Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014198.1 Kokia drynarioides strain JFW-HI SEQ_129231, 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: 218750
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 12 characters in sequence are not A, C, G, or T
Found at i:1021 original size:17 final size:17
Alignment explanation
Indices: 999--1077 Score: 86
Period size: 17 Copynumber: 4.6 Consensus size: 17
989 TGGACTTTTC
*
999 TAAATTTAATTTTATAA
1 TAAATTTAATTTTAAAA
* *
1016 TAAATTTAAATTTCAAA
1 TAAATTTAATTTTAAAA
* *
1033 TAAACTTAAATTTAAAA
1 TAAATTTAATTTTAAAA
* *
1050 TAAACTTAAATTTAAAA
1 TAAATTTAATTTTAAAA
*
1067 TAAATTCAATT
1 TAAATTTAATT
1078 CCCAACGGGC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAATTTTAAAA
Found at i:1052 original size:34 final size:34
Alignment explanation
Indices: 999--1070 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
989 TGGACTTTTC
* * * * *
999 TAAATTTAATTTTATAATAAATTTAAATTTCAAA
1 TAAACTTAAATTTAAAATAAACTTAAATTTAAAA
1033 TAAACTTAAATTTAAAATAAACTTAAATTTAAAA
1 TAAACTTAAATTTAAAATAAACTTAAATTTAAAA
1067 TAAA
1 TAAA
1071 TTCAATTCCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (34 bp):
TAAACTTAAATTTAAAATAAACTTAAATTTAAAA
Found at i:2125 original size:33 final size:33
Alignment explanation
Indices: 2071--2137 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
2061 TTAAGGGTTC
* *
2071 AAATTTTTTTTACTAATTTTTAAGGGACCTAAAA
1 AAATTTTTTTTA-TAACTTTTAAGGAACCTAAAA
2105 AAATTTTTTCTT-TAACTTTTAAGGAACCTAAAA
1 AAATTTTTT-TTATAACTTTTAAGGAACCTAAAA
2138 CCCTATTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 19 0.63
34 9 0.30
35 2 0.07
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.43
Consensus pattern (33 bp):
AAATTTTTTTTATAACTTTTAAGGAACCTAAAA
Found at i:6042 original size:6 final size:6
Alignment explanation
Indices: 6033--6057 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6023 TACTCCCTAA
6033 CTTGAG CTTGAG CTTGAG CTTGAG C
1 CTTGAG CTTGAG CTTGAG CTTGAG C
6058 CCGAACTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.20, G:0.32, T:0.32
Consensus pattern (6 bp):
CTTGAG
Found at i:7014 original size:114 final size:114
Alignment explanation
Indices: 6732--7014 Score: 362
Period size: 114 Copynumber: 2.5 Consensus size: 114
6722 TACTCTGGCG
*
6732 AGGGTATAGATACCTTTG-TTTTTGCTAATTTTTTTCAAACATCGAAGCTTAAA-TTGGTATAGA
1 AGGGTATAGATACCTTTGTTTTTTGCTAATTTTTTTCAAACATCGAAGCTAAAATTTGGTATAGA
* * * * *
6795 TACCAAGTAAGGGTGTCGATACTTTGACCTTGGTATCGATACTATGGAA
66 TACCAAGAAAAGGTATCGATACTTTGACCCTGGTATCGATACTATAGAA
* *
6844 AGGGTATCA-ACACCTTTGTTTTTTTGCTAATTTTTTTCAAACATCGAA--TATCAATTTGGTAT
1 AGGGTAT-AGATACCTTTG-TTTTTTGCTAATTTTTTTCAAACATCGAAGCTA-AAATTTGGTAT
* *
6906 TGATACC-AGAAAAAGGTATCGATACTTTGACCCTGGTATCTATACTATAGAA
63 AGATACCAAG-AAAAGGTATCGATACTTTGACCCTGGTATCGATACTATAGAA
* * * *
6958 AGGGTATTGATACATTTGTTTTTTGCTAAATTTTTTCAAATATCGAAGCTAAAATTT
1 AGGGTATAGATACCTTTGTTTTTTGCTAATTTTTTTCAAACATCGAAGCTAAAATTT
7015 ATAGACTTTA
Statistics
Matches: 146, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
112 16 0.11
113 32 0.22
114 96 0.66
115 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (114 bp):
AGGGTATAGATACCTTTGTTTTTTGCTAATTTTTTTCAAACATCGAAGCTAAAATTTGGTATAGA
TACCAAGAAAAGGTATCGATACTTTGACCCTGGTATCGATACTATAGAA
Found at i:11053 original size:36 final size:36
Alignment explanation
Indices: 10997--11348 Score: 411
Period size: 36 Copynumber: 9.8 Consensus size: 36
10987 TACTTCGATG
* *
10997 GATTGCGTATGTCTCGATTAGAGCATAATGCTAAGA
1 GATTGCTTATGTCTCGATTAGAGCATAATGCTAAGT
* * * * *
11033 GATTACTTATGTCTCAATTAGAGCGTAAAGCTAAGA
1 GATTGCTTATGTCTCGATTAGAGCATAATGCTAAGT
* *
11069 GATTG-TGTATGTCTCGGTTAGAGCATAATGCTACGT
1 GATTGCT-TATGTCTCGATTAGAGCATAATGCTAAGT
* * ** *
11105 GATTGCTTACGTCTCGGTTAGAGTGTAATGCTATGT
1 GATTGCTTATGTCTCGATTAGAGCATAATGCTAAGT
* *
11141 GATTGCTTATGTATCGATTAGAGCATAATGCTAAGA
1 GATTGCTTATGTCTCGATTAGAGCATAATGCTAAGT
* * * * *
11177 GATTACTTATGTCTCAATTAGAGCGTAAAGCTAAGA
1 GATTGCTTATGTCTCGATTAGAGCATAATGCTAAGT
* * * *
11213 GATTG-TGTATGACTCGGTTAGAGCGTAATGCTACGT
1 GATTGCT-TATGTCTCGATTAGAGCATAATGCTAAGT
* * *
11249 GATTGCTTACGTCTCGGTTAGAGCATAATGCTATGT
1 GATTGCTTATGTCTCGATTAGAGCATAATGCTAAGT
*
11285 GATTGCTTATGTCTCGATTAGAGCATAATGATAAGT
1 GATTGCTTATGTCTCGATTAGAGCATAATGCTAAGT
11321 GATTGCTTATGTCTCGATTAGAGCATAA
1 GATTGCTTATGTCTCGATTAGAGCATAA
11349 GGCCATTTCA
Statistics
Matches: 269, Mismatches: 43, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
35 2 0.01
36 265 0.99
37 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (36 bp):
GATTGCTTATGTCTCGATTAGAGCATAATGCTAAGT
Found at i:11257 original size:144 final size:144
Alignment explanation
Indices: 10997--11344 Score: 606
Period size: 144 Copynumber: 2.4 Consensus size: 144
10987 TACTTCGATG
*
10997 GATTGCGTATGTCTCGATTAGAGCATAATGCTAAGAGATTACTTATGTCTCAATTAGAGCGTAAA
1 GATTGCTTATGTCTCGATTAGAGCATAATGCTAAGAGATTACTTATGTCTCAATTAGAGCGTAAA
*
11062 GCTAAGAGATTGTGTATGTCTCGGTTAGAGCATAATGCTACGTGATTGCTTACGTCTCGGTTAGA
66 GCTAAGAGATTGTGTATGACTCGGTTAGAGCATAATGCTACGTGATTGCTTACGTCTCGGTTAGA
**
11127 GTGTAATGCTATGT
131 GCATAATGCTATGT
*
11141 GATTGCTTATGTATCGATTAGAGCATAATGCTAAGAGATTACTTATGTCTCAATTAGAGCGTAAA
1 GATTGCTTATGTCTCGATTAGAGCATAATGCTAAGAGATTACTTATGTCTCAATTAGAGCGTAAA
*
11206 GCTAAGAGATTGTGTATGACTCGGTTAGAGCGTAATGCTACGTGATTGCTTACGTCTCGGTTAGA
66 GCTAAGAGATTGTGTATGACTCGGTTAGAGCATAATGCTACGTGATTGCTTACGTCTCGGTTAGA
11271 GCATAATGCTATGT
131 GCATAATGCTATGT
* * * *
11285 GATTGCTTATGTCTCGATTAGAGCATAATGATAAGTGATTGCTTATGTCTCGATTAGAGC
1 GATTGCTTATGTCTCGATTAGAGCATAATGCTAAGAGATTACTTATGTCTCAATTAGAGC
11345 ATAAGGCCAT
Statistics
Matches: 193, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
144 193 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (144 bp):
GATTGCTTATGTCTCGATTAGAGCATAATGCTAAGAGATTACTTATGTCTCAATTAGAGCGTAAA
GCTAAGAGATTGTGTATGACTCGGTTAGAGCATAATGCTACGTGATTGCTTACGTCTCGGTTAGA
GCATAATGCTATGT
Found at i:13826 original size:26 final size:26
Alignment explanation
Indices: 13790--13844 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
13780 TAATGTCTCT
*
13790 AATGGTATATGAATTATTAGCATAAA
1 AATGATATATGAATTATTAGCATAAA
13816 AATGATATATGAATTATTAGCATAAA
1 AATGATATATGAATTATTAGCATAAA
13842 AAT
1 AAT
13845 TGTTATATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.35
Consensus pattern (26 bp):
AATGATATATGAATTATTAGCATAAA
Found at i:14712 original size:23 final size:23
Alignment explanation
Indices: 14647--14712 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
14637 CTTTTATTAA
* *
14647 CACTGTGTGTGCTCTCTGATTAG
1 CACTATGTGTGCTCTCTGTTTAG
* * * *
14670 TACTTTGTGTACTCTTTGTTTAG
1 CACTATGTGTGCTCTCTGTTTAG
14693 CACTATGTGTGCTCTCTGTT
1 CACTATGTGTGCTCTCTGTT
14713 GCCCAACACT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.47
Consensus pattern (23 bp):
CACTATGTGTGCTCTCTGTTTAG
Found at i:21811 original size:23 final size:23
Alignment explanation
Indices: 21772--21907 Score: 105
Period size: 23 Copynumber: 5.9 Consensus size: 23
21762 CATTAAGGAA
*
21772 CACTA-GCGCGCTCTCTGTTTAG
1 CACTATGCGTGCTCTCTGTTTAG
*
21794 CACGTCT-CGTGCTCTCTGTGATTAG
1 CAC-TATGCGTGCTCTCTGT--TTAG
* *
21819 CACTATGTGTGCTCTCTGATTAG
1 CACTATGCGTGCTCTCTGTTTAG
* * *
21842 CACTTTGTGTGCTCTCTGATTAG
1 CACTATGCGTGCTCTCTGTTTAG
* * * *
21865 TACTTTGTGTACTCTCTGTTTAG
1 CACTATGCGTGCTCTCTGTTTAG
* * *
21888 CACAAAGTGTGCTCTCTGTT
1 CACTATGCGTGCTCTCTGTT
21908 GCGCAGCACT
Statistics
Matches: 95, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
22 3 0.03
23 73 0.77
24 2 0.02
25 17 0.18
ACGTcount: A:0.15, C:0.24, G:0.21, T:0.40
Consensus pattern (23 bp):
CACTATGCGTGCTCTCTGTTTAG
Found at i:21880 original size:46 final size:46
Alignment explanation
Indices: 21802--21905 Score: 127
Period size: 46 Copynumber: 2.2 Consensus size: 46
21792 AGCACGTCTC
* ***
21802 GTGCTCTCTGTGATTAGCACTATGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTC--TGATTAGCACTATGTGTACTCTCTGATTAGCACAAAGT
* * *
21850 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACAAAGT
1 GTGCTCTCTGATTAGCACTATGTGTACTCTCTGATTAGCACAAAGT
21896 GTGCTCTCTG
1 GTGCTCTCTG
21906 TTGCGCAGCA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
46 41 0.84
48 8 0.16
ACGTcount: A:0.15, C:0.21, G:0.22, T:0.41
Consensus pattern (46 bp):
GTGCTCTCTGATTAGCACTATGTGTACTCTCTGATTAGCACAAAGT
Found at i:21902 original size:69 final size:66
Alignment explanation
Indices: 21805--21954 Score: 185
Period size: 69 Copynumber: 2.2 Consensus size: 66
21795 ACGTCTCGTG
* * *
21805 CTCTCTGTGATTAGCACTATGTGTGCTCTCTGATT-AGCACTTTGTGTGCTCTCTGATTAGTACT
1 CTCTCTGT--TTAGCACAAAGTGTGCTCTCTG-TTCAGCAC-TTATGTGCTCTCTG-TTAGTACT
21869 TTGTGTA
61 TTG-GTA
21876 CTCTCTGTTTAGCACAAAGTGTGCTCTCTGTTGCGCAGCACTTATGTGCTCTCTGTTAGTACTTT
1 CTCTCTGTTTAGCACAAAGTGTGCTCTCTGTT---CAGCACTTATGTGCTCTCTGTTAGTACTTT
21941 GGTA
63 GGTA
21945 CTCTCTGTTT
1 CTCTCTGTTT
21955 GTTCCGTATA
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
68 2 0.03
69 33 0.46
70 11 0.15
71 21 0.29
72 5 0.07
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.43
Consensus pattern (66 bp):
CTCTCTGTTTAGCACAAAGTGTGCTCTCTGTTCAGCACTTATGTGCTCTCTGTTAGTACTTTGGT
A
Found at i:26567 original size:9 final size:11
Alignment explanation
Indices: 26543--26567 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
26533 TAAACTCGTT
26543 TATATACAGAA
1 TATATACAGAA
26554 TATATACAGAA
1 TATATACAGAA
26565 TAT
1 TAT
26568 CACCATAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (11 bp):
TATATACAGAA
Found at i:38245 original size:53 final size:53
Alignment explanation
Indices: 38184--38428 Score: 303
Period size: 53 Copynumber: 4.6 Consensus size: 53
38174 TTGTTCCAAA
* * *
38184 GATTAAAGGTCCAATGACTCTGTGTCATCGTGAATTATATGAATCCTATCACA
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
* * *
38237 GATTAAAGGTCCGATGACTCTGTGTTATTGTGAGTTATATGAATCCTATCATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
* * * * *
38290 GATTAAAGGTCAGATGACTATGAGTCATCGTGAGTTATATGAATCTTATTACG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
* * * * ** *
38343 GATTAAGGGTCTGATGACTTTGTGTCATCGTGAGTTACACAAATCC-ATCATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
* *
38395 GATTAAAGGTTCGATGACTTTGTGTCATCGTGAG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAG
38429 CTATCAAATG
Statistics
Matches: 165, Mismatches: 27, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
52 35 0.21
53 130 0.79
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (53 bp):
GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
Found at i:45520 original size:53 final size:53
Alignment explanation
Indices: 45440--45688 Score: 338
Period size: 53 Copynumber: 4.7 Consensus size: 53
45430 TTGTTTCAAA
* *
45440 GATTAAAGGTCCGATGACTCTATGTCATCGTGAGTTATATGAATCCTATCACG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATG
45493 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATG
* * * * * *
45546 GATTAATGGTTCGATGATTATGTGTCATCTTGAGTTATATGAATCCTATTATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATG
* * * * *
45599 GATTAAGGGTCCGATGATTTTGTGTCATCGTGAGTTACACGAATCC-ATCATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATG
* * * *
45651 GATTAAAGGTCTGATGACTCTATGTCATCATGGGTTAT
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
45689 CAAATGCGAA
Statistics
Matches: 173, Mismatches: 23, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
52 35 0.20
53 138 0.80
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (53 bp):
GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATG
Found at i:48395 original size:45 final size:45
Alignment explanation
Indices: 48276--48422 Score: 143
Period size: 45 Copynumber: 3.2 Consensus size: 45
48266 TTTTCAAACA
* **
48276 AGTAAGACCATAGCCGAAAGACACTAGTGGAAACATGACGGAAACA
1 AGTAAGACCATAGCCAAAAGACACTA-TGGAAACATGACGGAAATG
* ** * * **
48322 AGTAAGACCATAGCCGAAAGGA-GTTATGGTAACATGCCAAAAATG
1 AGTAAGACCATAGCC-AAAAGACACTATGGAAACATGACGGAAATG
* * * *
48367 AGTAAGACCATAGCTAAAAGACACTATGGCATCATGACGGAAGTG
1 AGTAAGACCATAGCCAAAAGACACTATGGAAACATGACGGAAATG
48412 AGTAAGACCAT
1 AGTAAGACCAT
48423 GGATGAAAGA
Statistics
Matches: 79, Mismatches: 20, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
44 5 0.06
45 53 0.67
46 17 0.22
47 4 0.05
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.16
Consensus pattern (45 bp):
AGTAAGACCATAGCCAAAAGACACTATGGAAACATGACGGAAATG
Found at i:65546 original size:9 final size:9
Alignment explanation
Indices: 65532--65591 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
65522 TATATATATA
65532 TTCTTTTTT
1 TTCTTTTTT
65541 TTCTTTCTTT
1 TTCTTT-TTT
* **
65551 TTATTAACTT
1 TTCTT-TTTT
65561 TTC-TTTTT
1 TTCTTTTTT
* *
65569 TTCTCTTTC
1 TTCTTTTTT
65578 TTCTTTTTT
1 TTCTTTTTT
65587 TTCTT
1 TTCTT
65592 ATATGACTGA
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
8 5 0.13
9 22 0.58
10 11 0.29
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:65561 original size:24 final size:22
Alignment explanation
Indices: 65530--65591 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 22
65520 TATATATATA
*
65530 TATTCTTTTTTTTCTTTCTTTT
1 TATTCTTTTTTTTCTTTCTCTT
65552 TATTAACTTTTCTTTT-TTTCTCTT
1 TATT--CTTTT-TTTTCTTTCTCTT
*
65576 TCTTCTTTTTTTTCTT
1 TATTCTTTTTTTTCTT
65592 ATATGACTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
21 4 0.12
22 11 0.32
24 15 0.44
25 4 0.12
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (22 bp):
TATTCTTTTTTTTCTTTCTCTT
Found at i:76623 original size:61 final size:62
Alignment explanation
Indices: 76527--76654 Score: 231
Period size: 61 Copynumber: 2.1 Consensus size: 62
76517 TTGAATTAGT
* *
76527 GAAAGTCTTGTGGCATTATCACGGGGTTGAAGAAGCAACTTGGGAACCCGAAGAAGCTATGA
1 GAAAGTCTTGTGGCATCATCACAGGGTTGAAGAAGCAACTTGGGAACCCGAAGAAGCTATGA
76589 -AAAGTCTTGTGGCATCATCACAGGGTTGAAGAAGCAACTTGGGAACCCGAAGAAGCTATGA
1 GAAAGTCTTGTGGCATCATCACAGGGTTGAAGAAGCAACTTGGGAACCCGAAGAAGCTATGA
76650 GAAAG
1 GAAAG
76655 CAATACCCGA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
61 59 0.94
62 4 0.06
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (62 bp):
GAAAGTCTTGTGGCATCATCACAGGGTTGAAGAAGCAACTTGGGAACCCGAAGAAGCTATGA
Found at i:77785 original size:20 final size:21
Alignment explanation
Indices: 77746--77785 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
77736 TAGGTTAAGT
*
77746 CTTAAGATAGTATGATAATGA
1 CTTAAGATAGTATGAAAATGA
*
77767 CTTAA-ATATTATGAAAATG
1 CTTAAGATAGTATGAAAATG
77786 GGTTTGACCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (21 bp):
CTTAAGATAGTATGAAAATGA
Found at i:80996 original size:52 final size:52
Alignment explanation
Indices: 80918--81154 Score: 305
Period size: 52 Copynumber: 4.4 Consensus size: 52
80908 CAAAAGATCT
*
80918 GATGATTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCC
**
80970 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTGTGGATTATAAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCC
* * *
81022 AATGACTATGTGTCATCGTGAGTATATGAATCATTTTCGGATTATAAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCC
* *
81074 GATGACAATGTGTCATCGTGAGTATTAAATGAATTGAATCCTATTACGCATTA-AAGGTCC
1 GATGACTATGTGTCATCGTGAG---T--AT--A-TGAATCCT-TTACGGATTATAAGGTCC
*
81134 GATGACTCTGTGTCATCGTGA
1 GATGACTATGTGTCATCGTGA
81155 CTTACCAAAT
Statistics
Matches: 162, Mismatches: 14, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
52 117 0.72
55 1 0.01
57 2 0.01
59 1 0.01
60 33 0.20
61 8 0.05
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (52 bp):
GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCC
Found at i:88516 original size:7 final size:7
Alignment explanation
Indices: 88504--88529 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
88494 CGAAGTGATG
88504 GAGGGGA
1 GAGGGGA
88511 GAGGGGA
1 GAGGGGA
88518 GAGGGGA
1 GAGGGGA
88525 GAGGG
1 GAGGG
88530 AATAACAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.73, T:0.00
Consensus pattern (7 bp):
GAGGGGA
Found at i:114047 original size:27 final size:26
Alignment explanation
Indices: 113990--114060 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
113980 GTTGAGGTAA
*
113990 TTTCTTCTTGTTCTTTCTACTCTTCCT
1 TTTCTTCTTGTTC-TTCTACTATTCCT
*
114017 TTTCTTCTTGTTCTTCTTCTTATT-CT
1 TTTCTTCTTGTTCTTCTAC-TATTCCT
* *
114043 CTTTCTCCTTTTTCTTCT
1 -TTTCTTCTTGTTCTTCT
114061 CCACTTCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 7 0.18
27 31 0.82
ACGTcount: A:0.03, C:0.28, G:0.03, T:0.66
Consensus pattern (26 bp):
TTTCTTCTTGTTCTTCTACTATTCCT
Found at i:125583 original size:21 final size:21
Alignment explanation
Indices: 125542--125585 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
125532 ATAACAAAAG
125542 AAAAAAAATAACTAAAGCCTA
1 AAAAAAAATAACTAAAGCCTA
*
125563 AAAAAGAAATGACTAAA-CCTA
1 AAAAA-AAATAACTAAAGCCTA
125584 AA
1 AA
125586 TTACAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.66, C:0.14, G:0.07, T:0.14
Consensus pattern (21 bp):
AAAAAAAATAACTAAAGCCTA
Found at i:160286 original size:22 final size:21
Alignment explanation
Indices: 160236--160288 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
160226 TTTGAAAAAA
*
160236 TAAATTATTATATTAGATCAT
1 TAAATTATTTTATTAGATCAT
*
160257 TATA-TATTTTATATA-ATCAT
1 TAAATTATTTTAT-TAGATCAT
160277 TAAAATTATTTT
1 T-AAATTATTTT
160289 TTAAAATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 13 0.50
21 7 0.27
22 6 0.23
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (21 bp):
TAAATTATTTTATTAGATCAT
Found at i:160551 original size:46 final size:46
Alignment explanation
Indices: 160484--160577 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
160474 TCTCGAACTT
160484 GAGGTCGAATCAATCTCAAGCTCAAGCCTAGGCTTAGATCGATCTC
1 GAGGTCGAATCAATCTCAAGCTCAAGCCTAGGCTTAGATCGATCTC
*
160530 GAGGTCGAATCAATCTCAAGCTCAAGCCTAGGTTTAGATCGATCTC
1 GAGGTCGAATCAATCTCAAGCTCAAGCCTAGGCTTAGATCGATCTC
160576 GA
1 GA
160578 AATCAAATTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (46 bp):
GAGGTCGAATCAATCTCAAGCTCAAGCCTAGGCTTAGATCGATCTC
Found at i:160599 original size:16 final size:16
Alignment explanation
Indices: 160574--160606 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
160564 TAGATCGATC
160574 TCGAAATCAAATTATT
1 TCGAAATCAAATTATT
*
160590 TCGAATTCAAATTATT
1 TCGAAATCAAATTATT
160606 T
1 T
160607 TTTAGATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (16 bp):
TCGAAATCAAATTATT
Found at i:163618 original size:22 final size:22
Alignment explanation
Indices: 163582--163627 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
163572 AAAGATTTAG
*
163582 AAATTGAATTTGAAAATTTGAA
1 AAATTGAATTTGAAAATTTCAA
*
163604 AAATTG-ATTTGGAAACTTTCAA
1 AAATTGAATTT-GAAAATTTCAA
163626 AA
1 AA
163628 TTACATGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (22 bp):
AAATTGAATTTGAAAATTTCAA
Found at i:168563 original size:22 final size:22
Alignment explanation
Indices: 168511--168563 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
168501 TTTTATTCTA
168511 AAATAA-TTTTGAATAAAATTG
1 AAATAATTTTTGAATAAAATTG
* *
168532 AAAGATATTTTTTAATAAAA-TG
1 AAATA-ATTTTTGAATAAAATTG
168554 AGAATAATTT
1 A-AATAATTT
168564 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 4 0.15
22 8 0.31
23 14 0.54
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (22 bp):
AAATAATTTTTGAATAAAATTG
Found at i:172084 original size:6 final size:6
Alignment explanation
Indices: 172075--172111 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
172065 TCATCACTAT
172075 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC C
1 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC C
172112 ATCATTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CCTCTC
Found at i:173824 original size:16 final size:17
Alignment explanation
Indices: 173795--173830 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
173785 AGAAGGATTT
173795 TAATTTTAATTTTTATA
1 TAATTTTAATTTTTATA
173812 TAATTTT-ATTTTTATA
1 TAATTTTAATTTTTATA
173828 TAA
1 TAA
173831 ACAGACATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TAATTTTAATTTTTATA
Found at i:174990 original size:30 final size:31
Alignment explanation
Indices: 174943--175007 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
174933 AATAGTATAG
*
174943 TGACTTAAATAAAAACTTTTGAATCGTTCAA
1 TGACTTAAATAAAAACTTTTGAATAGTTCAA
* *
174974 TGACTTAAA-CAAAACTTTTGAATAGTTTAA
1 TGACTTAAATAAAAACTTTTGAATAGTTCAA
175004 TGAC
1 TGAC
175008 AATTTTGTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTGAATAGTTCAA
Found at i:179789 original size:105 final size:104
Alignment explanation
Indices: 179640--179879 Score: 322
Period size: 105 Copynumber: 2.3 Consensus size: 104
179630 ATTTCATTTA
** * *
179640 ATACTCACGATGACACATAGTCATTGGACCTCCTAATTCATAAAGGAATT-TTATACTCACAATG
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATTCATAAAGG-ATTCATATACTCACAATG
* * * *
179704 TCATATAGTCATCGGACCTCATAATCCGTAATAGGATTCAT
65 ACACATACTAATCGGACCTCATAATCCGTAA-AGGATTCAT
* * *
179745 ATACTCATGATGACACATAGTCATCAGACCTCATAA-TCTGTAAAGGATTCATATACTCACGATG
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATTC-ATAAAGGATTCATATACTCACAATG
179809 ACACATACTAATCGGACCTCATAATCCGTAAAGGATTCAT
65 ACACATACTAATCGGACCTCATAATCCGTAAAGGATTCAT
* *
179849 ATATTCACGATGACACATAGTCATCTGACCT
1 ATACTCACGATGACACATAGTCATCAGACCT
179880 TTTTCATTTA
Statistics
Matches: 119, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
104 42 0.35
105 77 0.65
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (104 bp):
ATACTCACGATGACACATAGTCATCAGACCTCATAATTCATAAAGGATTCATATACTCACAATGA
CACATACTAATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:179809 original size:52 final size:52
Alignment explanation
Indices: 179640--179879 Score: 320
Period size: 52 Copynumber: 4.6 Consensus size: 52
179630 ATTTCATTTA
* * * * *
179640 ATACTCACGATGACACATAGTCATTGGACCTCCTAATTCATAAAGGAATT-TT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGG-ATTCAT
* * *
179692 ATACTCACAATGTCATATAGTCATCGGACCTCATAATCCGTAATAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAA-AGGATTCAT
* * *
179745 ATACTCATGATGACACATAGTCATCAGACCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
179797 ATACTCACGATGACACATACTAATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
179849 ATATTCACGATGACACATAGTCATCTGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
179880 TTTTCATTTA
Statistics
Matches: 163, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
52 122 0.75
53 41 0.25
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:180536 original size:10 final size:10
Alignment explanation
Indices: 180521--180547 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
180511 AGTCCTTGCA
180521 TAAGCTAGAT
1 TAAGCTAGAT
180531 TAAGCTAGAT
1 TAAGCTAGAT
180541 TAAGCTA
1 TAAGCTA
180548 ATACGGACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.30
Consensus pattern (10 bp):
TAAGCTAGAT
Found at i:182437 original size:52 final size:52
Alignment explanation
Indices: 182354--182635 Score: 387
Period size: 52 Copynumber: 5.5 Consensus size: 52
182344 ATTTCATTTA
* * *
182354 ATACTCACGATGACACATAGTCATC-AGACCTCTTAATTCGTAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGA-ACCTCATAATCCGTAAAGGATTCAT
* * *
182406 ATACGCACGATGTCACATAGTCATCGAACCTCATAATTCGTAATAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAA-AGGATTCAT
*
182459 ATACTCACGATGACATATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
* * *
182511 ATACTCGCGATGACACATAGTAAT-TAGACCTCATAATCCGTAAAGGATTC--
1 ATACTCACGATGACACATAGTCATCGA-ACCTCATAATCCGTAAAGGATTCAT
* *
182561 ATA--CACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
182611 ATACTCACGATGACACATAGTCATC
1 ATACTCACGATGACACATAGTCATC
182636 AGACCTTTTT
Statistics
Matches: 205, Mismatches: 17, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
48 39 0.19
50 6 0.03
51 1 0.00
52 111 0.54
53 48 0.23
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
Found at i:182610 original size:100 final size:103
Alignment explanation
Indices: 182353--182641 Score: 388
Period size: 105 Copynumber: 2.8 Consensus size: 103
182343 CATTTCATTT
* * * * *
182353 AATACTCACGATGACACATAGTCATCAGACCTCTTAATTCGTAAAGGAATCATATACGCACGATG
1 AATAC-CACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGATG
* * *
182418 TCACATAGTCA-TCGAACCTCATAATTCGTAATAGGATTC
65 ACACATAGTCATTAG-ACCTCATAATCCGTAATAGGATTC
* * *
182457 ATATACTCACGATGACATATAGTCATCGAACCTCATAATCCGTAAAGGATTCATATACTCGCGAT
1 A-ATAC-CACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGAT
*
182522 GACACATAGTAATTAGACCTCATAATCCGTAA-AGGATTC
64 GACACATAGTCATTAGACCTCATAATCCGTAATAGGATTC
*
182561 -ATA-CACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCATATACTCACGATGA
1 AATACCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGATGA
*
182624 CACATAGTCATCAGACCT
66 CACATAGTCATTAGACCT
182642 TTTTCATTTA
Statistics
Matches: 165, Mismatches: 18, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
100 72 0.44
102 3 0.02
104 8 0.05
105 80 0.48
106 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AATACCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGATGA
CACATAGTCATTAGACCTCATAATCCGTAATAGGATTC
Found at i:194241 original size:24 final size:25
Alignment explanation
Indices: 194208--194258 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
194198 AGTCATTTGA
*
194208 AAAAGAAAAATGAGAAA-AAGGAAGA
1 AAAAGAAAAAAGA-AAAGAAGGAAGA
194233 AAAAG-AAAAAGAAAAGAAGGAA-A
1 AAAAGAAAAAAGAAAAGAAGGAAGA
194256 AAA
1 AAA
194259 TTATGATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 7 0.29
24 12 0.50
25 5 0.21
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (25 bp):
AAAAGAAAAAAGAAAAGAAGGAAGA
Found at i:194255 original size:15 final size:14
Alignment explanation
Indices: 194206--194257 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
194196 TCAGTCATTT
*
194206 GAAAAAGAAAAATG
1 GAAAAAGAAAAAAG
*
194220 AGAAAAAGGAAGAAAAA
1 -GAAAAA-GAA-AAAAG
194237 GAAAAAGAAAAGAAG
1 GAAAAAGAAAA-AAG
194252 GAAAAA
1 GAAAAA
194258 ATTATGATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 2 0.06
15 17 0.55
16 9 0.29
17 3 0.10
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (14 bp):
GAAAAAGAAAAAAG
Found at i:199195 original size:21 final size:21
Alignment explanation
Indices: 199165--199219 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
199155 TTTTAAAAAA
*
199165 GTCAATAATCAACAGTCAACG
1 GTCAACAATCAACAGTCAACG
*
199186 GTCAACAATCAACAGTTAACG
1 GTCAACAATCAACAGTCAACG
*
199207 GTCAACGATCAAC
1 GTCAACAATCAAC
199220 GGTCGGTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.18
Consensus pattern (21 bp):
GTCAACAATCAACAGTCAACG
Found at i:199242 original size:22 final size:22
Alignment explanation
Indices: 199215--199262 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
199205 CGGTCAACGA
* *
199215 TCAACGGTCGGTTAACAATCAG
1 TCAACGATCGGTAAACAATCAG
**
199237 TCAACGATCGGTAAACGGTCAG
1 TCAACGATCGGTAAACAATCAG
199259 TCAA
1 TCAA
199263 TGATTTGACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (22 bp):
TCAACGATCGGTAAACAATCAG
Found at i:199307 original size:15 final size:15
Alignment explanation
Indices: 199289--199322 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
199279 GGGTTTGGAC
199289 TTGGTTCAATTGGGT
1 TTGGTTCAATTGGGT
199304 TTGGTTCAATTGGGT
1 TTGGTTCAATTGGGT
199319 TTGG
1 TTGG
199323 GCTTAATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.12, C:0.06, G:0.35, T:0.47
Consensus pattern (15 bp):
TTGGTTCAATTGGGT
Found at i:205366 original size:17 final size:17
Alignment explanation
Indices: 205344--205377 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
205334 ATCCAAAATC
205344 AAAAT-AATAATAATAAA
1 AAAATAAATAAT-ATAAA
205361 AAAATAAATAATATAAA
1 AAAATAAATAATATAAA
205378 TTTGTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATAAATAATATAAA
Found at i:206444 original size:7 final size:7
Alignment explanation
Indices: 206432--206483 Score: 68
Period size: 7 Copynumber: 7.4 Consensus size: 7
206422 TTCAAAAAAA
206432 GTCAACG
1 GTCAACG
206439 GTCAACG
1 GTCAACG
* *
206446 ATTAACG
1 GTCAACG
*
206453 GTCAATG
1 GTCAACG
206460 GTCAACG
1 GTCAACG
*
206467 ATCAACG
1 GTCAACG
206474 GTCAACG
1 GTCAACG
206481 GTC
1 GTC
206484 GATCAATGGT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:206462 original size:21 final size:21
Alignment explanation
Indices: 206432--206483 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
206422 TTCAAAAAAA
*
206432 GTCAACGGTCAACGATTAACG
1 GTCAACGGTCAACGATCAACG
*
206453 GTCAATGGTCAACGATCAACG
1 GTCAACGGTCAACGATCAACG
206474 GTCAACGGTC
1 GTCAACGGTC
206484 GATCAATGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (21 bp):
GTCAACGGTCAACGATCAACG
Found at i:206547 original size:15 final size:15
Alignment explanation
Indices: 206527--206560 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
206517 GGGTTTGGAC
206527 TTGGTTCAATTCGGT
1 TTGGTTCAATTCGGT
*
206542 TTGGTTCAATTGGGT
1 TTGGTTCAATTCGGT
206557 TTGG
1 TTGG
206561 GCTTAATGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.09, G:0.32, T:0.47
Consensus pattern (15 bp):
TTGGTTCAATTCGGT
Found at i:208301 original size:30 final size:30
Alignment explanation
Indices: 208265--208432 Score: 121
Period size: 30 Copynumber: 5.7 Consensus size: 30
208255 CCATAGATAT
*
208265 CCACAAAGGCATCTCATATAACTGAATCAA
1 CCACAAAGGCATCTCATATAACTGATTCAA
208295 CCACAAAGGC-TCTCATATAACAT-ATTTC-A
1 CCACAAAGGCATCTCATATAAC-TGA-TTCAA
* * *
208324 CCACAAAGGTATCACATATAACAGATTCAA
1 CCACAAAGGCATCTCATATAACTGATTCAA
* * ** **
208354 CCACAAAGACTTAACATATAA-TGGATTCTG
1 CCACAAAGGCATCTCATATAACT-GATTCAA
* * * **
208384 CCACAAGGGCATCACTTATAACAAATTCAA
1 CCACAAAGGCATCTCATATAACTGATTCAA
* *
208414 CCACATAGGC-TTTCATATA
1 CCACAAAGGCATCTCATATA
208433 TCAAAATTAG
Statistics
Matches: 106, Mismatches: 25, Indels: 15
0.73 0.17 0.10
Matches are distributed among these distances:
29 31 0.29
30 75 0.71
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.24
Consensus pattern (30 bp):
CCACAAAGGCATCTCATATAACTGATTCAA
Found at i:208357 original size:59 final size:58
Alignment explanation
Indices: 208265--208432 Score: 167
Period size: 60 Copynumber: 2.8 Consensus size: 58
208255 CCATAGATAT
* * * *
208265 CCACAAAGGCATCTCATATAACTGAATCAACCACAAAGGCTCTCATATAACATATT-TCA
1 CCACAAAGGCATCACATATAACAGATTCAACCACAAAGGCT-TCATATAACAGATTCT-A
* * ** *
208324 CCACAAAGGTATCACATATAACAGATTCAACCACAAAGACTTAACATATAATGGATTCTG
1 CCACAAAGGCATCACATATAACAGATTCAACCACAAAGGCTT--CATATAACAGATTCTA
* * * *
208384 CCACAAGGGCATCACTTATAACAAATTCAACCACATAGGCTTTCATATA
1 CCACAAAGGCATCACATATAACAGATTCAACCACAAAGGC-TTCATATA
208433 TCAAAATTAG
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
58 1 0.01
59 42 0.47
60 44 0.49
61 3 0.03
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.24
Consensus pattern (58 bp):
CCACAAAGGCATCACATATAACAGATTCAACCACAAAGGCTTCATATAACAGATTCTA
Found at i:208437 original size:29 final size:28
Alignment explanation
Indices: 208400--208459 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
208390 GGGCATCACT
*
208400 TATAAC-AAATTCAACCACATAGGCTTTCA
1 TATAACAAAATT-AACCACAAAGGC-TTCA
* *
208429 TATATCAAAATTAGCCACAAAGGCTTCA
1 TATAACAAAATTAACCACAAAGGCTTCA
208457 TAT
1 TAT
208460 CGGTAAATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.26
29 15 0.56
30 5 0.19
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (28 bp):
TATAACAAAATTAACCACAAAGGCTTCA
Found at i:210891 original size:12 final size:12
Alignment explanation
Indices: 210874--210902 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
210864 TTATTAATTC
210874 TATTTATTTTAA
1 TATTTATTTTAA
210886 TATTTATTTTAA
1 TATTTATTTTAA
210898 TATTT
1 TATTT
210903 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTTATTTTAA
Found at i:213882 original size:20 final size:20
Alignment explanation
Indices: 213834--213888 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
213824 TTATTTAAAA
* *
213834 CCCTGTATGCACTTCGATGC
1 CCCTGTATGCACTACGATAC
* * *
213854 CTCTATATGCACTACGGTAC
1 CCCTGTATGCACTACGATAC
213874 CCCTGTATGCACTAC
1 CCCTGTATGCACTAC
213889 AATGCCCTCG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.35, G:0.16, T:0.29
Consensus pattern (20 bp):
CCCTGTATGCACTACGATAC
Found at i:216384 original size:29 final size:29
Alignment explanation
Indices: 216351--216410 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
216341 TAGGAATAGG
*
216351 AAATTCCATTAGGATATCTTAGGTTAATT
1 AAATTCCATTAGGATATCTTAAGTTAATT
* * *
216380 AAATTCCATTAGGTTCTTTTAAGTTAATT
1 AAATTCCATTAGGATATCTTAAGTTAATT
216409 AA
1 AA
216411 TTTAATTAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (29 bp):
AAATTCCATTAGGATATCTTAAGTTAATT
Found at i:216815 original size:15 final size:15
Alignment explanation
Indices: 216795--216823 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
216785 GTGTGTTAAC
216795 TTTTAATTATTTTTA
1 TTTTAATTATTTTTA
216810 TTTTAATTATTTTT
1 TTTTAATTATTTTT
216824 GTTATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTAATTATTTTTA
Found at i:216819 original size:9 final size:9
Alignment explanation
Indices: 216795--216849 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
216785 GTGTGTTAAC
216795 TTTTAATTA
1 TTTTAATTA
216804 -TTT--TTA
1 TTTTAATTA
216810 TTTTAATTA
1 TTTTAATTA
**
216819 TTTTTGTTA
1 TTTTAATTA
216828 TTTTTAATTA
1 -TTTTAATTA
216838 -TTTAATTA
1 TTTTAATTA
216846 TTTT
1 TTTT
216850 TAGATACCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
6 3 0.08
7 3 0.08
8 11 0.30
9 13 0.35
10 7 0.19
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTTAATTA
Found at i:218619 original size:17 final size:17
Alignment explanation
Indices: 218594--218627 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
218584 AAATCACCTC
*
218594 AATACCATATTATGCAA
1 AATACCATAATATGCAA
*
218611 AATATCATAATATGCAA
1 AATACCATAATATGCAA
218628 TAATTAAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (17 bp):
AATACCATAATATGCAA
Done.