Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003580.1 Kokia drynarioides strain JFW-HI SEQ_116453, 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: 70392
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:4813 original size:16 final size:17
Alignment explanation
Indices: 4792--4838 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
4782 CATTGTCCCT
*
4792 AATGCACTAAC-ATTAA
1 AATGCAATAACAATTAA
*
4808 AATGCAATGACAATTAA
1 AATGCAATAACAATTAA
* *
4825 AATGAAATGACAAT
1 AATGCAATAACAAT
4839 GTGCACTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 9 0.33
17 18 0.67
ACGTcount: A:0.53, C:0.13, G:0.11, T:0.23
Consensus pattern (17 bp):
AATGCAATAACAATTAA
Found at i:4825 original size:17 final size:17
Alignment explanation
Indices: 4803--4838 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
4793 ATGCACTAAC
*
4803 ATTAAAATGCAATGACA
1 ATTAAAATGAAATGACA
4820 ATTAAAATGAAATGACA
1 ATTAAAATGAAATGACA
4837 AT
1 AT
4839 GTGCACTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.08, G:0.11, T:0.25
Consensus pattern (17 bp):
ATTAAAATGAAATGACA
Found at i:11091 original size:21 final size:21
Alignment explanation
Indices: 11067--11113 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
11057 GTGTTGTGGT
*
11067 TGCATCTGATTTTGGTGTGAA
1 TGCATCTGACTTTGGTGTGAA
* * *
11088 TGCATCTGGCTTTGTTGTGGA
1 TGCATCTGACTTTGGTGTGAA
11109 TGCAT
1 TGCAT
11114 TTGAGTGTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.13, G:0.30, T:0.43
Consensus pattern (21 bp):
TGCATCTGACTTTGGTGTGAA
Found at i:16357 original size:31 final size:31
Alignment explanation
Indices: 16281--16378 Score: 101
Period size: 31 Copynumber: 3.1 Consensus size: 31
16271 ACCACAAAGA
* *
16281 AAAGTTCGCT-GAGACAGTAAACAAAGAACAG
1 AAAGTTCGCTAG-GACAATAAACAAAGAATAG
* *
16312 AGATAGTTCACTAGGACAATAAACATAGAATAG
1 A-A-AGTTCGCTAGGACAATAAACAAAGAATAG
*
16345 AAAGTTCGCTAGGACATTAAACACAA-AATAG
1 AAAGTTCGCTAGGACAATAAACA-AAGAATAG
16376 AAA
1 AAA
16379 TAGTCTGTTG
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
31 28 0.50
32 3 0.05
33 24 0.43
34 1 0.02
ACGTcount: A:0.50, C:0.14, G:0.18, T:0.17
Consensus pattern (31 bp):
AAAGTTCGCTAGGACAATAAACAAAGAATAG
Found at i:16402 original size:33 final size:33
Alignment explanation
Indices: 16362--16448 Score: 108
Period size: 31 Copynumber: 2.7 Consensus size: 33
16352 GCTAGGACAT
* *
16362 TAAACACAAAATAGAAATAGTCTGTTGGGATAG
1 TAAACACAAAATAGAAATAGTCTCTTGGGATAA
*
16395 TAAACACAAAATAG--ATAGTCCCTTGGGATAA
1 TAAACACAAAATAGAAATAGTCTCTTGGGATAA
*
16426 TAAA-AAAAGAATAGAAATAGTCT
1 TAAACACAA-AATAGAAATAGTCT
16449 ACTAGAATAG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
30 3 0.07
31 23 0.50
33 20 0.43
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.23
Consensus pattern (33 bp):
TAAACACAAAATAGAAATAGTCTCTTGGGATAA
Found at i:20867 original size:25 final size:25
Alignment explanation
Indices: 20822--20880 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
20812 CTTTTTCATA
20822 TTTTTTTCGTACTCATGATTTTCTTC
1 TTTTTTTCGTACTCA-GATTTTCTTC
* *
20848 TTTTGTTTCTTACTCA-ATTTTCTTT
1 TTTT-TTTCGTACTCAGATTTTCTTC
20873 TTCTTTTT
1 TT-TTTTT
20881 TATTTTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 13 0.45
26 6 0.21
27 10 0.34
ACGTcount: A:0.10, C:0.17, G:0.05, T:0.68
Consensus pattern (25 bp):
TTTTTTTCGTACTCAGATTTTCTTC
Found at i:23540 original size:21 final size:20
Alignment explanation
Indices: 23477--23554 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 20
23467 TTTTTGGTTT
23477 AATTAGGGTTTAAGGTTTTTTA
1 AATTA-GGTTT-AGGTTTTTTA
* **
23499 AATTAGGGTTAGTGTAATTTA
1 AATTAGGTTTAG-GTTTTTTA
*
23520 AATTGAGGTTTTGGTTTTTTA
1 AATT-AGGTTTAGGTTTTTTA
23541 AATTAAGGTTTAGG
1 AATT-AGGTTTAGG
23555 GTATTTTAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
20 2 0.04
21 32 0.71
22 11 0.24
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.47
Consensus pattern (20 bp):
AATTAGGTTTAGGTTTTTTA
Found at i:23565 original size:21 final size:21
Alignment explanation
Indices: 23474--23569 Score: 70
Period size: 21 Copynumber: 4.5 Consensus size: 21
23464 GTGTTTTTGG
* * *
23474 TTTAATTAGGGTTTAAGGTTT
1 TTTAATTAAGGTTTAGGGTAT
* *
23495 TTTAAATT-AGGGTTAGTGTAAT
1 TTT-AATTAAGGTTTAGGGT-AT
* * * *
23517 TTAAATTGAGGTTT-TGGTTT
1 TTTAATTAAGGTTTAGGGTAT
23537 TTTAAATTAAGGTTTAGGGTAT
1 TTT-AATTAAGGTTTAGGGTAT
23559 TTTAATTAAGG
1 TTTAATTAAGG
23570 GTTTTGAAAA
Statistics
Matches: 56, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
20 3 0.05
21 34 0.61
22 19 0.34
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.49
Consensus pattern (21 bp):
TTTAATTAAGGTTTAGGGTAT
Found at i:23573 original size:43 final size:42
Alignment explanation
Indices: 23474--23575 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 42
23464 GTGTTTTTGG
* *
23474 TTTAATTAGGGTTTAAGGTTTTTTAAATTAGGGTTAGTGTAAT
1 TTTAATTAGGGTTT-TGGTTTTTTAAATTAGGGTTAGGGTAAT
* *
23517 TTAAATT-GAGGTTTTGGTTTTTTAAATTAAGGTTTAGGGT-AT
1 TTTAATTAG-GGTTTTGGTTTTTTAAATT-AGGGTTAGGGTAAT
23559 TTTAATTAAGGGTTTTG
1 TTTAATT-AGGGTTTTG
23576 AAAATGGTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
42 22 0.44
43 27 0.54
44 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (42 bp):
TTTAATTAGGGTTTTGGTTTTTTAAATTAGGGTTAGGGTAAT
Found at i:23862 original size:29 final size:29
Alignment explanation
Indices: 23825--23913 Score: 72
Period size: 28 Copynumber: 3.1 Consensus size: 29
23815 CTAAGTATAG
*
23825 TTCTGGAAAAAATAATTTTGAGAAGATGGA
1 TTCT-GAAAAAATAATTTTGACAAGATGGA
* * *** **
23855 TTCTGAAAAATTAA-ATTGATTTGATGTT
1 TTCTGAAAAAATAATTTTGACAAGATGGA
* *
23883 TTCTGAAAAAATTATTTTGACAATATGGA
1 TTCTGAAAAAATAATTTTGACAAGATGGA
23912 TT
1 TT
23914 TTTTTTTTAA
Statistics
Matches: 42, Mismatches: 16, Indels: 3
0.69 0.26 0.05
Matches are distributed among these distances:
28 20 0.48
29 18 0.43
30 4 0.10
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.39
Consensus pattern (29 bp):
TTCTGAAAAAATAATTTTGACAAGATGGA
Found at i:27549 original size:59 final size:58
Alignment explanation
Indices: 27389--27608 Score: 280
Period size: 59 Copynumber: 3.7 Consensus size: 58
27379 TTGGTTCTCA
* * * * **
27389 ATTAAATGAAACAATATGTCAAAACTAATGTCTATAATAATATTCAAATGAACTTCGACGTT
1 ATTAAATG-AACAATA--T-AAAAATAATGTGTACAAAAATATTCAAATGAACTTCGATTTT
* *
27451 ATTAAATGAA-AATATAAAAATAATGTGTACAAAATTATTCAAATGAACTTTGATTTT
1 ATTAAATGAACAATATAAAAATAATGTGTACAAAAATATTCAAATGAACTTCGATTTT
*
27508 ATTAAATGAATCAATATAAAAATAACGTGTACAAAAATATTCAAATGAACTTCGATTTT
1 ATTAAATGAA-CAATATAAAAATAATGTGTACAAAAATATTCAAATGAACTTCGATTTT
* *
27567 ATTAAATGAAACAAGATAAAAATAATGTTTACAAAAATATTC
1 ATTAAATG-AACAATATAAAAATAATGTGTACAAAAATATTC
27609 GAATTAAATC
Statistics
Matches: 141, Mismatches: 14, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
57 44 0.31
58 1 0.01
59 80 0.57
60 6 0.04
61 2 0.01
62 8 0.06
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.33
Consensus pattern (58 bp):
ATTAAATGAACAATATAAAAATAATGTGTACAAAAATATTCAAATGAACTTCGATTTT
Found at i:28586 original size:34 final size:34
Alignment explanation
Indices: 28543--28611 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
28533 CAATGGGACC
28543 CTAATGTGCCTAGTGTTCGAATTCTATAGGAATT
1 CTAATGTGCCTAGTGTTCGAATTCTATAGGAATT
28577 CTAATGTGCCTAGTGTTCGAATTCTATAGGAATT
1 CTAATGTGCCTAGTGTTCGAATTCTATAGGAATT
28611 C
1 C
28612 CTCTGGAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (34 bp):
CTAATGTGCCTAGTGTTCGAATTCTATAGGAATT
Found at i:29656 original size:22 final size:23
Alignment explanation
Indices: 29606--29653 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
29596 ATTCACATAA
* *
29606 AAATTATTAAAAATATATGAATT
1 AAATTATTAAAAATATATAAAAT
29629 AAATTA-TAAAAATAATATAAAAT
1 AAATTATTAAAAAT-ATATAAAAT
29652 AA
1 AA
29654 TTAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
AAATTATTAAAAATATATAAAAT
Found at i:29659 original size:18 final size:17
Alignment explanation
Indices: 29634--29724 Score: 50
Period size: 18 Copynumber: 5.5 Consensus size: 17
29624 GAATTAAATT
29634 ATAA-AAATAATATAAA
1 ATAATAAATAATATAAA
**
29650 ATAATTAAAT-AT-TATT
1 ATAA-TAAATAATATAAA
* *
29666 TTAAAAAATAAT-TAAA
1 ATAATAAATAATATAAA
*
29682 TTATAA-AAATAAAATAAA
1 --ATAATAAATAATATAAA
*
29700 AAAATTAAATAATATAAA
1 ATAA-TAAATAATATAAA
29718 A-AATAAA
1 ATAATAAA
29725 ATTAACTCTT
Statistics
Matches: 57, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
15 4 0.07
16 20 0.35
17 10 0.18
18 23 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
ATAATAAATAATATAAA
Found at i:29698 original size:22 final size:23
Alignment explanation
Indices: 29670--29729 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
29660 ATTATTTTAA
*
29670 AAAATAATTAAATTATAA-AA-AT
1 AAAATAATAAAATTA-AATAATAT
*
29692 AAAATAAAAAAATTAAATAATAT
1 AAAATAATAAAATTAAATAATAT
29715 AAAA-AATAAAATTAA
1 AAAATAATAAAATTAA
29730 CTCTTACCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 2 0.06
22 25 0.76
23 6 0.18
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAATAATAAAATTAAATAATAT
Found at i:29704 original size:30 final size:30
Alignment explanation
Indices: 29669--29726 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
29659 TATTATTTTA
29669 AAAAATAATTAAAT--TAT-AAAAATAAAAT
1 AAAAA-AATTAAATAATATAAAAAATAAAAT
29697 AAAAAAATTAAATAATATAAAAAATAAAAT
1 AAAAAAATTAAATAATATAAAAAATAAAAT
29727 TAACTCTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 8 0.30
28 5 0.19
29 3 0.11
30 11 0.41
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (30 bp):
AAAAAAATTAAATAATATAAAAAATAAAAT
Found at i:32808 original size:24 final size:23
Alignment explanation
Indices: 32781--32871 Score: 59
Period size: 20 Copynumber: 4.0 Consensus size: 23
32771 AAAGAAAGTA
32781 TTTGCAGTTGCTTTAAATTGATTG
1 TTTGCAG-TGCTTTAAATTGATTG
* *
32805 TTTG-A-TG-TTTAAATCGATTCATT
1 TTTGCAGTGCTTTAAATTGA-T--TG
32828 TCTTGCAGCTGCTTTAAATTGATTG
1 T-TTGCAG-TGCTTTAAATTGATTG
*
32853 TTTG-A-TG-TTTAAATCGATT
1 TTTGCAGTGCTTTAAATTGATT
32872 CATTTATACT
Statistics
Matches: 54, Mismatches: 5, Indels: 20
0.68 0.06 0.25
Matches are distributed among these distances:
20 20 0.37
21 5 0.09
23 4 0.07
24 10 0.19
25 3 0.06
27 3 0.06
28 9 0.17
ACGTcount: A:0.23, C:0.10, G:0.18, T:0.49
Consensus pattern (23 bp):
TTTGCAGTGCTTTAAATTGATTG
Found at i:32817 original size:20 final size:20
Alignment explanation
Indices: 32792--32871 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 20
32782 TTGCAGTTGC
*
32792 TTTAAATTGATTGTTTGATG
1 TTTAAATCGATTGTTTGATG
*
32812 TTTAAATCGATTCATTTCTTGCAGCTG
1 TTTAAATCGA-T--TGT-TTG-A--TG
*
32839 CTTTAAATTGATTGTTTGATG
1 -TTTAAATCGATTGTTTGATG
32860 TTTAAATCGATT
1 TTTAAATCGATT
32872 CATTTATACT
Statistics
Matches: 47, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
20 20 0.43
21 3 0.06
23 3 0.06
24 6 0.13
25 3 0.06
27 3 0.06
28 9 0.19
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.50
Consensus pattern (20 bp):
TTTAAATCGATTGTTTGATG
Found at i:32853 original size:48 final size:48
Alignment explanation
Indices: 32782--32876 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
32772 AAGAAAGTAT
*
32782 TTGCAGTTGCTTTAAATTGATTGTTTGATGTTTAAATCGATTCATTTC
1 TTGCAGCTGCTTTAAATTGATTGTTTGATGTTTAAATCGATTCATTTC
32830 TTGCAGCTGCTTTAAATTGATTGTTTGATGTTTAAATCGATTCATTT
1 TTGCAGCTGCTTTAAATTGATTGTTTGATGTTTAAATCGATTCATTT
32877 ATACTTTTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.49
Consensus pattern (48 bp):
TTGCAGCTGCTTTAAATTGATTGTTTGATGTTTAAATCGATTCATTTC
Found at i:33111 original size:44 final size:46
Alignment explanation
Indices: 33052--33140 Score: 112
Period size: 44 Copynumber: 2.0 Consensus size: 46
33042 TTACAAAATC
* * *
33052 ATTCTATTTAACCAAATACAAT-AA-TACT-ATTACAGTTCTATTCT
1 ATTCCATTCAACCAAATA-AATGAATTACTGATTACAATTCTATTCT
*
33096 ATTCCATTCAACCAAATAATTGAATTACTGATTACAATTCTATTC
1 ATTCCATTCAACCAAATAAATGAATTACTGATTACAATTCTATTC
33141 CATTACAACT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
43 2 0.05
44 18 0.47
45 4 0.11
46 14 0.37
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.39
Consensus pattern (46 bp):
ATTCCATTCAACCAAATAAATGAATTACTGATTACAATTCTATTCT
Found at i:33147 original size:16 final size:16
Alignment explanation
Indices: 33126--33180 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
33116 TGAATTACTG
33126 ATTACAATTCTATTCC
1 ATTACAATTCTATTCC
* *
33142 ATTACAACTCTATTTC
1 ATTACAATTCTATTCC
* * *
33158 ATTACAGTTTTATTCT
1 ATTACAATTCTATTCC
33174 ATTACAA
1 ATTACAA
33181 CGAACCAAAC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.45
Consensus pattern (16 bp):
ATTACAATTCTATTCC
Found at i:33698 original size:18 final size:19
Alignment explanation
Indices: 33657--33698 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
33647 AATTAATCGA
*
33657 CTAATTAACCAAATTCGAT
1 CTAATTAACCAAATTCAAT
*
33676 C-AATTAACCGAATT-AAT
1 CTAATTAACCAAATTCAAT
33693 CTAATT
1 CTAATT
33699 TTATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 3 0.15
18 16 0.80
19 1 0.05
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (19 bp):
CTAATTAACCAAATTCAAT
Found at i:44912 original size:33 final size:34
Alignment explanation
Indices: 44832--44913 Score: 89
Period size: 33 Copynumber: 2.5 Consensus size: 34
44822 CCTATTTACT
* * **
44832 TAAAATAAATAATTTTAGTCAAAATGAAATTAGGA
1 TAAAATAAATAAATTTAATCAAAACAAAATTA-GA
*
44867 -AAAAT-AACAAATTTAATCAAAACAAAATTA-A
1 TAAAATAAATAAATTTAATCAAAACAAAATTAGA
44898 TAAAATAAATAAATTT
1 TAAAATAAATAAATTT
44914 GACTAAGTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
31 1 0.03
32 5 0.13
33 28 0.72
34 5 0.13
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (34 bp):
TAAAATAAATAAATTTAATCAAAACAAAATTAGA
Found at i:45537 original size:18 final size:17
Alignment explanation
Indices: 45514--45548 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
45504 AACTTACTGC
45514 TACTGATGGTCACTCTTT
1 TACTGATGGTCAC-CTTT
*
45532 TACTGATGTTCACCTTT
1 TACTGATGGTCACCTTT
45549 ATCGGCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.17, C:0.23, G:0.14, T:0.46
Consensus pattern (17 bp):
TACTGATGGTCACCTTT
Found at i:46676 original size:11 final size:10
Alignment explanation
Indices: 46660--46716 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 10
46650 CATGAAATTA
46660 ATATTTTTAAT
1 ATATTTTT-AT
46671 ATATTTTTAT
1 ATATTTTTAT
*
46681 -TATTTTTCT
1 ATATTTTTAT
46690 AT-TTTTTAT
1 ATATTTTTAT
46699 ATTTATTTTTAT
1 A--TATTTTTAT
46711 A-ATTTT
1 ATATTTT
46717 AAAATATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
9 20 0.50
10 3 0.08
11 9 0.22
12 8 0.20
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (10 bp):
ATATTTTTAT
Found at i:46716 original size:20 final size:20
Alignment explanation
Indices: 46661--46717 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
46651 ATGAAATTAA
46661 TATTTTTAATATATTTT-TAT
1 TATTTTT-ATATATTTTATAT
* *
46681 TATTTTTCTATTTTTTATATT
1 TATTTTTATATATTTTATA-T
46702 TATTTTTATA-ATTTTA
1 TATTTTTATATATTTTA
46718 AAATATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 7 0.23
20 14 0.45
21 10 0.32
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (20 bp):
TATTTTTATATATTTTATAT
Found at i:53041 original size:24 final size:24
Alignment explanation
Indices: 52996--53041 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
52986 GATCAAGTAA
*
52996 ATTACACTAATAAATGTAAAATAT
1 ATTACACTAATAAATATAAAATAT
* *
53020 ATTATACTAATAAATATTAAAT
1 ATTACACTAATAAATATAAAAT
53042 CTTCTAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (24 bp):
ATTACACTAATAAATATAAAATAT
Found at i:55007 original size:24 final size:24
Alignment explanation
Indices: 54956--55007 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
54946 TTCTTAGGTC
* *
54956 AAATAAATTATGCTAATAAATGCA
1 AAATAAATTATACTAATAAATACA
* *
54980 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACA
55004 AAAT
1 AAAT
55008 CTTTTGGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:59006 original size:42 final size:41
Alignment explanation
Indices: 58824--59014 Score: 154
Period size: 42 Copynumber: 4.6 Consensus size: 41
58814 ATAATAACAT
* *
58824 ACAT-AGTGCATCATCGAATAAACTAAAGC-AATCATGTTAGC
1 ACATAAGTGCATCATCG-ATAAACTGAAGCAAAT-ATATTAGC
* * ** *
58865 ACATAAGTGCATTATTGGATGTACTGAAAG-AAATATATTAGT
1 ACATAAGTGCATCA-TCGATAAACTG-AAGCAAATATATTAGC
** * * * * *
58907 ATGTAAGTGCATCATTGGATATACTGAAGCAATTATAATAGT
1 ACATAAGTGCATCA-TCGATAAACTGAAGCAAATATATTAGC
* *
58949 ACACAAGTGCATCATCAGATAAACTGAAGCAAATATATTGGC
1 ACATAAGTGCATCATC-GATAAACTGAAGCAAATATATTAGC
58991 ACATAAGTGCATCATCGATTAAAC
1 ACATAAGTGCATCATCGA-TAAAC
59015 CAAAGTATAA
Statistics
Matches: 120, Mismatches: 23, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
41 10 0.08
42 102 0.85
43 8 0.07
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (41 bp):
ACATAAGTGCATCATCGATAAACTGAAGCAAATATATTAGC
Done.