Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011559.1 Kokia drynarioides strain JFW-HI SEQ_126548, 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: 75325
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:2494 original size:19 final size:19
Alignment explanation
Indices: 2472--2516 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2462 TTTTATTAGG
2472 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
2491 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
2510 ATTTAAT
1 ATTTAAT
2517 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:3634 original size:17 final size:17
Alignment explanation
Indices: 3602--3647 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
3592 TTTTTAATTT
*
3602 TAATTTATAATTTTTTA
1 TAATTTATATTTTTTTA
*
3619 TAATTTATATTTTTTTC
1 TAATTTATATTTTTTTA
3636 TATATTT-TATTT
1 TA-ATTTATATTT
3648 ATATTTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
TAATTTATATTTTTTTA
Found at i:3639 original size:29 final size:28
Alignment explanation
Indices: 3607--3662 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
3597 AATTTTAATT
*
3607 TATAATTT-TTTATAATTTATATTTTTTTC
1 TATAATTTATTTAT-ATTT-GATTTTTTTC
*
3636 TATATTTTATTTATATTTGATTTTTTT
1 TATAATTTATTTATATTTGATTTTTTT
3663 ATTTTTTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.33
29 11 0.46
30 5 0.21
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (28 bp):
TATAATTTATTTATATTTGATTTTTTTC
Found at i:3647 original size:23 final size:22
Alignment explanation
Indices: 3621--3692 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 22
3611 ATTTTTTATA
*
3621 ATTTATATTTTTTTCTATATTTT
1 ATTTATATTTTTTT-TATTTTTT
3644 ATTTATATTTGATTTTTTTATTTTTT
1 ATTTATA--T--TTTTTTTATTTTTT
3670 AGTTT-TATTTTTTTTATTTTTT
1 A-TTTATATTTTTTTTATTTTTT
3692 A
1 A
3693 ATGTGTATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
22 15 0.35
23 7 0.16
24 1 0.02
25 1 0.02
26 10 0.23
27 9 0.21
ACGTcount: A:0.19, C:0.01, G:0.03, T:0.76
Consensus pattern (22 bp):
ATTTATATTTTTTTTATTTTTT
Found at i:3659 original size:26 final size:26
Alignment explanation
Indices: 3630--3679 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3620 AATTTATATT
3630 TTTTTCTATATTTTA-TTTATATTTGA
1 TTTTTCTATATTTTAGTTT-TATTTGA
* *
3656 TTTTTTTATTTTTTAGTTTTATTT
1 TTTTTCTATATTTTAGTTTTATTT
3680 TTTTTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (26 bp):
TTTTTCTATATTTTAGTTTTATTTGA
Found at i:4047 original size:19 final size:19
Alignment explanation
Indices: 4023--4089 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 19
4013 CTAAAATAGT
4023 AAAAAACCACAAAACAGTA
1 AAAAAACCACAAAACAGTA
*
4042 AAAAAACAACACCAAAACAGCA
1 AAAAAAC--CA-CAAAACAGTA
*
4064 AAAAATA--ACTAAAATAGTA
1 AAAAA-ACCAC-AAAACAGTA
4083 AAAAAAC
1 AAAAAAC
4090 AGCACAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
18 2 0.05
19 20 0.51
21 2 0.05
22 14 0.36
23 1 0.03
ACGTcount: A:0.70, C:0.18, G:0.04, T:0.07
Consensus pattern (19 bp):
AAAAAACCACAAAACAGTA
Found at i:4048 original size:41 final size:41
Alignment explanation
Indices: 4003--4099 Score: 106
Period size: 41 Copynumber: 2.4 Consensus size: 41
3993 AAAAAACACC
* * * *
4003 AAAACAACAACTAAAATAGTAAAAAACCAC-AAAACAGTAAA
1 AAAACAAC-ACCAAAACAGCAAAAAACAACTAAAACAGTAAA
* *
4044 AAAACAACACCAAAACAGCAAAAAATAACTAAAATAGTAAA
1 AAAACAACACCAAAACAGCAAAAAACAACTAAAACAGTAAA
* *
4085 AAAACAGCACAAAAA
1 AAAACAACACCAAAA
4100 TAATAATATA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 16 0.34
41 31 0.66
ACGTcount: A:0.69, C:0.18, G:0.05, T:0.08
Consensus pattern (41 bp):
AAAACAACACCAAAACAGCAAAAAACAACTAAAACAGTAAA
Found at i:4089 original size:30 final size:31
Alignment explanation
Indices: 3985--4102 Score: 93
Period size: 30 Copynumber: 3.9 Consensus size: 31
3975 TAACAGCATC
* *
3985 AAAACAGT-AAAAAACACCAAAACAACAACT
1 AAAACAGTAAAAAAACAGCAAAACAATAACT
* * * *
4015 AAAATAGTAAAAAACCA-CAAAACAGTAA-A
1 AAAACAGTAAAAAAACAGCAAAACAATAACT
** **
4044 AAAACAACACCAAAACAGCAAAA-AATAACT
1 AAAACAGTAAAAAAACAGCAAAACAATAACT
*
4074 AAAATAGTAAAAAAACAGCACAAA-AATAA
1 AAAACAGTAAAAAAACAGCA-AAACAATAA
4103 TAATATAATT
Statistics
Matches: 66, Mismatches: 18, Indels: 7
0.73 0.20 0.08
Matches are distributed among these distances:
29 15 0.23
30 36 0.55
31 15 0.23
ACGTcount: A:0.69, C:0.18, G:0.05, T:0.08
Consensus pattern (31 bp):
AAAACAGTAAAAAAACAGCAAAACAATAACT
Found at i:6541 original size:21 final size:21
Alignment explanation
Indices: 6517--6564 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
6507 TTTAAAATTT
6517 AATTTTTATATATATTTTTTA
1 AATTTTTATATATATTTTTTA
** * *
6538 AATTAATCTATTTATTTTTTA
1 AATTTTTATATATATTTTTTA
6559 AATTTT
1 AATTTT
6565 AAAATTCAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTTTTATATATATTTTTTA
Found at i:12541 original size:13 final size:13
Alignment explanation
Indices: 12523--12547 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12513 GTCCCATCTC
12523 TTATTAGATACAA
1 TTATTAGATACAA
12536 TTATTAGATACA
1 TTATTAGATACA
12548 TCACAATGAA
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
TTATTAGATACAA
Found at i:13247 original size:13 final size:13
Alignment explanation
Indices: 13229--13269 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
13219 TATCAAATAA
13229 AATTTAATTTAAC
1 AATTTAATTTAAC
*
13242 AATTT-ATATT-AG
1 AATTTAAT-TTAAC
13254 AATTTAATTTAAC
1 AATTTAATTTAAC
13267 AAT
1 AAT
13270 AACATAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (13 bp):
AATTTAATTTAAC
Found at i:15737 original size:22 final size:22
Alignment explanation
Indices: 15712--15758 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
15702 AAAAAAAAAT
15712 ATATCT-AT-ATTGTTTTATTTTA
1 ATATCTAATAATT-TTTTA-TTTA
*
15734 ATATTTAATAATTTTTTATTTA
1 ATATCTAATAATTTTTTATTTA
15756 ATA
1 ATA
15759 AATTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 12 0.55
23 7 0.32
24 3 0.14
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
ATATCTAATAATTTTTTATTTA
Found at i:15755 original size:15 final size:16
Alignment explanation
Indices: 15735--15766 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
15725 TTTATTTTAA
15735 TATTTAAT-AATTTTT
1 TATTTAATAAATTTTT
15750 TATTTAATAAATTTTT
1 TATTTAATAAATTTTT
15766 T
1 T
15767 TATATAGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTTAATAAATTTTT
Found at i:18313 original size:27 final size:25
Alignment explanation
Indices: 18283--18346 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 25
18273 ATATAAATAC
*
18283 AAATAAAAATTCTAAAATTTATGGAAA
1 AAATAAAAATTC-AAAATTTA-AGAAA
*
18310 AAATAAAATCTTCAAAATTTAAGAAA
1 AAATAAAA-ATTCAAAATTTAAGAAA
*
18336 AAGTAAAAATT
1 AAATAAAAATT
18347 TCTTTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 2 0.06
26 11 0.34
27 16 0.50
28 3 0.09
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.28
Consensus pattern (25 bp):
AAATAAAAATTCAAAATTTAAGAAA
Found at i:21223 original size:2 final size:2
Alignment explanation
Indices: 21216--21242 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21206 TTAAAAGTTA
21216 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
21243 ATGAATTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28987 original size:160 final size:160
Alignment explanation
Indices: 28721--29017 Score: 454
Period size: 160 Copynumber: 1.9 Consensus size: 160
28711 GACACCAGAG
* * *
28721 AGCTTAAGGTGGTGGTCCATGTAATTTCAAACTGTATCATGATTGCTAAGTGATACCTTAATTGC
1 AGCTTAAGGTGGTGGCCCATGTAATTCCAAAATGTATCATGATTGCTAAGTGATACCTTAATTGC
* ** *
28786 TCAAAGAGTCTCTATATGATAAAGGCATCAGATTTAAATCATATTGCACTTTTCAACGCAACACC
66 CCAAAGAACCTCTATATGACAAAGGCATCAGATTTAAATCATATTGCACTTTTCAACGCAACACC
28851 ATGCACTTTTAAAATTCTAACTCTGAAAAA
131 ATGCACTTTTAAAATTCTAACTCTGAAAAA
* * * *
28881 AGCTTAAGGTGGTGGCCCGTGTAATTCCAAAATGTATCGTGGTTGTTAAGTGATA-CTCTAATTG
1 AGCTTAAGGTGGTGGCCCATGTAATTCCAAAATGTATCATGATTGCTAAGTGATACCT-TAATTG
*
28945 CCCAAAGAACCTCTATATGACAAAGGCATTAG-TTTCAAATCATATTGCACTTTTCAACGCAACA
65 CCCAAAGAACCTCTATATGACAAAGGCATCAGATTT-AAATCATATTGCACTTTTCAACGCAACA
29009 CCATGCACT
129 CCATGCACT
29018 CTTGCTCTTC
Statistics
Matches: 123, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
159 5 0.04
160 118 0.96
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (160 bp):
AGCTTAAGGTGGTGGCCCATGTAATTCCAAAATGTATCATGATTGCTAAGTGATACCTTAATTGC
CCAAAGAACCTCTATATGACAAAGGCATCAGATTTAAATCATATTGCACTTTTCAACGCAACACC
ATGCACTTTTAAAATTCTAACTCTGAAAAA
Found at i:34024 original size:17 final size:16
Alignment explanation
Indices: 34001--34083 Score: 54
Period size: 17 Copynumber: 5.4 Consensus size: 16
33991 ACAAATATTC
34001 ATATACTAAATATATA
1 ATATACTAAATATATA
*
34017 ATATTACTCTAATATA-A
1 ATA-TACT-AAATATATA
*
34034 ACAT--TAAA-ATA-A
1 ATATACTAAATATATA
* *
34046 TTAAAC-AAATATAT-
1 ATATACTAAATATATA
34060 ATATACTAAATATATA
1 ATATACTAAATATATA
34076 ATACTACT
1 ATA-TACT
34084 CTAATATAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 17
0.67 0.11 0.23
Matches are distributed among these distances:
12 5 0.10
13 5 0.10
14 8 0.16
15 8 0.16
16 7 0.14
17 11 0.22
18 6 0.12
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (16 bp):
ATATACTAAATATATA
Found at i:34046 original size:28 final size:28
Alignment explanation
Indices: 34014--34105 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 28
34004 TACTAAATAT
34014 ATAATATTACTCTAATATAAACATTAAA
1 ATAATATTACTCTAATATAAACATTAAA
** * * *
34042 AT-A-ATTAAACAAATATATATATACTAAATA
1 ATAATATTACTCTAATATA-A-ACA-TTAA-A
*
34072 TATAATACTACTCTAATATAAACATTAAA
1 -ATAATATTACTCTAATATAAACATTAAA
34101 ATAAT
1 ATAAT
34106 GTTAAGATAA
Statistics
Matches: 46, Mismatches: 11, Indels: 14
0.65 0.15 0.20
Matches are distributed among these distances:
26 11 0.24
27 2 0.04
28 9 0.20
29 4 0.09
30 4 0.09
31 4 0.09
32 2 0.04
33 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (28 bp):
ATAATATTACTCTAATATAAACATTAAA
Found at i:34074 original size:13 final size:14
Alignment explanation
Indices: 34052--34081 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
34042 ATAATTAAAC
34052 AAATATATATATACT
1 AAATATATA-ATACT
34067 AAATATATAATACT
1 AAATATATAATACT
34081 A
1 A
34082 CTCTAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATATATAATACT
Found at i:34078 original size:59 final size:59
Alignment explanation
Indices: 33986--34105 Score: 215
Period size: 59 Copynumber: 2.0 Consensus size: 59
33976 TTTAGAACAC
*
33986 ATTAAACAAATATTCATATACTAAATATATAATATTACTCTAATATAAACATTAAAATA
1 ATTAAACAAATATTCATATACTAAATATATAATACTACTCTAATATAAACATTAAAATA
34045 ATTAAACAAATATAT-ATATACTAAATATATAATACTACTCTAATATAAACATTAAAATA
1 ATTAAACAAATAT-TCATATACTAAATATATAATACTACTCTAATATAAACATTAAAATA
34104 AT
1 AT
34106 GTTAAGATAA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
59 58 0.98
60 1 0.02
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (59 bp):
ATTAAACAAATATTCATATACTAAATATATAATACTACTCTAATATAAACATTAAAATA
Found at i:34154 original size:16 final size:16
Alignment explanation
Indices: 34135--34181 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
34125 AAAATTTCAT
*
34135 AAATAAAAAATATATA
1 AAATATAAAATATATA
*
34151 AAATTATTAAATAT-TA
1 AAA-TATAAAATATATA
34167 AAATATTAAAATATA
1 AAATA-TAAAATATA
34182 AATATATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 2 0.08
16 15 0.60
17 8 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATATAAAATATATA
Found at i:34202 original size:7 final size:8
Alignment explanation
Indices: 34141--34202 Score: 65
Period size: 8 Copynumber: 7.5 Consensus size: 8
34131 TCATAAATAA
34141 AAAATATAT
1 AAAATAT-T
34150 AAAATTATT
1 AAAA-TATT
34159 -AAATATT
1 AAAATATT
34166 AAAATATT
1 AAAATATT
34174 AAAATA-T
1 AAAATATT
34181 AAATATATTT
1 AAA-ATA-TT
*
34191 AAAAAATT
1 AAAATATT
34199 AAAA
1 AAAA
34203 AATAATATCA
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
7 8 0.17
8 25 0.53
9 7 0.15
10 7 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAAATATT
Found at i:36526 original size:42 final size:42
Alignment explanation
Indices: 36467--36558 Score: 184
Period size: 42 Copynumber: 2.2 Consensus size: 42
36457 AAACCAAACT
36467 TGCTTCTGCTCCATCTATGGGCCTAAACAACACTGTAAGAAC
1 TGCTTCTGCTCCATCTATGGGCCTAAACAACACTGTAAGAAC
36509 TGCTTCTGCTCCATCTATGGGCCTAAACAACACTGTAAGAAC
1 TGCTTCTGCTCCATCTATGGGCCTAAACAACACTGTAAGAAC
36551 TGCTTCTG
1 TGCTTCTG
36559 TCTGTAAATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (42 bp):
TGCTTCTGCTCCATCTATGGGCCTAAACAACACTGTAAGAAC
Found at i:40792 original size:22 final size:20
Alignment explanation
Indices: 40764--40810 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
40754 TTTTCTATAA
40764 TTTTTTATTAGAAAAAAATTAT
1 TTTTTTATT--AAAAAAATTAT
**
40786 TTTTTTATTTTAAAAATTAT
1 TTTTTTATTAAAAAAATTAT
40806 TTTTT
1 TTTTT
40811 ATTTAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 14 0.61
22 9 0.39
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTTTATTAAAAAAATTAT
Found at i:40800 original size:20 final size:18
Alignment explanation
Indices: 40777--40818 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 18
40767 TTTATTAGAA
40777 AAAAATTATTTTTTTATTTT
1 AAAAATTA-TTTTTTA-TTT
40797 AAAAATTATTTTTTATTT
1 AAAAATTATTTTTTATTT
40815 AAAA
1 AAAA
40819 TATGACCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AAAAATTATTTTTTATTT
Found at i:43712 original size:5 final size:5
Alignment explanation
Indices: 43702--43744 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
43692 TTATAGGGTT
43702 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
43745 GATCTCGCAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:44291 original size:22 final size:23
Alignment explanation
Indices: 44266--44326 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
44256 AACTTTCTTT
*
44266 TTTTTGCTATTGTTTTG-T-TTCA
1 TTTTTGTTATTGTTTTGCTATT-A
* *
44288 TTTTCGTTATTGTATTGCTATTA
1 TTTTTGTTATTGTTTTGCTATTA
44311 TTTGTTGTTATTGTTT
1 TTT-TTGTTATTGTTT
44327 GGATATTGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 14 0.45
23 5 0.16
24 12 0.39
ACGTcount: A:0.11, C:0.07, G:0.15, T:0.67
Consensus pattern (23 bp):
TTTTTGTTATTGTTTTGCTATTA
Found at i:45204 original size:29 final size:29
Alignment explanation
Indices: 45168--45242 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
45158 GAACCAAAAT
45168 TGAGAAAAATTGTCAAGTTTTAGAATTAA
1 TGAGAAAAATTGTCAAGTTTTAGAATTAA
45197 TGAGAAAAATTGTCAAGTTTTAGAATTAA
1 TGAGAAAAATTGTCAAGTTTTAGAATTAA
*
45226 TGTGAAAAAATT-TCAAG
1 TGAG-AAAAATTGTCAAG
45243 AACCAATTGT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 37 0.84
30 7 0.16
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.33
Consensus pattern (29 bp):
TGAGAAAAATTGTCAAGTTTTAGAATTAA
Found at i:65217 original size:22 final size:22
Alignment explanation
Indices: 65192--65248 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
65182 AACTTAAATT
65192 ATATATTTTTATAATAGTAAAA
1 ATATATTTTTATAATAGTAAAA
* * ** *
65214 ATATAGTTTTATTATTTTAATA
1 ATATATTTTTATAATAGTAAAA
*
65236 ACATATTTTTATA
1 ATATATTTTTATA
65249 GTTTTTAAAT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (22 bp):
ATATATTTTTATAATAGTAAAA
Found at i:65462 original size:5 final size:5
Alignment explanation
Indices: 65452--65497 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
65442 AAATTATAAT
65452 AATTA AATTA AATTA AATTA TAA--A AATTCA AATT- AATTA AATTA AA
1 AATTA AATTA AATTA AATTA -AATTA AATT-A AATTA AATTA AATTA AA
65498 ACTTTACAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
3 2 0.06
4 5 0.14
5 22 0.61
6 7 0.19
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (5 bp):
AATTA
Found at i:65473 original size:24 final size:24
Alignment explanation
Indices: 65441--65495 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
65431 TATAAAATCA
*
65441 TAAATTATAATAATT-AAATTAAAT
1 TAAATTATAAAAATTCAAATT-AAT
65465 TAAATTATAAAAATTCAAATTAAT
1 TAAATTATAAAAATTCAAATTAAT
65489 TAAATTA
1 TAAATTA
65496 AAACTTTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
TAAATTATAAAAATTCAAATTAAT
Found at i:65728 original size:26 final size:25
Alignment explanation
Indices: 65691--65746 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 25
65681 AAATAAAATT
65691 ATTTTTTTT-AAA-ATAATATATGA
1 ATTTTTTTTAAAATATAATATATGA
65714 ACTTTTTTTGATAAAATATAATATATGA
1 A-TTTTTTT--TAAAATATAATATATGA
65742 ATTTT
1 ATTTT
65747 GAATTAGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 1 0.04
24 7 0.25
26 1 0.04
27 7 0.25
28 12 0.43
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (25 bp):
ATTTTTTTTAAAATATAATATATGA
Found at i:65931 original size:15 final size:15
Alignment explanation
Indices: 65911--65944 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
65901 ACTATGTTTA
65911 TTTATAATATTTATT
1 TTTATAATATTTATT
* *
65926 TTTATATTTTTTATT
1 TTTATAATATTTATT
65941 TTTA
1 TTTA
65945 AAATTACCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATAATATTTATT
Found at i:68018 original size:57 final size:57
Alignment explanation
Indices: 67891--68301 Score: 374
Period size: 57 Copynumber: 7.0 Consensus size: 57
67881 AAATTCATGT
* *** * **
67891 AATGGTCGACACCCCCTTTTGGAGAAAAAAAATTTCAATTTTTTTTGTGTTGGCCATCA
1 AATGGCCGACACCCCCTTTTCTCGAAAAAAAATTGC-A-TTTTTGGGTGTTGGCCATCA
* * * * * **
67950 AATAGCTGACACCCCATTTTCTCGAAAAAAAATTGCATGTTTGGGTGTTGGTCATTG
1 AATGGCCGACACCCCCTTTTCTCGAAAAAAAATTGCATTTTTGGGTGTTGGCCATCA
* * * * * *
68007 CATGACCGACACCCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGATGTTGGCTATCA
1 AATGGCCGACACCCCCTTTTCTCGA-AAAAAAATTGC---ATTTTTGGGTGTTGGCCATCA
* * * * *
68068 AATGGCCGACA-CCCCTTTTCTTGAAAAAAAAATGCATTTTTGGGTGTTGACTATTGTA
1 AATGGCCGACACCCCCTTTTCTCGAAAAAAAATTGCATTTTTGGGTGTTGGCCA-T-CA
* * ** **
68126 TAATGGTCGACACCCTCTTTTCTCGAGAAAAAAATTTTAAAATTTTTTAGTGTTGGCCATCA
1 -AATGGCCGACACCCCCTTTTCTCGA-AAAAAAA--TT-GCATTTTTGGGTGTTGGCCATCA
*
68188 AATGGTCGACACCCCCTTTTCTCGAAAAAAAATTGCATTTTTGGGTGTTGGCCATCA
1 AATGGCCGACACCCCCTTTTCTCGAAAAAAAATTGCATTTTTGGGTGTTGGCCATCA
* *
68245 AATGGCTGACACCCCCTTTTCTCGAAAAAGAAAATTGTATTTTTGGGTGTTGGCCAT
1 AATGGCCGACACCCCCTTTTCTCG-AAAA-AAAATTGCATTTTTGGGTGTTGGCCAT
68302 GAAAATTTTC
Statistics
Matches: 283, Mismatches: 55, Indels: 28
0.77 0.15 0.08
Matches are distributed among these distances:
56 15 0.05
57 76 0.27
58 18 0.06
59 73 0.26
60 30 0.11
61 54 0.19
62 1 0.00
63 2 0.01
64 14 0.05
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (57 bp):
AATGGCCGACACCCCCTTTTCTCGAAAAAAAATTGCATTTTTGGGTGTTGGCCATCA
Found at i:68168 original size:120 final size:117
Alignment explanation
Indices: 67888--68280 Score: 442
Period size: 117 Copynumber: 3.3 Consensus size: 117
67878 AAAAAATTCA
* * **
67888 TGTAATGGTCGACACCCCCTTT-TGGAGAAAAAAAATTTCAATTTTTTTTG-TGTTGGCCATCAA
1 TGTAATGGTCGACACCCCTTTTCTCGAG-AAAAAAATTTCAAAATTTTTTGATGTTGGCCATCAA
* * * *
67951 ATAGCTGACACCCCATTTTCTCGAAAAAAAATTGCATGTTTGGGTGTTGGTCAT
65 ATGGCCGACACCCC-TTTTCTCGAAAAAAAATTGCATTTTTGGGTGTTGCTCAT
* ** *
68005 TG-CATGACCGACACCCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGATGTTGGCTATCAA
1 TGTAATGGTCGACA-CCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGATGTTGGCCATCAA
* *
68069 ATGGCCGACACCCCTTTTCTTGAAAAAAAAATGCATTTTTGGGTGTTGACT-AT
65 ATGGCCGACACCCCTTTTCTCGAAAAAAAATTGCATTTTTGGGTGTTG-CTCAT
*
68122 TGTATAATGGTCGACACCCTCTTTTCTCGAGAAAAAAATTTTAAAATTTTTT-AGTGTTGGCCAT
1 TG--TAATGGTCGACACCC-CTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGA-TGTTGGCCAT
*
68186 CAAATGGTCGACACCCCCTTTTCTCGAAAAAAAATTGCATTTTTGGGTGTTGGC-CA-
62 CAAATGGCCGACA-CCCCTTTTCTCGAAAAAAAATTGCATTTTTGGGTGTT-GCTCAT
** *
68242 TCAAATGG-CTGACACCCCCTTTTCTCGAAAAAGAAAATT
1 TGTAATGGTC-GACA-CCCCTTTTCTCGAGAAA-AAAATT
68281 GTATTTTTGG
Statistics
Matches: 236, Mismatches: 25, Indels: 28
0.82 0.09 0.10
Matches are distributed among these distances:
116 8 0.03
117 65 0.28
118 51 0.22
119 13 0.06
120 61 0.26
121 37 0.16
122 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (117 bp):
TGTAATGGTCGACACCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGATGTTGGCCATCAAA
TGGCCGACACCCCTTTTCTCGAAAAAAAATTGCATTTTTGGGTGTTGCTCAT
Found at i:71954 original size:11 final size:11
Alignment explanation
Indices: 71940--72005 Score: 80
Period size: 11 Copynumber: 5.9 Consensus size: 11
71930 GCCCTTTTTT
*
71940 AATTTATTTTA
1 AATTTAATTTA
*
71951 AATTTGATTTA
1 AATTTAATTTA
*
71962 AATTTAAATT-
1 AATTTAATTTA
71972 AATCTTAAATTTA
1 AAT-TT-AATTTA
71985 AATTTAATTTA
1 AATTTAATTTA
71996 AATTTAATTT
1 AATTTAATTT
72006 CAAAATTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
10 3 0.06
11 35 0.74
12 6 0.13
13 3 0.06
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:71968 original size:6 final size:6
Alignment explanation
Indices: 71947--72015 Score: 67
Period size: 6 Copynumber: 12.0 Consensus size: 6
71937 TTTAATTTAT
*
71947 TTTAAA TTT-GA TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA
*
71992 TTTAAA TTT-AA TTTCAAA ATTAAA
1 TTTAAA TTTAAA TTT-AAA TTTAAA
72016 AAGTCCAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
4 2 0.04
5 16 0.30
6 28 0.53
7 7 0.13
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:71969 original size:17 final size:17
Alignment explanation
Indices: 71937--72002 Score: 91
Period size: 17 Copynumber: 3.9 Consensus size: 17
71927 TGGGCCCTTT
*
71937 TTTAATTT-ATTTTAAA
1 TTTAATTTAAATTTAAA
*
71953 TTTGATTTAAATTTAAA
1 TTTAATTTAAATTTAAA
71970 -TTAATCTTAAATTTAAA
1 TTTAAT-TTAAATTTAAA
71987 TTTAATTTAAATTTAA
1 TTTAATTTAAATTTAA
72003 TTTCAAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
16 11 0.25
17 28 0.64
18 5 0.11
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTAATTTAAATTTAAA
Found at i:72620 original size:18 final size:19
Alignment explanation
Indices: 72606--72643 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
72596 AAATATTTTA
72606 AATGAGTTCATTA-TTAAT
1 AATGAGTTCATTATTTAAT
*
72624 AATGGGTTCATTA-TTAAT
1 AATGAGTTCATTATTTAAT
72642 AA
1 AA
72644 GTACTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.42
Consensus pattern (19 bp):
AATGAGTTCATTATTTAAT
Found at i:73895 original size:29 final size:28
Alignment explanation
Indices: 73863--74149 Score: 132
Period size: 29 Copynumber: 9.8 Consensus size: 28
73853 GAAATTACCA
*
73863 TTTTACCCTCGAACTTCTAAAAATCCCAT
1 TTTTACCC-CAAACTTCTAAAAATCCCAT
* * **
73892 TTTTAACCCCGAAACTACAAAAAATTAACA-
1 TTTT-ACCCC-AAACTTCTAAAAA-TCCCAT
* * * *
73922 TTTCACCCCTAAACTCCCAAAAATTCCAT
1 TTTTACCCC-AAACTTCTAAAAATCCCAT
* ** *
73951 TTTAACCCCAAAACTTCTAAAAATTACAA
1 TTTTACCCC-AAACTTCTAAAAATCCCAT
*
73980 TTTTACCCCAAAACTTCAAAAAATCCCAT
1 TTTTACCCC-AAACTTCTAAAAATCCCAT
* * * * *
74009 TTTTGATCTCGAACCCTCTAAAAATTACCA-
1 TTTT-A-CCCCAAACTTCTAAAAA-TCCCAT
* * * *
74039 TTTAACCCTAAACTCCCAAAAATCCCAT
1 TTTTACCCCAAACTTCTAAAAATCCCAT
*
74067 TTTTGACCCCGAAACTTCTAAAAATTACCA-
1 TTTT-ACCCC-AAACTTCTAAAAA-TCCCAT
* * ** *
74097 TTTCACCCCCAAAC-ACCCAAAATCCTAT
1 TTTTA-CCCCAAACTTCTAAAAATCCCAT
*
74125 TTTTGACCCTAAAACTTCTAAAAAT
1 TTTT-ACCC-CAAACTTCTAAAAAT
74150 TACAATTTTA
Statistics
Matches: 190, Mismatches: 52, Indels: 31
0.70 0.19 0.11
Matches are distributed among these distances:
27 7 0.04
28 28 0.15
29 87 0.46
30 55 0.29
31 13 0.07
ACGTcount: A:0.39, C:0.30, G:0.02, T:0.29
Consensus pattern (28 bp):
TTTTACCCCAAACTTCTAAAAATCCCAT
Found at i:73988 original size:58 final size:59
Alignment explanation
Indices: 73849--74218 Score: 356
Period size: 58 Copynumber: 6.3 Consensus size: 59
73839 CCCTAAAATG
* * * * * *
73849 TCTAGAAATTACCATTTTA-CCCTCGAACTTCTAAAAATCCCATTTTTAACCCCGAAACT
1 TCTAAAAATTACAATTTTACCCCT-AAACTCCCAAAAATCCCATTTTTGACCCCGAAACT
* * * * * *
73908 ACAAAAAATTA-ACATTTCACCCCTAAACTCCCAAAAATTCCA-TTTTAACCCCAAAACT
1 TCTAAAAATTACA-ATTTTACCCCTAAACTCCCAAAAATCCCATTTTTGACCCCGAAACT
* * * * * * *
73966 TCTAAAAATTACAATTTTACCCCAAAACTTCAAAAAATCCCATTTTTGATCTCGAACCC
1 TCTAAAAATTACAATTTTACCCCTAAACTCCCAAAAATCCCATTTTTGACCCCGAAACT
* *
74025 TCTAAAAATTACCA-TTTAACCCTAAACTCCCAAAAATCCCATTTTTGACCCCGAAACT
1 TCTAAAAATTACAATTTTACCCCTAAACTCCCAAAAATCCCATTTTTGACCCCGAAACT
* * * * * **
74083 TCTAAAAATTACCATTTCACCCCCAAACACCC-AAAATCCTATTTTTGACCCTAAAACT
1 TCTAAAAATTACAATTTTACCCCTAAACTCCCAAAAATCCCATTTTTGACCCCGAAACT
* * * * * *
74141 TCTAAAAATTACAATTTTACCCTTGAGCTCCCAAAAATCTCA-TTTTGACCTCGAAACA
1 TCTAAAAATTACAATTTTACCCCTAAACTCCCAAAAATCCCATTTTTGACCCCGAAACT
* *
74199 TCCAAAAATTACTATTTTAC
1 TCTAAAAATTACAATTTTAC
74219 TCTCGGATGT
Statistics
Matches: 251, Mismatches: 54, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
58 176 0.70
59 71 0.28
60 4 0.02
ACGTcount: A:0.38, C:0.29, G:0.03, T:0.29
Consensus pattern (59 bp):
TCTAAAAATTACAATTTTACCCCTAAACTCCCAAAAATCCCATTTTTGACCCCGAAACT
Found at i:74076 original size:117 final size:113
Alignment explanation
Indices: 73849--74218 Score: 364
Period size: 117 Copynumber: 3.2 Consensus size: 113
73839 CCCTAAAATG
* * * * * *
73849 TCTAGAAATTACCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTAACCCCGAAACTACAAAA
1 TCTAAAAATTACCATTTTACCC-CAAACTTCAAAAAATCCCATTTTTGA-CCCGAACCT-CTAAA
* * * * *
73914 AATTAACATTTCACCCCTAAACTCCCAAAAATTCCATTTTAACCCCAAAACT
63 AATTACCATTT-AACCCTAAACTCCCAAAAATCCCATTTTGACCCCGAAACT
* *
73966 TCTAAAAATTACAATTTTACCCCAAAACTTCAAAAAATCCCATTTTTGATCTCGAACCCTCTAAA
1 TCTAAAAATTACCATTTTACCCC-AAACTTCAAAAAATCCCATTTTTGA-CCCGAA-CCTCTAAA
74031 AATTACCATTTAACCCTAAACTCCCAAAAATCCCATTTTTGACCCCGAAACT
63 AATTACCATTTAACCCTAAACTCCCAAAAATCCCA-TTTTGACCCCGAAACT
* * ** * * *
74083 TCTAAAAATTACCATTTCACCCCCAAAC-ACCCAAAATCCTATTTTTGACCCTAAAACTTCTAAA
1 TCTAAAAATTACCATTTTA-CCCCAAACTTCAAAAAATCCCATTTTTGACCC--GAACCTCTAAA
* * * * * * *
74147 AATTACAATTTTACCCTTGAGCTCCCAAAAATCTCATTTTGACCTCGAAACA
63 AATTACCATTTAACCC-TAAACTCCCAAAAATCCCATTTTGACCCCGAAACT
* *
74199 TCCAAAAATTACTATTTTAC
1 TCTAAAAATTACCATTTTAC
74219 TCTCGGATGT
Statistics
Matches: 213, Mismatches: 33, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
115 3 0.01
116 90 0.42
117 114 0.54
118 6 0.03
ACGTcount: A:0.38, C:0.29, G:0.03, T:0.29
Consensus pattern (113 bp):
TCTAAAAATTACCATTTTACCCCAAACTTCAAAAAATCCCATTTTTGACCCGAACCTCTAAAAAT
TACCATTTAACCCTAAACTCCCAAAAATCCCATTTTGACCCCGAAACT
Found at i:74162 original size:29 final size:29
Alignment explanation
Indices: 73839--74163 Score: 117
Period size: 29 Copynumber: 11.1 Consensus size: 29
73829 CCCCGAAGGT
* *
73839 CCCTAAAA-TGTCTAGAAATTACCATTTTA
1 CCCTAAAACT-TCTAAAAATTACAATTTTA
** ** *
73868 CCCTCGAACTTCTAAAAATCCCATTTTTAA
1 CCCTAAAACTTCTAAAAATTACAATTTT-A
** * * *
73898 CCCCGAAACTACAAAAAATTA-ACATTTCA
1 CCCTAAAACTTCTAAAAATTACA-ATTTTA
* * *
73927 CCCCT-AAACTCCCAAAAATT-CCATTTTAA
1 -CCCTAAAACTTCTAAAAATTACAATTTT-A
*
73956 CCCCAAAACTTCTAAAAATTACAATTTTA
1 CCCTAAAACTTCTAAAAATTACAATTTTA
* * ** *
73985 CCCCAAAACTTCAAAAAATCCCATTTTTGA
1 CCCTAAAACTTCTAAAAATTACAATTTT-A
* * * * * *
74015 -TCTCGAACCCTCTAAAAATTACCATTTAA
1 CCCT-AAAACTTCTAAAAATTACAATTTTA
* * ** *
74044 CCCT-AAACTCCCAAAAATCCCATTTTTGA
1 CCCTAAAACTTCTAAAAATTACAATTTT-A
** * *
74073 CCCCGAAACTTCTAAAAATTACCATTTCA
1 CCCTAAAACTTCTAAAAATTACAATTTTA
** * ** * *
74102 CCCCCAAAC-ACCCAAAA-TCCTATTTTTGA
1 CCCTAAAACTTCTAAAAATTAC-AATTTT-A
74131 CCCTAAAACTTCTAAAAATTACAATTTTA
1 CCCTAAAACTTCTAAAAATTACAATTTTA
74160 CCCT
1 CCCT
74164 TGAGCTCCCA
Statistics
Matches: 206, Mismatches: 73, Indels: 34
0.66 0.23 0.11
Matches are distributed among these distances:
27 2 0.01
28 29 0.14
29 101 0.49
30 72 0.35
31 2 0.01
ACGTcount: A:0.39, C:0.30, G:0.03, T:0.29
Consensus pattern (29 bp):
CCCTAAAACTTCTAAAAATTACAATTTTA
Done.