Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011621.1 Kokia drynarioides strain JFW-HI SEQ_126612, 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: 123396
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69 characters in sequence are not A, C, G, or T
Found at i:8400 original size:27 final size:28
Alignment explanation
Indices: 8362--8414 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 28
8352 TTGGTATTTT
8362 GGATTAAGGGTTT-ATGGTTCG-GGTTTG
1 GGATTAAGGGTTTGA-GGTTCGAGGTTTG
8389 GGATTCAA-GGTTTGAGGTTCGAGGTT
1 GGATT-AAGGGTTTGAGGTTCGAGGTT
8415 CGGAGTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.17, C:0.06, G:0.40, T:0.38
Consensus pattern (28 bp):
GGATTAAGGGTTTGAGGTTCGAGGTTTG
Found at i:10550 original size:21 final size:22
Alignment explanation
Indices: 10524--10567 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
10514 CACATATTTA
*
10524 TATATAACATAGTTTTA-GACT
1 TATATAACATAGGTTTATGACT
*
10545 TATATAGCATAGGTTTATGACT
1 TATATAACATAGGTTTATGACT
10567 T
1 T
10568 TCATAAGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (22 bp):
TATATAACATAGGTTTATGACT
Found at i:14256 original size:28 final size:29
Alignment explanation
Indices: 14211--14265 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
14201 CAAATACCCA
14211 TTTTCATAATTAATTTATTTTTTATATAT
1 TTTTCATAATTAATTTATTTTTTATATAT
*
14240 TTTTCGTAATTAA-TTATTTTTTATAT
1 TTTTCATAATTAATTTATTTTTTATAT
14266 TATATGGGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (29 bp):
TTTTCATAATTAATTTATTTTTTATATAT
Found at i:16778 original size:13 final size:15
Alignment explanation
Indices: 16756--16789 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
16746 TGTTTCATTG
16756 AAAATAGATTTC-GA
1 AAAATAGATTTCTGA
16770 AAAAT-GATTTCTGA
1 AAAATAGATTTCTGA
16784 AAAATA
1 AAAATA
16790 CATTGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (15 bp):
AAAATAGATTTCTGA
Found at i:35535 original size:16 final size:17
Alignment explanation
Indices: 35514--35557 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
35504 TTTGTATTAA
*
35514 TAATTAATATTAATA-T
1 TAATTAATATTAAGATT
35530 TAATTAA-ATTAAGATT
1 TAATTAATATTAAGATT
35546 TAATTTAATATT
1 TAA-TTAATATT
35558 TCTTAAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 6 0.25
16 11 0.46
17 4 0.17
18 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TAATTAATATTAAGATT
Found at i:47147 original size:6 final size:6
Alignment explanation
Indices: 47136--47168 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
47126 ACCCTAAACC
*
47136 CCCTAA CCCTAA CCCTAA CACTAA CCCTAA CCC
1 CCCTAA CCCTAA CCCTAA CCCTAA CCCTAA CCC
47169 CTATAAGCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.33, C:0.52, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCTAA
Found at i:48673 original size:28 final size:28
Alignment explanation
Indices: 48612--48673 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
48602 TTTTTTTTAC
*
48612 CATTATCCACACTTAACCATCTATCCAT
1 CATTATCCAAACTTAACCATCTATCCAT
*
48640 -ATTTATCCAAATTTAACCA-CTCATCCAT
1 CA-TTATCCAAACTTAACCATCT-ATCCAT
48668 CATTAT
1 CATTAT
48674 TTTATTCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
27 3 0.10
28 25 0.86
29 1 0.03
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.35
Consensus pattern (28 bp):
CATTATCCAAACTTAACCATCTATCCAT
Found at i:49222 original size:14 final size:15
Alignment explanation
Indices: 49194--49222 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
49184 TATTACAATT
49194 ATAAATATATTTATA
1 ATAAATATATTTATA
49209 ATAAATAT-TTTATA
1 ATAAATATATTTATA
49223 GTATAAAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAAATATATTTATA
Found at i:56684 original size:31 final size:31
Alignment explanation
Indices: 56648--56714 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
56638 TCACAAGATG
* *
56648 GTCACTTAACTATTT-AAAAGTTTTCATTTAA
1 GTCACTAAACTATTTGAAAA-TTTTCATTCAA
*
56679 GTCACTAAACTATTTGAAAATTTTTATTCAA
1 GTCACTAAACTATTTGAAAATTTTCATTCAA
56710 GTCAC
1 GTCAC
56715 AAAGATTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (31 bp):
GTCACTAAACTATTTGAAAATTTTCATTCAA
Found at i:60884 original size:22 final size:20
Alignment explanation
Indices: 60849--60889 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
60839 ATTGGGTATT
*
60849 TAAATTTTTAAAATGTTAAA
1 TAAATTTTTAAAATATTAAA
60869 TAAATTGTTCTAAAATATTAA
1 TAAATT-TT-TAAAATATTAA
60890 CTGTGTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 2 0.11
22 10 0.56
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (20 bp):
TAAATTTTTAAAATATTAAA
Found at i:64997 original size:2 final size:2
Alignment explanation
Indices: 64990--65015 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
64980 TTCATCCTTT
64990 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
65016 AAAGCTGGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:65493 original size:2 final size:2
Alignment explanation
Indices: 65486--65511 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
65476 ATATGTTTGA
65486 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
65512 TTATTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65545 original size:100 final size:100
Alignment explanation
Indices: 65400--65588 Score: 279
Period size: 100 Copynumber: 1.9 Consensus size: 100
65390 ATATATTTGA
* * * *
65400 ATATATATATATATATATATATTTGAATTTTGAAAGTATGTAAGAAATTTAATATCATAGTTTTG
1 ATATATATATATATATATATATTTGAATTTTGAAAATATGCAAGAAAATTAATATCATAATTTTG
* *
65465 AAAATCAATCCATATGTTTGAATATATATATATAT
66 AAAATCAATCCATACGTGTGAATATATATATATAT
* * * *
65500 ATATATATATATTTATTTTTTTTTGAATTTTGAAAATATGCAAGAAAATTAATATCATAATTTTG
1 ATATATATATATATATATATATTTGAATTTTGAAAATATGCAAGAAAATTAATATCATAATTTTG
*
65565 AAATTCAATCCATACGTGTGAATA
66 AAAATCAATCCATACGTGTGAATA
65589 CATGTATTTG
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
100 78 1.00
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (100 bp):
ATATATATATATATATATATATTTGAATTTTGAAAATATGCAAGAAAATTAATATCATAATTTTG
AAAATCAATCCATACGTGTGAATATATATATATAT
Found at i:65735 original size:25 final size:25
Alignment explanation
Indices: 65707--65756 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
65697 AAAATTATAG
65707 AAAA-CAAAAAATCATAAA-ATTTTTA
1 AAAATCAAAAAA--ATAAATATTTTTA
65732 AAAATTCAAAAAAATAAATATTTTT
1 AAAA-TCAAAAAAATAAATATTTTT
65757 TCCAAGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
25 9 0.41
26 6 0.27
27 7 0.32
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (25 bp):
AAAATCAAAAAAATAAATATTTTTA
Found at i:69915 original size:21 final size:21
Alignment explanation
Indices: 69891--69978 Score: 103
Period size: 21 Copynumber: 4.3 Consensus size: 21
69881 TTTATATTGT
*
69891 TGTTTTGATGCTATTTTTTAC
1 TGTTTTGATGCTTTTTTTTAC
*
69912 TGTTTTGATTG-TTTTTTTTGC
1 TGTTTTGA-TGCTTTTTTTTAC
*
69933 TGTTTT--TGTTTTTTTTTAC
1 TGTTTTGATGCTTTTTTTTAC
*
69952 TGTTTTGATAC-TTTTTTTAC
1 TGTTTTGATGCTTTTTTTTAC
69972 TGTTTTG
1 TGTTTTG
69979 GTTGTTGTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
18 2 0.03
19 15 0.26
20 16 0.28
21 23 0.40
22 2 0.03
ACGTcount: A:0.09, C:0.07, G:0.15, T:0.69
Consensus pattern (21 bp):
TGTTTTGATGCTTTTTTTTAC
Found at i:69929 original size:20 final size:20
Alignment explanation
Indices: 69891--69989 Score: 96
Period size: 21 Copynumber: 4.8 Consensus size: 20
69881 TTTATATTGT
69891 TGTTTTGA-TGCTATTTTTTAC
1 TGTTTTGATTG-T-TTTTTTAC
*
69912 TGTTTTGATTGTTTTTTTTGC
1 TGTTTTGATTG-TTTTTTTAC
69933 TGTTTTTG-TT-TTTTTTTAC
1 TG-TTTTGATTGTTTTTTTAC
**
69952 TGTTTTGATACTTTTTTTAC
1 TGTTTTGATTGTTTTTTTAC
*
69972 TGTTTTGGTTGTTGTTTT
1 TGTTTTGATTGTT-TTTT
69990 CATGTTGCTT
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
18 5 0.08
19 11 0.17
20 19 0.29
21 23 0.35
22 8 0.12
ACGTcount: A:0.08, C:0.06, G:0.16, T:0.70
Consensus pattern (20 bp):
TGTTTTGATTGTTTTTTTAC
Found at i:70007 original size:12 final size:12
Alignment explanation
Indices: 69972--70040 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
69962 CTTTTTTTAC
*
69972 TGTTTTGGTTGT
1 TGTTTTTGTTGT
**
69984 TG-TTTTCATGT
1 TGTTTTTGTTGT
*
69995 TGCTTTTGTTGT
1 TGTTTTTGTTGT
* *
70007 TATTTTTGTTAT
1 TGTTTTTGTTGT
* *
70019 TATTTTTGTTGC
1 TGTTTTTGTTGT
70031 TGTTTTTGTT
1 TGTTTTTGTT
70041 ACTATTTTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
11 8 0.18
12 37 0.82
ACGTcount: A:0.06, C:0.04, G:0.20, T:0.70
Consensus pattern (12 bp):
TGTTTTTGTTGT
Found at i:70025 original size:24 final size:24
Alignment explanation
Indices: 69998--70107 Score: 86
Period size: 24 Copynumber: 4.8 Consensus size: 24
69988 TTCATGTTGC
*
69998 TTTTGTTGTTATTTTTGTTATTAT
1 TTTTGTTGTTATTTTTGTTACTAT
* *
70022 TTTTGTTGCTGTTTTTGTTACTAT
1 TTTTGTTGTTATTTTTGTTACTAT
* **
70046 TTTTTTTGTT-TTAATG-T--TA-
1 TTTTGTTGTTATTTTTGTTACTAT
** *
70065 TTTTACTGTTATTTTTGTTACTGT
1 TTTTGTTGTTATTTTTGTTACTAT
* *
70089 TTTGGTTGCTATTTTTGTT
1 TTTTGTTGTTATTTTTGTT
70108 GTTTGGATGC
Statistics
Matches: 65, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
19 8 0.12
20 6 0.09
21 1 0.02
22 1 0.02
23 5 0.08
24 44 0.68
ACGTcount: A:0.11, C:0.05, G:0.15, T:0.70
Consensus pattern (24 bp):
TTTTGTTGTTATTTTTGTTACTAT
Found at i:70046 original size:27 final size:27
Alignment explanation
Indices: 70016--70110 Score: 86
Period size: 27 Copynumber: 3.5 Consensus size: 27
70006 TTATTTTTGT
*
70016 TATTATTTTTGTTGCTGTTTTTGTTAC
1 TATTATTTTTGTTACTGTTTTTGTTAC
* * *
70043 TATTTTTTTTGTTTTAATGTTATT-TTAC
1 TATTATTTTTG--TTACTGTTTTTGTTAC
* * *
70071 TGTTATTTTTGTTACTGTTTTGGTTGC
1 TATTATTTTTGTTACTGTTTTTGTTAC
70098 TATT-TTTGTTGTT
1 TATTATTT-TTGTT
70111 TGGATGCTAT
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
26 11 0.21
27 21 0.40
28 13 0.25
29 8 0.15
ACGTcount: A:0.12, C:0.05, G:0.15, T:0.68
Consensus pattern (27 bp):
TATTATTTTTGTTACTGTTTTTGTTAC
Found at i:70048 original size:12 final size:12
Alignment explanation
Indices: 70007--70049 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
69997 CTTTTGTTGT
*
70007 TATTTTTGTTAT
1 TATTTTTGTTAC
*
70019 TATTTTTGTTGC
1 TATTTTTGTTAC
*
70031 TGTTTTTGTTAC
1 TATTTTTGTTAC
70043 TATTTTT
1 TATTTTT
70050 TTTGTTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.12, C:0.05, G:0.12, T:0.72
Consensus pattern (12 bp):
TATTTTTGTTAC
Found at i:70122 original size:55 final size:55
Alignment explanation
Indices: 70018--70123 Score: 149
Period size: 55 Copynumber: 1.9 Consensus size: 55
70008 ATTTTTGTTA
* * * * *
70018 TTATTTTTGTTGCTGTTTTTGTTACTATTTTTTTTGTTTTAATGTTATTTTACTG
1 TTATTTTTGTTACTGTTTTGGTTACTATTTTTGTTGTTTGAATGCTATTTTACTG
* *
70073 TTATTTTTGTTACTGTTTTGGTTGCTATTTTTGTTGTTTGGATGCTATTTT
1 TTATTTTTGTTACTGTTTTGGTTACTATTTTTGTTGTTTGAATGCTATTTT
70124 TTATGCATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.11, C:0.06, G:0.16, T:0.67
Consensus pattern (55 bp):
TTATTTTTGTTACTGTTTTGGTTACTATTTTTGTTGTTTGAATGCTATTTTACTG
Found at i:70134 original size:55 final size:54
Alignment explanation
Indices: 69963--70135 Score: 145
Period size: 55 Copynumber: 3.1 Consensus size: 54
69953 GTTTTGATAC
* * *
69963 TTTTT-TTACTGTTTTGGTTGTTGTTTTCATGTTGCTTTTGTTGTTATTTTTGTTAT-TA
1 TTTTTGTTACTGTTTTGGTTGCTATTTT--TGTTG-TTTTGATG-TA-TTTT-TTATGTA
* * * * * *
70021 TTTTTGTTGCTGTTTTTGTTACTATTTTTTTTGTTTTAATGT-TATTTTACTGTTA
1 TTTTTGTTACTGTTTTGGTTGCTATTTTTGTTGTTTTGATGTATTTTTTA-TG-TA
* *
70076 TTTTTGTTACTGTTTTGGTTGCTATTTTTGTTGTTTGGATGCTATTTTTTATGCA
1 TTTTTGTTACTGTTTTGGTTGCTATTTTTGTTGTTTTGATG-TATTTTTTATGTA
70131 TTTTT
1 TTTTT
70136 ACTATTGTTT
Statistics
Matches: 92, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
52 3 0.03
53 4 0.04
55 44 0.48
56 9 0.10
57 10 0.11
58 5 0.05
59 17 0.18
ACGTcount: A:0.10, C:0.06, G:0.16, T:0.68
Consensus pattern (54 bp):
TTTTTGTTACTGTTTTGGTTGCTATTTTTGTTGTTTTGATGTATTTTTTATGTA
Found at i:74173 original size:29 final size:30
Alignment explanation
Indices: 74129--74188 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
74119 ACTTTATAAG
*
74129 TTTTTAAAAGATTAAATTAAAATTTTATTA
1 TTTTTAAAAGATTAAAATAAAATTTTATTA
*
74159 TTTTTAAAAG-TTAAAATGAAATTTTATTA
1 TTTTTAAAAGATTAAAATAAAATTTTATTA
74188 T
1 T
74189 ATACTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (30 bp):
TTTTTAAAAGATTAAAATAAAATTTTATTA
Found at i:77137 original size:11 final size:11
Alignment explanation
Indices: 77121--77145 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
77111 AGAAATAAGA
77121 AATTATGTATC
1 AATTATGTATC
77132 AATTATGTATC
1 AATTATGTATC
77143 AAT
1 AAT
77146 AAGTTATTTC
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
AATTATGTATC
Found at i:87377 original size:15 final size:14
Alignment explanation
Indices: 87345--87387 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
87335 TTTCAATCCC
87345 TTTAATTTAAAATTT
1 TTTAATTT-AAATTT
87360 TTTAATTTAAATTAT
1 TTTAATTTAAATT-T
*
87375 TTTGGATTTAAAT
1 TTT-AATTTAAAT
87388 CAATTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 5 0.20
15 12 0.48
16 8 0.32
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (14 bp):
TTTAATTTAAATTT
Found at i:90599 original size:6 final size:6
Alignment explanation
Indices: 90584--90613 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
90574 TTACATAATT
90584 TTTG-A TTTGAA TTTGAA TTTGAA TTTGAA T
1 TTTGAA TTTGAA TTTGAA TTTGAA TTTGAA T
90614 CATTTGTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (6 bp):
TTTGAA
Found at i:92373 original size:35 final size:35
Alignment explanation
Indices: 92332--92399 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
92322 TTTTCAGATG
92332 ATATTCAAAACAAATAAATTAATATTTAAATTCGA
1 ATATTCAAAACAAATAAATTAATATTTAAATTCGA
* *
92367 ATATTCAAAACGAATGAATTAATATTTAAATTC
1 ATATTCAAAACAAATAAATTAATATTTAAATTC
92400 AAATTAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.35
Consensus pattern (35 bp):
ATATTCAAAACAAATAAATTAATATTTAAATTCGA
Found at i:111252 original size:31 final size:30
Alignment explanation
Indices: 111216--111301 Score: 93
Period size: 31 Copynumber: 2.9 Consensus size: 30
111206 GATTAAATCA
* *
111216 AAATTAAAGTTTCAAGTATATATTTGAACC
1 AAATTAAAGTTTCAAGTATACAATTGAACC
* * *
111246 ACAATTAAAGTTTGACGTATACAATTGCACC
1 A-AATTAAAGTTTCAAGTATACAATTGAACC
* *
111277 AAATTAAAG-CTCATGTATACAATTG
1 AAATTAAAGTTTCAAGTATACAATTG
111302 CACATTAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 13 0.28
30 9 0.19
31 25 0.53
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.33
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATACAATTGAACC
Found at i:116559 original size:18 final size:18
Alignment explanation
Indices: 116536--116576 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
116526 ATTTCAATCC
116536 ATATAATAATAA-ACATTA
1 ATATAATAATAATA-ATTA
*
116554 ATATAATGATAATAATTA
1 ATATAATAATAATAATTA
116572 ATATA
1 ATATA
116577 TTATATACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
ATATAATAATAATAATTA
Found at i:119952 original size:8 final size:9
Alignment explanation
Indices: 119924--119958 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
119914 CGAAATTAAA
119924 TTATATATTT
1 TTAT-TATTT
119934 TTATTATTT
1 TTATTATTT
119943 TTATTATTT
1 TTATTATTT
*
119952 TTTTTAT
1 TTATTAT
119959 AAAATTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 20 0.83
10 4 0.17
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTATTATTT
Found at i:120190 original size:12 final size:11
Alignment explanation
Indices: 120156--120201 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
120146 TTTTATATTC
*
120156 TAATACATAAA
1 TAATACAAAAA
*
120167 TAATAAAAAAA
1 TAATACAAAAA
120178 TAATTACAAAAA
1 TAA-TACAAAAA
120190 T-ATA-AAAAA
1 TAATACAAAAA
120199 TAA
1 TAA
120202 AGAAAAATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
9 6 0.20
10 3 0.10
11 13 0.43
12 8 0.27
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (11 bp):
TAATACAAAAA
Done.