Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012599.1 Kokia drynarioides strain JFW-HI SEQ_127608, 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: 123879
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:4783 original size:13 final size:13
Alignment explanation
Indices: 4765--4811 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
4755 TATAAAACTC
4765 TTCATATAACTAT
1 TTCATATAACTAT
* *
4778 TTCATATATCTTT
1 TTCATATAACTAT
4791 TTCCATATAAC-AT
1 TT-CATATAACTAT
*
4804 TTCGTATA
1 TTCATATA
4812 GTCATTTCGT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 5 0.18
13 16 0.57
14 7 0.25
ACGTcount: A:0.32, C:0.17, G:0.02, T:0.49
Consensus pattern (13 bp):
TTCATATAACTAT
Found at i:4819 original size:26 final size:27
Alignment explanation
Indices: 4767--4819 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
4757 TAAAACTCTT
*
4767 CATATAACTATTTCATATATCTTTTTC
1 CATATAACTATTTCATATATCTATTTC
*
4794 CATATAAC-ATTTCGTATAGTC-ATTTC
1 CATATAACTATTTCATATA-TCTATTTC
4820 GTATAACCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.30, C:0.19, G:0.04, T:0.47
Consensus pattern (27 bp):
CATATAACTATTTCATATATCTATTTC
Found at i:35796 original size:43 final size:43
Alignment explanation
Indices: 35650--35794 Score: 179
Period size: 43 Copynumber: 3.4 Consensus size: 43
35640 CCATCGAGTT
35650 ATAAGTTCTTCCATTTACAATAATCTTATGCTCTTAC-CGAGAC
1 ATAAG-TCTTCCATTTACAATAATCTTATGCTCTTACTCGAGAC
*
35693 ATAAGTTCTTCCATTTACAATATTCTTATGCTCTTACT-GAGAC
1 ATAAG-TCTTCCATTTACAATAATCTTATGCTCTTACTCGAGAC
* * * * *
35736 AAAAATCTTCCATTTATATATAATCTCATGCTCAT-CTCGAGAC
1 ATAAGTCTTCCATTTACA-ATAATCTTATGCTCTTACTCGAGAC
*
35779 ATGAGTCTTCCATTTA
1 ATAAGTCTTCCATTTA
35795 TACATCAAGT
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
42 14 0.16
43 75 0.84
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (43 bp):
ATAAGTCTTCCATTTACAATAATCTTATGCTCTTACTCGAGAC
Found at i:47212 original size:22 final size:21
Alignment explanation
Indices: 47186--47232 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 21
47176 TTTAATCATA
*
47186 TTTAATCGATGTTGTTGTTTT
1 TTTAATCGATATTGTTGTTTT
47207 GTTTAATCGATATTGTTGTTTT
1 -TTTAATCGATATTGTTGTTTT
47229 TTTA
1 TTTA
47233 TTCCTTCTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.17, C:0.04, G:0.17, T:0.62
Consensus pattern (21 bp):
TTTAATCGATATTGTTGTTTT
Found at i:49377 original size:159 final size:159
Alignment explanation
Indices: 48979--49429 Score: 613
Period size: 159 Copynumber: 2.8 Consensus size: 159
48969 AATGTCATCC
* * * * * * *
48979 TTTTTTGGCTTCTAGTTCTCATACTCGTACCAGACTGAGAAC-AATAATCAGAACCCAAATTAGA
1 TTTTTTGGGTTGTAGTTCTCGTACTCGTACCAGACTAAGAACAAAAAATCAAAACCAAAATTAGA
* * *
49043 TT-TAAATAATTTGGTATTGACAATGAGAAAGTGTTTATGATATACCTATGATCCAGTTGTGTTA
66 TTAT-TATAATTTGGAATTGACAATGAGAAAGTGTTTACGATATACCTATGATCCAGTTGTGTTA
*
49107 GGCTGAATAAATGGTGGTGCTTTGTCGTTCTT
130 GGCTGAATAAATGGTGGTGCTTTGTC--TATT
* * *
49139 TTTTTTGGGTTGTAGTTCTCGTACTCGTACCAAACTAAGACAAAAAAAATCAAAATCAAAATTAG
1 TTTTTTGGGTTGTAGTTCTCGTACTCGTACCAGACTAAGA-ACAAAAAATCAAAACCAAAATTAG
*
49204 ATTATTATAATTTGGAATTGACAATGAGAAAGTGTTTACGATATACCTATGATCCAATTGTGTTA
65 ATTATTATAATTTGGAATTGACAATGAGAAAGTGTTTACGATATACCTATGATCCAGTTGTGTTA
**
49269 GGCTGAATGCATGGTGGTG-TTCTGTC-ATT
130 GGCTGAATAAATGGTGGTGCTT-TGTCTATT
*
49298 TTTTTTGGGTTGTAGTTCTCGTACTCGTACCAGACAAAGATACAAAAAATCAAAACCAAAATTAG
1 TTTTTTGGGTTGTAGTTCTCGTACTCGTACCAGACTAAGA-ACAAAAAATCAAAACCAAAATTAG
* * * * *
49363 ATTATTATAGTTTGGAATTGACAATGAGAAAGTGTTTACAATATACCTGTGTTCCCGTTGTGTTA
65 ATTATTATAATTTGGAATTGACAATGAGAAAGTGTTTACGATATACCTATGATCCAGTTGTGTTA
49428 GG
130 GG
49430 ATCTTGTTTG
Statistics
Matches: 259, Mismatches: 28, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
159 123 0.47
160 35 0.14
161 3 0.01
162 97 0.37
163 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (159 bp):
TTTTTTGGGTTGTAGTTCTCGTACTCGTACCAGACTAAGAACAAAAAATCAAAACCAAAATTAGA
TTATTATAATTTGGAATTGACAATGAGAAAGTGTTTACGATATACCTATGATCCAGTTGTGTTAG
GCTGAATAAATGGTGGTGCTTTGTCTATT
Found at i:58881 original size:39 final size:39
Alignment explanation
Indices: 58832--58936 Score: 140
Period size: 39 Copynumber: 2.7 Consensus size: 39
58822 ACAGTAATCT
*
58832 TACCCGAACCCTCACCACCTCCCTGACCCAT-AACACCCA
1 TACCCGAACCCTCACCACCTCCCTCACCC-TCAACACCCA
* *
58871 TACCCAAACCCTCACCACCTCCCTCACCCTCAACACCCT
1 TACCCGAACCCTCACCACCTCCCTCACCCTCAACACCCA
* * *
58910 TACTCGAACCCTCACCTCCTCTCTCAC
1 TACCCGAACCCTCACCACCTCCCTCAC
58937 ACCACCTCCC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 1 0.02
39 57 0.98
ACGTcount: A:0.25, C:0.55, G:0.03, T:0.17
Consensus pattern (39 bp):
TACCCGAACCCTCACCACCTCCCTCACCCTCAACACCCA
Found at i:60717 original size:23 final size:23
Alignment explanation
Indices: 60691--60749 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
60681 AAAATCCAAA
*
60691 AAAT-CCCTAAATCTTTAAAACCT
1 AAATCCCCAAAAT-TTTAAAACCT
*
60714 AAATCCCCAAAATTTTGAAACCT
1 AAATCCCCAAAATTTTAAAACCT
* *
60737 AAAACCCAAAAAT
1 AAATCCCCAAAAT
60750 CCCAAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 24 0.77
24 7 0.23
ACGTcount: A:0.49, C:0.25, G:0.02, T:0.24
Consensus pattern (23 bp):
AAATCCCCAAAATTTTAAAACCT
Found at i:61017 original size:19 final size:21
Alignment explanation
Indices: 60995--61041 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
60985 GGGTAAATAT
60995 TTTATTGTTTTTAA-TTT-AA
1 TTTATTGTTTTTAACTTTAAA
61014 TTTA-TG-TTTTAACTTTAAA
1 TTTATTGTTTTTAACTTTAAA
*
61033 TTTTTTGTT
1 TTTATTGTT
61042 AACGTGGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
17 6 0.26
18 5 0.22
19 9 0.39
20 2 0.09
21 1 0.04
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.68
Consensus pattern (21 bp):
TTTATTGTTTTTAACTTTAAA
Found at i:61771 original size:7 final size:7
Alignment explanation
Indices: 61761--61800 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
61751 AAAATAAACA
*
61761 ATAATAG
1 ATAATAT
*
61768 ATAATAA
1 ATAATAT
61775 ATAATAT
1 ATAATAT
61782 ATAATAT
1 ATAATAT
61789 ATAATAT
1 ATAATAT
61796 ATAAT
1 ATAAT
61801 GCACTACTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (7 bp):
ATAATAT
Found at i:61827 original size:13 final size:15
Alignment explanation
Indices: 61809--61841 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
61799 ATGCACTACT
61809 ATTATTATA-TATA-
1 ATTATTATATTATAG
61822 ATTATTATATTATAG
1 ATTATTATATTATAG
61837 ATTAT
1 ATTAT
61842 AATAAAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 4 0.22
15 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
ATTATTATATTATAG
Found at i:63403 original size:20 final size:20
Alignment explanation
Indices: 63349--63403 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
63339 ATTTCCCAAC
63349 AAAAAGAAAAAGAAAAAATTG
1 AAAAAGAAAAA-AAAAAATTG
* * *
63370 AAAAATCAACAAAAAAGA-TG
1 AAAAA-GAAAAAAAAAAATTG
63390 AAAAAGAAAAAAAA
1 AAAAAGAAAAAAAA
63404 TGAAAAAAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 7 0.25
20 7 0.25
21 10 0.36
22 4 0.14
ACGTcount: A:0.78, C:0.04, G:0.11, T:0.07
Consensus pattern (20 bp):
AAAAAGAAAAAAAAAAATTG
Found at i:63414 original size:17 final size:16
Alignment explanation
Indices: 63349--63410 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 16
63339 ATTTCCCAAC
63349 AAAAA-GAAAAAG-AA
1 AAAAATGAAAAAGAAA
* *
63363 AAAATTGAAAAATCAACAA
1 AAAAATGAAAAA--GA-AA
63382 AAAAGATGAAAAAGAAA
1 AAAA-ATGAAAAAGAAA
63399 AAAAATGAAAAA
1 AAAAATGAAAAA
63411 AGAATTCAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 4 0.11
15 6 0.16
16 8 0.21
17 6 0.16
18 1 0.03
19 6 0.16
20 7 0.18
ACGTcount: A:0.77, C:0.03, G:0.11, T:0.08
Consensus pattern (16 bp):
AAAAATGAAAAAGAAA
Found at i:66070 original size:14 final size:14
Alignment explanation
Indices: 66051--66079 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
66041 CGGAGTTTCT
66051 TGGGGTTAGCTGGC
1 TGGGGTTAGCTGGC
66065 TGGGGTTAGCTGGC
1 TGGGGTTAGCTGGC
66079 T
1 T
66080 ACTACCGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.14, G:0.48, T:0.31
Consensus pattern (14 bp):
TGGGGTTAGCTGGC
Found at i:72097 original size:13 final size:14
Alignment explanation
Indices: 72069--72097 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
72059 TCAGTACATA
72069 GACATTTAACCTCT
1 GACATTTAACCTCT
72083 GACATTTAA-CTCT
1 GACATTTAACCTCT
72096 GA
1 GA
72098 TTACGTTGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (14 bp):
GACATTTAACCTCT
Found at i:75286 original size:31 final size:32
Alignment explanation
Indices: 75250--75309 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
75240 AGATTGCTCC
*
75250 CCCTTA-ATAAAAGTCATTTTCAATTTAAGCT
1 CCCTTATATAAAAATCATTTTCAATTTAAGCT
75281 CCCTTATATAAAAATCATTTTCAATTTAA
1 CCCTTATATAAAAATCATTTTCAATTTAA
75310 TGCATAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 6 0.22
32 21 0.78
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.40
Consensus pattern (32 bp):
CCCTTATATAAAAATCATTTTCAATTTAAGCT
Found at i:76437 original size:48 final size:48
Alignment explanation
Indices: 76360--76492 Score: 203
Period size: 48 Copynumber: 2.8 Consensus size: 48
76350 TATTTATGCT
* *
76360 TCATTAAGTGTTTTTTTTTGTTAAATGCATCTTTGTTTAATAATCTGCA
1 TCATTAAGTG-TTTTGTTTGTTAAATGCATCTTTGTTTAATAACCTGCA
*
76409 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAGTAACCTGCA
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAACCTGCA
* * *
76457 TTATTAACTATTTTGTTTGTTAAATGCATCTTTGTT
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTT
76493 AAATGCCTTG
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
48 68 0.87
49 10 0.13
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.53
Consensus pattern (48 bp):
TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAACCTGCA
Found at i:76505 original size:48 final size:47
Alignment explanation
Indices: 76371--76507 Score: 159
Period size: 48 Copynumber: 2.9 Consensus size: 47
76361 CATTAAGTGT
* ** * * *
76371 TTTTTTTTGTTAAATGCATCTTTGTTTAATAATCTGCATCATTAAGTG
1 TTTTGTTTGTTAAATGCATCTTTGTTTAATCCT-TGCATTATTAACTA
*
76419 TTTTGTTTGTTAAATGCATCTTTGTTTAGTAACC-TGCATTATTAACTA
1 TTTTGTTTGTTAAATGCATCTTTGTTTA--ATCCTTGCATTATTAACTA
*
76467 TTTTGTTTGTTAAATGCATCTTTGTTAAATGCCTTGCATTA
1 TTTTGTTTGTTAAATGCATCTTTGTTTAAT-CCTTGCATTA
76508 ATGCATCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
46 1 0.01
47 2 0.03
48 72 0.95
50 1 0.01
ACGTcount: A:0.24, C:0.12, G:0.13, T:0.51
Consensus pattern (47 bp):
TTTTGTTTGTTAAATGCATCTTTGTTTAATCCTTGCATTATTAACTA
Found at i:78920 original size:21 final size:21
Alignment explanation
Indices: 78891--78931 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
78881 GATACTTGAT
78891 AAAAAGTATCGATACTTTTTG
1 AAAAAGTATCGATACTTTTTG
* *
78912 AAAAGGTATTGATACTTTTT
1 AAAAAGTATCGATACTTTTT
78932 ATCATTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (21 bp):
AAAAAGTATCGATACTTTTTG
Found at i:85537 original size:31 final size:31
Alignment explanation
Indices: 85499--85562 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
85489 GAGATGAAGT
85499 AAAATTATATTGAGTGAACATATTTAACTCA
1 AAAATTATATTGAGTGAACATATTTAACTCA
85530 AAAATTATATTGAGTGAACATATTTAACTCA
1 AAAATTATATTGAGTGAACATATTTAACTCA
85561 AA
1 AA
85563 TGAATCAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.34
Consensus pattern (31 bp):
AAAATTATATTGAGTGAACATATTTAACTCA
Found at i:89304 original size:29 final size:29
Alignment explanation
Indices: 89257--89334 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
89247 TCCCTGTAAT
89257 TATTA-TATTATTTTAATTTAAT-CCTTTA
1 TATTATTATT-TTTTAATTTAATACCTTTA
*
89285 TATTATTATTTTTTAAATTT-GTACCTTTA
1 TATTATTATTTTTT-AATTTAATACCTTTA
* *
89314 TTTTTTTATTATTTTAATTTA
1 TATTATTATT-TTTTAATTTA
89335 GCCTTATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
28 10 0.24
29 28 0.67
30 4 0.10
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.65
Consensus pattern (29 bp):
TATTATTATTTTTTAATTTAATACCTTTA
Found at i:89516 original size:30 final size:32
Alignment explanation
Indices: 89446--89520 Score: 84
Period size: 30 Copynumber: 2.4 Consensus size: 32
89436 ATTATTTGTA
*
89446 TTTATTCATTTATTTTAGTATTTAATTTATAT
1 TTTATTCATTTATTATAGTATTTAATTTATAT
* * * *
89478 TTGA-TCATTT-TTATATTTTTTATTTTAT-T
1 TTTATTCATTTATTATAGTATTTAATTTATAT
89507 TTTATTCATTTATT
1 TTTATTCATTTATT
89521 TGTTATTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
29 4 0.11
30 20 0.57
31 8 0.23
32 3 0.09
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.69
Consensus pattern (32 bp):
TTTATTCATTTATTATAGTATTTAATTTATAT
Found at i:89530 original size:30 final size:30
Alignment explanation
Indices: 89446--89532 Score: 81
Period size: 30 Copynumber: 2.8 Consensus size: 30
89436 ATTATTTGTA
*
89446 TTTATTCATTTATTTTAGTATTTAATTTATAT
1 TTTATTCATTTATTTT--TATTTATTTTATAT
* *
89478 TTGA-TCATTT-TTATATTTTTTATTTTAT-T
1 TTTATTCATTTATT-T-TTATTTATTTTATAT
89507 TTTATTCATTTATTTGTTATTTATTT
1 TTTATTCATTTATTT-TTATTTATTT
89533 CCTATGCCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
29 4 0.09
30 28 0.62
31 9 0.20
32 4 0.09
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.70
Consensus pattern (30 bp):
TTTATTCATTTATTTTTATTTATTTTATAT
Found at i:89743 original size:22 final size:20
Alignment explanation
Indices: 89709--89748 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
89699 TTATCACTAC
*
89709 TATTTTTTATTTATTTGTGT
1 TATTTTTTATTTAATTGTGT
89729 TATTTGTTGTATTTAATTGT
1 TATTT-TT-TATTTAATTGT
89749 ATTTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 2 0.12
22 10 0.59
ACGTcount: A:0.17, C:0.00, G:0.12, T:0.70
Consensus pattern (20 bp):
TATTTTTTATTTAATTGTGT
Found at i:89795 original size:26 final size:26
Alignment explanation
Indices: 89746--89795 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
89736 TGTATTTAAT
* *
89746 TGTATTTATTTATTTTATTCTATTCA
1 TGTATGTATTTATTTTATTATATTCA
* *
89772 TGTATGTATTTTTTTTTTTATATT
1 TGTATGTATTTATTTTATTATATT
89796 TTTCCATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.70
Consensus pattern (26 bp):
TGTATGTATTTATTTTATTATATTCA
Found at i:95485 original size:13 final size:12
Alignment explanation
Indices: 95465--95494 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
95455 AAAATTTCAC
95465 AAAAAAAAAAAG
1 AAAAAAAAAAAG
95477 AAAAGAAAAAAAG
1 AAAA-AAAAAAAG
95490 AAAAA
1 AAAAA
95495 GGAGAGGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:97968 original size:60 final size:60
Alignment explanation
Indices: 97875--98039 Score: 251
Period size: 60 Copynumber: 2.7 Consensus size: 60
97865 GTTCAATGAC
* *
97875 TGTGTCATCGTGAGTATT-AATGAAATGAATCCTTTACGGATTATATGGTCTGATGACTA
1 TGTGTCATCGTGAGTATTAAATGAAATGAATCCTTTACGGATTATAAGGTCCGATGACTA
*
97934 TGTTTCATCGTGAGTATTAAATGAAATGAATCCTTTACGGATTATAAGGTCCGATGACTA
1 TGTGTCATCGTGAGTATTAAATGAAATGAATCCTTTACGGATTATAAGGTCCGATGACTA
* *
97994 TGTGTCATCGTGACTATTAAATGAGAAATAAATCCTATTACGGATT
1 TGTGTCATCGTGAGTATTAAAT--GAAATGAATCCT-TTACGGATT
98040 GAAGTTTGGT
Statistics
Matches: 96, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
59 17 0.18
60 59 0.61
62 11 0.11
63 9 0.09
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.36
Consensus pattern (60 bp):
TGTGTCATCGTGAGTATTAAATGAAATGAATCCTTTACGGATTATAAGGTCCGATGACTA
Found at i:100007 original size:74 final size:74
Alignment explanation
Indices: 99878--100024 Score: 258
Period size: 74 Copynumber: 2.0 Consensus size: 74
99868 CCTGCTACGG
* *
99878 ATGCGGAAGTGCAGATCATTTTCTGAGAAACTGTCCGATGAAATCTAAAGTAAAAGAGGATCAAA
1 ATGCGGAAGTGCAAATCATTTTCTGAGAAACTGTCCGATGAAATCTAAAGCAAAAGAGGATCAAA
99943 GTGTAAAAT
66 GTGTAAAAT
* *
99952 ATGCGGAAGTGCAAATCATTTTCTGAGAAATTGTCCGATGAAATCTGAAGCAAAAGAGGATCAAA
1 ATGCGGAAGTGCAAATCATTTTCTGAGAAACTGTCCGATGAAATCTAAAGCAAAAGAGGATCAAA
100017 GTGTAAAA
66 GTGTAAAA
100025 CCTCCTTTTA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.24
Consensus pattern (74 bp):
ATGCGGAAGTGCAAATCATTTTCTGAGAAACTGTCCGATGAAATCTAAAGCAAAAGAGGATCAAA
GTGTAAAAT
Found at i:108596 original size:32 final size:32
Alignment explanation
Indices: 108560--108622 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
108550 AGCTAAAATT
* *
108560 AATTAGCTGATTAATGTGTTTCAGGTACATGA
1 AATTAGCTGATTAATATATTTCAGGTACATGA
108592 AATTAGCTGATTAATATATTTCAGGTACATG
1 AATTAGCTGATTAATATATTTCAGGTACATG
108623 TATGGATGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (32 bp):
AATTAGCTGATTAATATATTTCAGGTACATGA
Found at i:116150 original size:62 final size:61
Alignment explanation
Indices: 115987--116184 Score: 213
Period size: 60 Copynumber: 3.2 Consensus size: 61
115977 TCATCGTAAG
* * * *
115987 TAAAT-GAAAGGAATCCTTTACGGATTACATGGTCCGATGACTATGTTTCATCATGAGTAT
1 TAAATGGAAATGAATCCTTTACGGATTACAAGGTCCGATGACTATGTGTCATCGTGAGTAT
* * *
116047 TAAAT-GAAATGATTCCTTCACGGATTATAAGGTCCGATGACTATGTGTCATCGTGAGTAT
1 TAAATGGAAATGAATCCTTTACGGATTACAAGGTCCGATGACTATGTGTCATCGTGAGTAT
* * * * * *
116107 TAAATGAGAAATGAATCCTATTACAGATTA-AAGGTCTGATGACTCTATGTCATTGTGAGTTAC
1 TAAATG-GAAATGAATCCT-TTACGGATTACAAGGTCCGATGACTATGTGTCATCGTGAG-TAT
*
116170 CAAATGCGAAATGAA
1 TAAATG-GAAATGAA
116185 ACCAACCTCG
Statistics
Matches: 117, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
60 58 0.50
62 36 0.31
63 23 0.20
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (61 bp):
TAAATGGAAATGAATCCTTTACGGATTACAAGGTCCGATGACTATGTGTCATCGTGAGTAT
Found at i:118035 original size:25 final size:25
Alignment explanation
Indices: 117986--118200 Score: 205
Period size: 25 Copynumber: 8.6 Consensus size: 25
117976 ACAGAGTTTA
* * * *
117986 GCTCTTACGAGCCTAGATAAAACATC
1 GCTCTTATGAGCC-AGACAGAATATC
* * * *
118012 GCTTTTATGAGCCAGTCAGAACATT
1 GCTCTTATGAGCCAGACAGAATATC
* *
118037 GCTCTTACGAGCCAGACAGAAGATC
1 GCTCTTATGAGCCAGACAGAATATC
* *
118062 GCTCTTATGAACCAGATAGAATATC
1 GCTCTTATGAGCCAGACAGAATATC
* * *
118087 ACTCTTACGAGCCAAACAGAATATC
1 GCTCTTATGAGCCAGACAGAATATC
* *
118112 GCTCTTGTGATCCAGACAGAATATC
1 GCTCTTATGAGCCAGACAGAATATC
* * *
118137 GCTCTTGTGAACCAAACAGAATATC
1 GCTCTTATGAGCCAGACAGAATATC
* * *
118162 GCTCTTACGAGCCAAACAGAATATT
1 GCTCTTATGAGCCAGACAGAATATC
*
118187 GCTCTTATAAGCCA
1 GCTCTTATGAGCCA
118201 ATCTTTAGTA
Statistics
Matches: 156, Mismatches: 33, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
25 145 0.93
26 11 0.07
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
GCTCTTATGAGCCAGACAGAATATC
Found at i:118107 original size:75 final size:75
Alignment explanation
Indices: 118028--118193 Score: 242
Period size: 75 Copynumber: 2.2 Consensus size: 75
118018 ATGAGCCAGT
* * *
118028 CAGAACATTGCTCTTACGAGCCAGACAGAAGATCGCTCTTATGAACCAGATAGAATATCACTCTT
1 CAGAATATTGCTCTTACGAGCCAGACAGAAGATCGCTCTTATGAACCAAACAGAATATCACTCTT
118093 ACGAGCCAAA
66 ACGAGCCAAA
* ** * * * *
118103 CAGAATATCGCTCTTGTGATCCAGACAGAATATCGCTCTTGTGAACCAAACAGAATATCGCTCTT
1 CAGAATATTGCTCTTACGAGCCAGACAGAAGATCGCTCTTATGAACCAAACAGAATATCACTCTT
118168 ACGAGCCAAA
66 ACGAGCCAAA
118178 CAGAATATTGCTCTTA
1 CAGAATATTGCTCTTA
118194 TAAGCCAATC
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 79 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (75 bp):
CAGAATATTGCTCTTACGAGCCAGACAGAAGATCGCTCTTATGAACCAAACAGAATATCACTCTT
ACGAGCCAAA
Found at i:119714 original size:14 final size:15
Alignment explanation
Indices: 119695--119727 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
119685 ACTAACTTCT
*
119695 AATTCACTAATT-AA
1 AATTCACCAATTGAA
119709 AATTCACCAATTGAA
1 AATTCACCAATTGAA
119724 AATT
1 AATT
119728 TTCATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.33
Consensus pattern (15 bp):
AATTCACCAATTGAA
Found at i:123472 original size:46 final size:46
Alignment explanation
Indices: 123414--123516 Score: 170
Period size: 46 Copynumber: 2.2 Consensus size: 46
123404 CAACAAAATA
* *
123414 TCATCCTTATCACTATACGTGTTAGCTTCAAAAAGAAGAAGAGATG
1 TCATACTTATCACTATACGTGTCAGCTTCAAAAAGAAGAAGAGATG
*
123460 TCATACTTATCACTATACGTGTCAGCTTCAAAAAGATGAAGAGATG
1 TCATACTTATCACTATACGTGTCAGCTTCAAAAAGAAGAAGAGATG
*
123506 TCATGCTTATC
1 TCATACTTATC
123517 CCGGCACTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (46 bp):
TCATACTTATCACTATACGTGTCAGCTTCAAAAAGAAGAAGAGATG
Done.