment explanation
Indices: 100296129--100296174 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
100296119 CTAGATCGGC
100296129 AAAAGCCG
1 AAAAGCCG
*
100296137 AAAAGCTG
1 AAAAGCCG
*
100296145 AAATGCCG
1 AAAAGCCG
*
100296153 AAAAGCTG
1 AAAAGCCG
*
100296161 AAATGCCG
1 AAAAGCCG
100296169 AAAAGC
1 AAAAGC
100296175 TGGCATCTTG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.48, C:0.20, G:0.24, T:0.09
Consensus pattern (8 bp):
AAAAGCCG
Found at i:100296154 original size:16 final size:16
Alignment explanation
Indices: 100296133--100296176 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
100296123 ATCGGCAAAA
100296133 GCCGAAAAGCTGAAAT
1 GCCGAAAAGCTGAAAT
100296149 GCCGAAAAGCTGAAAT
1 GCCGAAAAGCTGAAAT
100296165 GCCGAAAAGCTG
1 GCCGAAAAGCTG
100296177 GCATCTTGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.27, T:0.11
Consensus pattern (16 bp):
GCCGAAAAGCTGAAAT
Found at i:100296832 original size:20 final size:21
Alignment explanation
Indices: 100296789--100296834 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
100296779 ACTGTTTTGT
100296789 TATGGG-CCAACTGTATTGAA
1 TATGGGCCCAACTGTATTGAA
*
100296809 -ATGGGCCCAACTGTGTT-AA
1 TATGGGCCCAACTGTATTGAA
100296828 TATGGGC
1 TATGGGC
100296835 AAGGCCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGGGCCCAACTGTATTGAA
Found at i:100296901 original size:27 final size:28
Alignment explanation
Indices: 100296864--100296975 Score: 79
Period size: 27 Copynumber: 3.9 Consensus size: 28
100296854 CTTGTAATAG
100296864 GGCTACGGCCCAGATTAATACTGATATA
1 GGCTACGGCCCAGATTAATACTGATATA
*
100296892 GGCTA-GGCCCA-ATATACT-CTGATACTGTAA
1 GGCTACGGCCCAGAT-TAATACTGATA---T-A
* * *
100296922 GGGGCTATGGCCCAGATTAATATTGATATG
1 --GGCTACGGCCCAGATTAATACTGATATA
* *
100296952 GGCTAAGGCCCAG-TTAACACTGAT
1 GGCTACGGCCCAGATTAATACTGAT
100296976 TTCTGAATAG
Statistics
Matches: 67, Mismatches: 7, Indels: 21
0.71 0.07 0.22
Matches are distributed among these distances:
26 8 0.12
27 18 0.27
28 17 0.25
29 1 0.01
30 1 0.01
31 1 0.01
32 5 0.07
33 9 0.13
34 7 0.10
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (28 bp):
GGCTACGGCCCAGATTAATACTGATATA
Found at i:100302906 original size:27 final size:27
Alignment explanation
Indices: 100302871--100302926 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
100302861 TTCGTCTTTT
* *
100302871 TCTTCATTTATTGAAATTTGATCCATA
1 TCTTAATTTATTGAAAGTTGATCCATA
100302898 TCTTAATTTATTGAAAGTTGATCCATA
1 TCTTAATTTATTGAAAGTTGATCCATA
100302925 TC
1 TC
100302927 GTTTTCCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.46
Consensus pattern (27 bp):
TCTTAATTTATTGAAAGTTGATCCATA
Found at i:100303883 original size:46 final size:47
Alignment explanation
Indices: 100303827--100303928 Score: 188
Period size: 47 Copynumber: 2.2 Consensus size: 47
100303817 GATAGATAAA
100303827 AATATTAAATTAAACGTCAGTTACT-AAAAAAATACGAACATAAAAT
1 AATATTAAATTAAACGTCAGTTACTAAAAAAAATACGAACATAAAAT
*
100303873 AATATTAAATTAAACGTCAGTTATTAAAAAAAATACGAACATAAAAT
1 AATATTAAATTAAACGTCAGTTACTAAAAAAAATACGAACATAAAAT
100303920 AATATTAAA
1 AATATTAAA
100303929 ACATAAGTAC
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 24 0.44
47 30 0.56
ACGTcount: A:0.58, C:0.09, G:0.06, T:0.27
Consensus pattern (47 bp):
AATATTAAATTAAACGTCAGTTACTAAAAAAAATACGAACATAAAAT
Found at i:100308301 original size:39 final size:39
Alignment explanation
Indices: 100308252--100308328 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
100308242 ACAGGTGTCA
*
100308252 TGTGACCAGGCTGGGTCAAATTTGTCTGGTTCAAATTCT
1 TGTGAACAGGCTGGGTCAAATTTGTCTGGTTCAAATTCT
*
100308291 TGTGAACAGGCTGGGTCAAGTTTGTCTGGTTCAAATTC
1 TGTGAACAGGCTGGGTCAAATTTGTCTGGTTCAAATTC
100308329 ATCCAGCTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (39 bp):
TGTGAACAGGCTGGGTCAAATTTGTCTGGTTCAAATTCT
Found at i:100316691 original size:9 final size:9
Alignment explanation
Indices: 100316677--100316732 Score: 85
Period size: 9 Copynumber: 6.2 Consensus size: 9
100316667 TTTGGTTAAA
*
100316677 AATTACCCG
1 AATTAACCG
*
100316686 AATTACCCG
1 AATTAACCG
*
100316695 AATTACCCG
1 AATTAACCG
100316704 AATTAACCG
1 AATTAACCG
100316713 AATTAACCG
1 AATTAACCG
100316722 AATTAACCG
1 AATTAACCG
100316731 AA
1 AA
100316733 AAATACCCGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.41, C:0.27, G:0.11, T:0.21
Consensus pattern (9 bp):
AATTAACCG
Found at i:100316700 original size:18 final size:18
Alignment explanation
Indices: 100316677--100316732 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
100316667 TTTGGTTAAA
*
100316677 AATTACCCGAATTACCCG
1 AATTACCCGAATTAACCG
100316695 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
*
100316713 AATTAACCGAATTAACCG
1 AATTACCCGAATTAACCG
100316731 AA
1 AA
100316733 AAATACCCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.41, C:0.27, G:0.11, T:0.21
Consensus pattern (18 bp):
AATTACCCGAATTAACCG
Found at i:100318630 original size:24 final size:23
Alignment explanation
Indices: 100318579--100318630 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
100318569 ATTAAATTTT
100318579 CAAAATTAAAAAAAATGAGGAAA
1 CAAAATTAAAAAAAATGAGGAAA
* * **
100318602 AAAAATTATAAAACAATGATTAAA
1 CAAAATTA-AAAAAAATGAGGAAA
100318626 CAAAA
1 CAAAA
100318631 AAATTACTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.69, C:0.06, G:0.08, T:0.17
Consensus pattern (23 bp):
CAAAATTAAAAAAAATGAGGAAA
Found at i:100328664 original size:19 final size:20
Alignment explanation
Indices: 100328626--100328680 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
100328616 TTTGAACCTG
* **
100328626 AACCTTGAATCTCGAACCCA
1 AACCTTGAAACTTAAACCCA
*
100328646 AATCTT-AAACTTAAACCCA
1 AACCTTGAAACTTAAACCCA
*
100328665 AACCTTGAATCTTAAA
1 AACCTTGAAACTTAAA
100328681 TCTCAAACCC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.42, C:0.27, G:0.05, T:0.25
Consensus pattern (20 bp):
AACCTTGAAACTTAAACCCA
Found at i:100328693 original size:27 final size:26
Alignment explanation
Indices: 100328646--100328703 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
100328636 CTCGAACCCA
*
100328646 AATCTTAAACTTAAACCCAAA-CCTT
1 AATCTTAAACTCAAACCCAAATCCTT
100328671 GAATCTTAAATCTCAAACCCAAATCCTT
1 -AATCTTAAA-CTCAAACCCAAATCCTT
100328699 AATCT
1 AATCT
100328704 CGAGTTTGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 9 0.31
27 16 0.55
28 4 0.14
ACGTcount: A:0.41, C:0.28, G:0.02, T:0.29
Consensus pattern (26 bp):
AATCTTAAACTCAAACCCAAATCCTT
Found at i:100328869 original size:18 final size:18
Alignment explanation
Indices: 100328846--100328880 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
100328836 TTGTTTATAA
100328846 TTTAAAAAAATTAATTAT
1 TTTAAAAAAATTAATTAT
* *
100328864 TTTAAATAATTTAATTA
1 TTTAAAAAAATTAATTA
100328881 AAGTTAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAAAAAAATTAATTAT
Found at i:100329045 original size:19 final size:21
Alignment explanation
Indices: 100329004--100329043 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
100328994 TTTTAGGATG
*
100329004 ATCCTAATATAATTTATTCTC
1 ATCCTAATAAAATTTATTCTC
100329025 ATCCTAATAAAATTTATTC
1 ATCCTAATAAAATTTATTC
100329044 ATGTGTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (21 bp):
ATCCTAATAAAATTTATTCTC
Found at i:100329164 original size:124 final size:124
Alignment explanation
Indices: 100328925--100329147 Score: 376
Period size: 124 Copynumber: 1.8 Consensus size: 124
100328915 GATGAGTGTA
* *
100328925 TAATAATACATTGTTATCTTCAAATTTTAATGACGTGACACTATTTTATTGGTGCCTAAAAACTA
1 TAATAATACATTGTTATCTTCAAAATTTAATGACGTGACACTATTTTATTAGTGCCTAAAAACTA
100328990 TACTTTTTAGGATGATCCTAATATAATTTATTCTCATCCTAATAAAATTTATTCATGTG
66 TACTTTTTAGGATGATCCTAATATAATTTATTCTCATCCTAATAAAATTTATTCATGTG
** * *
100329049 TAATAATATTTTGTTATCTTTAAAATTTAATGACGTGACACTATTTTATTAGTGCCTAAAAGCTA
1 TAATAATACATTGTTATCTTCAAAATTTAATGACGTGACACTATTTTATTAGTGCCTAAAAACTA
*
100329114 TACTTTTTA-GATGATCTTAATATAATTTATTCTC
66 TACTTTTTAGGATGATCCTAATATAATTTATTCTC
100329148 TTTAATTAAT
Statistics
Matches: 92, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
123 24 0.26
124 68 0.74
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (124 bp):
TAATAATACATTGTTATCTTCAAAATTTAATGACGTGACACTATTTTATTAGTGCCTAAAAACTA
TACTTTTTAGGATGATCCTAATATAATTTATTCTCATCCTAATAAAATTTATTCATGTG
Found at i:100331146 original size:29 final size:29
Alignment explanation
Indices: 100331113--100331169 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
100331103 GTACAATAAT
*
100331113 CTATACAAGTCACAAAATTAAATAGAATC
1 CTATAAAAGTCACAAAATTAAATAGAATC
**
100331142 CTATAAAAGTCACTCAATTAAATAGAAT
1 CTATAAAAGTCACAAAATTAAATAGAAT
100331170 ATTTCCAGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.26
Consensus pattern (29 bp):
CTATAAAAGTCACAAAATTAAATAGAATC
Found at i:100334105 original size:14 final size:13
Alignment explanation
Indices: 100334072--100334122 Score: 52
Period size: 14 Copynumber: 4.0 Consensus size: 13
100334062 ATTGGAATTA
100334072 AAAATTTAAATAT
1 AAAATTTAAATAT
* *
100334085 TAAATTTAAGTTAT
1 AAAATTTAA-ATAT
*
100334099 AAAATTTTAAT-T
1 AAAATTTAAATAT
100334111 AAAA-TTAAATAT
1 AAAATTTAAATAT
100334123 CGAACATGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
11 5 0.17
12 6 0.20
13 9 0.30
14 10 0.33
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (13 bp):
AAAATTTAAATAT
Found at i:100336782 original size:27 final size:27
Alignment explanation
Indices: 100336747--100336801 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
100336737 AAGAACCTAA
*
100336747 AAGTGGTTGCATCCACCACAAGAGAGT
1 AAGTAGTTGCATCCACCACAAGAGAGT
100336774 AAGTAGTTGCATCCACCACAAGAGAGT
1 AAGTAGTTGCATCCACCACAAGAGAGT
100336801 A
1 A
100336802 TGTCTCTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
AAGTAGTTGCATCCACCACAAGAGAGT
Found at i:100345420 original size:54 final size:54
Alignment explanation
Indices: 100345361--100345475 Score: 153
Period size: 52 Copynumber: 2.1 Consensus size: 54
100345351 GGTGTTAGAG
*
100345361 ATTAAAGTATAAGAATTAAATATCTAATTTAAGCATATT-AGGACTAAAATTG-AA
1 ATTAAAGTATAAGAATT--ATATCAAATTTAAGCATATTAAGGACTAAAATTGAAA
* *
100345415 ATTAAAGTATAAGAATTATTTCAAATTTAAGCATATTAAAAGGACTAAAGTTGAAA
1 ATTAAAGTATAAGAATTATATCAAATTTAAGCATATT--AAGGACTAAAATTGAAA
100345471 ATTAA
1 ATTAA
100345476 CCGATTTATA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
52 18 0.33
54 17 0.31
55 12 0.22
56 7 0.13
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.33
Consensus pattern (54 bp):
ATTAAAGTATAAGAATTATATCAAATTTAAGCATATTAAGGACTAAAATTGAAA
Found at i:100349464 original size:23 final size:24
Alignment explanation
Indices: 100349429--100349474 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
100349419 AAATTATTAT
* *
100349429 TAAAATTTCAAATT-TTAAAAACA
1 TAAAAATTAAAATTATTAAAAACA
100349452 TAAAAATTAAAATTGATTAAAAA
1 TAAAAATTAAAATT-ATTAAAAA
100349475 AATTGATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
25 7 0.37
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (24 bp):
TAAAAATTAAAATTATTAAAAACA
Found at i:100349995 original size:14 final size:13
Alignment explanation
Indices: 100349976--100350012 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
100349966 TTTTAATTTC
100349976 AATTATATTAGGAT
1 AATTAT-TTAGGAT
*
100349990 AATTATTAAGGAT
1 AATTATTTAGGAT
100350003 AATTATTTAG
1 AATTATTTAG
100350013 ATTTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (13 bp):
AATTATTTAGGAT
Found at i:100350042 original size:10 final size:10
Alignment explanation
Indices: 100350027--100350092 Score: 62
Period size: 10 Copynumber: 6.6 Consensus size: 10
100350017 AAATTTTAAG
100350027 ATTTAT-TTT
1 ATTTATATTT
100350036 CATTTATATTT
1 -ATTTATATTT
* *
100350047 AATTATCTTT
1 ATTTATATTT
100350057 ATTTATATTT
1 ATTTATATTT
* *
100350067 AATTATCTTT
1 ATTTATATTT
*
100350077 ATTTATTTTT
1 ATTTATATTT
*
100350087 AATTAT
1 ATTTAT
100350093 CTTTTAGAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
10 43 0.93
11 3 0.07
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (10 bp):
ATTTATATTT
Found at i:100350060 original size:20 final size:20
Alignment explanation
Indices: 100350037--100350096 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
100350027 ATTTATTTTC
100350037 ATTTATATTTAATTATCTTT
1 ATTTATATTTAATTATCTTT
100350057 ATTTATATTTAATTATCTTT
1 ATTTATATTTAATTATCTTT
*
100350077 ATTTATTTTTAATTATCTTT
1 ATTTATATTTAATTATCTTT
100350097 TAGAATTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTATATTTAATTATCTTT
Found at i:100351395 original size:10 final size:10
Alignment explanation
Indices: 100351380--100351419 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
100351370 TATTAATATG
100351380 TCTTTTTTTT
1 TCTTTTTTTT
100351390 TCTTTTTTTT
1 TCTTTTTTTT
*
100351400 T-TAATTTTTT
1 TCT-TTTTTTT
100351410 TCTTTTTTTT
1 TCTTTTTTTT
100351420 AATTTTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 1 0.04
10 24 0.92
11 1 0.04
ACGTcount: A:0.05, C:0.07, G:0.00, T:0.88
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:100351605 original size:96 final size:97
Alignment explanation
Indices: 100351431--100351617 Score: 295
Period size: 96 Copynumber: 1.9 Consensus size: 97
100351421 ATTTTCTTTA
* * * *
100351431 TTTATTTTTACTTAGGAATATATTGAACTTTTTGACGCGAAGAGAGATGACAGCTAAGCACCCCA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCTAAGCACCCCA
*
100351496 CCCCGGTTGCTCAGCCCAACACATTCCTAATT
66 CCCCGGTTACTCAGCCCAACACATTCCTAATT
* *
100351528 TTTATTTTT-CTTAAGAACATATCGAACCTTTTGATGCGAAGAGAGATGACAGCTAAGCACCTCA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCTAAGCACCCCA
*
100351592 CCCTGGTTACTCAGCCCAACACATTC
66 CCCCGGTTACTCAGCCCAACACATTC
100351618 TTAAAAATTA
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
96 73 0.89
97 9 0.11
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (97 bp):
TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCTAAGCACCCCA
CCCCGGTTACTCAGCCCAACACATTCCTAATT
Found at i:100352367 original size:7 final size:7
Alignment explanation
Indices: 100352355--100352388 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
100352345 TAATATCTGA
100352355 AAATAAT
1 AAATAAT
100352362 AAATAAT
1 AAATAAT
100352369 AAAATAAT
1 -AAATAAT
100352377 AAATAA-
1 AAATAAT
100352383 AAATAA
1 AAATAA
100352389 AATAAACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 6 0.23
7 13 0.50
8 7 0.27
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAATAAT
Found at i:100352374 original size:15 final size:16
Alignment explanation
Indices: 100352359--100352424 Score: 66
Period size: 15 Copynumber: 4.1 Consensus size: 16
100352349 ATCTGAAAAT
100352359 AATAAAT-AATAA-AA
1 AATAAATAAATAATAA
100352373 TAATAAATAAA-AATAA
1 -AATAAATAAATAATAA
*
100352389 AATAAACTAAACTAAAAA
1 AATAAA-TAAA-TAATAA
*
100352407 AATAAAAAAATAATAA
1 AATAAATAAATAATAA
100352423 AA
1 AA
100352425 ATTAGGTTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
15 15 0.35
16 15 0.35
17 3 0.07
18 10 0.23
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (16 bp):
AATAAATAAATAATAA
Found at i:100352375 original size:8 final size:8
Alignment explanation
Indices: 100352354--100352424 Score: 63
Period size: 8 Copynumber: 8.5 Consensus size: 8
100352344 TTAATATCTG
100352354 AAAATAAT
1 AAAATAAT
100352362 -AAATAAT
1 AAAATAAT
100352369 AAAATAAT
1 AAAATAAT
*
100352377 AAATAAAAAT
1 -AA-AATAAT
100352387 AAAATAAACT
1 AAAAT-AA-T
* *
100352397 AAACTAAA
1 AAAATAAT
*
100352405 AAAATAAA
1 AAAATAAT
100352413 AAAATAAT
1 AAAATAAT
100352421 AAAA
1 AAAA
100352425 ATTAGGTTAC
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
7 7 0.13
8 27 0.52
9 8 0.15
10 10 0.19
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (8 bp):
AAAATAAT
Found at i:100353173 original size:15 final size:15
Alignment explanation
Indices: 100353153--100353182 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
100353143 CATTTTATTT
*
100353153 ATATTAGGATAATTA
1 ATATTAAGATAATTA
100353168 ATATTAAGATAATTA
1 ATATTAAGATAATTA
100353183 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:100360880 original size:20 final size:20
Alignment explanation
Indices: 100360833--100360880 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
100360823 TTAAATTCTA
100360833 AAAGATAATTACAAATAAAT
1 AAAGATAATTACAAATAAAT
*
100360853 AAATATAATTA-AAGATAAAT
1 AAAGATAATTACAA-ATAAAT
*
100360873 GAAGATAA
1 AAAGATAA
100360881 ATCCTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (20 bp):
AAAGATAATTACAAATAAAT
Found at i:100360933 original size:14 final size:13
Alignment explanation
Indices: 100360897--100360933 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
100360887 AAATTTAAAT
100360897 CTAAATAATTATC
1 CTAAATAATTATC
*
100360910 CTTAATAATTATC
1 CTAAATAATTATC
100360923 CTAATATAATT
1 CTAA-ATAATT
100360934 GAAATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (13 bp):
CTAAATAATTATC
Found at i:100364480 original size:18 final size:18
Alignment explanation
Indices: 100364447--100364518 Score: 58
Period size: 19 Copynumber: 3.9 Consensus size: 18
100364437 CTTAAATATA
*
100364447 ATAAAAAATA-AAAAATT
1 ATAAAAAATATATAAATT
*
100364464 ATAAAAAATATTTAAATT
1 ATAAAAAATATATAAATT
* *
100364482 GATATAAACT-TATAGATATT
1 -ATAAAAAATATATA-A-ATT
100364502 ATAAAAAATATAATAAA
1 ATAAAAAATAT-ATAAA
100364519 ACTAATAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
17 10 0.24
18 8 0.19
19 16 0.38
20 5 0.12
21 3 0.07
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (18 bp):
ATAAAAAATATATAAATT
Found at i:100364873 original size:16 final size:18
Alignment explanation
Indices: 100364852--100364888 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
100364842 CAGTTCAATT
100364852 AAATAAAAAAT-TAA-AA
1 AAATAAAAAATATAATAA
100364868 AAATAAAAAATATAATAA
1 AAATAAAAAATATAATAA
100364886 AAA
1 AAA
100364889 AAGTTGGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.58
17 3 0.16
18 5 0.26
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (18 bp):
AAATAAAAAATATAATAA
Found at i:100365016 original size:8 final size:9
Alignment explanation
Indices: 100365004--100365208 Score: 76
Period size: 9 Copynumber: 21.6 Consensus size: 9
100364994 CCAATTTAAG
*
100365004 TTTTTATGA
1 TTTTTATAA
100365013 TTTTTATAA
1 TTTTTATAA
*
100365022 TTTTATTTCAA
1 TTTT-TAT-AA
* *
100365033 TTTTAATAC
1 TTTTTATAA
*
100365042 TTTTAAT-A
1 TTTTTATAA
*
100365050 TTTTTATGAC
1 TTTTTAT-AA
* *
100365060 GTTTTATGA
1 TTTTTATAA
*
100365069 TTTTTTTAGTA
1 TTTTTATA--A
*
100365080 TTTTAATACA
1 TTTTTATA-A
100365090 TTTTTATAA
1 TTTTTATAA
*
100365099 TATTTTAAATA
1 T-TTTTATA-A
100365110 TGTTTTATTAA
1 T-TTTTA-TAA
100365121 -TTTTATAA
1 TTTTTATAA
100365129 TTTATTATAA
1 TTT-TTATAA
* *
100365139 ATTTTA-CA
1 TTTTTATAA
100365147 TCTTTTATAA
1 T-TTTTATAA
* *
100365157 TATTTATAT
1 TTTTTATAA
*
100365166 TTTTTTTAA
1 TTTTTATAA
*
100365175 GTTTATATCAA
1 -TTTTTAT-AA
* *
100365186 TTTTCATAT
1 TTTTTATAA
100365195 TTTTTGA-AA
1 TTTTT-ATAA
100365204 TTTTT
1 TTTTT
100365209 TTCTGATTTT
Statistics
Matches: 143, Mismatches: 37, Indels: 32
0.67 0.17 0.15
Matches are distributed among these distances:
8 10 0.07
9 65 0.45
10 44 0.31
11 23 0.16
12 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:100365072 original size:47 final size:46
Alignment explanation
Indices: 100365004--100365093 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 46
100364994 CCAATTTAAG
*
100365004 TTTTTATGATTTTTATAATTTTATTTCA-ATTTTAATAC-TTTTAATA
1 TTTTTATGAGTTTTATAATTTT-TTT-AGATTTTAATACATTTTAATA
*
100365050 TTTTTATGACGTTTTATGATTTTTTTAGTATTTTAATACATTTT
1 TTTTTATGA-GTTTTATAATTTTTTTAG-ATTTTAATACATTTT
100365094 TATAATATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
45 1 0.03
46 12 0.32
47 21 0.55
48 4 0.11
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (46 bp):
TTTTTATGAGTTTTATAATTTTTTTAGATTTTAATACATTTTAATA
Found at i:100365104 original size:10 final size:10
Alignment explanation
Indices: 100365078--100365161 Score: 54
Period size: 10 Copynumber: 8.5 Consensus size: 10
100365068 ATTTTTTTAG
100365078 TATTTTAATACA
1 TATTTT-ATA-A
100365090 T-TTTTATAA
1 TATTTTATAA
100365099 TATTTTA-AA
1 TATTTTATAA
*
100365108 TATGTTT-TAT
1 TAT-TTTATAA
100365118 TAATTTTATAA
1 T-ATTTTATAA
100365129 T-TTATTATAA
1 TATT-TTATAA
*
100365139 -ATTTTA-CA
1 TATTTTATAA
*
100365147 TCTTTTATAA
1 TATTTTATAA
100365157 TATTT
1 TATTT
100365162 ATATTTTTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
8 1 0.02
9 17 0.30
10 29 0.51
11 9 0.16
12 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.60
Consensus pattern (10 bp):
TATTTTATAA
Found at i:100365115 original size:21 final size:20
Alignment explanation
Indices: 100365068--100365161 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
100365058 ACGTTTTATG
* *
100365068 ATTTTTTTAGTATTTTAATAC
1 ATTTTTATAATATTTTAA-AC
*
100365089 ATTTTTATAATATTTTAAAT
1 ATTTTTATAATATTTTAAAC
* *
100365109 ATGTTTTATTA-ATTTTATA-
1 AT-TTTTATAATATTTTAAAC
100365128 ATTTATTATAA-ATTTT--AC
1 ATTT-TTATAATATTTTAAAC
100365146 ATCTTTTATAATATTT
1 AT-TTTTATAATATTT
100365162 ATATTTTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
17 1 0.02
18 10 0.16
19 18 0.29
20 10 0.16
21 23 0.37
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTTTATAATATTTTAAAC
Found at i:100368872 original size:9 final size:9
Alignment explanation
Indices: 100368854--100368899 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
100368844 TGAGTTTTCG
*
100368854 AATTCAAAT
1 AATTCGAAT
100368863 AATTCGAAT
1 AATTCGAAT
*
100368872 AATTCAAAT
1 AATTCGAAT
*
100368881 AATTTGAAT
1 AATTCGAAT
*
100368890 AAATCGAAT
1 AATTCGAAT
100368899 A
1 A
100368900 TGAAACTATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.33
Consensus pattern (9 bp):
AATTCGAAT
Found at i:100368875 original size:18 final size:18
Alignment explanation
Indices: 100368854--100368891 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
100368844 TGAGTTTTCG
100368854 AATTCAAATAATTCGAAT
1 AATTCAAATAATTCGAAT
*
100368872 AATTCAAATAATTTGAAT
1 AATTCAAATAATTCGAAT
100368890 AA
1 AA
100368892 ATCGAATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (18 bp):
AATTCAAATAATTCGAAT
Found at i:100371236 original size:10 final size:10
Alignment explanation
Indices: 100371217--100371248 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
100371207 ATTTAGGATT
100371217 TTAT-TTTAA
1 TTATCTTTAA
100371226 TTATCTTTAA
1 TTATCTTTAA
100371236 TTATCTTTAA
1 TTATCTTTAA
100371246 TTA
1 TTA
100371249 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:100372000 original size:18 final size:19
Alignment explanation
Indices: 100371963--100371998 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
100371953 ATTTTTCCTC
100371963 ATTTCAATTTCTGCAATTT
1 ATTTCAATTTCTGCAATTT
100371982 ATTT-AATTTC-GCAATTT
1 ATTTCAATTTCTGCAATTT
100371999 TAATTCACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 6 0.35
19 4 0.24
ACGTcount: A:0.28, C:0.14, G:0.06, T:0.53
Consensus pattern (19 bp):
ATTTCAATTTCTGCAATTT
Done.