Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007388.1 Kokia drynarioides strain JFW-HI SEQ_122006, 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: 159069
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:7728 original size:158 final size:158
Alignment explanation
Indices: 7440--7765 Score: 447
Period size: 158 Copynumber: 2.1 Consensus size: 158
7430 AACATCTTTG
** * *
7440 TATCATGTGGTGCTCACACGAGCTGTGGAATGAGTCTGCTCACATGAGCTGTGAGTCGAGATATT
1 TATCATGTAATGCTCACACGAGCTGTGGAATGAGTCTGCTCACACGAGCTGTGAGTCAAGATATT
* * *
7505 AAGCTACACAATGCTGCTCACACGAGCTGTGGAGAATCCGCAACATATGTCGAATCTCAGCCATC
66 AAGCTACACAATGATACTCACACGAGCTGTGGAGAATCCGCAACATATGTCGAACCTCAGCCATC
*
7570 GGTACGACATCTAAGACCAGCACCCATA
131 GGTAAGACATCTAAGACCAGCACCCATA
* * * * *
7598 TATCATGTAATGCTCACATGAGTTGT-GAAGTGGGTCTGCTCACACGAGCTGTGGGTCAAGATGT
1 TATCATGTAATGCTCACACGAGCTGTGGAA-TGAGTCTGCTCACACGAGCTGTGAGTCAAGATAT
* * * * *
7662 TAAGCTATACGATGATACTCATACGAGTTGTGGAGAATCCGCAACATATGTCGGACCTCAGCCAT
65 TAAGCTACACAATGATACTCACACGAGCTGTGGAGAATCCGCAACATATGTCGAACCTCAGCCAT
* * *
7727 CGGTAAGACATCTAAGACTAGCACTCATG
130 CGGTAAGACATCTAAGACCAGCACCCATA
7756 TATCATGTAA
1 TATCATGTAA
7766 ATCTTGAAAT
Statistics
Matches: 146, Mismatches: 21, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
157 3 0.02
158 143 0.98
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.25
Consensus pattern (158 bp):
TATCATGTAATGCTCACACGAGCTGTGGAATGAGTCTGCTCACACGAGCTGTGAGTCAAGATATT
AAGCTACACAATGATACTCACACGAGCTGTGGAGAATCCGCAACATATGTCGAACCTCAGCCATC
GGTAAGACATCTAAGACCAGCACCCATA
Found at i:11099 original size:24 final size:24
Alignment explanation
Indices: 11072--11135 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
11062 GTAATCAGAT
11072 TTTAATTGGGAAAAGATAACAAAG
1 TTTAATTGGGAAAAGATAACAAAG
**
11096 TTTAATTGGGAAATTATAACAAAG
1 TTTAATTGGGAAAAGATAACAAAG
11120 TTTAATTGGGAAAAGA
1 TTTAATTGGGAAAAGA
11136 AACTTGATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (24 bp):
TTTAATTGGGAAAAGATAACAAAG
Found at i:21375 original size:2 final size:2
Alignment explanation
Indices: 21368--21397 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21358 CTCCAAAATA
21368 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
21398 CAACCACTTA
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:23127 original size:20 final size:20
Alignment explanation
Indices: 23102--23148 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
23092 ATTTAGTGTT
23102 GGAGCCACGTTAAGGTCCAA
1 GGAGCCACGTTAAGGTCCAA
23122 GGAGCCACGTTAAGGTCCAA
1 GGAGCCACGTTAAGGTCCAA
23142 GGAGCCA
1 GGAGCCA
23149 TGACCCACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.26, G:0.32, T:0.13
Consensus pattern (20 bp):
GGAGCCACGTTAAGGTCCAA
Found at i:23651 original size:25 final size:26
Alignment explanation
Indices: 23613--23662 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
23603 TACAATGATA
* *
23613 TATATAAAGAATTTATGTAATAAATT
1 TATATAAAGAATTTATATAACAAATT
23639 TATA-AAAGAATTTATATAACAAAT
1 TATATAAAGAATTTATATAACAAAT
23663 AAATGTTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (26 bp):
TATATAAAGAATTTATATAACAAATT
Found at i:25034 original size:2 final size:2
Alignment explanation
Indices: 24975--25022 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
24965 TAGAAATTTA
24975 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25017 AT AT AT
1 AT AT AT
25023 TAAGGAATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30462 original size:21 final size:21
Alignment explanation
Indices: 30422--30475 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 21
30412 TATAATAAAA
*
30422 TAAAAATATTGAAAAAAATATTTCT
1 TAAAAA-ATTGAAAATAA-A-TT-T
30447 TAAAAAATTGAAAATAAATTT
1 TAAAAAATTGAAAATAAATTT
30468 TAAAAAAT
1 TAAAAAAT
30476 ATGTATACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 9 0.32
22 2 0.07
23 1 0.04
24 10 0.36
25 6 0.21
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (21 bp):
TAAAAAATTGAAAATAAATTT
Found at i:44612 original size:102 final size:103
Alignment explanation
Indices: 44419--44618 Score: 244
Period size: 102 Copynumber: 2.0 Consensus size: 103
44409 GTGAATTGCT
** * * * *
44419 GGTGGACATGGCAAAATACTTTAAATGGCTTTTGGCAAAAGCTCCTTTCTATCTATTGGCAAAAT
1 GGTGGACATGGCAAAATACTTTAAATAACTTTTGGCAAAAGCTCCTTCCAATCTACTGACAAAAT
* **
44484 ATCCAGTGACCCTTATAGAGGGGTGTTTGATGTCTAAG
66 ATCCAGTGACCCTTATAAAGAAGTGTTTGATGTCTAAG
* *
44522 GGTGGACATGG-AAAATACTTTGAATAACTTTTGG-AAAATGCTCCTTCCAATCTACTGACACAA
1 GGTGGACATGGCAAAATACTTTAAATAACTTTTGGCAAAA-GCTCCTTCCAATCTACTGACAAAA
* *
44585 TATCTATTGATCCC-TATAAAGAAGTGTTTGATGT
65 TATCCAGTGA-CCCTTATAAAGAAGTGTTTGATGT
44619 AAGACCTATG
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
101 4 0.05
102 64 0.78
103 14 0.17
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (103 bp):
GGTGGACATGGCAAAATACTTTAAATAACTTTTGGCAAAAGCTCCTTCCAATCTACTGACAAAAT
ATCCAGTGACCCTTATAAAGAAGTGTTTGATGTCTAAG
Found at i:55530 original size:18 final size:17
Alignment explanation
Indices: 55507--55540 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
55497 ATGCTTTAAT
55507 AATAATAATAACAACAAC
1 AATAATAATAA-AACAAC
55525 AATAATAATAAAACAA
1 AATAATAATAAAACAA
55541 TTTTTTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.18
Consensus pattern (17 bp):
AATAATAATAAAACAAC
Found at i:58643 original size:2 final size:2
Alignment explanation
Indices: 58638--58684 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
58628 TCCATATATA
58638 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
58680 TG TG T
1 TG TG T
58685 AAAATTGACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:65712 original size:30 final size:31
Alignment explanation
Indices: 65650--65712 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 31
65640 ACGTCGTTTC
* *
65650 TATTTTGGTCACTTTAAATTGTTTTTTGTTAAT
1 TATTTTGATCACTTTAAA-T-TTTTTTATTAAT
65683 TATTTTGATCACTTTAAA-TTTTTTATTAAT
1 TATTTTGATCACTTTAAATTTTTTTATTAAT
65713 CCGTTAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 11 0.39
33 17 0.61
ACGTcount: A:0.25, C:0.06, G:0.08, T:0.60
Consensus pattern (31 bp):
TATTTTGATCACTTTAAATTTTTTTATTAAT
Found at i:66072 original size:24 final size:23
Alignment explanation
Indices: 66026--66077 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
66016 GCAAAAGAAA
*
66026 AAAAAAAACTCAAAATTTCCTTT
1 AAAAAAAACTCAAAATTTACTTT
* *
66049 AAAAAAACCTTAAAATCTTACTTT
1 AAAAAAAACTCAAAAT-TTACTTT
*
66073 CAAAA
1 AAAAA
66078 TCACCCTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAAAAAACTCAAAATTTACTTT
Found at i:70333 original size:19 final size:20
Alignment explanation
Indices: 70311--70357 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
70301 TATAATTTTA
* *
70311 TTTTGTTATTATTTTCAT-T
1 TTTTGTTATGATTTTAATAT
*
70330 TTTTGTCATGATTTTAATAT
1 TTTTGTTATGATTTTAATAT
70350 TTTT-TTAT
1 TTTTGTTAT
70358 AAATGGTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.70
Consensus pattern (20 bp):
TTTTGTTATGATTTTAATAT
Found at i:70727 original size:30 final size:30
Alignment explanation
Indices: 70691--70752 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
70681 GTAACTTAAC
* * *
70691 AACAAATGCCTCTAAAATAGTAATAAAATT
1 AACAAATGCATCTAAAATAATAACAAAATT
70721 AACAAATGCATCTAAAATAATAACAAAATT
1 AACAAATGCATCTAAAATAATAACAAAATT
70751 AA
1 AA
70753 TAATAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.58, C:0.13, G:0.05, T:0.24
Consensus pattern (30 bp):
AACAAATGCATCTAAAATAATAACAAAATT
Found at i:70807 original size:11 final size:11
Alignment explanation
Indices: 70793--70819 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
70783 CAATAACAAC
70793 AAAATAATAGT
1 AAAATAATAGT
70804 AAAATAATAGT
1 AAAATAATAGT
70815 AAAAT
1 AAAAT
70820 TGTAACAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (11 bp):
AAAATAATAGT
Found at i:70851 original size:22 final size:20
Alignment explanation
Indices: 70823--70875 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
70813 GTAAAATTGT
70823 AACAAAATAGCGATGAAACAAA
1 AACAAAATAGC-ATGAAA-AAA
* *
70845 AAGAAAATAGCATTAAAAAA
1 AACAAAATAGCATGAAAAAA
70865 AACAAAA-AGCA
1 AACAAAATAGCA
70876 ATTTTTTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 9 0.32
21 5 0.18
22 10 0.36
ACGTcount: A:0.68, C:0.11, G:0.11, T:0.09
Consensus pattern (20 bp):
AACAAAATAGCATGAAAAAA
Found at i:70872 original size:21 final size:22
Alignment explanation
Indices: 70826--70872 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
70816 AAATTGTAAC
*
70826 AAAATAGCGATGAAACAAAAAG
1 AAAATAGCGATGAAACAAAAAA
*
70848 AAAATAGC-ATTAAA-AAAAACA
1 AAAATAGCGATGAAACAAAAA-A
70869 AAAA
1 AAAA
70873 GCAATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.70, C:0.09, G:0.11, T:0.11
Consensus pattern (22 bp):
AAAATAGCGATGAAACAAAAAA
Found at i:76964 original size:16 final size:16
Alignment explanation
Indices: 76943--76974 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
76933 TAAGTCCTTT
76943 TTATTTAACCACAACC
1 TTATTTAACCACAACC
76959 TTATTTAACCACAACC
1 TTATTTAACCACAACC
76975 CATTTCTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (16 bp):
TTATTTAACCACAACC
Found at i:94497 original size:19 final size:19
Alignment explanation
Indices: 94460--94497 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
94450 GTTGTTGGTA
*
94460 GGTGTCTATTATTGTAATT
1 GGTGTCTATTATTGGAATT
94479 GGTGT-TATTACTTGGAATT
1 GGTGTCTATTA-TTGGAATT
94498 TCTATTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.05, G:0.24, T:0.50
Consensus pattern (19 bp):
GGTGTCTATTATTGGAATT
Found at i:108485 original size:15 final size:15
Alignment explanation
Indices: 108465--108503 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
108455 GCACATCAAA
*
108465 CAAGAATTAATATAT
1 CAAGAATTAATAAAT
*
108480 CAAGAA-TACTAAAT
1 CAAGAATTAATAAAT
108494 CAAGAATTAA
1 CAAGAATTAA
108504 GCACACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (15 bp):
CAAGAATTAATAAAT
Found at i:108911 original size:25 final size:23
Alignment explanation
Indices: 108883--108928 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
108873 GTTGGATCCA
108883 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
108908 AATTAAATCTAAATAATAATT
1 AATTAAATCTAAAAAATAATT
108929 CCCTAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:110667 original size:26 final size:29
Alignment explanation
Indices: 110604--110669 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
110594 AAAATTGACC
*
110604 TATTTTTGTAATTAATCTGTATGTTACAT
1 TATTTTTGTAATTAACCTGTATGTTACAT
* *
110633 TATTTTTGTATTTAACCT-T-T-TTATAT
1 TATTTTTGTAATTAACCTGTATGTTACAT
110659 TATTTTTGTAA
1 TATTTTTGTAA
110670 AAGCCGCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 15 0.45
27 1 0.03
28 1 0.03
29 16 0.48
ACGTcount: A:0.26, C:0.06, G:0.08, T:0.61
Consensus pattern (29 bp):
TATTTTTGTAATTAACCTGTATGTTACAT
Found at i:112580 original size:47 final size:47
Alignment explanation
Indices: 112511--112609 Score: 180
Period size: 47 Copynumber: 2.1 Consensus size: 47
112501 TAGAGTAGAA
*
112511 TTGAAACTAAAAGATGCATCAATTGATACAATAACATCACATTAAGC
1 TTGAAACTAAAAGATGCATCAATTGATACAATAACATCACATTAACC
*
112558 TTGAAACTAAAAGATGCATCAATTGATATAATAACATCACATTAACC
1 TTGAAACTAAAAGATGCATCAATTGATACAATAACATCACATTAACC
112605 TTGAA
1 TTGAA
112610 TATCAGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.27
Consensus pattern (47 bp):
TTGAAACTAAAAGATGCATCAATTGATACAATAACATCACATTAACC
Found at i:112583 original size:22 final size:22
Alignment explanation
Indices: 112509--112583 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
112499 ATTAGAGTAG
112509 AATTGAAACTAAAAGATGCATC
1 AATTGAAACTAAAAGATGCATC
* * * *
112531 AATTGATAC-AATAACATCACATT
1 AATTGAAACTAA-AAGAT-GCATC
112554 AAGCTTGAAACTAAAAGATGCATC
1 AA--TTGAAACTAAAAGATGCATC
112578 AATTGA
1 AATTGA
112584 TATAATAACA
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
21 2 0.05
22 16 0.40
23 5 0.12
24 5 0.12
25 10 0.25
26 2 0.05
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.25
Consensus pattern (22 bp):
AATTGAAACTAAAAGATGCATC
Found at i:114757 original size:10 final size:11
Alignment explanation
Indices: 114741--114765 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
114731 CACAGCTGAT
114741 TTTTTTTTTTG
1 TTTTTTTTTTG
114752 TTTTTTTTTTG
1 TTTTTTTTTTG
114763 TTT
1 TTT
114766 CTTTCTCGCT
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:120518 original size:96 final size:96
Alignment explanation
Indices: 120341--120525 Score: 230
Period size: 96 Copynumber: 1.9 Consensus size: 96
120331 GAAAAGGATG
* ** * *
120341 TTCGATTATCTCGATTTGAAGAAAGGTTGCATCTAGTAAGTTAAGGCGCAAATTTTTAGAATCTA
1 TTCGATTATCTCGATCTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTTAGAAACTA
* *
120406 AGATAAGGAAACATTGCCTCGATTAAGGGTA
66 AAATAAAGAAACATTGCCTCGATTAAGGGTA
* * * *
120437 TTCGATTATTTCGATCTGAATAAAAATTTCACCTAGTAAGTTAAGGCGCAAA-TTTTCGAAACTC
1 TTCGATTATCTCGATCTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTTAGAAACT-
*
120501 AAAATAAA-AGAATATTGCCTCGATT
65 AAAATAAAGA-AACATTGCCTCGATT
120526 TTAAAGTTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
95 10 0.13
96 65 0.87
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (96 bp):
TTCGATTATCTCGATCTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTTAGAAACTA
AAATAAAGAAACATTGCCTCGATTAAGGGTA
Found at i:120922 original size:29 final size:27
Alignment explanation
Indices: 120889--121112 Score: 123
Period size: 29 Copynumber: 7.8 Consensus size: 27
120879 AAAATGAAAA
* *
120889 TTTTGGACATTCTGTGGTAAAAGGGTAAT
1 TTTTGGA-ATTTTGGGGTAAAA-GGTAAT
*
120918 TTTTGAGAGTTTTGGGGTCAAAATGG-AAT
1 TTTTG-GAATTTTGGGGT-AAAA-GGTAAT
*
120947 TTTTGGAAGTTTTGGGGTAAAATGTAAT
1 TTTTGGAA-TTTTGGGGTAAAAGGTAAT
*
120975 TTTTGGAAGTTTTGAGGTCAAAAATGG-AAT
1 TTTTGGAA-TTTTGGGGT--AAAA-GGTAAT
* * * *
121005 TTTTAGAAGTTTAGGGTAAAAATGTAAT
1 TTTTGGAATTTTGGGGT-AAAAGGTAAT
* *
121033 TTTTGAAAGTTTTAGGGTCAAAATGG-AAT
1 TTTTGGAA-TTTTGGGGT-AAAA-GGTAAT
* * *
121062 TTTTGGAAGTTCGAGGGTAAAAAAGTAA-
1 TTTTGGAATTTTG-GGGT-AAAAGGTAAT
*
121090 TTTTGGAAGTTTTAGGGTTAAAA
1 TTTTGGAA-TTTT-GGGGTAAAA
121113 ATGGAATTTT
Statistics
Matches: 154, Mismatches: 27, Indels: 29
0.73 0.13 0.14
Matches are distributed among these distances:
27 2 0.01
28 55 0.36
29 72 0.47
30 24 0.16
31 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.38
Consensus pattern (27 bp):
TTTTGGAATTTTGGGGTAAAAGGTAAT
Found at i:120966 original size:58 final size:57
Alignment explanation
Indices: 120904--121162 Score: 281
Period size: 58 Copynumber: 4.5 Consensus size: 57
120894 GACATTCTGT
**
120904 GGTAAAAGGGTAATTTTTGAGAGTTTTGGGGTCAAAATGGAATTTTTGGAAGTTTTGG
1 GGTAAAAATGTAATTTTTGAGAGTTTTGGGGTCAAAATGGAATTTTTGGAAG-TTTGG
* * *
120962 GGT-AAAATGTAATTTTTG-GAAGTTTTGAGGTCAAAAATGGAATTTTTAGAAGTTTAG
1 GGTAAAAATGTAATTTTTGAG-AGTTTTGGGGTC-AAAATGGAATTTTTGGAAGTTTGG
* * *
121019 GGTAAAAATGTAATTTTTGAAAGTTTTAGGGTCAAAATGGAATTTTTGGAAGTTCGAG
1 GGTAAAAATGTAATTTTTGAGAGTTTTGGGGTCAAAATGGAATTTTTGGAAGTTTG-G
* * * * *
121077 GGTAAAAAAGTAATTTTGGA-AGTTTTAGGGTTAAAAATGGAATTTTGGAGAAGTTTGG
1 GGTAAAAATGTAATTTTTGAGAGTTTT-GGGGTCAAAATGGAATTTTTG-GAAGTTTGG
* * *
121135 GGGATAAAATATAATTTTTAGATAGTTT
1 GGTA-AAAATGTAATTTTT-GAGAGTTT
121163 AAGGATCTTC
Statistics
Matches: 169, Mismatches: 22, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
56 1 0.01
57 57 0.34
58 86 0.51
59 18 0.11
60 2 0.01
61 5 0.03
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.37
Consensus pattern (57 bp):
GGTAAAAATGTAATTTTTGAGAGTTTTGGGGTCAAAATGGAATTTTTGGAAGTTTGG
Found at i:121113 original size:29 final size:29
Alignment explanation
Indices: 120915--121132 Score: 239
Period size: 29 Copynumber: 7.5 Consensus size: 29
120905 GTAAAAGGGT
* *
120915 AATTTTT-GAGAGTTTTGGGGTCAAAATGG
1 AATTTTTGGA-AGTTTTAGGGTAAAAATGG
* *
120944 AATTTTTGGAAGTTTTGGGGT-AAAATGT
1 AATTTTTGGAAGTTTTAGGGTAAAAATGG
120972 AATTTTTGGAAGTTTT-GAGGTCAAAAATGG
1 AATTTTTGGAAGTTTTAG-GGT-AAAAATGG
* *
121002 AATTTTTAGAAG-TTTAGGGTAAAAATGT
1 AATTTTTGGAAGTTTTAGGGTAAAAATGG
* *
121030 AATTTTTGAAAGTTTTAGGGTCAAAATGG
1 AATTTTTGGAAGTTTTAGGGTAAAAATGG
** * *
121059 AATTTTTGGAAGTTCGAGGGTAAAAAAGT
1 AATTTTTGGAAGTTTTAGGGTAAAAATGG
121088 AA-TTTTGGAAGTTTTAGGGTTAAAAATGG
1 AATTTTTGGAAGTTTTAGGG-TAAAAATGG
*
121117 AATTTTGGAGAAGTTT
1 AATTTTTG-GAAGTTT
121133 GGGGGATAAA
Statistics
Matches: 161, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
27 1 0.01
28 57 0.35
29 72 0.45
30 24 0.15
31 7 0.04
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.38
Consensus pattern (29 bp):
AATTTTTGGAAGTTTTAGGGTAAAAATGG
Found at i:122972 original size:6 final size:6
Alignment explanation
Indices: 122961--123044 Score: 70
Period size: 6 Copynumber: 14.7 Consensus size: 6
122951 TAATTCAAAA
* * *
122961 TAAATT TAAATT TAAA-A TAAATT TAAATT CAACA-- TGAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAA-ATT TAAATT TAAATT
* * *
123007 TAAA-T TAAATT CAAATT TAAA-C TAAATT AAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
123045 AATTAAAAGT
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
4 1 0.02
5 14 0.23
6 44 0.73
7 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (6 bp):
TAAATT
Found at i:122972 original size:17 final size:17
Alignment explanation
Indices: 122942--123045 Score: 118
Period size: 17 Copynumber: 6.1 Consensus size: 17
122932 TTTTATTATT
* * *
122942 AATAATTTTTAATTCAA
1 AATAAATTTAAATTTAA
122959 AATAAATTTAAATTTAA
1 AATAAATTTAAATTTAA
*
122976 AATAAATTTAAATTCAA
1 AATAAATTTAAATTTAA
* *
122993 CATGAATTTAAATTTAA
1 AATAAATTTAAATTTAA
* *
123010 ATTAAATTCAAATTTAA
1 AATAAATTTAAATTTAA
* *
123027 ACTAAATTAAAATTTAA
1 AATAAATTTAAATTTAA
123044 AA
1 AA
123046 ATTAAAAGTT
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 73 1.00
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (17 bp):
AATAAATTTAAATTTAA
Found at i:128011 original size:90 final size:90
Alignment explanation
Indices: 127880--128131 Score: 263
Period size: 90 Copynumber: 2.8 Consensus size: 90
127870 TTTGCAACTT
** * * *
127880 TGGTGGTTCATCCACAGATTTTCTGGCATCTTTTATTTGCAAATACGTTGTGCATTCACAACCAT
1 TGGTGGTTCATCCACCCATTTTCTGGCATCTCTAATCTGCAAATACGTTGTGCATTCACAACCAT
* *
127945 CTAGCAACGTTTTAACAAGCAACAC
66 CTGGCAACGTATTAACAAGCAACAC
* * *
127970 TGGTGGTTCATCCACCCATTTTCTGGTATCTCTAATCTGCAAGTACGTTATGCATTCACAACCAT
1 TGGTGGTTCATCCACCCATTTTCTGGCATCTCTAATCTGCAAATACGTTGTGCATTCACAACCAT
** ** *
128035 CTGGCAGTGTATTAACCTGTAACAC
66 CTGGCAACGTATTAACAAGCAACAC
* * ** * * * * * * *
128060 TGGTGGTTCCTCTACCCACATTCTGACAGCTGTCATCTG-TAATATGTTGTGTATTCACAACCAT
1 TGGTGGTTCATCCACCCATTTTCTGGCATCTCTAATCTGCAAATACGTTGTGCATTCACAACCAT
128124 CTGGCAAC
66 CTGGCAAC
128132 ACATTAACCT
Statistics
Matches: 131, Mismatches: 31, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
89 26 0.20
90 105 0.80
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (90 bp):
TGGTGGTTCATCCACCCATTTTCTGGCATCTCTAATCTGCAAATACGTTGTGCATTCACAACCAT
CTGGCAACGTATTAACAAGCAACAC
Found at i:129620 original size:24 final size:24
Alignment explanation
Indices: 129588--129633 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
129578 ATATATAATA
129588 TATAAAAAATTTAAAAAA-ATTTGT
1 TATAAAAAA-TTAAAAAATATTTGT
129612 TATAAAAAATTAAAAAATATTT
1 TATAAAAAATTAAAAAATATTT
129634 AAATTTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
TATAAAAAATTAAAAAATATTTGT
Found at i:130701 original size:22 final size:23
Alignment explanation
Indices: 130676--130762 Score: 99
Period size: 22 Copynumber: 3.8 Consensus size: 23
130666 ATTATATTGT
130676 TGTTTTGG-TGCTGTTTTTTTAC
1 TGTTTTGGTTGCTGTTTTTTTAC
* *
130698 TGTTTTGGTTACT-ATTTTTTAC
1 TGTTTTGGTTGCTGTTTTTTTAC
*
130720 TGTTTTGGTGTTGTTGTTTTTTTAC
1 TGTTTT-G-GTTGCTGTTTTTTTAC
*
130745 TGTTTT-GATGCTGTTTTT
1 TGTTTTGGTTGCTGTTTTT
130763 ACTGTTATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
22 32 0.59
23 4 0.07
24 4 0.07
25 14 0.26
ACGTcount: A:0.07, C:0.07, G:0.21, T:0.66
Consensus pattern (23 bp):
TGTTTTGGTTGCTGTTTTTTTAC
Found at i:130759 original size:25 final size:25
Alignment explanation
Indices: 130712--130759 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
130702 TTGGTTACTA
* *
130712 TTTTTTACTGTTTTGGTGTTGTTGT
1 TTTTTTACTGTTTTGATGCTGTTGT
130737 TTTTTTACTGTTTTGATGCTGTT
1 TTTTTTACTGTTTTGATGCTGTT
130760 TTTACTGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.06, C:0.06, G:0.21, T:0.67
Consensus pattern (25 bp):
TTTTTTACTGTTTTGATGCTGTTGT
Found at i:132517 original size:22 final size:22
Alignment explanation
Indices: 132492--132546 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
132482 TTAGCTTTAT
132492 AACCCTAATTTAT-AAATACTAA
1 AACCCTAATTTATAAAATA-TAA
* *
132514 AACCCTAA-TAATAAAATATCA
1 AACCCTAATTTATAAAATATAA
132535 AACCCTAATTTA
1 AACCCTAATTTA
132547 ACAAACCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (22 bp):
AACCCTAATTTATAAAATATAA
Found at i:132843 original size:68 final size:68
Alignment explanation
Indices: 132751--132897 Score: 233
Period size: 68 Copynumber: 2.2 Consensus size: 68
132741 GTTCAACTAG
* * *
132751 ACGCATTTTTCCTTAGCTCTCTGAGCTGGAAGCGCTTTATTAG-TCAAGGGAAAAAAGCGTTGAG
1 ACGCGTTTTTCCTTAGCACGCTGAGCTGGAAGCGCTTTATT-GTTCAAGGGAAAAAAGCGTTGAG
132815 CTAA
65 CTAA
*
132819 ACGCGTTTTTCCTTAGCACGCTGAGTTGGAAGCGCTTTATTGTTCAAGGGAAAAAAGCGTTGAGC
1 ACGCGTTTTTCCTTAGCACGCTGAGCTGGAAGCGCTTTATTGTTCAAGGGAAAAAAGCGTTGAGC
*
132884 TAG
66 TAA
132887 ACGCGTTTTTC
1 ACGCGTTTTTC
132898 TGAATTTCCC
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 1 0.01
68 72 0.99
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (68 bp):
ACGCGTTTTTCCTTAGCACGCTGAGCTGGAAGCGCTTTATTGTTCAAGGGAAAAAAGCGTTGAGC
TAA
Found at i:137103 original size:19 final size:19
Alignment explanation
Indices: 137079--137116 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
137069 TATATGATAT
137079 GCATACTTGAGCAAAAGCC
1 GCATACTTGAGCAAAAGCC
137098 GCATACTTGAGCAAAAGCC
1 GCATACTTGAGCAAAAGCC
137117 AACTAAAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.16
Consensus pattern (19 bp):
GCATACTTGAGCAAAAGCC
Found at i:139113 original size:29 final size:29
Alignment explanation
Indices: 139071--139128 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
139061 CTCACTACTG
*
139071 CACCTTTTTATGAAT-ATGTCATGCTTTGA
1 CACCTTCTTATGAATAAT-TCATGCTTTGA
*
139100 CACCTTCTTGTGAATAATTCATGCTTTGA
1 CACCTTCTTATGAATAATTCATGCTTTGA
139129 AGAAGCTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (29 bp):
CACCTTCTTATGAATAATTCATGCTTTGA
Found at i:147485 original size:19 final size:19
Alignment explanation
Indices: 147463--147503 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
147453 TAATGATATA
*
147463 ATAATTAATTTATACATTC
1 ATAATTAACTTATACATTC
*
147482 ATAATTTACTTATACATTC
1 ATAATTAACTTATACATTC
147501 ATA
1 ATA
147504 TTGATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.46
Consensus pattern (19 bp):
ATAATTAACTTATACATTC
Found at i:157030 original size:20 final size:20
Alignment explanation
Indices: 157005--157044 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
156995 TCATTTTATC
*
157005 TTTTTTAAAAATTAATTTTA
1 TTTTTTAAAAATTAAGTTTA
* *
157025 TTTTTTTATAATTAAGTTTA
1 TTTTTTAAAAATTAAGTTTA
157045 GTTGTTTTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTTTAAAAATTAAGTTTA
Found at i:158072 original size:22 final size:23
Alignment explanation
Indices: 158046--158088 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
158036 ATAAAGGAAA
158046 ACTTGAGATTTTAC-AGAAAATT
1 ACTTGAGATTTTACAAGAAAATT
* *
158068 ACTTGTGTTTTTACAAGAAAA
1 ACTTGAGATTTTACAAGAAAA
158089 ACCCATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (23 bp):
ACTTGAGATTTTACAAGAAAATT
Done.