Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014476.1 Kokia drynarioides strain JFW-HI SEQ_129515, 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: 323745
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 306 characters in sequence are not A, C, G, or T
Found at i:976 original size:24 final size:26
Alignment explanation
Indices: 940--987 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
930 AGAGAAATGT
940 AAATGTGATATATGA-A-ATTATGAG
1 AAATGTGATATATGAGAGATTATGAG
964 AAATGATGA-ATATGAGAGATTATG
1 AAATG-TGATATATGAGAGATTATG
988 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGTGATATATGAGAGATTATGAG
Found at i:1106 original size:23 final size:23
Alignment explanation
Indices: 1050--1176 Score: 93
Period size: 23 Copynumber: 5.5 Consensus size: 23
1040 ACGCTAGCGC
* *
1050 GCTTACTG-TTCAGCACTATATGT
1 GCTTACTGTTTC-GCACTGTGTGT
1073 GCTTACTGTTTCGCACT-TCGTGT
1 GCTTACTGTTTCGCACTGT-GTGT
* *
1096 GCTTACTGTTTCACACCT-CGTGT
1 GCTTACTGTTTCGCA-CTGTGTGT
* *
1119 GCCTACTGATTT-GCGCTGTGTGT
1 GCTTACTG-TTTCGCACTGTGTGT
* *
1142 GCCTACTGGATT-GCACTGTGTGT
1 GCTTACT-GTTTCGCACTGTGTGT
*
1165 GCTGACTGTTTC
1 GCTTACTGTTTC
1177 CCCAACACTT
Statistics
Matches: 85, Mismatches: 12, Indels: 14
0.77 0.11 0.13
Matches are distributed among these distances:
22 6 0.07
23 70 0.82
24 9 0.11
ACGTcount: A:0.13, C:0.24, G:0.24, T:0.39
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTGTGTGT
Found at i:2057 original size:21 final size:22
Alignment explanation
Indices: 2033--2073 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2023 TATAATTTTT
2033 TAAATTT-AAAAAATAAAAAAC
1 TAAATTTCAAAAAATAAAAAAC
*
2054 TAAATTTCTAAAAATAAAAA
1 TAAATTTCAAAAAATAAAAA
2074 TATATAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAATTTCAAAAAATAAAAAAC
Found at i:7684 original size:5 final size:5
Alignment explanation
Indices: 7674--7703 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
7664 GCAAAAATTA
7674 TGCTT TGCTT TGCTT TGCTT TGCTT TGCTT
1 TGCTT TGCTT TGCTT TGCTT TGCTT TGCTT
7704 CAAGGATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.20, G:0.20, T:0.60
Consensus pattern (5 bp):
TGCTT
Found at i:14721 original size:2 final size:2
Alignment explanation
Indices: 14711--14741 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
14701 ACGAAAAAAA
*
14711 AC AC GC 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 A
14742 AAATTCTGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.48, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:21416 original size:32 final size:31
Alignment explanation
Indices: 21360--21441 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 31
21350 TAAAATAATA
* ** *
21360 TTTTAAGTTTTTAAAAAATT-GTAAAAACTTTT
1 TTTTAA-TTTTT-AAAAGTTGGTAAAAAAATGT
*
21392 TTTTCATCTTTTAAAAGTTGGTAAAAAAATGT
1 TTTTAAT-TTTTAAAAGTTGGTAAAAAAATGT
21424 TTTTAATTTTTAAAAGTT
1 TTTTAATTTTTAAAAGTT
21442 TAATTTTTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
31 18 0.43
32 24 0.57
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.50
Consensus pattern (31 bp):
TTTTAATTTTTAAAAGTTGGTAAAAAAATGT
Found at i:22208 original size:29 final size:29
Alignment explanation
Indices: 22149--22218 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
22139 AAAATTTGAA
*
22149 ATTAAAATTAAATTGTATATTTTTACGAT
1 ATTAAAAATAAATTGTATATTTTTACGAT
* *
22178 ATTAAAAATATAATTTTATATTTTTA-TAT
1 ATTAAAAATA-AATTGTATATTTTTACGAT
*
22207 ATTATAAATAAA
1 ATTAAAAATAAA
22219 ATATATAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 2 0.06
29 20 0.56
30 14 0.39
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (29 bp):
ATTAAAAATAAATTGTATATTTTTACGAT
Found at i:27050 original size:26 final size:27
Alignment explanation
Indices: 27013--27071 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
27003 TTATATTATA
*
27013 TTATATTATTTTA-ATATTTAAAAATT
1 TTATATTATTTTATATATTGAAAAATT
* *
27039 TTATACTT-TTTTATTTATTGAAAATTT
1 TTATA-TTATTTTATATATTGAAAAATT
27066 TTATAT
1 TTATAT
27072 AGTAATCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (27 bp):
TTATATTATTTTATATATTGAAAAATT
Found at i:31238 original size:2 final size:2
Alignment explanation
Indices: 31231--31260 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31221 ATTGCAGGTG
31231 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
31261 TATTGCATTA
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:35185 original size:24 final size:21
Alignment explanation
Indices: 35148--35203 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 21
35138 TTGTTTATTT
35148 TTTTTAAAAAAATATTTATATA
1 TTTTTAAAAAAATATTTATA-A
*
35170 TTTTTAAAAATTAATATTTTTAA
1 TTTTTAAAAA--AATATTTATAA
35193 TTTTTAAAAAA
1 TTTTTAAAAAA
35204 TGAATGATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 1 0.03
22 10 0.32
23 11 0.35
24 9 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTTAAAAAAATATTTATAA
Found at i:35204 original size:24 final size:24
Alignment explanation
Indices: 35148--35215 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 24
35138 TTGTTTATTT
*
35148 TTTTTAAAAA--AATATTTATATA
1 TTTTTAAAAATGAATATTTTTATA
*
35170 TTTTTAAAAATTAATATTTTTA-A
1 TTTTTAAAAATGAATATTTTTATA
35193 TTTTTAAAAAATGAATGATTTTT
1 TTTTT-AAAAATGAAT-ATTTTT
35216 TTTTCTTGCT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
22 10 0.25
23 6 0.15
24 18 0.45
25 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (24 bp):
TTTTTAAAAATGAATATTTTTATA
Found at i:37591 original size:2 final size:2
Alignment explanation
Indices: 37584--37618 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
37574 GTTAAACTTT
37584 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
37619 GATAAATGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40381 original size:116 final size:112
Alignment explanation
Indices: 40153--40370 Score: 262
Period size: 112 Copynumber: 1.9 Consensus size: 112
40143 ATAAAATTTG
* * * * * *
40153 TTTCATTAGTCACAGGGCGAAAAAGGTTTTAATTGAATAATTGATTAATGAGACTAAACTTGAAA
1 TTTCAATAGTCAAAGGGCGAAAAAGGGTTCAATTGAATAATTAATTAAAGAGACTAAACTTGAAA
*
40218 TTATCCCAATCAACCAAAAAAGGCAAGGCTAGCCTGCCTATATTTTT
66 TTATCCCAATCAACCAAAAAAGGCAAGGCTAGCCTGCCTATACTTTT
* *
40265 TTTCAATAGTCAAAGGGCTAAAAAGGGTTCAATTGAATAGTTAATTAGAAGAAGAGGCTCAAA-T
1 TTTCAATAGTCAAAGGGCGAAAAAGGGTTCAATTGAATAATTAATTA-AAG-AGA--CT-AAACT
* *
40329 TGAAATTATCCCAATTAACC-AAAGAGG-AAGGCTATGCCTGCC
61 TGAAATTATCCCAATCAACCAAAAAAGGCAAGGCTA-GCCTGCC
40371 CTTGGCTTTT
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
112 40 0.44
113 2 0.02
114 10 0.11
115 13 0.14
116 22 0.24
117 3 0.03
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (112 bp):
TTTCAATAGTCAAAGGGCGAAAAAGGGTTCAATTGAATAATTAATTAAAGAGACTAAACTTGAAA
TTATCCCAATCAACCAAAAAAGGCAAGGCTAGCCTGCCTATACTTTT
Found at i:42220 original size:2 final size:2
Alignment explanation
Indices: 42213--42240 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42203 ATGGTTACTC
42213 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
42241 TTTGAGTAGA
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):
AT
Found at i:56839 original size:25 final size:25
Alignment explanation
Indices: 56802--56873 Score: 126
Period size: 25 Copynumber: 2.8 Consensus size: 25
56792 CTCTCTGTTT
*
56802 AGCACTTTGTGTGCTCTCTGTTGCCC
1 AGCAC-TTATGTGCTCTCTGTTGCCC
56828 AGCACTTATGTGCTCTCTGTTGCCC
1 AGCACTTATGTGCTCTCTGTTGCCC
56853 AGCACTTATGTGCTCTCTGTT
1 AGCACTTATGTGCTCTCTGTT
56874 TAGTACTTCG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 40 0.89
26 5 0.11
ACGTcount: A:0.11, C:0.29, G:0.21, T:0.39
Consensus pattern (25 bp):
AGCACTTATGTGCTCTCTGTTGCCC
Found at i:59715 original size:12 final size:12
Alignment explanation
Indices: 59698--59722 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59688 CCAACCAACC
59698 TCTTTTTTTTTT
1 TCTTTTTTTTTT
59710 TCTTTTTTTTTT
1 TCTTTTTTTTTT
59722 T
1 T
59723 AATTCGGTAC
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:60971 original size:16 final size:15
Alignment explanation
Indices: 60945--60975 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
60935 AACTTCTCTG
60945 TAAAAAAAATAATAA
1 TAAAAAAAATAATAA
60960 TAAAATAAAATAATAA
1 TAAAA-AAAATAATAA
60976 GCATTTGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAAAAAAATAATAA
Found at i:68189 original size:27 final size:27
Alignment explanation
Indices: 68137--68190 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
68127 AAAACACCCC
*
68137 TTAGTGCCGCCACTTTATATTCCTCCA
1 TTAGTGCCGCCACTTCATATTCCTCCA
* *
68164 TTAGTGCCGCCACTTCATGTTTCTCCA
1 TTAGTGCCGCCACTTCATATTCCTCCA
68191 CTAGGTGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.13, T:0.37
Consensus pattern (27 bp):
TTAGTGCCGCCACTTCATATTCCTCCA
Found at i:71546 original size:21 final size:21
Alignment explanation
Indices: 71518--71558 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
71508 TTAACAATAC
71518 TTTAATTAT-TATTTAAAAAT
1 TTTAATTATATATTTAAAAAT
71538 TTTATATTATAATATTTAAAA
1 TTTA-ATTAT-ATATTTAAAA
71559 TGATAAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 5 0.28
23 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAATTATATATTTAAAAAT
Found at i:77877 original size:47 final size:47
Alignment explanation
Indices: 77826--78000 Score: 242
Period size: 47 Copynumber: 3.7 Consensus size: 47
77816 GTTGTAGATG
** * * *
77826 TAGGACTCTTAATTTAAGTTGCTTTATTGTATTTAGGATAAGTTAGA
1 TAGGACTCTTAATAAAAGTTGTTTTATTATTTTTAGGATAAGTTAGA
* *
77873 TAGGACTCTTAATAAAAGTTGTTTTAGTATTTTTAGGATAAGTTAAA
1 TAGGACTCTTAATAAAAGTTGTTTTATTATTTTTAGGATAAGTTAGA
* *
77920 TAGGACTCTTAATAAAAGTTGTTTTATTATTTTTAGGAGAAGTTAGG
1 TAGGACTCTTAATAAAAGTTGTTTTATTATTTTTAGGATAAGTTAGA
77967 TAGGACTCTTAATAAAATAAGTTGTTTTATTATT
1 TAGGACTCTTAAT--AA-AAGTTGTTTTATTATT
78001 CTTGGAAGTT
Statistics
Matches: 114, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
47 96 0.84
49 2 0.02
50 16 0.14
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (47 bp):
TAGGACTCTTAATAAAAGTTGTTTTATTATTTTTAGGATAAGTTAGA
Found at i:78009 original size:47 final size:45
Alignment explanation
Indices: 77826--78022 Score: 207
Period size: 47 Copynumber: 4.2 Consensus size: 45
77816 GTTGTAGATG
** * * *
77826 TAGGACTCTTAATTTAAGTTGCTTTATTGTATTTAGGATAAGTTAGA
1 TAGGACTCTTAATAAAAGTTGTTTTATTATTTTTAGG--AAGTTAGA
* *
77873 TAGGACTCTTAATAAAAGTTGTTTTAGTATTTTTAGGATAAGTTAAA
1 TAGGACTCTTAATAAAAGTTGTTTTATTATTTTTAGG--AAGTTAGA
*
77920 TAGGACTCTTAATAAAAGTTGTTTTATTATTTTTAGGAGAAGTTAGG
1 TAGGACTCTTAATAAAAGTTGTTTTATTATTTTTA-G-GAAGTTAGA
* *
77967 TAGGACTCTTAATAAAATAAGTTGTTTTATTATTCTT-GGAAGTTAGG
1 TAGGACTCTTAAT--AA-AAGTTGTTTTATTATTTTTAGGAAGTTAGA
*
78014 TAGAACTCT
1 TAGGACTCT
78023 CATGATAAAA
Statistics
Matches: 133, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
47 110 0.83
48 2 0.02
49 3 0.02
50 18 0.14
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (45 bp):
TAGGACTCTTAATAAAAGTTGTTTTATTATTTTTAGGAAGTTAGA
Found at i:82081 original size:18 final size:18
Alignment explanation
Indices: 82058--82095 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
82048 ACAAAGGCAT
82058 ATCAAAACTA-AAAAAAAA
1 ATCAAAA-TATAAAAAAAA
*
82076 ATCAAAATATAAAAGAAA
1 ATCAAAATATAAAAAAAA
82094 AT
1 AT
82096 AAGAATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.16
Consensus pattern (18 bp):
ATCAAAATATAAAAAAAA
Found at i:82857 original size:36 final size:36
Alignment explanation
Indices: 82810--82888 Score: 158
Period size: 36 Copynumber: 2.2 Consensus size: 36
82800 GTGTTTTGAG
82810 AAGGTTGCACAATCGATTCGCTAACTTATTACGTCA
1 AAGGTTGCACAATCGATTCGCTAACTTATTACGTCA
82846 AAGGTTGCACAATCGATTCGCTAACTTATTACGTCA
1 AAGGTTGCACAATCGATTCGCTAACTTATTACGTCA
82882 AAGGTTG
1 AAGGTTG
82889 ACTAGAGTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (36 bp):
AAGGTTGCACAATCGATTCGCTAACTTATTACGTCA
Found at i:85649 original size:15 final size:15
Alignment explanation
Indices: 85611--85649 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
85601 AAATAATCCT
*
85611 ATAAAAAATTAAAAA
1 ATAAAAAACTAAAAA
* *
85626 AAAAAAAACTAAAGA
1 ATAAAAAACTAAAAA
85641 ATAAAAAAC
1 ATAAAAAAC
85650 ACCAGCACTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.79, C:0.05, G:0.03, T:0.13
Consensus pattern (15 bp):
ATAAAAAACTAAAAA
Found at i:88132 original size:15 final size:16
Alignment explanation
Indices: 88100--88135 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
88090 TAATCCTTTA
*
88100 AAAATAATGAAATTAT
1 AAAATAATGAAATGAT
88116 AAAATAAT-AAATGAT
1 AAAATAATGAAATGAT
88131 AAAAT
1 AAAAT
88136 TATCATTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (16 bp):
AAAATAATGAAATGAT
Found at i:90923 original size:14 final size:15
Alignment explanation
Indices: 90895--90932 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
90885 TTATTATTAT
90895 TAATAAT-AGTAAAAA
1 TAATAATGA-TAAAAA
90910 TAA-AATGATAAAAA
1 TAATAATGATAAAAA
90924 TAATAATGA
1 TAATAATGA
90933 AATATGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (15 bp):
TAATAATGATAAAAA
Found at i:96629 original size:30 final size:31
Alignment explanation
Indices: 96560--96618 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
96550 AAAAAAATAT
*
96560 TTTTATATATAAAATTTATGTTATTTTTACTA
1 TTTTAAATATAAAA-TTATGTTATTTTTACTA
96592 TTTTAAATATAAAA-TAT-TTATTTTTAC
1 TTTTAAATATAAAATTATGTTATTTTTAC
96619 ATGATTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 10 0.38
30 3 0.12
32 13 0.50
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (31 bp):
TTTTAAATATAAAATTATGTTATTTTTACTA
Found at i:107464 original size:108 final size:108
Alignment explanation
Indices: 107270--107488 Score: 384
Period size: 108 Copynumber: 2.0 Consensus size: 108
107260 GCACTGACAA
*
107270 CAAATATTTCTCAGGCTTCCTGCTAAAGATTTTTGAATCAGAGTGGCAATCACTTTCTGACAAAT
1 CAAATATTTCTCAGGCTTCCTGCTAAAGATTTTTGAATCAGAGTCGCAATCACTTTCTGACAAAT
107335 CTTTCTTCTCAATGGCATCACATGCTACCTGCACCATCGAATC
66 CTTTCTTCTCAATGGCATCACATGCTACCTGCACCATCGAATC
* * * *
107378 CAAATATTTCTCAGGCTTGCTGCTCAAGATTTTTGAATCGGGGTCGCAATCACTTTCTGACAAAT
1 CAAATATTTCTCAGGCTTCCTGCTAAAGATTTTTGAATCAGAGTCGCAATCACTTTCTGACAAAT
*
107443 CTTTCTTCTCAATGGCGTCACATGCTACCTGCACCATCGAATC
66 CTTTCTTCTCAATGGCATCACATGCTACCTGCACCATCGAATC
107486 CAA
1 CAA
107489 GTTATCCAAC
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 105 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (108 bp):
CAAATATTTCTCAGGCTTCCTGCTAAAGATTTTTGAATCAGAGTCGCAATCACTTTCTGACAAAT
CTTTCTTCTCAATGGCATCACATGCTACCTGCACCATCGAATC
Found at i:112070 original size:29 final size:29
Alignment explanation
Indices: 112037--112092 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
112027 GATATAAACA
*
112037 TTATTATCAATATAAATTAAATTCTAACT
1 TTATTATCAATACAAATTAAATTCTAACT
* *
112066 TTATTATCAATGCAGATTAAATTCTAA
1 TTATTATCAATACAAATTAAATTCTAA
112093 TTCGAGTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (29 bp):
TTATTATCAATACAAATTAAATTCTAACT
Found at i:120218 original size:29 final size:30
Alignment explanation
Indices: 120158--120228 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
120148 AACTCAAAAA
* **
120158 TAGTCACTTTTATTTGACTTAGGTTACATTT
1 TAGTCACTTATATTTGAAATA-GTTACATTT
*
120189 TAGTCACTTATATTTGAAATA-TTACGTTT
1 TAGTCACTTATATTTGAAATAGTTACATTT
120218 TAGTCACTTAT
1 TAGTCACTTAT
120229 GTTAGTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 18 0.50
31 18 0.50
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (30 bp):
TAGTCACTTATATTTGAAATAGTTACATTT
Found at i:121080 original size:18 final size:16
Alignment explanation
Indices: 121049--121092 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
121039 AGTTTAGGGT
*
121049 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
121066 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
121080 TTAAAAATTTATT
1 TTAAAAATTTATT
121093 CTCATTCCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:133809 original size:27 final size:27
Alignment explanation
Indices: 133775--133848 Score: 96
Period size: 26 Copynumber: 2.8 Consensus size: 27
133765 AAACTTTTTA
133775 TTAATTTTAAAATATATTTTACATATT
1 TTAATTTTAAAATATATTTTACATATT
** *
133802 TTAATTTTAAAAT-TATTAAATATATT
1 TTAATTTTAAAATATATTTTACATATT
* *
133828 TTAATTGTCAAATATATTTTA
1 TTAATTTTAAAATATATTTTA
133849 ATTTTTTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 21 0.54
27 18 0.46
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (27 bp):
TTAATTTTAAAATATATTTTACATATT
Found at i:133830 original size:20 final size:20
Alignment explanation
Indices: 133805--133849 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
133795 ACATATTTTA
*
133805 ATTTTAAAATTATTAAATAT
1 ATTTTAAAATTATCAAATAT
*
133825 ATTTT--AATTGTCAAATAT
1 ATTTTAAAATTATCAAATAT
133843 ATTTTAA
1 ATTTTAA
133850 TTTTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
18 16 0.76
20 5 0.24
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
ATTTTAAAATTATCAAATAT
Found at i:133855 original size:26 final size:26
Alignment explanation
Indices: 133770--133855 Score: 86
Period size: 26 Copynumber: 3.2 Consensus size: 26
133760 ATTATAAACT
133770 TTTTATTAATTTTAAAATATATTTTACA
1 TTTT-TTAATTTTAAAATATATTTTA-A
* *
133798 TATTTTAATTTTAAAAT-TA-TTAAA
1 TTTTTTAATTTTAAAATATATTTTAA
* *
133822 TATATTTTAATTGTCAAATATATTTTAA
1 T-T-TTTTAATTTTAAAATATATTTTAA
133850 TTTTTT
1 TTTTTT
133856 TAAAACATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
24 2 0.04
25 3 0.06
26 19 0.40
27 16 0.33
28 8 0.17
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (26 bp):
TTTTTTAATTTTAAAATATATTTTAA
Found at i:133856 original size:27 final size:27
Alignment explanation
Indices: 133775--133858 Score: 93
Period size: 27 Copynumber: 3.1 Consensus size: 27
133765 AAACTTTTTA
133775 TTAATTTTAAAATATATTTTACA-TATT
1 TTAATTTTAAAATATATTTTA-ATTATT
*
133802 TTAATTTTAAAAT-TA-TTAAATATATT
1 TTAATTTTAAAATATATTTTAAT-TATT
* * *
133828 TTAATTGTCAAATATATTTTAATTTTT
1 TTAATTTTAAAATATATTTTAATTATT
133855 TTAA
1 TTAA
133859 AACATATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
24 1 0.02
25 3 0.06
26 17 0.35
27 22 0.46
28 5 0.10
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.56
Consensus pattern (27 bp):
TTAATTTTAAAATATATTTTAATTATT
Found at i:134341 original size:27 final size:27
Alignment explanation
Indices: 134311--134373 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
134301 ACTTTTACTG
*
134311 TAAATTTTAAATTACTTACGTATTTAA
1 TAAATTTTAAATTACTTACGTAATTAA
*** *
134338 TAAAAAATAAATTATTTACGTAATTAA
1 TAAATTTTAAATTACTTACGTAATTAA
*
134365 TTAATTTTA
1 TAAATTTTA
134374 TAAAAAAACC
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (27 bp):
TAAATTTTAAATTACTTACGTAATTAA
Found at i:138667 original size:6 final size:6
Alignment explanation
Indices: 138658--138683 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
138648 ATTTTAATTT
138658 TTTTTC TTTTTC TTTTTC TTTTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TT
138684 AGCAACTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:140318 original size:6 final size:6
Alignment explanation
Indices: 140307--140346 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
140297 ATCCAATTAG
140307 TATTTA TATTTA TATTTA TATTTA T-TCTTA TATTATA TAT
1 TATTTA TATTTA TATTTA TATTTA TAT-TTA TATT-TA TAT
140347 AATGTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 1 0.03
6 24 0.77
7 6 0.19
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (6 bp):
TATTTA
Found at i:144877 original size:20 final size:20
Alignment explanation
Indices: 144849--144887 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
144839 TTCGATTTGA
*
144849 GTTTAGAGTTCAAGTTTTAG
1 GTTTAGAGTTCAAGATTTAG
*
144869 GTTTTGAGTTCAAGATTTA
1 GTTTAGAGTTCAAGATTTA
144888 AGATTTATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.05, G:0.23, T:0.46
Consensus pattern (20 bp):
GTTTAGAGTTCAAGATTTAG
Found at i:156162 original size:19 final size:19
Alignment explanation
Indices: 156138--156176 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
156128 ATCGGGGAAA
156138 ATCCCC-TTTCCATCAATCG
1 ATCCCCGTTT-CATCAATCG
*
156157 ATCCCCGTTTGATCAATCG
1 ATCCCCGTTTCATCAATCG
156176 A
1 A
156177 CATCATCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.23, C:0.36, G:0.10, T:0.31
Consensus pattern (19 bp):
ATCCCCGTTTCATCAATCG
Found at i:159074 original size:2 final size:2
Alignment explanation
Indices: 159069--159096 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
159059 TTCTTTTTAA
159069 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
159097 TCACATCAAT
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):
AT
Found at i:197460 original size:339 final size:338
Alignment explanation
Indices: 196840--198199 Score: 2236
Period size: 339 Copynumber: 4.0 Consensus size: 338
196830 TTCAACAGCA
* * *
196840 CATCCAGAAGCTCAATTTTCCTAAAATTATCATTCAATCCGCTTGCATTTGTATCTGAATGGACT
1 CATCCAGAAGCTTAATTTTCCTAAAATTATCATTCAATCTGCTTGCATTTGTATCCGAATGGACT
* * *
196905 GTCCCAGTTTCGTTAACATTCGGTTCCTCATCAGCTTTCTCACCATCCTCCGCTTTGCCCTTAGA
66 GTCCCGGTTTCATTAACATTCGGTTCTTCATCAGCTTTCTCACCATCCTCCGCTTTGCCCTTAGA
* * * *
196970 CAATGAAGGCAACTCTGTTTCAAAATCCAACGGCTGTGAAGGCAATACCAGTTTCTTCTTAGTGC
131 CAATGAAGGCAACTCTGCTTCAAAATCCAACGGCCGTGAAGGCAATACCCGTTCCTTCTTAGTGC
* * * * *
197035 CATCTGGATTCGAAGTGCTTTTAATCTTCTTCGCCGAATCAACTTCCTCCTCAGAAAATCCTGAA
196 CATCTGGATTCGAAGTGCTTTTTATCTTCCTCGCCAAATCAACTTCCTCCTCAGAAAACCCTAAA
* *
197100 TCTGTATCCTTTCCCAAATCAACTGCCCTCCTACTGTCAGCACTAACAGTTCTTCCGCTGTGATT
261 TCTGTATCCTTTCCCAAATCAACTGCCCTCCTAGTGTCAGCACTAACAGTTTTTCCGCT-TGATT
197165 GTCGATCATTTCAT
325 GTCGATCATTTCAT
*
197179 CATCCAGAAGCTTAATTTTCCTAAAATTATCATTCAATCTGCTTGCATTTGTATCCAAATGGACT
1 CATCCAGAAGCTTAATTTTCCTAAAATTATCATTCAATCTGCTTGCATTTGTATCCGAATGGACT
* **
197244 GTTCCGGTTTCATTAACATTCGGTTCTTCATCAGCTTTCTCACCATCCAACGCTTTGCCCTTAGA
66 GTCCCGGTTTCATTAACATTCGGTTCTTCATCAGCTTTCTCACCATCCTCCGCTTTGCCCTTAGA
* * *
197309 CAATAAAGGCAACTCTG-TATCAAAATCCAACGGCTGTGAAGGCAATACCCGTTTCTTCTTAGTG
131 CAATGAAGGCAACTCTGCT-TCAAAATCCAACGGCCGTGAAGGCAATACCCGTTCCTTCTTAGTG
*
197373 CCATCTGGATTCGAAGTGCTTTTTATCTTCCTGGCCAAATCAACTTCCTCCTCAGAAAACCCTAA
195 CCATCTGGATTCGAAGTGCTTTTTATCTTCCTCGCCAAATCAACTTCCTCCTCAGAAAACCCTAA
* *
197438 ATCCGTATCCTTTCCCAAATCAACTGCCCTCCTAGTGTCAGCACTAACTGTTTTTCCGCTGTGAT
260 ATCTGTATCCTTTCCCAAATCAACTGCCCTCCTAGTGTCAGCACTAACAGTTTTTCCGCT-TGAT
197503 TGTCGATCATTTCAT
324 TGTCGATCATTTCAT
*
197518 CATCCAGAAGCTTAGTTTTCCTAAAATTATCATTCAATCTGCTTGCATTTGTATCCGAATGGACT
1 CATCCAGAAGCTTAATTTTCCTAAAATTATCATTCAATCTGCTTGCATTTGTATCCGAATGGACT
* *
197583 GTCCCGGTTTCATTAACATTCGGTTCTTCATGAGCTTTCTCACCATCCTCCGCTTTGCCGTTAGA
66 GTCCCGGTTTCATTAACATTCGGTTCTTCATCAGCTTTCTCACCATCCTCCGCTTTGCCCTTAGA
197648 CAATGAAGGCAACTCTGCTTCAAAATCCAACGGCCGTGAAGGCAATACCCGTTCCTTCTTAGTGC
131 CAATGAAGGCAACTCTGCTTCAAAATCCAACGGCCGTGAAGGCAATACCCGTTCCTTCTTAGTGC
* *
197713 CATCTGGATTCGAAGTGCTTTTTATCTTCCTGGCCAAATCAACTTCCTCCGCAGAAAACCCTAAA
196 CATCTGGATTCGAAGTGCTTTTTATCTTCCTCGCCAAATCAACTTCCTCCTCAGAAAACCCTAAA
* * *
197778 TCTGTATCCTTTCCTAAATCAACTGCCCTCCTAGGGTCAGAACTAACAGTTTTTCCGCCTTGATT
261 TCTGTATCCTTTCCCAAATCAACTGCCCTCCTAGTGTCAGCACTAACAGTTTTTCCG-CTTGATT
197843 GTCGATCATTTCAT
325 GTCGATCATTTCAT
* *
197857 CATCCTGAAGCTTAGTTTTCCTAAAATTATCATTCAATCTGCTTGCATTTGTATCCGAATGGACT
1 CATCCAGAAGCTTAATTTTCCTAAAATTATCATTCAATCTGCTTGCATTTGTATCCGAATGGACT
* *
197922 GTCCCGGTTTCATTAACATTCGGTTCTTCATGAGCTTTCTCACCATCCTCCGCTTTGCCGTTAGA
66 GTCCCGGTTTCATTAACATTCGGTTCTTCATCAGCTTTCTCACCATCCTCCGCTTTGCCCTTAGA
197987 CAATGAAGGCAACTCTGCTTCAAAATCCAACGGCCGTGAAGGCAATACCCGTTCCTTCTTAGTGC
131 CAATGAAGGCAACTCTGCTTCAAAATCCAACGGCCGTGAAGGCAATACCCGTTCCTTCTTAGTGC
* * * * * *
198052 CATCTGGATTCGAAGTGCTGTTCATCTTCCTCGACGAATCAACTTCCCCCTCAGAAAACTCTAAA
196 CATCTGGATTCGAAGTGCTTTTTATCTTCCTCGCCAAATCAACTTCCTCCTCAGAAAACCCTAAA
* * *
198117 TCTGTTTCCTTTTCCAAATCAACTGCCCTCCTAGTGTCAGCACTAACAGTTTTTCCACCTTGATT
261 TCTGTATCCTTTCCCAAATCAACTGCCCTCCTAGTGTCAGCACTAACAGTTTTTCC-GCTTGATT
198182 GTCGATCATTTCAT
325 GTCGATCATTTCAT
198196 CATC
1 CATC
198200 ATTGCAATCA
Statistics
Matches: 964, Mismatches: 53, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
338 1 0.00
339 960 1.00
340 3 0.00
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (338 bp):
CATCCAGAAGCTTAATTTTCCTAAAATTATCATTCAATCTGCTTGCATTTGTATCCGAATGGACT
GTCCCGGTTTCATTAACATTCGGTTCTTCATCAGCTTTCTCACCATCCTCCGCTTTGCCCTTAGA
CAATGAAGGCAACTCTGCTTCAAAATCCAACGGCCGTGAAGGCAATACCCGTTCCTTCTTAGTGC
CATCTGGATTCGAAGTGCTTTTTATCTTCCTCGCCAAATCAACTTCCTCCTCAGAAAACCCTAAA
TCTGTATCCTTTCCCAAATCAACTGCCCTCCTAGTGTCAGCACTAACAGTTTTTCCGCTTGATTG
TCGATCATTTCAT
Found at i:199411 original size:16 final size:16
Alignment explanation
Indices: 199358--199403 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
199348 ATATATATAT
* *
199358 AAGAAATAAAAGAATA
1 AAGAAACAAAAGAAAA
* *
199374 AAGAAAGAAAAAAAAA
1 AAGAAACAAAAGAAAA
199390 AAGAAACAAAAGAA
1 AAGAAACAAAAGAA
199404 GGAAGAAAGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.04
Consensus pattern (16 bp):
AAGAAACAAAAGAAAA
Found at i:202083 original size:20 final size:19
Alignment explanation
Indices: 202058--202096 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
202048 TATAAAGTTT
*
202058 ATCAATGAGTATTTTATATA
1 ATCAATGAATATTTT-TATA
*
202078 ATCAATTAATATTTTTATA
1 ATCAATGAATATTTTTATA
202097 TTTAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (19 bp):
ATCAATGAATATTTTTATA
Found at i:202343 original size:16 final size:17
Alignment explanation
Indices: 202322--202353 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
202312 GAGAATAGTG
202322 AAATA-TTAAAAAAAAT
1 AAATATTTAAAAAAAAT
202338 AAATATTTAAAAAAAA
1 AAATATTTAAAAAAAA
202354 GACATGATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATATTTAAAAAAAAT
Found at i:203652 original size:5 final size:5
Alignment explanation
Indices: 203644--203673 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
203634 CGATTTGAAA
203644 GGTGT GGTGT GGTGT GGTGT GGTGT GGTGT
1 GGTGT GGTGT GGTGT GGTGT GGTGT GGTGT
203674 CCACGGAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.60, T:0.40
Consensus pattern (5 bp):
GGTGT
Found at i:203927 original size:24 final size:22
Alignment explanation
Indices: 203899--203943 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
203889 TTATTTTTCA
*
203899 ATTTTCTTATTAATCATTAATTTT
1 ATTTTATTATTAA--ATTAATTTT
*
203923 ATTTTATTCTTAAATTAATTT
1 ATTTTATTATTAAATTAATTT
203944 AATTCTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
24 11 0.58
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTTATTATTAAATTAATTTT
Found at i:205616 original size:15 final size:16
Alignment explanation
Indices: 205596--205631 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
205586 TTATTTTAAG
*
205596 ATTTTA-TTTTATAAA
1 ATTTTATTTTTAAAAA
205611 ATTTTATTTTTAAAAA
1 ATTTTATTTTTAAAAA
205627 ATTTT
1 ATTTT
205632 CACATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTATTTTTAAAAA
Found at i:205973 original size:30 final size:29
Alignment explanation
Indices: 205937--205995 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
205927 TAAGCACACT
205937 TTTACAAAATTAATATATTTTAGTAAATAA
1 TTTACAAAA-TAATATATTTTAGTAAATAA
* * * *
205967 TTTACAATATGATTTATTTTCGTAAATAA
1 TTTACAAAATAATATATTTTAGTAAATAA
205996 AATTAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (29 bp):
TTTACAAAATAATATATTTTAGTAAATAA
Found at i:208434 original size:16 final size:16
Alignment explanation
Indices: 208381--208426 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
208371 ATATATATAT
* *
208381 AAGAAATAAAAGAATA
1 AAGAAACAAAAGAAAA
* *
208397 AAGAAAGAAAAAAAAA
1 AAGAAACAAAAGAAAA
208413 AAGAAACAAAAGAA
1 AAGAAACAAAAGAA
208427 GGAAGAAAGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.04
Consensus pattern (16 bp):
AAGAAACAAAAGAAAA
Found at i:211106 original size:20 final size:19
Alignment explanation
Indices: 211081--211119 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
211071 TATAAAGTTT
*
211081 ATCAATGAGTATTTTATATA
1 ATCAATGAATATTTT-TATA
*
211101 ATCAATTAATATTTTTATA
1 ATCAATGAATATTTTTATA
211120 TTTAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (19 bp):
ATCAATGAATATTTTTATA
Found at i:211366 original size:16 final size:17
Alignment explanation
Indices: 211345--211376 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
211335 GAGAATAGTG
211345 AAATA-TTAAAAAAAAT
1 AAATATTTAAAAAAAAT
211361 AAATATTTAAAAAAAA
1 AAATATTTAAAAAAAA
211377 GACATGATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATATTTAAAAAAAAT
Found at i:212675 original size:5 final size:5
Alignment explanation
Indices: 212667--212696 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
212657 CGATTTGAAA
212667 GGTGT GGTGT GGTGT GGTGT GGTGT GGTGT
1 GGTGT GGTGT GGTGT GGTGT GGTGT GGTGT
212697 CCACGGAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.60, T:0.40
Consensus pattern (5 bp):
GGTGT
Found at i:212950 original size:24 final size:22
Alignment explanation
Indices: 212922--212966 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
212912 TTATTTTTCA
*
212922 ATTTTCTTATTAATCATTAATTTT
1 ATTTTATTATTAA--ATTAATTTT
*
212946 ATTTTATTCTTAAATTAATTT
1 ATTTTATTATTAAATTAATTT
212967 AATTCTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
24 11 0.58
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTTATTATTAAATTAATTTT
Found at i:214639 original size:15 final size:16
Alignment explanation
Indices: 214619--214654 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
214609 TTATTTTAAG
*
214619 ATTTTA-TTTTATAAA
1 ATTTTATTTTTAAAAA
214634 ATTTTATTTTTAAAAA
1 ATTTTATTTTTAAAAA
214650 ATTTT
1 ATTTT
214655 CACATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTATTTTTAAAAA
Found at i:214996 original size:30 final size:29
Alignment explanation
Indices: 214960--215018 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
214950 TAAGCACACT
214960 TTTACAAAATTAATATATTTTAGTAAATAA
1 TTTACAAAA-TAATATATTTTAGTAAATAA
* * * *
214990 TTTACAATATGATTTATTTTCGTAAATAA
1 TTTACAAAATAATATATTTTAGTAAATAA
215019 AATTAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (29 bp):
TTTACAAAATAATATATTTTAGTAAATAA
Found at i:225370 original size:31 final size:29
Alignment explanation
Indices: 225335--225416 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 29
225325 AAATCAAAAT
*
225335 TAAAGTTTCAAGTATATATTTGAACCATAA
1 TAAAGTTTCAAGTATATAATTGAACCA-AA
* * *
225365 CTAAAGTTTCACGTGTATAATTGTACCAAA
1 -TAAAGTTTCAAGTATATAATTGAACCAAA
* * *
225395 TAAAATTTCATGTATACAATTG
1 TAAAGTTTCAAGTATATAATTG
225417 CACATTAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 18 0.42
30 2 0.05
31 23 0.53
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (29 bp):
TAAAGTTTCAAGTATATAATTGAACCAAA
Found at i:226702 original size:2 final size:2
Alignment explanation
Indices: 226648--226685 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
226638 AGTAGATAGA
226648 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
226686 TTTTTAATAT
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):
AT
Found at i:226711 original size:21 final size:20
Alignment explanation
Indices: 226650--226702 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
226640 TAGATAGAAT
* *
226650 ATATATATATATATATATATA
1 ATATATATATATAT-TTTTTA
226671 TATATATATATATATTTTTTA
1 -ATATATATATATATTTTTTA
226692 ATATGATATAT
1 ATAT-ATATAT
226703 GTGTTTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 4 0.14
21 10 0.36
22 14 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
ATATATATATATATTTTTTA
Found at i:227596 original size:24 final size:24
Alignment explanation
Indices: 227546--227593 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
227536 GGGAAACGTT
* *
227546 AAAAAAAATATTATAACATTCACC
1 AAAAAAAATATTACAACAATCACC
*
227570 AAAAGAAATATTACAACCAATCAC
1 AAAAAAAATATTACAA-CAATCAC
227594 AAAGCTCTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.58, C:0.19, G:0.02, T:0.21
Consensus pattern (24 bp):
AAAAAAAATATTACAACAATCACC
Found at i:227679 original size:23 final size:21
Alignment explanation
Indices: 227653--227695 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
227643 ACATATGCAT
227653 AAAAAATATAAATAAATATATAA
1 AAAAAAT-TAAA-AAATATATAA
227676 AAAAAATTAAAAAATATATA
1 AAAAAATTAAAAAATATATA
227696 TATAATTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 4 0.20
23 7 0.35
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAAATTAAAAAATATATAA
Found at i:227687 original size:31 final size:32
Alignment explanation
Indices: 227652--227712 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
227642 TACATATGCA
*
227652 TAAAAAATATAAATA-AATATATAAAAAAAAT
1 TAAAAAATATAAATATAATATAGAAAAAAAAT
* *
227683 TAAAAAATATATATATAATTTAGAAAAAAA
1 TAAAAAATATAAATATAATATAGAAAAAAA
227713 CAATATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (32 bp):
TAAAAAATATAAATATAATATAGAAAAAAAAT
Found at i:227696 original size:23 final size:23
Alignment explanation
Indices: 227653--227697 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
227643 ACATATGCAT
*
227653 AAAAAATATAAATAAATATATAA
1 AAAAAATATAAAAAAATATATAA
227676 AAAAAAT-TAAAAAATATATATA
1 AAAAAATATAAAAAA-ATATATA
227698 TAATTTAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAAAATATAAAAAAATATATAA
Found at i:236217 original size:1 final size:1
Alignment explanation
Indices: 236211--236236 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
236201 NNNNNNNNNN
236211 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
236237 GTCATTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:246445 original size:1 final size:1
Alignment explanation
Indices: 246441--246465 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
246431 NNNNNNNNNN
246441 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
246466 AATATGATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:247691 original size:19 final size:19
Alignment explanation
Indices: 247667--247705 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
247657 TAAATATGGA
247667 ATTAAAGCTTATTGAGTGT
1 ATTAAAGCTTATTGAGTGT
247686 ATTAAAGCTTATTGAGTGT
1 ATTAAAGCTTATTGAGTGT
247705 A
1 A
247706 GTTTCATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (19 bp):
ATTAAAGCTTATTGAGTGT
Found at i:248072 original size:54 final size:54
Alignment explanation
Indices: 248009--248148 Score: 262
Period size: 54 Copynumber: 2.6 Consensus size: 54
247999 ATTTACTGTA
248009 CAAATTGACTAAAGTAAAAATTCTGGAAATTTTATGGTAAAAAGATATTTGAGT
1 CAAATTGACTAAAGTAAAAATTCTGGAAATTTTATGGTAAAAAGATATTTGAGT
*
248063 CAAATTGACTAAAGTAAAAATTCTGGAAATTTTATGGTAAAAATATATTTGAGT
1 CAAATTGACTAAAGTAAAAATTCTGGAAATTTTATGGTAAAAAGATATTTGAGT
*
248117 CTAATTGACTAAAGTAAAAATTCTGGAAATTT
1 CAAATTGACTAAAGTAAAAATTCTGGAAATTT
248149 ACTGTACAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 84 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.34
Consensus pattern (54 bp):
CAAATTGACTAAAGTAAAAATTCTGGAAATTTTATGGTAAAAAGATATTTGAGT
Found at i:248586 original size:23 final size:23
Alignment explanation
Indices: 248570--248624 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
248560 GCACTTCGTA
248570 TGCTTACTGGATTGCACTGTGTG
1 TGCTTACTGGATTGCACTGTGTG
*
248593 TGCCTACTGGATTGCACTGTGTG
1 TGCTTACTGGATTGCACTGTGTG
248616 TGCTTACTG
1 TGCTTACTG
248625 TTTCCCCAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.13, C:0.20, G:0.29, T:0.38
Consensus pattern (23 bp):
TGCTTACTGGATTGCACTGTGTG
Found at i:259866 original size:16 final size:17
Alignment explanation
Indices: 259845--259876 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
259835 TTAATAAATT
259845 TTTTTATAA-TTTATAA
1 TTTTTATAAGTTTATAA
259861 TTTTTATAAGTTTATA
1 TTTTTATAAGTTTATA
259877 TCAATTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTTTATAAGTTTATAA
Found at i:259868 original size:9 final size:9
Alignment explanation
Indices: 259845--259968 Score: 82
Period size: 9 Copynumber: 13.8 Consensus size: 9
259835 TTAATAAATT
259845 TTTTTATAA
1 TTTTTATAA
259854 --TTTATAA
1 TTTTTATAA
259861 TTTTTATAA
1 TTTTTATAA
*
259870 GTTTATATCAA
1 -TTTTTAT-AA
*
259881 TTTTCAT-A
1 TTTTTATAA
259889 -TTTT-TAA
1 TTTTTATAA
*
259896 TGTTTTTTAA
1 T-TTTTATAA
259906 TATTTTATAA
1 T-TTTTATAA
259916 -TTTTATAA
1 TTTTTATAA
*
259924 TTTTGATAA
1 TTTTTATAA
259933 TTTTATATATA
1 TTTT-TATA-A
*
259944 TTTTTTACAA
1 -TTTTTATAA
*
259954 TTTTAAT-A
1 TTTTTATAA
259962 TTTTTAT
1 TTTTTAT
259969 GAGAAATATA
Statistics
Matches: 91, Mismatches: 12, Indels: 25
0.71 0.09 0.20
Matches are distributed among these distances:
6 1 0.01
7 11 0.12
8 16 0.18
9 27 0.30
10 26 0.29
11 6 0.07
12 4 0.04
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:259943 original size:21 final size:20
Alignment explanation
Indices: 259919--259962 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
259909 TTTATAATTT
*
259919 TATAATTTTGATAATTTTATA
1 TATAATTTTGACAATTTTA-A
* *
259940 TATATTTTTTACAATTTTAA
1 TATAATTTTGACAATTTTAA
259960 TAT
1 TAT
259963 TTTTATGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
TATAATTTTGACAATTTTAA
Found at i:259966 original size:63 final size:62
Alignment explanation
Indices: 259846--259967 Score: 149
Period size: 63 Copynumber: 2.0 Consensus size: 62
259836 TAATAAATTT
* * * *
259846 TTTTATAATTTATAATTTTTATAAGTTTATATCAATTTTCATATTTTTAATGTTTTTTAATA
1 TTTTATAATTTATAATTTTGATAAGTTTATATCAATTTTCACAATTTTAATGATTTTTAATA
* *
259908 TTTTATAATTTTATAATTTTGATAATTTTATAT-ATATTTTTTACAATTTTAAT-ATTTTTA
1 TTTTATAA-TTTATAATTTTGATAAGTTTATATCA-A-TTTTCACAATTTTAATGATTTTTA
259968 TGAGAAATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
62 9 0.18
63 29 0.57
64 13 0.25
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (62 bp):
TTTTATAATTTATAATTTTGATAAGTTTATATCAATTTTCACAATTTTAATGATTTTTAATA
Found at i:259967 original size:17 final size:17
Alignment explanation
Indices: 259770--259968 Score: 65
Period size: 17 Copynumber: 11.2 Consensus size: 17
259760 TTTATTAACC
*
259770 TTATAATTTTTTATGATTT
1 TTATAA-TTTTAAT-ATTT
259789 TTATAGAATTTTAATATTT
1 TTAT--AATTTTAATATTT
*
259808 TT-TAAATTCTAAATATGTT
1 TTAT-AATT-TTAATAT-TT
*
259827 TTAT-TTCTTTAATAAATTTTT
1 TTATAAT-TTTAAT--A--TTT
259848 TTATAA-TTT-ATAATTT
1 TTATAATTTTAAT-ATTT
*
259864 TTATAAGTTTATATCAATTT
1 TTATAATTTTA-AT--ATTT
* * *
259884 TCATATTTTTAATGTTT
1 TTATAATTTTAATATTT
* *
259901 TT-TAATATTTTATAATT
1 TTATAAT-TTTAATATTT
* *
259918 TTATAATTTTGATAATT
1 TTATAATTTTAATATTT
*
259935 TTAT-A-TAT-AT-TTT
1 TTATAATTTTAATATTT
*
259948 TTACAATTTTAATATTT
1 TTATAATTTTAATATTT
259965 TTAT
1 TTAT
259969 GAGAAATATA
Statistics
Matches: 138, Mismatches: 21, Indels: 44
0.68 0.10 0.22
Matches are distributed among these distances:
13 5 0.04
14 3 0.02
15 4 0.03
16 15 0.11
17 39 0.28
18 18 0.13
19 21 0.15
20 24 0.17
21 8 0.06
22 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
TTATAATTTTAATATTT
Found at i:260113 original size:15 final size:15
Alignment explanation
Indices: 260093--260127 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
260083 ATTGATCATT
260093 TTAATTAACAAGAAC
1 TTAATTAACAAGAAC
* *
260108 TTAATTAACACGAAT
1 TTAATTAACAAGAAC
260123 TTAAT
1 TTAAT
260128 ATAAAAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (15 bp):
TTAATTAACAAGAAC
Found at i:260402 original size:8 final size:7
Alignment explanation
Indices: 260383--260416 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
260373 GGGAACGGAG
260383 TAAAAAA
1 TAAAAAA
260390 TAAAAAA
1 TAAAAAA
260397 TAAAAAA
1 TAAAAAA
260404 TAAAAAA
1 TAAAAAA
260411 GTAAAA
1 -TAAAA
260417 TCTCCGGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.81
8 5 0.19
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:260402 original size:14 final size:15
Alignment explanation
Indices: 260381--260416 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
260371 GGGGGAACGG
260381 AGTAAAAAATAAAAA
1 AGTAAAAAATAAAAA
260396 A-TAAAAAATAAAAA
1 AGTAAAAAATAAAAA
260410 AGTAAAA
1 AGTAAAA
260417 TCTCCGGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.14
Consensus pattern (15 bp):
AGTAAAAAATAAAAA
Found at i:269932 original size:25 final size:25
Alignment explanation
Indices: 269878--269932 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
269868 GAATAAAATA
* *
269878 AAAT-ATTTAAAATATATCTTTCTT
1 AAATAATTTAAAATATATATTTCTC
*
269902 ATATAATTTAAAATATATATTTAC-C
1 AAATAATTTAAAATATATATTT-CTC
269927 AAATAA
1 AAATAA
269933 GCAATTTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 3 0.12
25 21 0.84
26 1 0.04
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATAATTTAAAATATATATTTCTC
Found at i:287954 original size:163 final size:163
Alignment explanation
Indices: 287667--287994 Score: 514
Period size: 163 Copynumber: 2.0 Consensus size: 163
287657 TAACGAATCG
287667 TTCCTATGACGTTTCCTCCCAGAATAGAACAAAATCCTTTTGTCTTTAATCCTCATCCTGTTTTC
1 TTCCTATGACGTTTCCTCCCAGAATAGAACAAAATCCTTTTGTCTTTAATCCTCATCCTGTTTTC
* **
287732 TGGCTCTGCATTTAATGTATTTGATCTGTAATTTTGAAAAAAGGACAAATTCCGGGAACTATTTG
66 TGGCTCTGCATTTAATGTATTTGATCTGTAATTTTGAAAAAACGACAAATTCCGGGAACTATTCA
* *
287797 CTAACCAAAGACATGTTTTTGTTGAGTTTTTAC
131 CTAACCAAAAACACGTTTTTGTTGAGTTTTTAC
** * *
287830 TTCCTATGTTGTTTCCTCTCAGAATAGAATAAAATCCTTTTGTCTTTAATCCTCATCCTGTTTTC
1 TTCCTATGACGTTTCCTCCCAGAATAGAACAAAATCCTTTTGTCTTTAATCCTCATCCTGTTTTC
* * *
287895 TGGTTCTGCATTTAATGTATTTGATCTGTAATTTTGAAAAGCACGACAAATT-TGGGAACTATTC
66 TGGCTCTGCATTTAATGTATTTGATCTGTAATTTTGAAAA-AACGACAAATTCCGGGAACTATTC
**
287959 ACTAATGAAAAACACGTTTTTGTTGAGTTTTTAC
130 ACTAACCAAAAACACGTTTTTGTTGAGTTTTTAC
287993 TT
1 TT
287995 GTATACGTAA
Statistics
Matches: 150, Mismatches: 14, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
163 141 0.94
164 9 0.06
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (163 bp):
TTCCTATGACGTTTCCTCCCAGAATAGAACAAAATCCTTTTGTCTTTAATCCTCATCCTGTTTTC
TGGCTCTGCATTTAATGTATTTGATCTGTAATTTTGAAAAAACGACAAATTCCGGGAACTATTCA
CTAACCAAAAACACGTTTTTGTTGAGTTTTTAC
Found at i:295220 original size:22 final size:22
Alignment explanation
Indices: 295195--295303 Score: 57
Period size: 22 Copynumber: 4.9 Consensus size: 22
295185 ATCAAAATAC
295195 ATAAATATTTTAAATATGTATA
1 ATAAATATTTTAAATATGTATA
* ***
295217 ATAAAT-TTTAAAAACATAAAAATAA
1 ATAAATATTT--TAA-ATATGTAT-A
**
295242 ATAAATATTTTCAAA-ACAATATA
1 ATAAATATTTT-AAATA-TGTATA
*
295265 AT-AATAATTTTAAATATGTATT
1 ATAAAT-ATTTTAAATATGTATA
295287 ATAAATA-TTT-AATATGT
1 ATAAATATTTTAAATATGT
295304 TTATGTTTAT
Statistics
Matches: 68, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
20 7 0.10
21 6 0.09
22 18 0.26
23 15 0.22
24 10 0.15
25 9 0.13
26 3 0.04
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (22 bp):
ATAAATATTTTAAATATGTATA
Found at i:295358 original size:29 final size:29
Alignment explanation
Indices: 295325--295414 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
295315 ATGATTATAT
295325 TTTTTAAATTATTTATTTATTTTTATTTA
1 TTTTTAAATTATTTATTTATTTTTATTTA
* * *
295354 TTTTTAAATTTTATTA-TTATATATATATT-
1 TTTTTAAATTAT-TTATTTATTTTTAT-TTA
* * * *
295383 TTTTTAAAATATTTATGTACTTTTATATA
1 TTTTTAAATTATTTATTTATTTTTATTTA
295412 TTT
1 TTT
295415 CTTTGATTTT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
28 4 0.09
29 38 0.81
30 5 0.11
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (29 bp):
TTTTTAAATTATTTATTTATTTTTATTTA
Found at i:295366 original size:27 final size:29
Alignment explanation
Indices: 295309--295412 Score: 83
Period size: 29 Copynumber: 3.6 Consensus size: 29
295299 TATGTTTATG
*
295309 TTTATTATGAT-TATAT-TTTTTAAATTA
1 TTTATTATTATATATATATTTTTAAATTA
* *
295336 TTTATTTATT-TTTATTTATTTTTAAA-T-
1 TTTA-TTATTATATATATATTTTTAAATTA
*
295363 TTTATTATTATATATATATTTTTTTAAAATA
1 TTTATTATTATATATATA--TTTTTAAATTA
*
295394 TTTATGTACTTTTATATAT
1 TTTAT-TA-TTATATATAT
295413 TTCTTTGATT
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
26 5 0.08
27 15 0.24
28 9 0.15
29 16 0.26
30 1 0.02
31 5 0.08
32 2 0.03
33 9 0.15
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (29 bp):
TTTATTATTATATATATATTTTTAAATTA
Found at i:295410 original size:31 final size:29
Alignment explanation
Indices: 295320--295414 Score: 92
Period size: 31 Copynumber: 3.2 Consensus size: 29
295310 TTATTATGAT
*
295320 TATA-TTTTTTAAATTATTTATTTATTTT-
1 TATATTTTTTTAAAATATTTA-TTATTTTA
295348 TAT-TTATTTTT-AAAT-TTTATTATTATATA
1 TATATT-TTTTTAAAATATTTATTATT-T-TA
295377 TATATTTTTTTAAAATATTTATGTACTTTTA
1 TATATTTTTTTAAAATATTTAT-TA-TTTTA
295408 TATATTT
1 TATATTT
295415 CTTTGATTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 17
0.76 0.01 0.23
Matches are distributed among these distances:
26 5 0.09
27 5 0.09
28 8 0.14
29 13 0.23
30 6 0.11
31 14 0.25
32 3 0.05
33 2 0.04
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (29 bp):
TATATTTTTTTAAAATATTTATTATTTTA
Found at i:295822 original size:24 final size:25
Alignment explanation
Indices: 295770--295824 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
295760 TTATTTGAAA
*
295770 TATTT-AAAAAATATTTTTATAATT
1 TATTTAAAAAAATATTCTTATAATT
*
295794 AATTTAAAAAAATA-TCTTA-AATAT
1 TATTTAAAAAAATATTCTTATAAT-T
295818 TATTTAA
1 TATTTAA
295825 TGATATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 3 0.12
24 15 0.58
25 8 0.31
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
TATTTAAAAAAATATTCTTATAATT
Found at i:297295 original size:15 final size:15
Alignment explanation
Indices: 297249--297295 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
297239 ATTATTTATA
* *
297249 AAAATGATTTAAGTT
1 AAAATAATTTAAATT
*
297264 AAAA-AATATAAATT
1 AAAATAATTTAAATT
*
297278 AAAATAATTTAAAAT
1 AAAATAATTTAAATT
297293 AAA
1 AAA
297296 CTGTAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (15 bp):
AAAATAATTTAAATT
Found at i:297830 original size:57 final size:57
Alignment explanation
Indices: 297654--297826 Score: 180
Period size: 56 Copynumber: 3.1 Consensus size: 57
297644 AAAATACGAA
* * * * *
297654 TAAAAAATATTTTTTGAAGTGTTTGCCA-CTCAATGGCCTACAC--CTCTTTTCCAGAT
1 TAAAAAATATTTTTTTAAGTGTTTGTCATC-CAATGACTTACACTACT-TTTTCCAAAT
* * * *
297710 TTAAAAATATTTTTTTAATTGTTTGTCATCCAGTGACTTACACTACTTTTTTCAAAT
1 TAAAAAATATTTTTTTAAGTGTTTGTCATCCAATGACTTACACTACTTTTTCCAAAT
* *
297767 TTAAAAATATTTTTTT-AGTGTTTGTCA-CCAATGATTTAC-C-ACTTTTTCCAAAT
1 TAAAAAATATTTTTTTAAGTGTTTGTCATCCAATGACTTACACTACTTTTTCCAAAT
297820 TAAAAAA
1 TAAAAAA
297827 AAAAAATTTA
Statistics
Matches: 100, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
53 18 0.18
54 1 0.01
55 10 0.10
56 44 0.44
57 25 0.25
58 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (57 bp):
TAAAAAATATTTTTTTAAGTGTTTGTCATCCAATGACTTACACTACTTTTTCCAAAT
Found at i:298161 original size:57 final size:56
Alignment explanation
Indices: 298094--298211 Score: 134
Period size: 57 Copynumber: 2.1 Consensus size: 56
298084 CCTAATTTTT
* *
298094 TTTTTTAATTTAGAAAAAAT-AG-TGCAGGTCATTTGGTGACAAACA-CTCAAAAAAATA
1 TTTTTAAATTT-G-AAAAATGAGATGCAGGTCATTAGGTGACAAACATCT-AAAAAAA-A
* * *
298151 TTTTTAAATTTGAAAAATGTGATGTAGGTCATTAGGTGGCAAACATCTAAAAAAAA
1 TTTTTAAATTTGAAAAATGAGATGCAGGTCATTAGGTGACAAACATCTAAAAAAAA
298207 TTTTT
1 TTTTT
298212 GAGACCTGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
55 6 0.11
56 8 0.15
57 37 0.70
58 2 0.04
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (56 bp):
TTTTTAAATTTGAAAAATGAGATGCAGGTCATTAGGTGACAAACATCTAAAAAAAA
Found at i:298238 original size:56 final size:57
Alignment explanation
Indices: 298119--298226 Score: 130
Period size: 57 Copynumber: 1.9 Consensus size: 57
298109 AAAATAGTGC
* ** *
298119 AGGTCATTTGGTGACAAACACTCAAAAAAATATTTTTAAATTTGAAAAATGTGATGT
1 AGGTCATTAGGTGACAAACACTCAAAAAAATATTTTTAAACCTGAAAAAAGTGATGT
* *
298176 AGGTCATTAGGTGGCAAACA-TCTAAAAAAA-ATTTTTGAGACCTGAAAAAAG
1 AGGTCATTAGGTGACAAACACTC-AAAAAAATATTTTT-AAACCTGAAAAAAG
298227 GGTGTTGGTC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
56 8 0.19
57 35 0.81
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.29
Consensus pattern (57 bp):
AGGTCATTAGGTGACAAACACTCAAAAAAATATTTTTAAACCTGAAAAAAGTGATGT
Found at i:301110 original size:18 final size:18
Alignment explanation
Indices: 301087--301123 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
301077 TAATCAATCT
* *
301087 TAAAATTTGATATTTAAA
1 TAAAATATGAAATTTAAA
301105 TAAAATATGAAATTTAAA
1 TAAAATATGAAATTTAAA
301123 T
1 T
301124 TTAAATTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
TAAAATATGAAATTTAAA
Found at i:302487 original size:21 final size:21
Alignment explanation
Indices: 302463--302511 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
302453 AAATTAATAA
302463 TATATAATTTATG-TTAATATT
1 TATATAATTTATGATTAA-ATT
*
302484 TATATATTTTTATGATTAAATT
1 TATATA-ATTTATGATTAAATT
302506 TA-ATAA
1 TATATAA
302512 AATATGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 9 0.38
22 11 0.46
23 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (21 bp):
TATATAATTTATGATTAAATT
Found at i:303847 original size:18 final size:20
Alignment explanation
Indices: 303808--303847 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
303798 ATTCCTTGCT
303808 TAATTTTACTAATATATTAAA
1 TAATTTTACTAATATA-TAAA
303829 TAATTTTA-TAATATA-AAA
1 TAATTTTACTAATATATAAA
303847 T
1 T
303848 TCAATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
20 7 0.37
21 8 0.42
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TAATTTTACTAATATATAAA
Found at i:304254 original size:23 final size:21
Alignment explanation
Indices: 304212--304257 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
304202 ATAATAGTAA
*
304212 AATATATAATTTTATCAATTT
1 AATATATAATTTTATAAATTT
*
304233 AATATTTATATTTTATAAAATTT
1 AATATATA-ATTTTAT-AAATTT
304256 AA
1 AA
304258 AGGATTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 7 0.33
23 7 0.33
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
AATATATAATTTTATAAATTT
Found at i:304276 original size:30 final size:31
Alignment explanation
Indices: 304242--304309 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
304232 TAATATTTAT
* *
304242 ATTTTATAAAATTTAAAG-GATTAAATTAAA
1 ATTTTATAAAATTTAAAGAGATCAAAGTAAA
** *
304272 ATTTTATAATTTTTAAAGAGATCAAAGTATA
1 ATTTTATAAAATTTAAAGAGATCAAAGTAAA
304303 ATTTTAT
1 ATTTTAT
304310 TTTTATTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.44
Consensus pattern (31 bp):
ATTTTATAAAATTTAAAGAGATCAAAGTAAA
Found at i:308606 original size:22 final size:23
Alignment explanation
Indices: 308578--308620 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
308568 ACCAGAATTT
308578 TAAAA-TTTAAAAAATAAAAATA
1 TAAAATTTTAAAAAATAAAAATA
*
308600 TAAAATTTTAAAAAGTAAAAA
1 TAAAATTTTAAAAAATAAAAA
308621 CATATGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
TAAAATTTTAAAAAATAAAAATA
Found at i:316376 original size:19 final size:19
Alignment explanation
Indices: 316340--316386 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
316330 ATCATCATGT
316340 ATAAA-TTATAATTATTAA
1 ATAAATTTATAATTATTAA
* * *
316358 TTAAATTTATAGTTTTTAA
1 ATAAATTTATAATTATTAA
316377 ATATAATTTA
1 ATA-AATTTA
316387 AGTAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 4 0.17
19 13 0.57
20 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
ATAAATTTATAATTATTAA
Found at i:319833 original size:23 final size:23
Alignment explanation
Indices: 319791--319845 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
319781 TAAAATGACA
319791 AATTTTG-TAAACATTGAGGGCT
1 AATTTTGTTAAACATTGAGGGCT
*
319813 AATTTTGTTAAA-ATTGAAGGGTT
1 AATTTTGTTAAACATTG-AGGGCT
319836 AATTTTGTTA
1 AATTTTGTTA
319846 CTAGATCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 11 0.37
23 19 0.63
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.44
Consensus pattern (23 bp):
AATTTTGTTAAACATTGAGGGCT
Done.