Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010289.1 Kokia drynarioides strain JFW-HI SEQ_125138, 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: 25337
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:18 original size:3 final size:3
Alignment explanation
Indices: 5--128 Score: 61
Period size: 3 Copynumber: 39.0 Consensus size: 3
1 ACAT
* * *
5 TAA TAG TAA TAA TAGT TAA TAA TAA TAA TAA CTATT TAA TAAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA -TA-A TAA T-AA TAA TAA
* * * * * *
54 TAA TAT TAA TAA TAAA TAG TAG TAA TAAA TAA CAT TAA TAAA TAT TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA T-AA TAA TAA TAA T-AA TAA TAA
* * *
102 TAA AAA TAT TAG TAA TAA -AA TGAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA
129 AAAAGGGAAA
Statistics
Matches: 91, Mismatches: 21, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
2 2 0.02
3 68 0.75
4 21 0.23
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:25 original size:16 final size:16
Alignment explanation
Indices: 4--34 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1 ACA
*
4 TTAATAGTAATAATAG
1 TTAATAATAATAATAG
20 TTAATAATAATAATA
1 TTAATAATAATAATA
35 ACTATTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (16 bp):
TTAATAATAATAATAG
Found at i:29 original size:13 final size:12
Alignment explanation
Indices: 11--119 Score: 69
Period size: 12 Copynumber: 8.5 Consensus size: 12
1 ACATTAATAG
11 TAATAATAGTTAA
1 TAATAATA-TTAA
*
24 TAATAATAATAA
1 TAATAATATTAA
* *
36 CTATTTAATAAATAA
1 -TA-ATAAT-ATTAA
51 TAATAATATTAA
1 TAATAATATTAA
63 TAATAAATAGTAGTAA
1 TAAT-AATA-T--TAA
*
79 TAAATAACATTAA
1 T-AATAATATTAA
92 T-A-AATATTAA
1 TAATAATATTAA
* *
102 TAAAAATATTAG
1 TAATAATATTAA
114 TAATAA
1 TAATAA
120 AATGAATAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
10 8 0.10
11 2 0.03
12 23 0.29
13 22 0.28
14 7 0.09
15 6 0.08
16 7 0.09
17 3 0.04
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.36
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:1209 original size:29 final size:29
Alignment explanation
Indices: 1159--1619 Score: 339
Period size: 30 Copynumber: 15.9 Consensus size: 29
1149 CCCTGGAGGT
1159 CCCT-GAACTTCCAAAAATTCCATTTTTA
1 CCCTCGAACTTCCAAAAATTCCATTTTTA
*
1187 CCCTCGAA-TTCCCAAAAATTCCATTTTCAA
1 CCCTCGAACTT-CCAAAAATTCCATTTT-TA
**
1217 CCCTAAAACTTCCAAAAATTCCATTTTTTA
1 CCCTCGAACTTCCAAAAATTCCA-TTTTTA
* * *
1247 CCCCCGAACTCCCAAAAATTCCATTTTCGA
1 CCCTCGAACTTCCAAAAATTCCATTTT-TA
* *
1277 -CCTCGAAACTTCCAAAAAATCAATTTTTA
1 CCCTCG-AACTTCCAAAAATTCCATTTTTA
*
1306 CCC-CGAACTTCCATAAATTCCATTTTTGA
1 CCCTCGAACTTCCAAAAATTCCATTTTT-A
* *
1335 CCC-CAAAACTTTCAAAAATTCCATTTTTA
1 CCCTC-GAACTTCCAAAAATTCCATTTTTA
* * *
1364 CCC-CTAAACTTCAAAAAAATCCATTTTTGA
1 CCCTC-GAACTTCCAAAAATTCCATTTTT-A
1394 CCCT-GAAACTTCCAAAAAATTCCATTTTTGA
1 CCCTCG-AACTTCC-AAAAATTCCATTTTT-A
* * ** *
1425 CCC-CAAAATTTTAAAAAAATCCATTTTTA
1 CCCTC-GAACTTCCAAAAATTCCATTTTTA
*
1454 CCCTCGAACTTCCAAAAATTCCATTTTCA
1 CCCTCGAACTTCCAAAAATTCCATTTTTA
* * * *
1483 ACNT--AA----AAAAAAATCCATTTTTA
1 CCCTCGAACTTCCAAAAATTCCATTTTTA
*
1506 CCCTCGAACTTCCAAAAATTCCATTTTCAA
1 CCCTCGAACTTCCAAAAATTCCATTTT-TA
* * *
1536 CCC-CGTAACTCCCAAAAATTCTATTTTTG
1 CCCTCG-AACTTCCAAAAATTCCATTTTTA
* * *
1565 CCC-CGAA-TGTCCAAAAACTCTATTTTCGA
1 CCCTCGAACT-TCCAAAAATTCCATTTT-TA
*
1594 -CCTCAAAAC-TCCAAAAATTCCATTTT
1 CCCTC-GAACTTCCAAAAATTCCATTTT
1620 ATCCCCGAAT
Statistics
Matches: 344, Mismatches: 59, Indels: 59
0.74 0.13 0.13
Matches are distributed among these distances:
23 16 0.05
25 2 0.01
27 3 0.01
28 44 0.13
29 120 0.35
30 130 0.38
31 29 0.08
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.32
Consensus pattern (29 bp):
CCCTCGAACTTCCAAAAATTCCATTTTTA
Found at i:1403 original size:59 final size:59
Alignment explanation
Indices: 1159--1532 Score: 337
Period size: 59 Copynumber: 6.5 Consensus size: 59
1149 CCCTGGAGGT
* * **
1159 CCCTG-AACTTCCAAAAATTCCATTTTTA-CCCTCGAA-TTCCCAAAAATTCCATTTTCAA
1 CCCTGAAACTTCCAAAAATTCCATTTTTACCCCT-GAACTT-CAAAAAAATCCATTTTTGA
* * * * * *
1217 CCCTAAAACTTCCAAAAATTCCATTTTTTACCCCCGAACTCCCAAAAATTCCATTTTCGA
1 CCCTGAAACTTCCAAAAATTCCA-TTTTTACCCCTGAACTTCAAAAAAATCCATTTTTGA
* * * * *
1277 -CCTCGAAACTTCCAAAAAATCAATTTTTACCCC-GAACTTCCATAAATTCCATTTTTGA
1 CCCT-GAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCAAAAAAATCCATTTTTGA
** * *
1335 CCCCAAAACTTTCAAAAATTCCATTTTTACCCCTAAACTTCAAAAAAATCCATTTTTGA
1 CCCTGAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCAAAAAAATCCATTTTTGA
** * *
1394 CCCTGAAACTTCCAAAAAATTCCATTTTTGACCCCAAAATTTTAAAAAAATCCATTTTT-A
1 CCCTGAAACTTCC-AAAAATTCCATTTTT-ACCCCTGAACTTCAAAAAAATCCATTTTTGA
* * *
1454 CCCTCG-AACTTCCAAAAATTCCATTTTCA-ACNT-AA----AAAAAAATCCATTTTT-A
1 CCCT-GAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCAAAAAAATCCATTTTTGA
1506 CCCTCG-AACTTCCAAAAATTCCATTTT
1 CCCT-GAAACTTCCAAAAATTCCATTTT
1533 CAACCCCGTA
Statistics
Matches: 277, Mismatches: 29, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
52 44 0.16
56 2 0.01
57 1 0.00
58 52 0.19
59 77 0.28
60 70 0.25
61 31 0.11
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.32
Consensus pattern (59 bp):
CCCTGAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCAAAAAAATCCATTTTTGA
Found at i:1501 original size:52 final size:51
Alignment explanation
Indices: 1437--1536 Score: 191
Period size: 52 Copynumber: 1.9 Consensus size: 51
1427 CCAAAATTTT
1437 AAAAAAATCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTCAACNTAA
1 AAAAAAATCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTCAAC-TAA
1489 AAAAAAATCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTCAAC
1 AAAAAAATCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTCAAC
1537 CCCGTAACTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.40, C:0.26, G:0.02, T:0.31
Consensus pattern (51 bp):
AAAAAAATCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTCAACTAA
Found at i:3666 original size:28 final size:28
Alignment explanation
Indices: 3635--3696 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
3625 AAAATGAGAC
* *
3635 TTTGGATACCCAAGGGCAAAATGGTAAT
1 TTTGGACACCCAAGGGCAAAATGATAAT
* ** *
3663 TTTGGACACTCGGGGGCAAAATTATAAT
1 TTTGGACACCCAAGGGCAAAATGATAAT
3691 TTTGGA
1 TTTGGA
3697 AAAGTTTGGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (28 bp):
TTTGGACACCCAAGGGCAAAATGATAAT
Found at i:3750 original size:59 final size:56
Alignment explanation
Indices: 3660--3899 Score: 148
Period size: 59 Copynumber: 4.1 Consensus size: 56
3650 GCAAAATGGT
* *
3660 AATTTTGGACACTCGGGGGCAAAATTA-TAATTTTGGAAAAGTTTGGGGTTAAAAAATGA
1 AATTTTGGACATTC-GGGGTAAAA--AGTAATTTTGGAAAAGTTTGGGGTT-AAAAATGA
* * * * * *
3719 AATTTTAGACATTCGAGGGTAAAACAGTAATTTTTAGAAAAATTT-TGGATAAAAACGCA
1 AATTTTGGACATTCG-GGGTAAAA-AGTAA-TTTTGGAAAAGTTTGGGGTTAAAAATG-A
* * * * * * *
3778 AATTTTGGACATTCGGGGGTAAAATGGTAATTTTTGATAACTTCGAGGTAAAAAATGGA
1 AATTTTGGACATTC-GGGGTAAAA-AGTAATTTTGGAAAAGTTTGGGGTTAAAAAT-GA
* * *
3837 ATTTTTGGA-AGTTCGGTGATAAAAATGGAATTTTGG-AAAGTTTTGGGGTT-AAAATGA
1 AATTTTGGACA-TTCGG-GGTAAAAA-GTAATTTTGGAAAAG-TTTGGGGTTAAAAATGA
3894 AATTTT
1 AATTTT
3900 TGGAAGTCTG
Statistics
Matches: 139, Mismatches: 31, Indels: 24
0.72 0.16 0.12
Matches are distributed among these distances:
57 7 0.05
58 28 0.20
59 90 0.65
60 14 0.10
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (56 bp):
AATTTTGGACATTCGGGGTAAAAAGTAATTTTGGAAAAGTTTGGGGTTAAAAATGA
Found at i:3851 original size:29 final size:28
Alignment explanation
Indices: 3798--3906 Score: 80
Period size: 29 Copynumber: 3.7 Consensus size: 28
3788 ATTCGGGGGT
* *
3798 AAAATGGTAATTTTTGATAACTTCGAGGTAA
1 AAAATGG-AATTTTTG-GAAGTTCG-GGTAA
3829 AAAATGGAATTTTTGGAAGTTC-GGTGATA
1 AAAATGGAATTTTTGGAAGTTCGGGT-A-A
* *
3858 AAAATGGAA-TTTTGGAAAGTTTTGGGGT-T
1 AAAATGGAATTTTTGG-AAG--TTCGGGTAA
*
3887 AAAATGAAATTTTTGGAAGT
1 AAAATGGAATTTTTGGAAGT
3907 CTGGGAGTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
27 4 0.06
28 7 0.11
29 29 0.44
30 14 0.21
31 9 0.14
32 3 0.05
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTCGGGTAA
Found at i:3920 original size:28 final size:27
Alignment explanation
Indices: 3829--3921 Score: 75
Period size: 29 Copynumber: 3.3 Consensus size: 27
3819 TTCGAGGTAA
*
3829 AAAATGGAATTTTTGGAAGTTCGGTGA-T
1 AAAATGAAATTTTTGGAAGTT-GG-GAGT
*
3857 AAAAATGGAA-TTTTGGAAAGTTTTGGG-GTT
1 -AAAATGAAATTTTTGG-AAG--TTGGGAG-T
3887 AAAATGAAATTTTTGGAAGTCTGGGAGT
1 AAAATGAAATTTTTGGAAGT-TGGGAGT
3915 AAAATGA
1 AAAATGA
3922 TAAATTTCAA
Statistics
Matches: 55, Mismatches: 1, Indels: 17
0.75 0.01 0.23
Matches are distributed among these distances:
27 1 0.02
28 18 0.33
29 25 0.45
30 9 0.16
31 2 0.04
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (27 bp):
AAAATGAAATTTTTGGAAGTTGGGAGT
Found at i:4022 original size:59 final size:59
Alignment explanation
Indices: 3828--4024 Score: 181
Period size: 58 Copynumber: 3.4 Consensus size: 59
3818 CTTCGAGGTA
* * ** *
3828 AAAAATGGAATTTTTGGAAGTTCGGTGATAAAAATGG-AATTTT-GGAAAGTTTTGGGGTT
1 AAAAATGAAATTTTTGGAAGTTTGG-GAGCAAAATGGTAATTTTCAG-AAGTTTTGGGGTT
* * * * * * *
3887 -AAAATGAAATTTTTGGAAGTCTGGGAGTAAAATGATAAATTTCAAAAATTTTAGGG-T
1 AAAAATGAAATTTTTGGAAGTTTGGGAGCAAAATGGTAATTTTCAGAAGTTTTGGGGTT
*
3944 AAAAAT-ATAATTTTTGGAAGTTTGAGG-GCAAAATGGTAATTTTCAGAAGTTTCGGGGTT
1 AAAAATGA-AATTTTTGGAAGTTTG-GGAGCAAAATGGTAATTTTCAGAAGTTTTGGGGTT
**
4003 AAAAATGGGATTTTTGGAAGTT
1 AAAAATGAAATTTTTGGAAGTT
4025 CAAGGGTTAA
Statistics
Matches: 110, Mismatches: 21, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
57 10 0.09
58 78 0.71
59 22 0.20
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (59 bp):
AAAAATGAAATTTTTGGAAGTTTGGGAGCAAAATGGTAATTTTCAGAAGTTTTGGGGTT
Found at i:6081 original size:6 final size:6
Alignment explanation
Indices: 6072--6190 Score: 99
Period size: 6 Copynumber: 20.7 Consensus size: 6
6062 TTTGAACATT
6072 AATTTA AATTTA AATTTA AATTTA AATTTA TAA--TA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA
* * * * * *
6119 AACTTA TAA--TA AATTTA AATTTT AA-GTA AATTTA GACTTA AA-ATA
1 AATTTA -AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* *
6164 AATTTA ATTTTA AA-ATA AATTTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATT
6191 ATGTTGGATC
Statistics
Matches: 90, Mismatches: 14, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
4 4 0.04
5 15 0.17
6 67 0.74
7 4 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:6108 original size:17 final size:17
Alignment explanation
Indices: 6072--6190 Score: 98
Period size: 17 Copynumber: 6.6 Consensus size: 17
6062 TTTGAACATT
6072 AATTTAAATTTA-AATTTA
1 AATTTAAATTTATAA--TA
6090 AATTTAAATTTATAATA
1 AATTTAAATTTATAATA
6107 AATTTAAATTTAAACTTATAATA
1 AATTTAAA--T----TTATAATA
6130 AATTTAAATTT-TAAGTA
1 AATTTAAATTTATAA-TA
* * *
6147 AATTTAGACTTAAAATA
1 AATTTAAATTTATAATA
* *
6164 AATTTAATTTTAAAATA
1 AATTTAAATTTATAATA
6181 AATTTAAATT
1 AATTTAAATT
6191 ATGTTGGATC
Statistics
Matches: 85, Mismatches: 7, Indels: 19
0.77 0.06 0.17
Matches are distributed among these distances:
16 3 0.04
17 48 0.56
18 14 0.16
19 3 0.04
21 1 0.01
23 16 0.19
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
AATTTAAATTTATAATA
Found at i:6108 original size:23 final size:23
Alignment explanation
Indices: 6082--6140 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
6072 AATTTAAATT
*
6082 TAAATTTAAATTTAAATTTATAA
1 TAAATTTAAATTTAAACTTATAA
6105 TAAATTTAAATTTAAACTTATAA
1 TAAATTTAAATTTAAACTTATAA
6128 TAAATTTAAATTT
1 TAAATTTAAATTT
6141 TAAGTAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAATTTAAATTTAAACTTATAA
Found at i:6110 original size:11 final size:11
Alignment explanation
Indices: 6094--6135 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
6084 AATTTAAATT
6094 TAAATTTATAA
1 TAAATTTATAA
6105 TAAATTTA-AA
1 TAAATTTATAA
*
6115 TTTAAACTTATAA
1 --TAAATTTATAA
6128 TAAATTTA
1 TAAATTTA
6136 AATTTTAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 2 0.08
11 15 0.58
12 7 0.27
13 2 0.08
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (11 bp):
TAAATTTATAA
Found at i:6149 original size:34 final size:34
Alignment explanation
Indices: 6111--6192 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 34
6101 ATAATAAATT
*
6111 TAAATTTAAACTTATAATAAATTTAAATTTT-AAG
1 TAAATTTAAACTTATAATAAATTT-AATTTTAAAA
* *
6145 TAAATTTAGACTTAAAATAAATTTAATTTTAAAA
1 TAAATTTAAACTTATAATAAATTTAATTTTAAAA
6179 TAAATTTAAA-TTAT
1 TAAATTTAAACTTAT
6193 GTTGGATCCG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 9 0.21
34 33 0.79
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (34 bp):
TAAATTTAAACTTATAATAAATTTAATTTTAAAA
Found at i:6190 original size:23 final size:23
Alignment explanation
Indices: 6072--6190 Score: 96
Period size: 23 Copynumber: 4.9 Consensus size: 23
6062 TTTGAACATT
*
6072 AATTTAAATTTAAATTTAAATTTA
1 AATTTAAA-ATAAATTTAAATTTA
*
6096 AATTTATAATAAATTTAAATTTA
1 AATTTAAAATAAATTTAAATTTA
* *
6119 AACTTATAATAAATTTAAATTTTAAGTA
1 AATTTAAAATAAATTTAAA--TT---TA
** *
6147 AATTTAGACTTAAA-ATAAATTTA
1 AATTTA-AAATAAATTTAAATTTA
*
6170 ATTTTAAAATAAATTTAAATT
1 AATTTAAAATAAATTTAAATT
6191 ATGTTGGATC
Statistics
Matches: 76, Mismatches: 12, Indels: 15
0.74 0.12 0.15
Matches are distributed among these distances:
22 5 0.07
23 45 0.59
24 7 0.09
25 2 0.03
26 2 0.03
28 11 0.14
29 4 0.05
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
AATTTAAAATAAATTTAAATTTA
Found at i:9463 original size:6 final size:6
Alignment explanation
Indices: 9452--9479 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
9442 AATGACACCA
9452 ACCCCG ACCCCG ACCCCG ACCCCG ACCC
1 ACCCCG ACCCCG ACCCCG ACCCCG ACCC
9480 GTTCCGTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.68, G:0.14, T:0.00
Consensus pattern (6 bp):
ACCCCG
Found at i:14118 original size:3 final size:3
Alignment explanation
Indices: 14110--14139 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
14100 ATATATCAAG
14110 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
14140 TATGCGATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:23082 original size:24 final size:24
Alignment explanation
Indices: 23051--23101 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
23041 ACATACAACA
* *
23051 TTAGCTCTTATGAGCCTAGAATGG
1 TTAGCTCTTATGAGCCCAGAATAG
23075 TTAGCTCTTATGAGCCCAGAATAG
1 TTAGCTCTTATGAGCCCAGAATAG
23099 TTA
1 TTA
23102 ACCAGTATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (24 bp):
TTAGCTCTTATGAGCCCAGAATAG
Found at i:23259 original size:82 final size:82
Alignment explanation
Indices: 23112--23266 Score: 231
Period size: 82 Copynumber: 1.9 Consensus size: 82
23102 ACCAGTATAC
* * *
23112 GATGCTGCTCACACAAGCTGATGAGAATTCGCGACATACGTGAAGACTCAACCATCAATATGGTC
1 GATGCTGCTCACACAAGCTGATGAGAATTCACAACATACGTGAAGACTCAACCATCAATAGGGTC
*
23177 CAGAATTTCCCACTCTT
66 CACAATTTCCCACTCTT
* * *
23194 GATGCTGCTTACACAAGCTGATGAGAATTCACAACATACGTGAAGACTCAGCCATCAGA-GGGGT
1 GATGCTGCTCACACAAGCTGATGAGAATTCACAACATACGTGAAGACTCAACCATCA-ATAGGGT
23258 CCACAATTT
65 CCACAATTT
23267 AGTATTCATT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
82 64 0.98
83 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (82 bp):
GATGCTGCTCACACAAGCTGATGAGAATTCACAACATACGTGAAGACTCAACCATCAATAGGGTC
CACAATTTCCCACTCTT
Found at i:25309 original size:17 final size:16
Alignment explanation
Indices: 25287--25333 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 16
25277 ACTCATTCTA
25287 AAATTTATTTTAAGGT-T
1 AAATTTATTTTAA--TAT
25304 AAATTTATTTTGAATAT
1 AAATTTATTTT-AATAT
25321 AAATTTATTTTAA
1 AAATTTATTTTAA
25334 ATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.11
17 23 0.82
18 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
AAATTTATTTTAATAT
Done.