Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004271.1 Kokia drynarioides strain JFW-HI SEQ_117559, 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: 16174
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Found at i:1034 original size:19 final size:20
Alignment explanation
Indices: 1002--1039 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
992 AATATGAATG
*
1002 TTTTAACTTTCAACCTCAAT
1 TTTTAACTTGCAACCTCAAT
*
1022 TTTTAAC-TGCAACGTCAA
1 TTTTAACTTGCAACCTCAA
1040 ACACAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (20 bp):
TTTTAACTTGCAACCTCAAT
Found at i:4744 original size:3 final size:3
Alignment explanation
Indices: 4736--4775 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
4726 CTTTAAGGTT
4736 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4776 AAAATGACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5053 original size:17 final size:16
Alignment explanation
Indices: 5031--5062 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5021 ATTTTAATGA
5031 TTTTTTAAAATGTTTTT
1 TTTTTTAAAAT-TTTTT
5048 TTTTTTAAAATTTTT
1 TTTTTTAAAATTTTT
5063 AAATTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTTTAAAATTTTTT
Found at i:6994 original size:21 final size:20
Alignment explanation
Indices: 6970--7044 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 20
6960 ATATGGAAAT
6970 TTATTTAAAAATTATTAATAA
1 TTATTTAAAAATTATTAA-AA
*
6991 TTA--TAGTAAATTATTAAAA
1 TTATTTA-AAAATTATTAAAA
* * *
7010 TTATTAAAAAAATACTTAGAA
1 TTATTTAAAAATTA-TTAAAA
*
7031 TTAGTTAAAAATTA
1 TTATTTAAAAATTA
7045 GTATTAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
19 7 0.17
20 15 0.36
21 20 0.48
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.41
Consensus pattern (20 bp):
TTATTTAAAAATTATTAAAA
Found at i:7012 original size:9 final size:9
Alignment explanation
Indices: 6977--7018 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
6967 AATTTATTTA
6977 AAAATTATT
1 AAAATTATT
6986 AATAATTA-T
1 AA-AATTATT
6995 AGTAAATTATT
1 A--AAATTATT
7006 AAAATTATT
1 AAAATTATT
7015 AAAA
1 AAAA
7019 AAATACTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 16 0.55
10 10 0.34
11 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (9 bp):
AAAATTATT
Found at i:7019 original size:10 final size:10
Alignment explanation
Indices: 6974--7019 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
6964 GGAAATTTAT
6974 TTAAAAATTA
1 TTAAAAATTA
*
6984 TTAATAATTA
1 TTAAAAATTA
*
6994 -TAGTAAATTA
1 TTA-AAAATTA
7004 TT-AAAATTA
1 TTAAAAATTA
7013 TTAAAAA
1 TTAAAAA
7020 AATACTTAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
9 10 0.34
10 18 0.62
11 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:8407 original size:30 final size:29
Alignment explanation
Indices: 8376--8852 Score: 219
Period size: 30 Copynumber: 16.2 Consensus size: 29
8366 AAAAATGAAT
*
8376 TTTTTGGAAGTTTGGGGGTAAAATGGTAA
1 TTTTTGGAAGTTTAGGGGTAAAATGGTAA
* * * **
8405 TTTTGGGAAGAATCAGGATTAAAAATGG-AA
1 TTTTTGGAAG-TTTAGGGGT-AAAATGGTAA
*
8435 TTTTGGGAAGTTTAGGGGTAAAATGGTAA
1 TTTTTGGAAGTTTAGGGGTAAAATGGTAA
** *
8464 TTTTTGGAA-AATAGGGTTCAAAATGG-AA
1 TTTTTGGAAGTTTAGGGGT-AAAATGGTAA
* *
8492 TTTTTTGGAAGTTCAAGGGTAAAATGGTAA
1 -TTTTTGGAAGTTTAGGGGTAAAATGGTAA
* ** **
8522 TTTTAGGAAGAATCAAGGTTTAAAATGG-AA
1 TTTTTGGAAG--TTTAGGGGTAAAATGGTAA
*
8552 TTTTGGGAAGTTTAGGGGTAAAATGGTAA
1 TTTTTGGAAGTTTAGGGGTAAAATGGTAA
* ** *
8581 TTTTAGGAAAAATTAGGGTTAAAAATGG-AA
1 TTTTTGG-AAGTTTAGGGGT-AAAATGGTAA
* *
8611 TTTTTGGATG-TTCGAGGGTAAAATGGTAA
1 TTTTTGGAAGTTTAG-GGGTAAAATGGTAA
* ** * * *
8640 TTTTGGGAAGAATCGAGGTTAAAAAT-GAAA
1 TTTTTGGAAGTTTAG-GGGT-AAAATGGTAA
* *
8670 TTTTGGGAAGTTTAGGGGTAAAATGGTTA
1 TTTTTGGAAGTTTAGGGGTAAAATGGTAA
* ****
8699 -TTTTGGAAAAAG-TAAGATCAAAAATGG-AA
1 TTTTTGG---AAGTTTAGGGGTAAAATGGTAA
*
8728 TTTTTTGGAAG-TTCGAGGGTAAAATGGTAA
1 -TTTTTGGAAGTTTAG-GGGTAAAATGGTAA
** * **
8758 TTTTTAAAAAG-TTCGAGGGTCAAAA-CATAA
1 TTTTT-GGAAGTTTAG-GGGT-AAAATGGTAA
* *
8788 TTTTAGAGAAGTTTAGGGGTCAAAAT-ATAA
1 TTTTTG-GAAGTTTAGGGGT-AAAATGGTAA
* *
8818 TTTTAGAAAAGTTTAGGGGTTAAAAT-GTAA
1 TTTTTG-GAAGTTTAGGGG-TAAAATGGTAA
8848 TTTTT
1 TTTTT
8853 TAAAAATTTA
Statistics
Matches: 344, Mismatches: 74, Indels: 59
0.72 0.16 0.12
Matches are distributed among these distances:
28 52 0.15
29 96 0.28
30 149 0.43
31 47 0.14
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.34
Consensus pattern (29 bp):
TTTTTGGAAGTTTAGGGGTAAAATGGTAA
Found at i:8444 original size:59 final size:59
Alignment explanation
Indices: 8273--8761 Score: 480
Period size: 59 Copynumber: 8.3 Consensus size: 59
8263 TGGGTACCCG
* * * * * * *
8273 GGGGTGAAATGGTAATTTTGGGAA-AGTTCAGGGTTAAAAAT-GAAATTTAGGCA-TCCA
1 GGGGTAAAATGGTAATTTTGGGAAGA-ATCAGGATTAAAAATGGAATTTTTGGAAGTTCA
** * * * **
8330 GGGGTAAAATGGTAATTTTTGAAAAGAACCAAGATAAAAAAT-GAATTTTTTGGAAGTTTG
1 GGGGTAAAATGGTAA-TTTTGGGAAGAATCAGGATTAAAAATGGAA-TTTTTGGAAGTTCA
* *
8390 GGGGTAAAATGGTAATTTTGGGAAGAATCAGGATTAAAAATGGAATTTTGGGAAGTTTA
1 GGGGTAAAATGGTAATTTTGGGAAGAATCAGGATTAAAAATGGAATTTTTGGAAGTTCA
* * *
8449 GGGGTAAAATGGTAATTTTTGGAA-AAT-AGGGTTCAAAATGGAATTTTTTGGAAGTTCA
1 GGGGTAAAATGGTAATTTTGGGAAGAATCAGGATTAAAAATGGAA-TTTTTGGAAGTTCA
* * * * *
8507 AGGGTAAAATGGTAATTTTAGGAAGAATCAAGG-TTTAAAATGGAATTTTGGGAAGTTTA
1 GGGGTAAAATGGTAATTTTGGGAAGAATC-AGGATTAAAAATGGAATTTTTGGAAGTTCA
* * * * *
8566 GGGGTAAAATGGTAATTTTAGGAAAAATTAGGGTTAAAAATGGAATTTTTGGATGTTC-
1 GGGGTAAAATGGTAATTTTGGGAAGAATCAGGATTAAAAATGGAATTTTTGGAAGTTCA
* * *
8624 GAGGGTAAAATGGTAATTTTGGGAAGAATCGAGG-TTAAAAATGAAATTTTGGGAAGTTTA
1 G-GGGTAAAATGGTAATTTTGGGAAGAATC-AGGATTAAAAATGGAATTTTTGGAAGTTCA
* * * *
8684 GGGGTAAAATGGTTATTTT-GGAAAAAGT-AAGATCAAAAATGGAATTTTTTGGAAGTTC-
1 GGGGTAAAATGGTAATTTTGGGAAGAA-TCAGGATTAAAAATGGAA-TTTTTGGAAGTTCA
8742 GAGGGTAAAATGGTAATTTT
1 G-GGGTAAAATGGTAATTTT
8762 TAAAAAGTTC
Statistics
Matches: 362, Mismatches: 53, Indels: 32
0.81 0.12 0.07
Matches are distributed among these distances:
57 30 0.08
58 78 0.22
59 217 0.60
60 34 0.09
61 3 0.01
ACGTcount: A:0.37, C:0.03, G:0.28, T:0.32
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTGGGAAGAATCAGGATTAAAAATGGAATTTTTGGAAGTTCA
Found at i:8659 original size:118 final size:117
Alignment explanation
Indices: 8274--8761 Score: 621
Period size: 117 Copynumber: 4.2 Consensus size: 117
8264 GGGTACCCGG
* * * * * **
8274 GGGTGAAATGGTAATTTTGGGAA-AGTTCAGGGTTAAAAAT-GAAATTTAGGCA-TCCAGGGGTA
1 GGGTAAAATGGTAATTTTGGGAAGA-ATCA-GGTTAAAAATGGAATTTTGGGAAGTTTAGGGGTA
* * * * *
8336 AAATGGTAATTTTTGAAAAGAACCAAGATAAAAAAT-GAATTTTTTGGAAGTTTGG
64 AAATGGTAATTTTTGGAAA-AA-TAAGATTAAAAATGGAATTTTTTGGAAGTTCGA
8391 GGGTAAAATGGTAATTTTGGGAAGAATCAGGATTAAAAATGGAATTTTGGGAAGTTTAGGGGTAA
1 GGGTAAAATGGTAATTTTGGGAAGAATCAGG-TTAAAAATGGAATTTTGGGAAGTTTAGGGGTAA
* * * *
8456 AATGGTAATTTTTGG-AAAATAGGGTTCAAAATGGAATTTTTTGGAAGTTCAA
65 AATGGTAATTTTTGGAAAAATAAGATTAAAAATGGAATTTTTTGGAAGTTCGA
* *
8508 GGGTAAAATGGTAATTTTAGGAAGAATCAAGGTTTAAAATGGAATTTTGGGAAGTTTAGGGGTAA
1 GGGTAAAATGGTAATTTTGGGAAGAATC-AGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGTAA
* * * *
8573 AATGGTAATTTTAGGAAAAATTAGGGTTAAAAATGGAA-TTTTTGGATGTTCGA
65 AATGGTAATTTTTGGAAAAA-TAAGATTAAAAATGGAATTTTTTGGAAGTTCGA
*
8626 GGGTAAAATGGTAATTTTGGGAAGAATCGAGGTTAAAAATGAAATTTTGGGAAGTTTAGGGGTAA
1 GGGTAAAATGGTAATTTTGGGAAGAATC-AGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGTAA
* *
8691 AATGGTTA-TTTTGGAAAAAGTAAGATCAAAAATGGAATTTTTTGGAAGTTCGA
65 AATGGTAATTTTTGGAAAAA-TAAGATTAAAAATGGAATTTTTTGGAAGTTCGA
8744 GGGTAAAATGGTAATTTT
1 GGGTAAAATGGTAATTTT
8762 TAAAAAGTTC
Statistics
Matches: 329, Mismatches: 33, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
116 10 0.03
117 148 0.45
118 132 0.40
119 39 0.12
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.32
Consensus pattern (117 bp):
GGGTAAAATGGTAATTTTGGGAAGAATCAGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGTAAA
ATGGTAATTTTTGGAAAAATAAGATTAAAAATGGAATTTTTTGGAAGTTCGA
Found at i:8819 original size:60 final size:61
Alignment explanation
Indices: 8755--8885 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 61
8745 GGTAAAATGG
* *
8755 TAATTTTTA-AAAAGTTCGA-GGGTCAAAACATAATTTTAGAGAAGTTTAGGGGTCAAAATA
1 TAATTTTTAGAAAAGTT-GAGGGGTCAAAACATAATTTTAGAAAAATTTAGGGGTCAAAATA
* * ** ** *
8815 TAA-TTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTTTAAAAATTTAGGGGTTAAAATA
1 TAATTTTTAGAAAAGTTGAGGGGTCAAAACATAATTTTAGAAAAATTTAGGGGTCAAAATA
*
8875 TGATTTTTAGA
1 TAATTTTTAGA
8886 CAGTTTAGGG
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
59 6 0.10
60 45 0.78
61 7 0.12
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.37
Consensus pattern (61 bp):
TAATTTTTAGAAAAGTTGAGGGGTCAAAACATAATTTTAGAAAAATTTAGGGGTCAAAATA
Found at i:8829 original size:118 final size:117
Alignment explanation
Indices: 8274--8827 Score: 567
Period size: 117 Copynumber: 4.7 Consensus size: 117
8264 GGGTACCCGG
* * * * * **
8274 GGGTGAAATGGTAATTTTGGGAA-AGTTC-AGGGTTAAAAATGAAATTTAGGCA-TCCAGGGGTA
1 GGGTAAAATGGTAATTTT-GGAAGA-ATCGAGGGTTAAAAATGAATTTTGGGAAGTTTAGGGGTA
* ** * * *
8336 AAATGGTAATTTTTGAAAAGAACCAAGATAAAAAAT-GAATTTTTTGGAAGTTTGG
64 AAATGGTAATTTTAG-AAA-AAGTAAGATCAAAAATGGAATTTTTTGGAAGTTCGA
*
8391 GGGTAAAATGGTAATTTTGGGAAGAATC-AGGATTAAAAATGGAATTTTGGGAAGTTTAGGGGTA
1 GGGTAAAATGGTAATTTT-GGAAGAATCGAGGGTTAAAAAT-GAATTTTGGGAAGTTTAGGGGTA
* * * * *
8455 AAATGGTAATTTTTGGAAAA-TAGGGTTC-AAAATGGAATTTTTTGGAAGTTCAA
64 AAATGGTAATTTTAGAAAAAGTA-AGATCAAAAATGGAATTTTTTGGAAGTTCGA
* *
8508 GGGTAAAATGGTAATTTTAGGAAGAATC-AAGGTTTAAAATGGAATTTTGGGAAGTTTAGGGGTA
1 GGGTAAAATGGTAATTTT-GGAAGAATCGAGGGTTAAAAAT-GAATTTTGGGAAGTTTAGGGGTA
* * * * *
8572 AAATGGTAATTTTAGGAAAAATTAGGGTTAAAAATGGAA-TTTTTGGATGTTCGA
64 AAATGGTAATTTTA-GAAAAAGTAAGATCAAAAATGGAATTTTTTGGAAGTTCGA
8626 GGGTAAAATGGTAATTTTGGGAAGAATCGA-GGTTAAAAATGAAATTTTGGGAAGTTTAGGGGTA
1 GGGTAAAATGGTAATTTT-GGAAGAATCGAGGGTTAAAAATG-AATTTTGGGAAGTTTAGGGGTA
* *
8690 AAATGGTTATTTTGGAAAAAGTAAGATCAAAAATGGAATTTTTTGGAAGTTCGA
64 AAATGGTAATTTTAGAAAAAGTAAGATCAAAAATGGAATTTTTTGGAAGTTCGA
* * * *
8744 GGGTAAAATGGTAATTTT-TAAAAAGTTCGAGGGTCAAAACAT-AATTTTAGAGAAGTTTAGGGG
1 GGGTAAAATGGTAATTTTGGAAGAA--TCGAGGGTTAAAA-ATGAATTTT-GGGAAGTTTAGGGG
*
8807 TCAAAAT-ATAATTTTAGAAAA
62 T-AAAATGGTAATTTTAGAAAA
8828 GTTTAGGGGT
Statistics
Matches: 378, Mismatches: 42, Indels: 32
0.84 0.09 0.07
Matches are distributed among these distances:
116 10 0.03
117 149 0.39
118 145 0.38
119 67 0.18
120 7 0.02
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (117 bp):
GGGTAAAATGGTAATTTTGGAAGAATCGAGGGTTAAAAATGAATTTTGGGAAGTTTAGGGGTAAA
ATGGTAATTTTAGAAAAAGTAAGATCAAAAATGGAATTTTTTGGAAGTTCGA
Found at i:8863 original size:30 final size:30
Alignment explanation
Indices: 8755--8882 Score: 123
Period size: 30 Copynumber: 4.3 Consensus size: 30
8745 GGTAAAATGG
* * * *
8755 TAATTTTT-AAAAAGTTCGAGGGTCAAAACA
1 TAATTTTTGAAAAATTTAG-GGGTTAAAATA
* * * *
8785 TAATTTTAGAGAAGTTTAGGGGTCAAAATA
1 TAATTTTTGAAAAATTTAGGGGTTAAAATA
* * *
8815 TAATTTTAGAAAAGTTTAGGGGTTAAAATG
1 TAATTTTTGAAAAATTTAGGGGTTAAAATA
*
8845 TAATTTTTTAAAAATTTAGGGGTTAAAATA
1 TAATTTTTGAAAAATTTAGGGGTTAAAATA
*
8875 TGATTTTT
1 TAATTTTT
8883 AGACAGTTTA
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
30 77 0.93
31 6 0.07
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.38
Consensus pattern (30 bp):
TAATTTTTGAAAAATTTAGGGGTTAAAATA
Found at i:9979 original size:3 final size:3
Alignment explanation
Indices: 9951--10034 Score: 62
Period size: 3 Copynumber: 26.7 Consensus size: 3
9941 ATTTATTAAA
* * * *
9951 TAT TAA TAT TAAT TAT TAA TAGT TAT TAT TAAT TAT CAT TAT TAA TACT
1 TAT TAT TAT T-AT TAT TAT TA-T TAT TAT T-AT TAT TAT TAT TAT TA-T
* *
10000 TAT TAA TAT TAT TAT TAT TAAT TAT T-G TAT TAT TA
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TA
10035 CTTAATGTTA
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
2 1 0.02
3 49 0.78
4 13 0.21
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:9986 original size:10 final size:10
Alignment explanation
Indices: 9952--10025 Score: 64
Period size: 10 Copynumber: 7.6 Consensus size: 10
9942 TTTATTAAAT
*
9952 ATTAATATTA
1 ATTATTATTA
*
9962 ATTATTAATA
1 ATTATTATTA
*
9972 GTTATTATTA
1 ATTATTATTA
*
9982 ATTATCATT-
1 ATTATTATTA
*
9991 ATTAATACTT-
1 ATTATTA-TTA
*
10001 ATTAATATT-
1 ATTATTATTA
10010 ATTATTATTA
1 ATTATTATTA
10020 ATTATT
1 ATTATT
10026 GTATTATTAC
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
9 15 0.28
10 38 0.72
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (10 bp):
ATTATTATTA
Found at i:10025 original size:13 final size:12
Alignment explanation
Indices: 9951--10021 Score: 79
Period size: 13 Copynumber: 5.6 Consensus size: 12
9941 ATTTATTAAA
9951 TATTAATATTAAT
1 TATTAATATT-AT
9964 TATTAATAGTTAT
1 TATTAATA-TTAT
*
9977 TATTAATTATCAT
1 TATTAA-TATTAT
9990 TATTAATACTTAT
1 TATTAATA-TTAT
* *
10003 TAATATTATTAT
1 TATTAATATTAT
10015 TATTAAT
1 TATTAAT
10022 TATTGTATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
12 11 0.22
13 34 0.69
14 4 0.08
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (12 bp):
TATTAATATTAT
Found at i:10048 original size:21 final size:18
Alignment explanation
Indices: 9951--10040 Score: 60
Period size: 19 Copynumber: 4.7 Consensus size: 18
9941 ATTTATTAAA
* *
9951 TATTAATATTAATTATTAA
1 TATTATTATTAATTATT-G
9970 TAGTTATTATTAATTATCAT-
1 TA-TTATTATTAATTAT--TG
*
9990 TATTAATACTT-ATTAATAT-
1 TATTATTA-TTAATT-AT-TG
10009 TATTATTATTAATTATTG
1 TATTATTATTAATTATTG
10027 TATTATTACTTAAT
1 TATTATTA-TTAAT
10041 GTTATTGTTA
Statistics
Matches: 60, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
17 1 0.02
18 12 0.20
19 27 0.45
20 19 0.32
22 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (18 bp):
TATTATTATTAATTATTG
Found at i:10646 original size:16 final size:16
Alignment explanation
Indices: 10625--10673 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
10615 TGGTTGAGGG
10625 TTTGGGTTAAGTGTAA
1 TTTGGGTTAAGTGTAA
10641 TTTGGGTT---TGT--
1 TTTGGGTTAAGTGTAA
10652 TTTGGGTTAAGTGTAA
1 TTTGGGTTAAGTGTAA
*
10668 ATTGGG
1 TTTGGG
10674 CCCCAATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
11 8 0.30
13 3 0.11
14 3 0.11
16 13 0.48
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (16 bp):
TTTGGGTTAAGTGTAA
Found at i:10782 original size:6 final size:6
Alignment explanation
Indices: 10773--10825 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
10763 TTATAATATT
** * **
10773 TTTAAA TTTAAA AATAAA TTTAAA CTTAAA -TTAAA TTTAAA AATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
10820 TTTAAA
1 TTTAAA
10826 ATGAGTTGGT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
5 5 0.14
6 32 0.86
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (6 bp):
TTTAAA
Found at i:10809 original size:17 final size:18
Alignment explanation
Indices: 10773--10813 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
10763 TTATAATATT
*
10773 TTTAAATTTAAAAATAAA
1 TTTAAACTTAAAAATAAA
*
10791 TTTAAACTT-AAATTAAA
1 TTTAAACTTAAAAATAAA
10808 TTTAAA
1 TTTAAA
10814 AATAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTAAACTTAAAAATAAA
Found at i:10819 original size:17 final size:17
Alignment explanation
Indices: 10787--10821 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
10777 AATTTAAAAA
**
10787 TAAATTTAAACTTAAAT
1 TAAATTTAAAAATAAAT
10804 TAAATTTAAAAATAAAT
1 TAAATTTAAAAATAAAT
10821 T
1 T
10822 TAAAATGAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAAAATAAAT
Found at i:11960 original size:3 final size:3
Alignment explanation
Indices: 11816--11942 Score: 83
Period size: 3 Copynumber: 42.3 Consensus size: 3
11806 TATTATATGT
* * *
11816 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TGA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * * * * * * * * *
11864 TGA TGA TGA TGA TGA TGA TAA TAA TGA TGA TGA TGA TGA TGA TGA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
11912 TGA TAA TAA TAA TAG TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
11943 TATTATTATT
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 118 1.00
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (3 bp):
TAA
Done.