Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_pilon, whole genome shotgun sequence
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: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 30 of 56
Found at i:6303106 original size:67 final size:67
Alignment explanation
Indices: 6302998--6303129 Score: 219
Period size: 67 Copynumber: 2.0 Consensus size: 67
6302988 GCTCCATATG
* * *
6302998 GAAATCCATACACTCAATATGATTTCTTTATCATTTTAGCACATATAGTGCTCCATATGGAAATC
1 GAAATCCATACACTCAACATGATTTCCTTATCAATTTAGCACATATAGTGCTCCATATGGAAATC
6303063 AT
66 AT
* *
6303065 GAAATCCATACACTCAGCATGATTTCCTTATCAATTTAGCACATATAGTGCTCCGTATGGAAATC
1 GAAATCCATACACTCAACATGATTTCCTTATCAATTTAGCACATATAGTGCTCCATATGGAAATC
6303130 CATACACTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (67 bp):
GAAATCCATACACTCAACATGATTTCCTTATCAATTTAGCACATATAGTGCTCCATATGGAAATC
AT
Found at i:6303174 original size:126 final size:126
Alignment explanation
Indices: 6302878--6303175 Score: 321
Period size: 126 Copynumber: 2.4 Consensus size: 126
6302868 GTGCTTTTTC
* * * * *
6302878 TGGAAATCCATACACTCAGTATGATTCCCTTACCATTTTAGCACATATAATGC-CC---T----A
1 TGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATACAGTGCTCCATATGGAAA
* * * ** *
6302935 TC-TGGAAATCCATATATTCAATATGATTTCCTTATCCTTTTATCACACTCAGTGCTCCATA
66 TCAT-GAAATCCATACACTCAACATGATTTCCTTATCAATTTAGCACACTCAGTGCTCCATA
* *
6302996 TGGAAATCCATACACTCAATATGATTTCTTTATCATTTTAGCACATATAGTGCTCCATATGGAAA
1 TGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATACAGTGCTCCATATGGAAA
* * *
6303061 TCATGAAATCCATACACTCAGCATGATTTCCTTATCAATTTAGCACA-TATAGTGCTCCGTA
66 TCATGAAATCCATACACTCAACATGATTTCCTTATCAATTTAGCACACT-CAGTGCTCCATA
***
6303122 TGGAAATCCATACACTTTGTATGATTTCCTTATCATTTTAGCACACT-CAGTGCT
1 TGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACA-TACAGTGCT
6303176 ACATTCAATA
Statistics
Matches: 150, Mismatches: 19, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
118 48 0.32
119 2 0.01
122 1 0.01
125 1 0.01
126 96 0.64
127 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (126 bp):
TGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATACAGTGCTCCATATGGAAA
TCATGAAATCCATACACTCAACATGATTTCCTTATCAATTTAGCACACTCAGTGCTCCATA
Found at i:6306355 original size:20 final size:18
Alignment explanation
Indices: 6306332--6306386 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
6306322 CAATATTCCT
6306332 TTTTTATTTATATTATATCA
1 TTTTTA-TTATA-TATATCA
6306352 TTTTTATTATATATATC-
1 TTTTTATTATATATATCA
*
6306369 TTATATCATTATATATAT
1 TT-T-TTATTATATATAT
6306387 ATATGTATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 2 0.06
18 7 0.22
19 17 0.53
20 6 0.19
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTTATTATATATATCA
Found at i:6306359 original size:14 final size:14
Alignment explanation
Indices: 6306337--6306390 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
6306327 TTCCTTTTTT
6306337 ATTTATATTATATC
1 ATTTATATTATATC
*
6306351 ATTTTTATTATAT-
1 ATTTATATTATATC
*
6306364 A--TATCTTATATC
1 ATTTATATTATATC
6306376 ATTATATATATATAT
1 ATT-TATAT-TATAT
6306391 GTATAGATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
11 8 0.26
12 1 0.03
13 1 0.03
14 12 0.39
15 4 0.13
16 5 0.16
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTATATTATATC
Found at i:6306366 original size:23 final size:22
Alignment explanation
Indices: 6306331--6306395 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 22
6306321 ACAATATTCC
*
6306331 TTTT-TTATTTATATTATATCA
1 TTTTATTATATATATTATATCA
6306352 TTTTTATTATATATATCTTATATCA
1 -TTTTATTATATATA--TTATATCA
*
6306377 TTATA-TATATATATGTATA
1 TTTTATTATATATAT-TATA
6306396 GATGTATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
21 1 0.03
22 8 0.22
23 16 0.43
24 4 0.11
25 8 0.22
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTATTATATATATTATATCA
Found at i:6306377 original size:25 final size:23
Alignment explanation
Indices: 6306344--6306390 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
6306334 TTTATTTATA
*
6306344 TTATATCATTTTTATTATATATATC
1 TTATATCA-TTATA-TATATATATC
6306369 TTATATCATTATATATATATAT
1 TTATATCATTATATATATATAT
6306391 GTATAGATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 4 0.19
25 8 0.38
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (23 bp):
TTATATCATTATATATATATATC
Found at i:6306452 original size:18 final size:18
Alignment explanation
Indices: 6306429--6306494 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
6306419 ACTATGTATA
6306429 TATATTTTTTCTTAATAT
1 TATATTTTTTCTTAATAT
* *
6306447 TATATTTTATACGTTTATAT
1 TATATTTT-TTC-TTAATAT
* *
6306467 ATATATATATTCTTAATAT
1 -TATATTTTTTCTTAATAT
*
6306486 TCTATTTTT
1 TATATTTTT
6306495 GTTTTTATTT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
18 14 0.39
19 8 0.22
20 8 0.22
21 6 0.17
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (18 bp):
TATATTTTTTCTTAATAT
Found at i:6306537 original size:31 final size:30
Alignment explanation
Indices: 6306498--6306557 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
6306488 TATTTTTGTT
6306498 TTTATTTATTTATATATATTATATTTTTAC
1 TTTATTTATTTATATATATTATATTTTTAC
* * * *
6306528 TTTATTTTATTTTTTTCTATTATTTTTTTA
1 TTTA-TTTATTTATATATATTATATTTTTA
6306558 ATATCATGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (30 bp):
TTTATTTATTTATATATATTATATTTTTAC
Found at i:6306542 original size:18 final size:18
Alignment explanation
Indices: 6306497--6306553 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
6306487 CTATTTTTGT
* *
6306497 TTTTATTTATTTA-TATA
1 TTTTATTTTTTTACTTTA
* *
6306514 TATTATATTTTTACTTTA
1 TTTTATTTTTTTACTTTA
6306532 TTTTATTTTTTT-CTATTA
1 TTTTATTTTTTTACT-TTA
6306550 TTTT
1 TTTT
6306554 TTTAATATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 12 0.38
18 20 0.62
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATTTTTTTACTTTA
Found at i:6306689 original size:18 final size:17
Alignment explanation
Indices: 6306657--6306701 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
6306647 TGTACACATT
6306657 ATTTTTATT-CCTTTTTA
1 ATTTTT-TTACCTTTTTA
*
6306674 ATTTCTTTTACCTTTTTT
1 ATTT-TTTTACCTTTTTA
6306692 ATTTTTTTAC
1 ATTTTTTTAC
6306702 TCCATTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTTACCTTTTTA
Found at i:6306699 original size:17 final size:17
Alignment explanation
Indices: 6306655--6306701 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
6306645 TATGTACACA
6306655 TTATTTTTATT-CCTTTT
1 TTATTTTT-TTACCTTTT
*
6306672 TAATTTCTTTTACCTTTT
1 TTATTT-TTTTACCTTTT
6306690 TTATTTTTTTAC
1 TTATTTTTTTAC
6306702 TCCATTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTTTTTACCTTTT
Found at i:6309946 original size:7 final size:7
Alignment explanation
Indices: 6309936--6309973 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
6309926 AAAAGAGAAA
6309936 AAAAGAG
1 AAAAGAG
*
6309943 AAAAAAG
1 AAAAGAG
6309950 AAAAGAG
1 AAAAGAG
*
6309957 AAAATA-
1 AAAAGAG
6309963 AAAAGAG
1 AAAAGAG
6309970 AAAA
1 AAAA
6309974 ACAAAGGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (7 bp):
AAAAGAG
Found at i:6309955 original size:14 final size:13
Alignment explanation
Indices: 6309933--6309974 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
6309923 ACAAAAAGAG
6309933 AAAAAAAGAGAAA
1 AAAAAAAGAGAAA
6309946 AAAGAAAAGAGAAA
1 AAA-AAAAGAGAAA
*
6309960 ATAAAAAGAGAAA
1 AAAAAAAGAGAAA
6309973 AA
1 AA
6309975 CAAAGGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (13 bp):
AAAAAAAGAGAAA
Found at i:6309966 original size:13 final size:13
Alignment explanation
Indices: 6309935--6309985 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
6309925 AAAAAGAGAA
*
6309935 AAAAAGAGAAAAA
1 AAAAAGAGAAAAT
6309948 AGAAAAGAGAAAAT
1 A-AAAAGAGAAAAT
6309962 AAAAAGAGAAAA-
1 AAAAAGAGAAAAT
*
6309974 ACAAAG-GAAAAT
1 AAAAAGAGAAAAT
6309986 TGAAGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 5 0.15
12 5 0.15
13 12 0.35
14 12 0.35
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (13 bp):
AAAAAGAGAAAAT
Found at i:6310175 original size:69 final size:69
Alignment explanation
Indices: 6310057--6310194 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
6310047 GATTCAAACT
*
6310057 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
6310122 TCAA
66 TCAA
* *
6310126 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAATCACTCCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
6310191 TCAA
66 TCAA
6310195 GAGAGAGACA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
TCAA
Found at i:6311792 original size:36 final size:36
Alignment explanation
Indices: 6311745--6311970 Score: 207
Period size: 36 Copynumber: 6.4 Consensus size: 36
6311735 ATTGAAAACA
* * * *
6311745 TTTCCCTTGAAATAAAATTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
6311781 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
6311817 TTTCCCTTGAAA-AAA----AT-TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA-G
*** ** *
6311846 TTTTATTTGAAACAAATTTCATCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
** * *
6311882 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
6311919 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
6311955 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
6311971 ATCTATGAAT
Statistics
Matches: 157, Mismatches: 23, Indels: 20
0.79 0.12 0.10
Matches are distributed among these distances:
28 2 0.01
29 14 0.09
30 5 0.03
31 1 0.01
34 2 0.01
35 4 0.03
36 97 0.62
37 32 0.20
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:6311921 original size:138 final size:138
Alignment explanation
Indices: 6311765--6312024 Score: 380
Period size: 138 Copynumber: 1.9 Consensus size: 138
6311755 AATAAAATTC
* *
6311765 GTCTCTCTTGAGATAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA-
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * ** *
6311829 AAAAT-TATTTGAATATGTTTTATTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGA
66 AAAATCTA--TGAATATATTTCACCTAAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGA
6311893 ACTAAGTTTT
129 ACTAAGTTTT
*
6311903 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * * *
6311968 AAAATCTATGAATTTATTTCCCCTAAAACAAATTTTATGTCCCTTGAGACAGTTTCT
66 AAAATCTATGAATATATTTCACCTAAAACAAATTTCATCTCCCTTGAGACAGTTTCT
6312025 CTTGAAACAC
Statistics
Matches: 108, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
138 101 0.94
139 5 0.05
140 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (138 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
AAAATCTATGAATATATTTCACCTAAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAAC
TAAGTTTT
Found at i:6311929 original size:102 final size:101
Alignment explanation
Indices: 6311658--6311936 Score: 301
Period size: 101 Copynumber: 2.8 Consensus size: 101
6311648 TAAAAAGAAG
* * * * * *
6311658 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCT
1 ATTTCATCTCCCTTGAGATAGTTTCCCTTGGAACTAAATTTTGTCTCTCTTGAGACAGTTTCTCT
* * *
6311723 TGAAATATAAA-CATTGAAAACATTTCCCTTGAAATAA
66 TGAAA-A-AAATTATTGAAAACATTTCACTTGAAACAA
* * * * *
6311760 AATTCGTCTCTCTTGAGATAGTTTCCCTT-GAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCT
1 ATTTCATCTCCCTTGAGATAGTTTCCCTTGGAACTAAATTTTGTCTCTCTTGAGACAGTTTCTCT
* ** * *
6311824 TGAAAAAAATTATTTGAATATGTTTTATTTGAAACAA
66 TGAAAAAAATTA-TTGAAAACATTTCACTTGAAACAA
* ** *
6311861 ATTTCATCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCT
1 ATTTCATCTCCCTTGAGATAGTTTCCCTTGGAACTAAATTTTGTCTCTCTTGAGACAGTTTCTCT
*
6311926 TGAAACAAATT
66 TGAAAAAAATT
6311937 TTGTCTCTCT
Statistics
Matches: 146, Mismatches: 28, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
99 3 0.02
100 2 0.01
101 74 0.51
102 67 0.46
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (101 bp):
ATTTCATCTCCCTTGAGATAGTTTCCCTTGGAACTAAATTTTGTCTCTCTTGAGACAGTTTCTCT
TGAAAAAAATTATTGAAAACATTTCACTTGAAACAA
Found at i:6312032 original size:65 final size:65
Alignment explanation
Indices: 6311928--6312102 Score: 217
Period size: 65 Copynumber: 2.6 Consensus size: 65
6311918 GTTTCTCTTG
* * *
6311928 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTAT-GAATTTATTTCCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCT-TCAAATTTATTTCCCCT
6311992 A
65 A
* * *
6311993 AAACAAATTTTATGTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
6312058 TA
64 TA
* * * *
6312060 AAACAAAATTTTGTTTCCCTTGAGACTGTTTTTCATGAAACAA
1 AAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
6312103 CAAATATCTT
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
65 32 0.34
66 7 0.07
67 29 0.31
68 27 0.28
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:6314460 original size:20 final size:18
Alignment explanation
Indices: 6314390--6314491 Score: 59
Period size: 19 Copynumber: 5.5 Consensus size: 18
6314380 TTTCGTCCCC
6314390 TATATATAT-ATTTTTAAT
1 TATATATATCATTTTT-AT
* * * *
6314408 TATATTTTTTATTTAT-T
1 TATATATATCATTTTTAT
*
6314425 TACTATAT-TCCTTTTTTATT
1 TA-TATATAT-CATTTTTA-T
6314445 TATATTATATCATTTTTAT
1 TATA-TATATCATTTTTAT
*
6314464 TATATATATC-TTATATCAT
1 TATATATATCATT-T-TTAT
6314483 TATATATAT
1 TATATATAT
6314492 ATGTATAGAT
Statistics
Matches: 66, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
17 6 0.09
18 22 0.33
19 24 0.36
20 13 0.20
21 1 0.02
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (18 bp):
TATATATATCATTTTTAT
Found at i:6314471 original size:23 final size:23
Alignment explanation
Indices: 6314436--6314483 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
6314426 ACTATATTCC
*
6314436 TTTTTTATTTATA-TTATATCAT
1 TTTTTTATATATACTTATATCAT
6314458 TTTTATTATATATATCTTATATCAT
1 TTTT-TTATATATA-CTTATATCAT
6314483 T
1 T
6314484 ATATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 4 0.18
23 8 0.36
25 10 0.45
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTTTATATATACTTATATCAT
Found at i:6314640 original size:31 final size:32
Alignment explanation
Indices: 6314582--6314660 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 32
6314572 ATATATATTC
* * *
6314582 TATATATTCTATTTTT-GTTTTTATTTATTTA
1 TATATATTATATTTTTACTTTATATTTATTTA
*
6314613 TATATATTATATTTTTACTTTAT-TTTATTTT
1 TATATATTATATTTTTACTTTATATTTATTTA
* * *
6314644 TTTCTATTATTTTTTTA
1 TATATATTATATTTTTA
6314661 ATATCATGTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 36 0.90
32 4 0.10
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (32 bp):
TATATATTATATTTTTACTTTATATTTATTTA
Found at i:6314645 original size:18 final size:18
Alignment explanation
Indices: 6314600--6314656 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
6314590 CTATTTTTGT
* *
6314600 TTTTATTTATTTA-TATA
1 TTTTATTTTTTTACTTTA
* *
6314617 TATTATATTTTTACTTTA
1 TTTTATTTTTTTACTTTA
6314635 TTTTATTTTTTT-CTATTA
1 TTTTATTTTTTTACT-TTA
6314653 TTTT
1 TTTT
6314657 TTTAATATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 12 0.38
18 20 0.62
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATTTTTTTACTTTA
Found at i:6314790 original size:18 final size:17
Alignment explanation
Indices: 6314758--6314802 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
6314748 TGTACACATT
6314758 ATTTTTATT-CCTTTTTA
1 ATTTTT-TTACCTTTTTA
6314775 ATTTCTTTTACCTTTTTA
1 ATTT-TTTTACCTTTTTA
6314793 ATTTTTTTAC
1 ATTTTTTTAC
6314803 TCCATTGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTTACCTTTTTA
Found at i:6314887 original size:9 final size:9
Alignment explanation
Indices: 6314854--6314887 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
6314844 CATTTTATTC
*
6314854 ATTTTGTTT
1 ATTTTTTTT
*
6314863 ATTTTTATT
1 ATTTTTTTT
6314872 ATTTTTTTT
1 ATTTTTTTT
6314881 ATTTTTT
1 ATTTTTT
6314888 ACGTGTTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:6314888 original size:19 final size:19
Alignment explanation
Indices: 6314846--6314886 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
6314836 TTTTTTAACA
6314846 TTTTATTCATTTTGTTTAT
1 TTTTATTCATTTTGTTTAT
*
6314865 TTTTATT-ATTTTTTTTAT
1 TTTTATTCATTTTGTTTAT
6314883 TTTT
1 TTTT
6314887 TACGTGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTATTCATTTTGTTTAT
Found at i:6317429 original size:45 final size:45
Alignment explanation
Indices: 6317363--6317542 Score: 249
Period size: 45 Copynumber: 4.0 Consensus size: 45
6317353 AATTTCTTAT
* * *
6317363 CAATATACATACCATTTAATCCACAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTAAATCCATAAGCTCGTAAGCTTATTTTAC
*
6317408 CAATATACTTACCATTAAATCCATAAGCTCGTAAGCTTATTTTAT
1 CAATATACTTACCATTAAATCCATAAGCTCGTAAGCTTATTTTAC
* *
6317453 CAATATACTTACCATT-ATTCCATAAGCTCGTAAGCTTATTTTTAT
1 CAATATACTTACCATTAAATCCATAAGCTCGTAAGCTTA-TTTTAC
* * *
6317498 CAATATACTTACTA-TAATTTCATAAGCTCGTAAGCTTA-TTTAC
1 CAATATACTTACCATTAAATCCATAAGCTCGTAAGCTTATTTTAC
6317541 CA
1 CA
6317543 GTTTCATAAG
Statistics
Matches: 125, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
43 6 0.05
44 22 0.18
45 97 0.78
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (45 bp):
CAATATACTTACCATTAAATCCATAAGCTCGTAAGCTTATTTTAC
Found at i:6317494 original size:89 final size:90
Alignment explanation
Indices: 6317359--6317538 Score: 274
Period size: 89 Copynumber: 2.0 Consensus size: 90
6317349 ATAAAATTTC
6317359 TTATCAATATACATACCATTTAATCCACAAGCTCGTAAGCTTA-TTTTACCAATATACTTACCAT
1 TTATCAATATACATACCATTTAATCCACAAGCTCGTAAGCTTATTTTTACCAATATACTTACCA-
6317423 TAAATCCATAAGCTCGTAAGCTTATT
65 TAAATCCATAAGCTCGTAAGCTTATT
* * * * *
6317449 TTATCAATATACTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTTATCAATATACTTACTAT
1 TTATCAATATACATACCATTTAATCCACAAGCTCGTAAGCTTATTTTTACCAATATACTTACCAT
* *
6317513 AATTTCATAAGCTCGTAAGCTTATT
66 AAATCCATAAGCTCGTAAGCTTATT
6317538 T
1 T
6317539 ACCAGTTTCA
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
89 47 0.57
90 35 0.43
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (90 bp):
TTATCAATATACATACCATTTAATCCACAAGCTCGTAAGCTTATTTTTACCAATATACTTACCAT
AAATCCATAAGCTCGTAAGCTTATT
Found at i:6317548 original size:29 final size:29
Alignment explanation
Indices: 6317515--6317571 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
6317505 CTTACTATAA
*
6317515 TTTCATAAGCTCGTAAGCTTATTTACCAG
1 TTTCATAAGCTCGTAAGATTATTTACCAG
*
6317544 TTTCATAAGCTCGTTAGATTATTTACCA
1 TTTCATAAGCTCGTAAGATTATTTACCA
6317572 ATATTCTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (29 bp):
TTTCATAAGCTCGTAAGATTATTTACCAG
Found at i:6317591 original size:72 final size:73
Alignment explanation
Indices: 6317473--6317614 Score: 223
Period size: 72 Copynumber: 1.9 Consensus size: 73
6317463 ACCATTATTC
* *
6317473 CATAAGCTCGTAAGCTTATTTTTATCAATATACTTACTATAATTTCATAAGCTCGTAAGCTTATT
1 CATAAGCTCGTAAGATTA-TTTTACCAATATACTTACTATAATTTCATAAGCTCGTAAGCTTATT
6317538 TACCAGTTT
65 TACCAGTTT
* * *
6317547 CATAAGCTCGTTAGATTA-TTTACCAATATTCTTTCTATAATTTCATAAGCTCGTAAGCTTATTT
1 CATAAGCTCGTAAGATTATTTTACCAATATACTTACTATAATTTCATAAGCTCGTAAGCTTATTT
6317611 ACCA
66 ACCA
6317615 ATATACTTAC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
72 47 0.75
74 16 0.25
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (73 bp):
CATAAGCTCGTAAGATTATTTTACCAATATACTTACTATAATTTCATAAGCTCGTAAGCTTATTT
ACCAGTTT
Found at i:6317609 original size:43 final size:43
Alignment explanation
Indices: 6317544--6317632 Score: 133
Period size: 43 Copynumber: 2.1 Consensus size: 43
6317534 TATTTACCAG
* * * *
6317544 TTTCATAAGCTCGTTAGATTATTTACCAATATTCTTTCTATAA
1 TTTCATAAGCTCGTAAGATTATTTACCAATATACTTACTACAA
*
6317587 TTTCATAAGCTCGTAAGCTTATTTACCAATATACTTACTACAA
1 TTTCATAAGCTCGTAAGATTATTTACCAATATACTTACTACAA
6317630 TTT
1 TTT
6317633 GCATCACTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (43 bp):
TTTCATAAGCTCGTAAGATTATTTACCAATATACTTACTACAA
Found at i:6317950 original size:59 final size:59
Alignment explanation
Indices: 6317929--6318274 Score: 475
Period size: 59 Copynumber: 5.9 Consensus size: 59
6317919 GTTCTTTTTC
* * *
6317929 TGGAAATCCATACACTCAGTATGATTCCCTTA-CAATTTTAGCACATATAATGC-CCTATC
1 TGGAAATCCATACACTCAGTATGATTTCCTTATC-ATTTTAGCACATATAGTGCTCC-ATA
* * * * *
6317988 TGGAAATCCATATATTCAATATGATTTCCTTATCCTTTTAGCACACT-CAGTGCTCCATA
1 TGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACA-TATAGTGCTCCATA
* *
6318047 TGGAAATCCATACACTCATTATGATTTCTTTATCATTTTAGCACATATAGTGCTCCATA
1 TGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACATATAGTGCTCCATA
*
6318106 TGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACATATAGTGCTCCGTA
1 TGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACATATAGTGCTCCATA
* *
6318165 TGGAAATCCATGCACTCAGTATGATTTCCTTATCATTTTAGCACACT-CAGTGCTCCATA
1 TGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACA-TATAGTGCTCCATA
* * * *
6318224 TGGAAATTCATACATTCAATATGATTTCCTTATCATTTTATCACATATAGT
1 TGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACATATAGT
6318275 ACCATTTGGT
Statistics
Matches: 255, Mismatches: 26, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
58 2 0.01
59 248 0.97
60 5 0.02
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (59 bp):
TGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACATATAGTGCTCCATA
Found at i:6318014 original size:118 final size:118
Alignment explanation
Indices: 6317814--6318263 Score: 468
Period size: 118 Copynumber: 3.8 Consensus size: 118
6317804 CCTGTTCGAG
* * * *
6317814 AATCCATAC-CATTAGTATGA-TCCCATTACCATTTTTAGCACATGA-AGTGC-CTTATATGAAA
1 AATCCATACAC-TCAGTATGATTCCC-TTATCA-TTTTAGCACAT-ATAGTGCTC-CATATGGAA
* * * * * *** *
6317875 ATCCATAC-TGTTAGTATGATTTTCTTATCCTTGTAGCACCCTTAGTTCTTTTTCTGGA
61 ATCCATACAT-TCAATATGATTTCCTTATCCTTTTAGCACCCTTAGTGCTCCATATGGA
* *
6317933 AATCCATACACTCAGTATGATTCCCTTA-CAATTTTAGCACATATAATGC-CCTATCTGGAAATC
1 AATCCATACACTCAGTATGATTCCCTTATC-ATTTTAGCACATATAGTGCTCC-ATATGGAAATC
* * *
6317996 CATATATTCAATATGATTTCCTTATCCTTTTAGCACACTCAGTGCTCCATATGGA
64 CATACATTCAATATGATTTCCTTATCCTTTTAGCACCCTTAGTGCTCCATATGGA
* * *
6318051 AATCCATACACTCATTATGATTTCTTTATCATTTTAGCACATATAGTGCTCCATATGGAAATCCA
1 AATCCATACACTCAGTATGATTCCCTTATCATTTTAGCACATATAGTGCTCCATATGGAAATCCA
* * * * *
6318116 TACACTCAGTATGATTTCCTTATCATTTTAGCA-CATATAGTGCTCCGTATGGA
66 TACATTCAATATGATTTCCTTATCCTTTTAGCACCCT-TAGTGCTCCATATGGA
* * * *
6318169 AATCCATGCACTCAGTATGATTTCCTTATCATTTTAGCACACT-CAGTGCTCCATATGGAAATTC
1 AATCCATACACTCAGTATGATTCCCTTATCATTTTAGCACA-TATAGTGCTCCATATGGAAATCC
*
6318233 ATACATTCAATATGATTTCCTTATCATTTTA
65 ATACATTCAATATGATTTCCTTATCCTTTTA
6318264 TCACATATAG
Statistics
Matches: 284, Mismatches: 37, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
117 2 0.01
118 251 0.88
119 26 0.09
120 5 0.02
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (118 bp):
AATCCATACACTCAGTATGATTCCCTTATCATTTTAGCACATATAGTGCTCCATATGGAAATCCA
TACATTCAATATGATTTCCTTATCCTTTTAGCACCCTTAGTGCTCCATATGGA
Found at i:6318072 original size:177 final size:177
Alignment explanation
Indices: 6317889--6318274 Score: 503
Period size: 177 Copynumber: 2.2 Consensus size: 177
6317879 ATACTGTTAG
* * * *** *
6317889 TATGATTTTCTTATCCTTGTAGCACCCT-TAGTTCTTTTTCTGGAAATCCATACACTCAGTATGA
1 TATGATTTTCTTATCATTGTAGCA-CATATAGTGCTCCATATGGAAATCCATACACTCAGTATGA
* *
6317953 TTCCCTTA-CAATTTTAGCACATATAATGC-CC-TATCTGGAAATCCATATATTCAATATGATTT
65 TTCCCTTATC-ATTTTAGCACATATAATGCTCCGTA--TGGAAATCCATACACTCAATATGATTT
* *
6318015 CCTTATCCTTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAT
127 CCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAA
*
6318066 TATGA-TTTCTTTATCATTTTAGCACATATAGTGCTCCATATGGAAATCCATACACTCAGTATGA
1 TATGATTTTC-TTATCATTGTAGCACATATAGTGCTCCATATGGAAATCCATACACTCAGTATGA
* * * *
6318130 TTTCCTTATCATTTTAGCACATATAGTGCTCCGTATGGAAATCCATGCACTCAGTATGATTTCCT
65 TTCCCTTATCATTTTAGCACATATAATGCTCCGTATGGAAATCCATACACTCAATATGATTTCCT
* *
6318195 TATCATTTTAGCACACTCAGTGCTCCATATGGAAATTCATACATTCAA
130 TATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAA
* * *
6318243 TATGATTTCCTTATCATTTTATCACATATAGT
1 TATGATTTTCTTATCATTGTAGCACATATAGT
6318275 ACCATTTGGT
Statistics
Matches: 183, Mismatches: 20, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
176 6 0.03
177 169 0.92
178 6 0.03
179 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.38
Consensus pattern (177 bp):
TATGATTTTCTTATCATTGTAGCACATATAGTGCTCCATATGGAAATCCATACACTCAGTATGAT
TCCCTTATCATTTTAGCACATATAATGCTCCGTATGGAAATCCATACACTCAATATGATTTCCTT
ATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAA
Found at i:6321382 original size:61 final size:61
Alignment explanation
Indices: 6321263--6321382 Score: 143
Period size: 61 Copynumber: 2.0 Consensus size: 61
6321253 TGCATGTGGA
* * **
6321263 GGGCACAACCTTATGTGTCTTATCCGGATTAGCAAAAGAGTGTAAACCTAGTGTAGGTTGT
1 GGGCACAACCTTATGTGTCTTATCCGAATTAGCAAAAGAGCGTAAACCTAGTACAGGTTGT
* ** * *
6321324 GGGCACGACCTTATGTGT-TATATCCGAATTAGCACTAGAGCGTAAGCTTAGTACAGGTT
1 GGGCACAACCTTATGTGTCT-TATCCGAATTAGCAAAAGAGCGTAAACCTAGTACAGGTT
6321383 TAACACTACA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 1 0.02
61 48 0.98
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (61 bp):
GGGCACAACCTTATGTGTCTTATCCGAATTAGCAAAAGAGCGTAAACCTAGTACAGGTTGT
Found at i:6329880 original size:10 final size:10
Alignment explanation
Indices: 6329865--6329897 Score: 52
Period size: 9 Copynumber: 3.5 Consensus size: 10
6329855 TTTTTCATTA
6329865 AAAAATTCAC
1 AAAAATTCAC
6329875 AAAAATTCA-
1 AAAAATTCAC
6329884 AAAAATT-AC
1 AAAAATTCAC
6329893 AAAAA
1 AAAAA
6329898 AAGAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 1 0.05
9 12 0.55
10 9 0.41
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAAATTCAC
Found at i:6329898 original size:10 final size:9
Alignment explanation
Indices: 6329864--6329898 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
6329854 GTTTTTCATT
6329864 AAAAAATTC
1 AAAAAATTC
6329873 ACAAAAATTC
1 A-AAAAATTC
6329883 AAAAAATTAC
1 AAAAAATT-C
6329893 AAAAAA
1 AAAAAA
6329899 AGAATTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAAAATTC
Found at i:6330130 original size:13 final size:15
Alignment explanation
Indices: 6330086--6330125 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
6330076 GTGAAAAGTT
6330086 ATATATTGAAACTAC
1 ATATATTGAAACTAC
6330101 ATATATTGAAACTAC
1 ATATATTGAAACTAC
6330116 ATATATTGAA
1 ATATATTGAA
6330126 TACATTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.35
Consensus pattern (15 bp):
ATATATTGAAACTAC
Found at i:6330630 original size:3 final size:3
Alignment explanation
Indices: 6330617--6330652 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
6330607 TCTACAAAAA
6330617 TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
6330653 TACACGTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:6335666 original size:54 final size:53
Alignment explanation
Indices: 6335430--6335745 Score: 348
Period size: 54 Copynumber: 5.8 Consensus size: 53
6335420 CCGATACAAT
* * * ** *
6335430 AATTCACAAACTCATTATGAATTACGTGGGGTTGCACACATAGTGTCAATACGGA
1 AATTCATAAACTTATTATGAATTTC-TTAGGTTGCACACATAGT-ACAATACGGA
* * * * * * *
6335485 AATTCATAAAATCATTATGAATTTCGTGAGATTGCAAACATAGTGCCAATAAGGA
1 AATTCATAAACTTATTATGAATTTC-TTAGGTTGCACACATAGT-ACAATACGGA
*
6335540 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACA-ATACTGT-CAATACGAA
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATA--GTACAATACGGA
* * * * *
6335593 AATTCATAAACTTGTTATGAACTTCTTAAGTTGCACACAAAGTACAAATATGGA
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTAC-AATACGGA
* *
6335647 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTTCCAATACAGA
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAG-TACAATACGGA
*
6335701 AATTCATAAACTTATTATGAATTTCCTAGGTTGCACACATAGTAC
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTAC
6335746 CCATTCGGTA
Statistics
Matches: 225, Mismatches: 30, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
52 2 0.01
53 47 0.21
54 102 0.45
55 74 0.33
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (53 bp):
AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTACAATACGGA
Found at i:6335745 original size:108 final size:107
Alignment explanation
Indices: 6335430--6335745 Score: 393
Period size: 108 Copynumber: 2.9 Consensus size: 107
6335420 CCGATACAAT
* * * **
6335430 AATTCACAAACTCATTATGAATTACGTGGGGTTGCACACATAGTGTCAATACGGAAATTCATAAA
1 AATTCATAAACTTATTATGAATTTC-TTAGGTTGCACACATAGTGTCAATAC-GAAATTCATAAA
* * * * * * *
6335495 ATCATTATGAATTTCGTGAGATTGCAAACATAGTGCCAATAAGGA
64 CTTATTATGAATTTCCT-AGGTTGCACACATAGTACAAATAAGGA
*
6335540 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACA-ATACTGTCAATACGAAAATTCATAAAC
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGTCAATACG-AAATTCATAAAC
* * * * * *
6335604 TTGTTATGAACTTCTTAAGTTGCACACAAAGTACAAATATGGA
65 TTATTATGAATTTCCTAGGTTGCACACATAGTACAAATAAGGA
6335647 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGT-TCCAATACAGAAATTCATAAA
1 AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGT-CAATAC-GAAATTCATAAA
6335711 CTTATTATGAATTTCCTAGGTTGCACACATAGTAC
64 CTTATTATGAATTTCCTAGGTTGCACACATAGTAC
6335746 CCATTCGGTA
Statistics
Matches: 178, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
107 59 0.33
108 86 0.48
109 11 0.06
110 22 0.12
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (107 bp):
AATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGTCAATACGAAATTCATAAACT
TATTATGAATTTCCTAGGTTGCACACATAGTACAAATAAGGA
Found at i:6342569 original size:54 final size:54
Alignment explanation
Indices: 6342370--6342758 Score: 534
Period size: 54 Copynumber: 7.2 Consensus size: 54
6342360 ACGTGGGGTA
* * *
6342370 GCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAAGTT
1 GCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTC-TTAAGTT
** *
6342425 GCACACATAGTGCCAATACGGGAATTCATAAACTTATTATGAATTTCTT-AGCCT
1 GCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG-TT
* *
6342479 GCACACA-AGTGCCAATAC-AGAAATTCATAAATTTATTATGAACTTCTTAAGTT
1 GCACACATAGTGCCAATACGA-AAATTCATAAACTTATTATGAATTTCTTAAGTT
* *
6342532 GCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTATGTT
1 GCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTT
* *
6342586 GCACACATAGTGCCAATAC-AGAAATTCATAAACTTATTATGAACTTCATAAGTT
1 GCACACATAGTGCCAATACGA-AAATTCATAAACTTATTATGAATTTCTTAAGTT
* * * * *
6342640 GCACACAAAGTACAAATATGAAAATTCATAAACTTATTATGAATTTCTTAGGTT
1 GCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTT
* * *
6342694 GCACACATAGTTCCAATACAAAAATTCATAAACTTATTATGAATTTCTTAGGTT
1 GCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTT
6342748 GCACACATAGT
1 GCACACATAGT
6342759 ACCATTCAGT
Statistics
Matches: 299, Mismatches: 28, Indels: 15
0.87 0.08 0.04
Matches are distributed among these distances:
53 47 0.16
54 205 0.69
55 47 0.16
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (54 bp):
GCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTT
Found at i:6343182 original size:20 final size:20
Alignment explanation
Indices: 6343157--6343205 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
6343147 TTTTCAAAAA
6343157 TGGTATCGAAACCTTCCTCT
1 TGGTATCGAAACCTTCCTCT
*
6343177 TGGTATCGATACCTTCCTCT
1 TGGTATCGAAACCTTCCTCT
*
6343197 TGGCATCGA
1 TGGTATCGA
6343206 TGCCCCCACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (20 bp):
TGGTATCGAAACCTTCCTCT
Found at i:6346157 original size:16 final size:16
Alignment explanation
Indices: 6346136--6346167 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6346126 AAAAAATATT
6346136 TCCATTAAGAAACATA
1 TCCATTAAGAAACATA
6346152 TCCATTAAGAAACATA
1 TCCATTAAGAAACATA
6346168 ATAAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (16 bp):
TCCATTAAGAAACATA
Found at i:6350815 original size:25 final size:24
Alignment explanation
Indices: 6350765--6350819 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
6350755 TAAAATAACA
6350765 TTTTTTTCATTTTTTGTTTCTATT
1 TTTTTTTCATTTTTTGTTTCTATT
* *
6350789 TTTTTTTTATTTTTT-TATTCT-TC
1 TTTTTTTCATTTTTTGT-TTCTATT
6350812 TTTTTTTC
1 TTTTTTTC
6350820 GCATGCTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.07, C:0.09, G:0.02, T:0.82
Consensus pattern (24 bp):
TTTTTTTCATTTTTTGTTTCTATT
Found at i:6352411 original size:31 final size:31
Alignment explanation
Indices: 6352375--6352477 Score: 188
Period size: 31 Copynumber: 3.3 Consensus size: 31
6352365 AATCTATAAT
6352375 TAAAATTTTATATAAAGTTCAGGGGTTAAAA
1 TAAAATTTTATATAAAGTTCAGGGGTTAAAA
6352406 TAAAATTTTATATAAAGTTCAGGGGTTAAAA
1 TAAAATTTTATATAAAGTTCAGGGGTTAAAA
* *
6352437 TAAAATTTTATATGAAGTTTAGGGGTTAAAA
1 TAAAATTTTATATAAAGTTCAGGGGTTAAAA
6352468 TAAAATTTTA
1 TAAAATTTTA
6352478 CCCTTTCATT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 70 1.00
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.38
Consensus pattern (31 bp):
TAAAATTTTATATAAAGTTCAGGGGTTAAAA
Found at i:6353256 original size:50 final size:50
Alignment explanation
Indices: 6353191--6353291 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
6353181 TCTATTTCAT
* *
6353191 GCGTTTTCTCGAACTACGAAATTTCCAATGAGAACTTCTATGATCGACAA
1 GCGTTTTCTCAAACTAAGAAATTTCCAATGAGAACTTCTATGATCGACAA
6353241 GCGTTTTCTCAAACTAAGAAATTTCCAATGAGAACTTCTATGATCGACAA
1 GCGTTTTCTCAAACTAAGAAATTTCCAATGAGAACTTCTATGATCGACAA
6353291 G
1 G
6353292 ATCCTTCAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.30
Consensus pattern (50 bp):
GCGTTTTCTCAAACTAAGAAATTTCCAATGAGAACTTCTATGATCGACAA
Found at i:6353520 original size:22 final size:22
Alignment explanation
Indices: 6353492--6353533 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
6353482 GATTTAAAAC
6353492 GAACCAAATGCGAACCAGAAAG
1 GAACCAAATGCGAACCAGAAAG
* *
6353514 GAACCAAATGTGAATCAGAA
1 GAACCAAATGCGAACCAGAA
6353534 TTAATCGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.19, G:0.21, T:0.10
Consensus pattern (22 bp):
GAACCAAATGCGAACCAGAAAG
Found at i:6372303 original size:29 final size:29
Alignment explanation
Indices: 6372232--6372297 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
6372222 AACAAAGGGA
6372232 TTAGAAACTCGTTTTAAAGCTCTAAGTAG
1 TTAGAAACTCGTTTTAAAGCTCTAAGTAG
6372261 TTAGAAACTCGTTTTAAAGCTCTAAGTAG
1 TTAGAAACTCGTTTTAAAGCTCTAAGTAG
6372290 TTAGAAAC
1 TTAGAAAC
6372298 ATGTTTCCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (29 bp):
TTAGAAACTCGTTTTAAAGCTCTAAGTAG
Found at i:6379253 original size:26 final size:26
Alignment explanation
Indices: 6379224--6379274 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
6379214 CCAAATAACA
*
6379224 TATATATACATATGACACGAATATAC
1 TATATAAACATATGACACGAATATAC
*
6379250 TATATAAACATATGACACGCATATA
1 TATATAAACATATGACACGAATATA
6379275 AAAAATATGT
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:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (26 bp):
TATATAAACATATGACACGAATATAC
Found at i:6379775 original size:26 final size:27
Alignment explanation
Indices: 6379746--6379809 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
6379736 TTAAAGCAAT
6379746 TTATAACATTTTTTTAAT-AAAAAAAC
1 TTATAACATTTTTTTAATAAAAAAAAC
6379772 TTATAACATTTTTTTAATAAAAAAAAC
1 TTATAACATTTTTTTAATAAAAAAAAC
6379799 TTATAACATTT
1 TTATAACATTT
6379810 CTGGTCTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 18 0.49
27 19 0.51
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (27 bp):
TTATAACATTTTTTTAATAAAAAAAAC
Found at i:6382374 original size:20 final size:20
Alignment explanation
Indices: 6382339--6382376 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6382329 ATCTTATATT
6382339 TTTAATAAATATTATAAAAA
1 TTTAATAAATATTATAAAAA
6382359 TTTAA-AAATATATATAAA
1 TTTAATAAATAT-TATAAA
6382377 TAAATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TTTAATAAATATTATAAAAA
Found at i:6382385 original size:23 final size:21
Alignment explanation
Indices: 6382338--6382387 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 21
6382328 TATCTTATAT
6382338 TTTTAATAAATATTATAAAAA
1 TTTTAATAAATATTATAAAAA
6382359 -TTTAA-AAATATATATAAATAAA
1 TTTTAATAAATAT-TAT-AA-AAA
6382381 TTTTAAT
1 TTTTAAT
6382388 TTAATCACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 6 0.25
20 8 0.33
21 2 0.08
22 3 0.12
23 5 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTTAATAAATATTATAAAAA
Found at i:6382438 original size:2 final size:2
Alignment explanation
Indices: 6382431--6382467 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6382421 ATATCAGAGA
6382431 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6382468 AAGAAGGCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6382774 original size:5 final size:5
Alignment explanation
Indices: 6382755--6382792 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
6382745 CGCCGTCTGT
* *
6382755 CTCGT CTCGG CTCGG CTCGG CACGG CTCGG CTCGG CTC
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTC
6382793 ATGGTCGTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.03, C:0.42, G:0.34, T:0.21
Consensus pattern (5 bp):
CTCGG
Found at i:6388691 original size:6 final size:6
Alignment explanation
Indices: 6388680--6388704 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6388670 TCGGCTCGGC
6388680 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
6388705 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:6398990 original size:47 final size:47
Alignment explanation
Indices: 6398937--6399031 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
6398927 ACTTAGACAC
*
6398937 ATAGTTAACAACAACAAGAATGTAAAGATTACTAAAGGATGATGGAT
1 ATAGTTAACAACAACAAGAATGTAAACATTACTAAAGGATGATGGAT
**
6398984 ATAGTTAACAATGACAAGAATGTAAACATTACTAAAGGATGATGGAT
1 ATAGTTAACAACAACAAGAATGTAAACATTACTAAAGGATGATGGAT
6399031 A
1 A
6399032 AGGTCCCATG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.48, C:0.08, G:0.19, T:0.24
Consensus pattern (47 bp):
ATAGTTAACAACAACAAGAATGTAAACATTACTAAAGGATGATGGAT
Found at i:6407015 original size:10 final size:10
Alignment explanation
Indices: 6407000--6407027 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
6406990 CTACATAAAC
6407000 AAACAACCGA
1 AAACAACCGA
6407010 AAACAACCGA
1 AAACAACCGA
6407020 AAACAACC
1 AAACAACC
6407028 CTATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.32, G:0.07, T:0.00
Consensus pattern (10 bp):
AAACAACCGA
Found at i:6415649 original size:20 final size:20
Alignment explanation
Indices: 6415615--6415661 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
6415605 GAATAGTATT
**
6415615 GTACTGTATGTATAGTACCG
1 GTACTGTATCAATAGTACCG
*
6415635 GTACTGTATCAATAGTATCG
1 GTACTGTATCAATAGTACCG
*
6415655 ATACTGT
1 GTACTGT
6415662 GTGAACAGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
GTACTGTATCAATAGTACCG
Found at i:6415738 original size:19 final size:21
Alignment explanation
Indices: 6415710--6415751 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
6415700 AATGTAAAAT
*
6415710 GTGTATCGATAC-CT-CTACA
1 GTGTACCGATACACTGCTACA
6415729 GTGTACCGATACACTGCTACA
1 GTGTACCGATACACTGCTACA
6415750 GT
1 GT
6415752 AATTTCAGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
20 2 0.10
21 7 0.35
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (21 bp):
GTGTACCGATACACTGCTACA
Found at i:6418234 original size:2 final size:2
Alignment explanation
Indices: 6418227--6418256 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6418217 ATGTGTAACA
6418227 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6418257 GCACAGTGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6420424 original size:245 final size:243
Alignment explanation
Indices: 6419984--6420461 Score: 762
Period size: 245 Copynumber: 2.0 Consensus size: 243
6419974 TGTGTCTAAC
6419984 ATAAACTAAAAATAATAAAGTCCATATAATAATATGATTATTATTAAATATCCTTAGTCGAATAT
1 ATAAACTAAAAATAATAAAGTCCATATAATAATATGATTATTATTAAATATCCTTAGTCGAATAT
* * ** *
6420049 TATTATGGGTATGGACAATAATAATATGTTTAAGACTAATGTGTTATTGATTGATGACAATGAGT
66 TATTATGGGCATGGACAATAATAATACGTTTAAGACTAACATGTTATTAATTGATGACAATGAGT
* * *
6420114 TGTCATTGACATAAAGATGTCAGGATCGATACAAGAATATATTGTTAGAGAACAATGTATTGGAT
131 TGTCATTAACATAAAGATGTCAGAATCGATACAAGAATATATTGTTAGAGAACAATATATTGGAT
6420179 TGACCCGCCATGAGAATATGTATTGGATTATTATGTGATTATTATTAA
196 TGACCCGCCATGAGAATATGTATTGGATTATTATGTGATTATTATTAA
*
6420227 ATAAACTAAAAGATAATAATGTCCATATAATAATATGATTATTATTAAAATATCCTTAGTC-AAG
1 ATAAACTAAAA-ATAATAAAGTCCATATAATAATATGATTATTATT-AAATATCCTTAGTCGAA-
6420291 TATTATTATGGGCATGGACAATAATAATACGCTTT-AGACTAACATGTTATTAATTGATGACAAT
63 TATTATTATGGGCATGGACAATAATAATACG-TTTAAGACTAACATGTTATTAATTGATGACAAT
* * * *
6420355 GAGTTGTCATTAACATAGAGATGTCAGAATTGATACATGAATATATTGTTAGAGAATAATATATT
127 GAGTTGTCATTAACATAAAGATGTCAGAATCGATACAAGAATATATTGTTAGAGAACAATATATT
* * *
6420420 GGATTGACCCGCTATGAGTATATGTCTTGGATTATTATGTGA
192 GGATTGACCCGCCATGAGAATATGTATTGGATTATTATGTGA
6420462 CAGTCATGAT
Statistics
Matches: 215, Mismatches: 16, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
243 11 0.05
244 35 0.16
245 166 0.77
246 3 0.01
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.36
Consensus pattern (243 bp):
ATAAACTAAAAATAATAAAGTCCATATAATAATATGATTATTATTAAATATCCTTAGTCGAATAT
TATTATGGGCATGGACAATAATAATACGTTTAAGACTAACATGTTATTAATTGATGACAATGAGT
TGTCATTAACATAAAGATGTCAGAATCGATACAAGAATATATTGTTAGAGAACAATATATTGGAT
TGACCCGCCATGAGAATATGTATTGGATTATTATGTGATTATTATTAA
Found at i:6434801 original size:44 final size:45
Alignment explanation
Indices: 6434679--6434803 Score: 189
Period size: 46 Copynumber: 2.8 Consensus size: 45
6434669 GATAAAATCT
*
6434679 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATATA
*
6434724 CTTACCATTTAATACCATAAGTTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTT-ATACCATAAGCTCGTAAGCTTATTTTACCAATATA
* * *
6434770 CTTGCCA-TTATTCCATAAGCTCTTAAGCTTATTT
1 CTTACCATTTATACCATAAGCTCGTAAGCTTATTT
6434804 GCCTGGTTAC
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
44 22 0.30
45 12 0.16
46 39 0.53
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:6434964 original size:40 final size:40
Alignment explanation
Indices: 6434891--6434966 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
6434881 GTCAATTGTC
* * *
6434891 GCACCGAAGTGCTGAGGTCGTGCTTTGCTCACCTAATAAT
1 GCACCGAAGTGCTGAGGTCGGGCTTTACCCACCTAATAAT
* *
6434931 GCACCGTAGTGCTGAGGTCGGGTTTTACCCACCTAA
1 GCACCGAAGTGCTGAGGTCGGGCTTTACCCACCTAA
6434967 CTTGTACTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (40 bp):
GCACCGAAGTGCTGAGGTCGGGCTTTACCCACCTAATAAT
Found at i:6436904 original size:30 final size:30
Alignment explanation
Indices: 6436868--6436940 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 30
6436858 AAAATTACAT
* *
6436868 TTTGGTCCCTAAACTTT-TCAAAGTTTATAC
1 TTTGGTCCCTAAACTTTACCAAA-TTTATAA
6436898 TTTGGTCACC-AAACTTTACCAAATTTATAA
1 TTTGGTC-CCTAAACTTTACCAAATTTATAA
6436928 TTTGG-CCACTAAA
1 TTTGGTCC-CTAAA
6436941 TAAATCCATT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
28 1 0.03
29 2 0.05
30 28 0.76
31 6 0.16
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.38
Consensus pattern (30 bp):
TTTGGTCCCTAAACTTTACCAAATTTATAA
Found at i:6438594 original size:2 final size:2
Alignment explanation
Indices: 6438587--6438624 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6438577 ACCAGTGAAG
6438587 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6438625 ATCATTTCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6438679 original size:38 final size:36
Alignment explanation
Indices: 6438636--6438715 Score: 99
Period size: 38 Copynumber: 2.2 Consensus size: 36
6438626 TCATTTCTCA
*
6438636 TTTTTTC-TCTTTTTCTTTTCTTTTCTTTTTCTATATGT
1 TTTTTTCGTCTTTTTCTTTT-TATTCTTTTT-T-TATGT
* *
6438674 TTTTTTCGTTTTTTTCTTTTTATTCTTTTTTTTTGT
1 TTTTTTCGTCTTTTTCTTTTTATTCTTTTTTTATGT
6438710 TTTTTT
1 TTTTTT
6438716 GTTTTCTGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 10 0.26
37 1 0.03
38 16 0.42
39 11 0.29
ACGTcount: A:0.04, C:0.11, G:0.04, T:0.81
Consensus pattern (36 bp):
TTTTTTCGTCTTTTTCTTTTTATTCTTTTTTTATGT
Found at i:6438686 original size:9 final size:9
Alignment explanation
Indices: 6438672--6438720 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
6438662 TTTTCTATAT
6438672 GTTTTTTTC
1 GTTTTTTTC
6438681 GTTTTTTTC
1 GTTTTTTTC
6438690 -TTTTTATTC
1 GTTTTT-TTC
* *
6438699 TTTTTTTTT
1 GTTTTTTTC
6438708 GTTTTTTT-
1 GTTTTTTTC
6438716 GTTTT
1 GTTTT
6438721 CTGTTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
8 10 0.28
9 21 0.58
10 5 0.14
ACGTcount: A:0.02, C:0.06, G:0.08, T:0.84
Consensus pattern (9 bp):
GTTTTTTTC
Found at i:6441702 original size:179 final size:179
Alignment explanation
Indices: 6441402--6441768 Score: 700
Period size: 179 Copynumber: 2.1 Consensus size: 179
6441392 ATACGCTAAG
* *
6441402 TATATACTTAGTGAGGTAATTAAAACAATAAACAGTGCAATACAATTCATGCATGATTTTCAAAG
1 TATATACTTAGTGAGGCAATTAAAACAATAAACAGTGCAATACAATTCATGCATGATTTCCAAAG
6441467 TAAAAAACAAATGCCATTAGATCATGTTACAAACATATCTAACATTTTTCCATGATCAAAATAAG
66 TAAAAAACAAATGCCATTAGATCATGTTACAAACATATCTAACATTTTTCCATGATCAAAATAAG
6441532 ATAAAATCTCTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCA
131 ATAAAATCTCTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCA
6441581 TATATACTTAGTGAGGCAATTAAAACAATAAACAGTGCAATACAATTCATGCATGATTTCCAAAG
1 TATATACTTAGTGAGGCAATTAAAACAATAAACAGTGCAATACAATTCATGCATGATTTCCAAAG
*
6441646 TCAAAAACAAATGCCATTAGATCATGTTACAAACATATCTAACATTTTTCCATGATCAAAATAAG
66 TAAAAAACAAATGCCATTAGATCATGTTACAAACATATCTAACATTTTTCCATGATCAAAATAAG
6441711 ATAAAATCTCTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCA
131 ATAAAATCTCTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCA
6441760 -ATATACTTA
1 TATATACTTA
6441769 CCATTTAATA
Statistics
Matches: 185, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
178 9 0.05
179 176 0.95
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (179 bp):
TATATACTTAGTGAGGCAATTAAAACAATAAACAGTGCAATACAATTCATGCATGATTTCCAAAG
TAAAAAACAAATGCCATTAGATCATGTTACAAACATATCTAACATTTTTCCATGATCAAAATAAG
ATAAAATCTCTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCA
Found at i:6441842 original size:44 final size:45
Alignment explanation
Indices: 6441720--6441844 Score: 180
Period size: 46 Copynumber: 2.8 Consensus size: 45
6441710 GATAAAATCT
*
6441720 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
6441765 CTTACCATTTAATACCATAAGTTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT-ATACCATAAGCTCGTAAGCTTATTTTACCAATATA
** *
6441811 CTTGGCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATACCATAAGCTCGTAAGCTTATTT
6441845 GTCTGGTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
44 23 0.32
45 12 0.17
46 37 0.51
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:6442005 original size:40 final size:40
Alignment explanation
Indices: 6441931--6442007 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
6441921 AGTCAATTGT
* *
6441931 TGCACCGAAGTGCTGAGATCGAGCTTTGCTCACCTAATAA
1 TGCACCGAAGTGCTGAGATCGAGCTTTACCCACCTAATAA
* * * *
6441971 TGCACCGTAGTGCTGAGGTCGGGTTTTACCCACCTAA
1 TGCACCGAAGTGCTGAGATCGAGCTTTACCCACCTAA
6442008 CTTGTACTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
TGCACCGAAGTGCTGAGATCGAGCTTTACCCACCTAATAA
Found at i:6446372 original size:2 final size:2
Alignment explanation
Indices: 6446367--6446394 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6446357 CATAATTCCC
6446367 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6446395 GCATTTCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6446715 original size:57 final size:56
Alignment explanation
Indices: 6446651--6446777 Score: 152
Period size: 57 Copynumber: 2.2 Consensus size: 56
6446641 TAAATTTTAT
** *
6446651 ATTCGGATCGGATATTTGA-ATATCCGAAATTTTGGATATCCGGTTTTTTCGGATCGG
1 ATTCGGATC-GATATTTGAGATATCCGAAATTTTGGATAT-CGGAATTTTCGGATAGG
* *
6446708 ATTCGGATC-ATGATTTTAGATATCCGAAATTTTGGATATCTGAATTTTCGGATAGG
1 ATTCGGATCGAT-ATTTGAGATATCCGAAATTTTGGATATCGGAATTTTCGGATAGG
6446764 ATT-GGATCCGATAT
1 ATTCGGAT-CGATAT
6446778 CCGAATTTGC
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
55 6 0.10
56 24 0.39
57 31 0.51
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (56 bp):
ATTCGGATCGATATTTGAGATATCCGAAATTTTGGATATCGGAATTTTCGGATAGG
Found at i:6446755 original size:15 final size:16
Alignment explanation
Indices: 6446720--6446761 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
6446710 TCGGATCATG
*
6446720 ATTTTAGATATCCGAA
1 ATTTTGGATATCCGAA
*
6446736 ATTTTGGATATCTG-A
1 ATTTTGGATATCCGAA
6446751 ATTTTCGGATA
1 ATTTT-GGATA
6446762 GGATTGGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.43
Consensus pattern (16 bp):
ATTTTGGATATCCGAA
Found at i:6449015 original size:33 final size:33
Alignment explanation
Indices: 6448973--6449035 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
6448963 TACATGCATC
*
6448973 ATCCCATTGATTGACTTTGGTGATCAAGTCAAT
1 ATCCCATTGATTGACTTTGATGATCAAGTCAAT
* *
6449006 ATCCCATTGATTTATTTTGATGATCAAGTC
1 ATCCCATTGATTGACTTTGATGATCAAGTC
6449036 GATCAAACCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (33 bp):
ATCCCATTGATTGACTTTGATGATCAAGTCAAT
Found at i:6460623 original size:19 final size:20
Alignment explanation
Indices: 6460599--6460650 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
6460589 TAGAAAATTA
*
6460599 ATCCCCAATGGCTCC-AAAC
1 ATCCCCAACGGCTCCAAAAC
6460618 ATCCCCAACGGCTCCAAAAC
1 ATCCCCAACGGCTCCAAAAC
6460638 ATCCCCAACGGCT
1 ATCCCCAACGGCT
6460651 AGAAACATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.31, C:0.44, G:0.12, T:0.13
Consensus pattern (20 bp):
ATCCCCAACGGCTCCAAAAC
Found at i:6460658 original size:19 final size:18
Alignment explanation
Indices: 6460599--6460658 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 18
6460589 TAGAAAATTA
* *
6460599 ATCCCCAATGGCTCCAAAC
1 ATCCCCAACGGCT-AAAAC
6460618 ATCCCCAACGGCTCCAAAAC
1 ATCCCCAACGGCT--AAAAC
6460638 ATCCCCAACGGCTAGAAAC
1 ATCCCCAACGGCTA-AAAC
6460657 AT
1 AT
6460659 TCACAAACTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.03
19 18 0.49
20 18 0.49
ACGTcount: A:0.35, C:0.40, G:0.12, T:0.13
Consensus pattern (18 bp):
ATCCCCAACGGCTAAAAC
Found at i:6480532 original size:19 final size:19
Alignment explanation
Indices: 6480508--6480557 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
6480498 AATCTCTTTA
6480508 ATTTGTTTATTTAATTATT
1 ATTTGTTTATTTAATTATT
6480527 ATTTGTTTATTTAATTATT
1 ATTTGTTTATTTAATTATT
6480546 ATTTGTTTATTT
1 ATTTGTTTATTT
6480558 TAACCACAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (19 bp):
ATTTGTTTATTTAATTATT
Found at i:6486418 original size:28 final size:28
Alignment explanation
Indices: 6486336--6486428 Score: 97
Period size: 28 Copynumber: 3.5 Consensus size: 28
6486326 AACAAAAAAT
*
6486336 CAGTGCAGAAAAACTGACTTGGTTCAAA
1 CAGTGCAGAAAAACTGATTTGGTTCAAA
* * **
6486364 CTGTGCAG-AAAA---ATTCGAAT-AGAA
1 CAGTGCAGAAAAACTGATTTGGTTCA-AA
6486388 CAGTGCAGAAAAACTGATTTGGTTCAAA
1 CAGTGCAGAAAAACTGATTTGGTTCAAA
6486416 CAGTGCAGAAAAA
1 CAGTGCAGAAAAA
6486429 TACACAGCAG
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
23 1 0.02
24 13 0.26
25 4 0.08
27 4 0.08
28 27 0.54
29 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (28 bp):
CAGTGCAGAAAAACTGATTTGGTTCAAA
Found at i:6488191 original size:76 final size:76
Alignment explanation
Indices: 6488100--6488269 Score: 254
Period size: 76 Copynumber: 2.2 Consensus size: 76
6488090 TTACACTCAA
*
6488100 ATTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGGATATTATTTTAAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGT
6488164 ATTTTAATTAAG
65 ATTTTAATTAAG
* * * *
6488176 TTTTAGGATATTATTTT-TATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTA
1 ATTTAGGATATTATTTTAAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTA
*
6488240 TTTTAATTAGG
66 TTTTAATTAAG
*
6488251 ATTTAGGATATTATATTAA
1 ATTTAGGATATTATTTTAA
6488270 TTTTAGGTAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
75 40 0.48
76 43 0.52
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (76 bp):
ATTTAGGATATTATTTTAAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTA
TTTTAATTAAG
Found at i:6488250 original size:19 final size:19
Alignment explanation
Indices: 6488222--6488283 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
6488212 TGTATTTTAG
*
6488222 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
6488241 TTTAATTAGGATTTAGGAT
1 TTTAATTAGGTTTTAGTAT
* *
6488260 ATTATATTA-ATTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
6488280 TTTA
1 TTTA
6488284 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
19 23 0.70
20 10 0.30
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:6490644 original size:15 final size:15
Alignment explanation
Indices: 6490621--6490654 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
6490611 CCAGTAGAAA
*
6490621 AAGATGCACATCAGG
1 AAGACGCACATCAGG
6490636 AAGACGCACATCAGG
1 AAGACGCACATCAGG
6490651 AAGA
1 AAGA
6490655 ATAAGAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.26, T:0.09
Consensus pattern (15 bp):
AAGACGCACATCAGG
Found at i:6494589 original size:11 final size:11
Alignment explanation
Indices: 6494549--6494594 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
6494539 AGGCAACCCA
*
6494549 TTTCGTTATAT
1 TTTCGTTTTAT
*
6494560 TTTTGTTTTTAT
1 TTTCG-TTTTAT
6494572 TTT--TTTTAT
1 TTTCGTTTTAT
6494581 TTTCGTTTTAT
1 TTTCGTTTTAT
6494592 TTT
1 TTT
6494595 TATATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 9 0.30
11 13 0.43
12 8 0.27
ACGTcount: A:0.11, C:0.04, G:0.07, T:0.78
Consensus pattern (11 bp):
TTTCGTTTTAT
Found at i:6496441 original size:76 final size:75
Alignment explanation
Indices: 6496350--6496514 Score: 235
Period size: 76 Copynumber: 2.2 Consensus size: 75
6496340 TTAAACTCAA
*
6496350 ATTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGGATATTATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGT
6496414 ATTTTAATTCA-G
64 ATTTTAATT-AGG
* * * *
6496426 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
6496491 TTTAATTAGG
66 TTTAATTAGG
*
6496501 ATTTAGAATATTAT
1 ATTTAGGATATTAT
6496515 ATTATTTTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
74 1 0.01
75 36 0.45
76 43 0.54
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.56
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
TTTAATTAGG
Found at i:6496500 original size:19 final size:19
Alignment explanation
Indices: 6496472--6496534 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
6496462 TGTATTTTAG
*
6496472 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
6496491 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
6496510 ATTATATTATTTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
6496531 TTTA
1 TTTA
6496535 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 8 0.24
21 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:6498329 original size:2 final size:2
Alignment explanation
Indices: 6498322--6498354 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6498312 AATTAAAATT
6498322 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
6498355 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:6503678 original size:11 final size:11
Alignment explanation
Indices: 6503659--6503706 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
6503649 TCTTTAAATT
6503659 TTTTCTTTTTTG
1 TTTT-TTTTTTG
6503671 -TTTTTTTTTG
1 TTTTTTTTTTG
6503681 TTTTTTTTTTG
1 TTTTTTTTTTG
**
6503692 CCTTTTTTTTG
1 TTTTTTTTTTG
6503703 TTTT
1 TTTT
6503707 CATGTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
10 7 0.23
11 24 0.77
ACGTcount: A:0.00, C:0.06, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:6503679 original size:17 final size:16
Alignment explanation
Indices: 6503657--6503690 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
6503647 TTTCTTTAAA
6503657 TTTTTTCTTTTTTGTTT
1 TTTTTTCTTTTTT-TTT
*
6503674 TTTTTTGTTTTTTTTT
1 TTTTTTCTTTTTTTTT
6503690 T
1 T
6503691 GCCTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.00, C:0.03, G:0.06, T:0.91
Consensus pattern (16 bp):
TTTTTTCTTTTTTTTT
Found at i:6504076 original size:11 final size:11
Alignment explanation
Indices: 6504047--6504093 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
6504037 TTTGGTGCTG
6504047 AAAACAAGATA
1 AAAACAAGATA
*
6504058 AGAAACAAGATT
1 A-AAACAAGATA
6504070 AAAACAAGATA
1 AAAACAAGATA
6504081 AATAA-AAGATA
1 AA-AACAAGATA
6504092 AA
1 AA
6504094 GGAATTGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 20 0.62
12 12 0.38
ACGTcount: A:0.70, C:0.06, G:0.11, T:0.13
Consensus pattern (11 bp):
AAAACAAGATA
Found at i:6510801 original size:13 final size:13
Alignment explanation
Indices: 6510783--6510807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6510773 ATTAAAGTTA
6510783 ATATATATATTTG
1 ATATATATATTTG
6510796 ATATATATATTT
1 ATATATATATTT
6510808 AATTTAATTA
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:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
ATATATATATTTG
Found at i:6513403 original size:56 final size:56
Alignment explanation
Indices: 6513336--6513448 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
6513326 AAAATGTCTC
6513336 CGCTACAACAAGACTGGACACTAGAAAAGAAATTGCCCTATTTACCTTGAAGAGTT
1 CGCTACAACAAGACTGGACACTAGAAAAGAAATTGCCCTATTTACCTTGAAGAGTT
*
6513392 CGCTACAACAAGACTGGACACTGGAAAAGAAATTGCCCTATTTACCTTGAAGAGTT
1 CGCTACAACAAGACTGGACACTAGAAAAGAAATTGCCCTATTTACCTTGAAGAGTT
6513448 C
1 C
6513449 AGAAAGGCAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (56 bp):
CGCTACAACAAGACTGGACACTAGAAAAGAAATTGCCCTATTTACCTTGAAGAGTT
Found at i:6516446 original size:21 final size:23
Alignment explanation
Indices: 6516422--6516503 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 23
6516412 GTAATTTACA
6516422 CCGAAGTG-CCACA-AA-ATTGTC
1 CCGAAG-GACCACATAAGATTGTC
*
6516443 CCGAAGGACCACATAAGCTTGTC
1 CCGAAGGACCACATAAGATTGTC
**
6516466 CCGAAGGACCACATAATTTTGTC
1 CCGAAGGACCACATAAGATTGTC
* *
6516489 TCGAAAGACCACATA
1 CCGAAGGACCACATA
6516504 GAACCCTCGA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
20 1 0.02
21 11 0.21
22 2 0.04
23 39 0.74
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (23 bp):
CCGAAGGACCACATAAGATTGTC
Found at i:6516468 original size:23 final size:23
Alignment explanation
Indices: 6516438--6516503 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
6516428 TGCCACAAAA
6516438 TTGTCCCGAAGGACCACATAAGC
1 TTGTCCCGAAGGACCACATAAGC
**
6516461 TTGTCCCGAAGGACCACATAATT
1 TTGTCCCGAAGGACCACATAAGC
* *
6516484 TTGTCTCGAAAGACCACATA
1 TTGTCCCGAAGGACCACATA
6516504 GAACCCTCGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (23 bp):
TTGTCCCGAAGGACCACATAAGC
Found at i:6517092 original size:19 final size:20
Alignment explanation
Indices: 6517044--6517095 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
6517034 TCCCACTACA
*
6517044 GTACCGATACTTCCCTTCTATG
1 GTACCGATAC--CCCTCCTATG
*
6517066 GTATCGATACCCCTCCT-TG
1 GTACCGATACCCCTCCTATG
6517085 GTACCGATACC
1 GTACCGATACC
6517096 ATTTCGACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 12 0.44
20 6 0.22
22 9 0.33
ACGTcount: A:0.19, C:0.35, G:0.15, T:0.31
Consensus pattern (20 bp):
GTACCGATACCCCTCCTATG
Found at i:6523256 original size:23 final size:21
Alignment explanation
Indices: 6523198--6523267 Score: 79
Period size: 23 Copynumber: 3.2 Consensus size: 21
6523188 CACCACAGCT
*
6523198 CATAATTTTCACCGAAGTG-CCA
1 CATAATTGTC-CCGAAG-GACCA
6523220 CATAATTGTCCCGAAGGACCA
1 CATAATTGTCCCGAAGGACCA
*
6523241 CATAAGTTTGTGCCGAAGGACCA
1 CATAA--TTGTCCCGAAGGACCA
6523264 CATA
1 CATA
6523268 GAACCCTCGA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
20 1 0.02
21 14 0.33
22 9 0.21
23 19 0.44
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (21 bp):
CATAATTGTCCCGAAGGACCA
Found at i:6523851 original size:22 final size:20
Alignment explanation
Indices: 6523826--6523877 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 20
6523816 TACAGTACCG
6523826 ATACTTCCCTTCTATGGTATCA
1 ATAC-TCCCTTCT-TGGTATCA
* *
6523848 ATAC-CCCTCCTTGGTATCG
1 ATACTCCCTTCTTGGTATCA
6523867 ATACTACCCTT
1 ATACT-CCCTT
6523878 TCAGTATCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 11 0.44
20 6 0.24
21 4 0.16
22 4 0.16
ACGTcount: A:0.21, C:0.33, G:0.10, T:0.37
Consensus pattern (20 bp):
ATACTCCCTTCTTGGTATCA
Found at i:6526420 original size:2 final size:2
Alignment explanation
Indices: 6526415--6526453 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
6526405 ATTAGAGTTA
*
6526415 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
6526454 TAAACTTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:6527002 original size:22 final size:22
Alignment explanation
Indices: 6526977--6527025 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
6526967 AGTGCCTCGA
6526977 CATTGATACGAAAATGCAATAG
1 CATTGATACGAAAATGCAATAG
6526999 CATTGATACGAAAATGCAATAG
1 CATTGATACGAAAATGCAATAG
*
6527021 AATTG
1 CATTG
6527026 CTGAGAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.24
Consensus pattern (22 bp):
CATTGATACGAAAATGCAATAG
Found at i:6529553 original size:577 final size:577
Alignment explanation
Indices: 6528772--6530485 Score: 3173
Period size: 574 Copynumber: 3.0 Consensus size: 577
6528762 TAACGGAATG
* * *
6528772 ACCTGAGATAGGCCAAAACGATAACTTATAAGCATAGACATATGGAACACATTGTTGATGCACTC
1 ACCTGAGATGGGCCAAAACGATATCTTCTAAGCATAGACATATGGAACACATTGTTGATGCACTC
6528837 CATCTCGAGATGGTAAGCAATTGGATCAACCCTATTAAGTACCTCATAGGTTCTATAGCACCTTA
66 CATCTCGAGATGGTAAGCAATTGGATCAACCCTATTAAGTACCTCATAGGTTCTATAGCACCTTA
* *
6528902 GACCACTACAACACATATTCAACCGATGTAGGATGCCATACGGAACCACCAGAGTGGCTTACAAA
131 GACCACTACAACACATAGTCAACCGATGTAGGATGCCACACGGAACCACCAGAGTGGCTTACAAA
*
6528967 TACCTTACTCTTTTCTTGTACTATAAAACGACCATTTCCATAAATAAAACATCCCTGAAATAATA
196 TACCTTACTCTTTTCTTGTACTATAAAACGACCATTTCCATAAATAAAACATCCCTAAAATAATA
6529032 TAGTTTAAAACTTTATATTAGTGAGCTCCCAAAATAAATATTTACAATCAAAATATTATAGATTG
261 TAGTTTAAAACTTTATATTAGTGAGCTCCCAAAATAAATATTTACAATCAAAATATTATAGATTG
*
6529097 AATCTTAATAAAATTTATGACTCAATTGATATAACAGGGTTTATAAAATATACATGCCCTTCAAC
326 AATCTTAATAAAATTTATGACTCAACTGATATAACAGGGTTTATAAAATATACATGCCCTTCAAC
6529162 AACTACTGAGACATACTCTGAATCTGCACTGGGTCTGGACCTTGATCTATCTACTGCTCCTCGAA
391 AACTACTGAGACATACTCTGAATCTGCACTGGGTCTGGACCTTGATCTATCTACTGCTCCTCGAA
* *
6529227 CACTTGATCTACTTATCTATCCATAGAAAATAATCTGAAGTTAGGGCCACACGAACAACTAAAAC
456 CACTTGATCTACTGATCTATCCATAGAAAATAATCTGAAGTTAGCGCCACACGAACAACTAAAAC
*
6529292 ATACTAAAGGTTTATCACTGAAATGCTCAAGCTATCAAGTATACTGCTATATGGTCT
521 ATACTAAAAGTTTATCACTGAAATGCTCAAGCTATCAAGTATACTGCTATATGGTCT
*
6529349 ACCTGAGATGGGCCAAAACGATATCTTCTAAGCATAGACATATGGAACACATTGTTAATGCACTC
1 ACCTGAGATGGGCCAAAACGATATCTTCTAAGCATAGACATATGGAACACATTGTTGATGCACTC
6529414 CATCTCGAGATGGTAAGCAATTGGATCAACCCTATTAAGTACCTCATAGGTTCTATAGCACCTTA
66 CATCTCGAGATGGTAAGCAATTGGATCAACCCTATTAAGTACCTCATAGGTTCTATAGCACCTTA
*
6529479 GACCACTACAACACATAGTCAACCGATGTATGATGCCACACGGAACCACCAGAGTGGCTTACAAA
131 GACCACTACAACACATAGTCAACCGATGTAGGATGCCACACGGAACCACCAGAGTGGCTTACAAA
*
6529544 TACCTTACTCTTTTCTTGTACTATAAAATGACCATTTCCATAAATAAAACATCCCTAAAATAATA
196 TACCTTACTCTTTTCTTGTACTATAAAACGACCATTTCCATAAATAAAACATCCCTAAAATAATA
*
6529609 TAGTTTAAAACTTTATATTAGTGAGTTCCCAAAATAAATATTTACAATCAAAATATTATAGATTG
261 TAGTTTAAAACTTTATATTAGTGAGCTCCCAAAATAAATATTTACAATCAAAATATTATAGATTG
*
6529674 AATCTTAATAAAATTTATGAATCAACTGATATAACAGGGTTTATAAAATATACATGCCCTTCAAC
326 AATCTTAATAAAATTTATGACTCAACTGATATAACAGGGTTTATAAAATATACATGCCCTTCAAC
6529739 AACTACTGAGACATACTCTGAATCTGCACTGGGTCTGGACCTTGATCTATCTACTGCTCCTCGAA
391 AACTACTGAGACATACTCTGAATCTGCACTGGGTCTGGACCTTGATCTATCTACTGCTCCTCGAA
* *
6529804 CACTTGATATACTGATCTATCCATAGAAAATAATCTGAAGTTAGCGCCACATGAACAACTAAAAC
456 CACTTGATCTACTGATCTATCCATAGAAAATAATCTGAAGTTAGCGCCACACGAACAACTAAAAC
6529869 ATACTAAAAGTTTATCACTGAAATGCTCAAGCTAT---GTATACTGCTATATGGTCT
521 ATACTAAAAGTTTATCACTGAAATGCTCAAGCTATCAAGTATACTGCTATATGGTCT
6529923 ACCTGAGATGGGCCAAAACGATATCTTCTAAGCATAGACATATGGAACACATTGTTGATGCACTC
1 ACCTGAGATGGGCCAAAACGATATCTTCTAAGCATAGACATATGGAACACATTGTTGATGCACTC
* * *
6529988 CATCTCGAGATGGTAAGCTATTGGATTAACCCTACTAAGTACCTCATAGGTTCTATAGCACCTTA
66 CATCTCGAGATGGTAAGCAATTGGATCAACCCTATTAAGTACCTCATAGGTTCTATAGCACCTTA
6530053 GACCACTACAACACATAGTCAACCGATGTAGGATGCCACACGGAACCACCAGAGTGGCTTACAAA
131 GACCACTACAACACATAGTCAACCGATGTAGGATGCCACACGGAACCACCAGAGTGGCTTACAAA
**
6530118 TACCTTACTCTTTTCTTGTACTATAAAACGACCATTTCCATAAATAAAACATCATTAAAATAATA
196 TACCTTACTCTTTTCTTGTACTATAAAACGACCATTTCCATAAATAAAACATCCCTAAAATAATA
*
6530183 TAGTTTAAAACTTTATATTAGTGATCTCCCAAAATAAATATTTACAATCAAAATATTATAGATTG
261 TAGTTTAAAACTTTATATTAGTGAGCTCCCAAAATAAATATTTACAATCAAAATATTATAGATTG
*
6530248 AATCTTAAAAAAATTTATGACTCAACTGATATAACAGGGTTTATAAAATATACATGCCCTTCAAC
326 AATCTTAATAAAATTTATGACTCAACTGATATAACAGGGTTTATAAAATATACATGCCCTTCAAC
*
6530313 AACTACTGAGACATACTCTGAATCTGCACTGGGTCTGGACCTTGATCTATCTACTGCTCCTCAAA
391 AACTACTGAGACATACTCTGAATCTGCACTGGGTCTGGACCTTGATCTATCTACTGCTCCTCGAA
*
6530378 CACTTGATCTACTGATCTATCCACAGAAAATAATCTGAAGTTAGCGCCACACGAACAACTAAAAC
456 CACTTGATCTACTGATCTATCCATAGAAAATAATCTGAAGTTAGCGCCACACGAACAACTAAAAC
6530443 ATACTAAAAGTTTATCACTGAAATGCTCAAGCTATCAAGTATA
521 ATACTAAAAGTTTATCACTGAAATGCTCAAGCTATCAAGTATA
6530486 ATGTTATTTG
Statistics
Matches: 1101, Mismatches: 33, Indels: 6
0.97 0.03 0.01
Matches are distributed among these distances:
574 558 0.51
577 543 0.49
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (577 bp):
ACCTGAGATGGGCCAAAACGATATCTTCTAAGCATAGACATATGGAACACATTGTTGATGCACTC
CATCTCGAGATGGTAAGCAATTGGATCAACCCTATTAAGTACCTCATAGGTTCTATAGCACCTTA
GACCACTACAACACATAGTCAACCGATGTAGGATGCCACACGGAACCACCAGAGTGGCTTACAAA
TACCTTACTCTTTTCTTGTACTATAAAACGACCATTTCCATAAATAAAACATCCCTAAAATAATA
TAGTTTAAAACTTTATATTAGTGAGCTCCCAAAATAAATATTTACAATCAAAATATTATAGATTG
AATCTTAATAAAATTTATGACTCAACTGATATAACAGGGTTTATAAAATATACATGCCCTTCAAC
AACTACTGAGACATACTCTGAATCTGCACTGGGTCTGGACCTTGATCTATCTACTGCTCCTCGAA
CACTTGATCTACTGATCTATCCATAGAAAATAATCTGAAGTTAGCGCCACACGAACAACTAAAAC
ATACTAAAAGTTTATCACTGAAATGCTCAAGCTATCAAGTATACTGCTATATGGTCT
Found at i:6531390 original size:19 final size:18
Alignment explanation
Indices: 6531366--6531402 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
6531356 ATATCATGCT
6531366 TATAACATAAATCATATAA
1 TATAACATAAA-CATATAA
*
6531385 TATAACATTAACATATAA
1 TATAACATAAACATATAA
6531403 CAATAAACTT
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:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (18 bp):
TATAACATAAACATATAA
Found at i:6531408 original size:19 final size:19
Alignment explanation
Indices: 6531367--6531408 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
6531357 TATCATGCTT
*
6531367 ATAACATAAATCATATAAT
1 ATAACATAAATCATATAAA
*
6531386 ATAACATTAA-CATATAACA
1 ATAACATAAATCATATAA-A
6531405 ATAA
1 ATAA
6531409 ACTTCATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.29
Consensus pattern (19 bp):
ATAACATAAATCATATAAA
Found at i:6540617 original size:81 final size:81
Alignment explanation
Indices: 6540397--6540899 Score: 575
Period size: 81 Copynumber: 6.2 Consensus size: 81
6540387 TAATATTATG
* * * * ** *
6540397 GTAAAAGATTAAATGCCTAACTATACACTTGGCTGAAATATGTCAATCATGCTAGTTAGATGAAA
1 GTAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGACAATCATGCTAGTTAGATGAAA
*
6540462 GGTTAAATG-TTTATGA
66 GGTTAAATGCCTT-TGA
* * *
6540478 GTAAAAGATAAAAATGCCTAACTGTGCAATTT-GCAGAAAGGTGTCAATCATGCCAGTTAGATGA
1 GTAAAAGAT-TAAATGCCTAACTGTGC-ATTTGGCAGAAAGGTGACAATCATGCTAGTTAGATGA
6540542 AAGGTTAAATGCCTTTGA
64 AAGGTTAAATGCCTTTGA
* * **
6540560 GTAAAAGATAAAATGCCTAACTATGCAATTT-ATAGAAAGGTGACAATCATGCTAGTTAGATGAA
1 GTAAAAGATTAAATGCCTAACTGTGC-ATTTGGCAGAAAGGTGACAATCATGCTAGTTAGATGAA
*
6540624 AGGTTATATGCCTTTGA
65 AGGTTAAATGCCTTTGA
* * * * * * *
6540641 TTAAAAGATTAAATGCCTAATTGTGTATTTGGCATAAAGGTGTCAATCATTCTAGTTAGATAAAA
1 GTAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGACAATCATGCTAGTTAGATGAAA
6540706 GGTTAAATGCCTTTGA
66 GGTTAAATGCCTTTGA
* * * *
6540722 GTAAAAGATTAAATGTCTAATTGTGCATTTGACAGAAAAGGT-ATCAATCATACTAGTTAGATGA
1 GTAAAAGATTAAATGCCTAACTGTGCATTTGGCAG-AAAGGTGA-CAATCATGCTAGTTAGATGA
*
6540786 AAGGTTAAATGCCTTTGG
64 AAGGTTAAATGCCTTTGA
* * * * * * *
6540804 GTAAAAGATTAAATGCATAAATGTGCATTTGGCACAAAGGTGCCAATAATGCAAGTTAGACGAAA
1 GTAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGACAATCATGCTAGTTAGATGAAA
6540869 GGTTAAATGCCTTTAGA
66 GGTTAAATGCCTTT-GA
* *
6540886 G-GAAAGAATAAATG
1 GTAAAAGATTAAATG
6540900 TTTAACAGTC
Statistics
Matches: 365, Mismatches: 49, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
80 4 0.01
81 218 0.60
82 138 0.38
83 5 0.01
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (81 bp):
GTAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGACAATCATGCTAGTTAGATGAAA
GGTTAAATGCCTTTGA
Found at i:6540780 original size:163 final size:163
Alignment explanation
Indices: 6540397--6540905 Score: 591
Period size: 163 Copynumber: 3.1 Consensus size: 163
6540387 TAATATTATG
* * * ** * **
6540397 GTAAAAGATTAAATGCCTAACTATACACTTGGCTGAAATATG-TCAATCATGCTAGTTAGATGAA
1 GTAAAAGATTAAATGTCTAACTATGCAATTTACAGAAAGGTGATCAATCATGCTAGTTAGATGAA
* * * *
6540461 AGGTTAAATG-TTTATGAGTAAAAGATAAAAATGCCTAACTGTGCAATTT-GCAGAAAGGTGTCA
66 AGGTTAAATGCCTT-TGAGTAAAAGAT-TAAATGCCTAAATGTG-AATTTGGCACAAAGGTGTCA
*
6540524 ATCATGCCAGTTAGATGAAAGGTTAAATGCCTTTGA
128 ATCATGCAAGTTAGATGAAAGGTTAAATGCCTTTGA
* * *
6540560 GTAAAAGATAAAATGCCTAACTATGCAATTTATAGAAAGGTGA-CAATCATGCTAGTTAGATGAA
1 GTAAAAGATTAAATGTCTAACTATGCAATTTACAGAAAGGTGATCAATCATGCTAGTTAGATGAA
* * * * *
6540624 AGGTTATATGCCTTTGATTAAAAGATTAAATGCCTAATTGTGTATTTGGCATAAAGGTGTCAATC
66 AGGTTAAATGCCTTTGAGTAAAAGATTAAATGCCTAAATGTGAATTTGGCACAAAGGTGTCAATC
* * *
6540689 ATTCTAGTTAGATAAAAGGTTAAATGCCTTTGA
131 ATGCAAGTTAGATGAAAGGTTAAATGCCTTTGA
* * *
6540722 GTAAAAGATTAAATGTCTAATTGTGC-ATTTGACAGAAAAGGT-ATCAATCATACTAGTTAGATG
1 GTAAAAGATTAAATGTCTAACTATGCAATTT-ACAG-AAAGGTGATCAATCATGCTAGTTAGATG
* * * *
6540785 AAAGGTTAAATGCCTTTGGGTAAAAGATTAAATGCATAAATGTGCATTTGGCACAAAGGTGCCAA
64 AAAGGTTAAATGCCTTTGAGTAAAAGATTAAATGCCTAAATGTGAATTTGGCACAAAGGTGTCAA
* *
6540850 TAATGCAAGTTAGACGAAAGGTTAAATGCCTTTAGA
129 TCATGCAAGTTAGATGAAAGGTTAAATGCCTTT-GA
* * *
6540886 G-GAAAGAATAAATGTTTAAC
1 GTAAAAGATTAAATGTCTAAC
6540906 AGTCCATTTT
Statistics
Matches: 297, Mismatches: 42, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
161 8 0.03
162 86 0.29
163 198 0.67
164 5 0.02
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (163 bp):
GTAAAAGATTAAATGTCTAACTATGCAATTTACAGAAAGGTGATCAATCATGCTAGTTAGATGAA
AGGTTAAATGCCTTTGAGTAAAAGATTAAATGCCTAAATGTGAATTTGGCACAAAGGTGTCAATC
ATGCAAGTTAGATGAAAGGTTAAATGCCTTTGA
Found at i:6540845 original size:244 final size:244
Alignment explanation
Indices: 6540437--6540882 Score: 630
Period size: 244 Copynumber: 1.8 Consensus size: 244
6540427 GGCTGAAATA
* *
6540437 TGTCAATCATGCTAGTTAGATGAAAGGTTAAATGTTTATGAGTAAAAGATAAAAATGCCTAACTG
1 TGTCAATCATGCTAGTTAGATAAAAGGTTAAATGCTTATGAGTAAAAGATAAAAATGCCTAACTG
* *
6540502 TGCAATTTGCAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATGCCTTTGAGTAAAAG
66 TGCAATTTGCAGAAAGGTATCAATCATACCAGTTAGATGAAAGGTTAAATGCCTTTGAGTAAAAG
* * * * * * * *
6540567 ATAAAATGCCTAACTATGCAATTTATAGAAAGGTGACAATCATGCTAGTTAGATGAAAGGTTATA
131 ATAAAATGCATAAATATGCAATTTACACAAAGGTGACAATAATGCAAGTTAGACGAAAGGTTAAA
6540632 TGCCTTTGATTAAAAGATTAAATGCCTAATTGTGTATTTGGCATAAAGG
196 TGCCTTTGATTAAAAGATTAAATGCCTAATTGTGTATTTGGCATAAAGG
* * * *
6540681 TGTCAATCATTCTAGTTAGATAAAAGGTTAAATGCCTT-TGAGTAAAAGAT-TAAATGTCTAATT
1 TGTCAATCATGCTAGTTAGATAAAAGGTTAAATG-CTTATGAGTAAAAGATAAAAATGCCTAACT
* *
6540744 GTGC-ATTTGACAGAAAAGGTATCAATCATACTAGTTAGATGAAAGGTTAAATGCCTTTGGGTAA
65 GTGCAATTTG-CAG-AAAGGTATCAATCATACCAGTTAGATGAAAGGTTAAATGCCTTTGAGTAA
* * * *
6540808 AAGATTAAATGCATAAATGTGC-ATTTGGCACAAAGGTGCCAATAATGCAAGTTAGACGAAAGGT
128 AAGATAAAATGCATAAATATGCAATTT-ACACAAAGGTGACAATAATGCAAGTTAGACGAAAGGT
6540872 TAAATGCCTTT
192 TAAATGCCTTT
6540883 AGAGGAAAGA
Statistics
Matches: 176, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
242 5 0.03
243 21 0.12
244 148 0.84
245 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.31
Consensus pattern (244 bp):
TGTCAATCATGCTAGTTAGATAAAAGGTTAAATGCTTATGAGTAAAAGATAAAAATGCCTAACTG
TGCAATTTGCAGAAAGGTATCAATCATACCAGTTAGATGAAAGGTTAAATGCCTTTGAGTAAAAG
ATAAAATGCATAAATATGCAATTTACACAAAGGTGACAATAATGCAAGTTAGACGAAAGGTTAAA
TGCCTTTGATTAAAAGATTAAATGCCTAATTGTGTATTTGGCATAAAGG
Found at i:6547617 original size:81 final size:81
Alignment explanation
Indices: 6547468--6548128 Score: 1036
Period size: 81 Copynumber: 8.2 Consensus size: 81
6547458 AAATTATGAC
*
6547468 TAAAAGATTAAATGCCTAACTGTGCATTTGGCAAAAAGGTGTCAATCATGCTAGTTAGATGAAAG
1 TAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATGAAAG
6547533 GTTAAATGCCTTTGAG
66 GTTAAATGCCTTTGAG
* * * *
6547549 TAATAGATAAAATTCCTAACTGTGCATTTGGCAGAAAGGTGTTAATCATGCTAGTTAGATGAAAG
1 TAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATGAAAG
* *
6547614 GTTAAATACCCTTGAG
66 GTTAAATGCCTTTGAG
* * * *
6547630 TAAAAGATTAAATGCCTAACTGTGCATTTAGCAAAAAGGTATCAATCATGCTAGTTAAATGAAAG
1 TAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATGAAAG
6547695 GTTAAATGCCTTTGAG
66 GTTAAATGCCTTTGAG
* * *
6547711 TAAAATATTAAATGTCTAACTGTGCATTTGGCAGAAAGGTGTAAATCATGCTAGTTAGATGAAAG
1 TAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATGAAAG
6547776 GTTAAATGCCTTTGAG
66 GTTAAATGCCTTTGAG
* *
6547792 TAAAAGATTAAATGTCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCTAGTTAGATGAAAG
1 TAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATGAAAG
6547857 GTTAAATGCCTTTGAG
66 GTTAAATGCCTTTGAG
* *
6547873 TAAAAGATTAAATGCCTAATTGTGAATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATGAAAG
1 TAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATGAAAG
*
6547938 GTTAAATGCCCTTGAG
66 GTTAAATGCCTTTGAG
* * *
6547954 TAAAAGATTAAATGTCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCTAGTTAGATGAAAT
1 TAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATGAAAG
*
6548019 GTTAAATGCCTTTGGG
66 GTTAAATGCCTTTGAG
* * * * * *
6548035 TAAAAGATTAAATGCCTAACTGTGCATTTGGCAAAAAGGTGCCAATAATGCAAGTTACACGAAAG
1 TAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATGAAAG
6548100 GTTAAATGCCTTTAGAG
66 GTTAAATGCCTTT-GAG
*
6548117 -GAAAGATTAAAT
1 TAAAAGATTAAAT
6548129 ATTTAACAGT
Statistics
Matches: 529, Mismatches: 50, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
81 527 1.00
82 2 0.00
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.30
Consensus pattern (81 bp):
TAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATGAAAG
GTTAAATGCCTTTGAG
Found at i:6551448 original size:2 final size:2
Alignment explanation
Indices: 6551382--6551428 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
6551372 TTAGTTTTAA
6551382 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6551424 AT AT A
1 AT AT A
6551429 ATAAGGTTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6551628 original size:12 final size:12
Alignment explanation
Indices: 6551611--6551635 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6551601 GAACGCATGC
6551611 TTGTTTAACTAT
1 TTGTTTAACTAT
6551623 TTGTTTAACTAT
1 TTGTTTAACTAT
6551635 T
1 T
6551636 AGTGAAGATT
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:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TTGTTTAACTAT
Found at i:6558651 original size:19 final size:20
Alignment explanation
Indices: 6558615--6558652 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6558605 GTTCGTTATT
6558615 GCCGCGATTGGCTGTGATCC
1 GCCGCGATTGGCTGTGATCC
*
6558635 GCCGCTATTGG-TGTGATC
1 GCCGCGATTGGCTGTGATC
6558653 TTGTTTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.11, C:0.26, G:0.34, T:0.29
Consensus pattern (20 bp):
GCCGCGATTGGCTGTGATCC
Found at i:6558845 original size:2 final size:2
Alignment explanation
Indices: 6558838--6558876 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6558828 TTTGTTTTAA
6558838 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6558877 GAGAGAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6558881 original size:2 final size:2
Alignment explanation
Indices: 6558876--6558913 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6558866 ATATATATAT
6558876 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
6558914 GGGTGTTGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6564084 original size:16 final size:16
Alignment explanation
Indices: 6564063--6564112 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
6564053 TATATCTTTA
6564063 GATTTTAATTTATTTT
1 GATTTTAATTTATTTT
*
6564079 GATTTT-ATCTTTTTTT
1 GATTTTAAT-TTATTTT
6564095 G-TTATTAATTATATTTT
1 GATT-TTAATT-TATTTT
6564112 G
1 G
6564113 TCACCTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 4 0.14
16 16 0.57
17 8 0.29
ACGTcount: A:0.22, C:0.02, G:0.08, T:0.68
Consensus pattern (16 bp):
GATTTTAATTTATTTT
Found at i:6564480 original size:33 final size:33
Alignment explanation
Indices: 6564413--6564480 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
6564403 TTTTAAACAT
** *
6564413 TAATATACACCTTAATAATATAAATTTTTTTAA
1 TAATATACACCTTAATAATATAAACCTTTATAA
* *
6564446 TAATATACGCCTTAATGATATAAACCTTTATAA
1 TAATATACACCTTAATAATATAAACCTTTATAA
6564479 TA
1 TA
6564481 TTTTGTTGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (33 bp):
TAATATACACCTTAATAATATAAACCTTTATAA
Found at i:6573321 original size:15 final size:16
Alignment explanation
Indices: 6573282--6573323 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 16
6573272 TATTCTCTTA
6573282 TTTTTACTTTAATTGCGT
1 TTTTTA-TTTAATT-CGT
6573300 TTATTTATTTAATT-GT
1 TT-TTTATTTAATTCGT
6573316 TTTTTATT
1 TTTTTATT
6573324 ATTATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 6 0.26
16 4 0.17
18 9 0.39
19 4 0.17
ACGTcount: A:0.19, C:0.05, G:0.07, T:0.69
Consensus pattern (16 bp):
TTTTTATTTAATTCGT
Found at i:6574956 original size:28 final size:27
Alignment explanation
Indices: 6574901--6574956 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
6574891 AGGGCTTGGA
*
6574901 GGTATTTGGGTAATTTTACACTTCAAG
1 GGTATTTGGGTAATTTTACACTTAAAG
* * *
6574928 GGTATTTTGGTCATTTTACAGTTTAAAG
1 GGTATTTGGGTAATTTTACA-CTTAAAG
6574956 G
1 G
6574957 TGTTTCAGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.25, C:0.09, G:0.23, T:0.43
Consensus pattern (27 bp):
GGTATTTGGGTAATTTTACACTTAAAG
Found at i:6577467 original size:17 final size:18
Alignment explanation
Indices: 6577434--6577467 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6577424 TTGAAATGTG
6577434 TAAATAATAAAACAATTA
1 TAAATAATAAAACAATTA
*
6577452 TAAATAA-AATACAATT
1 TAAATAATAAAACAATT
6577468 TCAGAAAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAATAATAAAACAATTA
Found at i:6585018 original size:19 final size:19
Alignment explanation
Indices: 6584994--6585054 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 19
6584984 TTTTGGTGCA
*
6584994 GAGGGAATCGATCCCCCCT
1 GAGGGAACCGATCCCCCCT
*
6585013 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGA-TCCCCC-CT
6585034 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGA-TCCCCCC
6585055 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 10 0.29
20 6 0.17
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.16
Consensus pattern (19 bp):
GAGGGAACCGATCCCCCCT
Found at i:6587709 original size:21 final size:23
Alignment explanation
Indices: 6587685--6587729 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
6587675 TTCCAGATTG
6587685 CTCAGA-G-GGAACCGATTCCCC
1 CTCAGAGGAGGAACCGATTCCCC
*
6587706 CTCATAGGAGGAACCGATTCCCC
1 CTCAGAGGAGGAACCGATTCCCC
6587729 C
1 C
6587730 ATGAATGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 1 0.05
23 15 0.71
ACGTcount: A:0.24, C:0.38, G:0.22, T:0.16
Consensus pattern (23 bp):
CTCAGAGGAGGAACCGATTCCCC
Found at i:6588881 original size:18 final size:19
Alignment explanation
Indices: 6588860--6588905 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
6588850 CAACAGGTAG
*
6588860 GTCAACGG-TCATGTCAAA
1 GTCAACGGTTCAAGTCAAA
*
6588878 GTCAACGGTTCAAGTCAAG
1 GTCAACGGTTCAAGTCAAA
6588897 GTCCAACGG
1 GT-CAACGG
6588906 GTCAGACCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.33
19 10 0.42
20 6 0.25
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.20
Consensus pattern (19 bp):
GTCAACGGTTCAAGTCAAA
Found at i:6590363 original size:8 final size:8
Alignment explanation
Indices: 6590350--6590388 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
6590340 ATATAATTTT
6590350 AATTTTAG
1 AATTTTAG
6590358 AATTTTAG
1 AATTTTAG
6590366 AATTTTAG
1 AATTTTAG
*
6590374 AAATTTAG
1 AATTTTAG
6590382 AAATTTT
1 -AATTTT
6590389 TTATATAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
8 23 0.82
9 5 0.18
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (8 bp):
AATTTTAG
Found at i:6590531 original size:25 final size:26
Alignment explanation
Indices: 6590474--6590534 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
6590464 AATTATATAT
6590474 AATATAATTTTTATATATATTAACTTA
1 AATAT-ATTTTTATATATATTAACTTA
*
6590501 AA-ATATTTTTATATCA-ATTTA-TTA
1 AATATATTTTTATAT-ATATTAACTTA
6590525 AATATATTTT
1 AATATATTTT
6590535 ATTAGTAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 5 0.16
25 21 0.68
26 3 0.10
27 2 0.06
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (26 bp):
AATATATTTTTATATATATTAACTTA
Done.