Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 126 of 211
Found at i:39819217 original size:18 final size:18
Alignment explanation
Indices: 39819194--39819229 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
39819184 ATCTCTCTTT
39819194 ATTTTATAACAACATAGA
1 ATTTTATAACAACATAGA
39819212 ATTTTATAACAACATAGA
1 ATTTTATAACAACATAGA
39819230 CTTAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (18 bp):
ATTTTATAACAACATAGA
Found at i:39819375 original size:22 final size:23
Alignment explanation
Indices: 39819327--39819378 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
39819317 TGATTTAAAC
* *
39819327 AAATACTCATATTTATATAATTA
1 AAATATTCATAATTATATAATTA
39819350 AAATATTCATAATT-TATAA-TA
1 AAATATTCATAATTATATAATTA
39819371 TAAATATT
1 -AAATATT
39819379 TATTAGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 2 0.08
22 12 0.46
23 12 0.46
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATATTCATAATTATATAATTA
Found at i:39819584 original size:24 final size:24
Alignment explanation
Indices: 39819557--39819604 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
39819547 ACATGTATGT
*
39819557 TTAATAAAATTAAAAATTATAATA
1 TTAACAAAATTAAAAATTATAATA
*
39819581 TTAACAAAATTAAAATTTATAATA
1 TTAACAAAATTAAAAATTATAATA
39819605 CTTTATATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
TTAACAAAATTAAAAATTATAATA
Found at i:39820034 original size:7 final size:7
Alignment explanation
Indices: 39820033--39820064 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
39820023 TAAAATATAA
39820033 AAATATT
1 AAATATT
39820040 AAATATT
1 AAATATT
39820047 AAATATT
1 AAATATT
39820054 AAATATT
1 AAATATT
39820061 AAAT
1 AAAT
39820065 TAAAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATATT
Found at i:39820050 original size:22 final size:22
Alignment explanation
Indices: 39819999--39820064 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
39819989 AAAATGTTAT
*
39819999 TATTATATATAAAAAT-TTAATA
1 TATTAAATATAAAAATATTAA-A
* *
39820021 AATAAAATATAAAAATATTAAA
1 TATTAAATATAAAAATATTAAA
*
39820043 TATTAAATAT-TAAATATTAAA
1 TATTAAATATAAAAATATTAAA
39820064 T
1 T
39820065 TAAAATAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 11 0.30
22 22 0.59
23 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TATTAAATATAAAAATATTAAA
Found at i:39824147 original size:18 final size:20
Alignment explanation
Indices: 39824132--39824177 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
39824122 ATGTAAAAAT
39824132 GAAAGAAGAAAAAAAAACTGC
1 GAAAGAAGAAAAAAAAACT-C
*
39824153 GAAAGAAGAAAAAGGAAACTC
1 GAAAGAAGAAAAA-AAAACTC
39824174 GAAA
1 GAAA
39824178 TCACCTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.65, C:0.09, G:0.22, T:0.04
Consensus pattern (20 bp):
GAAAGAAGAAAAAAAAACTC
Found at i:39825171 original size:132 final size:131
Alignment explanation
Indices: 39824901--39825209 Score: 428
Period size: 132 Copynumber: 2.3 Consensus size: 131
39824891 AGTCTGATAC
* * * *
39824901 GATCTGCTCTACTACAACTTCAGAGAGATAAGACCTG-TAAT-TTTCAACCTACTCCACTGCTGC
1 GATCTGCTCCACTACTACTT-AGGGAGATAAGATCTGCT-ATCTTT-AACCTACTCCACTGCTGC
* *
39824964 TCAGGGAGACAAGGCTCATTGGCTTAAATCTCTTCCTACTATCCTGGAAAGATAAGATTTGTCGT
63 TCAGGGAGACAAGGCTCATTGGCTTAAATCTCTTCCCACTATCCTGGAAAGATAAGATTTGTCAT
39825029 ATTT
128 ATTT
* *
39825033 GATCTGCTCCACTACTTCTTAGGGAGATAAGATCTGCTATCTTTAACCTACTCCGCTGCTGCTCA
1 GATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCTATCTTTAACCTACTCCACTGCTGCTCA
* *
39825098 GGGAGACAAGGC-C-TGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTTAT
66 GGGAGACAAGGCTCAT--TGGCTTAAATCT-CTTCCCACTATCCTGGAAAGATAAGATTTGTCAT
*
39825161 CTTT
128 ATTT
*
39825165 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCTATCTTTA
1 GATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCTATCTTTA
39825210 CTGATCATTT
Statistics
Matches: 160, Mismatches: 12, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
129 1 0.01
130 1 0.01
131 60 0.38
132 98 0.61
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (131 bp):
GATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCTATCTTTAACCTACTCCACTGCTGCTCA
GGGAGACAAGGCTCATTGGCTTAAATCTCTTCCCACTATCCTGGAAAGATAAGATTTGTCATATT
T
Found at i:39825193 original size:44 final size:44
Alignment explanation
Indices: 39825034--39825209 Score: 151
Period size: 44 Copynumber: 4.0 Consensus size: 44
39825024 GTCGTATTTG
*
39825034 ATCTGCTCCACTACTTCTTAGGGAGATAAGATCTGCTATCTTTA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCTATCTTTA
* * * * * * ** * ** *
39825078 ACCTACTCCGCTGCTGCTCAGGGAGACAAGGCCTGGTGGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCTATCTTTA
* * * *
39825122 ATCTGCTTCCCACTA-T-CTT-GGAAAGATAAGATTTGTTATCTTTG
1 ATCTGC-T-CCACTACTGCTTAGG-GAGATAAGATCTGCTATCTTTA
39825166 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCTATCTTTA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCTATCTTTA
39825210 CTGATCATTT
Statistics
Matches: 94, Mismatches: 32, Indels: 12
0.68 0.23 0.09
Matches are distributed among these distances:
42 6 0.06
43 4 0.04
44 76 0.81
45 4 0.04
46 4 0.04
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (44 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCTATCTTTA
Found at i:39838487 original size:18 final size:20
Alignment explanation
Indices: 39838472--39838517 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
39838462 ATGTAAAAAT
39838472 GAAAGAAGAAAAAAAAACTGC
1 GAAAGAAGAAAAAAAAACT-C
*
39838493 GAAAGAAGAAAAAGGAAACTC
1 GAAAGAAGAAAAA-AAAACTC
39838514 GAAA
1 GAAA
39838518 TCACCTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.65, C:0.09, G:0.22, T:0.04
Consensus pattern (20 bp):
GAAAGAAGAAAAAAAAACTC
Found at i:39847493 original size:8 final size:8
Alignment explanation
Indices: 39847468--39847526 Score: 68
Period size: 8 Copynumber: 7.5 Consensus size: 8
39847458 CAATGATGTG
*
39847468 AATAATAA
1 AATATTAA
39847476 AATATATAA
1 AATAT-TAA
39847485 AATATT-A
1 AATATTAA
39847492 AATATT-A
1 AATATTAA
39847499 AATATTAA
1 AATATTAA
*
39847507 AATATAAA
1 AATATTAA
*
39847515 AATATTAG
1 AATATTAA
39847523 AATA
1 AATA
39847527 ATAATAATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
7 14 0.31
8 23 0.51
9 8 0.18
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (8 bp):
AATATTAA
Found at i:39847494 original size:7 final size:7
Alignment explanation
Indices: 39847479--39847526 Score: 51
Period size: 7 Copynumber: 6.4 Consensus size: 7
39847469 ATAATAAAAT
*
39847479 ATATAAA
1 ATATTAA
39847486 ATATTAA
1 ATATTAA
39847493 ATATTAA
1 ATATTAA
39847500 ATATTAAA
1 ATATT-AA
*
39847508 ATATAAAA
1 ATAT-TAA
39847516 ATATTAGA
1 ATATTA-A
39847524 ATA
1 ATA
39847527 ATAATAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
7 19 0.54
8 16 0.46
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (7 bp):
ATATTAA
Found at i:39847496 original size:14 final size:14
Alignment explanation
Indices: 39847479--39847526 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 14
39847469 ATAATAAAAT
39847479 ATATAAAATATTAA
1 ATATAAAATATTAA
*
39847493 ATATTAAATATTAAA
1 ATATAAAATATT-AA
39847508 ATATAAAAATATTAGA
1 ATAT-AAAATATTA-A
39847524 ATA
1 ATA
39847527 ATAATAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 11 0.38
15 7 0.24
16 11 0.38
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
ATATAAAATATTAA
Found at i:39847537 original size:31 final size:31
Alignment explanation
Indices: 39847468--39847537 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
39847458 CAATGATGTG
*
39847468 AATAA-TAAAATATATAAAATATTAAATATT
1 AATAATTAAAATATATAAAATATTAAATAAT
39847498 AA-ATATTAAAATATA-AAAATATTAGAATAAT
1 AATA-ATTAAAATATATAAAATATTA-AATAAT
39847529 AATAATTAA
1 AATAATTAA
39847538 TATTGAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
29 1 0.03
30 12 0.34
31 21 0.60
32 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (31 bp):
AATAATTAAAATATATAAAATATTAAATAAT
Found at i:39847556 original size:17 final size:18
Alignment explanation
Indices: 39847505--39847556 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 18
39847495 ATTAAATATT
39847505 AAAATATAAAAATATTAGA
1 AAAATA-AAAAATATTAGA
*
39847524 ATAATAATAATTAATATT-GA
1 AAAATAA-AA--AATATTAGA
39847544 AAAATAAAAAATA
1 AAAATAAAAAATA
39847557 AAATAGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 4 0.14
18 1 0.04
19 9 0.32
20 8 0.29
21 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (18 bp):
AAAATAAAAAATATTAGA
Found at i:39847704 original size:25 final size:25
Alignment explanation
Indices: 39847676--39847827 Score: 94
Period size: 25 Copynumber: 5.9 Consensus size: 25
39847666 CGTGATAATA
*
39847676 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAGTG
39847701 TTAAAAATATATACATAATATA--G
1 TTAAAAATATATACATAATATAGTG
* * *
39847724 TT-AAGATATATACATAAGATAACATG
1 TTAAAAATATATACATAATAT-A-GTG
* * * *
39847750 TAGAAAATATATATATAAATAATATAATA
1 T--TAAA-A-ATATATACATAATATAGTG
* * * *
39847779 TTAAAGATATATAAATAAAATAGTA
1 TTAAAAATATATACATAATATAGTG
* *
39847804 TAAAAATATATATACGTAATATAG
1 TTAAAA-ATATATACATAATATAG
39847828 AATTTAAAAT
Statistics
Matches: 100, Mismatches: 17, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
22 16 0.16
23 4 0.04
25 42 0.42
26 16 0.16
27 3 0.03
29 5 0.05
30 1 0.01
31 13 0.13
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (25 bp):
TTAAAAATATATACATAATATAGTG
Found at i:39847797 original size:14 final size:13
Alignment explanation
Indices: 39847753--39847817 Score: 53
Period size: 13 Copynumber: 4.8 Consensus size: 13
39847743 TAACATGTAG
*
39847753 AAAATATATATAT
1 AAAATATATAAAT
39847766 -AAATAATATAATATT
1 AAAAT-ATATAA-A-T
39847781 AAAGATATATAAAT
1 AAA-ATATATAAAT
39847795 AAAATAGTATAAA-
1 AAAATA-TATAAAT
*
39847808 AATATATATA
1 AAAATATATA
39847818 CGTAATATAG
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
12 8 0.18
13 13 0.30
14 11 0.25
15 2 0.05
16 8 0.18
17 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (13 bp):
AAAATATATAAAT
Found at i:39848439 original size:29 final size:29
Alignment explanation
Indices: 39848371--39848512 Score: 162
Period size: 29 Copynumber: 4.8 Consensus size: 29
39848361 TAGGTACAAG
* *
39848371 TGGTGGTGGAGCAAGTGTGGTTAGTGGAGT
1 TGGTGGTGGA-AAAGTGTGGCTAGTGGAGT
* ** * *
39848401 AGGTAATGGAGCAA-TGTGGCTAGTGGATT
1 TGGTGGTGGA-AAAGTGTGGCTAGTGGAGT
*
39848430 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAA-GTGTGGCTAGTGGAGT
39848460 TGGTGGTGGAAAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGTGTGGCTAGTGGAGT
39848489 T-GTGGTGGAAAAGGTGTGGCTAGT
1 TGGTGGTGGAAAA-GTGTGGCTAGT
39848513 TGAGAAAAGT
Statistics
Matches: 97, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
28 13 0.13
29 47 0.48
30 37 0.38
ACGTcount: A:0.22, C:0.04, G:0.46, T:0.27
Consensus pattern (29 bp):
TGGTGGTGGAAAAGTGTGGCTAGTGGAGT
Found at i:39848452 original size:30 final size:30
Alignment explanation
Indices: 39848415--39848512 Score: 164
Period size: 29 Copynumber: 3.3 Consensus size: 30
39848405 AATGGAGCAA
*
39848415 TGTGGCTAGTGGATTTGGTGGTGGAAAAGG
1 TGTGGCTAGTGGAGTTGGTGGTGGAAAAGG
*
39848445 AGTGGCTAGTGGAGTTGGTGGTGGAAAA-G
1 TGTGGCTAGTGGAGTTGGTGGTGGAAAAGG
39848474 TGTGGCTAGTGGAGTT-GTGGTGGAAAAGG
1 TGTGGCTAGTGGAGTTGGTGGTGGAAAAGG
39848503 TGTGGCTAGT
1 TGTGGCTAGT
39848513 TGAGAAAAGT
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
28 11 0.17
29 27 0.42
30 26 0.41
ACGTcount: A:0.20, C:0.04, G:0.47, T:0.29
Consensus pattern (30 bp):
TGTGGCTAGTGGAGTTGGTGGTGGAAAAGG
Found at i:39849306 original size:72 final size:72
Alignment explanation
Indices: 39849230--39849777 Score: 633
Period size: 72 Copynumber: 7.6 Consensus size: 72
39849220 TCAGCGAGCC
* * *
39849230 AGGCTCAACTCACATCTCGCAATATGAGTTG-CTTTTGAAAAACAGAAATTTAAAATACCTCAGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATTGAAAATACCTCAGC
39849294 GTGTCCTG
65 GTGTCCTG
* *** *
39849302 AGGCTCAACTCACCTCTCGCAATATGCGTTGATTTTTGTTTACAGAAATTGAAATTACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAGCG
39849367 TGTCCTG
66 TGTCCTG
* * *
39849374 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTTACGAACAGAAAATTGAAGAACAGAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGA-AAACAG-AAATT---G---A-AAA
** **
39849439 TTGAAATTACCTCAGTGT-CTG
56 -T--ACCT-CAGC-GTGTCCTG
39849460 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAACAGAAATTGAAAATACCTCA---
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAGCG
*
39849521 TGTGCTG
66 TGTCCTG
39849528 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAACAGAAATTG-AAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAGCG
39849591 TGT-CTG
66 TGTCCTG
*
39849597 AGGCTCAACTCA-CTCT-GCAATATGAGTTGA-TTTTGAAAACA-AAATTGAAATTACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAGCG
39849658 TGTCCTG
66 TGTCCTG
* * *
39849665 AGGCTCAACTCA-TTCTCGCAATATGAGTTGATTTTTTTAACAACAG-AATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAA-AACAGAAATTGAAAATACCTCAG
39849728 CGTGTCCTG
64 CGTGTCCTG
*
39849737 AGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
39849778 AAAAATTAAA
Statistics
Matches: 416, Mismatches: 31, Indels: 60
0.82 0.06 0.12
Matches are distributed among these distances:
66 11 0.03
67 47 0.11
68 75 0.18
69 29 0.07
70 5 0.01
71 13 0.03
72 132 0.32
73 27 0.06
74 5 0.01
75 8 0.02
76 1 0.00
78 1 0.00
79 1 0.00
81 1 0.00
82 7 0.02
83 6 0.01
85 7 0.02
86 36 0.09
87 4 0.01
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (72 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAGCG
TGTCCTG
Found at i:39849441 original size:14 final size:15
Alignment explanation
Indices: 39849415--39849443 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39849405 ATTTTTTTAC
39849415 GAACAGAAAATTGAA
1 GAACAGAAAATTGAA
39849430 GAACAG-AAATTGAA
1 GAACAGAAAATTGAA
39849444 ATTACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.59, C:0.07, G:0.21, T:0.14
Consensus pattern (15 bp):
GAACAGAAAATTGAA
Found at i:39849625 original size:67 final size:70
Alignment explanation
Indices: 39849431--39849776 Score: 509
Period size: 68 Copynumber: 5.0 Consensus size: 70
39849421 AAAATTGAAG
39849431 AACAGAAATTGAAATTACCTCA--GTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 AACAGAAATTGAAATTACCTCAGCGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
39849494 TTTGA
66 TTTGA
* *
39849499 AACAGAAATTGAAAATACCTCA-TGTG-CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 AACAGAAATTGAAATTACCTCAGCGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
39849562 TTTGA
66 TTTGA
39849567 AACAGAAATTGAAA-TACCTCAGCGTGTCTGAGGCTCAACTCA-CTCT-GCAATATGAGTTGA-T
1 AACAGAAATTGAAATTACCTCAGCGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
39849628 TTTGAA
66 TTTG-A
*
39849634 AACA-AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCA-TTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAATTACCTCAGCGTGT-CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
*
39849697 TTTTTTAA
64 -TTTTTGA
*
39849705 CAACAG-AATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA
1 -AACAGAAATTGAAATTACCTCAGCGTGT-CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
39849769 -TTTTGA
64 TTTTTGA
39849775 AA
1 AA
39849777 AAAAAATTAA
Statistics
Matches: 258, Mismatches: 7, Indels: 25
0.89 0.02 0.09
Matches are distributed among these distances:
66 14 0.05
67 39 0.15
68 102 0.40
69 34 0.13
70 5 0.02
71 1 0.00
72 46 0.18
73 17 0.07
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (70 bp):
AACAGAAATTGAAATTACCTCAGCGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
TTTGA
Found at i:39849906 original size:69 final size:71
Alignment explanation
Indices: 39849788--39849960 Score: 214
Period size: 69 Copynumber: 2.5 Consensus size: 71
39849778 AAAAATTAAA
* * * **
39849788 AGGCTTAACTCAC-TCTCGCAATATGAG-TCA-ATTTAAAACATAAACTAAAAATACCTCGGCGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACATAAACTAAAAATACCTCAACGT
39849850 GCCCCG
66 GCCCCG
*
39849856 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAA-A-AAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACATAAACTAAAAATACCTCAACGT
* **
39849919 GTCTTG
66 GCCCCG
39849925 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT
39849961 CCTTGGAAAG
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
68 13 0.14
69 69 0.75
70 3 0.03
71 7 0.08
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (71 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACATAAACTAAAAATACCTCAACGT
GCCCCG
Found at i:39849956 original size:188 final size:190
Alignment explanation
Indices: 39849597--39849960 Score: 513
Period size: 188 Copynumber: 1.9 Consensus size: 190
39849587 AGCGTGTCTG
* * * * * *
39849597 AGGCTCAACTCACTCTGCAATATGAGTTGATTTTGAAAACAAAATTGAAATTACCTCAGCGTGTC
1 AGGCTCAACTCACTCTGCAATATGAGTTCAATTTGAAAACAAAACTAAAAATACCTCAGCGTGCC
* * * *
39849662 CTGAGGCTCAACTCATTCTCGCAATATGAGTTGATTTTTTTAACAACAGAATTGAAATTACCTCA
66 CCGAGGCTCAACTCATTCTCGCAATATGAGTTGA-TTTTTTAACAACAAAATTAAAAATACCTCA
*
39849727 GCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAAAAATTAAA
130 ACGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAAAAATTAAA
* *
39849788 AGGCTTAACTCACTCTCGCAATATGAG-TCAATTT-AAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACTCT-GCAATATGAGTTCAATTTGAAAACA-AAACTAAAAATACCTCAGCGTG
39849851 CCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTAA-AA-AAAATTAAAAATACCT
64 CCCCGAGGCTCAACTCA-TTCTCGCAATATGAGTTGATTTTTTAACAACAAAATTAAAAATACCT
* * *
39849913 CAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTT
128 CAACGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTT
39849961 CCTTGGAAAG
Statistics
Matches: 154, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
188 57 0.37
189 2 0.01
190 13 0.08
191 53 0.34
192 29 0.19
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (190 bp):
AGGCTCAACTCACTCTGCAATATGAGTTCAATTTGAAAACAAAACTAAAAATACCTCAGCGTGCC
CCGAGGCTCAACTCATTCTCGCAATATGAGTTGATTTTTTAACAACAAAATTAAAAATACCTCAA
CGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAAAAATTAAA
Found at i:39858209 original size:12 final size:12
Alignment explanation
Indices: 39858189--39858224 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
39858179 TGGGATATGC
*
39858189 AATGTATGAATG
1 AATGCATGAATG
39858201 AATGCATGAATG
1 AATGCATGAATG
39858213 AATGCATGAATG
1 AATGCATGAATG
39858225 TCAAATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:39859815 original size:16 final size:15
Alignment explanation
Indices: 39859794--39859843 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 15
39859784 CAATGATGTG
39859794 AATATAAAATATATAA
1 AATATAAAATAT-TAA
39859810 AATAT-AAATATTAA
1 AATATAAAATATTAA
*
39859824 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
39859840 AATA
1 AATA
39859844 ATAATAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 8 0.26
15 6 0.19
16 17 0.55
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:39859820 original size:22 final size:22
Alignment explanation
Indices: 39859794--39859836 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39859784 CAATGATGTG
*
39859794 AATA-TAAAATATATAAAATATA
1 AATATTAAAATAT-CAAAATATA
39859816 AATATTAAAATATCAAAATAT
1 AATATTAAAATATCAAAATAT
39859837 TAGAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
AATATTAAAATATCAAAATATA
Found at i:39859828 original size:8 final size:8
Alignment explanation
Indices: 39859794--39859843 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
39859784 CAATGATGTG
39859794 AATA-TAA
1 AATATTAA
39859801 AATATATAA
1 AATAT-TAA
39859810 AATA-T-A
1 AATATTAA
39859816 AATATTAA
1 AATATTAA
*
39859824 AATATCAA
1 AATATTAA
*
39859832 AATATTAG
1 AATATTAA
39859840 AATA
1 AATA
39859844 ATAATAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
6 5 0.14
7 6 0.17
8 18 0.50
9 7 0.19
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (8 bp):
AATATTAA
Found at i:39860020 original size:25 final size:25
Alignment explanation
Indices: 39859992--39860056 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
39859982 CGTGATAATA
*
39859992 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAGTG
39860017 TTAAAAATATATACATAATATA--G
1 TTAAAAATATATACATAATATAGTG
*
39860040 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
39860057 GATAACATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 14 0.37
23 3 0.08
25 21 0.55
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (25 bp):
TTAAAAATATATACATAATATAGTG
Found at i:39860114 original size:14 final size:13
Alignment explanation
Indices: 39860070--39860126 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 13
39860060 AACATGTAGA
*
39860070 AAAATATATATAT
1 AAAATATATAAAT
39860083 -AAATAATATAATATT
1 AAAAT-ATATAA-A-T
39860098 AAAGATATATAAAT
1 AAA-ATATATAAAT
39860112 AAAATAGTATAAAT
1 AAAATA-TATAAAT
39860126 A
1 A
39860127 TATATATACG
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
12 4 0.11
13 8 0.22
14 13 0.35
15 2 0.05
16 8 0.22
17 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (13 bp):
AAAATATATAAAT
Found at i:39860780 original size:30 final size:30
Alignment explanation
Indices: 39860746--39860814 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
39860736 TGGAGCAAGT
*
39860746 GTGGCTAGTGGATTTGGTGGTGGAAAAGGA
1 GTGGCTAGTGGAGTTGGTGGTGGAAAAGGA
*
39860776 GTGGCTAGTGGAGTTGGTGGTGGAAAAGGT
1 GTGGCTAGTGGAGTTGGTGGTGGAAAAGGA
39860806 GTGGCTAGT
1 GTGGCTAGT
39860815 TGAGAAAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.20, C:0.04, G:0.48, T:0.28
Consensus pattern (30 bp):
GTGGCTAGTGGAGTTGGTGGTGGAAAAGGA
Found at i:39864916 original size:31 final size:30
Alignment explanation
Indices: 39864881--39864940 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
39864871 AATTAGTAAC
*
39864881 AATAA-AATTATAGTTTAATTTTCTTAAAAAT
1 AATAATAATT-TAATTTAATTTT-TTAAAAAT
39864912 AATAATAATTTAATTTAATTTTTTAAAAA
1 AATAATAATTTAATTTAATTTTTTAAAAA
39864941 CTATAAAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 7 0.26
31 16 0.59
32 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (30 bp):
AATAATAATTTAATTTAATTTTTTAAAAAT
Found at i:39865818 original size:151 final size:150
Alignment explanation
Indices: 39865608--39865902 Score: 518
Period size: 151 Copynumber: 2.0 Consensus size: 150
39865598 CGCGATATAT
*
39865608 ATCATCATCATCATCAAGGCATGTTTTGTTCACTCTCCTCCAAACCTTCCAGCAGTACTGCTGGG
1 ATCATCATCATCATCAAGGCATGTTTTGTTCAATCTCCTCCAAACCTTCCAGCAGTACTGCTGGG
* *
39865673 GGGTAGTGTGTAGCATATTGCCGGAAGCGTTTGAGGGAGACTGAGCAACCAATTCCTTGTAAGCT
66 GAGTAGTGTGTAGCATATTGCCGGAAGCGTTTGAGGGAGACTGAGCAACCAATTCCTTCTAAGCT
39865738 TTAAAAAATATATATATCATC
131 TT-AAAAATATATATATCATC
39865759 ATCATCATCATCATCAAGGCATGTTTTGTTCAATCTCCTCCAAACCTTCCAGCAGTACTGCTGGG
1 ATCATCATCATCATCAAGGCATGTTTTGTTCAATCTCCTCCAAACCTTCCAGCAGTACTGCTGGG
* * *
39865824 GAGTAGTGTGTAGCATATTGCTGGAAGCGTTTGAGGGAGATTGAGCAACCGATTCCTTCTAAGCT
66 GAGTAGTGTGTAGCATATTGCCGGAAGCGTTTGAGGGAGACTGAGCAACCAATTCCTTCTAAGCT
*
39865889 TTAATAATATATAT
131 TTAAAAATATATAT
39865903 TCTTCTCTTG
Statistics
Matches: 137, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
150 11 0.08
151 126 0.92
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (150 bp):
ATCATCATCATCATCAAGGCATGTTTTGTTCAATCTCCTCCAAACCTTCCAGCAGTACTGCTGGG
GAGTAGTGTGTAGCATATTGCCGGAAGCGTTTGAGGGAGACTGAGCAACCAATTCCTTCTAAGCT
TTAAAAATATATATATCATC
Found at i:39867355 original size:20 final size:19
Alignment explanation
Indices: 39867322--39867367 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
39867312 TTAATGTGGT
39867322 AATATAATAAAAAATAAAA
1 AATATAATAAAAAATAAAA
*
39867341 AATACTAATAGAAAAT-AAA
1 AATA-TAATAAAAAATAAAA
39867360 AATATAAT
1 AATATAAT
39867368 CTTTCTCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 4 0.16
19 11 0.44
20 10 0.40
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
AATATAATAAAAAATAAAA
Found at i:39869847 original size:18 final size:19
Alignment explanation
Indices: 39869798--39869844 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
39869788 AAAAAATTAT
*
39869798 AAAAAATTTTAAATTTTAG
1 AAAAAATATTAAATTTTAG
39869817 AAAAAATATTAAATTTTA-
1 AAAAAATATTAAATTTTAG
39869835 ATAAAAATAT
1 A-AAAAATAT
39869845 AAAAAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 1 0.04
19 25 0.96
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAAAATATTAAATTTTAG
Found at i:39869898 original size:20 final size:19
Alignment explanation
Indices: 39869875--39869923 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
39869865 TAGAAATTTT
39869875 TTTATAAAAACTGTAAAAAA
1 TTTATAAAAACTGT-AAAAA
* * *
39869895 TTTAAAAAAATTGTAAAAT
1 TTTATAAAAACTGTAAAAA
39869914 TTTATAAAAA
1 TTTATAAAAA
39869924 TCATAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (19 bp):
TTTATAAAAACTGTAAAAA
Found at i:39869932 original size:20 final size:20
Alignment explanation
Indices: 39869874--39869932 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
39869864 TTAGAAATTT
39869874 TTTTATAAAAA-CTGTAAAAA
1 TTTTATAAAAATC-GTAAAAA
* * *
39869894 ATTTAAAAAAATTGT-AAAA
1 TTTTATAAAAATCGTAAAAA
*
39869913 TTTTATAAAAATCATAAAAA
1 TTTTATAAAAATCGTAAAAA
39869933 ATTAACGACC
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (20 bp):
TTTTATAAAAATCGTAAAAA
Found at i:39870146 original size:67 final size:67
Alignment explanation
Indices: 39870069--39870215 Score: 163
Period size: 67 Copynumber: 2.2 Consensus size: 67
39870059 ATAATTTTTA
* *
39870069 TAAATTTTTTTACA-AAATTTATATTTCTTTACATTTTGTATAATTTTCTTACGA-TTGTATAAA
1 TAAATTTTTTTA-ATAAATTTAAATTTCTATACATTTTGTATAA-TTTCTTACGATTTGTATAAA
39870132 ATTT
64 ATTT
*** * * * * *
39870136 TAAATTTTTTTAATTTTTTTAAATTTCTATATATTTTTTATAATTTGTTATGATTTTTATAAAAT
1 TAAATTTTTTTAATAAATTTAAATTTCTATACATTTTGTATAATTTCTTACGATTTGTATAAAAT
39870201 TT
66 TT
39870203 TACAATTTTTTTA
1 TA-AATTTTTTTA
39870216 TATTTTTTAC
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
66 9 0.13
67 48 0.72
68 10 0.15
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (67 bp):
TAAATTTTTTTAATAAATTTAAATTTCTATACATTTTGTATAATTTCTTACGATTTGTATAAAAT
TT
Found at i:39870150 original size:9 final size:9
Alignment explanation
Indices: 39870133--39870266 Score: 60
Period size: 10 Copynumber: 14.4 Consensus size: 9
39870123 TTGTATAAAA
*
39870133 TTTTAAATT
1 TTTTTAATT
39870142 TTTTTAATT
1 TTTTTAATT
39870151 TTTTTAAATT
1 TTTTT-AATT
* *
39870161 TCTATATATT
1 TTTTTA-ATT
39870171 TTTTATAATT
1 TTTT-TAATT
* *
39870181 TGTTATGATT
1 T-TTTTAATT
* *
39870191 TTTATAAAAT
1 TTT-TTAATT
**
39870201 TTTACAATT
1 TTTTTAATT
39870210 TTTTTATATT
1 TTTTTA-ATT
*
39870220 TTTTACAATT
1 TTTT-TAATT
*
39870230 TTTAT-ATT
1 TTTTTAATT
39870238 TTTTCTAA--
1 TTTT-TAATT
39870246 TTTTTAA-T
1 TTTTTAATT
*
39870254 ATTTTAATT
1 TTTTTAATT
39870263 TTTT
1 TTTT
39870267 ATTAAAATTT
Statistics
Matches: 92, Mismatches: 22, Indels: 22
0.68 0.16 0.16
Matches are distributed among these distances:
7 3 0.03
8 16 0.17
9 28 0.30
10 40 0.43
11 5 0.05
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (9 bp):
TTTTTAATT
Found at i:39870157 original size:19 final size:19
Alignment explanation
Indices: 39870061--39870250 Score: 93
Period size: 19 Copynumber: 9.8 Consensus size: 19
39870051 TTGGTACGAT
39870061 AATTTTTATAAATTTTTTTA
1 AATTTTTAT-AATTTTTTTA
** *
39870081 CAAAATTTAT-ATTTCTTTA
1 -AATTTTTATAATTTTTTTA
* *
39870100 CATTTTGTATAATTTTCTTA
1 AATTTT-TATAATTTTTTTA
* * **
39870120 CGA-TTGTATAA-AATTTTA
1 -AATTTTTATAATTTTTTTA
*
39870138 AATTTTTTTAATTTTTTTA
1 AATTTTTATAATTTTTTTA
*
39870157 AATTTCTAT-ATATTTTTTA
1 AATTTTTATAAT-TTTTTTA
* *
39870176 TAATTTGTTATGATTTTTATA
1 -AATTT-TTATAATTTTTTTA
* *
39870197 AAATTTTACAATTTTTTTA
1 AATTTTTATAATTTTTTTA
* * *
39870216 TATTTTTTACAATTTTTAT-
1 -AATTTTTATAATTTTTTTA
* *
39870235 ATTTTTTCTAATTTTT
1 AATTTTTATAATTTTT
39870251 AATATTTTAA
Statistics
Matches: 128, Mismatches: 31, Indels: 23
0.70 0.17 0.13
Matches are distributed among these distances:
17 1 0.01
18 29 0.23
19 46 0.36
20 33 0.26
21 17 0.13
22 2 0.02
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (19 bp):
AATTTTTATAATTTTTTTA
Found at i:39870181 original size:10 final size:10
Alignment explanation
Indices: 39870133--39870250 Score: 88
Period size: 9 Copynumber: 12.3 Consensus size: 10
39870123 TTGTATAAAA
39870133 TTTTA-AATT
1 TTTTATAATT
39870142 TTTT-TAATT
1 TTTTATAATT
*
39870151 TTTT-TAAAT
1 TTTTATAATT
*
39870160 TTCTATATATT
1 TTTTATA-ATT
39870171 TTTTATAATT
1 TTTTATAATT
* *
39870181 TGTTATGA-T
1 TTTTATAATT
**
39870190 TTTTATAAAA
1 TTTTATAATT
*
39870200 TTTTACAATT
1 TTTTATAATT
39870210 TTTT-TATATT
1 TTTTATA-ATT
*
39870220 TTTTACAA-T
1 TTTTATAATT
39870229 TTTTAT-ATT
1 TTTTATAATT
*
39870238 TTTTCTAATT
1 TTTTATAATT
39870248 TTT
1 TTT
39870251 AATATTTTAA
Statistics
Matches: 85, Mismatches: 16, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
8 1 0.01
9 39 0.46
10 36 0.42
11 9 0.11
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:39870209 original size:29 final size:28
Alignment explanation
Indices: 39870171--39870231 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
39870161 TCTATATATT
*
39870171 TTTTATAA-TTTGTTATGATTTTTATAAAA
1 TTTTACAATTTTGTTAT-ATTTTT-TAAAA
* *
39870200 TTTTACAATTTTTTTATATTTTTTACAA
1 TTTTACAATTTTGTTATATTTTTTAAAA
39870228 TTTT
1 TTTT
39870232 TATATTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 8 0.29
29 13 0.46
30 7 0.25
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (28 bp):
TTTTACAATTTTGTTATATTTTTTAAAA
Found at i:39870222 original size:67 final size:66
Alignment explanation
Indices: 39870086--39870248 Score: 188
Period size: 67 Copynumber: 2.4 Consensus size: 66
39870076 TTTTACAAAA
* * *
39870086 TTTATATTTCTTTACATTTTGTATAATTTTCTTACGATTGTATAAAATTTTAAATTTTTTTAAT-
1 TTTAAATTTC-TTATATTTTTTATAA-TTTCTTACGATTGTATAAAATTTTAAATTTTTTTAATA
39870150 TTT
64 TTT
* * *
39870153 TTTAAATTTCTATATATTTTTTATAATTTGTTATGATTTTTATAAAATTTTACAATTTTTTT-AT
1 TTTAAATTTCT-TATATTTTTTATAATTTCTTACGA-TTGTATAAAATTTTA-AATTTTTTTAAT
39870217 ATTT
63 ATTT
*
39870221 TTTACAATTT-TTATATTTTTTCTAATTT
1 TTTA-AATTTCTTATATTTTTTATAATTT
39870249 TTAATATTTT
Statistics
Matches: 84, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
66 9 0.11
67 53 0.63
68 17 0.20
69 5 0.06
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (66 bp):
TTTAAATTTCTTATATTTTTTATAATTTCTTACGATTGTATAAAATTTTAAATTTTTTTAATATT
T
Found at i:39870249 original size:27 final size:25
Alignment explanation
Indices: 39870209--39870268 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 25
39870199 ATTTTACAAT
*
39870209 TTTTTTATATTTTTTACA-ATTTTTATA
1 TTTTTTATAATTTTTA-ATA-TTTTA-A
*
39870236 TTTTTTCTAATTTTTAATATTTTAA
1 TTTTTTATAATTTTTAATATTTTAA
39870261 TTTTTTAT
1 TTTTTTAT
39870269 TAAAATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 8 0.28
26 6 0.21
27 15 0.52
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTTTTATAATTTTTAATATTTTAA
Found at i:39880780 original size:12 final size:12
Alignment explanation
Indices: 39880763--39880787 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39880753 AACGAGCAAC
39880763 ATAATATAAATG
1 ATAATATAAATG
39880775 ATAATATAAATG
1 ATAATATAAATG
39880787 A
1 A
39880788 AAGCACAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATAATATAAATG
Found at i:39881201 original size:31 final size:30
Alignment explanation
Indices: 39881144--39881214 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 30
39881134 TATGTATTAT
* * *
39881144 ATATATCAAAACAAATTAATATATAAA-AA
1 ATATATAAAAACAAATTAAAAAATAAAGAA
39881173 ATATATAAAAACTAAAATTAAAAAATAAAGAA
1 ATATATAAAAAC--AAATTAAAAAATAAAGAA
*
39881205 A-ATAAAAAAA
1 ATATATAAAAA
39881215 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 11 0.31
31 21 0.60
32 3 0.09
ACGTcount: A:0.72, C:0.04, G:0.01, T:0.23
Consensus pattern (30 bp):
ATATATAAAAACAAATTAAAAAATAAAGAA
Found at i:39882573 original size:23 final size:20
Alignment explanation
Indices: 39882551--39882588 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39882541 CATATCTTTA
*
39882551 TTAAATAATTATATTATTTT
1 TTAAAAAATTATATTATTTT
*
39882571 TTAAGAAATTATATTATT
1 TTAAAAAATTATATTATT
39882589 AAATATTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTAAAAAATTATATTATTTT
Found at i:39883202 original size:15 final size:16
Alignment explanation
Indices: 39883182--39883215 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
39883172 TATTTTTCAA
39883182 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
39883197 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
39883213 AAA
1 AAA
39883216 ATTACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:39887527 original size:15 final size:15
Alignment explanation
Indices: 39887507--39887538 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39887497 CATTTCACTA
*
39887507 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
39887522 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
39887537 TT
1 TT
39887539 TGTATGAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:39895886 original size:43 final size:43
Alignment explanation
Indices: 39895839--39895940 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 43
39895829 TGTAATCTCG
39895839 TATCGATGCCAATATCCCAGCCATGGTCATACACGAAATCACA
1 TATCGATGCCAATATCCCAGCCATGGTCATACACGAAATCACA
* * * * * *
39895882 TATCGATACCAATGTCCTAGCCATGGTCTTACACGAATTCTCA
1 TATCGATGCCAATATCCCAGCCATGGTCATACACGAAATCACA
*
39895925 TATCGACGCC-ATATCC
1 TATCGATGCCAATATCC
39895941 TAGATATGGT
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 5 0.10
43 45 0.90
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (43 bp):
TATCGATGCCAATATCCCAGCCATGGTCATACACGAAATCACA
Found at i:39897800 original size:17 final size:17
Alignment explanation
Indices: 39897778--39897810 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
39897768 TTAGTCACTA
39897778 TTAGGCGAATCCAAGTT
1 TTAGGCGAATCCAAGTT
39897795 TTAGGCGAATCCAAGT
1 TTAGGCGAATCCAAGT
39897811 CTCAGGCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (17 bp):
TTAGGCGAATCCAAGTT
Found at i:39897817 original size:17 final size:17
Alignment explanation
Indices: 39897780--39897817 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
39897770 AGTCACTATT
* *
39897780 AGGCGAATCCAAGTTTT
1 AGGCGAATCCAAGTCTC
39897797 AGGCGAATCCAAGTCTC
1 AGGCGAATCCAAGTCTC
39897814 AGGC
1 AGGC
39897818 ATTGGCAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (17 bp):
AGGCGAATCCAAGTCTC
Found at i:39904344 original size:31 final size:31
Alignment explanation
Indices: 39904309--39904372 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
39904299 AAAATTTCAA
*
39904309 AATTCAAAAAGTACGGAG-ACTAAAATTGATC
1 AATTCAAAAAGTA-GAAGAACTAAAATTGATC
*
39904340 AATTCAAAAAGTATAAGAACTAAAATTGATC
1 AATTCAAAAAGTAGAAGAACTAAAATTGATC
39904371 AA
1 AA
39904373 ATTAAAGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.53, C:0.11, G:0.12, T:0.23
Consensus pattern (31 bp):
AATTCAAAAAGTAGAAGAACTAAAATTGATC
Found at i:39904390 original size:29 final size:28
Alignment explanation
Indices: 39904325--39904392 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 28
39904315 AAAAGTACGG
39904325 AGACTAAAATTGATCAATTCAAAAAGTATA
1 AGACTAAAATTGATCAATT--AAAAGTATA
39904355 AGAACTAAAATTGATCAAATT-AAAGTATAA
1 AG-ACTAAAATTGATC-AATTAAAAGTAT-A
39904385 AGACTAAA
1 AGACTAAA
39904393 TCAACAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
29 13 0.37
30 5 0.14
31 13 0.37
32 4 0.11
ACGTcount: A:0.56, C:0.09, G:0.10, T:0.25
Consensus pattern (28 bp):
AGACTAAAATTGATCAATTAAAAGTATA
Found at i:39905052 original size:32 final size:32
Alignment explanation
Indices: 39905015--39905082 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
39905005 TTTTTGATAT
*
39905015 CTAAATTTGACACTTTTTTCCTAATTTGGTAC
1 CTAAATTTGACACTCTTTTCCTAATTTGGTAC
* *
39905047 CTAAATTTGACTCTCTTTTCTTAATTTGGTAC
1 CTAAATTTGACACTCTTTTCCTAATTTGGTAC
39905079 CTAA
1 CTAA
39905083 TTTTATTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (32 bp):
CTAAATTTGACACTCTTTTCCTAATTTGGTAC
Found at i:39905481 original size:61 final size:59
Alignment explanation
Indices: 39905410--39905522 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
39905400 TTTGAACCTA
* *
39905410 AAAAAAGTTTAGATATCAAATTAGAAAAAAAAATGCCAACTTCAGGTACCAAATTGGGCCC
1 AAAAAAGTTTAGATACCAAATT--AAAAAAAAATGCCAACTTCAAGTACCAAATTGGGCCC
* * * *
39905471 AAAAAAGTTTAGGTACCAAATTAAAAAAAAGTGTCAAGTTCAAGTACCAAAT
1 AAAAAAGTTTAGATACCAAATTAAAAAAAAATGCCAACTTCAAGTACCAAAT
39905523 ATTATATTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 26 0.57
61 20 0.43
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.22
Consensus pattern (59 bp):
AAAAAAGTTTAGATACCAAATTAAAAAAAAATGCCAACTTCAAGTACCAAATTGGGCCC
Found at i:39906110 original size:6 final size:6
Alignment explanation
Indices: 39906099--39906132 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
39906089 GTTTTCTTAC
*
39906099 CAAAAA CAAAAA CAAAAA CAAAAA -AAAAA GAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAA
39906133 CAAGGCTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:39906122 original size:18 final size:17
Alignment explanation
Indices: 39906099--39906132 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39906089 GTTTTCTTAC
39906099 CAAAAACAAAAACAAAAA
1 CAAAAA-AAAAACAAAAA
*
39906117 CAAAAAAAAAAGAAAA
1 CAAAAAAAAAACAAAA
39906133 CAAGGCTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (17 bp):
CAAAAAAAAAACAAAAA
Found at i:39909035 original size:25 final size:23
Alignment explanation
Indices: 39908982--39909028 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 23
39908972 AAGAGCATGT
*
39908982 CAAACTAAATATTTAAATATGTTA
1 CAAA-TAAATATTTAAATAAGTTA
39909006 CAAATAAATATATTAAAATAAGT
1 CAAATAAATAT-TT-AAATAAGT
39909029 ACTAAATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 6 0.30
25 7 0.35
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.34
Consensus pattern (23 bp):
CAAATAAATATTTAAATAAGTTA
Found at i:39909110 original size:3 final size:3
Alignment explanation
Indices: 39909102--39909136 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
39909092 ATAAAGAAGG
39909102 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
39909137 TAATAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:39913807 original size:41 final size:41
Alignment explanation
Indices: 39913762--39913931 Score: 252
Period size: 41 Copynumber: 4.1 Consensus size: 41
39913752 GGCTCGGTGC
* * **
39913762 CTAGCAGGCTTGATGCCAGTGATATGTTTCAGACTTTAAGT
1 CTAGCAGGCTTGATGCCGGTGAAACATTTCAGACTTTAAGT
39913803 CTAGCAGGCTTG-TCGCCGGTGAAACATTTCAGACTTTAAGT
1 CTAGCAGGCTTGAT-GCCGGTGAAACATTTCAGACTTTAAGT
** *
39913844 CTAGCAGGCTTGGCGCCGATGAAACATTTCAGACTTTAAGT
1 CTAGCAGGCTTGATGCCGGTGAAACATTTCAGACTTTAAGT
*
39913885 CTAGCAGGCTTGATGCCGGTGAAACATTTCAGACTTTATGT
1 CTAGCAGGCTTGATGCCGGTGAAACATTTCAGACTTTAAGT
39913926 CTAGCA
1 CTAGCA
39913932 AGCTAAGTGC
Statistics
Matches: 117, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
40 1 0.01
41 116 0.99
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (41 bp):
CTAGCAGGCTTGATGCCGGTGAAACATTTCAGACTTTAAGT
Found at i:39925375 original size:7 final size:7
Alignment explanation
Indices: 39925363--39925416 Score: 65
Period size: 7 Copynumber: 7.9 Consensus size: 7
39925353 TTCTAAAATA
39925363 CATTTCC
1 CATTTCC
39925370 CATTTCC
1 CATTTCC
*
39925377 CACTTCC
1 CATTTCC
39925384 CATTTCC
1 CATTTCC
* *
39925391 C-CTCCC
1 CATTTCC
39925397 CATTTCC
1 CATTTCC
*
39925404 TATTTCC
1 CATTTCC
39925411 CATTTC
1 CATTTC
39925417 TCCGTGCATC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
6 4 0.11
7 34 0.89
ACGTcount: A:0.13, C:0.46, G:0.00, T:0.41
Consensus pattern (7 bp):
CATTTCC
Found at i:39925400 original size:13 final size:14
Alignment explanation
Indices: 39925368--39925403 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
39925358 AAATACATTT
*
39925368 CCCATTTCCCACTT
1 CCCATTTCCCACTC
39925382 CCCATTTCCC-CTC
1 CCCATTTCCCACTC
39925395 CCCATTTCC
1 CCCATTTCC
39925404 TATTTCCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.11, C:0.56, G:0.00, T:0.33
Consensus pattern (14 bp):
CCCATTTCCCACTC
Found at i:39925672 original size:6 final size:6
Alignment explanation
Indices: 39925662--39925695 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
39925652 GCTTTTTGCT
*
39925662 TTTTGA TTTTGA TTTTAA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
39925696 TGCTGTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.71
Consensus pattern (6 bp):
TTTTGA
Found at i:39925997 original size:128 final size:128
Alignment explanation
Indices: 39925769--39926023 Score: 465
Period size: 128 Copynumber: 2.0 Consensus size: 128
39925759 GGAATTTTGG
39925769 TTTTGATTTTAATTTTTACTATTAACCCTATTTCCTGTTCGAACAATTAGACTAATAGGTTTAAA
1 TTTTGATTTTAATTTTTACTATTAACCCTATTTCCTGTTCGAACAATTAGACTAATAGGTTTAAA
*
39925834 GCAGTCAAAGATTGTATTGACATTTTTAACCTTTAAATGTTGCGTGTTTTAATCTTGTTATGA
66 GCAGTCAAAGATTGTATTGACATATTTAACCTTTAAATGTTGCGTGTTTTAATCTTGTTATGA
* * *
39925897 TTTTGATTTTAATTTTTGCTGTTAACCCTATTTCCTGTTCGAATAATTAGACTAATAGGTTTAAA
1 TTTTGATTTTAATTTTTACTATTAACCCTATTTCCTGTTCGAACAATTAGACTAATAGGTTTAAA
*
39925962 GCAGTCAAAGATTGTGTTGACATATTTAACCTTTAAATGTTGCGTGTTTTAATCTTGTTATG
66 GCAGTCAAAGATTGTATTGACATATTTAACCTTTAAATGTTGCGTGTTTTAATCTTGTTATG
39926024 CTTAAAATGA
Statistics
Matches: 122, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 122 1.00
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (128 bp):
TTTTGATTTTAATTTTTACTATTAACCCTATTTCCTGTTCGAACAATTAGACTAATAGGTTTAAA
GCAGTCAAAGATTGTATTGACATATTTAACCTTTAAATGTTGCGTGTTTTAATCTTGTTATGA
Found at i:39926376 original size:28 final size:28
Alignment explanation
Indices: 39926343--39926397 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
39926333 TATTTGATTT
39926343 AACTGACAGTGAGAGTGTCCTTTTGAAG
1 AACTGACAGTGAGAGTGTCCTTTTGAAG
*
39926371 AACTGATAGTGAGAGTGTCCTTTTGAA
1 AACTGACAGTGAGAGTGTCCTTTTGAA
39926398 CCCTTGTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (28 bp):
AACTGACAGTGAGAGTGTCCTTTTGAAG
Found at i:39928417 original size:26 final size:26
Alignment explanation
Indices: 39928384--39928434 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
39928374 ATGGGAAAGA
*
39928384 AAAAACTAAGTTAGGAATTTGGGGAG
1 AAAAACTAAGTCAGGAATTTGGGGAG
*
39928410 AAAAACTAAGTCAGGGATTTGGGGA
1 AAAAACTAAGTCAGGAATTTGGGGA
39928435 AAACAATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.06, G:0.31, T:0.22
Consensus pattern (26 bp):
AAAAACTAAGTCAGGAATTTGGGGAG
Found at i:39931998 original size:27 final size:27
Alignment explanation
Indices: 39931941--39931998 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
39931931 AATTTACTTT
*
39931941 TTATATAAATTTAATTTAATTATTATT
1 TTATATAAATTTAATTTAATTATTATA
*
39931968 TTATAT-AATATT-ATTTCATTATATATA
1 TTATATAAAT-TTAATTTAATTAT-TATA
39931995 TTAT
1 TTAT
39931999 TATTTAGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (27 bp):
TTATATAAATTTAATTTAATTATTATA
Found at i:39932467 original size:19 final size:19
Alignment explanation
Indices: 39932443--39932484 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
39932433 AAAATTGAAG
39932443 GGAGACTTGGTCAGAAATT
1 GGAGACTTGGTCAGAAATT
*
39932462 GGAGACTTGGTCAGCAATT
1 GGAGACTTGGTCAGAAATT
39932481 GGAG
1 GGAG
39932485 TTTTGACCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.12, G:0.36, T:0.24
Consensus pattern (19 bp):
GGAGACTTGGTCAGAAATT
Found at i:39939577 original size:10 final size:10
Alignment explanation
Indices: 39939562--39939592 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
39939552 ATTACAAATC
39939562 ATTTTCTATT
1 ATTTTCTATT
39939572 ATTTTCTATT
1 ATTTTCTATT
39939582 ATTTTCATATT
1 ATTTTC-TATT
39939593 GAAATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (10 bp):
ATTTTCTATT
Found at i:39940190 original size:24 final size:25
Alignment explanation
Indices: 39940150--39940196 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
39940140 AGTTATCATC
39940150 AAATCCATGATGAAGACAAAAAAAG
1 AAATCCATGATGAAGACAAAAAAAG
*
39940175 AAATCCA-GATGCAGACAAAAAA
1 AAATCCATGATGAAGACAAAAAA
39940197 GTCTTGCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.60, C:0.15, G:0.15, T:0.11
Consensus pattern (25 bp):
AAATCCATGATGAAGACAAAAAAAG
Found at i:39940212 original size:72 final size:72
Alignment explanation
Indices: 39940095--39940234 Score: 176
Period size: 72 Copynumber: 1.9 Consensus size: 72
39940085 GGCAACCTGA
* * * * *
39940095 AAAAAAAGAAATCCACATACCAACAACAAAGATTGGCAATGTGGAAGTTATCATCAAATCCATGA
1 AAAAAAAGAAATCCACATACCAACAAAAAAGATTGGCAACGTGGAAGCTATCATCAAAACAATGA
39940160 TGAAGAC
66 TGAAGAC
* * *
39940167 AAAAAAAGAAATCCAGAT-GCAGACAAAAAAG-TCTTGCAACGTGGAAGCTATCATCAAAACAAT
1 AAAAAAAGAAATCCACATACCA-ACAAAAAAGAT-TGGCAACGTGGAAGCTATCATCAAAACAAT
39940230 GATGA
64 GATGA
39940235 TGTAAGCAGT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
71 3 0.05
72 55 0.95
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.17
Consensus pattern (72 bp):
AAAAAAAGAAATCCACATACCAACAAAAAAGATTGGCAACGTGGAAGCTATCATCAAAACAATGA
TGAAGAC
Found at i:39941038 original size:18 final size:19
Alignment explanation
Indices: 39941003--39941039 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
39940993 TAAAGTAGAA
39941003 GAGAAAGTAAATAATTTAG
1 GAGAAAGTAAATAATTTAG
*
39941022 GAGAAATTAAA-AATTTAG
1 GAGAAAGTAAATAATTTAG
39941040 ATTTAAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.19, T:0.27
Consensus pattern (19 bp):
GAGAAAGTAAATAATTTAG
Found at i:39942044 original size:14 final size:14
Alignment explanation
Indices: 39942022--39942054 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
39942012 AATTTCTAAC
39942022 AAAAGAAAAGAAGTT
1 AAAAGAAAAGAA-TT
39942037 AAAA-AAAAGAATT
1 AAAAGAAAAGAATT
39942050 AAAAG
1 AAAAG
39942055 TCTTGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.35
14 7 0.41
15 4 0.24
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (14 bp):
AAAAGAAAAGAATT
Found at i:39943384 original size:34 final size:32
Alignment explanation
Indices: 39943345--39943418 Score: 107
Period size: 30 Copynumber: 2.3 Consensus size: 32
39943335 AATTAATAAC
39943345 AAAACCTATAAAAATAATAGGTATAGATGGTAAT
1 AAAACC-ATAAAAATAAT-GGTATAGATGGTAAT
*
39943379 AAAACCAT--AATTAATGGTATAGATGGTAAT
1 AAAACCATAAAAATAATGGTATAGATGGTAAT
39943409 AAAACCATAA
1 AAAACCATAA
39943419 TTAATTATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
30 23 0.62
31 6 0.16
33 2 0.05
34 6 0.16
ACGTcount: A:0.53, C:0.08, G:0.14, T:0.26
Consensus pattern (32 bp):
AAAACCATAAAAATAATGGTATAGATGGTAAT
Found at i:39943398 original size:30 final size:31
Alignment explanation
Indices: 39943359--39943423 Score: 123
Period size: 30 Copynumber: 2.1 Consensus size: 31
39943349 CCTATAAAAA
39943359 TAATAGGTATAGATGGTAATAAAACCATAAT
1 TAATAGGTATAGATGGTAATAAAACCATAAT
39943390 TAAT-GGTATAGATGGTAATAAAACCATAAT
1 TAATAGGTATAGATGGTAATAAAACCATAAT
39943420 TAAT
1 TAAT
39943424 TATAAAGCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 30 0.88
31 4 0.12
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (31 bp):
TAATAGGTATAGATGGTAATAAAACCATAAT
Found at i:39952224 original size:21 final size:19
Alignment explanation
Indices: 39952181--39952228 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
39952171 CGAATATGCC
*
39952181 AACAGAAGCTCGAAAGCTG
1 AACAGAAGCTCGAAAGCTA
*
39952200 AACATAAGCTCGTAAGAGCTA
1 AACAGAAGCTCG-AA-AGCTA
39952221 AACAGAAG
1 AACAGAAG
39952229 TTCATTAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 11 0.46
20 2 0.08
21 11 0.46
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
AACAGAAGCTCGAAAGCTA
Found at i:39955854 original size:10 final size:9
Alignment explanation
Indices: 39955831--39955855 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
39955821 TAGTATAAAT
39955831 ACCCCCTTC
1 ACCCCCTTC
39955840 ACCCCCTTC
1 ACCCCCTTC
39955849 ACCCCCT
1 ACCCCCT
39955856 CATTCCATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.68, G:0.00, T:0.20
Consensus pattern (9 bp):
ACCCCCTTC
Found at i:39957799 original size:26 final size:26
Alignment explanation
Indices: 39957770--39957852 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
39957760 AAAGTAGTTA
39957770 AGTAATACAATTTAATTGTGACATTC
1 AGTAATACAATTTAATTGTGACATTC
* * * ** * *
39957796 AGTACCTAGAAGTTAGAAAAGT-A-GTTA
1 AGTA-ATACAA-TT-TAATTGTGACATTC
39957823 AGTAATACAATTTAATTGTGACATTC
1 AGTAATACAATTTAATTGTGACATTC
39957849 AGTA
1 AGTA
39957853 CCTAGACCCG
Statistics
Matches: 38, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
24 4 0.11
25 3 0.08
26 14 0.37
27 10 0.26
28 3 0.08
29 4 0.11
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.34
Consensus pattern (26 bp):
AGTAATACAATTTAATTGTGACATTC
Found at i:39957810 original size:53 final size:53
Alignment explanation
Indices: 39957750--39957858 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
39957740 TGTAAATAAA
39957750 AGAAGTTAGAAAAGTAGTTAAGTAATACAATTTAATTGTGACATTCAGTACCT
1 AGAAGTTAGAAAAGTAGTTAAGTAATACAATTTAATTGTGACATTCAGTACCT
39957803 AGAAGTTAGAAAAGTAGTTAAGTAATACAATTTAATTGTGACATTCAGTACCT
1 AGAAGTTAGAAAAGTAGTTAAGTAATACAATTTAATTGTGACATTCAGTACCT
39957856 AGA
1 AGA
39957859 CCCGACGATC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.31
Consensus pattern (53 bp):
AGAAGTTAGAAAAGTAGTTAAGTAATACAATTTAATTGTGACATTCAGTACCT
Found at i:39972944 original size:25 final size:25
Alignment explanation
Indices: 39972910--39972965 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
39972900 GATTACTTGA
* *
39972910 AAAGCATTTGTGGTGTATCATTTGG
1 AAAGCCTTTGTGATGTATCATTTGG
39972935 AAAGCCTTTGTGATGTATCATTTGG
1 AAAGCCTTTGTGATGTATCATTTGG
39972960 AAAGCC
1 AAAGCC
39972966 ATCATGGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (25 bp):
AAAGCCTTTGTGATGTATCATTTGG
Found at i:39975978 original size:20 final size:18
Alignment explanation
Indices: 39975953--39975989 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
39975943 ACCTAACATG
39975953 AATTAAATTGAAACCATATT
1 AATTAAATT-AAA-CATATT
39975973 AATTAAATTAAACATAT
1 AATTAAATTAAACATAT
39975990 CAACATCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35
Consensus pattern (18 bp):
AATTAAATTAAACATATT
Found at i:39978991 original size:32 final size:32
Alignment explanation
Indices: 39978955--39979020 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
39978945 CATTTGAGGT
* *
39978955 ATGCTTACTTGGGAGATAATAGCACATTGCCA
1 ATGCTTACTTAGGAGATAATAACACATTGCCA
39978987 ATGCTTACTTAGGAGATAATAACACATTGCCA
1 ATGCTTACTTAGGAGATAATAACACATTGCCA
39979019 AT
1 AT
39979021 AGTTATCTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (32 bp):
ATGCTTACTTAGGAGATAATAACACATTGCCA
Found at i:39979785 original size:24 final size:24
Alignment explanation
Indices: 39979753--39979799 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
39979743 TAGAGTTAGC
39979753 TCTTTGTCGGTGTCAAGAAACTAT
1 TCTTTGTCGGTGTCAAGAAACTAT
*
39979777 TCTTTGTCGGTGTGAAGAAACTA
1 TCTTTGTCGGTGTCAAGAAACTA
39979800 ACCTTGTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (24 bp):
TCTTTGTCGGTGTCAAGAAACTAT
Found at i:39981733 original size:35 final size:35
Alignment explanation
Indices: 39981685--39981752 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
39981675 GAATCTCTCT
* *
39981685 TTTTAATTCTATTTTAGTTTTTCTCTTT-TTTTAGG
1 TTTTAATTCTATTTCAATTTTT-TCTTTGTTTTAGG
39981720 TTTTAGATT-TATTTCAATTTTTTCTTTGTTTTA
1 TTTTA-ATTCTATTTCAATTTTTTCTTTGTTTTA
39981753 TCTTAGGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 5 0.17
35 21 0.72
36 3 0.10
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.69
Consensus pattern (35 bp):
TTTTAATTCTATTTCAATTTTTTCTTTGTTTTAGG
Found at i:39983812 original size:22 final size:23
Alignment explanation
Indices: 39983739--39983811 Score: 85
Period size: 23 Copynumber: 3.0 Consensus size: 23
39983729 AAGAATATAG
*
39983739 AATGGAAAAAATAAAAACCACAAAA
1 AATGGACAAAAT-AAAACCAC-AAA
*
39983764 AATGTGGAC-AAATAAAAACACAAA
1 AA--TGGACAAAATAAAACCACAAA
39983788 AATGGACAAAATAAAACCACAAA
1 AATGGACAAAATAAAACCACAAA
39983811 A
1 A
39983812 TCGTGAACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.12
23 15 0.36
24 5 0.12
25 9 0.21
26 4 0.10
27 4 0.10
ACGTcount: A:0.67, C:0.14, G:0.10, T:0.10
Consensus pattern (23 bp):
AATGGACAAAATAAAACCACAAA
Found at i:39990769 original size:31 final size:31
Alignment explanation
Indices: 39990734--39990829 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
39990724 TGCACAGAGA
* * *
39990734 CTTATCACAGAAAGCTCGCATAGGGAGCTTG
1 CTTATCATAGAGAGCTCACATAGGGAGCTTG
39990765 CTTATCATAGAGAGCTCACATAGGGAGCTTG
1 CTTATCATAGAGAGCTCACATAGGGAGCTTG
39990796 CTTATCATAGAGAGCTCACATAGGGAGCTTG
1 CTTATCATAGAGAGCTCACATAGGGAGCTTG
39990827 CTT
1 CTT
39990830 GAAAACACTT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (31 bp):
CTTATCATAGAGAGCTCACATAGGGAGCTTG
Found at i:39990779 original size:18 final size:18
Alignment explanation
Indices: 39990752--39990811 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
39990742 AGAAAGCTCG
*
39990752 CATAGGGAGCTTGCTTAT
1 CATAGAGAGCTTGCTTAT
39990770 CATAGAGAGC-T-C--A-
1 CATAGAGAGCTTGCTTAT
*
39990783 CATAGGGAGCTTGCTTAT
1 CATAGAGAGCTTGCTTAT
39990801 CATAGAGAGCT
1 CATAGAGAGCT
39990812 CACATAGGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
13 9 0.26
14 2 0.06
15 1 0.03
16 1 0.03
17 2 0.06
18 19 0.56
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (18 bp):
CATAGAGAGCTTGCTTAT
Found at i:39990969 original size:27 final size:26
Alignment explanation
Indices: 39990939--39990994 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
39990929 GCACACATAA
* *
39990939 AACATATCTTTAAAATCATAGCTTAAG
1 AACATATCTTGAAAAT-AGAGCTTAAG
*
39990966 AACATATCTTGAAAATAGAGTTTAAG
1 AACATATCTTGAAAATAGAGCTTAAG
39990992 AAC
1 AAC
39990995 TTGAAAACAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.30
Consensus pattern (26 bp):
AACATATCTTGAAAATAGAGCTTAAG
Found at i:39990997 original size:21 final size:22
Alignment explanation
Indices: 39990973--39991015 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
39990963 AAGAACATAT
*
39990973 CTTGAAAATAGAGTTT-AAGAA
1 CTTGAAAACAGAGTTTGAAGAA
39990994 CTTGAAAACAGAGTTTGAAGAA
1 CTTGAAAACAGAGTTTGAAGAA
39991016 AACTTACTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (22 bp):
CTTGAAAACAGAGTTTGAAGAA
Found at i:39991571 original size:27 final size:27
Alignment explanation
Indices: 39991540--39991594 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
39991530 ACTGGCGAAT
* *
39991540 CCTAGTTTGAAACTTAAGTAGCAAACC
1 CCTAGTTCGAAACTTAACTAGCAAACC
* *
39991567 CCTAGTTCGCAACTTACCTAGCAAACC
1 CCTAGTTCGAAACTTAACTAGCAAACC
39991594 C
1 C
39991595 TAGCTCGCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.31, G:0.13, T:0.24
Consensus pattern (27 bp):
CCTAGTTCGAAACTTAACTAGCAAACC
Found at i:39991614 original size:27 final size:26
Alignment explanation
Indices: 39991558--39991633 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 26
39991548 GAAACTTAAG
* *
39991558 TAGCAAACCCCTAGTTCG-CAACTTACC
1 TAGCAAA-CCCTAGCTCGCCAA-ATACC
39991585 TAGCAAACCCTAGCTCGCCAAATACAC
1 TAGCAAACCCTAGCTCGCCAAATAC-C
** *
39991612 TAGTGAACCCTAGCTCACCAAA
1 TAGCAAACCCTAGCTCGCCAAA
39991634 CATACTGGCG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 12 0.29
27 30 0.71
ACGTcount: A:0.34, C:0.36, G:0.12, T:0.18
Consensus pattern (26 bp):
TAGCAAACCCTAGCTCGCCAAATACC
Found at i:39991646 original size:27 final size:27
Alignment explanation
Indices: 39991584--39991647 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
39991574 CGCAACTTAC
* * *
39991584 CTAGCAAACCCTAGCTCGCCAAATACA
1 CTAGCGAACCCTAGCTCACCAAACACA
* *
39991611 CTAGTGAACCCTAGCTCACCAAACATA
1 CTAGCGAACCCTAGCTCACCAAACACA
*
39991638 CTGGCGAACC
1 CTAGCGAACC
39991648 TACATGCAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.34, C:0.36, G:0.14, T:0.16
Consensus pattern (27 bp):
CTAGCGAACCCTAGCTCACCAAACACA
Found at i:39993653 original size:21 final size:21
Alignment explanation
Indices: 39993629--39993669 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
39993619 TATATTTATC
39993629 ATGTTGATAATTTATTGAATG
1 ATGTTGATAATTTATTGAATG
*
39993650 ATGTTTATAATTTATTGAAT
1 ATGTTGATAATTTATTGAAT
39993670 AATATTTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (21 bp):
ATGTTGATAATTTATTGAATG
Found at i:39993677 original size:21 final size:21
Alignment explanation
Indices: 39993635--39993678 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
39993625 TATCATGTTG
* *
39993635 ATAATTTATTGAATGATGTTT
1 ATAATTTATTGAATAATATTT
39993656 ATAATTTATTGAATAATATTT
1 ATAATTTATTGAATAATATTT
39993677 AT
1 AT
39993679 GAGTAGAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (21 bp):
ATAATTTATTGAATAATATTT
Found at i:39996647 original size:30 final size:30
Alignment explanation
Indices: 39996613--39996674 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
39996603 GCTAGAAAAC
*
39996613 TAAACCTATAAAATATCATGAGGACCACAA
1 TAAACCCATAAAATATCATGAGGACCACAA
39996643 TAAACCCATAAAATATCATGAGGACCACAA
1 TAAACCCATAAAATATCATGAGGACCACAA
39996673 TA
1 TA
39996675 TTAATCAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.50, C:0.21, G:0.10, T:0.19
Consensus pattern (30 bp):
TAAACCCATAAAATATCATGAGGACCACAA
Found at i:39999765 original size:140 final size:140
Alignment explanation
Indices: 39999505--40000332 Score: 1035
Period size: 140 Copynumber: 6.0 Consensus size: 140
39999495 TATAACAAAA
* * * * * *
39999505 GTTGACATAGTGTTGGACAAAGCTGACTCTTATTTAATTGCTGCATTAGGCATACATATCCCAAC
1 GTTGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGTGTTGCCTTAGGCATGCATATCCCAAC
* ** * * *
39999570 CCTTATACAAAGAGTTGGCCAAAGCGTATATCAGTAAGTCTATCCCAACAATTAGGAAAGTGCCG
66 CCTTATACAAAGAGTTGGCCAAAGCGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTCG
39999635 GCCCAAAAGT
131 GCCCAAAAGT
* *
39999645 GTTGGCATAGTGTTGTACAAAGCCGACTCTTATTTAAGTGTTGCCTTAGGAAAT-CATATCCCAA
1 GTTGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGTGTTGCCTTAGG-CATGCATATCCCAA
* * * *
39999709 CCCTTTTACAAAGAGTTGGCCAAAGTGTATGTTGGCAAGTTTATCCCAACACTTAGGAAAGTTTC
65 CCCTTATACAAAGAGTTGGCCAAAGCGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTC
39999774 GGCCCAAAAGT
130 GGCCCAAAAGT
* * * * *
39999785 GTCGGCATAGCT-TTGGACAAAGTCGACTCTTATTTAAGTGTTACCTTAAGTATGCATATCCCAA
1 GTTGGCATAG-TGTTGGACAAAGCCGACTCTTATTTAAGTGTTGCCTTAGGCATGCATATCCCAA
* * * *
39999849 CCCTTATACAAAGAGTTGGCTAAAGCATATGTCT-GTAAGTCTATCCCAACATTTAGGAAAGTGT
65 CCCTTATACAAAGAGTTGGCCAAAGCGTATGT-TGGCAAGTCTATCCCAACACTTAGGAAAGTGT
39999913 CGGCCCAAAAGT
129 CGGCCCAAAAGT
* * *
39999925 GTTGTCATAGTGTTGGTCAAAGCCCACTCTTATTTAAGTGTTGCCTTAGGCATGCATATCCCAAC
1 GTTGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGTGTTGCCTTAGGCATGCATATCCCAAC
* * * *
39999990 CTTTATATAAAGAGTTGGCCAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAAGAAAGTGTCG
66 CCTTATACAAAGAGTTGGCCAAAGCGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTCG
40000055 GCCCAAAAGT
131 GCCCAAAAGT
* * * *
40000065 GTTGGCATAGTGTTGGACAAAGCTGACCCTTATTTAAGCGTTGCCTTAGGCATGAATATCCCAAC
1 GTTGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGTGTTGCCTTAGGCATGCATATCCCAAC
* * * * **
40000130 CCTTATAGAAAGAGTTGGCCAACGTGTCTGTCAAG-AAGTCTATCCCAACACTTAGGAAAGTGT-
66 CCTTATACAAAGAGTTGGCCAAAGCGTATGT-TGGCAAGTCTATCCCAACACTTAGGAAAGTGTC
40000193 ----C------
130 GGCCCAAAAGT
* **
40000194 ---GGCATAGTATTGGACAAAGCCGACTCTTATTTAACCGTTGCCTTAGGCATGCATATCCCAAC
1 GTTGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGTGTTGCCTTAGGCATGCATATCCCAAC
* * *
40000256 CCTTATACAAAGAGTTGGCCAAATCATATGTTGGCAAGTCTATCCCAACACTTAGAAAAGTGTCG
66 CCTTATACAAAGAGTTGGCCAAAGCGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTCG
*
40000321 TCCCAAAAGT
131 GCCCAAAAGT
40000331 GT
1 GT
40000333 CGTCTTAGGA
Statistics
Matches: 591, Mismatches: 76, Indels: 43
0.83 0.11 0.06
Matches are distributed among these distances:
125 1 0.00
126 109 0.18
131 1 0.00
135 1 0.00
139 3 0.01
140 471 0.80
141 5 0.01
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (140 bp):
GTTGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGTGTTGCCTTAGGCATGCATATCCCAAC
CCTTATACAAAGAGTTGGCCAAAGCGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGTCG
GCCCAAAAGT
Found at i:40000295 original size:126 final size:126
Alignment explanation
Indices: 40000059--40000320 Score: 375
Period size: 126 Copynumber: 2.1 Consensus size: 126
40000049 GTGTCGGCCC
* * * *
40000059 AAAAGTGTTGGCATAGTGTTGGACAAAGCTGACCCTTATTTAAGCGTTGCCTTAGGCATGAATAT
1 AAAAGTGTCGGCATAGTATTGGACAAAGCCGACCCTTATTTAACCGTTGCCTTAGGCATGAATAT
* * * *
40000124 CCCAACCCTTATAGAAAGAGTTGGCCAACGTGTCTGTCAAGAAGTCTATCCCAACACTTAG
66 CCCAACCCTTATACAAAGAGTTGGCCAACATATATGTCAAGAAGTCTATCCCAACACTTAG
* * *
40000185 GAAAGTGTCGGCATAGTATTGGACAAAGCCGACTCTTATTTAACCGTTGCCTTAGGCATGCATAT
1 AAAAGTGTCGGCATAGTATTGGACAAAGCCGACCCTTATTTAACCGTTGCCTTAGGCATGAATAT
**
40000250 CCCAACCCTTATACAAAGAGTTGGCCAA-ATCATATGT-TGGCAAGTCTATCCCAACACTTAG
66 CCCAACCCTTATACAAAGAGTTGGCCAACAT-ATATGTCAAG-AAGTCTATCCCAACACTTAG
40000311 AAAAGTGTCG
1 AAAAGTGTCG
40000321 TCCCAAAAGT
Statistics
Matches: 120, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
125 2 0.02
126 118 0.98
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.27
Consensus pattern (126 bp):
AAAAGTGTCGGCATAGTATTGGACAAAGCCGACCCTTATTTAACCGTTGCCTTAGGCATGAATAT
CCCAACCCTTATACAAAGAGTTGGCCAACATATATGTCAAGAAGTCTATCCCAACACTTAG
Found at i:40006877 original size:20 final size:19
Alignment explanation
Indices: 40006834--40006877 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
40006824 AAAAACTTAG
* *
40006834 ATTTTCTAGAAGATATCAT
1 ATTTTCTAGAAAATAACAT
*
40006853 ATTTTCTAGAAAATCAACCT
1 ATTTTCTAGAAAAT-AACAT
40006873 ATTTT
1 ATTTT
40006878 TCGTTAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (19 bp):
ATTTTCTAGAAAATAACAT
Found at i:40008356 original size:41 final size:41
Alignment explanation
Indices: 40008260--40008381 Score: 154
Period size: 41 Copynumber: 2.9 Consensus size: 41
40008250 AATACACCGG
* * *
40008260 TTTGTGGACAAACCACCAGTAATTGTAGATATACTGCCAAAAA
1 TTTGTGGACAAGCCACCAGT-ATTGTAGATAAATTGCC-AAAA
* * *
40008303 TATGTGGACAAGCCACCAGTATTGTATACAAATTGCCAAAA
1 TTTGTGGACAAGCCACCAGTATTGTAGATAAATTGCCAAAA
* *
40008344 TTTGTGGACAAGCCATCAATATTGTAGATAAATTGCCA
1 TTTGTGGACAAGCCACCAGTATTGTAGATAAATTGCCA
40008382 GTACTTCCTC
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 37 0.54
42 13 0.19
43 18 0.26
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (41 bp):
TTTGTGGACAAGCCACCAGTATTGTAGATAAATTGCCAAAA
Found at i:40008594 original size:6 final size:6
Alignment explanation
Indices: 40008585--40008661 Score: 118
Period size: 6 Copynumber: 12.8 Consensus size: 6
40008575 AATGTAGAAT
* * * *
40008585 AGTGAT AGTGAC AGTGAT AGTGAC AGTGAC AGTGAT AGTGAC GGTGAC
1 AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC
40008633 AGTGAC AGTGAC AGTGAC AGTGAC AGTGA
1 AGTGAC AGTGAC AGTGAC AGTGAC AGTGA
40008662 TAGTATCAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.32, C:0.12, G:0.35, T:0.21
Consensus pattern (6 bp):
AGTGAC
Found at i:40025205 original size:29 final size:29
Alignment explanation
Indices: 40025171--40025232 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
40025161 ATGTGGTTAT
*
40025171 GTTTGGGTTATTACCTACTTTGTTACTTA
1 GTTTGGGTTATTACCGACTTTGTTACTTA
40025200 GTTTGGGTTATTACCGACTTTGTTACTTA
1 GTTTGGGTTATTACCGACTTTGTTACTTA
40025229 GTTT
1 GTTT
40025233 TTTTTTGGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.16, C:0.13, G:0.19, T:0.52
Consensus pattern (29 bp):
GTTTGGGTTATTACCGACTTTGTTACTTA
Found at i:40037651 original size:17 final size:18
Alignment explanation
Indices: 40037609--40037652 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
40037599 GCCCAATATT
40037609 CCCACACGCCCGTATGGGG
1 CCCACACGCCCG-ATGGGG
* *
40037628 CCAACACGCCCG-TGTGG
1 CCCACACGCCCGATGGGG
40037645 CCCACACG
1 CCCACACG
40037653 GCCCAATTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 11 0.50
19 11 0.50
ACGTcount: A:0.18, C:0.45, G:0.27, T:0.09
Consensus pattern (18 bp):
CCCACACGCCCGATGGGG
Found at i:40039813 original size:138 final size:138
Alignment explanation
Indices: 40039660--40040080 Score: 682
Period size: 138 Copynumber: 3.1 Consensus size: 138
40039650 TGAACATAGT
*
40039660 TATAATTAATCTATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCAAATTTATTA
1 TATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCAAATTTATTA
* * *
40039725 ATATCAACAATTATATTAATTAATTTCAATTAAAATATAAAAGACATGGAAATTAATATTCTTTT
66 ATATAAAAAATTATATTAATTAATTTCAATCAAAATATAAAAGACATGGAAATTAATATTCTTTT
40039790 GGAAAGAA
131 GGAAAGAA
*
40039798 TATAATTAATATATGAATTTGATTTATACAAAATATTAATTGTATATATTTTA-CTAAATTTATT
1 TATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATC-AAATTTATT
* *
40039862 AATATAAAAAATTATATTAATTACTTTCAATCAAAATATAAAAGACATGGAAATTAATATTATTT
65 AATATAAAAAATTATATTAATTAATTTCAATCAAAATATAAAAGACATGGAAATTAATATTCTTT
40039927 TGGAAAGAA
130 TGGAAAGAA
* *
40039936 TATAATTAATATATGAATTTGATTCATACAAAACATTAATTGTATATATTTTATCGAATTTATTA
1 TATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCAAATTTATTA
* * * * * * *
40040001 GTATAAATAATTATATTAATTAATTTCGATCAAGATATAAAGGACATGAAAATTAATGTTCTTTT
66 ATATAAAAAATTATATTAATTAATTTCAATCAAAATATAAAAGACATGGAAATTAATATTCTTTT
40040066 GGAAAGAA
131 GGAAAGAA
40040074 TATAATT
1 TATAATT
40040081 TATTTTTCTA
Statistics
Matches: 262, Mismatches: 19, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
137 1 0.00
138 260 0.99
139 1 0.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (138 bp):
TATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCAAATTTATTA
ATATAAAAAATTATATTAATTAATTTCAATCAAAATATAAAAGACATGGAAATTAATATTCTTTT
GGAAAGAA
Found at i:40040187 original size:75 final size:75
Alignment explanation
Indices: 40040059--40040203 Score: 245
Period size: 75 Copynumber: 1.9 Consensus size: 75
40040049 AAAATTAATG
* * * * *
40040059 TTCTTTTGGAAAGAATATAATTTATTTTTCTAACTTTTCATTTGTCTTTTCTATTATTAAGGGAA
1 TTCTTTTGGAAAGAATATAACTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGGGAA
40040124 TAATCCTATA
66 TAATCCTATA
40040134 TTCTTTTGGAAAGAATATAACTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGGGAA
1 TTCTTTTGGAAAGAATATAACTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGGGAA
40040199 TAATC
66 TAATC
40040204 ATGGTTTTCC
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.48
Consensus pattern (75 bp):
TTCTTTTGGAAAGAATATAACTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGGGAA
TAATCCTATA
Found at i:40051304 original size:10 final size:11
Alignment explanation
Indices: 40051291--40051339 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 11
40051281 TAAATAAAGC
40051291 TAATAATA-AT
1 TAATAATATAT
40051301 TAAT-ATATAT
1 TAATAATATAT
*
40051311 T-ATAATAGAT
1 TAATAATATAT
*
40051321 ATAATTATATAT
1 -TAATAATATAT
40051333 TAATAAT
1 TAATAAT
40051340 TATCATCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
9 5 0.16
10 12 0.39
11 7 0.23
12 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
TAATAATATAT
Found at i:40051329 original size:22 final size:20
Alignment explanation
Indices: 40051291--40051339 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
40051281 TAAATAAAGC
40051291 TAATAATAATTAATATATAT
1 TAATAATAATTAATATATAT
40051311 T-ATAATAGATATAATTATATAT
1 TAATAATA-AT-TAA-TATATAT
40051333 TAATAAT
1 TAATAAT
40051340 TATCATCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.24
20 3 0.12
21 3 0.12
22 8 0.32
23 5 0.20
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
TAATAATAATTAATATATAT
Found at i:40051368 original size:11 final size:12
Alignment explanation
Indices: 40051345--40051373 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
40051335 ATAATTATCA
40051345 TCTTTTCTTTTT
1 TCTTTTCTTTTT
40051357 TCTTTT-TTTTT
1 TCTTTTCTTTTT
40051368 TCTTTT
1 TCTTTT
40051374 ATTGAACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TCTTTTCTTTTT
Found at i:40051468 original size:30 final size:30
Alignment explanation
Indices: 40051411--40051472 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
40051401 TCTTTTTGAA
* *
40051411 AATATTTACAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGCAACAAATTTTT
40051441 AATATTTACAAAAAGA-GCAACAAAATTTTT
1 AATATTTACAAAAAGAGGCAAC-AAATTTTT
40051471 AA
1 AA
40051473 AAATAATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.32
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCAACAAATTTTT
Found at i:40071737 original size:26 final size:26
Alignment explanation
Indices: 40071691--40071740 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
40071681 AACCCAAGAA
*
40071691 GTTAAGATAGGGATGTCTACACAACT
1 GTTAAGATAGGGATATCTACACAACT
* *
40071717 GTTAAGATAGGGCTATTTACACAA
1 GTTAAGATAGGGATATCTACACAA
40071741 ATTTTAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (26 bp):
GTTAAGATAGGGATATCTACACAACT
Found at i:40071747 original size:26 final size:26
Alignment explanation
Indices: 40071691--40071747 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
40071681 AACCCAAGAA
* *
40071691 GTTAAGATAGGGATGTCTACACAACT
1 GTTAAGATAGGGATATCTACACAAAT
* *
40071717 GTTAAGATAGGGCTATTTACACAAAT
1 GTTAAGATAGGGATATCTACACAAAT
*
40071743 TTTAA
1 GTTAA
40071748 TATATTGTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (26 bp):
GTTAAGATAGGGATATCTACACAAAT
Found at i:40072939 original size:27 final size:29
Alignment explanation
Indices: 40072909--40072978 Score: 90
Period size: 27 Copynumber: 2.5 Consensus size: 29
40072899 GTATAGTATA
40072909 TGTGGCAAAGCCACCAGTAACAGTA-AT-
1 TGTGGCAAAGCCACCAGTAACAGTATATG
* * *
40072936 TGTGGCAAAGCCACTAGTATCAGTATGTG
1 TGTGGCAAAGCCACCAGTAACAGTATATG
*
40072965 TGTGGCAGAGCCAC
1 TGTGGCAAAGCCAC
40072979 AAGAAATAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 23 0.62
28 1 0.03
29 13 0.35
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.21
Consensus pattern (29 bp):
TGTGGCAAAGCCACCAGTAACAGTATATG
Found at i:40073153 original size:27 final size:27
Alignment explanation
Indices: 40073105--40073377 Score: 329
Period size: 27 Copynumber: 10.2 Consensus size: 27
40073095 CCTAGAAGTC
* * *
40073105 ATTTTGCCCTATCGAGAGTATTTCGATA
1 ATTTTACCC-ATCGAGGGTATTTCGGTA
* * *
40073133 ACTTTACCCATCGGGGGTATTTTGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
*
40073160 ATTTTACCCAT-TAGGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
* *
40073186 ATTTTACCCATAGAGGGTATTTTGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
*
40073213 ATTTTACCCATTGAGGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
* *
40073240 ATTTTACCCAT-TAGGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCGGTA
* * *
40073266 ATTTTACCCATTGAGGGTATTTTGATA
1 ATTTTACCCATCGAGGGTATTTCGGTA
* *
40073293 ATTTTACCCATCGGGGGTATTTCAGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
* *
40073320 ATTTCACTCATCGA-GGTA-TTCGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
40073345 ATTTTACCCATCGAGGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
*
40073372 GTTTTA
1 ATTTTA
40073378 GGCTGATAAC
Statistics
Matches: 211, Mismatches: 30, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
25 18 0.09
26 55 0.26
27 131 0.62
28 7 0.03
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (27 bp):
ATTTTACCCATCGAGGGTATTTCGGTA
Found at i:40073192 original size:53 final size:54
Alignment explanation
Indices: 40073122--40073377 Score: 340
Period size: 53 Copynumber: 4.8 Consensus size: 54
40073112 CCTATCGAGA
* * * *
40073122 GTATTTCGATAACTTTACCCATCGGGGGTATTTTGGTAATTTTACCCATT-AGG
1 GTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATTGAGG
* *
40073175 GTATTTCGGTAATTTTACCCATAGAGGGTATTTTGGTAATTTTACCCATTGAGG
1 GTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATTGAGG
* *
40073229 GTATTTCGGTAATTTTACCCAT-TAGGGTATTTCGATAATTTTACCCATTGAGG
1 GTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATTGAGG
* * * * * * *
40073282 GTATTTTGATAATTTTACCCATCGGGGGTATTTCAGTAATTTCACTCATCGA-G
1 GTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATTGAGG
*
40073335 GTA-TTCGGTAATTTTACCCATCGAGGGTATTTCGGTAGTTTTA
1 GTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTA
40073378 GGCTGATAAC
Statistics
Matches: 179, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
52 34 0.19
53 98 0.55
54 47 0.26
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (54 bp):
GTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATTGAGG
Found at i:40073255 original size:80 final size:80
Alignment explanation
Indices: 40073135--40073377 Score: 346
Period size: 80 Copynumber: 3.0 Consensus size: 80
40073125 TTTCGATAAC
*
40073135 TTTACCCATCGGGGGTATTTTGGTAATTTTACCCATTAGGGTATTTCGGTAATTTTACCCATAGA
1 TTTACCCATCGGGGGTATTTCGGTAATTTTACCCATTAGGGTATTTCGGTAATTTTACCCATAGA
40073200 GGGTATTTTGGTAAT
66 GGGTATTTTGGTAAT
* * * *
40073215 TTTACCCATTGAGGGTATTTCGGTAATTTTACCCATTAGGGTATTTCGATAATTTTACCCATTGA
1 TTTACCCATCGGGGGTATTTCGGTAATTTTACCCATTAGGGTATTTCGGTAATTTTACCCATAGA
*
40073280 GGGTATTTTGATAAT
66 GGGTATTTTGGTAAT
* * * * *
40073295 TTTACCCATCGGGGGTATTTCAGTAATTTCACTCA-TCGAGGTA-TTCGGTAATTTTACCCATCG
1 TTTACCCATCGGGGGTATTTCGGTAATTTTACCCATTAG-GGTATTTCGGTAATTTTACCCATAG
* *
40073358 AGGGTATTTCGGTAGT
65 AGGGTATTTTGGTAAT
40073374 TTTA
1 TTTA
40073378 GGCTGATAAC
Statistics
Matches: 145, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
79 37 0.26
80 108 0.74
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (80 bp):
TTTACCCATCGGGGGTATTTCGGTAATTTTACCCATTAGGGTATTTCGGTAATTTTACCCATAGA
GGGTATTTTGGTAAT
Found at i:40084353 original size:52 final size:52
Alignment explanation
Indices: 40084292--40084439 Score: 149
Period size: 57 Copynumber: 2.8 Consensus size: 52
40084282 GATAAATTGA
* *
40084292 AAATTATTATGGTTTTCTCCAAAAATGAAAATGGAGAAATGAAATCAACTGG
1 AAATGATTATGGTTTTCTCCAAAAATGAAAATGAAGAAATGAAATCAACTGG
* * ***
40084344 AAATGATTATGGTTTTCTCCAAAATAAAAATTAAAATGAAGAAATGGAATCCTTTGG
1 AAATGATTATGGTTTTCTCC-----AAAAATGAAAATGAAGAAATGAAATCAACTGG
* *
40084401 AAATGAATGTGGTTTTCTCC-AAAATGAAAAT-AA-AAATGA
1 AAATGATTATGGTTTTCTCCAAAAATGAAAATGAAGAAATGA
40084440 TCTGGAAATG
Statistics
Matches: 80, Mismatches: 11, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
49 5 0.06
50 2 0.03
51 10 0.12
52 19 0.24
57 44 0.55
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (52 bp):
AAATGATTATGGTTTTCTCCAAAAATGAAAATGAAGAAATGAAATCAACTGG
Found at i:40084387 original size:57 final size:57
Alignment explanation
Indices: 40084312--40084439 Score: 166
Period size: 57 Copynumber: 2.2 Consensus size: 57
40084302 GGTTTTCTCC
* * *
40084312 AAAAATGAAAATGGAGAAATGAAATCAACTGGAAATGATTATGGTTTTCTCCAAAAT
1 AAAAATAAAAATGAAGAAATGAAATCAACTGGAAATGAATATGGTTTTCTCCAAAAT
* * *** *
40084369 AAAAATTAAAATGAAGAAATGGAATCCTTTGGAAATGAATGTGGTTTTCTCCAAAAT
1 AAAAATAAAAATGAAGAAATGAAATCAACTGGAAATGAATATGGTTTTCTCCAAAAT
*
40084426 GAAAATAAAAATGA
1 AAAAATAAAAATGA
40084440 TCTGGAAATG
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (57 bp):
AAAAATAAAAATGAAGAAATGAAATCAACTGGAAATGAATATGGTTTTCTCCAAAAT
Found at i:40085898 original size:20 final size:19
Alignment explanation
Indices: 40085862--40085900 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
40085852 TTTTTCTAAA
* *
40085862 ATTTAAAATTATTAAAATT
1 ATTTAAAACTATAAAAATT
40085881 ATTTAAAAACTATAAAAATT
1 ATTT-AAAACTATAAAAATT
40085901 TATATATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTAAAACTATAAAAATT
Found at i:40089683 original size:42 final size:42
Alignment explanation
Indices: 40089623--40089970 Score: 362
Period size: 42 Copynumber: 8.3 Consensus size: 42
40089613 AAAGAAATCA
*
40089623 TTCATTACATTT-GAAGGCCCAGATGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAG-AGGCCCAGATGTGGAGGTCCATTTACTT
* * ** * * *
40089665 TTCATTACATTTAGAGGCCTAGGCGTGTAAGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTT
*
40089707 TTCATTGCATTTAGAGGCCC-GAGTGTGGAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGA-TGTGGAGGTCCATTTACTT
* *
40089749 TTCATTGCATTTAGAGGCTC-GAAGTGTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAG-A-TGTGGAGGTCCATTTACTT
** * ** *
40089792 TTCATTGCATTTAGAGGCTTAGGTGTGGAAATTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTT
* * * * **
40089834 TTCATTGCATTTAGAGGCTCGGGTATGGAAATCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTT
* **
40089876 TTCATTGCATTTAGAGGCTCAGATGTGGAGGTTAATTTACTT
1 TTCATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTT
* * *
40089918 TACATTGCATTTAAAGGCCCA-AGTGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGA-TGTGGAGGTCCATTTACTT
40089960 TTCATTGCATT
1 TTCATTGCATT
40089971 GTATAATAAG
Statistics
Matches: 262, Mismatches: 39, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
41 2 0.01
42 220 0.84
43 39 0.15
44 1 0.00
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTT
Found at i:40089805 original size:127 final size:126
Alignment explanation
Indices: 40089623--40089970 Score: 434
Period size: 127 Copynumber: 2.8 Consensus size: 126
40089613 AAAGAAATCA
* * *
40089623 TTCATTACATTT-GAAGGCCCAGATGTGGAGGTCCATTTACTTTTCATTACATTTAGAGGCCTAG
1 TTCATTGCATTTAG-AGGCTCAGATGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAG
* * ** *
40089687 GCGTGTAAGTTCATTTACTTTTCATTGCATTTAGAGGCCCGAGTGTGGAGGTTCATTTACTT
65 GAGTGTAAGTTCATTTACTTTTCATTGCATTTAGAGGCCCGAGTATGGAAATCCATTTACTT
* *
40089749 TTCATTGCATTTAGAGGCTC-GAAGTGTGGAGGTCCATTTATTTTTCATTGCATTTAGAGGCTTA
1 TTCATTGCATTTAGAGGCTCAG-A-TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTA
* * * * *
40089813 GGTGTGGAAATTCATTTACTTTTCATTGCATTTAGAGGCTCGGGTATGGAAATCCATTTACTT
64 GGAGTGTAAGTTCATTTACTTTTCATTGCATTTAGAGGCCCGAGTATGGAAATCCATTTACTT
** * * *
40089876 TTCATTGCATTTAGAGGCTCAGATGTGGAGGTTAATTTACTTTACATTGCATTTAAAGGCCCA--
1 TTCATTGCATTTAGAGGCTCAGATGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAGG
*
40089939 AGTGTAGAGGTCCATTTACTTTTCATTGCATT
66 AGTGTA-A-GTTCATTTACTTTTCATTGCATT
40089971 GTATAATAAG
Statistics
Matches: 191, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
124 4 0.02
125 2 0.01
126 71 0.37
127 113 0.59
128 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (126 bp):
TTCATTGCATTTAGAGGCTCAGATGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAGG
AGTGTAAGTTCATTTACTTTTCATTGCATTTAGAGGCCCGAGTATGGAAATCCATTTACTT
Found at i:40091211 original size:21 final size:22
Alignment explanation
Indices: 40091185--40091229 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
40091175 AAAGCTTTGA
*
40091185 TTTTTAAGA-AAAA-TTGTGATT
1 TTTTTAAAACAAAACTT-TGATT
40091206 TTTTTAAAACAAAACTTTGATT
1 TTTTTAAAACAAAACTTTGATT
40091228 TT
1 TT
40091230 GCAAAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 11 0.52
23 2 0.10
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (22 bp):
TTTTTAAAACAAAACTTTGATT
Done.