Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012419.1 Kokia drynarioides strain JFW-HI SEQ_127423, 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: 174257
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 38 characters in sequence are not A, C, G, or T
Found at i:657 original size:36 final size:36
Alignment explanation
Indices: 558--657 Score: 128
Period size: 36 Copynumber: 2.8 Consensus size: 36
548 CGTTATTCGT
* * *
558 TTTACTCCTTATTGACCCAAAGGTCATAATGCTCAT
1 TTTACTCCCTATTGACCCAAAGGTCATGATGCTCAA
* **
594 TTTACTACCTATTGACCCGGAGGTCATGATGCTCAA
1 TTTACTCCCTATTGACCCAAAGGTCATGATGCTCAA
* *
630 TTTACTCCCTATTGACTCAAATGTCATG
1 TTTACTCCCTATTGACCCAAAGGTCATG
658 CCTATTATCA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (36 bp):
TTTACTCCCTATTGACCCAAAGGTCATGATGCTCAA
Found at i:30072 original size:6 final size:6
Alignment explanation
Indices: 30061--30094 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
30051 CCCTGACCCA
30061 ACCCCC ACCCCC ACCCCC ACCCCC ACCCCC ACCC
1 ACCCCC ACCCCC ACCCCC ACCCCC ACCCCC ACCC
30095 AAAGTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.82, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCCCC
Found at i:34713 original size:26 final size:26
Alignment explanation
Indices: 34684--34736 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
34674 GCAATGATGA
34684 AGAATAGTCTGGGAGAATCATTGCTG
1 AGAATAGTCTGGGAGAATCATTGCTG
34710 AGAATAGTCTGGGAGAATCATTGCTG
1 AGAATAGTCTGGGAGAATCATTGCTG
34736 A
1 A
34737 TAATGGTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.26
Consensus pattern (26 bp):
AGAATAGTCTGGGAGAATCATTGCTG
Found at i:39680 original size:23 final size:24
Alignment explanation
Indices: 39654--39698 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
39644 TTTAAATATA
39654 CAAATATTTCAG-TTTTTTTACGG
1 CAAATATTTCAGCTTTTTTTACGG
39677 CAAATATTTCAGCTTTTTTTAC
1 CAAATATTTCAGCTTTTTTTAC
39699 AGTTCTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.49
Consensus pattern (24 bp):
CAAATATTTCAGCTTTTTTTACGG
Found at i:47288 original size:18 final size:19
Alignment explanation
Indices: 47265--47300 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
47255 ATATTCAAGT
*
47265 AAAGTGTT-TTATGAAAGC
1 AAAGTGTTAATATGAAAGC
47283 AAAGTGTTAATATGAAAG
1 AAAGTGTTAATATGAAAG
47301 TGAATTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (19 bp):
AAAGTGTTAATATGAAAGC
Found at i:50487 original size:17 final size:17
Alignment explanation
Indices: 50479--50559 Score: 103
Period size: 17 Copynumber: 4.8 Consensus size: 17
50469 AAATAAATTT
50479 TAAATTTAAATTT-ATAA
1 TAAATTTAAATTTCA-AA
* *
50496 TATATTTAATTTTCAAA
1 TAAATTTAAATTTCAAA
50513 TAAATTTAAATTT-AGAA
1 TAAATTTAAATTTCA-AA
*
50530 TAAATTTAATTTTCAAA
1 TAAATTTAAATTTCAAA
50547 TAAATTTAAATTT
1 TAAATTTAAATTT
50560 ATTGGGCCCA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
16 1 0.02
17 52 0.95
18 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:50488 original size:6 final size:6
Alignment explanation
Indices: 50472--50560 Score: 50
Period size: 6 Copynumber: 15.3 Consensus size: 6
50462 ATTATTTAAA
* *
50472 TAAATTT TAAATT TAAATT TATAA-- TATATT TAATTT TCAAA-- TAAATT
1 TAAA-TT TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT
*
50519 TAAATT TAGAA-- TAAATT TAATTT TCAAA-- TAAATT TAAATT TA
1 TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT TAAATT TA
50561 TTGGGCCCAG
Statistics
Matches: 64, Mismatches: 6, Indels: 25
0.67 0.06 0.26
Matches are distributed among these distances:
4 9 0.14
5 6 0.09
6 37 0.58
7 12 0.19
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (6 bp):
TAAATT
Found at i:50517 original size:34 final size:34
Alignment explanation
Indices: 50479--50561 Score: 148
Period size: 34 Copynumber: 2.4 Consensus size: 34
50469 AAATAAATTT
*
50479 TAAATTTAAATTTATAATATATTTAATTTTCAAA
1 TAAATTTAAATTTATAATAAATTTAATTTTCAAA
*
50513 TAAATTTAAATTTAGAATAAATTTAATTTTCAAA
1 TAAATTTAAATTTATAATAAATTTAATTTTCAAA
50547 TAAATTTAAATTTAT
1 TAAATTTAAATTTAT
50562 TGGGCCCAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (34 bp):
TAAATTTAAATTTATAATAAATTTAATTTTCAAA
Found at i:50705 original size:20 final size:22
Alignment explanation
Indices: 50682--50747 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 22
50672 ATCCAAACAT
50682 AAAAAAATATTAA-TT-TTTT-C
1 AAAAAAATA-TAATTTATTTTAC
50702 AAAAAAA-ATAATTTATTTTAC
1 AAAAAAATATAATTTATTTTAC
* *
50723 -AAAAAA-ATAACTTATTTTTC
1 AAAAAAATATAATTTATTTTAC
50743 AAAAA
1 AAAAA
50748 TCATTTTACG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 29 0.73
21 5 0.12
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAAAAATATAATTTATTTTAC
Found at i:50708 original size:21 final size:21
Alignment explanation
Indices: 50682--50747 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
50672 ATCCAAACAT
*
50682 AAAAAAAT-ATTAATTTTTTCA
1 AAAAAAATAATTAA-TTTTACA
*
50703 AAAAAAATAATTTATTTTAC-
1 AAAAAAATAATTAATTTTACA
*
50723 AAAAAAATAACTT-ATTTTTCA
1 AAAAAAATAA-TTAATTTTACA
50744 AAAA
1 AAAA
50748 TCATTTTACG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
20 16 0.41
21 19 0.49
22 4 0.10
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAAAATAATTAATTTTACA
Found at i:72421 original size:14 final size:14
Alignment explanation
Indices: 72402--72431 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
72392 CTTTCGACGT
72402 GAGATCATGATTTC
1 GAGATCATGATTTC
72416 GAGATCATGATTTC
1 GAGATCATGATTTC
72430 GA
1 GA
72432 ACACACAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33
Consensus pattern (14 bp):
GAGATCATGATTTC
Found at i:72918 original size:20 final size:20
Alignment explanation
Indices: 72875--72933 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
72865 TAGTTTACCC
72875 TAATAACAAATATGTACT-TATA
1 TAATAA-AAATAT-TA-TATATA
72897 TAATAAAAATATTATATATA
1 TAATAAAAATATTATATATA
* *
72917 TATTAAAAGTA-TATATA
1 TAATAAAAATATTATATA
72934 AAAATATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 7 0.21
20 15 0.44
21 6 0.18
22 6 0.18
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (20 bp):
TAATAAAAATATTATATATA
Found at i:73286 original size:3 final size:3
Alignment explanation
Indices: 73268--73301 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
73258 AAATATTTGA
73268 AAT AAT ATAT ATAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AA
73302 CAAGTGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 23 0.77
4 7 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:76044 original size:3 final size:3
Alignment explanation
Indices: 76036--76062 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
76026 TTAAGGAACA
76036 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
76063 GCTTCACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:80153 original size:31 final size:31
Alignment explanation
Indices: 80088--80146 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
80078 AACAACCAAG
* *
80088 TGACTTAAATAAAAACTTTCAAATAGTTCAA
1 TGACTTAAACAAAAACTTTCAAATAATTCAA
* *
80119 TGACTTAAACGAAAACTTTCGAATAATT
1 TGACTTAAACAAAAACTTTCAAATAATT
80147 TGATGACCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (31 bp):
TGACTTAAACAAAAACTTTCAAATAATTCAA
Found at i:90628 original size:22 final size:21
Alignment explanation
Indices: 90601--90649 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
90591 CAAATCTGAT
*
90601 TTTTTAGATGATATTTTTTTTA
1 TTTTTAG-TGAAATTTTTTTTA
*
90623 TTTTTAGTTAAATTTTTTTTA
1 TTTTTAGTGAAATTTTTTTTA
90644 TTTTTA
1 TTTTTA
90650 ATTAGTGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.71
Consensus pattern (21 bp):
TTTTTAGTGAAATTTTTTTTA
Found at i:91577 original size:21 final size:21
Alignment explanation
Indices: 91553--91594 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
91543 TTTTCACTTT
91553 ATTTATTTCATTT-TATTTTTG
1 ATTTATTT-ATTTATATTTTTG
91574 ATTTATTTATTTAATATTTTT
1 ATTTATTTATTT-ATATTTTT
91595 ATCATTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 8 0.42
22 7 0.37
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (21 bp):
ATTTATTTATTTATATTTTTG
Found at i:97472 original size:14 final size:14
Alignment explanation
Indices: 97449--97479 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
97439 ATAATATCCC
97449 ATTTAGTTCAAAAA
1 ATTTAGTTCAAAAA
*
97463 ATTTATTTCAAAAA
1 ATTTAGTTCAAAAA
97477 ATT
1 ATT
97480 AAAATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (14 bp):
ATTTAGTTCAAAAA
Found at i:103063 original size:2 final size:2
Alignment explanation
Indices: 103056--103085 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
103046 TAATTTCAAG
103056 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
103086 AATTAACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:104008 original size:27 final size:27
Alignment explanation
Indices: 103966--104030 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
103956 ACAAGGGGTG
* *
103966 GTGCCTATCTGACAGGCGGCACTAAAA
1 GTGCCTACCTGACAGGCGGCACCAAAA
*
103993 GTGCCTACCTGCCAGGCGGCACCAAAA
1 GTGCCTACCTGACAGGCGGCACCAAAA
*
104020 GTACCTACCTG
1 GTGCCTACCTG
104031 GCAAGCTACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.32, G:0.25, T:0.17
Consensus pattern (27 bp):
GTGCCTACCTGACAGGCGGCACCAAAA
Found at i:104042 original size:27 final size:27
Alignment explanation
Indices: 103989--104044 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
103979 AGGCGGCACT
* * *
103989 AAAAGTGCCTACCTGCCAGGCGGCACC
1 AAAAGTACCTACCTGCCAAGCGACACC
* *
104016 AAAAGTACCTACCTGGCAAGCTACACC
1 AAAAGTACCTACCTGCCAAGCGACACC
104043 AA
1 AA
104045 CCCCACATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.34, G:0.20, T:0.12
Consensus pattern (27 bp):
AAAAGTACCTACCTGCCAAGCGACACC
Found at i:105506 original size:26 final size:26
Alignment explanation
Indices: 105477--105526 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
105467 ATTAATTCTG
105477 TTTAAATTTGAATTTATTTAATAATT
1 TTTAAATTTGAATTTATTTAATAATT
**
105503 TTTATGTTTGAATTTATTTAATAA
1 TTTAAATTTGAATTTATTTAATAA
105527 GTTTAGCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (26 bp):
TTTAAATTTGAATTTATTTAATAATT
Found at i:106071 original size:6 final size:6
Alignment explanation
Indices: 106060--106089 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
106050 GTGCTGCGGG
106060 TCAGGC TCAGGC TCAGGC TCAGGC TCAGGC
1 TCAGGC TCAGGC TCAGGC TCAGGC TCAGGC
106090 GGTTGAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (6 bp):
TCAGGC
Found at i:107948 original size:42 final size:42
Alignment explanation
Indices: 107901--108027 Score: 98
Period size: 42 Copynumber: 3.0 Consensus size: 42
107891 TTTGATGAAA
107901 AAAAATTAAAATATTTACTACATTTATGTTTCTTTCTTTTTT
1 AAAAATTAAAATATTTACTACATTTATGTTTCTTTCTTTTTT
** * * ** * ** ****
107943 AAAAA-TATAAATATCAAATATA-AGA-GTTTTGTTTGATGAAA
1 AAAAATTA-AAATATTTACTACATTTATG-TTTCTTTCTTTTTT
107984 AAAAATTAAAATATTTACTACATTTATGTTTCTTTCTTTTTT
1 AAAAATTAAAATATTTACTACATTTATGTTTCTTTCTTTTTT
108026 AA
1 AA
108028 TTTTTAAAAA
Statistics
Matches: 54, Mismatches: 26, Indels: 10
0.60 0.29 0.11
Matches are distributed among these distances:
40 1 0.02
41 25 0.46
42 27 0.50
43 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (42 bp):
AAAAATTAAAATATTTACTACATTTATGTTTCTTTCTTTTTT
Found at i:107954 original size:83 final size:83
Alignment explanation
Indices: 107861--108027 Score: 325
Period size: 83 Copynumber: 2.0 Consensus size: 83
107851 GTAATTTATT
*
107861 AAAATATAAATATCGAATATAAGAGTTTTGTTTGATGAAAAAAAATTAAAATATTTACTACATTT
1 AAAATATAAATATCAAATATAAGAGTTTTGTTTGATGAAAAAAAATTAAAATATTTACTACATTT
107926 ATGTTTCTTTCTTTTTTA
66 ATGTTTCTTTCTTTTTTA
107944 AAAATATAAATATCAAATATAAGAGTTTTGTTTGATGAAAAAAAATTAAAATATTTACTACATTT
1 AAAATATAAATATCAAATATAAGAGTTTTGTTTGATGAAAAAAAATTAAAATATTTACTACATTT
108009 ATGTTTCTTTCTTTTTTA
66 ATGTTTCTTTCTTTTTTA
108027 A
1 A
108028 TTTTTAAAAA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (83 bp):
AAAATATAAATATCAAATATAAGAGTTTTGTTTGATGAAAAAAAATTAAAATATTTACTACATTT
ATGTTTCTTTCTTTTTTA
Found at i:107996 original size:41 final size:41
Alignment explanation
Indices: 107868--107997 Score: 97
Period size: 41 Copynumber: 3.1 Consensus size: 41
107858 ATTAAAATAT
*
107868 AAATATCGAATATAAGAGTTTTGTTTGATGAAAAAAAATTA
1 AAATATCAAATATAAGAGTTTTGTTTGATGAAAAAAAATTA
* * * ** * ** *
107909 AAATATTTACTACATTTATGTTTCTTTCTTT--TTTAAAAATA-T-
1 AAATA--T-C-AAATATAAGAGT-TTTGTTTGATGAAAAAAAATTA
107951 AAATATCAAATATAAGAGTTTTGTTTGATGAAAAAAAATTA
1 AAATATCAAATATAAGAGTTTTGTTTGATGAAAAAAAATTA
107992 AAATAT
1 AAATAT
107998 TTACTACATT
Statistics
Matches: 61, Mismatches: 19, Indels: 18
0.62 0.19 0.18
Matches are distributed among these distances:
37 6 0.10
38 7 0.11
39 8 0.13
40 2 0.03
41 11 0.18
42 5 0.08
43 2 0.03
44 8 0.13
45 6 0.10
46 6 0.10
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (41 bp):
AAATATCAAATATAAGAGTTTTGTTTGATGAAAAAAAATTA
Found at i:108169 original size:33 final size:32
Alignment explanation
Indices: 108132--108203 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 32
108122 TTATTTTGTC
* *
108132 ATTTTAAAAATTTAAAAATATTTTTTATTTCAA
1 ATTTTAAAAATTCAAAAATATTTTTT-TTTAAA
* * *
108165 ATTTTTAATATTCAAAAGTATTTTTTTTTAAA
1 ATTTTAAAAATTCAAAAATATTTTTTTTTAAA
108197 ATTTTAA
1 ATTTTAA
108204 TATAGTATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 11 0.33
33 22 0.67
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (32 bp):
ATTTTAAAAATTCAAAAATATTTTTTTTTAAA
Found at i:108205 original size:31 final size:33
Alignment explanation
Indices: 108145--108206 Score: 92
Period size: 31 Copynumber: 1.9 Consensus size: 33
108135 TTAAAAATTT
*
108145 AAAAATATTTTTTATTTCAAATTTTTAATATTC
1 AAAAATATTTTTTATTTCAAAATTTTAATATTC
*
108178 AAAAGTATTTTTT-TTT-AAAATTTTAATAT
1 AAAAATATTTTTTATTTCAAAATTTTAATAT
108207 AGTATAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 12 0.44
32 3 0.11
33 12 0.44
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (33 bp):
AAAAATATTTTTTATTTCAAAATTTTAATATTC
Found at i:109128 original size:18 final size:17
Alignment explanation
Indices: 109083--109128 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
109073 CCGTATCAAC
*
109083 ATTTTTTTAA-AATTTT
1 ATTTATTTAATAATTTT
109099 A-TTATTTAAATAATTTTT
1 ATTTATTT-AATAA-TTTT
109117 ATTTATTTAATA
1 ATTTATTTAATA
109129 TTAATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 5 0.20
16 3 0.12
17 2 0.08
18 9 0.36
19 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTATTTAATAATTTT
Found at i:114029 original size:17 final size:16
Alignment explanation
Indices: 113998--114031 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
113988 ATGTGAAAAA
113998 TTATATAAAAATATAT
1 TTATATAAAAATATAT
*
114014 TTATAGTAAAATTATAT
1 TTATA-TAAAAATATAT
114031 T
1 T
114032 AGAATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
TTATATAAAAATATAT
Found at i:124999 original size:2 final size:2
Alignment explanation
Indices: 124992--125025 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
124982 CTGCGTATAA
124992 TC TC TC TC TC TC TC TC TC TC TC TC TC TC ATC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC -TC TC T
125026 TTGTCGTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:128270 original size:22 final size:22
Alignment explanation
Indices: 128245--128286 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
128235 AAGTTTTGAT
128245 TTTAAAATTAGGTTTAAATTGG
1 TTTAAAATTAGGTTTAAATTGG
* **
128267 TTTAAATTTATTTTTAAATT
1 TTTAAAATTAGGTTTAAATT
128287 TAAATTTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.55
Consensus pattern (22 bp):
TTTAAAATTAGGTTTAAATTGG
Found at i:128302 original size:17 final size:17
Alignment explanation
Indices: 128267--128312 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 17
128257 TTTAAATTGG
*
128267 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TATTAAA
128285 TTTAAATTTATATTAAA
1 TTTAAATTTATATTAAA
128302 TTTAAATTTAT
1 TTTAAATTTAT
128313 CTTTTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 17 0.63
18 10 0.37
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTAAATTTATATTAAA
Found at i:128328 original size:6 final size:6
Alignment explanation
Indices: 128267--128311 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
128257 TTTAAATTGG
** *
128267 TTTAAA TTTATT TTTAAA TTTAAA TTTATA -TTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
128312 TCTTTTTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:129025 original size:9 final size:9
Alignment explanation
Indices: 129008--129082 Score: 51
Period size: 9 Copynumber: 8.0 Consensus size: 9
128998 TCAAAATGTC
*
129008 ATTAATAAT
1 ATTATTAAT
129017 ATTATTAATT
1 ATTATTAA-T
129027 ATTATGGTAAT
1 ATTAT--TAAT
* *
129038 AATAATAAT
1 ATTATTAAT
* *
129047 AATAATAAT
1 ATTATTAAT
*
129056 ATTACTAAT
1 ATTATTAAT
*
129065 ATTGTTAAT
1 ATTATTAAT
*
129074 AATATTAAT
1 ATTATTAAT
129083 GACGATAATA
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
9 41 0.76
10 6 0.11
11 4 0.07
12 3 0.06
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (9 bp):
ATTATTAAT
Found at i:129025 original size:12 final size:12
Alignment explanation
Indices: 129008--129080 Score: 69
Period size: 12 Copynumber: 6.1 Consensus size: 12
128998 TCAAAATGTC
129008 ATTAATAATATT
1 ATTAATAATATT
129020 ATTAAT--TATT
1 ATTAATAATATT
*
129030 ATGGTAATAATAAT
1 AT--TAATAATATT
* *
129044 AATAATAATAAT
1 ATTAATAATATT
*
129056 ATTACTAATATT
1 ATTAATAATATT
*
129068 GTTAATAATATT
1 ATTAATAATATT
129080 A
1 A
129081 ATGACGATAA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
10 6 0.12
12 39 0.80
14 4 0.08
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (12 bp):
ATTAATAATATT
Found at i:129040 original size:3 final size:3
Alignment explanation
Indices: 129034--129110 Score: 55
Period size: 3 Copynumber: 25.7 Consensus size: 3
129024 ATTATTATGG
* * * ** *
129034 TAA TAA TAA TAA TAA TAA TAA TAT TAC TAA TAT TGT TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* ** * *
129082 TGA CGA TAA TAA TAA TAA CAT TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
129111 GCATTAATTA
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:130213 original size:29 final size:29
Alignment explanation
Indices: 130181--130589 Score: 263
Period size: 30 Copynumber: 14.1 Consensus size: 29
130171 AAAATTACCA
*
130181 TTTTACCCCCAAACTTCCAAAAATCTCATT
1 TTTTACCCCCAAACTTCCAAAAATCCCA-T
* * * * *
130211 TTTTATCTCGAAACTTTCAAAAATTACCA-
1 TTTTACCCCCAAACTTCCAAAAA-TCCCAT
* *
130240 -TTTACCCTCGAACTTCCAAAAATCCCAT
1 TTTTACCCCCAAACTTCCAAAAATCCCAT
* * *
130268 TTTTGACCCCAAAATTTCCAAAAAATACCA-
1 TTTT-ACCCCCAAACTTCC-AAAAATCCCAT
* *
130298 TTTTACCCCTAAACTTCCAATAATCCCATT
1 TTTTACCCCCAAACTTCCAAAAATCCCA-T
* * *
130328 TTTTACCCCAAAATTTCCAAAAATTACCATT
1 TTTTACCCCCAAACTTCCAAAAA-TCCCA-T
* ** *
130359 ATTTTAACCATAAATTTCCAAAAATCCCAT
1 -TTTTACCCCCAAACTTCCAAAAATCCCAT
* * * *
130389 TTTTAACCTCAAAACTTCAAAAAATACCA-
1 TTTT-ACCCCCAAACTTCCAAAAATCCCAT
* *
130418 TTTTATCCCCAAACTTCCAAAAATCCTAT
1 TTTTACCCCCAAACTTCCAAAAATCCCAT
*
130447 TTTTGACCCCCAAAACTTCCAAAAATTACCA-
1 TTTT-ACCCCC-AAACTTCCAAAAA-TCCCAT
* * *
130478 TTTTACCCTCGAATTTCCAAAAATCCCATT
1 TTTTACCCCCAAACTTCCAAAAATCCCA-T
* *
130508 TTTTA-TCCCAAAATT------A--CCA-
1 TTTTACCCCCAAACTTCCAAAAATCCCAT
130527 TTTTACCCCCAAACTTCCAAAAATCCCAT
1 TTTTACCCCCAAACTTCCAAAAATCCCAT
* * *
130556 TTTTGACCCCAAAACTTTCAAAAATTACCAT
1 TTTT-ACCCCCAAACTTCCAAAAA-TCCCAT
130587 TTT
1 TTT
130590 ACTCCCTGAT
Statistics
Matches: 292, Mismatches: 59, Indels: 55
0.72 0.15 0.14
Matches are distributed among these distances:
19 5 0.02
20 8 0.03
21 3 0.01
23 1 0.00
26 1 0.00
27 4 0.01
28 49 0.17
29 48 0.16
30 103 0.35
31 47 0.16
32 23 0.08
ACGTcount: A:0.37, C:0.29, G:0.01, T:0.33
Consensus pattern (29 bp):
TTTTACCCCCAAACTTCCAAAAATCCCAT
Found at i:130293 original size:59 final size:59
Alignment explanation
Indices: 130171--130591 Score: 435
Period size: 59 Copynumber: 7.3 Consensus size: 59
130161 AAACTGTTCG
* * * * * *
130171 AAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTTATCTCGAAACTTT-CA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGA-CCCCAAAATTTCCA
*
130230 AAAATTACCA-TTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAAATTTCCA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAATTTCCA
* * *
130288 AAAAATACCATTTTACCC-CTAAACTTCCAATAATCCCATTTTTTACCCCAAAATTTCCA
1 AAAATTACCATTTTACCCTC-AAACTTCCAAAAATCCCATTTTTGACCCCAAAATTTCCA
* * * * *
130347 AAAATTACCATTATTTTAACCAT-AAATTTCCAAAAATCCCATTTTTAACCTCAAAACTT-CA
1 AAAATTACC---ATTTT-ACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAATTTCCA
* * *
130408 AAAAATACCATTTTATCCC-CAAACTTCCAAAAATCCTATTTTTGACCCCCAAAACTTCCA
1 AAAATTACCATTTTA-CCCTCAAACTTCCAAAAATCCCATTTTTGA-CCCCAAAATTTCCA
* * * *
130468 AAAATTACCATTTTACCCTCGAATTTCCAAAAATCCCATTTTT----------TATCCC
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAATTTCCA
*
130517 AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTT-CA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAA-TTTCCA
130576 AAAATTACCATTTTAC
1 AAAATTACCATTTTAC
130592 TCCCTGATGT
Statistics
Matches: 302, Mismatches: 36, Indels: 48
0.78 0.09 0.12
Matches are distributed among these distances:
49 43 0.14
57 9 0.03
58 71 0.24
59 91 0.30
60 39 0.13
61 10 0.03
62 36 0.12
63 3 0.01
ACGTcount: A:0.38, C:0.29, G:0.01, T:0.32
Consensus pattern (59 bp):
AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAATTTCCA
Found at i:130545 original size:49 final size:49
Alignment explanation
Indices: 130468--130569 Score: 159
Period size: 49 Copynumber: 2.1 Consensus size: 49
130458 AAAACTTCCA
* * * * *
130468 AAAATTACCATTTTACCCTCGAATTTCCAAAAATCCCATTTTTTATCCC
1 AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
130517 AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
1 AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
130566 AAAA
1 AAAA
130570 CTTTCAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.31
Consensus pattern (49 bp):
AAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
Found at i:135788 original size:6 final size:6
Alignment explanation
Indices: 135777--135895 Score: 54
Period size: 6 Copynumber: 20.7 Consensus size: 6
135767 TGAGATTTAT
** * * *
135777 TTTAAA TTTAAA TTT-GT TTTAAG TTTAAA ATT-AT TTTAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
* * * * * * *
135824 TTTAAA -TCAAG TTTAAA TTT-AT TTTGAA TTCAAAA GTT-AT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA
*
135870 TTTAAA -TT-AA TTTGAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA
135896 TAATAAATAA
Statistics
Matches: 81, Mismatches: 23, Indels: 18
0.66 0.19 0.15
Matches are distributed among these distances:
4 2 0.02
5 20 0.25
6 52 0.64
7 7 0.09
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:135796 original size:17 final size:17
Alignment explanation
Indices: 135771--135896 Score: 119
Period size: 17 Copynumber: 7.4 Consensus size: 17
135761 TCATTTTGAG
135771 ATTTATTTTAAATTTAA
1 ATTTATTTTAAATTTAA
* *
135788 ATTTGTTTTAAGTTTAA
1 ATTTATTTTAAATTTAA
*
135805 AATTATTTTAAAATTTAA
1 ATTTATTTT-AAATTTAA
** * *
135823 ATTTAAATCAAGTTTAA
1 ATTTATTTTAAATTTAA
* *
135840 ATTTATTTTGAATTCAAA
1 ATTTATTTTAAATT-TAA
*
135858 AGTTATTTTAAATTTAA
1 ATTTATTTTAAATTTAA
* *
135875 A-TTAATTTGAATTTAA
1 ATTTATTTTAAATTTAA
135891 ATTTAT
1 ATTTAT
135897 AATAAATAAG
Statistics
Matches: 84, Mismatches: 22, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
16 14 0.17
17 44 0.52
18 26 0.31
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (17 bp):
ATTTATTTTAAATTTAA
Found at i:135836 original size:35 final size:34
Alignment explanation
Indices: 135773--135853 Score: 99
Period size: 35 Copynumber: 2.4 Consensus size: 34
135763 ATTTTGAGAT
*** *
135773 TTATTTTAAATTTAAATTTGTTTTAAGTTTAAAA
1 TTATTTTAAATTTAAATTTAAATCAAGTTTAAAA
*
135807 TTATTTTAAAATTTAAATTTAAATCAAGTTTAAAT
1 TTATTTT-AAATTTAAATTTAAATCAAGTTTAAAA
*
135842 TTATTTTGAATT
1 TTATTTTAAATT
135854 CAAAAGTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
34 11 0.28
35 29 0.73
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (34 bp):
TTATTTTAAATTTAAATTTAAATCAAGTTTAAAA
Found at i:136539 original size:3 final size:3
Alignment explanation
Indices: 136531--136562 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
136521 GTATTGAATG
136531 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
136563 CAAAAAGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:137740 original size:30 final size:30
Alignment explanation
Indices: 137685--137889 Score: 167
Period size: 30 Copynumber: 7.0 Consensus size: 30
137675 ATTTTGACCC
*
137685 AAAC-TTCTCAAAAATTGCA-TTTAACCCCT
1 AAACTTTC-CAAAAATTACATTTTAACCCCT
*
137714 AAACTTTCCAAAAATTACATTTTAACCCTT
1 AAACTTTCCAAAAATTACATTTTAACCCCT
* * *
137744 AAA-TTTCTCAAAGATTACATTTTAACACTT
1 AAACTTTC-CAAAAATTACATTTTAACCCCT
* * *
137774 AAACTTTCTAAAAAATACATTTTCACCCC-
1 AAACTTTCCAAAAATTACATTTTAACCCCT
* *
137803 AAAC-TTACAAAAATCACATTTTTAA-CCCT
1 AAACTTTCCAAAAATTACA-TTTTAACCCCT
* * *
137832 AAATTTTCCAAAAATTATCA-TTTACCCCCC
1 AAACTTTCCAAAAATTA-CATTTTAACCCCT
* *
137862 AAAC-ATCC-AAAATTATCATTTTACCCCC
1 AAACTTTCCAAAAATTA-CATTTTAACCCC
137890 GAATGTCCAA
Statistics
Matches: 144, Mismatches: 22, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
28 23 0.16
29 46 0.32
30 69 0.48
31 6 0.04
ACGTcount: A:0.40, C:0.26, G:0.01, T:0.33
Consensus pattern (30 bp):
AAACTTTCCAAAAATTACATTTTAACCCCT
Found at i:137873 original size:59 final size:57
Alignment explanation
Indices: 137682--137873 Score: 170
Period size: 59 Copynumber: 3.3 Consensus size: 57
137672 CATATTTTGA
** *
137682 CCCAAACTTCTCAAAAATTGCA-TTTAACCCCTAAACTTTCCAAAAATTACATTTTAACC
1 CCCAAACTTC-CAAAAATCACATTTTAA-CCCTAAACTTTCCAAAAATTACA-TTTACCC
** * * * * * * * *
137741 CTTAAATTTCTCAAAGATTACATTTTAACACTTAAACTTTCTAAAAAATACATTTTCAC
1 CCCAAACTTC-CAAAAATCACATTTTAAC-CCTAAACTTTCCAAAAATTACATTTACCC
* *
137800 CCCAAACTTACAAAAATCACATTTTTAACCCTAAATTTTCCAAAAATTATCATTTACCC
1 CCCAAACTTCCAAAAATCACA-TTTTAACCCTAAACTTTCCAAAAATTA-CATTTACCC
*
137859 CCCAAACATCCAAAA
1 CCCAAACTTCCAAAA
137874 TTATCATTTT
Statistics
Matches: 104, Mismatches: 25, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
58 25 0.24
59 55 0.53
60 24 0.23
ACGTcount: A:0.41, C:0.26, G:0.01, T:0.32
Consensus pattern (57 bp):
CCCAAACTTCCAAAAATCACATTTTAACCCTAAACTTTCCAAAAATTACATTTACCC
Found at i:137902 original size:29 final size:29
Alignment explanation
Indices: 137838--138066 Score: 216
Period size: 29 Copynumber: 7.9 Consensus size: 29
137828 CCCTAAATTT
* **
137838 TCCAAAAATTATCA-TTTACCCCCCAAACA
1 TCCAAAAATTATCATTTTA-CCCCCGAATG
137867 TCC-AAAATTATCATTTTACCCCCGAATG
1 TCCAAAAATTATCATTTTACCCCCGAATG
* * * *
137895 TCCAAAAATT-TTATTTCTACCCTCGAGTT
1 TCCAAAAATTATCATTT-TACCCCCGAATG
* * *
137924 TCCAAAAGTTACCATTTTACTCCCGAATTG
1 TCCAAAAATTATCATTTTACCCCCGAA-TG
* * *
137954 TCCAAAAATTA-CATTTTGCCCCCGAGTT
1 TCCAAAAATTATCATTTTACCCCCGAATG
* *
137982 TTCAAAAATTATCATTTTACCCCCGGATG
1 TCCAAAAATTATCATTTTACCCCCGAATG
* * *
138011 TCCAAAAATTA-CATTTTTGCTCCCGAGTG
1 TCCAAAAATTATCA-TTTTACCCCCGAATG
*
138040 TCCAAAAATTATCGTTTTACCCCCGAA
1 TCCAAAAATTATCATTTTACCCCCGAA
138067 CCTCCGTAAA
Statistics
Matches: 159, Mismatches: 33, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
28 38 0.24
29 105 0.66
30 16 0.10
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (29 bp):
TCCAAAAATTATCATTTTACCCCCGAATG
Found at i:138092 original size:58 final size:57
Alignment explanation
Indices: 137870--138092 Score: 250
Period size: 58 Copynumber: 3.8 Consensus size: 57
137860 CCAAACATCC
**
137870 AAAATTATCATTTTACCCCCGAATGTCCAAAAATTTTATTTCTAC-CCTCGAGTTTCCA
1 AAAATTATCATTTTACCCCCGAATGTCCAAAAATTACATTT-TACTCC-CGAGTTTCCA
* * * * * *
137928 AAAGTTACCATTTTACTCCCGAATTGTCCAAAAATTACATTTTGCCCCCGAGTTTTCA
1 AAAATTATCATTTTACCCCCGAA-TGTCCAAAAATTACATTTTACTCCCGAGTTTCCA
* * *
137986 AAAATTATCATTTTACCCCCGGATGTCCAAAAATTACATTTTTGCTCCCGAGTGTCCA
1 AAAATTATCATTTTACCCCCGAATGTCCAAAAATTACA-TTTTACTCCCGAGTTTCCA
* ** **
138044 AAAATTATCGTTTTACCCCCGAACCTCCGTAAATTACTATTTTACTCCC
1 AAAATTATCATTTTACCCCCGAATGTCCAAAAATTAC-ATTTTACTCCC
138093 AGGCATCCAA
Statistics
Matches: 140, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
57 15 0.11
58 106 0.76
59 19 0.14
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.35
Consensus pattern (57 bp):
AAAATTATCATTTTACCCCCGAATGTCCAAAAATTACATTTTACTCCCGAGTTTCCA
Found at i:140849 original size:41 final size:41
Alignment explanation
Indices: 140804--140883 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
140794 GGAAAAACGT
* **
140804 CGCTAAAGGTCATAGCATTAACGGTGTTTATGGGAAAGCGC
1 CGCTAAAGGTCAAAGCATTAACGGCATTTATGGGAAAGCGC
*
140845 CGCTAAAGGTCAAAGCATTAGCGGCATTTATGGGAAAGC
1 CGCTAAAGGTCAAAGCATTAACGGCATTTATGGGAAAGC
140884 ACAGTTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (41 bp):
CGCTAAAGGTCAAAGCATTAACGGCATTTATGGGAAAGCGC
Found at i:142169 original size:2 final size:2
Alignment explanation
Indices: 142157--142186 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
142147 TTTATTGCAA
*
142157 AT AT TT 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
142187 GGTAAATGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:149868 original size:2 final size:2
Alignment explanation
Indices: 149861--149889 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
149851 TTCCACATAA
149861 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
149890 TTTCTAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:150477 original size:5 final size:5
Alignment explanation
Indices: 150472--150509 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
150462 GAATGAACCG
* *
150472 ATCCG ATCCG ATCCA ATCCA ATCCA ATCCA ATCCA ATC
1 ATCCA ATCCA ATCCA ATCCA ATCCA ATCCA ATCCA ATC
150510 TCCAAATATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.34, C:0.39, G:0.05, T:0.21
Consensus pattern (5 bp):
ATCCA
Found at i:151268 original size:14 final size:14
Alignment explanation
Indices: 151249--151276 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
151239 CCTTGTGTCG
151249 AAACCATCTTTTTT
1 AAACCATCTTTTTT
151263 AAACCATCTTTTTT
1 AAACCATCTTTTTT
151277 GGAAAACGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (14 bp):
AAACCATCTTTTTT
Found at i:152197 original size:29 final size:29
Alignment explanation
Indices: 152143--152575 Score: 116
Period size: 29 Copynumber: 14.7 Consensus size: 29
152133 TGCTTGGGTT
*
152143 AAATGGTAATTTTTGGAAGGCTCGAGGTCAA
1 AAATGG-AATTTTTGGAA-GTTCGAGGTCAA
152174 AAATGGAATTTTTGGACA-TTCGAGGGT--A
1 AAATGGAATTTTTGGA-AGTTCGA-GGTCAA
* * *
152202 AAATGGTAAATTTTGGAAGGTTCAAGATCAA
1 AAATGG-AATTTTTGGAA-GTTCGAGGTCAA
* * * * *
152233 AAACGGAGTTTTTAGACA-TCCAAGGGT--A
1 AAATGGAATTTTTGGA-AGTTCGA-GGTCAA
* * * * *
152261 AAATGATAATTTTCGAAAGTTTTGGGGTCAA
1 AAATG-GAATTTTTGGAAG-TTCGAGGTCAA
* **
152292 AAATGGAATTTTTGGAAGTTCGGGGGGAA
1 AAATGGAATTTTTGGAAGTTCGAGGTCAA
* *
152321 AAATGCTAA-TTTTGGAAAGTTTG-GGATCAA
1 AAATG-GAATTTTTGG-AAGTTCGAGG-TCAA
* *
152351 AAATGGAGTTTTTAGACA-TTCGAGGGT---
1 AAATGGAATTTTTGGA-AGTTCGA-GGTCAA
* *
152378 AAATGGTAAATTTTGGAAGTTTCG-GGATTAA
1 AAATGG-AATTTTTGGAAG-TTCGAGG-TCAA
* * * *
152409 AAACGGAGTTTTTAGACA-TTTGAGGGT-AA
1 AAATGGAATTTTTGGA-AGTTCGA-GGTCAA
* *
152438 AATTGTAATTTTTGGAAGTTTCGAGGTCAA
1 AAATGGAATTTTTGGAAG-TTCGAGGTCAA
* * * * *
152468 ATATGGAA-TTTTGAAAAATTCAAGGTAAA
1 AAATGGAATTTTTG-GAAGTTCGAGGTCAA
* * * *
152497 AAATGTAATTTATGAAAATATCG-GGTCAA
1 AAATGGAATTTTTGGAAGT-TCGAGGTCAA
*
152526 AATTGGAA-TTTTGGAAAGTTTGCG-GGTCAA
1 AAATGGAATTTTTGG-AAG-TT-CGAGGTCAA
152556 AATAT--AATTTTTGGATAGTT
1 AA-ATGGAATTTTTGGA-AGTT
152576 TAGGGACTTT
Statistics
Matches: 293, Mismatches: 66, Indels: 88
0.66 0.15 0.20
Matches are distributed among these distances:
27 9 0.03
28 27 0.09
29 121 0.41
30 105 0.36
31 31 0.11
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.33
Consensus pattern (29 bp):
AAATGGAATTTTTGGAAGTTCGAGGTCAA
Found at i:152303 original size:30 final size:29
Alignment explanation
Indices: 152268--152362 Score: 91
Period size: 30 Copynumber: 3.2 Consensus size: 29
152258 GTAAAATGAT
152268 AATTTTCGAAAGTTTTGGGGTCAAAAATGG
1 AATTTTCGAAAG-TTTGGGGTCAAAAATGG
* * * ** *
152298 AATTTTTGGAAGTTCGGGGGGAAAAATGCT
1 AATTTTCGAAAGTTTGGGGTCAAAAATG-G
* *
152328 AATTTTGGAAAGTTTGGGATCAAAAATGG
1 AATTTTCGAAAGTTTGGGGTCAAAAATGG
*
152357 AGTTTT
1 AATTTT
152363 TAGACATTCG
Statistics
Matches: 50, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
29 18 0.36
30 32 0.64
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (29 bp):
AATTTTCGAAAGTTTGGGGTCAAAAATGG
Found at i:152411 original size:58 final size:59
Alignment explanation
Indices: 152138--152479 Score: 329
Period size: 59 Copynumber: 5.8 Consensus size: 59
152128 TTGGATGCTT
* * ** * *
152138 GGGTTAAATGGTAATTTTTGGAAGGCTCGAGG-TCAAAAATGGAATTTTTGGACATTCGA
1 GGGTAAAATGGTAAATTTTGGAAGTTTCG-GGATCAAAAATGGAGTTTTTAGACATTCGA
* ** * * *
152197 GGGTAAAATGGTAAATTTTGGAAGGTTCAAGATCAAAAACGGAGTTTTTAGACATCCAA
1 GGGTAAAATGGTAAATTTTGGAAGTTTCGGGATCAAAAATGGAGTTTTTAGACATTCGA
* * * * * * *
152256 GGGTAAAATGAT-AATTTTCGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGA-AGTTCGGG
1 GGGTAAAATGGTAAATTTT-GGAAGTTTCGGGATCAAAAATGGAGTTTTTAGACA-TTC-GA
* *
152316 GGGAAAAATGCT-AATTTTGGAAAGTTT-GGGATCAAAAATGGAGTTTTTAGACATTCGA
1 GGGTAAAATGGTAAATTTTGG-AAGTTTCGGGATCAAAAATGGAGTTTTTAGACATTCGA
* * *
152374 GGGT-AAATGGTAAATTTTGGAAGTTTCGGGATTAAAAACGGAGTTTTTAGACATTTGA
1 GGGTAAAATGGTAAATTTTGGAAGTTTCGGGATCAAAAATGGAGTTTTTAGACATTCGA
* * * *
152432 GGGTAAAATTGTAATTTTTGGAAGTTTCGAGG-TCAAATATGGAATTTT
1 GGGTAAAATGGTAAATTTTGGAAGTTTCG-GGATCAAAAATGGAGTTTT
152480 GAAAAATTCA
Statistics
Matches: 232, Mismatches: 41, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
57 12 0.05
58 52 0.22
59 143 0.62
60 25 0.11
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.33
Consensus pattern (59 bp):
GGGTAAAATGGTAAATTTTGGAAGTTTCGGGATCAAAAATGGAGTTTTTAGACATTCGA
Found at i:152501 original size:176 final size:176
Alignment explanation
Indices: 152170--152537 Score: 449
Period size: 176 Copynumber: 2.1 Consensus size: 176
152160 AGGCTCGAGG
*
152170 TCAAAAATGGAATTTTTGGACATTCGAGGGTAAAATGGTAAATTTTGGAAGGTTCAAGATCAAAA
1 TCAAAAATGGAATTTTTAGACATTCGAGGGTAAAATGGTAAATTTTGGAAGGTTCAAGATCAAAA
* *
152235 ACGGAGTTTTTAGACATCCAAGGGTAAAATGATAATTTTCGAAAGTTTTGGGGTCAAAAATGGAA
66 ACGGAGTTTTTAGACATCCAAGGGTAAAATGATAATTTTCGAAAGTTTCGAGGTCAAAAATGGAA
* * ** *
152300 TTTTTGGAAGTTCGGGGGGAAAAATGCTAATTTTGGAAAGTTTGGGA
131 TTTTTGAAAATTCAAGGGAAAAAATG-TAATTTTGGAAAGTTTGGGA
* * ** *
152347 TCAAAAATGGAGTTTTTAGACATTCGAGGGT-AAATGGTAAATTTTGGAAGTTTCGGGATTAAAA
1 TCAAAAATGGAATTTTTAGACATTCGAGGGTAAAATGGTAAATTTTGGAAGGTTCAAGATCAAAA
*** * * *
152411 ACGGAGTTTTTAGACATTTGAGGGTAAAATTG-TAATTTTTGGAAGTTTCGAGGTCAAATATGGA
66 ACGGAGTTTTTAGACATCCAAGGGTAAAA-TGATAATTTTCGAAAGTTTCGAGGTCAAAAATGGA
* * *
152475 A-TTTTGAAAAATTCAAGGTAAAAAATGTAATTTAT-GAAAATATCGGG-
130 ATTTTTG-AAAATTCAAGGGAAAAAATGTAATTT-TGGAAAGT-TTGGGA
*
152522 TCAAAATTGGAATTTT
1 TCAAAAATGGAATTTT
152538 GGAAAGTTTG
Statistics
Matches: 163, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
175 30 0.18
176 102 0.63
177 31 0.19
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (176 bp):
TCAAAAATGGAATTTTTAGACATTCGAGGGTAAAATGGTAAATTTTGGAAGGTTCAAGATCAAAA
ACGGAGTTTTTAGACATCCAAGGGTAAAATGATAATTTTCGAAAGTTTCGAGGTCAAAAATGGAA
TTTTTGAAAATTCAAGGGAAAAAATGTAATTTTGGAAAGTTTGGGA
Found at i:152568 original size:30 final size:29
Alignment explanation
Indices: 152518--152576 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
152508 ATGAAAATAT
152518 CGGGTCAAAATTGGAATTTTGGAAAGTTTG
1 CGGGTCAAAATT-GAATTTTGGAAAGTTTG
*
152548 CGGGTCAAAATAT-AATTTTTGGATAGTTT
1 CGGGTCAAAAT-TGAA-TTTTGGAAAGTTT
152577 AGGGACTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 2 0.08
30 23 0.88
31 1 0.04
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.37
Consensus pattern (29 bp):
CGGGTCAAAATTGAATTTTGGAAAGTTTG
Found at i:153724 original size:3 final size:3
Alignment explanation
Indices: 153718--153803 Score: 172
Period size: 3 Copynumber: 28.7 Consensus size: 3
153708 CTACTACTAC
153718 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
153766 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
153804 ATGCTATTAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:154541 original size:19 final size:20
Alignment explanation
Indices: 154501--154542 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
154491 CAATTAGGCC
154501 TTTGTAAATTGGACATTTAA
1 TTTGTAAATTGGACATTTAA
154521 TTTGTAAA-TGGAC-TTTGAA
1 TTTGTAAATTGGACATTT-AA
154540 TTT
1 TTT
154543 AATTTTAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.14
19 10 0.48
20 8 0.38
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (20 bp):
TTTGTAAATTGGACATTTAA
Found at i:154603 original size:18 final size:18
Alignment explanation
Indices: 154580--154617 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
154570 TTTCAAATAT
154580 AAACTAAATTGAAATTTA
1 AAACTAAATTGAAATTTA
*
154598 AAACTAAATTTAAATTTA
1 AAACTAAATTGAAATTTA
154616 AA
1 AA
154618 TTTAAAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (18 bp):
AAACTAAATTGAAATTTA
Found at i:154611 original size:6 final size:6
Alignment explanation
Indices: 154584--154638 Score: 67
Period size: 6 Copynumber: 9.3 Consensus size: 6
154574 AAATATAAAC
* ** *
154584 TAAATT GAAATT TAAAAC TAAATT TAAATT TAAATT TAAA-G TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
154631 TAAATT TA
1 TAAATT TA
154639 GAAATAAATC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
5 4 0.10
6 36 0.90
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:154629 original size:41 final size:42
Alignment explanation
Indices: 154569--154652 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 42
154559 TTTTAAAATT
*
154569 ATTTCAAATATAAACTAAATTGAAATTTA-AAACTAAATTTAA
1 ATTTCAAATATAAACTAAATTGAAATTTAGAAA-TAAATCTAA
* * *
154611 ATTT-AAATTTAAAGTAAATTTAAATTTAGAAATAAATCTAA
1 ATTTCAAATATAAACTAAATTGAAATTTAGAAATAAATCTAA
154652 A
1 A
154653 ATAATTTGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 30 0.81
42 7 0.19
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.37
Consensus pattern (42 bp):
ATTTCAAATATAAACTAAATTGAAATTTAGAAATAAATCTAA
Found at i:154630 original size:17 final size:18
Alignment explanation
Indices: 154608--154652 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
154598 AAACTAAATT
*
154608 TAAATTTAAATTTA-AAG
1 TAAATTTAAATTTAGAAA
154625 TAAATTTAAATTTAGAAA
1 TAAATTTAAATTTAGAAA
*
154643 TAAATCTAAA
1 TAAATTTAAA
154653 ATAATTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (18 bp):
TAAATTTAAATTTAGAAA
Found at i:154646 original size:23 final size:23
Alignment explanation
Indices: 154584--154646 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
154574 AAATATAAAC
* * *
154584 TAAATTGAAATTTAAAACTAAATT
1 TAAATTTAAATAT-AAAGTAAATT
*
154608 TAAATTTAAATTTAAAGTAAATT
1 TAAATTTAAATATAAAGTAAATT
154631 TAAATTTAGAA-ATAAA
1 TAAATTTA-AATATAAA
154647 TCTAAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
23 21 0.60
24 14 0.40
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (23 bp):
TAAATTTAAATATAAAGTAAATT
Found at i:155374 original size:206 final size:206
Alignment explanation
Indices: 155010--155835 Score: 1190
Period size: 206 Copynumber: 4.0 Consensus size: 206
155000 TCTGGTTTCA
* * * * * * * *
155010 TTGACTTGGACTTCTTCTCAATATCTCATCAGGAAGATGACCGCATCACTTATTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTTAATCCGCTT
* * * *
155075 CTCTGTGTTTTATCAGGAAGACGGATTTGGTTCACTTCTTC-GTATCTCATCAGGAAGCTAACCA
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTC-TCAGTATCTCATCAGGAAGCTAACCA
* *
155139 TTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
130 TTTTATTTCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACA
155204 TCGAGCGTGAGT
195 TCGAGCGTGAGT
** * *
155216 TTGATTTGGTCTTCTTCTTTGTGTCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTTAATCCGCTT
155281 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* *
155346 TTTATTTCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTCTCACAT
131 TTTATTTCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACAT
*
155411 TGAGCGTGAGT
196 CGAGCGTGAGT
* *
155422 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGAAAGATGACCGAGTCATTTGTTTTAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTTAATCCGCTT
* * * * *
155487 CTCTGTGTTTCATTAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* *
155552 TTTATTGCTTCGACCTGCTTCTCAATATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACAT
131 TTTATTTCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACAT
* *
155617 CGAGTGTGGGT
196 CGAGCGTGAGT
* * * * * *
155628 TTTATTTGGTTTTCTTCTCAGTATCTCATTAAGAAGATGACCGCGTCGTTTGTTTTAATTCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTTAATCCGCTT
* * * *
155693 CTCTGTATCTCATCAGGAAGACGAATTT-GCTCTATTTCTCAATATCTCATAAGGAAGCTAACCA
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTTC-ACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * *
155757 TTTTATTGT-TTCGACCCGCTTCTCAGTATCTCATCAAGAAGCTGAGGTTCGAAGATTTGCTCAT
130 TTTTATT-TCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCAC
155821 ATCGAGCGCTGAGT
194 ATCGAGCG-TGAGT
155835 T
1 T
155836 GGTATACTTC
Statistics
Matches: 555, Mismatches: 61, Indels: 7
0.89 0.10 0.01
Matches are distributed among these distances:
205 4 0.01
206 546 0.98
207 5 0.01
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (206 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTTAATCCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
TTTATTTCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACAT
CGAGCGTGAGT
Found at i:156315 original size:50 final size:50
Alignment explanation
Indices: 156250--156363 Score: 228
Period size: 50 Copynumber: 2.3 Consensus size: 50
156240 TATCTTGCTC
156250 TTACTGCAACTTCAGAGAGATAAAGACTTGCTATTATTTTTAATCCAACT
1 TTACTGCAACTTCAGAGAGATAAAGACTTGCTATTATTTTTAATCCAACT
156300 TTACTGCAACTTCAGAGAGATAAAGACTTGCTATTATTTTTAATCCAACT
1 TTACTGCAACTTCAGAGAGATAAAGACTTGCTATTATTTTTAATCCAACT
156350 TTACTGCAACTTCA
1 TTACTGCAACTTCA
156364 AGTGGATAGG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 64 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.36
Consensus pattern (50 bp):
TTACTGCAACTTCAGAGAGATAAAGACTTGCTATTATTTTTAATCCAACT
Found at i:156641 original size:50 final size:50
Alignment explanation
Indices: 156537--156762 Score: 201
Period size: 50 Copynumber: 4.5 Consensus size: 50
156527 CGCCATTGTA
*** * *
156537 ACTTAAACCTTTCCCTTCAAATCTTC-GTGGTACTA-GATTCGCCGTTGCG
1 ACTTAAACCTTTCCCTTCTTGTCTTCTGAGGTAC-ACGATCCGCCGTTGCG
* * *
156586 GCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACACGGTCCGCCGTTGCG
1 ACTTAAACCTTTCCCTTCTTGTCTTCTGAGGTACACGATCCGCCGTTGCG
* *
156636 ACTTAAACCTTTCCCTT-TTGTATCTT-TGTGGTAC-TGAATCCGCCGTTGCG
1 ACTTAAACCTTTCCCTTCTTG--TCTTCTGAGGTACACG-ATCCGCCGTTGCG
* * * * * * *
156686 GCTTAAATCTTTCCTTTCGTGTCTTCTGAGGTACACGATCCTGCTGTTACA
1 ACTTAAACCTTTCCCTTCTTGTCTTCTGAGGTACACGATCC-GCCGTTGCG
* *
156737 ACTTAGACCTTTCCCTTCATGTCTTC
1 ACTTAAACCTTTCCCTTCTTGTCTTC
156763 ATGGTACTGA
Statistics
Matches: 141, Mismatches: 27, Indels: 16
0.77 0.15 0.09
Matches are distributed among these distances:
49 30 0.21
50 77 0.55
51 34 0.24
ACGTcount: A:0.16, C:0.28, G:0.17, T:0.38
Consensus pattern (50 bp):
ACTTAAACCTTTCCCTTCTTGTCTTCTGAGGTACACGATCCGCCGTTGCG
Found at i:156771 original size:100 final size:100
Alignment explanation
Indices: 156536--156774 Score: 313
Period size: 100 Copynumber: 2.4 Consensus size: 100
156526 TCGCCATTGT
** *
156536 AACTTAAACCTTTCCCTTCAAATCTTCGTGGTACT-AGATTCGCCGTTGCGGCTTAAATCTTTCC
1 AACTTAAACCTTTCCCTTCATGTCTTCGTGGTACTGAGATCCGCCGTTGCGGCTTAAATCTTTCC
* * *
156600 CTTCTTGTCTTCTGAGGTACACGGTCCGCCGTTGC
66 CTTCGTGTCTTCTGAGGTACACGATCCGCCGTTAC
* * *
156635 GACTTAAACCTTTCCCTT-TTGTATCTTTGTGGTACTGA-ATCCGCCGTTGCGGCTTAAATCTTT
1 AACTTAAACCTTTCCCTTCATG--TCTTCGTGGTACTGAGATCCGCCGTTGCGGCTTAAATCTTT
* *
156698 CCTTTCGTGTCTTCTGAGGTACACGATCCTGCTGTTAC
64 CCCTTCGTGTCTTCTGAGGTACACGATCC-GCCGTTAC
* *
156736 AACTTAGACCTTTCCCTTCATGTCTTCATGGTACTGAGA
1 AACTTAAACCTTTCCCTTCATGTCTTCGTGGTACTGAGA
156775 CCTATAGAAC
Statistics
Matches: 118, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
99 17 0.14
100 75 0.64
101 24 0.20
102 2 0.02
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.37
Consensus pattern (100 bp):
AACTTAAACCTTTCCCTTCATGTCTTCGTGGTACTGAGATCCGCCGTTGCGGCTTAAATCTTTCC
CTTCGTGTCTTCTGAGGTACACGATCCGCCGTTAC
Found at i:157996 original size:17 final size:17
Alignment explanation
Indices: 157970--158052 Score: 53
Period size: 17 Copynumber: 4.8 Consensus size: 17
157960 TCAACCTCTC
*
157970 TTTTTTTTCTATTTTTG
1 TTTTTCTTCTATTTTTG
*
157987 TTTTTCTTCTTGTTTTTG
1 TTTTTCTTC-TATTTTTG
* * *
158005 CTTTTCTT-TTTTCTTTC
1 TTTTTCTTCTATT-TTTG
* *
158022 TTCTTCTTCT-TTTTTT
1 TTTTTCTTCTATTTTTG
*
158038 TTTCTTTTTCTATTT
1 TTT-TTCTTCTATTT
158053 GTTTATTTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
16 8 0.16
17 25 0.49
18 18 0.35
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.80
Consensus pattern (17 bp):
TTTTTCTTCTATTTTTG
Found at i:157997 original size:26 final size:26
Alignment explanation
Indices: 157968--158048 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 26
157958 CCTCAACCTC
*
157968 TCTT-TTTTTTCTATTTTTGTTTTTCT
1 TCTTCTTTTTTCT-TTTTTCTTTTTCT
* * *
157994 TCTTGTTTTTGCTTTTCTTTTTTCTTTCT
1 TCTTCTTTTTTC-TTT-TTTCTT-TTTCT
158023 TCTTCTTCTTTT-TTTTTTCTTTTTCT
1 TCTTCTT-TTTTCTTTTTTCTTTTTCT
158049 ATTTGTTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
26 9 0.20
27 13 0.29
28 9 0.20
29 11 0.24
30 3 0.07
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.79
Consensus pattern (26 bp):
TCTTCTTTTTTCTTTTTTCTTTTTCT
Found at i:158015 original size:6 final size:6
Alignment explanation
Indices: 157968--158066 Score: 62
Period size: 6 Copynumber: 16.7 Consensus size: 6
157958 CCTCAACCTC
* * * * *
157968 TCTTTT T-TTTC TATTTT TGTTTT TCTTCT TGTTTT TGC-TTT TCTTTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT T-CTTTT TC-TTTT
* * * *
158016 TCTTTCT TCTTCT TCTTTT T-TTTT TCTTTT TCTATT TGTTTA T-TTTT
1 TCTTT-T TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
158063 TCTT
1 TCTT
158067 CATTGTATCT
Statistics
Matches: 71, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
5 14 0.20
6 47 0.66
7 10 0.14
ACGTcount: A:0.03, C:0.14, G:0.04, T:0.79
Consensus pattern (6 bp):
TCTTTT
Found at i:158026 original size:32 final size:30
Alignment explanation
Indices: 157970--158046 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 30
157960 TCAACCTCTC
* *
157970 TTTT-TTTTCTATTTTTGTTTTTCTTCTTGT
1 TTTTCTTTTCT-TTTTTCTTTTTCTTCTTCT
158000 TTTTGCTTTTCTTTTTTCTTTCTTCTTCTTCT
1 TTTT-CTTTTCTTTTTTCTTT-TTCTTCTTCT
*
158032 TTTTTTTTTCTTTTT
1 TTTTCTTTTCTTTTT
158047 CTATTTGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 4 0.10
31 18 0.44
32 19 0.46
ACGTcount: A:0.01, C:0.14, G:0.04, T:0.81
Consensus pattern (30 bp):
TTTTCTTTTCTTTTTTCTTTTTCTTCTTCT
Found at i:158033 original size:20 final size:20
Alignment explanation
Indices: 158008--158048 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
157998 GTTTTTGCTT
158008 TTCTTTTTTCTTTCTTCTTC
1 TTCTTTTTTCTTTCTTCTTC
* *
158028 TTCTTTTTTTTTTCTTTTTC
1 TTCTTTTTTCTTTCTTCTTC
158048 T
1 T
158049 ATTTGTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (20 bp):
TTCTTTTTTCTTTCTTCTTC
Found at i:162881 original size:28 final size:28
Alignment explanation
Indices: 162840--162897 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
162830 AACTATCGGA
*
162840 GTTGAAAATGAGACTTTTGGATACGGGG
1 GTTGAAAATAAGACTTTTGGATACGGGG
162868 GTTGAAAATAAGACTTTTGGATACGGGG
1 GTTGAAAATAAGACTTTTGGATACGGGG
162896 GT
1 GT
162898 AAAACGGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.29, C:0.07, G:0.34, T:0.29
Consensus pattern (28 bp):
GTTGAAAATAAGACTTTTGGATACGGGG
Found at i:162993 original size:59 final size:59
Alignment explanation
Indices: 162919--163406 Score: 539
Period size: 59 Copynumber: 8.4 Consensus size: 59
162909 TTTTGACGCT
* * * * *
162919 CAGGGGTGAAATGGTAATTTTTGGAAGGCTCGAGGTCAAAAATGGAATTTTTGGACATC
1 CAGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGATCAAAAATGGAGTTTTTAGACATC
* * *
162978 CAAGGGTAAAATGGTAATTTTTGGAAGGTTCTAGAT-AAAAATGGAGTTATT-GACATC
1 CAGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGATCAAAAATGGAGTTTTTAGACATC
* * * *
163035 TAGGGGTAAAATTGTAATTTTTGGAAGGTTTC-AGATCAAAAATAGAGTTTTTAGACATT
1 CAGGGGTAAAATGGTAATTTTTGGAAGG-TTCGAGATCAAAAATGGAGTTTTTAGACATC
* * *
163094 CAGGGGTAAAATGGTAAATTTTGGAAGGTTCGAGATTAAAAACGGAGTTTTTAGACATC
1 CAGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGATCAAAAATGGAGTTTTTAGACATC
*
163153 CAGGGGTAAAATGGTAAATTTTGGAAGGTTCGAGATCAAAAATGGAGTTTTTAGACATC
1 CAGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGATCAAAAATGGAGTTTTTAGACATC
* * * ** * * * * *
163212 C-GGGGATAAAATGATAA-TTTTCGAAAGTTTTAGGGTCGAAAATGGAATTTTTGGA-AGTT
1 CAGGGG-TAAAATGGTAATTTTTGGAAGGTTCGA-GATCAAAAATGGAGTTTTTAGACA-TC
* *
163271 C-GAGGGTAAAATGGTAA-TTTTGGAATGTTC-AGGAT-AAAAATGGAGTTTTTAGACATT
1 CAG-GGGTAAAATGGTAATTTTTGGAAGGTTCGA-GATCAAAAATGGAGTTTTTAGACATC
* * * * *
163328 CTGGGGTAAAATGG-AAATTTTGGAAGGTTCGATATCAAAAATTGAGTTTTTAGACATA
1 CAGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGATCAAAAATGGAGTTTTTAGACATC
*
163386 CGGGGGTAAAATGGTAATTTT
1 CAGGGGTAAAATGGTAATTTT
163407 CAAAAGTTTC
Statistics
Matches: 369, Mismatches: 46, Indels: 28
0.83 0.10 0.06
Matches are distributed among these distances:
56 2 0.01
57 78 0.21
58 88 0.24
59 198 0.54
60 3 0.01
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.32
Consensus pattern (59 bp):
CAGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGATCAAAAATGGAGTTTTTAGACATC
Found at i:163016 original size:29 final size:29
Alignment explanation
Indices: 162927--163017 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
162917 CTCAGGGGTG
* *
162927 AAATGGTAATTTTTGGAAGGCTCGAGGTCAA
1 AAATGGTAATTTTTGGAAGGTTCAAGGT--A
*
162958 AAATGG-AATTTTTGGACA--TCCAAGGGTA
1 AAATGGTAATTTTTGGA-AGGTTCAA-GGTA
* *
162986 AAATGGTAATTTTTGGAAGGTTCTAGATA
1 AAATGGTAATTTTTGGAAGGTTCAAGGTA
163015 AAA
1 AAA
163018 ATGGAGTTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
28 8 0.16
29 18 0.37
30 16 0.33
31 7 0.14
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (29 bp):
AAATGGTAATTTTTGGAAGGTTCAAGGTA
Found at i:163021 original size:30 final size:30
Alignment explanation
Indices: 162927--163021 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
162917 CTCAGGGGTG
* *
162927 AAATGGTAATTTTTGGAAGGCTCGAGGTCAA
1 AAATGGTAATTTTTGGAAGGTTCAAGGT-AA
*
162958 AAATGG-AATTTTTGGACA--TCCAAGGGT-A
1 AAATGGTAATTTTTGGA-AGGTTCAA-GGTAA
* *
162986 AAATGGTAATTTTTGGAAGGTTCTAGATAA
1 AAATGGTAATTTTTGGAAGGTTCAAGGTAA
163016 AAATGG
1 AAATGG
163022 AGTTATTGAC
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
28 8 0.15
29 14 0.27
30 23 0.44
31 7 0.13
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (30 bp):
AAATGGTAATTTTTGGAAGGTTCAAGGTAA
Found at i:163053 original size:116 final size:117
Alignment explanation
Indices: 162920--163406 Score: 535
Period size: 116 Copynumber: 4.2 Consensus size: 117
162910 TTTGACGCTC
* * * * * *
162920 AGGGGTGAAATGGTAATTTTTGGAAGGCTCGAGGTCAAAAATGGAATTTTTGGACATCCAAGGGT
1 AGGGGTAAAATGGTAATTTTTGGAAGGTTC-AGATCAAAAATGGAGTTTTTAGACATCCAGGGGT
* * *
162985 AAAATGGTAATTTTTGGAAGGTTCTAGAT-AAAAATGGAGTTATT-GACATCT
65 AAAATGGTAAATTTTGGAAGGTTCGAGATCAAAAATGGAGTTTTTAGACATCT
* * *
163036 AGGGGTAAAATTGTAATTTTTGGAAGGTTTCAGATCAAAAATAGAGTTTTTAGACATTCAGGGGT
1 AGGGGTAAAATGGTAATTTTTGGAAGG-TTCAGATCAAAAATGGAGTTTTTAGACATCCAGGGGT
* * *
163101 AAAATGGTAAATTTTGGAAGGTTCGAGATTAAAAACGGAGTTTTTAGACATCC
65 AAAATGGTAAATTTTGGAAGGTTCGAGATCAAAAATGGAGTTTTTAGACATCT
*
163154 AGGGGTAAAATGGTAAATTTTGGAAGGTTCGAGATCAAAAATGGAGTTTTTAGACATCC-GGGGA
1 AGGGGTAAAATGGTAATTTTTGGAAGGTTC-AGATCAAAAATGGAGTTTTTAGACATCCAGGGG-
* * * ** * * * *
163218 TAAAATGAT-AATTTTCGAAAGTTTTAGGGTCGAAAATGGAATTTTTGGA-AGT-T
64 TAAAATGGTAAATTTTGGAAGGTTCGA-GATCAAAAATGGAGTTTTTAGACA-TCT
* * * *
163271 CGAGGGTAAAATGGTAA-TTTTGGAATGTTCAGGAT-AAAAATGGAGTTTTTAGACATTCTGGGG
1 AG-GGGTAAAATGGTAATTTTTGGAAGGTTCA-GATCAAAAATGGAGTTTTTAGACATCCAGGGG
* *
163334 TAAAATGG-AAATTTTGGAAGGTTCGATATCAAAAATTGAGTTTTTAGACATAC-
64 TAAAATGGTAAATTTTGGAAGGTTCGAGATCAAAAATGGAGTTTTTAGACAT-CT
*
163387 GGGGGTAAAATGGTAATTTT
1 AGGGGTAAAATGGTAATTTT
163407 CAAAAGTTTC
Statistics
Matches: 311, Mismatches: 45, Indels: 30
0.81 0.12 0.08
Matches are distributed among these distances:
115 31 0.10
116 128 0.41
117 56 0.18
118 96 0.31
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.32
Consensus pattern (117 bp):
AGGGGTAAAATGGTAATTTTTGGAAGGTTCAGATCAAAAATGGAGTTTTTAGACATCCAGGGGTA
AAATGGTAAATTTTGGAAGGTTCGAGATCAAAAATGGAGTTTTTAGACATCT
Found at i:163270 original size:30 final size:29
Alignment explanation
Indices: 163218--163359 Score: 91
Period size: 28 Copynumber: 4.9 Consensus size: 29
163208 CATCCGGGGA
* * * **
163218 TAAAATGATAATTTTCGAAAGTTTTAGGG
1 TAAAATGGTAATTTTTGGAAGTTCGAGGG
163247 TCGAAAATGG-AATTTTTGGAAGTTCGAGGG
1 T--AAAATGGTAATTTTTGGAAGTTCGAGGG
*
163277 TAAAATGGTAA-TTTTGGAATGTTC-AGGA
1 TAAAATGGTAATTTTTGGAA-GTTCGAGGG
* *
163305 TAAAAATGG-AGTTTTTAGACA-TTCTG-GGG
1 T-AAAATGGTAATTTTTGGA-AGTTC-GAGGG
*
163334 TAAAATGG-AAATTTTGGAAGGTTCGA
1 TAAAATGGTAATTTTTGGAA-GTTCGA
163360 TATCAAAAAT
Statistics
Matches: 89, Mismatches: 12, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
27 1 0.01
28 38 0.43
29 26 0.29
30 18 0.20
31 6 0.07
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.34
Consensus pattern (29 bp):
TAAAATGGTAATTTTTGGAAGTTCGAGGG
Found at i:163318 original size:175 final size:171
Alignment explanation
Indices: 162922--163453 Score: 592
Period size: 175 Copynumber: 3.0 Consensus size: 171
162912 TGACGCTCAG
* * * * *
162922 GGGTGAAATGGTAATTTTTGGAAGGCTCGAGG-TCAAAAATGGAATTTTTGGACATCCAAGGGTA
1 GGGTAAAATGGTAA-TTTTGGAAGGTTC-AGGAT-AAAAATGGAGTTTTTAGACATCCAGGGGTA
* * * *
162986 AAATGGTAATTTTTGGAAGGTTCTAGAT-AAAAATGGAGTTATT-GACATCTAGGGGTAAAATTG
63 AAATGGTAAATTTTGGAAGGTTCGAGATCAAAAATGGAGTTTTTAGACATC-CGGGGTAAAA-TG
* * * * *
163049 TAATTTTTGGAAGGTTTCA-GATCAAAAATAGAGTTTTTAGACATTC-A
126 TAA-TTTTCGAAAGTTTCAGGGTCAAAAATGGAATTTTT-GA-ATTCGA
*
163096 GGGGTAAAATGGTAAATTTTGGAAGGTTC-GAGATTAAAAACGGAGTTTTTAGACATCCAGGGGT
1 -GGGTAAAATGGT-AATTTTGGAAGGTTCAG-GA-TAAAAATGGAGTTTTTAGACATCCAGGGGT
163160 AAAATGGTAAATTTTGGAAGGTTCGAGATCAAAAATGGAGTTTTTAGACATCCGGGGATAAAATG
62 AAAATGGTAAATTTTGGAAGGTTCGAGATCAAAAATGGAGTTTTTAGACATCCGGGG-TAAAATG
* *
163225 ATAATTTTCGAAAGTTTTAGGGTCGAAAATGGAATTTTTGGAAGTTCGA
126 -TAATTTTCGAAAGTTTCAGGGTCAAAAATGGAATTTTT-GAA-TTCGA
* * *
163274 GGGTAAAATGGTAATTTTGGAATGTTCAGGATAAAAATGGAGTTTTTAGACATTCTGGGGTAAAA
1 GGGTAAAATGGTAATTTTGGAAGGTTCAGGATAAAAATGGAGTTTTTAGACATCCAGGGGTAAAA
* * *
163339 TGG-AAATTTTGGAAGGTTCGATATCAAAAATTGAGTTTTTAGACATACGGGGGTAAAATGGTAA
66 TGGTAAATTTTGGAAGGTTCGAGATCAAAAATGGAGTTTTTAGACAT-CCGGGGTAAAAT-GTAA
* * * *
163403 TTTTCAAAAGTTTCGGGGTCAAAAATGAAATTTTATAAAATTCGA
129 TTTTCGAAAGTTTCAGGGTCAAAAATGGAATTTT-T-GAATTCGA
163448 GGGTAA
1 GGGTAA
163454 TTTATGAAAA
Statistics
Matches: 310, Mismatches: 32, Indels: 31
0.83 0.09 0.08
Matches are distributed among these distances:
173 1 0.00
174 91 0.29
175 118 0.38
176 52 0.17
177 47 0.15
178 1 0.00
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.32
Consensus pattern (171 bp):
GGGTAAAATGGTAATTTTGGAAGGTTCAGGATAAAAATGGAGTTTTTAGACATCCAGGGGTAAAA
TGGTAAATTTTGGAAGGTTCGAGATCAAAAATGGAGTTTTTAGACATCCGGGGTAAAATGTAATT
TTCGAAAGTTTCAGGGTCAAAAATGGAATTTTTGAATTCGA
Found at i:163491 original size:29 final size:29
Alignment explanation
Indices: 163454--163514 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
163444 TCGAGGGTAA
*
163454 TTTATGAAAAGATTT-GGGTTAAAATGGAAT
1 TTTATG-AAAG-TTTAGGGGTAAAATGGAAT
*
163484 TTTA-GAAAGTTTAGGGGTAAAATGTAAT
1 TTTATGAAAGTTTAGGGGTAAAATGGAAT
163512 TTT
1 TTT
163515 TGGAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 3 0.11
28 20 0.71
29 1 0.04
30 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.39
Consensus pattern (29 bp):
TTTATGAAAGTTTAGGGGTAAAATGGAAT
Found at i:163533 original size:29 final size:29
Alignment explanation
Indices: 163469--163534 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
163459 GAAAAGATTT
**
163469 GGGTTAAAATGGAATTTTAGAAAGTTTAG
1 GGGTTAAAATGGAATTTTAGAAAGAATAG
* *
163498 GGG-TAAAATGTAATTTTTGGAAA-AATAG
1 GGGTTAAAATGGAA-TTTTAGAAAGAATAG
163526 GGGTTAAAA
1 GGGTTAAAA
163535 ATAGCATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 15 0.48
29 16 0.52
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.32
Consensus pattern (29 bp):
GGGTTAAAATGGAATTTTAGAAAGAATAG
Found at i:164721 original size:3 final size:3
Alignment explanation
Indices: 164713--164742 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
164703 TTAATACTAT
164713 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
164743 ATGCTATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:165390 original size:11 final size:11
Alignment explanation
Indices: 165369--165398 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
165359 TTTTGGGCCA
165369 TTGTAATTGGAT
1 TTGT-ATTGGAT
165381 TTGTATTGGAT
1 TTGTATTGGAT
165392 TTGTATT
1 TTGTATT
165399 CTGGGTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (11 bp):
TTGTATTGGAT
Found at i:165526 original size:6 final size:6
Alignment explanation
Indices: 165517--165566 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
165507 AAATTAAAAC
** * *
165517 AAATTT AAATTT AAAAAT GAATTT AAATTT AAA-GT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
165564 AAA
1 AAA
165567 AATAAATCTA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
5 4 0.11
6 31 0.89
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (6 bp):
AAATTT
Found at i:165578 original size:18 final size:18
Alignment explanation
Indices: 165484--165578 Score: 97
Period size: 17 Copynumber: 5.4 Consensus size: 18
165474 TTTTAAAATT
*
165484 ATTTCAAATTT-AAACTAA
1 ATTT-AAATTTAAAAATAA
* * *
165502 ATTGAAAATT-AAAACAA
1 ATTTAAATTTAAAAATAA
*
165519 ATTTAAATTTAAAAATGA
1 ATTTAAATTTAAAAATAA
*
165537 ATTTAAATTT-AAAGTAA
1 ATTTAAATTTAAAAATAA
165554 ATTTAAATTTAAAAATAA
1 ATTTAAATTTAAAAATAA
*
165572 ATCTAAA
1 ATTTAAA
165579 ATAATTTAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
17 33 0.52
18 30 0.48
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (18 bp):
ATTTAAATTTAAAAATAA
Found at i:174032 original size:17 final size:16
Alignment explanation
Indices: 173991--174047 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 16
173981 TTTATATGAA
173991 ATTTAAAATAATATA-
1 ATTTAAAATAATATAT
174006 A--TAAATATAATTATAT
1 ATTTAAA-ATAA-TATAT
174022 ATTTAAAATAATATTAT
1 ATTTAAAATAATA-TAT
174039 ATTTGAAAA
1 ATTT-AAAA
174048 ATTAAAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
13 4 0.11
14 4 0.11
15 5 0.14
16 3 0.09
17 11 0.31
18 8 0.23
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
ATTTAAAATAATATAT
Found at i:174157 original size:2 final size:2
Alignment explanation
Indices: 174152--174176 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
174142 AAAAAAAAAA
174152 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 A
174177 GATAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.