Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004345.1 Kokia drynarioides strain JFW-HI SEQ_117683, 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: 67999
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:536 original size:17 final size:17
Alignment explanation
Indices: 514--590 Score: 93
Period size: 17 Copynumber: 4.5 Consensus size: 17
504 TAAATTTAAT
*
514 TTTAAATTTATAATAAA
1 TTTAAATTTAAAATAAA
***
531 TTTAAATTTCCCATAAA
1 TTTAAATTTAAAATAAA
548 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
565 CTT-AATGTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
582 TTTAAATTT
1 TTTAAATTT
591 TGTTTTGCTC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
16 3 0.06
17 44 0.88
18 3 0.06
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:1288 original size:201 final size:201
Alignment explanation
Indices: 925--1349 Score: 602
Period size: 201 Copynumber: 2.1 Consensus size: 201
915 TTCAGTCTTC
* * * * * * ** *
925 TTCTCAGTATCTCATCAGGAAGATGACCGCATTGCTTGTTTCAATTCGCTTCTTTTTATCTCATC
1 TTCTCTGTATCTCATCAGAAAGATGACCGCATTACCTGTTTCAATCCACTTCCCTGTATCTCATC
* * * * *
990 AAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGAC
66 AAAAAGACAAATTTGATCCACTCCTCAATATCTCATCAGGAAGCTAACCATTTTATTGCTTCGAC
** * * *
1055 TTGCTTCTCAGTATCTCATTAGGAAGCTGGGGTTCGAGGATTTGCTCGCATTGAGCCCTGAGTTG
131 CCGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTACTCGCATTGAGCCCTGAGTTG
1120 GTATAA
196 GTATAA
* *
1126 TTCTTTGTATCTCATCAGAAAGATGACCGCCTTACCTGTTTCAATCCACTTCCCTGTATCTCATC
1 TTCTCTGTATCTCATCAGAAAGATGACCGCATTACCTGTTTCAATCCACTTCCCTGTATCTCATC
* *
1191 AAAAAGACAAATTTGATTCACTCCTCAATATCTCATCAGGAAGCTGACCATTTTATTGCTTCGAC
66 AAAAAGACAAATTTGATCCACTCCTCAATATCTCATCAGGAAGCTAACCATTTTATTGCTTCGAC
1256 CCGCTTCTCAGTATC-CTATCAGGTAA-CTGGGGTTCGAAGATTTACTCGCATTGAGCCCTGAGT
131 CCGCTTCTCAGTATCTC-ATCAGG-AAGCTGGGGTTCGAAGATTTACTCGCATTGAGCCCTGAGT
*
1319 TGGTATAC
194 TGGTATAA
1327 TTCTCTGTATCTCATCAGAAAGA
1 TTCTCTGTATCTCATCAGAAAGA
1350 CAAATTTGGT
Statistics
Matches: 197, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
200 1 0.01
201 194 0.98
202 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (201 bp):
TTCTCTGTATCTCATCAGAAAGATGACCGCATTACCTGTTTCAATCCACTTCCCTGTATCTCATC
AAAAAGACAAATTTGATCCACTCCTCAATATCTCATCAGGAAGCTAACCATTTTATTGCTTCGAC
CCGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTACTCGCATTGAGCCCTGAGTTG
GTATAA
Found at i:1377 original size:152 final size:152
Alignment explanation
Indices: 1173--1491 Score: 491
Period size: 152 Copynumber: 2.1 Consensus size: 152
1163 GTTTCAATCC
* *
1173 ACTTCCCTGTATCTCATCAAAAAGACAAATTTGATTCACTCCTCAATATCTCATCAGGAAGCTGA
1 ACTTCCCTGTATCTCATCAAAAAGACAAATTTGATCCACTCCTCAATATCTCATCAGGAAGCTAA
*
1238 CCATTTTATTGCTTCGACCCGCTTCTCAGTATC-CTATCAGGTAA-CTGGGGTTCGAAGATTTAC
66 CCATTTTATTGCTTCAACCCGCTTCTCAGTATCTC-ATCAGG-AAGCTGGGGTTCGAAGATTTAC
1301 TCGCATTGAGCCCTGAGTTGGTAT
129 TCGCATTGAGCCCTGAGTTGGTAT
* * * * *
1325 ACTTCTCTGTATCTCATCAGAAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAA
1 ACTTCCCTGTATCTCATCAAAAAGACAAATTTGATCCACTCCTCAATATCTCATCAGGAAGCTAA
* * *
1390 CCATTTTTTTGCTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTC
66 CCATTTTATTGCTTCAACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTACTC
1455 GCATTGAGCCCTGAGTTGGTAT
131 GCATTGAGCCCTGAGTTGGTAT
1477 ACTTCGCC-GTATCTC
1 ACTTC-CCTGTATCTC
1492 GTAAGGAAGA
Statistics
Matches: 152, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
151 2 0.01
152 148 0.97
153 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (152 bp):
ACTTCCCTGTATCTCATCAAAAAGACAAATTTGATCCACTCCTCAATATCTCATCAGGAAGCTAA
CCATTTTATTGCTTCAACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTACTC
GCATTGAGCCCTGAGTTGGTAT
Found at i:12710 original size:7 final size:7
Alignment explanation
Indices: 12698--12722 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12688 CAAAAATCAA
12698 GAAATAC
1 GAAATAC
12705 GAAATAC
1 GAAATAC
12712 GAAATAC
1 GAAATAC
12719 GAAA
1 GAAA
12723 GCATATAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.16, T:0.12
Consensus pattern (7 bp):
GAAATAC
Found at i:12872 original size:30 final size:30
Alignment explanation
Indices: 12836--13305 Score: 276
Period size: 30 Copynumber: 15.9 Consensus size: 30
12826 TGGATACTTA
12836 AAAAATGGTAATTTT-GAAAGGTTTGGGGTT
1 AAAAATGGTAATTTTAGAAA-GTTTGGGGTT
* * *
12866 AAAAAT-GAAATTTTTAGACA-TTCGAGGG-T
1 AAAAATGGTAA-TTTTAGAAAGTTTG-GGGTT
* *
12895 -AAAATGGTAATTTTTGGAAAGTTTGAGGTT
1 AAAAATGGTAA-TTTTAGAAAGTTTGGGGTT
* *
12925 AAAAATGG-AATTTTTAGACA-TTCAGGGG-T
1 AAAAATGGTAA-TTTTAGAAAGTT-TGGGGTT
* * *
12954 -AAAATGGTAATTTTGGAAGGTTTGGGGGTC
1 AAAAATGGTAATTTTAGAAAGTTT-GGGGTT
* *
12984 AAAAATGG-AATTTTTAG-ACGTTCGAGGG-T
1 AAAAATGGTAA-TTTTAGAAAGTTTG-GGGTT
* * *
13013 -AAAATGGTAATTTTGGAAAGTTTAGGGTA
1 AAAAATGGTAATTTTAGAAAGTTTGGGGTT
*
13042 AAAAATGG-AATTTTAGAAAATTTTGGGG-T
1 AAAAATGGTAATTTTAG-AAAGTTTGGGGTT
**
13071 AAAAAT-GTAATTTTTAGAAAGTTAAGGGTT
1 AAAAATGGTAA-TTTTAGAAAGTTTGGGGTT
* * *
13101 AAAAAATGGT-GTTTTGGAAAGTTTGGTGGTA
1 -AAAAATGGTAATTTTAGAAAGTTTGG-GGTT
* *
13132 AAAAAT-GTAATTTTTAGAAAGTTTGGTGTC
1 AAAAATGGTAA-TTTTAGAAAGTTTGGGGTT
* *
13162 AAAAATGG-AATTTT-GGAAGTTCGAGGG-T
1 AAAAATGGTAATTTTAGAAAGTTTG-GGGTT
*
13190 AAAAA-AGTAATTTTTAGAAAGTTTGGGGTT
1 AAAAATGGTAA-TTTTAGAAAGTTTGGGGTT
* *
13220 AAAAAT-ATAATTTTTGGAAAGTTT-GGGTT
1 AAAAATGGTAA-TTTTAGAAAGTTTGGGGTT
* *
13249 CAAAAATGG-AATTTTAAAAAGTTTAAGGG-T
1 -AAAAATGGTAATTTTAGAAAGTTT-GGGGTT
* *
13279 -AAAAT-ATAATTTTTTGAAAGTTTGGGG
1 AAAAATGGTAA-TTTTAGAAAGTTTGGGG
13306 ATATTTTGGG
Statistics
Matches: 341, Mismatches: 58, Indels: 84
0.71 0.12 0.17
Matches are distributed among these distances:
27 1 0.00
28 58 0.17
29 103 0.30
30 128 0.38
31 49 0.14
32 2 0.01
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (30 bp):
AAAAATGGTAATTTTAGAAAGTTTGGGGTT
Found at i:12927 original size:59 final size:60
Alignment explanation
Indices: 12837--13234 Score: 332
Period size: 59 Copynumber: 6.8 Consensus size: 60
12827 GGATACTTAA
* *
12837 AAAATGGTAA-TTTT-GAAAGGTTTGGGGTTAAAAATGAAATTTTTAGACA-TTCGAGGGT
1 AAAATGGTAATTTTTAGAAA-GTTTGAGGTTAAAAATGGAATTTTTAGACAGTTCGAGGGT
*
12895 AAAATGGTAATTTTTGGAAAGTTTGAGGTTAAAAATGGAATTTTTAGACA-TTC-AGGGGT
1 AAAATGGTAATTTTTAGAAAGTTTGAGGTTAAAAATGGAATTTTTAGACAGTTCGA-GGGT
* * * *
12954 AAAATGGTAA-TTTTGGAAGGTTTGGGGGTCAAAAATGGAATTTTTAGAC-GTTCGAGGGT
1 AAAATGGTAATTTTTAGAAAGTTT-GAGGTTAAAAATGGAATTTTTAGACAGTTCGAGGGT
* * * * *
13013 AAAATGGTAA-TTTTGGAAAGTTT-AGGGTAAAAAATGGAA-TTTTAGAAAATTTTG-GGGT
1 AAAATGGTAATTTTTAGAAAGTTTGA-GGTTAAAAATGGAATTTTTAG-ACAGTTCGAGGGT
* * * *
13071 AAAAAT-GTAATTTTTAGAAAG-TTAAGGGTTAAAAAATGG--TGTTTTGGAAAGTTTG-GTGGT
1 -AAAATGGTAATTTTTAGAAAGTTTGA-GGTT-AAAAATGGAAT-TTTTAGACAGTTCGAG-GGT
* *
13131 AAAAAAT-GTAATTTTTAGAAAGTTTG-GTGTCAAAAATGGAA-TTTTGGA-AGTTCGAGGGT
1 --AAAATGGTAATTTTTAGAAAGTTTGAG-GTTAAAAATGGAATTTTTAGACAGTTCGAGGGT
** * **
13190 AAAAAAGTAATTTTTAGAAAGTTTGGGGTTAAAAATATAATTTTT
1 AAAATGGTAATTTTTAGAAAGTTTGAGGTTAAAAATGGAATTTTT
13235 GGAAAGTTTG
Statistics
Matches: 293, Mismatches: 22, Indels: 49
0.80 0.06 0.13
Matches are distributed among these distances:
57 10 0.03
58 76 0.26
59 144 0.49
60 38 0.13
61 23 0.08
62 2 0.01
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (60 bp):
AAAATGGTAATTTTTAGAAAGTTTGAGGTTAAAAATGGAATTTTTAGACAGTTCGAGGGT
Found at i:13070 original size:117 final size:118
Alignment explanation
Indices: 12836--13084 Score: 364
Period size: 117 Copynumber: 2.1 Consensus size: 118
12826 TGGATACTTA
*
12836 AAAAATGGTAATTTTGAAAGGTTTGGGGTTAAAAATGAAATTTTTAGACATTCGAGGGTAAAATG
1 AAAAATGGTAATTTTGAAAGGTTTGGGGTCAAAAATGAAATTTTTAGACATTCGAGGGTAAAATG
* *
12901 GTAATTTTTGGAAAGTTTGAGGTTAAAAATGGAATTTTTAGACATTCAGGGGT
66 GTAATTTTTGGAAAGTTTGAGGTAAAAAATGGAATTTTTAGAAATTCAGGGGT
* * *
12954 -AAAATGGTAATTTTGGAAGGTTTGGGGGTCAAAAATGGAATTTTTAGACGTTCGAGGGTAAAAT
1 AAAAATGGTAATTTTGAAAGGTTT-GGGGTCAAAAATGAAATTTTTAGACATTCGAGGGTAAAAT
**
13018 GGTAA-TTTTGGAAAGTTT-AGGGTAAAAAATGGAA-TTTTAGAAAATTTTGGGGT
65 GGTAATTTTTGGAAAGTTTGA-GGTAAAAAATGGAATTTTTAG-AAATTCAGGGGT
13071 AAAAAT-GTAATTTT
1 AAAAATGGTAATTTT
13085 TAGAAAGTTA
Statistics
Matches: 119, Mismatches: 8, Indels: 9
0.88 0.06 0.07
Matches are distributed among these distances:
116 7 0.06
117 65 0.55
118 47 0.39
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.35
Consensus pattern (118 bp):
AAAAATGGTAATTTTGAAAGGTTTGGGGTCAAAAATGAAATTTTTAGACATTCGAGGGTAAAATG
GTAATTTTTGGAAAGTTTGAGGTAAAAAATGGAATTTTTAGAAATTCAGGGGT
Found at i:13270 original size:59 final size:59
Alignment explanation
Indices: 12836--13305 Score: 294
Period size: 59 Copynumber: 8.0 Consensus size: 59
12826 TGGATACTTA
* * * *
12836 AAAAATGGTAA-TTTT-GAAAGGTTTGGGGTTAAAAATGA-AATTTTTAGACA-TTCGAGGGT
1 AAAAAT-GTAATTTTTAGAAA-GTTTAGGGTTAAAAAT-ATAATTTTTGGAAAGTTTG-GGGT
* ** * * *
12895 -AAAATGGTAATTTTTGGAAAGTTT-GAGGTTAAAAATGGAATTTTTAGACA-TTCAGGGGT
1 AAAAAT-GTAATTTTTAGAAAGTTTAG-GGTTAAAAATATAATTTTTGGAAAGTT-TGGGGT
* * * * ** * * *
12954 -AAAATGGTAA-TTTTGGAAGGTTTGGGGGTCAAAAATGGAATTTTTAG-ACGTTCGAGGGT
1 AAAAAT-GTAATTTTTAGAAAGTTT-AGGGTTAAAAATATAATTTTTGGAAAGTTTG-GGGT
* * ** * * *
13013 -AAAATGGTAA-TTTTGGAAAGTTTAGGGTAAAAAATGGAATTTTAGAAAATTTTGGGGT
1 AAAAAT-GTAATTTTTAGAAAGTTTAGGGTTAAAAATATAATTTTTGGAAAGTTTGGGGT
* **
13071 AAAAATGTAATTTTTAGAAAGTTAAGGGTTAAAAA-ATGGTGTTTTGGAAAGTTTGGTGGT
1 AAAAATGTAATTTTTAGAAAGTTTAGGGTTAAAAATATAAT-TTTTGGAAAGTTTGG-GGT
* ** *
13131 AAAAAATGTAATTTTTAGAAAGTTT-GGTGTCAAAAATGGAA-TTTTGG-AAGTTCGAGGGT
1 -AAAAATGTAATTTTTAGAAAGTTTAGG-GTTAAAAATATAATTTTTGGAAAGTTTG-GGGT
* * *
13190 AAAAAAGTAATTTTTAGAAAGTTTGGGGTTAAAAATATAATTTTTGGAAAGTTTGGGTT
1 AAAAATGTAATTTTTAGAAAGTTTAGGGTTAAAAATATAATTTTTGGAAAGTTTGGGGT
* * *
13249 CAAAAATGGAA-TTTTAAAAAGTTTAAGGG-T-AAAATATAATTTTTTGAAAGTTTGGGG
1 -AAAAATGTAATTTTTAGAAAGTTT-AGGGTTAAAAATATAATTTTTGGAAAGTTTGGGG
13306 ATATTTTGGG
Statistics
Matches: 343, Mismatches: 45, Indels: 47
0.79 0.10 0.11
Matches are distributed among these distances:
58 109 0.32
59 169 0.49
60 35 0.10
61 30 0.09
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (59 bp):
AAAAATGTAATTTTTAGAAAGTTTAGGGTTAAAAATATAATTTTTGGAAAGTTTGGGGT
Found at i:13844 original size:28 final size:28
Alignment explanation
Indices: 13789--13845 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
13779 ATTTTCAGAA
*
13789 AAAAAAAATCACTTTTCATTTCTTTTTC
1 AAAAAAAATCACTTTTCATTTCTCTTTC
*
13817 AAAAAAAATCCCTTTTC-TTCTCTCTTTC
1 AAAAAAAATCACTTTTCATT-TCTCTTTC
13845 A
1 A
13846 CTCTCTCATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 24 0.92
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (28 bp):
AAAAAAAATCACTTTTCATTTCTCTTTC
Found at i:15084 original size:17 final size:17
Alignment explanation
Indices: 15062--15137 Score: 89
Period size: 17 Copynumber: 4.5 Consensus size: 17
15052 TAAATTTAAT
*
15062 TTTAAATTTATAATAAA
1 TTTAAATTTAAAATAAA
**
15079 TTTAAATTTCCAATAAA
1 TTTAAATTTAAAATAAA
* *
15096 TTGAAATTAAAAATAAA
1 TTTAAATTTAAAATAAA
* *
15113 CTTAATTTTAAAATAAA
1 TTTAAATTTAAAATAAA
15130 TTTAAATT
1 TTTAAATT
15138 CTATTAGGCC
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 47 1.00
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:18125 original size:24 final size:24
Alignment explanation
Indices: 18080--18125 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
18070 TTTTTTAAAT
* *
18080 TTAAAAAGTATAAAGATTAAATTC
1 TTAAAAAGTATAAACATAAAATTC
18104 TTAAAAA-TATAAACATGAAAAT
1 TTAAAAAGTATAAACAT-AAAAT
18126 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (24 bp):
TTAAAAAGTATAAACATAAAATTC
Found at i:18455 original size:26 final size:26
Alignment explanation
Indices: 18397--18455 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
18387 AATCTTTATA
* *
18397 TTTTAATTTTTAATATAATATAATAT
1 TTTTATTTTTTAAAATAATATAATAT
*
18423 TTATATTTTTATAAAATAAT-TAATAT
1 TTTTATTTTT-TAAAATAATATAATAT
18449 TTTTATT
1 TTTTATT
18456 AAAATGTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TTTTATTTTTTAAAATAATATAATAT
Found at i:29071 original size:29 final size:29
Alignment explanation
Indices: 29038--29114 Score: 124
Period size: 28 Copynumber: 2.7 Consensus size: 29
29028 CAAATGATTT
29038 TAAAATTATTAAAATTATTTTTTACAAT-A
1 TAAAATTATTAAAATTATTTTTTA-AATAA
29067 TAAAATTATTAAAATTA-TTTTTAAATAA
1 TAAAATTATTAAAATTATTTTTTAAATAA
29095 TAAAATTATT-AAATTATTTT
1 TAAAATTATTAAAATTATTTT
29115 AATTTTCAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
27 9 0.20
28 20 0.43
29 17 0.37
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTTAAATAA
Found at i:35465 original size:28 final size:28
Alignment explanation
Indices: 35432--35485 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
35422 AAAATGTAAC
35432 AAATAAAAAAATTGTGTTCAAAAGAAAA
1 AAATAAAAAAATTGTGTTCAAAAGAAAA
* * *
35460 AAATAAAACATTTTTGTTCAAAAGAA
1 AAATAAAAAAATTGTGTTCAAAAGAA
35486 CAACAAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.26
Consensus pattern (28 bp):
AAATAAAAAAATTGTGTTCAAAAGAAAA
Found at i:37891 original size:16 final size:15
Alignment explanation
Indices: 37870--37900 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
37860 CTCACACCAT
37870 TTTTTATTTATTTTTA
1 TTTTTATTT-TTTTTA
37886 TTTTTATTTTTTTTA
1 TTTTTATTTTTTTTA
37901 GAACTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTATTTTTTTTA
Found at i:42671 original size:3 final size:3
Alignment explanation
Indices: 42663--42713 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
42653 AAAAACAAGA
42663 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42711 AAT
1 AAT
42714 TAAAGTGGGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:44965 original size:15 final size:16
Alignment explanation
Indices: 44936--44968 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
44926 TTCACTTGAA
44936 TTGATCTTTTGTTGTT
1 TTGATCTTTTGTTGTT
*
44952 TTGAT-TTTTTTTGTT
1 TTGATCTTTTGTTGTT
44967 TT
1 TT
44969 AAAGATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.06, C:0.03, G:0.15, T:0.76
Consensus pattern (16 bp):
TTGATCTTTTGTTGTT
Found at i:45301 original size:12 final size:12
Alignment explanation
Indices: 45264--45305 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
45254 CTTGATAAAT
*
45264 AATACAAATTTA
1 AATAAAAATTTA
45276 AGATGAAAAA-TTA
1 A-AT-AAAAATTTA
45289 AATAAAAATTTA
1 AATAAAAATTTA
45301 AATAA
1 AATAA
45306 TTTTTTTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 5 0.19
12 11 0.42
13 6 0.23
14 4 0.15
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (12 bp):
AATAAAAATTTA
Found at i:46948 original size:2 final size:2
Alignment explanation
Indices: 46941--46972 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
46931 AAAAGAAAAT
46941 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46973 AGTAATACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51375 original size:29 final size:30
Alignment explanation
Indices: 51332--51390 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
51322 GAATTGAATC
*
51332 AAATCAAAATTTCATGGATAAAATTACACA
1 AAATCAAAATTTCATAGATAAAATTACACA
* *
51362 AAATCAAAA-TTCATATATACAATTACACA
1 AAATCAAAATTTCATAGATAAAATTACACA
51391 TTAAATCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.54, C:0.15, G:0.03, T:0.27
Consensus pattern (30 bp):
AAATCAAAATTTCATAGATAAAATTACACA
Found at i:52093 original size:21 final size:21
Alignment explanation
Indices: 52045--52093 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
52035 AAACAAATCG
*
52045 GAAAATGAAAGAAAAATTGTA
1 GAAAAAGAAAGAAAAATTGTA
* *
52066 GAGAAAGAAAGTAAAATTG-A
1 GAAAAAGAAAGAAAAATTGTA
52086 TGAAAAAG
1 -GAAAAAG
52094 TTCACACCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.16
Consensus pattern (21 bp):
GAAAAAGAAAGAAAAATTGTA
Found at i:56542 original size:21 final size:21
Alignment explanation
Indices: 56492--56542 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
56482 GAAAACAAAC
*
56492 CAGAAAATGAAAGAAAAATTG
1 CAGAAAAAGAAAGAAAAATTG
* *
56513 CAGAGAAAGAAAGTAAAATTG
1 CAGAAAAAGAAAGAAAAATTG
56534 -ATGAAAAAG
1 CA-GAAAAAG
56543 TTCACACCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.61, C:0.04, G:0.22, T:0.14
Consensus pattern (21 bp):
CAGAAAAAGAAAGAAAAATTG
Found at i:61359 original size:32 final size:29
Alignment explanation
Indices: 61315--61381 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
61305 ACTTTCCTCA
* *
61315 TTAATTTTTTTTATATTTTATTTTCTTAGTTT
1 TTAATTTGTTTTA-ATTTTA-ATT-TTAGTTT
*
61347 TTAATTTGTTTTACTTTTAATTTTAGTTT
1 TTAATTTGTTTTAATTTTAATTTTAGTTT
61376 TTAATT
1 TTAATT
61382 CTAAAACCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 13 0.41
30 2 0.06
31 5 0.16
32 12 0.38
ACGTcount: A:0.21, C:0.03, G:0.04, T:0.72
Consensus pattern (29 bp):
TTAATTTGTTTTAATTTTAATTTTAGTTT
Done.