Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012681.1 Kokia drynarioides strain JFW-HI SEQ_127692, 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: 127815
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4767 original size:14 final size:14
Alignment explanation
Indices: 4730--4759 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4720 TTATCTTTAA
*
4730 TTTATATTTATCTT
1 TTTACATTTATCTT
4744 TTTACATTTATCTT
1 TTTACATTTATCTT
4758 TT
1 TT
4760 AGAGTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTACATTTATCTT
Found at i:6261 original size:23 final size:23
Alignment explanation
Indices: 6233--6358 Score: 153
Period size: 23 Copynumber: 5.5 Consensus size: 23
6223 AGTGCTGGGG
6233 AAACAGTAAGCACACACAGTGCA
1 AAACAGTAAGCACACACAGTGCA
* *
6256 AAACAGCAGGCACACACAGTGCA
1 AAACAGTAAGCACACACAGTGCA
*
6279 AAACAGTAAGCACACACAGTACA
1 AAACAGTAAGCACACACAGTGCA
* * * * *
6302 AATCAGTAAGCACATATAGTACG
1 AAACAGTAAGCACACACAGTGCA
* *
6325 AATCAGTAAGCACACACAGTGCT
1 AAACAGTAAGCACACACAGTGCA
*
6348 GAACAGTAAGC
1 AAACAGTAAGC
6359 GCGCTAATGT
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 88 1.00
ACGTcount: A:0.45, C:0.25, G:0.18, T:0.12
Consensus pattern (23 bp):
AAACAGTAAGCACACACAGTGCA
Found at i:11639 original size:35 final size:35
Alignment explanation
Indices: 11593--11663 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
11583 TGTGGAGCTG
11593 AACTACCTCTTGCAGACTGTTCAGTAGTATTCTCC
1 AACTACCTCTTGCAGACTGTTCAGTAGTATTCTCC
11628 AACTACCTCTTGCAGACTGTTCAGTAGTATTCTCC
1 AACTACCTCTTGCAGACTGTTCAGTAGTATTCTCC
11663 A
1 A
11664 TCAATCTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (35 bp):
AACTACCTCTTGCAGACTGTTCAGTAGTATTCTCC
Found at i:13666 original size:23 final size:23
Alignment explanation
Indices: 13533--13681 Score: 194
Period size: 23 Copynumber: 6.5 Consensus size: 23
13523 AAGTGCTGGG
*
13533 AAACAGTAAGCACACACAATGC-
1 AAACAGTAAGCACACACAGTGCT
* * *
13555 AAATCAGTAGGCACACACATTGCA
1 AAA-CAGTAAGCACACACAGTGCT
13579 AAACAGTAAGCACACACAGTG-T
1 AAACAGTAAGCACACACAGTGCT
13601 AAATCAGTAAGCACACACAGTGCT
1 AAA-CAGTAAGCACACACAGTGCT
* *
13625 GAACAGTAAGTACACACAGTGCT
1 AAACAGTAAGCACACACAGTGCT
*
13648 AAACAATAAGCACACACAGTGCT
1 AAACAGTAAGCACACACAGTGCT
*
13671 GAACAGTAAGC
1 AAACAGTAAGC
13682 GCGCTAATGT
Statistics
Matches: 111, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
22 6 0.05
23 99 0.89
24 6 0.05
ACGTcount: A:0.44, C:0.24, G:0.17, T:0.14
Consensus pattern (23 bp):
AAACAGTAAGCACACACAGTGCT
Found at i:18923 original size:16 final size:18
Alignment explanation
Indices: 18902--18934 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
18892 ATTGTCATGT
18902 AGTAAAA-AT-ATTAAAA
1 AGTAAAATATAATTAAAA
18918 AGTAAAATATAATTAAA
1 AGTAAAATATAATTAAA
18935 TAATCAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (18 bp):
AGTAAAATATAATTAAAA
Found at i:19002 original size:108 final size:111
Alignment explanation
Indices: 18863--19063 Score: 259
Period size: 108 Copynumber: 1.8 Consensus size: 111
18853 TTTTAAACTT
* * *
18863 TAAAAACACTTAAATATAGCTGATGAGATATTGTCATGTAGT-AAAAA-T-ATT-AAAAAGTAAA
1 TAAAAACACTTAAATATAGCTAATGAAATATTGTCATGCAGTAAAAAATTAATTAAAAAAGTAAA
18924 ATATAATTAAATAATCAAAACATAAAAAAACCCAAAATTTGAAATTC
66 ATATAATTAAATAATCAAAAC-TAAAAAAACCCAAAATTTGAAATTC
* * *
18971 TAAAAACACTTAAATTTA-ATCAATGAAATATTTTCATGCAGTAAAAAATTAAATTAAAAAAGTA
1 TAAAAACACTTAAATATAGCT-AATGAAATATTGTCATGCAGTAAAAAATT-AATTAAAAAAGTA
* * *
19035 AATTGTAATTAAATAATTAAAACTAAAAA
64 AAATATAATTAAATAATCAAAACTAAAAA
19064 GGATCATGGC
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
107 1 0.01
108 34 0.44
109 5 0.06
110 1 0.01
112 9 0.12
113 28 0.36
ACGTcount: A:0.56, C:0.08, G:0.07, T:0.29
Consensus pattern (111 bp):
TAAAAACACTTAAATATAGCTAATGAAATATTGTCATGCAGTAAAAAATTAATTAAAAAAGTAAA
ATATAATTAAATAATCAAAACTAAAAAAACCCAAAATTTGAAATTC
Found at i:20001 original size:31 final size:29
Alignment explanation
Indices: 19942--20022 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 29
19932 TGTTTTAGTC
*
19942 TAATTTAGTACTCAAACTTGACACTTTTTCT
1 TAATTTAGTACT-AAACTTTACACTTTTT-T
19973 TAATTTAGTATCTAAACTTTACGA-TTTTTT
1 TAATTTAGTA-CTAAACTTTAC-ACTTTTTT
* *
20003 TAAATTGGTACCTAAACTTT
1 TAATTTAGTA-CTAAACTTT
20023 TTGGGATCCA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
30 18 0.41
31 23 0.52
32 3 0.07
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.47
Consensus pattern (29 bp):
TAATTTAGTACTAAACTTTACACTTTTTT
Found at i:27839 original size:80 final size:80
Alignment explanation
Indices: 27706--27860 Score: 240
Period size: 80 Copynumber: 1.9 Consensus size: 80
27696 GGTGCAAAAC
* *
27706 CGTTGATTAATCCAAATAGAGCTGGGCTCACTTATTGCGGTTTATTCGCTAGGCA-CTAGGTGCC
1 CGTTGATTAATCCAAATAGAGCTGGGCTCACTTATCGCGGTTTATCCGCTAGGCATCT-GGTGCC
27770 ATGAATTGACGGATTT
65 ATGAATTGACGGATTT
* * * *
27786 CGTTGGTTAATCCAACTAGAGCTGGGCTCCCTTATCGTGGTTTATCCGCTAGGCATCTGGTGCCA
1 CGTTGATTAATCCAAATAGAGCTGGGCTCACTTATCGCGGTTTATCCGCTAGGCATCTGGTGCCA
27851 TGAATTGACG
66 TGAATTGACG
27861 AACTTGGTTA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
80 66 0.97
81 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (80 bp):
CGTTGATTAATCCAAATAGAGCTGGGCTCACTTATCGCGGTTTATCCGCTAGGCATCTGGTGCCA
TGAATTGACGGATTT
Found at i:28962 original size:59 final size:59
Alignment explanation
Indices: 28870--28990 Score: 224
Period size: 59 Copynumber: 2.1 Consensus size: 59
28860 AATTCCCTAG
*
28870 TTTCCTATGTGGTTTGCTAATTACTCGAAAATGATCCATGAATGATTATAATGTTTGCA
1 TTTCCTATGTGGTTTGATAATTACTCGAAAATGATCCATGAATGATTATAATGTTTGCA
*
28929 TTTCCTATGTGGTTTGATAATTACTCGAAAATGATCCATGAATGATTGTAATGTTTGCA
1 TTTCCTATGTGGTTTGATAATTACTCGAAAATGATCCATGAATGATTATAATGTTTGCA
28988 TTT
1 TTT
28991 GGAATTTGTG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.42
Consensus pattern (59 bp):
TTTCCTATGTGGTTTGATAATTACTCGAAAATGATCCATGAATGATTATAATGTTTGCA
Found at i:29729 original size:13 final size:13
Alignment explanation
Indices: 29713--29757 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
29703 TTTAAATTAA
* *
29713 ACTTTTTAAAAGT
1 ACTTTTCAAAATT
*
29726 ACTTCTCAAAATT
1 ACTTTTCAAAATT
29739 ACTTTTCAAAATT
1 ACTTTTCAAAATT
29752 ACTTTT
1 ACTTTT
29758 TTAAAAACAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.36, C:0.16, G:0.02, T:0.47
Consensus pattern (13 bp):
ACTTTTCAAAATT
Found at i:42505 original size:19 final size:19
Alignment explanation
Indices: 42468--42510 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
42458 TGATACAAAT
*
42468 TATTTTTAATTAGTATTTA
1 TATTTTTAATTAATATTTA
*
42487 -ATTTTATAATTAATTTTTA
1 TATTTT-TAATTAATATTTA
42506 TATTT
1 TATTT
42511 GTTTTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 5 0.25
19 11 0.55
20 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TATTTTTAATTAATATTTA
Found at i:43825 original size:59 final size:61
Alignment explanation
Indices: 43715--43842 Score: 154
Period size: 59 Copynumber: 2.1 Consensus size: 61
43705 TTAATATAAT
* * * ** *
43715 ATTTGGTATTTGTGAACTTAACATTTTTTTCTAATTTGGTACTTAAATTTTTTTCTATCTA
1 ATTTGGTATTTGTGAACTTAACAATTTTTTCTAATTTAGTACCTAAATTTTTTTAAATCCA
* *
43776 ATTTGGTA-TT-TGAACTTGACAATTTTTT-TAATTTAGTACCTATATTTTTTTTAAATCCA
1 ATTTGGTATTTGTGAACTTAACAATTTTTTCTAATTTAGTACCTA-AATTTTTTTAAATCCA
43835 ATTTGGTA
1 ATTTGGTA
43843 CCTAAACTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 12 0.21
59 36 0.62
60 2 0.03
61 8 0.14
ACGTcount: A:0.27, C:0.09, G:0.10, T:0.54
Consensus pattern (61 bp):
ATTTGGTATTTGTGAACTTAACAATTTTTTCTAATTTAGTACCTAAATTTTTTTAAATCCA
Found at i:44111 original size:58 final size:57
Alignment explanation
Indices: 44048--44156 Score: 148
Period size: 58 Copynumber: 1.9 Consensus size: 57
44038 AATAATATTA
* *
44048 AAAAAAATTAATTA-TCAAATTAAAAAAAATAATCAAGTTCAAGTACCAAATTGGATCC
1 AAAAAAATTAAGTACT-AAATTAAAAAAAAT-ATCAAATTCAAGTACCAAATTGGATCC
* * *
44106 AAAAAATTTAAGTACTAAGTTAAAAAAAATATCAAATTTAAGTACCAAATT
1 AAAAAAATTAAGTACTAAATTAAAAAAAATATCAAATTCAAGTACCAAATT
44157 AAAAAAATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
57 19 0.42
58 25 0.56
59 1 0.02
ACGTcount: A:0.56, C:0.10, G:0.06, T:0.28
Consensus pattern (57 bp):
AAAAAAATTAAGTACTAAATTAAAAAAAATATCAAATTCAAGTACCAAATTGGATCC
Found at i:44170 original size:29 final size:30
Alignment explanation
Indices: 44109--44171 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
44099 TGGATCCAAA
* *
44109 AAATTTAAGTACTAAGTTAAAAAAAATATC
1 AAATTTAAGTACCAAATTAAAAAAAATATC
44139 AAATTTAAGTACCAAATT-AAAAAAATATC
1 AAATTTAAGTACCAAATTAAAAAAAATATC
44168 AAAT
1 AAAT
44172 ATTATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.29
Consensus pattern (30 bp):
AAATTTAAGTACCAAATTAAAAAAAATATC
Found at i:61434 original size:26 final size:28
Alignment explanation
Indices: 61376--61427 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 28
61366 GAATTAATTA
61376 ATAATATTATAAAAATATAAACATCAAT
1 ATAATATTATAAAAATATAAACATCAAT
*
61404 ATAATA-TA-AAAAAT-TAAATATCAA
1 ATAATATTATAAAAATATAAACATCAA
61428 ATTTAATCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 9 0.39
26 6 0.26
27 2 0.09
28 6 0.26
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (28 bp):
ATAATATTATAAAAATATAAACATCAAT
Found at i:67694 original size:3 final size:3
Alignment explanation
Indices: 67686--67710 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
67676 TCCCAATTTC
67686 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
67711 TTTTAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:83284 original size:55 final size:55
Alignment explanation
Indices: 83140--83347 Score: 162
Period size: 55 Copynumber: 3.8 Consensus size: 55
83130 TTTGATCATT
* * * * * *
83140 ACCTAAAAAATATTTTTTCATCTAAAAAAAAAGTGATGATCATGGCTTGAC-A-A
1 ACCTCAAAAATATTTTTTTATCTATAAAAAGAGTGATGATCATGACTTAACAAGA
* * * ** * *
83193 ACACT---AATTTTTTTTTTATTTGATAAAAAGAGTGATGATCATGACTTGGCCATA
1 AC-CTCAAAAATATTTTTTTATCT-ATAAAAAGAGTGATGATCATGACTTAACAAGA
* * *
83247 ACC-CAAAAAATATTTTTTTATCTA-AAAAAGAAGTGATGGTTATGACTTAACAAGC
1 ACCTC-AAAAATATTTTTTTATCTATAAAAAG-AGTGATGATCATGACTTAACAAGA
*
83302 ACCTCAAAAATA-TTTTTTATCATATAAAAAGAGTGTTGATCATGAC
1 ACCTCAAAAATATTTTTTTATC-TATAAAAAGAGTGATGATCATGAC
83348 ATAGACGACA
Statistics
Matches: 122, Mismatches: 21, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
51 12 0.10
52 24 0.20
53 4 0.03
54 20 0.16
55 42 0.34
56 20 0.16
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (55 bp):
ACCTCAAAAATATTTTTTTATCTATAAAAAGAGTGATGATCATGACTTAACAAGA
Found at i:85085 original size:22 final size:21
Alignment explanation
Indices: 85045--85085 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
85035 GTTTTATCTT
* *
85045 ATACCAAATGTTTTCGAGTTA
1 ATACCAAATATTTTAGAGTTA
85066 ATACCAAATTATTTTAGAGT
1 ATACCAAA-TATTTTAGAGT
85086 GTTTAAGTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (21 bp):
ATACCAAATATTTTAGAGTTA
Found at i:86180 original size:2 final size:2
Alignment explanation
Indices: 86173--86216 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
86163 GATGAGCTCG
* * *
86173 TA TA TA TA -A TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
86214 TA T
1 TA T
86217 TTTCAAAGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:87917 original size:21 final size:19
Alignment explanation
Indices: 87892--87931 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
87882 TAACTCAAAA
87892 TAATCATCTTACTTACTCATT
1 TAATCATCTTA-TTA-TCATT
87913 TAATCATCTTATTATCATT
1 TAATCATCTTATTATCATT
87932 GTATTCGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 3 0.16
21 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (19 bp):
TAATCATCTTATTATCATT
Found at i:96185 original size:6 final size:6
Alignment explanation
Indices: 96174--96200 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
96164 AAGTGAAGGA
96174 GAATGG GAATGG GAATGG GAATGG GAA
1 GAATGG GAATGG GAATGG GAATGG GAA
96201 ATTGTAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.48, T:0.15
Consensus pattern (6 bp):
GAATGG
Found at i:96318 original size:13 final size:13
Alignment explanation
Indices: 96300--96324 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
96290 AATTTAGCAT
96300 TGTTTTTAAAAAG
1 TGTTTTTAAAAAG
96313 TGTTTTTAAAAA
1 TGTTTTTAAAAA
96325 ATTTAGTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TGTTTTTAAAAAG
Found at i:101166 original size:30 final size:31
Alignment explanation
Indices: 101126--101183 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
101116 TTGATAAAAT
101126 TAAAGGATAAG-ATTAA-ATCCATAATTTTTA
1 TAAAGGATAAGAATTAATA-CCATAATTTTTA
*
101156 TAAAGTATAAGAATTAATACCATAATTT
1 TAAAGGATAAGAATTAATACCATAATTT
101184 AACCTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 10 0.40
31 14 0.56
32 1 0.04
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (31 bp):
TAAAGGATAAGAATTAATACCATAATTTTTA
Found at i:101179 original size:31 final size:30
Alignment explanation
Indices: 101126--101183 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
101116 TTGATAAAAT
101126 TAAAGGATAAGATTAAATCCATAATTTTTA
1 TAAAGGATAAGATTAAATCCATAATTTTTA
*
101156 TAAAGTATAAGAATT-AATACCATAATTT
1 TAAAGGATAAG-ATTAAAT-CCATAATTT
101184 AACCTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (30 bp):
TAAAGGATAAGATTAAATCCATAATTTTTA
Found at i:107582 original size:20 final size:20
Alignment explanation
Indices: 107554--107610 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
107544 TCACATCAAC
*
107554 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
107574 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
107594 AAATTA--TTAAAATTATT
1 AAATTATTTTAAAATTATT
107611 TTTTTGAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 6 0.19
17 2 0.06
18 1 0.03
20 13 0.41
21 2 0.06
22 8 0.25
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:107605 original size:29 final size:31
Alignment explanation
Indices: 107563--107635 Score: 123
Period size: 29 Copynumber: 2.4 Consensus size: 31
107553 CAAATGATTT
107563 TAAAATTATTAAAATTA-TTTTTTAAAAT-A
1 TAAAATTATTAAAATTATTTTTTTAAAATAA
*
107592 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATTAAAATTATTTTTTTAAAATAA
107623 TAAAATTATTAAA
1 TAAAATTATTAAA
107636 TAATTTTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 17 0.41
30 10 0.24
31 14 0.34
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (31 bp):
TAAAATTATTAAAATTATTTTTTTAAAATAA
Found at i:107642 original size:30 final size:29
Alignment explanation
Indices: 107563--107642 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 29
107553 CAAATGATTT
*
107563 TAAAATTATTAAA-ATTATTTTTTAAAATA
1 TAAAATTATTAAATAAT-TTTTTTAAAATA
* *
107592 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATT-AAATAATTTTTTTAAAAT-A
107623 TAAAATTATTAAATAATTTT
1 TAAAATTATTAAATAATTTT
107643 AATTTCCAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
29 10 0.23
30 22 0.50
31 12 0.27
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
TAAAATTATTAAATAATTTTTTTAAAATA
Found at i:108147 original size:19 final size:19
Alignment explanation
Indices: 108125--108169 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
108115 TTATATTAGG
108125 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
108144 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
108163 ATTTAAT
1 ATTTAAT
108170 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:109010 original size:22 final size:22
Alignment explanation
Indices: 108970--109029 Score: 88
Period size: 21 Copynumber: 2.8 Consensus size: 22
108960 TTCGACTTCC
*
108970 CTATTTTCTATT-TTTTTAATT
1 CTATTTTCTTTTATTTTTAATT
108991 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTATTTTTAATT
*
109013 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTATTTTT
109030 CCTTAGATCG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 25 0.69
22 11 0.31
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (22 bp):
CTATTTTCTTTTATTTTTAATT
Found at i:109367 original size:14 final size:14
Alignment explanation
Indices: 109348--109374 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
109338 AGTTCCAATT
109348 TTTTTATTTTTTTA
1 TTTTTATTTTTTTA
109362 TTTTTATTTTTTT
1 TTTTTATTTTTTT
109375 GCAGGTGAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTATTTTTTTA
Found at i:119232 original size:3 final size:3
Alignment explanation
Indices: 119224--119256 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
119214 ATATTTACTT
119224 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
119257 AACTTTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:126726 original size:23 final size:22
Alignment explanation
Indices: 126678--126734 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
126668 CTGGGGAAAT
* *
126678 AGTAAGCACACATAGTGCAATC
1 AGTAGGCACACATAGCGCAATC
*
126700 AGTAGGCGCACATAGCGCAAATC
1 AGTAGGCACACATAGCGC-AATC
126723 AGTAGGCACACA
1 AGTAGGCACACA
126735 AGGTGCGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 15 0.50
23 15 0.50
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.14
Consensus pattern (22 bp):
AGTAGGCACACATAGCGCAATC
Found at i:126748 original size:23 final size:22
Alignment explanation
Indices: 126649--126798 Score: 124
Period size: 23 Copynumber: 6.5 Consensus size: 22
126639 CGAAGTACTT
126649 AACAGTAAGCACACAAGTGCTGGGGA
1 AACAGTAAGCACACAAGTGC----GA
*
126675 AATAGTAAGCACACATAGTGC-A
1 AACAGTAAGCACACA-AGTGCGA
* * * *
126697 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACA-AGTGCGA
*
126719 AATCAGTAGGCACACAAGGTGCGA
1 AA-CAGTAAGCACACAA-GTGCGA
126743 AACAGTAAGCACACGAAGTGCGA
1 AACAGTAAGCACAC-AAGTGCGA
*
126766 AATAGTAAGCACACGAAGTGCGA
1 AACAGTAAGCACAC-AAGTGCGA
*
126789 AATAGTAAGC
1 AACAGTAAGC
126799 GCGCTAGCGT
Statistics
Matches: 108, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
22 20 0.19
23 64 0.59
24 5 0.05
26 14 0.13
27 5 0.05
ACGTcount: A:0.41, C:0.20, G:0.26, T:0.13
Consensus pattern (22 bp):
AACAGTAAGCACACAAGTGCGA
Found at i:126778 original size:46 final size:44
Alignment explanation
Indices: 126649--126798 Score: 142
Period size: 46 Copynumber: 3.2 Consensus size: 44
126639 CGAAGTACTT
126649 AACAGTAAGCACACAAGTGCTGGGGAAATAGTAAGCACACATAGTGC-A
1 AACAGTAAGCACACAAGTGC----GAAATAGTAAGCACACA-AGTGCGA
* * * * *
126697 ATCAGTAGGCGCACATAGCGC-AAATCAGTAGGCACACAAGGTGCGA
1 AACAGTAAGCACACA-AGTGCGAAAT-AGTAAGCACACAA-GTGCGA
126743 AACAGTAAGCACACGAAGTGCGAAATAGTAAGCACACGAAGTGCGA
1 AACAGTAAGCACAC-AAGTGCGAAATAGTAAGCACAC-AAGTGCGA
*
126789 AATAGTAAGC
1 AACAGTAAGC
126799 GCGCTAGCGT
Statistics
Matches: 84, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
44 5 0.06
45 15 0.18
46 41 0.49
47 7 0.08
48 12 0.14
49 4 0.05
ACGTcount: A:0.41, C:0.20, G:0.26, T:0.13
Consensus pattern (44 bp):
AACAGTAAGCACACAAGTGCGAAATAGTAAGCACACAAGTGCGA
Done.