Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010410.1 Kokia drynarioides strain JFW-HI SEQ_125295, 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: 201824
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:8173 original size:96 final size:96
Alignment explanation
Indices: 7996--8180 Score: 241
Period size: 96 Copynumber: 1.9 Consensus size: 96
7986 GAAAATGATG
* ** *
7996 TTCGATTATCTCGATTGGAGGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTTAGAATCGA
1 TTCGATTATCTCGATTGGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTGAGAATCGA
8061 AGATAAGAAAACATTGCCTCGATTAAGGGTA
66 AGATAAGAAAACATTGCCTCGATTAAGGGTA
* * *
8092 TTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGTAAATTTTCGA-AACTC
1 TTCGATTATCTCGATTGGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTT-GAGAA-TC
* *
8156 GAA-ATAA-AAGAATATTGCCTTGATT
64 GAAGATAAGAA-AACATTGCCTCGATT
8181 TTAAAGTTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
95 2 0.03
96 69 0.90
97 6 0.08
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (96 bp):
TTCGATTATCTCGATTGGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTGAGAATCGA
AGATAAGAAAACATTGCCTCGATTAAGGGTA
Found at i:8511 original size:59 final size:60
Alignment explanation
Indices: 8434--8695 Score: 188
Period size: 58 Copynumber: 4.5 Consensus size: 60
8424 ATTTTGGATT
* *
8434 TTCGAGGGCAAAATGGTAATTTTGGGAAAATTC-ATAGTTAAAAATGGAATTTTTAGACA
1 TTCGAGGGTAAAAAGGTAATTTTGGGAAAATTCGATAGTTAAAAATGGAATTTTTAGACA
* * * ** * * *
8493 TTTGAGGGTAAAAAGGTAATTTTAAGGG---TTTCGA-GGTCGAAAATAGAGTTTTTTGACA
1 TTCGAGGGTAAAAAGGTAATTTT--GGGAAAATTCGATAGTTAAAAATGGAATTTTTAGACA
* * * * * * *
8551 TTCGGGGGTAAAATGGTAATTTT-AGAAAGTTTCGAT--TTTAAAATGGAAATTTTAGAGA
1 TTCGAGGGTAAAAAGGTAATTTTGGGAAA-ATTCGATAGTTAAAAATGGAATTTTTAGACA
* * * *
8609 TTCGAGGGTAAAAATGG-AATTTTTGGAAATTTTGA-GGTTAAAAATGGAATTTTTAGA-A
1 TTCGAGGGTAAAAA-GGTAATTTTGGGAAAATTCGATAGTTAAAAATGGAATTTTTAGACA
*
8667 GTTCGAGGGTAAAAAAGG-AATTTTTGGAA
1 -TTCGAGGGT-AAAAAGGTAATTTTGGGAA
8696 GTTTCGGGGT
Statistics
Matches: 162, Mismatches: 27, Indels: 28
0.75 0.12 0.13
Matches are distributed among these distances:
55 1 0.01
58 80 0.49
59 73 0.45
60 5 0.03
61 3 0.02
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (60 bp):
TTCGAGGGTAAAAAGGTAATTTTGGGAAAATTCGATAGTTAAAAATGGAATTTTTAGACA
Found at i:8652 original size:30 final size:30
Alignment explanation
Indices: 8415--8722 Score: 162
Period size: 29 Copynumber: 10.5 Consensus size: 30
8405 CTCGGGAGGT
* *
8415 AAAATGGTAA-TTTTGG-ATTTTCGAGGG-C
1 AAAATGG-AATTTTTGGAAATTTCGAGGGTA
* * * *
8443 AAAATGGTAATTTTGGGAAAATTC-ATAGTTA
1 AAAATGG-AATTTTTGGAAATTTCGA-GGGTA
* *
8474 AAAATGGAATTTTTAGACATTT-GAGGGTA
1 AAAATGGAATTTTTGGAAATTTCGAGGGTA
* * *
8503 AAAA-GGTAATTTTAAGG--GTTTCGA-GGTCG
1 AAAATGG-AATTTT-TGGAAATTTCGAGGGT-A
* * * * *
8532 AAAATAGAGTTTTTTGACA-TTCGGGGGT-
1 AAAATGGAATTTTTGGAAATTTCGAGGGTA
* ** *
8560 AAAATGGTAA-TTTTAGAAAGTTTCGA-TTTT
1 AAAATGG-AATTTTTGGAAA-TTTCGAGGGTA
* * *
8590 AAAATGGAAATTTTAGAGA-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAATTTCGAGGGTA
* *
8619 AAAATGGAATTTTTGGAAATTTTGAGGTTA
1 AAAATGGAATTTTTGGAAATTTCGAGGGTA
* *
8649 AAAATGGAATTTTTAG-AAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAATTTCGAGGGTA
* *
8678 AAAAAGGAATTTTTGGAAGTTTCG-GGGTA
1 AAAATGGAATTTTTGGAAATTTCGAGGGTA
*
8707 AAAATGGAAGTTTTGG
1 AAAATGGAATTTTTGG
8723 GGTCAAAATG
Statistics
Matches: 211, Mismatches: 48, Indels: 41
0.70 0.16 0.14
Matches are distributed among these distances:
28 37 0.18
29 98 0.46
30 69 0.33
31 7 0.03
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAATTTCGAGGGTA
Found at i:8721 original size:29 final size:29
Alignment explanation
Indices: 8555--8856 Score: 168
Period size: 29 Copynumber: 10.7 Consensus size: 29
8545 TTGACATTCG
* *
8555 GGGGT-AAAATGGTAATTTTAGAAAGTTTC
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTC
*** * * * *
8584 GATTTTAAAATGGAAATTTTAG-AGATTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
* *
8612 GAGGGTAAAAATGGAATTTTTGGAAATTTT
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTC
* *
8642 GAGGTTAAAAATGGAATTTTTAGAAG-TTC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTC
*
8671 GAGGGTAAAAAAGGAATTTTTGGAAGTTTC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTC
* *
8701 GGGGTAAAAATGGAAGTTTTGG--G-GTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
** * *
8727 -----AAAATGGAAATTTTTT-AAG-TTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
* *
8749 GAGGGT-AAAATGGAATTTTTAGAAGTTTTA
1 G-GGGTAAAAATGGAATTTTTGGAAG-TTTC
* *
8779 AGGTTAAAAATGGAATTTTTGGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
* * *
8808 GAGATCAAAAAT-AAGATTTTTGGAAG-TTC
1 GGGGT-AAAAATGGA-ATTTTTGGAAGTTTC
8837 TGGGGTAAAAATGGAATTTT
1 -GGGGTAAAAATGGAATTTT
8857 CAGACAGTTT
Statistics
Matches: 204, Mismatches: 49, Indels: 40
0.70 0.17 0.14
Matches are distributed among these distances:
21 11 0.05
22 3 0.01
26 2 0.01
27 12 0.06
28 9 0.04
29 89 0.44
30 78 0.38
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTC
Found at i:8741 original size:21 final size:20
Alignment explanation
Indices: 8691--8740 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
8681 AAGGAATTTT
*
8691 TGGAAGTTTCGGGGTAAAAA
1 TGGAAGTTTTGGGGTAAAAA
*
8711 TGGAAGTTTTGGGGTCAAAA
1 TGGAAGTTTTGGGGTAAAAA
*
8731 TGGAAATTTT
1 TGGAAGTTTT
8741 TTAAGTTCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.32
Consensus pattern (20 bp):
TGGAAGTTTTGGGGTAAAAA
Found at i:8787 original size:78 final size:78
Alignment explanation
Indices: 8649--8800 Score: 209
Period size: 78 Copynumber: 1.9 Consensus size: 78
8639 TTTGAGGTTA
* **
8649 AAAATGGAATTTTTAGAAGTTCGAGGGTAAAAAAGGAATTTTTGGAAGTTTCGGGGTAAAAATGG
1 AAAATGGAATTTTTAGAAGTTCGAGGGTAAAAAAGGAATTTTTAGAAGTTTAAGGGTAAAAATGG
8714 AAGTTTTGGGGTC
66 AAGTTTTGGGGTC
* * *
8727 AAAATGGAAATTTTT-TAAGTTCGAGGGT-AAAATGGAATTTTTAGAAGTTTTAAGGTTAAAAAT
1 AAAATGG-AATTTTTAGAAGTTCGAGGGTAAAAAAGGAATTTTTAGAAG-TTTAAGGGTAAAAAT
*
8790 GGAATTTTTGG
64 GGAAGTTTTGG
8801 AAGTTTCGAG
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
77 17 0.26
78 41 0.63
79 7 0.11
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (78 bp):
AAAATGGAATTTTTAGAAGTTCGAGGGTAAAAAAGGAATTTTTAGAAGTTTAAGGGTAAAAATGG
AAGTTTTGGGGTC
Found at i:8818 original size:30 final size:29
Alignment explanation
Indices: 8711--8856 Score: 113
Period size: 30 Copynumber: 5.0 Consensus size: 29
8701 GGGGTAAAAA
* * *
8711 TGGAAGTTTTGGGGTCAAAATGGAAATTTT
1 TGGAAGTTTCGAGGTAAAAATGG-AATTTT
*
8741 T-TAAG-TTCGAGGGT-AAAATGGAATTTT
1 TGGAAGTTTCGA-GGTAAAAATGGAATTTT
* **
8768 TAGAAGTTTTAAGGTTAAAAATGGAATTTT
1 TGGAAGTTTCGAGG-TAAAAATGGAATTTT
* *
8798 TGGAAGTTTCGAGATCAAAAAT-AAGATTTT
1 TGGAAGTTTCGAGGT-AAAAATGGA-ATTTT
*
8828 TGGAAG-TTCTGGGGTAAAAATGGAATTTT
1 TGGAAGTTTC-GAGGTAAAAATGGAATTTT
8857 CAGACAGTTT
Statistics
Matches: 93, Mismatches: 14, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
27 7 0.08
28 15 0.16
29 26 0.28
30 45 0.48
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.36
Consensus pattern (29 bp):
TGGAAGTTTCGAGGTAAAAATGGAATTTT
Found at i:9920 original size:3 final size:3
Alignment explanation
Indices: 9912--9964 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
9902 TTTCGATTTT
* * *
9912 TTA TTA TTA TTA ATA TCTA TTA TTA TTA TTA -TA TTA TTA ATA ATA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
9957 TTAA TTA T
1 TT-A TTA T
9965 AGTTTTCATT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:10002 original size:9 final size:9
Alignment explanation
Indices: 9916--10017 Score: 68
Period size: 9 Copynumber: 11.2 Consensus size: 9
9906 GATTTTTTAT
9916 TATTATTAA
1 TATTATTAA
*
9925 TATCTATTAT
1 TAT-TATTAA
9935 TATTATT-A
1 TATTATTAA
9943 TATTATTAA
1 TATTATTAA
*
9952 TAATATT-A
1 TATTATTAA
*
9960 -ATTA-TAG
1 TATTATTAA
*
9967 TTTTCATTAA
1 TATT-ATTAA
*
9977 TATTGTTATGA
1 TATTATTA--A
9988 TCATTATTAA
1 T-ATTATTAA
*
9998 TATTAATAA
1 TATTATTAA
*
10007 TATTAATAA
1 TATTATTAA
10016 TA
1 TA
10018 ATGATAACTT
Statistics
Matches: 73, Mismatches: 11, Indels: 18
0.72 0.11 0.18
Matches are distributed among these distances:
6 1 0.01
7 3 0.04
8 10 0.14
9 36 0.49
10 15 0.21
11 2 0.03
12 6 0.08
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (9 bp):
TATTATTAA
Found at i:10660 original size:6 final size:6
Alignment explanation
Indices: 10649--10683 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
10639 ATTATTTAAA
*
10649 TAAATT TAAATT TAAATT TAAA-A TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
10684 CTGTTGGGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
TAAATT
Found at i:10677 original size:11 final size:11
Alignment explanation
Indices: 10642--10681 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
10632 ATTAGACATT
10642 ATTT-AAATAA
1 ATTTAAAATAA
*
10652 ATTTAAATTTAA
1 ATTTAAA-ATAA
10664 ATTTAAAATAA
1 ATTTAAAATAA
10675 ATTTAAA
1 ATTTAAA
10682 TTCTGTTGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 4 0.15
11 12 0.46
12 10 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATTTAAAATAA
Found at i:10809 original size:21 final size:22
Alignment explanation
Indices: 10785--10827 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
10775 TAATATTCAA
*
10785 TTTAATT-GGTTCAATCGATTT
1 TTTAATTCGATTCAATCGATTT
*
10806 TTTAATTCGATTCAATTGATTT
1 TTTAATTCGATTCAATCGATTT
10828 ATATCGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.53
Consensus pattern (22 bp):
TTTAATTCGATTCAATCGATTT
Found at i:26334 original size:30 final size:30
Alignment explanation
Indices: 26298--26358 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
26288 TCCACTACCT
26298 TAGCTTTCCACAACTAAGGATTTTCCCAAA
1 TAGCTTTCCACAACTAAGGATTTTCCCAAA
26328 TAGCTTTCCACAACTAAGGATTTTCCCAAA
1 TAGCTTTCCACAACTAAGGATTTTCCCAAA
26358 T
1 T
26359 CTATTAGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (30 bp):
TAGCTTTCCACAACTAAGGATTTTCCCAAA
Found at i:27091 original size:20 final size:20
Alignment explanation
Indices: 27066--27103 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27056 TCTTCAAGGC
27066 ATCGGTAGAAATGAAGTTGT
1 ATCGGTAGAAATGAAGTTGT
*
27086 ATCGGTAGAAGTGAAGTT
1 ATCGGTAGAAATGAAGTT
27104 CTACCGGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.05, G:0.32, T:0.29
Consensus pattern (20 bp):
ATCGGTAGAAATGAAGTTGT
Found at i:27111 original size:20 final size:20
Alignment explanation
Indices: 27068--27117 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
27058 TTCAAGGCAT
* * *
27068 CGGTAGAAATGAAGTTGTAT
1 CGGTAGAAGTGAAGTTCTAC
27088 CGGTAGAAGTGAAGTTCTAC
1 CGGTAGAAGTGAAGTTCTAC
*
27108 CGGTTGAAGT
1 CGGTAGAAGT
27118 CTCACTGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.10, G:0.32, T:0.28
Consensus pattern (20 bp):
CGGTAGAAGTGAAGTTCTAC
Found at i:29307 original size:24 final size:24
Alignment explanation
Indices: 29263--29308 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
29253 TTAAATCAAA
* *
29263 TTGGATTAGTATTCAACAAATTCG
1 TTGGATTAGAATACAACAAATTCG
*
29287 TTGGATTAGAATACAATAAATT
1 TTGGATTAGAATACAACAAATT
29309 TTGATTCATT
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:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (24 bp):
TTGGATTAGAATACAACAAATTCG
Found at i:30902 original size:20 final size:19
Alignment explanation
Indices: 30857--30903 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
30847 CCATCGGTTA
* *
30857 AATTTAAATTTTAATGTTG
1 AATTTAAATTTCAATCTTG
30876 -ATATTAAATTTCAAGTCTTG
1 AAT-TTAAATTTCAA-TCTTG
30896 AATTTAAA
1 AATTTAAA
30904 ACTTAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 2 0.09
19 10 0.43
20 9 0.39
21 2 0.09
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (19 bp):
AATTTAAATTTCAATCTTG
Found at i:41496 original size:19 final size:19
Alignment explanation
Indices: 41472--41514 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
41462 TAAAAAATAA
*
41472 TTTTTACAA-TTTTTAAGAT
1 TTTTTACAACATTTTAA-AT
41491 TTTTTACAACATTTTAAAT
1 TTTTTACAACATTTTAAAT
41510 TTTTT
1 TTTTT
41515 TTAAAAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTTACAACATTTTAAAT
Found at i:41623 original size:20 final size:20
Alignment explanation
Indices: 41581--41623 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
41571 CAAGTTTTTT
* *
41581 TTTAAATAATTTTTATAACA
1 TTTAAACAATTTTAATAACA
41601 TTTAAACAATGTTTAATAA-A
1 TTTAAACAAT-TTTAATAACA
41621 TTT
1 TTT
41624 TAATCTACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (20 bp):
TTTAAACAATTTTAATAACA
Found at i:41625 original size:21 final size:21
Alignment explanation
Indices: 41580--41626 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
41570 GCAAGTTTTT
* *
41580 TTTTAAATAATTTTTATAACA
1 TTTTAAACAATTTTAATAACA
41601 -TTTAAACAATGTTTAATAA-A
1 TTTTAAACAAT-TTTAATAACA
41621 TTTTAA
1 TTTTAA
41627 TCTACTAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTTAAACAATTTTAATAACA
Found at i:59090 original size:24 final size:24
Alignment explanation
Indices: 59079--59264 Score: 255
Period size: 24 Copynumber: 7.8 Consensus size: 24
59069 TTGTCATTCG
* *
59079 CTATACGTTTATGCTCGTCAGTCT
1 CTATACGTTTATGCTCGTCAGCCA
*
59103 CTATACGTTTACGCTCGTCAGCCA
1 CTATACGTTTATGCTCGTCAGCCA
* * *
59127 TTACACGTTGATGCTCGTCAGCCA
1 CTATACGTTTATGCTCGTCAGCCA
*
59151 CTATACGTTTATGCTCGTCAACCA
1 CTATACGTTTATGCTCGTCAGCCA
* *
59175 CTATACGTTTATGCTCGCCAACCA
1 CTATACGTTTATGCTCGTCAGCCA
*
59199 CTATACGTTTATGCTCGTTAGCCA
1 CTATACGTTTATGCTCGTCAGCCA
* *
59223 CTATACGTTTATGCTCATCAGTCA
1 CTATACGTTTATGCTCGTCAGCCA
*
59247 CTATATGTTTATGCTCGT
1 CTATACGTTTATGCTCGT
59265 ATATTTGGTA
Statistics
Matches: 142, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 142 1.00
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.35
Consensus pattern (24 bp):
CTATACGTTTATGCTCGTCAGCCA
Found at i:66488 original size:15 final size:15
Alignment explanation
Indices: 66460--66489 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
66450 TCATAGTTAC
66460 TTAAGTTTAATTTTT
1 TTAAGTTTAATTTTT
66475 TTAA-TTTAATTTTT
1 TTAAGTTTAATTTTT
66489 T
1 T
66490 GTAAATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTAAGTTTAATTTTT
Found at i:70027 original size:30 final size:29
Alignment explanation
Indices: 69982--70041 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 29
69972 TTTGATGACT
*
69982 ACTCACTCGAGACTTTTGTAACCAGAATA
1 ACTCACTCAAGACTTTTGTAACCAGAATA
70011 ACTCACTACAAGACTTTTGTAACCAGAATA
1 ACTCACT-CAAGACTTTTGTAACCAGAATA
70041 A
1 A
70042 TTCTTCTTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (29 bp):
ACTCACTCAAGACTTTTGTAACCAGAATA
Found at i:75237 original size:4 final size:4
Alignment explanation
Indices: 75230--75336 Score: 106
Period size: 4 Copynumber: 26.8 Consensus size: 4
75220 CGAATATATA
* * * * *
75230 TATG TATG CATG CATG CATG CATG CATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * *
75278 TATG TGTG TGTG TATA TATG TGTG TATG TATG TTTG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
75326 CATG CATG TAT
1 TATG TATG TAT
75337 TGATGAAATG
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 91 1.00
ACGTcount: A:0.22, C:0.07, G:0.26, T:0.45
Consensus pattern (4 bp):
TATG
Found at i:77331 original size:20 final size:20
Alignment explanation
Indices: 77306--77343 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
77296 TGATACAAAT
77306 GATGAATAATAATAGATAAG
1 GATGAATAATAATAGATAAG
77326 GATGAATAATAATAGATA
1 GATGAATAATAATAGATA
77344 TAAGTACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.26
Consensus pattern (20 bp):
GATGAATAATAATAGATAAG
Found at i:79895 original size:16 final size:15
Alignment explanation
Indices: 79858--79896 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
79848 TTAAAATGTG
79858 ATTAAAAAAAATTAA
1 ATTAAAAAAAATTAA
* *
79873 ATAAAAAAAATATTAT
1 ATTAAAAAAA-ATTAA
79889 ATTAAAAA
1 ATTAAAAA
79897 TATTAAATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATTAAAAAAAATTAA
Found at i:105241 original size:2 final size:2
Alignment explanation
Indices: 105234--105258 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
105224 AAAGTTGGTG
105234 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
105259 GATCTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:107420 original size:30 final size:30
Alignment explanation
Indices: 107386--107483 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
107376 AGGTTGATGG
107386 TTAAATTTATTGAATTTTTTAGAATTTAA-A
1 TTAAATTTATTGAATTTTTTA-AATTTAACA
* * * * *
107416 TTAAAATGA-TAAATTTTATAAATATTAACGG
1 TTAAATTTATTGAATTTTTTAAAT-TTAAC-A
* * *
107447 TTAAATTTATTGAATATTTTATATTTAATA
1 TTAAATTTATTGAATTTTTTAAATTTAACA
107477 TTAAATT
1 TTAAATT
107484 AATAAAATGC
Statistics
Matches: 51, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
28 3 0.06
29 13 0.25
30 14 0.27
31 11 0.22
32 10 0.20
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (30 bp):
TTAAATTTATTGAATTTTTTAAATTTAACA
Found at i:107498 original size:61 final size:61
Alignment explanation
Indices: 107384--107504 Score: 154
Period size: 61 Copynumber: 2.0 Consensus size: 61
107374 CAAGGTTGAT
* * * ** *
107384 GGTTAAATTTATTGAATTTTTTAGAATTTAAATTAAAATGATAAATTTTATAAATATTAAC
1 GGTTAAATTTATTGAATATTTTAGAATTTAAATTAAAATAATAAAATGCATAAACATTAAC
* *
107445 GGTTAAATTTATTGAATATTTTA-TATTTAATATTAAATTAATAAAATGCATAAACATTAA
1 GGTTAAATTTATTGAATATTTTAGAATTTAA-ATTAAAATAATAAAATGCATAAACATTAA
107505 AAGATTGGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 6 0.12
61 45 0.88
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (61 bp):
GGTTAAATTTATTGAATATTTTAGAATTTAAATTAAAATAATAAAATGCATAAACATTAAC
Found at i:108401 original size:14 final size:13
Alignment explanation
Indices: 108370--108395 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
108360 AATATAGTAG
108370 AATATTAAAAAAA
1 AATATTAAAAAAA
108383 AATATTAAAAAAA
1 AATATTAAAAAAA
108396 GCATATGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AATATTAAAAAAA
Found at i:120210 original size:29 final size:31
Alignment explanation
Indices: 120177--120243 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 31
120167 AACCACCTAC
120177 ATGTGAACTGTTTATATGCAAACTG-TT-GT
1 ATGTGAACTGTTTATATGCAAACTGTTTGGT
* * *
120206 ATGTGAACTGTTTATGTGCGAGCTGTTTGGT
1 ATGTGAACTGTTTATATGCAAACTGTTTGGT
120237 ATGTGAA
1 ATGTGAA
120244 TCATTGATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 22 0.67
30 2 0.06
31 9 0.27
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.40
Consensus pattern (31 bp):
ATGTGAACTGTTTATATGCAAACTGTTTGGT
Found at i:120214 original size:14 final size:13
Alignment explanation
Indices: 120177--120223 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 13
120167 AACCACCTAC
120177 ATGTGAACTGTTT
1 ATGTGAACTGTTT
*
120190 ATATGCAAACTGTTGT
1 ATGTG--AACTGTT-T
120206 ATGTGAACTGTTT
1 ATGTGAACTGTTT
120219 ATGTG
1 ATGTG
120224 CGAGCTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 10 0.34
14 7 0.24
15 7 0.24
16 5 0.17
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.43
Consensus pattern (13 bp):
ATGTGAACTGTTT
Found at i:122297 original size:27 final size:29
Alignment explanation
Indices: 122241--122306 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
122231 TTTAAATTGA
*
122241 CAATACATATTTTTTAATTATAAGATATG
1 CAATACATATTTTTTAATTATAAGAAATG
*
122270 CAATACGTA-TTTTTAATTATAA-AAATG
1 CAATACATATTTTTTAATTATAAGAAATG
*
122297 CAATATATAT
1 CAATACATAT
122307 ATAAAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 11 0.34
28 13 0.41
29 8 0.25
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (29 bp):
CAATACATATTTTTTAATTATAAGAAATG
Found at i:123850 original size:28 final size:29
Alignment explanation
Indices: 123798--123853 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
123788 TCGCTCAAAT
123798 TCGAAAAGCAAAAAAAAAATAAAAAAAAA
1 TCGAAAAGCAAAAAAAAAATAAAAAAAAA
123827 TCGAAAAGCAAAAAAAAAATAAAAAAA
1 TCGAAAAGCAAAAAAAAAATAAAAAAA
123854 TCAAAACTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (29 bp):
TCGAAAAGCAAAAAAAAAATAAAAAAAAA
Found at i:124000 original size:11 final size:11
Alignment explanation
Indices: 123984--124009 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
123974 TCTCTTCGTT
123984 TTTTTTTTTTA
1 TTTTTTTTTTA
123995 TTTTTTTTTTA
1 TTTTTTTTTTA
124006 TTTT
1 TTTT
124010 ATGTTTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:124003 original size:16 final size:17
Alignment explanation
Indices: 123982--124016 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
123972 CATCTCTTCG
123982 TTTTTTTT-TTTTAT-T
1 TTTTTTTTATTTTATGT
123997 TTTTTTTTATTTTATGT
1 TTTTTTTTATTTTATGT
124014 TTT
1 TTT
124017 CATGCGTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 6 0.33
17 4 0.22
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.89
Consensus pattern (17 bp):
TTTTTTTTATTTTATGT
Found at i:125551 original size:13 final size:13
Alignment explanation
Indices: 125533--125566 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
125523 CTCCAAACCT
125533 ACTCCTATCCGTC
1 ACTCCTATCCGTC
125546 ACTCCTATCCGTC
1 ACTCCTATCCGTC
125559 ACTCCTAT
1 ACTCCTAT
125567 TCAGTAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.18, C:0.44, G:0.06, T:0.32
Consensus pattern (13 bp):
ACTCCTATCCGTC
Found at i:129208 original size:87 final size:87
Alignment explanation
Indices: 129104--129293 Score: 229
Period size: 87 Copynumber: 2.2 Consensus size: 87
129094 AAACCTTCGA
* * * *
129104 TATCAGACCTTTCATCTCAATCGTCAAAGGCCTAATTTAATAACTCACGATGCCATAAAAAAT-T
1 TATCGGACCTTTAATCTCAACCATCAAAGGCCTAATTTAATAACTCACGATGCCATAAAAAATCT
* *
129168 CGTAACAAATGCAGGATTTCCGT
66 -GCAACAAATGCAAGATTTCCGT
* * ** *
129191 TATCGGACCTTTAATCTCGACCATCATAGGCCTAATTTGGTAACTCATGATGCCATAAAAAATCT
1 TATCGGACCTTTAATCTCAACCATCAAAGGCCTAATTTAATAACTCACGATGCCATAAAAAATCT
* *
129256 GCAACAATTGCAAGATTTTCGT
66 GCAACAAATGCAAGATTTCCGT
* *
129278 CATCGGACGTTTAATC
1 TATCGGACCTTTAATC
129294 CGTAATAGGA
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
87 86 0.99
88 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (87 bp):
TATCGGACCTTTAATCTCAACCATCAAAGGCCTAATTTAATAACTCACGATGCCATAAAAAATCT
GCAACAAATGCAAGATTTCCGT
Found at i:142171 original size:102 final size:102
Alignment explanation
Indices: 141995--142192 Score: 317
Period size: 102 Copynumber: 1.9 Consensus size: 102
141985 TAATACCTAA
* * *
141995 AGTGATTACTAATTACTTTTATTCTTTGTAGGTATTTAATTCACTATTGCCTCACCCCTCCTTTG
1 AGTGATTACTAATTAATTCTATTCTTTGAAGGTATTTAATTCACTATTGCCTCACCCCTCCTTTG
*
142060 GGTACGATCCTCAGAATACTACCAAGTGTTCCATTAT
66 GGTACGATCCTCAGAATACTACCAAATGTTCCATTAT
*
142097 AGTGATTACTAATTAATTCTATTCTTTGCAAGG-ATTTAATTCACTATTGCCTCACGCCTCCTTT
1 AGTGATTACTAATTAATTCTATTCTTTG-AAGGTATTTAATTCACTATTGCCTCACCCCTCCTTT
* *
142161 GGGTACGATCCTCGGAATACTACTAAATGTTC
65 GGGTACGATCCTCAGAATACTACCAAATGTTC
142193 TGTTGTAACA
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
102 85 0.97
103 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (102 bp):
AGTGATTACTAATTAATTCTATTCTTTGAAGGTATTTAATTCACTATTGCCTCACCCCTCCTTTG
GGTACGATCCTCAGAATACTACCAAATGTTCCATTAT
Found at i:149974 original size:62 final size:62
Alignment explanation
Indices: 149895--150014 Score: 163
Period size: 62 Copynumber: 1.9 Consensus size: 62
149885 GTCATTATGG
*
149895 CTCTGAAATTTTTGAAAGTTTAAATTAAG-CCTCTCAT-AATTTTTAAAAATTCTTATTAAGC
1 CTCTGAAATTTTTGAAAGTTTAAATTAAGCCCTC-CATAAAATTTTAAAAATTCTTATTAAGC
* * * *
149956 CTCTGGAAGTTTTTGAAAGTTTGAATTAAGCCCTCCCTAAAATTTTAGAAATTCTTATT
1 CTCT-GAAATTTTTGAAAGTTTAAATTAAGCCCTCCATAAAATTTTAAAAATTCTTATT
150015 CCTTCCTCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
61 4 0.08
62 25 0.49
63 22 0.43
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (62 bp):
CTCTGAAATTTTTGAAAGTTTAAATTAAGCCCTCCATAAAATTTTAAAAATTCTTATTAAGC
Found at i:149984 original size:31 final size:29
Alignment explanation
Indices: 149895--149987 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 29
149885 GTCATTATGG
149895 CTCTGAAATTTTTGAAAGTTTAAATTAAGC
1 CTCTGAAATTTTTGAAAGTTT-AATTAAGC
* * * *
149925 CTCTCATAATTTTTAAAAATTCTTATTAAGC
1 CTCTGA-AATTTTTGAAAGTT-TAATTAAGC
*
149956 CTCTGGAAGTTTTTGAAAGTTTGAATTAAGC
1 CTCT-GAAATTTTTGAAAGTTT-AATTAAGC
149987 C
1 C
149988 CTCCCTAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
30 6 0.12
31 42 0.84
32 2 0.04
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (29 bp):
CTCTGAAATTTTTGAAAGTTTAATTAAGC
Found at i:152642 original size:66 final size:66
Alignment explanation
Indices: 152529--152660 Score: 189
Period size: 66 Copynumber: 2.0 Consensus size: 66
152519 AACTTTTGAC
*
152529 AACGTACACACATTGCACACACATGTGCTTGAACTCGAGTCTATTAAGATGAACATCATCTTCTT
1 AACGTACACACATTGCACACACATGTGCTTGAACTCGAGTCTATTAAGATGAACATCATCCTCTT
152594 T
66 T
* *
152595 AACGTACACACATTGCATACACA-GATG-TTCGAACTCGTA-TCTCTTAAGATGAACATCATCCT
1 AACGTACACACATTGCACACACATG-TGCTT-GAACTCG-AGTCTATTAAGATGAACATCATCCT
152657 CTTT
63 CTTT
152661 TTCACTAGAA
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
65 3 0.05
66 56 0.93
67 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (66 bp):
AACGTACACACATTGCACACACATGTGCTTGAACTCGAGTCTATTAAGATGAACATCATCCTCTT
T
Found at i:163217 original size:41 final size:41
Alignment explanation
Indices: 163072--163317 Score: 260
Period size: 41 Copynumber: 5.9 Consensus size: 41
163062 CCTTTAAACG
** * * *
163072 TAATCTCATGCTCATCCTAAGTCATGAGTCTTCCTTAAAACA
1 TAATCTCATGCTCATCCCGAGACATGAGTCTTCCTT-TAATA
* * * * * * *
163114 TAATCTCATTCTCTTTCTGAGTCACGAGTCTTCCTTTTAAACA
1 TAATCTCATGCTCATCCCGAGACATGAGTCTTCC-TTT-AATA
*
163157 TAATCTCATGCTCACCCCGAGACATGAGTCTTCCTTTAATA
1 TAATCTCATGCTCATCCCGAGACATGAGTCTTCCTTTAATA
* *
163198 TACTCTCATGCTCATCCCGACACATGAGTCTTCCTTTAATA
1 TAATCTCATGCTCATCCCGAGACATGAGTCTTCCTTTAATA
* * **
163239 TACTTTCATGCTCATCCTAAGACATGAGTCTTCCTTTAATA
1 TAATCTCATGCTCATCCCGAGACATGAGTCTTCCTTTAATA
* *
163280 TAGT-TCATGCTCATCCCGAGACATGAGTTTTCCATTTA
1 TAATCTCATGCTCATCCCGAGACATGAGTCTTCC-TTTA
163318 TACATCAATT
Statistics
Matches: 176, Mismatches: 25, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
40 26 0.15
41 85 0.48
42 32 0.18
43 33 0.19
ACGTcount: A:0.26, C:0.27, G:0.11, T:0.36
Consensus pattern (41 bp):
TAATCTCATGCTCATCCCGAGACATGAGTCTTCCTTTAATA
Found at i:167892 original size:106 final size:106
Alignment explanation
Indices: 167707--167914 Score: 407
Period size: 106 Copynumber: 2.0 Consensus size: 106
167697 AGGTTTTATA
167707 AATAAATAGTAATATAAGAAGTTTTGATCGTTTTTATAGGAAACTATCATACATGAAAAAAATAG
1 AATAAATAGTAATATAAGAAGTTTTGATCGTTTTTATAGGAAACTATCATACATGAAAAAAATAG
167772 AGAATTATTATTAGGAGCATGTGTTTAGTTAAAAATTCGTT
66 AGAATTATTATTAGGAGCATGTGTTTAGTTAAAAATTCGTT
*
167813 AATAAATAGTAGTATAAGAAGTTTTGATCGTTTTTATAGGAAACTATCATACATGAAAAAAATAG
1 AATAAATAGTAATATAAGAAGTTTTGATCGTTTTTATAGGAAACTATCATACATGAAAAAAATAG
167878 AGAATTATTATTAGGAGCATGTGTTTAGTTAAAAATT
66 AGAATTATTATTAGGAGCATGTGTTTAGTTAAAAATT
167915 TTGTTACCAA
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 101 1.00
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (106 bp):
AATAAATAGTAATATAAGAAGTTTTGATCGTTTTTATAGGAAACTATCATACATGAAAAAAATAG
AGAATTATTATTAGGAGCATGTGTTTAGTTAAAAATTCGTT
Found at i:168096 original size:18 final size:18
Alignment explanation
Indices: 168049--168104 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
168039 ATGATTTTTT
168049 TATTATTATAA-AAA-AA
1 TATTATTATAATAAATAA
*
168065 TA-TA-T-TAATTAATAA
1 TATTATTATAATAAATAA
168080 TATTATTATAATAAATAA
1 TATTATTATAATAAATAA
*
168098 TAATATT
1 TATTATT
168105 TTATTATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 3 0.09
14 3 0.09
15 6 0.19
16 4 0.12
17 1 0.03
18 15 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATTATTATAATAAATAA
Found at i:168109 original size:26 final size:26
Alignment explanation
Indices: 168080--168129 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
168070 TAATTAATAA
*
168080 TATTATTATAATA-AATAATAATATTT
1 TATTATT-TAATATAATAAAAATATTT
168106 TATTATTTAATATAATAAAAATAT
1 TATTATTTAATATAATAAAAATAT
168130 AAGAGAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TATTATTTAATATAATAAAAATATTT
Found at i:168117 original size:21 final size:21
Alignment explanation
Indices: 168068--168122 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
168058 AAAAAAATAT
168068 ATTAATTAATAATATTATTATA
1 ATTAA-TAATAATATTATTATA
*
168090 ATAAATAATAATATT-TTATTA
1 ATTAATAATAATATTATTA-TA
*
168111 TTTAAT-ATAATA
1 ATTAATAATAATA
168123 AAAATATAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 9 0.31
21 16 0.55
22 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTAATAATAATATTATTATA
Found at i:169794 original size:2 final size:2
Alignment explanation
Indices: 169787--169821 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
169777 TACATAGGCT
*
169787 TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
169822 TAAGTCTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:172877 original size:42 final size:42
Alignment explanation
Indices: 172809--172914 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
172799 ATCGAGCCAT
* *
172809 GAGTCTTCCTTTAAACGTAATCTCATGCTCA-TCTCAAGTCAC
1 GAGTCTTCCTTTAAACATAATATCATGCT-ATTCTCAAGTCAC
* * *
172851 GAGTCTTCCTTAAAACATAATATCATGCTATTTTTAAGTCAC
1 GAGTCTTCCTTTAAACATAATATCATGCTATTCTCAAGTCAC
172893 GAGTCTTCCTTTTAAACATAAT
1 GAGTCTTCC-TTTAAACATAAT
172915 CTGTAACACC
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
41 1 0.02
42 44 0.79
43 11 0.20
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (42 bp):
GAGTCTTCCTTTAAACATAATATCATGCTATTCTCAAGTCAC
Found at i:173658 original size:226 final size:226
Alignment explanation
Indices: 173264--173721 Score: 898
Period size: 226 Copynumber: 2.0 Consensus size: 226
173254 CTAATATTCA
173264 CATTTAGTCATTTCTTATAAGACCTTTACACATAACTAATCCTAGGTACATGCCAAAATAATCAA
1 CATTTAGTCATTTCTTATAAGACCTTTACACATAACTAATCCTAGGTACATGCCAAAATAATCAA
173329 AAAGTGACATCACTGACTTAGAGTTTGAGATTTCCACTTTGATGCTGAGTTGTAATCTACTATTA
66 AAAGTGACATCACTGACTTAGAGTTTGAGATTTCCACTTTGATGCTGAGTTGTAATCTACTATTA
173394 AGATAACCTGAAATCATGAAAGATTCAATTACATTAGTAACATTTATTCACCACAAACCATTTGC
131 AGATAACCTGAAATCATGAAAGATTCAATTACATTAGTAACATTTATTCACCACAAACCATTTGC
173459 ATGGATATTTACTATTTTCAAATAAAGCTTT
196 ATGGATATTTACTATTTTCAAATAAAGCTTT
*
173490 CATTTAGTCATTTCTTATAAGACCTTTACACATAACTAGTCCTAGGTACATGCCAAAATAATCAA
1 CATTTAGTCATTTCTTATAAGACCTTTACACATAACTAATCCTAGGTACATGCCAAAATAATCAA
173555 AAAGTGACATCACTGACTTAGAGTTTGAGATTTCCACTTTGATGCTGAGTTGTAATCTACTATTA
66 AAAGTGACATCACTGACTTAGAGTTTGAGATTTCCACTTTGATGCTGAGTTGTAATCTACTATTA
*
173620 AGATAACCTGAAATCATGGAAGATTCAATTACATTAGTAACATTTATTCACCACAAACCATTTGC
131 AGATAACCTGAAATCATGAAAGATTCAATTACATTAGTAACATTTATTCACCACAAACCATTTGC
173685 ATGGATATTTACTATTTTCAAATAAAGCTTT
196 ATGGATATTTACTATTTTCAAATAAAGCTTT
173716 CATTTA
1 CATTTA
173722 TACAAAATCA
Statistics
Matches: 230, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
226 230 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.35
Consensus pattern (226 bp):
CATTTAGTCATTTCTTATAAGACCTTTACACATAACTAATCCTAGGTACATGCCAAAATAATCAA
AAAGTGACATCACTGACTTAGAGTTTGAGATTTCCACTTTGATGCTGAGTTGTAATCTACTATTA
AGATAACCTGAAATCATGAAAGATTCAATTACATTAGTAACATTTATTCACCACAAACCATTTGC
ATGGATATTTACTATTTTCAAATAAAGCTTT
Found at i:179879 original size:20 final size:19
Alignment explanation
Indices: 179850--179890 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
179840 GAATCTGTCT
* *
179850 TTTGGGTTTTCTTTCTTTA
1 TTTGGGTTTTATTTATTTA
179869 TTTGTGGTTTTATTTATTTA
1 TTTG-GGTTTTATTTATTTA
179889 TT
1 TT
179891 ACACTTATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.10, C:0.05, G:0.15, T:0.71
Consensus pattern (19 bp):
TTTGGGTTTTATTTATTTA
Found at i:180760 original size:61 final size:61
Alignment explanation
Indices: 180685--180807 Score: 228
Period size: 61 Copynumber: 2.0 Consensus size: 61
180675 GTGAAATATA
* *
180685 TTTAAAACACGAGAATTAATTTGTAAATATATGTATACATATGGCATAGATAACTTCGATC
1 TTTAAAACACGAGAATCAATTTGTAAACATATGTATACATATGGCATAGATAACTTCGATC
180746 TTTAAAACACGAGAATCAATTTGTAAACATATGTATACATATGGCATAGATAACTTCGATC
1 TTTAAAACACGAGAATCAATTTGTAAACATATGTATACATATGGCATAGATAACTTCGATC
180807 T
1 T
180808 AATGTATTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (61 bp):
TTTAAAACACGAGAATCAATTTGTAAACATATGTATACATATGGCATAGATAACTTCGATC
Found at i:188246 original size:31 final size:31
Alignment explanation
Indices: 188186--188256 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
188176 TTGGTGTAAT
* *
188186 TATACACATGAAACTTTGATTGTAGTTCAAA
1 TATACACATGAAACTATGATTGTAATTCAAA
* * * *
188217 TATATACATGAAACTATGGTTTTAATTCAAT
1 TATACACATGAAACTATGATTGTAATTCAAA
188248 TATACACAT
1 TATACACAT
188257 TTAAAAAATA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (31 bp):
TATACACATGAAACTATGATTGTAATTCAAA
Found at i:188418 original size:29 final size:30
Alignment explanation
Indices: 188372--188430 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
188362 AAATTAAATC
* *
188372 AAATTAAAATTTCATGTATAAAATTGCACA
1 AAATCAAAATTTCATGTATAAAATTACACA
*
188402 AAATCAAAATTT-ATGTATAACATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
188431 TTAGACCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTACACA
Found at i:188863 original size:21 final size:22
Alignment explanation
Indices: 188837--188878 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
188827 ACTATCAATA
188837 TTTTTAAAAAAATG-TAATTAT
1 TTTTTAAAAAAATGTTAATTAT
**
188858 TTTTTATGAAAATGTTAATTA
1 TTTTTAAAAAAATGTTAATTA
188879 AAATTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (22 bp):
TTTTTAAAAAAATGTTAATTAT
Found at i:198627 original size:18 final size:18
Alignment explanation
Indices: 198604--198640 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
198594 GCTCCCATTT
198604 AGGAGTTGAGTAACAGTC
1 AGGAGTTGAGTAACAGTC
198622 AGGAGTTGAGTAACAGTC
1 AGGAGTTGAGTAACAGTC
198640 A
1 A
198641 TGCTTATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.11, G:0.32, T:0.22
Consensus pattern (18 bp):
AGGAGTTGAGTAACAGTC
Done.