Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold358
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: 583678
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 4 of 4
Found at i:497520 original size:28 final size:28
Alignment explanation
Indices: 497484--497560 Score: 118
Period size: 28 Copynumber: 2.8 Consensus size: 28
497474 ATTTTTCACA
497484 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
497512 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*** *
497540 CGAGGGGATACTCCATCCCCG
1 ATCGGGGATACTCCAACCCCG
497561 ACTTTATTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.25
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:497637 original size:50 final size:51
Alignment explanation
Indices: 497544--497661 Score: 159
Period size: 50 Copynumber: 2.3 Consensus size: 51
497534 TATTTCCGAG
* *
497544 GGGATACTCCATCCCC-GACTTTATTTCCAAAATATTGATTTCTCACAATCA
1 GGGATACTCCAACCCCAG-CCTTATTTCCAAAATATTGATTTCTCACAATCA
* * * *
497595 GGGATACTTCAACCCCAGCCTTATTT-CTAAATATTGATTTCTCATAATTA
1 GGGATACTCCAACCCCAGCCTTATTTCCAAAATATTGATTTCTCACAATCA
497645 GGGATACTCCAACCCCA
1 GGGATACTCCAACCCCA
497662 TTATTTTCAC
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
50 37 0.63
51 21 0.36
52 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (51 bp):
GGGATACTCCAACCCCAGCCTTATTTCCAAAATATTGATTTCTCACAATCA
Found at i:497670 original size:158 final size:158
Alignment explanation
Indices: 497354--497689 Score: 385
Period size: 158 Copynumber: 2.1 Consensus size: 158
497344 ATTTTTCATA
* ** *
497354 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAAC
* * * ** *
497419 ACTAATTCTCCACAATCGGGGATATTCCAACTCTGATTTTATTTCCAAAACACTAATTTTTCACA
66 ACTAATTCTCCACAATCAGGGATATTCCAACCCAGACCTTATTTCCAAAACACTAATTTCTCACA
* *
497484 ATCGGGGATACTCCAACCCCGTTATTTC
131 ATCAGGGATACTCCAACCCCATTATTTC
* *
497512 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCATCCCCGACTTTATTTCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAAC
* * * * * *
497577 ATTGATT-TCTCACAATCAGGGATACTT-CAACCCCAG-CCTTATTT-CTAAATATTGATTTCTC
66 ACTAATTCTC-CACAATCAGGGATA-TTCCAA-CCCAGACCTTATTTCCAAAACACTAATTTCTC
* *
497638 ATAATTAGGGATACTCCAACCCCATTATTTTC
128 ACAATCAGGGATACTCCAACCCCATTA-TTTC
* *
497670 A-CGAGGATACTCCAATCCCG
1 ATCGGGGATACTCCAACCCCG
497690 ATTTTATTTT
Statistics
Matches: 150, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
157 54 0.36
158 91 0.61
159 5 0.03
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (158 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAAC
ACTAATTCTCCACAATCAGGGATATTCCAACCCAGACCTTATTTCCAAAACACTAATTTCTCACA
ATCAGGGATACTCCAACCCCATTATTTC
Found at i:497846 original size:130 final size:128
Alignment explanation
Indices: 497512--497847 Score: 352
Period size: 129 Copynumber: 2.6 Consensus size: 128
497502 CCGTTATTTC
** * *
497512 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCATCCCCGACTTTATTTCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCC-ATTTTATTTCCAAAAT
* * * *
497577 ATTGATTTCTCACAATCAGGGATACTTCAACCCCAGCCTTATTTCTAAATATTGATTTCTCATA
65 ATTAATTTCTCACAATCAGGGACACTTCAACCCCAGCCTTATTTCTAAATATCGATTTCTCACA
** * * * * ***
497641 ATTAGGGATACTCCAACCCCATTA-TTTTCACGAGGATACTCCAATCCCGATTTTATTTTTGAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTTGA-GGGGATACTCCAA-CCCCATTTTATTTCCAAAA
* * * * ** * *
497705 CATCTATTTTCT-ATAATCGGGGACACTTCAACCCTTGTCTTATTTCTAAATCATCGATTTTTCA
64 TAT-TAATTTCTCACAATCAGGGACACTTCAACCCCAGCCTTATTTCTAAAT-ATCGATTTCTCA
497769 CA
127 CA
* *
497771 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCTTTATTATCTCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCATT-TTATTTCCAAAAT
497836 ATTAAATTTCTC
65 ATT-AATTTCTC
497848 GTCAGGAGAT
Statistics
Matches: 161, Mismatches: 38, Indels: 14
0.76 0.18 0.07
Matches are distributed among these distances:
128 3 0.02
129 84 0.52
130 69 0.43
131 5 0.03
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.35
Consensus pattern (128 bp):
ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCATTTTATTTCCAAAATA
TTAATTTCTCACAATCAGGGACACTTCAACCCCAGCCTTATTTCTAAATATCGATTTCTCACA
Found at i:501437 original size:21 final size:21
Alignment explanation
Indices: 501411--501486 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
501401 CTGCCAAGAA
*
501411 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
501432 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
501452 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
501473 ATGTATCGATACAT
1 ATGTATCGATACAT
501487 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:501457 original size:20 final size:20
Alignment explanation
Indices: 501432--501504 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
501422 CATCTTTTTT
501432 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
501452 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
501473 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
501493 ATGTATCGATAC
1 ATGTATCGATAC
501505 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:501468 original size:41 final size:41
Alignment explanation
Indices: 501411--501504 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
501401 CTGCCAAGAA
*
501411 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
501452 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
501493 ATGTATCGATAC
1 ATGTATCGATAC
501505 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:503975 original size:13 final size:13
Alignment explanation
Indices: 503957--503995 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
503947 ATAATCACCC
*
503957 TGTATCGATACAG
1 TGTATCGATACAA
503970 TGTATCGATACAA
1 TGTATCGATACAA
503983 TGTATCGATACAA
1 TGTATCGATACAA
503996 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:504006 original size:20 final size:20
Alignment explanation
Indices: 503981--504059 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
503971 GTATCGATAC
503981 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
504001 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
504026 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
504046 CATGTATCGATACA
1 AATGTATCGATACA
504060 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:510185 original size:13 final size:13
Alignment explanation
Indices: 510167--510192 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
510157 CAATTTTTTG
510167 TGTATCGATACAT
1 TGTATCGATACAT
510180 TGTATCGATACAT
1 TGTATCGATACAT
510193 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:510257 original size:21 final size:21
Alignment explanation
Indices: 510231--510306 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
510221 CTGCCAAGAA
*
510231 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
510252 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
510272 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
510293 ATGTATCGATACAT
1 ATGTATCGATACAT
510307 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:510277 original size:20 final size:20
Alignment explanation
Indices: 510252--510324 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
510242 CATCTTTTTT
510252 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
510272 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
510293 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
510313 ATGTATCGATAC
1 ATGTATCGATAC
510325 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:510288 original size:41 final size:41
Alignment explanation
Indices: 510231--510324 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
510221 CTGCCAAGAA
*
510231 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
510272 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
510313 ATGTATCGATAC
1 ATGTATCGATAC
510325 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:512795 original size:19 final size:19
Alignment explanation
Indices: 512771--512835 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
512761 TAGCCAAACT
512771 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
512790 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
512803 TGTATCGATACACATAAAATA
1 TGTATCGATACAC--AAAATA
512824 TGTATCGATACA
1 TGTATCGATACA
512836 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.29
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:512807 original size:13 final size:13
Alignment explanation
Indices: 512789--512814 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
512779 TACACAAAAT
512789 ATGTATCGATACA
1 ATGTATCGATACA
512802 ATGTATCGATACA
1 ATGTATCGATACA
512815 CATAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:512812 original size:32 final size:33
Alignment explanation
Indices: 512771--512835 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
512761 TAGCCAAACT
512771 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
512803 TGTATCGATACACATAAAATATGTATCGATACA
1 TGTATCGATACACA-AAAATATGTATCGATACA
512836 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.29
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:515068 original size:21 final size:21
Alignment explanation
Indices: 515035--515084 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
515025 TTGCAAGTTG
*
515035 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
515057 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
515078 AAATAAA
1 AAATAAA
515085 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:516898 original size:15 final size:15
Alignment explanation
Indices: 516878--516908 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
516868 TAAAAATGTC
*
516878 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
516893 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
516908 C
1 C
516909 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:519008 original size:13 final size:13
Alignment explanation
Indices: 518990--519025 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
518980 CATTTTTCTT
518990 TGTATCGATACAA
1 TGTATCGATACAA
*
519003 TGTATCGATACAC
1 TGTATCGATACAA
519016 TGTATCGATA
1 TGTATCGATA
519026 ATATGAACAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:519172 original size:20 final size:20
Alignment explanation
Indices: 519129--519174 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
519119 AAATCTTTTG
519129 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
519150 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
519170 CAAAA
1 CAAAA
519175 CTAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:521548 original size:19 final size:19
Alignment explanation
Indices: 521524--521588 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
521514 TAGCCAAACT
521524 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
521543 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
521556 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAATA
521577 TGTATCGATACA
1 TGTATCGATACA
521589 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:521560 original size:13 final size:13
Alignment explanation
Indices: 521542--521567 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
521532 TACACAAAAT
521542 ATGTATCGATACA
1 ATGTATCGATACA
521555 ATGTATCGATACA
1 ATGTATCGATACA
521568 CAAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:521565 original size:32 final size:33
Alignment explanation
Indices: 521524--521588 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
521514 TAGCCAAACT
521524 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
521556 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
521589 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:522870 original size:103 final size:103
Alignment explanation
Indices: 522661--522873 Score: 284
Period size: 103 Copynumber: 2.0 Consensus size: 103
522651 ATGACCTTAA
**
522661 GGTGATGAAAATTCCCATAATGACCTTAAATTAGGGAGAATACTCTAAATGGTACCAAAATGCAT
1 GGTGATGAAAATTCCCATAATGACCTTAAATT-----GAATACTCTAAATAATACCAAAATGCAT
* * * *
522726 AAAAATGCTAAAGTTATCTTAGATTATATAAAATAACCTAAAT
61 AAAAATGCTAAAGTGATCTTAGATTATACAAAACAAACTAAAT
* * *
522769 GGTGATGAAAATTCCCATAATTATCTTAAATT-AATACTCTAAATAATACTAAAATGCATAGAAA
1 GGTGATGAAAATTCCCATAATGACCTTAAATTGAATACTCTAAATAATACCAAAATGCATA-AAA
522833 ATGCTAAAGTGATCTTAGATTATACAAAACAAACTAAAT
65 ATGCTAAAGTGATCTTAGATTATACAAAACAAACTAAAT
522872 GG
1 GG
522874 CTTTAAAATG
Statistics
Matches: 95, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
102 25 0.26
103 40 0.42
108 30 0.32
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.29
Consensus pattern (103 bp):
GGTGATGAAAATTCCCATAATGACCTTAAATTGAATACTCTAAATAATACCAAAATGCATAAAAA
TGCTAAAGTGATCTTAGATTATACAAAACAAACTAAAT
Found at i:524335 original size:79 final size:78
Alignment explanation
Indices: 524241--524475 Score: 278
Period size: 80 Copynumber: 3.0 Consensus size: 78
524231 GAGCATCCTA
*
524241 AAAAATAATGAGGTTGGAGTATCCCCAATGGTGGAAAATCGATGTTTTAGAAATAAAACTAGGGT
1 AAAAATAACGAGGTTGGAGTATCCCCAATGGTGGAAAATCGATGTTTTA-AAATAAAACTAGGGT
524306 AGGAGTATCCCCTC
65 AGGAGTATCCCCTC
* * * * * *
524320 AGAAATAACGGGGTTGGAGTATCCCCGACGGTGGAAAAATCGATGCTTTAAAGATAAAATCGAGG
1 AAAAATAACGAGGTTGGAGTATCCCCAATGGTGG-AAAATCGATGTTTTAAA-ATAAAA-CTAGG
*
524385 TTA-GAGTATCCCCTC
63 GTAGGAGTATCCCCTC
** * *
524400 AAAAATAACGAGGTTGGAGTATCCCTTATGGTGAAAAAT-TAGTGTTTTAAAAATAAAACT-GGG
1 AAAAATAACGAGGTTGGAGTATCCCCAATGGTGGAAAATCGA-TGTTTT-AAAATAAAACTAGGG
*
524463 TTGGAGTATCCCC
64 TAGGAGTATCCCC
524476 AATAGTGGAA
Statistics
Matches: 131, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
77 3 0.02
78 12 0.09
79 47 0.36
80 63 0.48
81 6 0.05
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (78 bp):
AAAAATAACGAGGTTGGAGTATCCCCAATGGTGGAAAATCGATGTTTTAAAATAAAACTAGGGTA
GGAGTATCCCCTC
Found at i:524508 original size:51 final size:50
Alignment explanation
Indices: 524411--524508 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 50
524401 AAAATAACGA
** * *
524411 GGTTGGAGTATCCCTTATGGTGAAAAATTAGTGTTTTAAAAATAAAACTG
1 GGTTGGAGTATCCCCAATAGTGAAAAATTAGTGCTTTAAAAATAAAACTG
* * *
524461 GGTTGGAGTATCCCCAATAGTGGAAAAATTGGTGCTTTAGAGATAAAA
1 GGTTGGAGTATCCCCAATAGT-GAAAAATTAGTGCTTTAAAAATAAAA
524509 TCGGGCTCAG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
50 18 0.45
51 22 0.55
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.31
Consensus pattern (50 bp):
GGTTGGAGTATCCCCAATAGTGAAAAATTAGTGCTTTAAAAATAAAACTG
Found at i:524549 original size:28 final size:28
Alignment explanation
Indices: 524517--524583 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
524507 AATCGGGCTC
* *
524517 AGAGTATCCCCTCGAAAATAATGGGGTT
1 AGAGTATCCCCTCAAAAATAATAGGGTT
524545 AGAGTATCCCCTCAAAAATAATAGGGTT
1 AGAGTATCCCCTCAAAAATAATAGGGTT
*
524573 ATAGTATCCCC
1 AGAGTATCCCC
524584 GATGGTGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (28 bp):
AGAGTATCCCCTCAAAAATAATAGGGTT
Found at i:524629 original size:79 final size:79
Alignment explanation
Indices: 524539--524694 Score: 195
Period size: 79 Copynumber: 2.0 Consensus size: 79
524529 CGAAAATAAT
* * **
524539 GGGGTTAGAGTATCCCCTCAAAAATAATAGGGTTATAGTATCCCCGATGGTGGAAAATTGGTATT
1 GGGGTTAGAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCCCCGATGGTGGAAAATCAGTATT
524604 TAAGAAATAAAATC
66 TAAGAAATAAAATC
* *** * * * *
524618 GGGGTTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCTCGATGGTGGAAAATCAGTGTT
1 GGGGTTAGAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCCCCGATGGTGGAAAATCAGTATT
*
524683 TTAGAAATAAAA
66 TAAGAAATAAAA
524695 CATTAATGAA
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
79 64 1.00
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (79 bp):
GGGGTTAGAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCCCCGATGGTGGAAAATCAGTATT
TAAGAAATAAAATC
Found at i:524650 original size:107 final size:108
Alignment explanation
Indices: 524467--524660 Score: 266
Period size: 107 Copynumber: 1.8 Consensus size: 108
524457 ACTGGGTTGG
* *
524467 AGTATCCCCAATAGTGGAAAAATTGGTGCTTTAGAGATAAAATCGGGCTCAGAGTATCCCCTCGA
1 AGTATCCCCAATAGTGGAAAAATTGGTGATTTAGAAATAAAATCGGGCTCAGAGTATCCCCTCGA
*
524532 AAATAATGGGGTTAGAGTATCCCCTCAAAAATAATAGGGTTAT
66 AAATAACGGGGTTAGAGTATCCCCTCAAAAATAATAGGGTTAT
* * * ** *
524575 AGTATCCCCGATGGTGG-AAAATTGGT-ATTTAAGAAATAAAATCGGGGTTGGAGTATCCCCTTG
1 AGTATCCCCAATAGTGGAAAAATTGGTGATTT-AGAAATAAAATCGGGCTCAGAGTATCCCCTCG
* *
524638 GAAATAACGGGGTTGGAGTATCC
65 AAAATAACGGGGTTAGAGTATCC
524661 TCGATGGTGG
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
106 3 0.04
107 56 0.76
108 15 0.20
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.26
Consensus pattern (108 bp):
AGTATCCCCAATAGTGGAAAAATTGGTGATTTAGAAATAAAATCGGGCTCAGAGTATCCCCTCGA
AAATAACGGGGTTAGAGTATCCCCTCAAAAATAATAGGGTTAT
Found at i:525694 original size:19 final size:20
Alignment explanation
Indices: 525670--525724 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
525660 GTATCGATAT
*
525670 ATTGTATCGATACATGCTC-
1 ATTGTATCGATACATGCACA
*
525689 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGCACA
525709 ATTGTATCGATACATG
1 ATTGTATCGATACATG
525725 AGATTGGCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (20 bp):
ATTGTATCGATACATGCACA
Found at i:525799 original size:13 final size:13
Alignment explanation
Indices: 525775--525822 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
525765 ATGATACAAC
525775 GTATCGATACATT
1 GTATCGATACATT
525788 GTATCGATACA-T
1 GTATCGATACATT
525800 G-AT-GA-A-ATT
1 GTATCGATACATT
*
525809 GTATCTATACATT
1 GTATCGATACATT
525822 G
1 G
525823 CTTGTAATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 4 0.14
11 3 0.10
12 3 0.10
13 15 0.52
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:528228 original size:23 final size:23
Alignment explanation
Indices: 528196--528239 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
528186 CATTTTGTTC
* *
528196 CAAAGTCCACGACTCAGTGGCTT
1 CAAAGCCCACAACTCAGTGGCTT
*
528219 CAAAGCCCACAACTCCGTGGC
1 CAAAGCCCACAACTCAGTGGC
528240 ACTCTTTACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.36, G:0.20, T:0.16
Consensus pattern (23 bp):
CAAAGCCCACAACTCAGTGGCTT
Found at i:528294 original size:31 final size:31
Alignment explanation
Indices: 528259--528577 Score: 180
Period size: 31 Copynumber: 9.7 Consensus size: 31
528249 CCTTTCCCAG
*
528259 AGTCCACGACTTAGTGGCATCTTTTCTTCAA
1 AGTCCACGACTCAGTGGCATCTTTTCTTCAA
* *
528290 AGTCCATGACTTAGTGGCATCTCTTTC--CAA
1 AGTCCACGACTCAGTGGCATCT-TTTCTTCAA
* **
528320 AGTCCACGACTCAGTGGCATCTTTCCTTTTA
1 AGTCCACGACTCAGTGGCATCTTTTCTTCAA
* * **
528351 AGTCCACAACTCCGTGGCACTCTTCACCCTTTCCTTTTA
1 AGTCCACGACTCAGTGGCA-TC-T-----TTT-CTTCAA
* * * * *
528390 AGCCCACAATTTC-GTGGCACCCTTTTTCTTTTTAA
1 AGTCCACGA-CTCAGTGGCA-TC-TTTTC--TTCAA
* * * *
528425 AGCCCACAACTCCGTGGCACTCTTTACCATTTCCCAA
1 AGTCCACGACTCAGTGGCA-TCTTT-TC--TT--CAA
*
528462 AGTCCACGACTTAGTGGCATCTTTTCTTCAA
1 AGTCCACGACTCAGTGGCATCTTTTCTTCAA
*
528493 AGTCCATGACTCAGTGGCATCTCTTTC--CAA
1 AGTCCACGACTCAGTGGCATCT-TTTCTTCAA
*
528523 AGTCCACGACTCAGTGGCATCTTTTTTTCAA
1 AGTCCACGACTCAGTGGCATCTTTTCTTCAA
* * *
528554 AGCCCACAACTCTGTGGCACTCTT
1 AGTCCACGACTCAGTGGCA-TCTT
528578 CACCCTTTCC
Statistics
Matches: 236, Mismatches: 30, Indels: 43
0.76 0.10 0.14
Matches are distributed among these distances:
29 6 0.03
30 47 0.20
31 81 0.34
32 14 0.06
33 4 0.02
34 8 0.03
35 26 0.11
36 5 0.02
37 17 0.07
38 2 0.01
39 24 0.10
40 2 0.01
ACGTcount: A:0.22, C:0.31, G:0.14, T:0.33
Consensus pattern (31 bp):
AGTCCACGACTCAGTGGCATCTTTTCTTCAA
Found at i:528323 original size:30 final size:30
Alignment explanation
Indices: 528250--528341 Score: 123
Period size: 30 Copynumber: 3.0 Consensus size: 30
528240 ACTCTTTACC
*
528250 CTTTCCCAGAGTCCACGACTTAGTGGCATCT
1 CTTT-CCAAAGTCCACGACTTAGTGGCATCT
*
528281 -TTTCTTCAAAGTCCATGACTTAGTGGCATCT
1 CTTTC--CAAAGTCCACGACTTAGTGGCATCT
*
528312 CTTTCCAAAGTCCACGACTCAGTGGCATCT
1 CTTTCCAAAGTCCACGACTTAGTGGCATCT
528342 TTCCTTTTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
29 1 0.02
30 26 0.48
31 23 0.43
32 4 0.07
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (30 bp):
CTTTCCAAAGTCCACGACTTAGTGGCATCT
Found at i:528329 original size:61 final size:64
Alignment explanation
Indices: 528216--528578 Score: 288
Period size: 61 Copynumber: 5.5 Consensus size: 64
528206 GACTCAGTGG
* * *
528216 CTTCAAAGCCCACAACTCCGTGGCACTCTTTACCCTTTCCCAGAGTCCACGACTTAGTGGCATCT
1 CTTCAAAGTCCACAACTCAGTGGCACTC-TT--CCTTT-CCAAAGTCCACGACTTAGTGGCATCT
528281 TTT
62 TTT
** * * *
528284 CTTCAAAGTCCATGACTTAGTGGCA-TC-T-CTTTCCAAAGTCCACGACTCAGTGGCATCTTTC
1 CTTCAAAGTCCACAACTCAGTGGCACTCTTCCTTTCCAAAGTCCACGACTTAGTGGCATCTTTT
** * * * * * *
528345 CTTTTAAGTCCACAACTCCGTGGCACTCTTCACCCTTTCCTTTTAAGCCCACAATTTCGTGGCAC
1 CTTCAAAGTCCACAACTCAGTGGCACTCTT---CCTTTCC---AAAGTCCACGACTTAGTGGCA-
*
528410 CCTTTTT
59 TC-TTTT
* * *
528417 CTTTTTAAAGCCCACAACTCCGTGGCACTCTTTACCATTTCCCAAAGTCCACGACTTAGTGGCAT
1 C--TTCAAAGTCCACAACTCAGTGGCACTC-TT-CC-TTT-CCAAAGTCCACGACTTAGTGGCAT
528482 CTTTT
60 CTTTT
** *
528487 CTTCAAAGTCCATGACTCAGTGGCA-TC-T-CTTTCCAAAGTCCACGACTCAGTGGCATCTTTT
1 CTTCAAAGTCCACAACTCAGTGGCACTCTTCCTTTCCAAAGTCCACGACTTAGTGGCATCTTTT
* * *
528548 TTTCAAAGCCCACAACTCTGTGGCACTCTTC
1 CTTCAAAGTCCACAACTCAGTGGCACTCTTC
528579 ACCCTTTCCT
Statistics
Matches: 234, Mismatches: 42, Indels: 42
0.74 0.13 0.13
Matches are distributed among these distances:
61 93 0.40
62 11 0.05
63 3 0.01
65 2 0.01
67 10 0.04
68 39 0.17
70 20 0.09
71 2 0.01
72 20 0.09
73 2 0.01
74 28 0.12
75 4 0.02
ACGTcount: A:0.21, C:0.33, G:0.14, T:0.32
Consensus pattern (64 bp):
CTTCAAAGTCCACAACTCAGTGGCACTCTTCCTTTCCAAAGTCCACGACTTAGTGGCATCTTTT
Found at i:528397 original size:39 final size:38
Alignment explanation
Indices: 528340--528458 Score: 129
Period size: 39 Copynumber: 3.2 Consensus size: 38
528330 TCAGTGGCAT
*
528340 CTTTCCTTTTAAGTCCACAACTCCGTGGCACTCTTCACC
1 CTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTT-ACC
* * *
528379 CTTTCCTTTTAAGCCCACAATTTCGTGGCACCCTT---
1 CTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTTACC
*
528414 -TTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTACC
1 CTTTCCTTTT-AAGCCCACAACTCCGTGGCACTC-TTACC
*
528453 ATTTCC
1 CTTTCC
528459 CAAAGTCCAC
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
34 8 0.12
35 20 0.31
36 2 0.03
39 31 0.48
40 4 0.06
ACGTcount: A:0.18, C:0.35, G:0.10, T:0.36
Consensus pattern (38 bp):
CTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTTACC
Found at i:528441 original size:35 final size:34
Alignment explanation
Indices: 528380--528449 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
528370 CTCTTCACCC
* *
528380 TTTCCTTTTAAGCCCACAATTTCGTGGCACCCTT
1 TTTCCTTTTAAGCCCACAACTCCGTGGCACCCTT
* *
528414 TTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTT
1 TTTCCTTTT-AAGCCCACAACTCCGTGGCACCCTT
528449 T
1 T
528450 ACCATTTCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 8 0.26
35 23 0.74
ACGTcount: A:0.19, C:0.31, G:0.11, T:0.39
Consensus pattern (34 bp):
TTTCCTTTTAAGCCCACAACTCCGTGGCACCCTT
Found at i:528524 original size:30 final size:29
Alignment explanation
Indices: 528458--528547 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 29
528448 TTACCATTTC
*
528458 CCAAAGTCCACGACTTAGTGGCATCTTTT
1 CCAAAGTCCACGACTCAGTGGCATCTTTT
*
528487 CTTCAAAGTCCATGACTCAGTGGCATCTCTTT
1 C--CAAAGTCCACGACTCAGTGGCATCT-TTT
528519 CCAAAGTCCACGACTCAGTGGCATCTTTT
1 CCAAAGTCCACGACTCAGTGGCATCTTTT
528548 TTTCAAAGCC
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
29 4 0.07
30 24 0.44
31 23 0.42
32 4 0.07
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (29 bp):
CCAAAGTCCACGACTCAGTGGCATCTTTT
Found at i:528573 original size:203 final size:202
Alignment explanation
Indices: 528217--528661 Score: 766
Period size: 203 Copynumber: 2.2 Consensus size: 202
528207 ACTCAGTGGC
*
528217 TTCAAAGCCCACAACTCCGTGGCACTCTTTACCCTTTCCCAGAGTCCACGACTTAGTGGCATCTT
1 TTCAAAGCCCACAACTCCGTGGCACTCTTTACCCTTTCCCAAAGTCCACGACTTAGTGGCATCTT
*
528282 TTCTTCAAAGTCCATGACTTAGTGGCATCTCTTTCCAAAGTCCACGACTCAGTGGCATCTTTCCT
66 TTCTTCAAAGTCCATGACTCAGTGGCATCTCTTTCCAAAGTCCACGACTCAGTGGCATCTTT-CT
*
528347 TTTAAGTCCACAACTCCGTGGCACTCTTCACCCTTTCCTTTTAAGCCCACAATTTCGTGGCACCC
130 TTTAAGCCCACAACTCCGTGGCACTCTTCACCCTTTCCTTTTAAGCCCACAATTTCGTGGCACCC
528412 TTTTTCTT
195 TTTTTCTT
* *
528420 TTTAAAGCCCACAACTCCGTGGCACTCTTTACCATTTCCCAAAGTCCACGACTTAGTGGCATCTT
1 TTCAAAGCCCACAACTCCGTGGCACTCTTTACCCTTTCCCAAAGTCCACGACTTAGTGGCATCTT
528485 TTCTTCAAAGTCCATGACTCAGTGGCATCTCTTTCCAAAGTCCACGACTCAGTGGCATCTTT-TT
66 TTCTTCAAAGTCCATGACTCAGTGGCATCTCTTTCCAAAGTCCACGACTCAGTGGCATCTTTCTT
*
528549 TTCAAAGCCCACAACTCTGTGGCACTCTTCACCCTTTCCTTTTAAGCCCACAATTTCGTGGCACC
131 TT--AAGCCCACAACTCCGTGGCACTCTTCACCCTTTCCTTTTAAGCCCACAATTTCGTGGCACC
528614 CTTTTTCTT
194 CTTTTTCTT
* * * *
528623 TTCAATGCTCACAACTTCGTGGCACTCTTCACCCTTTCC
1 TTCAAAGCCCACAACTCCGTGGCACTCTTTACCCTTTCC
528662 TTTTAAGTCC
Statistics
Matches: 228, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
201 4 0.02
203 224 0.98
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (202 bp):
TTCAAAGCCCACAACTCCGTGGCACTCTTTACCCTTTCCCAAAGTCCACGACTTAGTGGCATCTT
TTCTTCAAAGTCCATGACTCAGTGGCATCTCTTTCCAAAGTCCACGACTCAGTGGCATCTTTCTT
TTAAGCCCACAACTCCGTGGCACTCTTCACCCTTTCCTTTTAAGCCCACAATTTCGTGGCACCCT
TTTTCTT
Found at i:528610 original size:39 final size:39
Alignment explanation
Indices: 528553--528689 Score: 146
Period size: 39 Copynumber: 3.6 Consensus size: 39
528543 CTTTTTTTCA
528553 AAGCCCACAAC-TCTGTGGCACTCTTCACCCTTTCCTTTT
1 AAGCCCACAACTTC-GTGGCACTCTTCACCCTTTCCTTTT
* *
528592 AAGCCCACAATTTCGTGGCACCCTT-----TTT-CTTTT
1 AAGCCCACAACTTCGTGGCACTCTTCACCCTTTCCTTTT
*
528625 CAATGCTCACAACTTCGTGGCACTCTTCACCCTTTCCTTTT
1 -AA-GCCCACAACTTCGTGGCACTCTTCACCCTTTCCTTTT
* *
528666 AAGTCCACAACTCCGTGGCA-TCTT
1 AAGCCCACAACTTCGTGGCACTCTT
528690 TCTCCTTTTA
Statistics
Matches: 81, Mismatches: 8, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
33 5 0.06
34 5 0.06
35 20 0.25
38 4 0.05
39 35 0.43
40 7 0.09
41 5 0.06
ACGTcount: A:0.19, C:0.35, G:0.12, T:0.34
Consensus pattern (39 bp):
AAGCCCACAACTTCGTGGCACTCTTCACCCTTTCCTTTT
Found at i:528698 original size:74 final size:72
Alignment explanation
Indices: 528522--528690 Score: 218
Period size: 74 Copynumber: 2.3 Consensus size: 72
528512 TCTCTTTCCA
* *
528522 AAGTCCACGACTCAGTGGCATC-TTT-TTTTCAAAGCCCACAACTCTGTGGCACTCTTCACCCTT
1 AAGTCCACAACTCCGTGGCATCTTTTCTTTTCAAAGCCCACAACTCTGTGGCACTCTTCACCCTT
528585 TCCTTTT
66 TCCTTTT
* * * * * *
528592 AAGCCCACAATTTCGTGGCACCCTTTTTCTTTTCAATGCTCACAACT-TCGTGGCACTCTTCACC
1 AAGTCCACAACTCCGTGGCA-TC-TTTTCTTTTCAAAGCCCACAACTCT-GTGGCACTCTTCACC
528656 CTTTCCTTTT
63 CTTTCCTTTT
528666 AAGTCCACAACTCCGTGGCATCTTT
1 AAGTCCACAACTCCGTGGCATCTTT
528691 CTCCTTTTAG
Statistics
Matches: 82, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
70 15 0.18
71 1 0.01
72 3 0.04
73 5 0.06
74 58 0.71
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (72 bp):
AAGTCCACAACTCCGTGGCATCTTTTCTTTTCAAAGCCCACAACTCTGTGGCACTCTTCACCCTT
TCCTTTT
Found at i:528761 original size:203 final size:201
Alignment explanation
Indices: 528217--528764 Score: 552
Period size: 203 Copynumber: 2.7 Consensus size: 201
528207 ACTCAGTGGC
* * * * *
528217 TTCAAAGCCCACAACTCCGTGGCACTCTTTACCCTTTCCCAGAGTCCACGACTTAGTGGCATCTT
1 TTCAAAGCCCACAACTCCGTGGCACTCTTCACCATTTCCCAAAGTCCACAACTCAGTGGCATCTT
* ** * * * * * *
528282 TTCTTCAAAGTCCATGACTTAGTGGCATCTCTTTCCAAAGTCCACGACTCAGTGGCATCTTTCCT
66 TTCTTCAAAGCCCACAACTCAGGGGCAACTCTTTCAAAAG-CCACGACTAAGTGGCAAC--TCCT
* *
528347 TT-TAAGTCCACAACTCCGTGGCACTCTTCACCCTTTCCTTTTAAGCCCACAATTTCGTGGCACC
128 TTCAAAGCCCACAACTCCGTGGCACTCTTCACCCTTTCCTTTTAAGCCCACAATTTCGTGGCACC
528411 CTTTTTCTT
193 CTTTTTCTT
* * * *
528420 TTTAAAGCCCACAACTCCGTGGCACTCTTTACCATTTCCCAAAGTCCACGACTTAGTGGCATCTT
1 TTCAAAGCCCACAACTCCGTGGCACTCTTCACCATTTCCCAAAGTCCACAACTCAGTGGCATCTT
* ** * * * * * **
528485 TTCTTCAAAGTCCATGACTCAGTGGCATCTCTTTCCAAAGTCCACGACTCAGTGGCATCTTTTTT
66 TTCTTCAAAGCCCACAACTCAGGGGCAACTCTTTCAAAAG-CCACGACTAAGTGGCAAC-TCCTT
*
528550 TCAAAGCCCACAACTCTGTGGCACTCTTCACCCTTTCCTTTTAAGCCCACAATTTCGTGGCACCC
129 TCAAAGCCCACAACTCCGTGGCACTCTTCACCCTTTCCTTTTAAGCCCACAATTTCGTGGCACCC
528615 TTTTTCTT
194 TTTTTCTT
* * * * ** *
528623 TTCAATGCTCACAACTTCGTGGCACTCTTCACCCTTTCCTTTTAAGTCCACAACTCCGTGGCATC
1 TTCAAAGCCCACAACTCCGTGGCACTCTTCACCATTTCC--CAAAGTCCACAACTCAGTGGCATC
** * *
528688 TTTCTCCTTTTAGGCCCACAAGTCAGGGGCAAC-C-TTCAAAAG-CAC-AC-AAGTTGGTACAAC
64 TTT-T-CTTCAAAGCCCACAACTCAGGGGCAACTCTTTCAAAAGCCACGACTAAG-TGG--CAAC
528748 -CCTTTCAAAAGCCCACA
124 TCCTTTC-AAAGCCCACA
528765 CAAGTTGGTG
Statistics
Matches: 302, Mismatches: 34, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
201 2 0.01
202 14 0.05
203 234 0.77
204 3 0.01
205 29 0.10
206 2 0.01
207 18 0.06
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.31
Consensus pattern (201 bp):
TTCAAAGCCCACAACTCCGTGGCACTCTTCACCATTTCCCAAAGTCCACAACTCAGTGGCATCTT
TTCTTCAAAGCCCACAACTCAGGGGCAACTCTTTCAAAAGCCACGACTAAGTGGCAACTCCTTTC
AAAGCCCACAACTCCGTGGCACTCTTCACCCTTTCCTTTTAAGCCCACAATTTCGTGGCACCCTT
TTTCTT
Found at i:528950 original size:49 final size:49
Alignment explanation
Indices: 528781--529686 Score: 930
Period size: 49 Copynumber: 18.9 Consensus size: 49
528771 GGTGGCATCT
*
528781 TCTTTAAGTCCAATGTAGCTGGCGTTGAATCAGCACATTGGCA-CTTCA
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
*
528829 TCTTTAAGTCCAATGTAGCTGGCCTTGAATTAGCACATTGGCACC-TCA
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
528877 CCTTTAAGTCCAATAG-AGCTGGCCTTGAATCAGCATATTGGCACCTTTA
1 TCTTTAAGTCCAAT-GTAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
528926 TCTTTAAGTCTAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * **
528975 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGTGCATTCAGTCA
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATT-G-GCA--CCTTCA
** * * *
529028 TCTTTAAAACCCAATGTCA-TTGGCCTTGAATCAACACATTGGCA--TTCT
1 TCTTT-AAGTCCAATGT-AGCTGGCCTTGAATCAGCACATTGGCACCTTCA
529076 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG------CA
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
529119 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCA
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
529167 CCTTTAAGTCCAATAG-AGCTGGCCTTGAATCAGCATATTGGCACCTTTA
1 TCTTTAAGTCCAAT-GTAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
529216 TCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTAGCACCTTCA
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * * *
529265 TCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCGCATACGTCA
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATT-G-GCA-CCTTCA
** * * * *
529317 TCTTTAAAACCCAATGTCGTTGGCCTTGAATCAACACATTGGCA--TTCT
1 TCTTT-AAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
529365 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG------CA
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
529408 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG------CA
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * *
529451 TCTTTAAGTCCAATATAGATGGCCTTGAATCAGCATATTGGCACTTTTA
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
*
529500 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCATCACATTGGCACC-T--
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * * * *
529546 TC---AAGCCCAATATCGTTGGCCGTGAATCAGCATATTGGCATCTTCA
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * *
529592 CCTTTAAGTCCAACAG-CGCTGGCCTTGAATCAGCATATTGGCACCTT-T
1 TCTTTAAGTCCAA-TGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
529640 TCCGTCTTGAGTCCAATGTAGCTGGCCTTGAATCAGCACATTAGCAC
1 T-C-T-TTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
529687 AAACCCAATA
Statistics
Matches: 724, Mismatches: 94, Indels: 77
0.81 0.11 0.09
Matches are distributed among these distances:
43 156 0.22
44 1 0.00
46 4 0.01
47 61 0.08
48 144 0.20
49 236 0.33
50 3 0.00
51 43 0.06
52 13 0.02
53 37 0.05
54 26 0.04
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (49 bp):
TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
Found at i:529137 original size:43 final size:43
Alignment explanation
Indices: 529048--529681 Score: 480
Period size: 43 Copynumber: 13.5 Consensus size: 43
529038 CCAATGTCAT
*
529048 TGGCCTTGAATCAACACATTGGCATTCTTCTTTAAGTCCAATGTAGC
1 TGGCCTTGAATCAGCACATTGGCA----TCTTTAAGTCCAATGTAGC
529095 TGGCCTTGAATCAGCACATTGGCATCTTTAAGTCCAATGTAGC
1 TGGCCTTGAATCAGCACATTGGCATCTTTAAGTCCAATGTAGC
529138 TGGCCTTGAATCAGCACATTGGCACCTCACCTTTAAGTCCAATAG-AGC
1 TGGCCTTGAATCAGCACATTGGCA--T---CTTTAAGTCCAAT-GTAGC
*
529186 TGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGC
1 TGGCCTTGAATCAGCACATTGG---C---ATCTTTAAGTCCAATGTAGC
* * * *
529235 TGGCCTTGACTCAGCACATTAGCACCTTCATCTTTAAGTCCAATATCGC
1 TGGCCTTGAATCAGCACATT-G-----GCATCTTTAAGTCCAATGTAGC
* * ** * *
529284 TAGCCTTGAATCAGCATATTGGCGCATACGTCATCTTTAAAACCCAATGTCGT
1 TGGCCTTGAATCAGCACATT---G-----G-CATCTTT-AAGTCCAATGTAGC
*
529337 TGGCCTTGAATCAACACATTGGCATTCTTCTTTAAGTCCAATGTAGC
1 TGGCCTTGAATCAGCACATTGGCA----TCTTTAAGTCCAATGTAGC
529384 TGGCCTTGAATCAGCACATTGGCATCTTTAAGTCCAATGTAGC
1 TGGCCTTGAATCAGCACATTGGCATCTTTAAGTCCAATGTAGC
* *
529427 TGGCCTTGAATCAGCACATTGGCATCTTTAAGTCCAATATAGA
1 TGGCCTTGAATCAGCACATTGGCATCTTTAAGTCCAATGTAGC
*
529470 TGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATGTAGC
1 TGGCCTTGAATCAGCACATTGG--C----ATCTTTAAGTCCAATGTAGC
* * * * * * *
529519 TGGCCTTGAATCATCACATTGGCACCTTCAAGCCCAATATCGT
1 TGGCCTTGAATCAGCACATTGGCATCTTTAAGTCCAATGTAGC
* * * *
529562 TGGCCGTGAATCAGCATATTGGCATCTTCACCTTTAAGTCCAACAG-CGC
1 TGGCCTTGAATCAGCACATTGGCA---T---CTTTAAGTCCAA-TGTAGC
* *
529611 TGGCCTTGAATCAGCATATTGGCACCTTTTCCGTCTTGAGTCCAATGTAGC
1 TGGCCTTGAATCAGCACATTGGCA-----T-C-T-TTAAGTCCAATGTAGC
529662 TGGCCTTGAATCAGCACATT
1 TGGCCTTGAATCAGCACATT
529682 AGCACAAACC
Statistics
Matches: 487, Mismatches: 55, Indels: 86
0.78 0.09 0.14
Matches are distributed among these distances:
43 159 0.33
44 2 0.00
45 3 0.01
47 57 0.12
48 43 0.09
49 145 0.30
50 4 0.01
51 37 0.08
52 9 0.02
53 27 0.06
54 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (43 bp):
TGGCCTTGAATCAGCACATTGGCATCTTTAAGTCCAATGTAGC
Found at i:529303 original size:290 final size:289
Alignment explanation
Indices: 528773--529681 Score: 1332
Period size: 290 Copynumber: 3.2 Consensus size: 289
528763 CACAAGTTGG
*
528773 TGGCA-TCTTCTTTAAGTCCAATGTAGCTGGCGTTGAATCAGCACATTGGCACTTCATCTTTAAG
1 TGGCATTCTTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG-----CATCTTTAAG
*
528837 TCCAATGTAGCTGGCCTTGAATTAGCACATTGGCACCTCACCTTTAAGTCCAATAGAGCTGGCCT
61 TCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCACCTTTAAGTCCAATAGAGCTGGCCT
*
528902 TGAATCAGCATATTGGCACCTTTATCTTTAAGTCTAATGTAGCTGGCCTTGACTCAGCACATTGG
126 TGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGG
* * *
528967 CACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGTGCATTCAGTCATCTT
191 CACCTTCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTAGCGCATAC-GTCATCTT
529032 TAAAACCCAATGTCATTGGCCTTGAATCAACACAT
255 TAAAACCCAATGTCATTGGCCTTGAATCAACACAT
529067 TGGCATTCTTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCTTTAAGTCCAA
1 TGGCATTCTTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCTTTAAGTCCAA
529132 TGTAGCTGGCCTTGAATCAGCACATTGGCACCTCACCTTTAAGTCCAATAGAGCTGGCCTTGAAT
66 TGTAGCTGGCCTTGAATCAGCACATTGGCACCTCACCTTTAAGTCCAATAGAGCTGGCCTTGAAT
*
529197 CAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTAGCACCT
131 CAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCT
*
529262 TCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCGCATACGTCATCTTTAAAAC
196 TCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTAGCGCATACGTCATCTTTAAAAC
*
529327 CCAATGTCGTTGGCCTTGAATCAACACAT
261 CCAATGTCATTGGCCTTGAATCAACACAT
529356 TGGCATTCTTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCTTTAAGTCCAA
1 TGGCATTCTTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCTTTAAGTCCAA
* *
529421 TGTAGCTGGCCTTGAATCAGCACATTGGCA--T---CTTTAAGTCCAATATAGATGGCCTTGAAT
66 TGTAGCTGGCCTTGAATCAGCACATTGGCACCTCACCTTTAAGTCCAATAGAGCTGGCCTTGAAT
* * *
529481 CAGCATATTGGCACTTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCATCACATTGGCACC-
131 CAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCT
* * * * * * **
529545 T--TC---AAGCCCAATATCGTTGGCCGTGAATCAGCATATT-G-GCAT-CTTCACCTTT-AAGT
196 TCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTAGCGCATACGTCATCTTTAAAAC
* ** * *
529601 CCAACAG-CGCTGGCCTTGAATCAGCATAT
261 CCAA-TGTCATTGGCCTTGAATCAACACAT
*
529630 TGGCACCTT-TTCCGTCTTGAGTCCAATGTAGCTGGCCTTGAATCAGCACATT
1 TGGCA--TTCTT-C-T-TTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATT
529682 AGCACAAACC
Statistics
Matches: 580, Mismatches: 28, Indels: 30
0.91 0.04 0.05
Matches are distributed among these distances:
274 30 0.05
275 11 0.02
276 7 0.01
277 2 0.00
278 65 0.11
281 2 0.00
283 1 0.00
284 87 0.15
287 1 0.00
289 137 0.24
290 189 0.33
294 5 0.01
295 43 0.07
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (289 bp):
TGGCATTCTTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCTTTAAGTCCAA
TGTAGCTGGCCTTGAATCAGCACATTGGCACCTCACCTTTAAGTCCAATAGAGCTGGCCTTGAAT
CAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCT
TCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTAGCGCATACGTCATCTTTAAAAC
CCAATGTCATTGGCCTTGAATCAACACAT
Found at i:530341 original size:32 final size:32
Alignment explanation
Indices: 530300--530362 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
530290 TTCAACGATT
530300 TGTATCGATACATAAGTGTTGTATCAATACAA
1 TGTATCGATACATAAGTGTTGTATCAATACAA
* *
530332 TGTATCGATACATATGTGTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCAATACA
530363 TATGAAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCAATACAA
Found at i:530365 original size:19 final size:19
Alignment explanation
Indices: 530299--530366 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
530289 TTTCAACGAT
*
530299 TTGTATCGATACATAAGTG
1 TTGTATCGATACATATGTG
*
530318 TTGTATCAATACA-A----
1 TTGTATCGATACATATGTG
530332 -TGTATCGATACATATGTG
1 TTGTATCGATACATATGTG
530350 TTGTATCGATACATATG
1 TTGTATCGATACATATG
530367 AAGCTACTGC
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 11 0.27
14 1 0.02
18 1 0.02
19 28 0.68
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATATGTG
Found at i:530424 original size:13 final size:13
Alignment explanation
Indices: 530406--530430 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
530396 ATTACTCAAA
530406 TGTATCGATACAT
1 TGTATCGATACAT
530419 TGTATCGATACA
1 TGTATCGATACA
530431 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:530476 original size:52 final size:52
Alignment explanation
Indices: 530439--530564 Score: 189
Period size: 52 Copynumber: 2.4 Consensus size: 52
530429 CACTGATCTT
530439 TGTATCAATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCAATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* * ** *
530491 TGTATCGATACTTGTAGGCAAATTTGCCTAGATGTATCGATACACTATGAAA
1 TGTATCAATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
530543 TGTATCGATACATGCAGGCAAA
1 TGTATCAATACATACAGGCAAA
530565 ATTTCATATT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCAATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:534926 original size:18 final size:19
Alignment explanation
Indices: 534887--534927 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
534877 AATAAATGTT
534887 TTAAAGGGGAGACAAGTTG
1 TTAAAGGGGAGACAAGTTG
* *
534906 TTAAAGGGG-GATAATTTG
1 TTAAAGGGGAGACAAGTTG
534924 TTAA
1 TTAA
534928 GGGAGGAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.37, C:0.02, G:0.32, T:0.29
Consensus pattern (19 bp):
TTAAAGGGGAGACAAGTTG
Found at i:535617 original size:13 final size:13
Alignment explanation
Indices: 535599--535624 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
535589 CACACCTAGA
535599 TGTATCGATACAT
1 TGTATCGATACAT
535612 TGTATCGATACAT
1 TGTATCGATACAT
535625 GTTCTTAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:535817 original size:20 final size:20
Alignment explanation
Indices: 535788--535826 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
535778 TCAAATACGT
*
535788 GTATCGATACATAATAGCAA
1 GTATCAATACATAATAGCAA
535808 GTATCAATACATAATAGCA
1 GTATCAATACATAATAGCA
535827 TATTTGTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (20 bp):
GTATCAATACATAATAGCAA
Found at i:538274 original size:25 final size:27
Alignment explanation
Indices: 538214--538280 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 27
538204 TTAATAATTT
* **
538214 ATATAAATATATAATATATTAAATTTA
1 ATATAAATATAAAATATATTAAATACA
538241 AT-TATAATATAAAAT-TA-TAAATACA
1 ATATA-AATATAAAATATATTAAATACA
*
538266 ATATAAATAAAAAAT
1 ATATAAATATAAAAT
538281 CTCTCTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 17 0.50
26 6 0.18
27 11 0.32
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (27 bp):
ATATAAATATAAAATATATTAAATACA
Found at i:541032 original size:16 final size:16
Alignment explanation
Indices: 540993--541032 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
540983 AGAATTAGAT
540993 TTAATTTTATGTAATA
1 TTAATTTTATGTAATA
*
541009 -TAAGTTTTATGTATTA
1 TTAA-TTTTATGTAATA
541025 TTAATTTT
1 TTAATTTT
541033 CAGTTACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 15 0.71
17 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (16 bp):
TTAATTTTATGTAATA
Found at i:545973 original size:28 final size:28
Alignment explanation
Indices: 545933--545988 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
545923 GCAAGCCTTG
545933 ACTTATCTGTTTTATTTTTCTTGTTCTT
1 ACTTATCTGTTTTATTTTTCTTGTTCTT
545961 ACTTAT-TAGTTTTATTTTTCTTGTTCTT
1 ACTTATCT-GTTTTATTTTTCTTGTTCTT
545989 TGATTTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.12, C:0.12, G:0.07, T:0.68
Consensus pattern (28 bp):
ACTTATCTGTTTTATTTTTCTTGTTCTT
Found at i:546811 original size:13 final size:13
Alignment explanation
Indices: 546793--546817 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
546783 ATTACTCAAA
546793 TGTATCGATACAT
1 TGTATCGATACAT
546806 TGTATCGATACA
1 TGTATCGATACA
546818 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:546882 original size:52 final size:52
Alignment explanation
Indices: 546826--546950 Score: 205
Period size: 52 Copynumber: 2.4 Consensus size: 52
546816 CACTGATCTT
* *
546826 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATAAAA
* *
546878 TGTATTGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATAAAA
*
546930 TGTATCTATACATGCAGGCAA
1 TGTATCGATACATGCAGGCAA
546951 CTTTTCATAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATAAAA
Found at i:554214 original size:15 final size:15
Alignment explanation
Indices: 554194--554224 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
554184 TAAAAATGTC
*
554194 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
554209 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
554224 C
1 C
554225 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:556316 original size:13 final size:13
Alignment explanation
Indices: 556298--556323 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
556288 ACATTTTTCT
556298 TTGTATCGATACA
1 TTGTATCGATACA
556311 TTGTATCGATACA
1 TTGTATCGATACA
556324 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:561260 original size:52 final size:51
Alignment explanation
Indices: 561180--561298 Score: 202
Period size: 52 Copynumber: 2.3 Consensus size: 51
561170 AAAAGTTGCT
*
561180 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTACC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA-TTACC
* *
561232 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
561283 TGCATGTATCGATACA
1 TGCATGTATCGATACA
561299 AAGATCAGTG
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
51 20 0.31
52 44 0.69
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (51 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
Found at i:561325 original size:13 final size:13
Alignment explanation
Indices: 561307--561331 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
561297 CAAAGATCAG
561307 TGTATCGATACAA
1 TGTATCGATACAA
561320 TGTATCGATACA
1 TGTATCGATACA
561332 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:561412 original size:13 final size:13
Alignment explanation
Indices: 561394--561418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
561384 CAAAAAAATA
561394 TGTATCGATACAT
1 TGTATCGATACAT
561407 TGTATCGATACA
1 TGTATCGATACA
561419 CCATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:562315 original size:52 final size:52
Alignment explanation
Indices: 562177--562370 Score: 216
Period size: 52 Copynumber: 3.7 Consensus size: 52
562167 GAAAAGTGAT
* * * * **
562177 AAAGATGCCAATATG-TCGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCT-GATTCAAGGCCAGCTATATTGAACTTAAAGATG-G-A
* * *
562231 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGGA
* * *
562284 AAAGGTGCCAATATGCTAATTCAAGGCCAGCTATATTGGACTTAAAGGT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGGA
562334 -AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTG
562371 GGCTTAGAAG
Statistics
Matches: 122, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
49 36 0.30
51 1 0.01
52 38 0.31
53 6 0.05
54 5 0.04
55 35 0.29
56 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGGA
Found at i:562357 original size:49 final size:51
Alignment explanation
Indices: 562177--562381 Score: 209
Period size: 49 Copynumber: 3.9 Consensus size: 51
562167 GAAAAGTGAT
* * * * * *
562177 AAAGATGCCAATATG-TCGATTCACGGCCAACGATATTGGGCTTAAAGATGAG
1 AAAGGTGCCAATATGCT-GATTCAAGGCCAGCTATATTGGACTTAAAGGTG-G
* * * * *
562229 AAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
1 --AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGG
*
562283 AAAAGGTGCCAATATGCTAATTCAAGGCCAGCTATATTGGACTTAAAGGT-G
1 -AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGG
*
562334 -AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAGAAGG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA-AAGG
562382 GTTGCCACCG
Statistics
Matches: 131, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
49 41 0.31
50 4 0.03
51 1 0.01
52 38 0.29
53 6 0.05
54 5 0.04
55 35 0.27
56 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.24
Consensus pattern (51 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGG
Found at i:562507 original size:30 final size:30
Alignment explanation
Indices: 562397--562850 Score: 384
Period size: 30 Copynumber: 15.5 Consensus size: 30
562387 CACCGACTTG
* * *
562397 TGTGGGCTTTGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
562427 TGTGGGC-TTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
562454 TGTGGGCTTTT--AAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
**
562482 TGTGGGCTTTTGAAAAATATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* * *
562512 TGTGGGCTTTTGAACAGGGTGCCACTAACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
562542 TGTGGGCTTTT--AAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
** *
562570 TGTGGGCTTTTGAAAAATATGCCACTAACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* *
562600 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* *
562630 TGTGGGC---TGAAAA-GAGTGCTA-TAGAGT
1 TGTGGGCTTTTGAAAAGGA-TGCCACT-GACT
* ** * * *
562657 TGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTT----TTGAAAAGGA-TGCCACTGACT
* * *
562692 TGTGGACTTTGGAAAA-GATGCCACCGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
** * *
562721 TGTGGGCTTCGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
562751 TGTGGGC-TTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
** *
562778 TGTGGGCTTTTGAAAAAAATGCCACCGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
**
562808 TGTGGGC-TTTGAAAAAAATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
562837 TGTGGACTTTTGAA
1 TGTGGGCTTTTGAA
562851 GGGTGATGAA
Statistics
Matches: 352, Mismatches: 50, Indels: 44
0.79 0.11 0.10
Matches are distributed among these distances:
26 2 0.01
27 60 0.17
28 59 0.17
29 55 0.16
30 148 0.42
31 5 0.01
34 5 0.01
35 18 0.05
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (30 bp):
TGTGGGCTTTTGAAAAGGATGCCACTGACT
Found at i:562563 original size:58 final size:59
Alignment explanation
Indices: 562381--562850 Score: 331
Period size: 57 Copynumber: 8.0 Consensus size: 59
562371 GGCTTAGAAG
* * * *
562381 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AA
1 GGTTGCCACTGAC-T-TGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAA
* *
562440 GGTTGCCACTGACTTGTGGGCTTTT--AAAGGTTGCCACTGACTTGTGGGCTTTTGAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAA
** *
562497 AATATGCCACTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTT-AAA
1 GGT-TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAA
***
562556 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTAACTTGTGGGCTTTTGAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTG-AAA
* * * * * * **
562616 GGGTGCCACTAACTTGTGGGC---TGAAAAGAGTGCTA-TAGAGTTGTGAGCTTACAAAAGAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTA-ACTTGTGGGCTT----TTG--AA
562677 A
59 A
* * * * * ** **
562678 GAG-TGCCACGGAGTTGTGGACTTTGGAAAA-GATGCCACCGACTTGTGGGCTTCGGAAAA
1 G-GTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTG-AAA
* * * *
562737 GGGTGCCACTGATTTGTGGGC-TTTG--AAGGTTGCCACTGACTTGTGGGCTTTTGAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTG-AAA
*** * *** * *
562794 AAATGCCACCGACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGACTTTTGAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAA
562851 GGGTGATGAA
Statistics
Matches: 333, Mismatches: 56, Indels: 45
0.77 0.13 0.10
Matches are distributed among these distances:
55 22 0.07
56 8 0.02
57 78 0.23
58 77 0.23
59 60 0.18
60 48 0.14
61 1 0.00
62 19 0.06
63 1 0.00
64 14 0.04
65 5 0.02
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (59 bp):
GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAA
Found at i:562566 original size:88 final size:87
Alignment explanation
Indices: 562381--562637 Score: 383
Period size: 88 Copynumber: 2.9 Consensus size: 87
562371 GGCTTAGAAG
* * *** * *
562381 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGGTT
1 GGTTGCCACTGAC-T-TGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGGT
*
562444 GCCACTGACTTGTGGGCTTTTAAA
64 GCCACTAACTTGTGGGCTTTTAAA
562468 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAACAGGGTG
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAA-AGGGTG
562533 CCACTAACTTGTGGGCTTTTAAA
65 CCACTAACTTGTGGGCTTTTAAA
*
562556 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTAACTTGTGGGCTTTTGAAAAGGGTG
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTG-AAAGGGTG
562621 CCACTAACTTGTGGGCT
65 CCACTAACTTGTGGGCT
562638 GAAAAGAGTG
Statistics
Matches: 157, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
85 32 0.20
86 5 0.03
87 13 0.08
88 105 0.67
89 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (87 bp):
GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGGTGC
CACTAACTTGTGGGCTTTTAAA
Found at i:562723 original size:29 final size:29
Alignment explanation
Indices: 562674--562846 Score: 170
Period size: 29 Copynumber: 5.9 Consensus size: 29
562664 TTACAAAAGA
* * *
562674 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACTGACTTGTGGGCTTTGG
* *
562704 AAAAGATGCCACCGACTTGTGGGCTTCGG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
562733 AAAAGGGTGCCACTGATTTGTGGGCTTT-G
1 AAAA-GATGCCACTGACTTGTGGGCTTTGG
* * *
562762 -AAGGTTGCCACTGACTTGTGGGCTTTTGA
1 AAAAGATGCCACTGACTTGTGGGC-TTTGG
* * *
562791 AAAAAATGCCACCGACTTGTGGGCTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
562820 AAAAAATGCCACTGACTTGTGGACTTT
1 AAAAGATGCCACTGACTTGTGGGCTTT
562847 TGAAGGGTGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
27 18 0.15
28 5 0.04
29 54 0.45
30 44 0.36
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.27
Consensus pattern (29 bp):
AAAAGATGCCACTGACTTGTGGGCTTTGG
Found at i:564266 original size:1 final size:1
Alignment explanation
Indices: 564262--564377 Score: 88
Period size: 1 Copynumber: 116.0 Consensus size: 1
564252 CCGGACCCCC
* * * * * ** * *
564262 TTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTTTTTTTCCTTTTGTTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** ** **
564327 TGTTTTTTTTTTTTTGGTTTTTCATTTTTTTTCGTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
564378 GGAGGACGCC
Statistics
Matches: 89, Mismatches: 26, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 89 1.00
ACGTcount: A:0.02, C:0.03, G:0.09, T:0.86
Consensus pattern (1 bp):
T
Found at i:564290 original size:11 final size:10
Alignment explanation
Indices: 564262--564377 Score: 114
Period size: 10 Copynumber: 11.5 Consensus size: 10
564252 CCGGACCCCC
564262 TTTTTTGTTT
1 TTTTTTGTTT
*
564272 TTGTTTGTTT
1 TTTTTTGTTT
564282 TTTTATTG-TT
1 TTTT-TTGTTT
564292 TTTTTT-TTT
1 TTTTTTGTTT
**
564301 CCTTTTGTTTT
1 TTTTTTG-TTT
564312 TTTTTTGTTT
1 TTTTTTGTTT
564322 TTTTTTGTTT
1 TTTTTTGTTT
564332 TTTTTT-TTT
1 TTTTTTGTTT
*
564341 TGGTTTTTCATTT
1 T--TTTTT-GTTT
*
564354 TTTTTCGTTT
1 TTTTTTGTTT
564364 TTTTTT-TTT
1 TTTTTTGTTT
564373 TTTTT
1 TTTTT
564378 GGAGGACGCC
Statistics
Matches: 89, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
9 20 0.22
10 45 0.51
11 20 0.22
13 4 0.04
ACGTcount: A:0.02, C:0.03, G:0.09, T:0.86
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:564321 original size:50 final size:49
Alignment explanation
Indices: 564262--564378 Score: 146
Period size: 50 Copynumber: 2.3 Consensus size: 49
564252 CCGGACCCCC
* ** *
564262 TTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTTTTTTTCCTTTTGTTT-T
1 TTTTTTGTTTTTTTTTGTTTTTTT-TT-TTTTGGTTTTTCATTTTGTTTCT
*
564312 TTTTTTGTTTTTTTTTGTTTTTTTTTTTTTGGTTTTTCATTTTTTTTCGT
1 TTTTTTGTTTTTTTTTGTTTTTTTTTTTTTGGTTTTTCATTTTGTTTC-T
*
564362 TTTTTTTTTTTTTTTTG
1 TTTTTTGTTTTTTTTTG
564379 GAGGACGCCG
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
48 17 0.29
49 2 0.03
50 40 0.68
ACGTcount: A:0.02, C:0.03, G:0.09, T:0.85
Consensus pattern (49 bp):
TTTTTTGTTTTTTTTTGTTTTTTTTTTTTTGGTTTTTCATTTTGTTTCT
Found at i:564323 original size:39 final size:39
Alignment explanation
Indices: 564264--564339 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 39
564254 GGACCCCCTT
564264 TTTTGTTTTTGTTTGTTTTTTTATTGTTTTTTTTTTTCC
1 TTTTGTTTTTGTTTGTTTTTTTATTGTTTTTTTTTTTCC
*
564303 TTTTGTTTTTTTTTTGTTTTTTT-TTGTTTTTTTTTTT
1 TTTTG-TTTTTGTTTGTTTTTTTATTGTTTTTTTTTTT
564340 TTGGTTTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
39 19 0.54
40 16 0.46
ACGTcount: A:0.01, C:0.03, G:0.09, T:0.87
Consensus pattern (39 bp):
TTTTGTTTTTGTTTGTTTTTTTATTGTTTTTTTTTTTCC
Found at i:564340 original size:40 final size:40
Alignment explanation
Indices: 564264--564377 Score: 128
Period size: 40 Copynumber: 2.9 Consensus size: 40
564254 GGACCCCCTT
*
564264 TTTTG-TTTTTGTTTGTTTTTTTATTG-TTTTTTTTTTTCC
1 TTTTGTTTTTTTTTTGTTTTTTT-TTGTTTTTTTTTTTTCC
**
564303 TTTTGTTTTTTTTTTGTTTTTTTTTGTTTTTTTTTTTTTGG
1 TTTTGTTTTTTTTTTGTTTTTTTTTG-TTTTTTTTTTTTCC
*
564344 TTTT-TCATTTTTTTTCGTTTTTTTTT-TTTTTTTT
1 TTTTGT--TTTTTTTTTGTTTTTTTTTGTTTTTTTT
564378 GGAGGACGCC
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
39 8 0.12
40 25 0.38
41 15 0.23
42 18 0.27
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.86
Consensus pattern (40 bp):
TTTTGTTTTTTTTTTGTTTTTTTTTGTTTTTTTTTTTTCC
Found at i:571875 original size:17 final size:17
Alignment explanation
Indices: 571853--571887 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
571843 TGAACATGCA
571853 TATGTAGTAGAGACAAT
1 TATGTAGTAGAGACAAT
571870 TATGTAGTAGAGACAAT
1 TATGTAGTAGAGACAAT
571887 T
1 T
571888 GATTCTTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (17 bp):
TATGTAGTAGAGACAAT
Found at i:574095 original size:10 final size:10
Alignment explanation
Indices: 574080--574106 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
574070 ATGCATCAAG
574080 CAAAAACAAA
1 CAAAAACAAA
574090 CAAAAACAAA
1 CAAAAACAAA
574100 CAAAAAC
1 CAAAAAC
574107 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:578321 original size:52 final size:51
Alignment explanation
Indices: 578241--578359 Score: 193
Period size: 52 Copynumber: 2.3 Consensus size: 51
578231 AAAAGTTGCT
* *
578241 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGTAAATTTACC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA-TTACC
* *
578293 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
578344 TGCATGTATCGATACA
1 TGCATGTATCGATACA
578360 AAGATCAGTG
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
51 20 0.32
52 43 0.68
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (51 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
Found at i:578386 original size:13 final size:13
Alignment explanation
Indices: 578368--578392 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
578358 CAAAGATCAG
578368 TGTATCGATACAA
1 TGTATCGATACAA
578381 TGTATCGATACA
1 TGTATCGATACA
578393 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:578470 original size:33 final size:33
Alignment explanation
Indices: 578433--578532 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
578423 AGTAGCTTAA
* ***
578433 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAACATTTTATGTATCGATAC
578466 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAACATTTTATGTATCGATAC
578499 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAACATTTTATGTATCGATAC
578532 A
1 A
578533 AATCGTTGAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (33 bp):
ATTGTATCGATACAACATTTTATGTATCGATAC
Found at i:578473 original size:13 final size:13
Alignment explanation
Indices: 578455--578512 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
578445 CAAAAAAATA
578455 TGTATCGATACAT
1 TGTATCGATACAT
578468 TGTATCGATACAACATTTT
1 TGTATCGAT---ACA---T
578487 ATGTATCGATACAT
1 -TGTATCGATACAT
578501 TGTATCGATACA
1 TGTATCGATACA
578513 ACATTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 3 0.08
17 3 0.08
19 1 0.03
20 9 0.24
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:578493 original size:20 final size:20
Alignment explanation
Indices: 578468--578533 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
578458 ATCGATACAT
578468 TGTATCGATACAACATTTTA
1 TGTATCGATACAACATTTTA
578488 TGTATCGAT---ACA---T-
1 TGTATCGATACAACATTTTA
578501 TGTATCGATACAACATTTTA
1 TGTATCGATACAACATTTTA
578521 TGTATCGATACAA
1 TGTATCGATACAA
578534 ATCGTTGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 9 0.23
14 1 0.03
16 3 0.08
17 3 0.08
19 1 0.03
20 22 0.56
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (20 bp):
TGTATCGATACAACATTTTA
Found at i:581050 original size:20 final size:22
Alignment explanation
Indices: 581027--581069 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
581017 AAAGCAATAA
581027 GTATCGATAC-TTCT-GGGTTT
1 GTATCGATACTTTCTAGGGTTT
*
581047 GTATTGATACTTTCTAGGGTTT
1 GTATCGATACTTTCTAGGGTTT
581069 G
1 G
581070 ACCTTTGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 4 0.20
22 7 0.35
ACGTcount: A:0.16, C:0.12, G:0.26, T:0.47
Consensus pattern (22 bp):
GTATCGATACTTTCTAGGGTTT
Found at i:582691 original size:48 final size:47
Alignment explanation
Indices: 582595--582736 Score: 220
Period size: 48 Copynumber: 3.1 Consensus size: 47
582585 TGAAGCTTGA
* *
582595 GTTTAAAC-TGTGATGCCCATCTCACCC-TT-ATC-TGGTTATGGAC
1 GTTTAAACTTGTGATGCCCATCTCACCCTTTCCTCTTGGTTATGGAT
582638 GTTTAAACTTGTGATGCCCATCTCAACCCTTTCCTCTTGGTTATGGAT
1 GTTTAAACTTGTGATGCCCATCTC-ACCCTTTCCTCTTGGTTATGGAT
582686 GTTTAAACTTTGTGATGCCCATCTCACCCTTTCCTCTTGGTTATGGAT
1 GTTTAAAC-TTGTGATGCCCATCTCACCCTTTCCTCTTGGTTATGGAT
582734 GTT
1 GTT
582737 GAACTTCCAT
Statistics
Matches: 91, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
43 8 0.09
44 15 0.16
45 4 0.04
46 2 0.02
47 2 0.02
48 44 0.48
49 16 0.18
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (47 bp):
GTTTAAACTTGTGATGCCCATCTCACCCTTTCCTCTTGGTTATGGAT
Done.