Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013151.1 Kokia drynarioides strain JFW-HI SEQ_128170, 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: 6927
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:1813 original size:379 final size:376
Alignment explanation
Indices: 1092--2168 Score: 1048
Period size: 379 Copynumber: 2.8 Consensus size: 376
1082 ATGATACATA
* * * * ***
1092 TTTCCTACAATATTTGTTTGTTGTTTCCATTGTAATTA-AGACTCTAATCTTTCTTTGAAAA-TT
1 TTTCCTACCATATTTCTATATTGTTTCCATTGTAATTATA-ACTCTAATCTTTCAACGAAAACTT
** ** * * * *
1155 ACGC-TATAATATCTTCAAAAACAGTAGTTTTTTTCTTTTATCATT-T-AACATTATGTACCACT
65 -CGCTTA-AATATCACCAAAAACA-T-GTGCTTCTCATTTAT--TTGTAAACATTATTTATCACT
** * * *** * *
1217 TATTTTGTGTTGTCAACTTTCACTACAATTCAAGTTTCCTATACGAGTCGAGTGAAAAAAGGGGT
124 TATTTTGCATTGTCAAATTTCACCACAATTCAAGTTTAAGATACGCGTCGAGTGAAAAAAGGGGG
* * * * * *
1282 TAAAAAAAAACATAAAATGGGTTTTGGGGATGTTTATACAATCATTTCTATTTCTCTTAAAGGCT
189 GAAAAAAACACA-AAAA-GAG-TTTGGGGGTGCTTATACAATCATGTCTATTTC-CTTAAAGGCT
* * * * * *
1347 TCGCTCTCTGTTTTCAACCTCACATTGGATATATACTATTTTCTTTAATTATCTTTTGTTTCAAG
250 TCGCTCCCTATTTTCAACCTCACTTTTGATATAAACTATTTTCTTTGATT-TCTTTTGTTTCAAG
* * *
1412 CATTTTGTGTCGAGTCTGAAAATGAAGAGTATCAAATTGGTTAGTGGCCAACCAAGATACC-TGC
314 TATTTTGTGTCGAGTCTGAAAATGAAGAATATCAAATTGGTTAGAGGCCAACC-A-ATACCATGC
* * * *
1476 -TTCCTAGCATAGTTT-TATGTTGTTTCCGTTGTAATTATAACTCTAATCTTTCAGCGAAAACTT
1 TTTCCTACCATA-TTTCTATATTGTTTCCATTGTAATTATAACTCTAATCTTTCAACGAAAACTT
* * * *
1539 CGCTTAAATATCACCAAAAATATGTGCTTCTCATTTATTTTTGAAA-TTTATTTATCACTTGTTT
65 CGCTTAAATATCACCAAAAACATGTGCTTCTCATTTATTTGT-AAACATTATTTATCACTTATTT
* *
1603 TGCATTGTCAAATTTCACCACAATTCAACTTTTAGATACGCGTCGAGTGAAAAAAGGGGGGAAAC
129 TGCATTGTCAAATTTCACCACAATTCAAGTTTAAGATACGCGTCGAGTGAAAAAAGGGGGGAAA-
*
1668 AAAACACAAAAAGAGTTTGGGGGTGCTTATACAATCATGTCTATTTGCCTAAAAGGCTTCGCTCC
193 AAAACACAAAAAGAGTTTGGGGGTGCTTATACAATCATGTCTATTT-CCTTAAAGGCTTCGCTCC
* *
1733 CTATTTTCAACTTCACTTTTGATATAAACTGTTTTCTTTGATATTCTTTTGTTTCAAGTATTTTG
257 CTATTTTCAACCTCACTTTTGATATAAACTATTTTCTTTGAT-TTCTTTTGTTTCAAGTATTTTG
* ** * * *
1798 TGTC-ATGTTTGAAAATTCAGAATATCCAATTGGTTAGAGGCTAACCAATACCATTC
321 TGTCGA-GTCTGAAAATGAAGAATATCAAATTGGTTAGAGGCCAACCAATACCATGC
* * * * * *
1854 TTTCGTACCATATTTCTCTATTGTTTCCATTGTATTTATGACTCTAATCTTTCAACGGAAAGTTC
1 TTTCCTACCATATTTCTATATTGTTTCCATTGTAATTATAACTCTAATCTTTCAACGAAAACTTC
* * * *
1919 GCTTAAATATCTCCAAAAGCATGTGTTTCTCCTTTATTTGTAAACATTATTTATCACTTATTTTG
66 GCTTAAATATCACCAAAAACATGTGCTTCTCATTTATTTGTAAACATTATTTATCACTTATTTTG
* * * * *
1984 CATTGTCAAATTTCACCACAATTAAAGTTTAAGATACGC-ACTGAGTG-AAAAAGAGTGGAAATG
131 CATTGTCAAATTTCACCACAATTCAAGTTTAAGATACGCGTC-GAGTGAAAAAAGGGGGGAAA-A
* * * * * * *
2047 AAACATAAAATGAGTGT-GAGGTGCTTAGACAATCGTGTGC-ATTTCCCTTAAAGGCTTCACTCC
194 AAACACAAAAAGAGTTTGGGGGTGCTTATACAATCATGT-CTATTT-CCTTAAAGGCTTCGCTCC
* * ** ** *
2110 TTATTTTCATCCTCACTTTTCTTATAAACCCTTTTCTTTGATCTTCTTTTGTGTCAAGT
257 CTATTTTCAACCTCACTTTTGATATAAACTATTTTCTTTGAT-TTCTTTTGTTTCAAGT
2169 TTAAGCTCTT
Statistics
Matches: 580, Mismatches: 96, Indels: 41
0.81 0.13 0.06
Matches are distributed among these distances:
377 93 0.16
378 38 0.07
379 281 0.48
380 5 0.01
381 82 0.14
382 10 0.02
383 63 0.11
384 8 0.01
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (376 bp):
TTTCCTACCATATTTCTATATTGTTTCCATTGTAATTATAACTCTAATCTTTCAACGAAAACTTC
GCTTAAATATCACCAAAAACATGTGCTTCTCATTTATTTGTAAACATTATTTATCACTTATTTTG
CATTGTCAAATTTCACCACAATTCAAGTTTAAGATACGCGTCGAGTGAAAAAAGGGGGGAAAAAA
ACACAAAAAGAGTTTGGGGGTGCTTATACAATCATGTCTATTTCCTTAAAGGCTTCGCTCCCTAT
TTTCAACCTCACTTTTGATATAAACTATTTTCTTTGATTTCTTTTGTTTCAAGTATTTTGTGTCG
AGTCTGAAAATGAAGAATATCAAATTGGTTAGAGGCCAACCAATACCATGC
Found at i:2956 original size:31 final size:29
Alignment explanation
Indices: 2917--3008 Score: 91
Period size: 28 Copynumber: 3.1 Consensus size: 29
2907 TTTTCAGTAG
2917 GTTTGGGGTAAAAAAATGAGATTTTTGGAA
1 GTTTGGGGTAAAAAAATG-GATTTTTGGAA
* *
2947 GTTTGGGGGT---AAAATGGTAATTTTAGAA
1 GTTT-GGGGTAAAAAAATGG-ATTTTTGGAA
*
2975 GGTTCGGGGTAAAAAAATGGGATTTTTGGAA
1 -GTTTGGGGTAAAAAAAT-GGATTTTTGGAA
3006 GTT
1 GTT
3009 CAGGGGAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
27 1 0.02
28 19 0.38
29 3 0.06
30 7 0.14
31 18 0.36
32 2 0.04
ACGTcount: A:0.33, C:0.01, G:0.33, T:0.34
Consensus pattern (29 bp):
GTTTGGGGTAAAAAAATGGATTTTTGGAA
Found at i:2988 original size:59 final size:59
Alignment explanation
Indices: 2868--3084 Score: 287
Period size: 59 Copynumber: 3.7 Consensus size: 59
2858 GTTCGGAATC
* *
2868 AAAAATGGGATTTTTGGAAGTTC-GAAGGTAAAATGGTAATTTTCAGTAGGTTTGGGGTAA
1 AAAAATGGGATTTTTGGAAGTTCAG-GGGTAAAATGGTAATTTT-AGAAGGTTTGGGGTAA
* ** *
2928 AAAAATGAGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTAGAAGGTTCGGGGTAA
1 AAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTAGAAGGTTTGGGGTAA
*
2987 AAAAATGGGATTTTTGGAAGTTCAGGGG-AAAATGGTAATTTTTAGAAGGTTTGGGGT-C
1 AAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATGGTAA-TTTTAGAAGGTTTGGGGTAA
* * *
3045 AAAATTGGTGATTTTTTGAAGTTTAGGGGTAAAATGGTAA
1 AAAAATGG-GATTTTTGGAAGTTCAGGGGTAAAATGGTAA
3085 AAATGGGATT
Statistics
Matches: 140, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
58 17 0.12
59 74 0.53
60 48 0.34
61 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.34
Consensus pattern (59 bp):
AAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTAGAAGGTTTGGGGTAA
Found at i:3058 original size:118 final size:119
Alignment explanation
Indices: 2868--3084 Score: 330
Period size: 118 Copynumber: 1.8 Consensus size: 119
2858 GTTCGGAATC
* *
2868 AAAAATGGGATTTTTGGAAGTTCGAAGGTAAAATGGTAATTTTCAGTAGGTTTGGGGTAAAAAAA
1 AAAAATGGGATTTTTGGAAGTTCGAAGGGAAAATGGTAATTTTCAGAAGGTTTGGGGTAAAAAAA
*
2933 TGAGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTAGAAGGTTCGGGGTAA
66 TGAGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTAGAAGGTTCGGGGTAA
* * * *
2987 AAAAATGGGATTTTTGGAAGTTC-AGGGGAAAATGGTAATTTTTAGAAGGTTTGGGGT-CAAAAT
1 AAAAATGGGATTTTTGGAAGTTCGAAGGGAAAATGGTAATTTTCAGAAGGTTTGGGGTAAAAAAA
* *
3050 TGGTGATTTTTTGAAGTTTAGGGGTAAAATGGTAA
66 T-GAGATTTTTGGAAGTTTAGGGGTAAAATGGTAA
3085 AAATGGGATT
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
117 5 0.06
118 60 0.68
119 23 0.26
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.34
Consensus pattern (119 bp):
AAAAATGGGATTTTTGGAAGTTCGAAGGGAAAATGGTAATTTTCAGAAGGTTTGGGGTAAAAAAA
TGAGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTAGAAGGTTCGGGGTAA
Found at i:3059 original size:31 final size:28
Alignment explanation
Indices: 2869--3202 Score: 151
Period size: 31 Copynumber: 11.1 Consensus size: 28
2859 TTCGGAATCA
* * *
2869 AAAATGG-GATTTTTGGAAGTTCGAAGGT
1 AAAATGGTGATTTTTAGAAGTTTG-GGGT
* * *
2897 AAAATGGTAATTTTCAGTAGGTTTGGGGT
1 AAAATGGTGATTTTTAG-AAGTTTGGGGT
* *
2926 AAAAAAAT-GAGATTTTTGGAAGTTTGGGGGT
1 ---AAAATGGTGATTTTTAGAAGTTT-GGGGT
* *
2957 AAAATGGT-AATTTTAGAAGGTTCGGGGT
1 AAAATGGTGATTTTTAGAA-GTTTGGGGT
* *
2985 AAAAAAATGG-GATTTTTGGAAGTTCAGGGG-
1 ---AAAATGGTGATTTTTAGAAGTT-TGGGGT
*
3015 AAAATGGTAATTTTTAGAAGGTTTGGGGT
1 AAAATGGTGATTTTTAGAA-GTTTGGGGT
*
3044 CAAAATTGGTGATTTTTTGAAGTTTAGGGGT
1 -AAAA-TGGTGATTTTTAGAAGTTT-GGGGT
* *
3075 AAAATGGTAAAAATGGGATTTTCAGAAGTTCGGGGGT
1 AAAATGG------T--GATTTTTAGAAGTT-TGGGGT
* *
3112 AAAATGGTAATTTTTAGAAGGTTCGGGGT
1 AAAATGGTGATTTTTAGAA-GTTTGGGGT
* *
3141 CAAAAATGG-GATTTTTGGAAGTTCGGGGGT
1 --AAAATGGTGATTTTTAGAAGTT-TGGGGT
* * *
3171 -AAATGGTAATTTTTGAAAAGTTTAGGGT
1 AAAATGGTGATTTTT-AGAAGTTTGGGGT
3199 AAAA
1 AAAA
3203 AATGGGATTT
Statistics
Matches: 234, Mismatches: 37, Indels: 69
0.69 0.11 0.20
Matches are distributed among these distances:
27 13 0.06
28 48 0.21
29 44 0.19
30 42 0.18
31 57 0.24
32 5 0.02
35 1 0.00
37 24 0.10
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (28 bp):
AAAATGGTGATTTTTAGAAGTTTGGGGT
Found at i:3095 original size:96 final size:95
Alignment explanation
Indices: 2987--3179 Score: 289
Period size: 96 Copynumber: 2.0 Consensus size: 95
2977 TTCGGGGTAA
** * *
2987 AAAAATGGGATTTTTGGAAGTTCAGGGG-AAAATGGTAATTTTTAGAAGGTTTGGGGTCAAAATT
1 AAAAATGGGATTTTCAGAAGTTCAGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAAT
* *
3051 GGTGATTTTTTGAAGTTTAGGGGTAAAATGGT
66 GG-GATTTTTGGAAGTTCAGGGGT-AAATGGT
*
3083 AAAAATGGGATTTTCAGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAAT
1 AAAAATGGGATTTTCAGAAGTTCAGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAAT
*
3148 GGGATTTTTGGAAGTTCGGGGGTAAATGGT
66 GGGATTTTTGGAAGTTCAGGGGTAAATGGT
3178 AA
1 AA
3180 TTTTTGAAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
95 9 0.10
96 43 0.49
97 36 0.41
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.33
Consensus pattern (95 bp):
AAAAATGGGATTTTCAGAAGTTCAGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAAT
GGGATTTTTGGAAGTTCAGGGGTAAATGGT
Found at i:3111 original size:155 final size:156
Alignment explanation
Indices: 2928--3228 Score: 448
Period size: 155 Copynumber: 1.9 Consensus size: 156
2918 TTTGGGGTAA
** *
2928 AAAAATGAGATTTTTGGAAGTTTGGGGGTAAAATGGTAA-TTTTAGAAGGTTCGGGGTAAAAAAA
1 AAAAATGAGATTTTCAGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGT-AAAAAA
* * * *
2992 TGGGATTTTTGGAAGTTCAGGGGAAAATGGTAATTTTT-AGAAGGTTTGGGGTCAAAATTGGTGA
65 TGGGATTTTTGGAAGTTCAGGGGAAAATGGTAATTTTTGA-AAAGTTTAGGGTAAAAAATGG-GA
3056 TTTTTT-G-AAGTTTAGGGGTAAAATGGT
128 TTTTTTGGAAAGTTTAGGGGTAAAATGGT
* *
3083 AAAAATGGGATTTTCAGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAAT
1 AAAAATGAGATTTTCAGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTAAAAAAT
* *
3148 GGGATTTTTGGAAGTTCGGGGGTAAATGGTAATTTTTGAAAAGTTTAGGGTAAAAAATGGGATTT
66 GGGATTTTTGGAAGTTCAGGGGAAAATGGTAATTTTTGAAAAGTTTAGGGTAAAAAATGGGATTT
3213 TTTGGAAAGTTTAGGG
131 TTTGGAAAGTTTAGGG
3229 ACCTTCGGGG
Statistics
Matches: 131, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
154 8 0.06
155 94 0.72
156 29 0.22
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.34
Consensus pattern (156 bp):
AAAAATGAGATTTTCAGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTAAAAAAT
GGGATTTTTGGAAGTTCAGGGGAAAATGGTAATTTTTGAAAAGTTTAGGGTAAAAAATGGGATTT
TTTGGAAAGTTTAGGGGTAAAATGGT
Found at i:3124 original size:29 final size:28
Alignment explanation
Indices: 3084--3184 Score: 107
Period size: 29 Copynumber: 3.5 Consensus size: 28
3074 TAAAATGGTA
* *
3084 AAAATGGGATTTTCAGAAGTTCGGGGGT
1 AAAATGGAATTTTTAGAAGTTCGGGGGT
3112 AAAATGGTAATTTTTAGAAGGTTC-GGGGT
1 AAAATGG-AATTTTTAGAA-GTTCGGGGGT
* *
3141 CAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 --AAAATGGAATTTTTAGAAGTTCGGGGGT
3171 -AAATGGTAATTTTT
1 AAAATGG-AATTTTT
3185 GAAAAGTTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
27 6 0.10
28 13 0.21
29 18 0.29
30 18 0.29
31 7 0.11
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTTAGAAGTTCGGGGGT
Found at i:3191 original size:29 final size:30
Alignment explanation
Indices: 3100--3192 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
3090 GGATTTTCAG
3100 AAGTTCGGGGGTAAAATGGTAATTTTT-AGA
1 AAGTTCGGGGGTAAAATGGTAATTTTTGA-A
* * *
3130 AGGTTC-GGGGTCAAAAATGG-GATTTTTG-G
1 AAGTTCGGGGGT--AAAATGGTAATTTTTGAA
3159 AAGTTCGGGGGT-AAATGGTAATTTTTGAA
1 AAGTTCGGGGGTAAAATGGTAATTTTTGAA
3188 AAGTT
1 AAGTT
3193 TAGGGTAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
27 6 0.12
28 7 0.14
29 15 0.29
30 16 0.31
31 7 0.14
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.33
Consensus pattern (30 bp):
AAGTTCGGGGGTAAAATGGTAATTTTTGAA
Found at i:3215 original size:59 final size:59
Alignment explanation
Indices: 3083--3219 Score: 188
Period size: 59 Copynumber: 2.3 Consensus size: 59
3073 GTAAAATGGT
** * * *
3083 AAAAATGGGATTTTCAGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTC
1 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTCAGGGTA
*
3142 AAAAATGGGATTTTTGGAAGTTCGGGGGT-AAATGGTAATTTTT-GAAAAGTTTAGGGTA
1 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAG-AAAGTTCAGGGTA
3200 AAAAATGGGATTTTTTGGAA
1 AAAAATGGGA-TTTTTGGAA
3220 AGTTTAGGGA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
57 1 0.01
58 33 0.47
59 36 0.51
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.33
Consensus pattern (59 bp):
AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTCAGGGTA
Found at i:4429 original size:7 final size:7
Alignment explanation
Indices: 4417--4460 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
4407 CCCCCTTTAT
4417 TTATTAA
1 TTATTAA
4424 TTATTAA
1 TTATTAA
*
4431 TTAATAA
1 TTATTAA
4438 TTATTAA
1 TTATTAA
4445 TATCATT-A
1 T-T-ATTAA
4453 TTATTAA
1 TTATTAA
4460 T
1 T
4461 ATCAAAACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 3 0.09
7 23 0.72
8 3 0.09
9 3 0.09
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (7 bp):
TTATTAA
Found at i:4457 original size:15 final size:15
Alignment explanation
Indices: 4421--4464 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
4411 CTTTATTTAT
*
4421 TAATTATTAAT-TAA
1 TAATTATTAATATCA
4435 TAATTATTAATATCA
1 TAATTATTAATATCA
*
4450 TTATTATTAATATCA
1 TAATTATTAATATCA
4465 AAACATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATTAATATCA
Found at i:5229 original size:18 final size:18
Alignment explanation
Indices: 5203--5317 Score: 137
Period size: 17 Copynumber: 6.5 Consensus size: 18
5193 TTATTTATTT
*
5203 TAAACTTTAAATTTGAAAA
1 TAAA-TTTAAATTTTAAAA
* * *
5222 TAATTTTAAA-CTTAAAT
1 TAAATTTAAATTTTAAAA
*
5239 TAAATTTAAATTTTAAAG
1 TAAATTTAAATTTTAAAA
5257 TAAATTTAAA-TTTAAAA
1 TAAATTTAAATTTTAAAA
*
5274 TAAATTTAAATTTTTAAA
1 TAAATTTAAATTTTAAAA
*
5292 CAAATTT-AATTTTAAAA
1 TAAATTTAAATTTTAAAA
5309 TAAATTTAA
1 TAAATTTAA
5318 TGAGAGTATG
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
17 44 0.54
18 34 0.42
19 3 0.04
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (18 bp):
TAAATTTAAATTTTAAAA
Found at i:5248 original size:35 final size:35
Alignment explanation
Indices: 5202--5317 Score: 124
Period size: 35 Copynumber: 3.3 Consensus size: 35
5192 TTTATTTATT
*
5202 TTAAACTTTAAATTTGAAAATAATTTTAAACTTAAA
1 TTAAA-TTTAAATTTGAAAATAAATTTAAACTTAAA
* * *
5238 TTAAATTTAAATTTTAAAGTAAATTTAAATTTAAA
1 TTAAATTTAAATTTGAAAATAAATTTAAACTTAAA
* ** * **
5273 ATAAATTTAAATTTTTAAACAAATTTAATTTTAAA
1 TTAAATTTAAATTTGAAAATAAATTTAAACTTAAA
*
5308 ATAAATTTAA
1 TTAAATTTAA
5318 TGAGAGTATG
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
35 66 0.93
36 5 0.07
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (35 bp):
TTAAATTTAAATTTGAAAATAAATTTAAACTTAAA
Found at i:5255 original size:7 final size:6
Alignment explanation
Indices: 5201--5286 Score: 72
Period size: 6 Copynumber: 14.5 Consensus size: 6
5191 TTTTATTTAT
* * *
5201 TTTAAA CTTTAAA TTTGAAA -ATAAT TTTAAA CTTAAA -TTAAA TTTAAA
1 TTTAAA -TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
5249 TTTTAAA -GTAAA TTTAAA TTTAAA -ATAAA TTTAAA TTT
1 -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
5287 TTAAACAAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
5 15 0.23
6 34 0.53
7 15 0.23
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:5889 original size:59 final size:54
Alignment explanation
Indices: 5811--5929 Score: 130
Period size: 54 Copynumber: 2.1 Consensus size: 54
5801 GCTGTGGTTC
* *
5811 GAAGATTTGCTCACATCGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAATATCTCATCAG
1 GAAGATTTGCTCACATCGAGCCT-CGTTT-G---GGTCTTCTTCTCAATATCTCATCAG
*** * *
5870 GAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAG
1 GAAGATTTGCTCACATCGAGCCTCGTTTGGGTCTTCTTCTCAATATCTCATCAG
5924 GAAGAT
1 GAAGAT
5930 GATCCCATCA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
54 29 0.55
57 1 0.02
58 4 0.08
59 19 0.36
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (54 bp):
GAAGATTTGCTCACATCGAGCCTCGTTTGGGTCTTCTTCTCAATATCTCATCAG
Found at i:6005 original size:37 final size:37
Alignment explanation
Indices: 5964--6049 Score: 145
Period size: 37 Copynumber: 2.3 Consensus size: 37
5954 TTCTTTGTAT
*
5964 CTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTAC
1 CTCATCAGGAAGACGAATTCGGTTCACTTCTCAGTAC
* *
6001 CTCATCTGGAAGACGAATTCGGTTCACTTCTCAGTAT
1 CTCATCAGGAAGACGAATTCGGTTCACTTCTCAGTAC
6038 CTCATCAGGAAG
1 CTCATCAGGAAG
6050 CTAATTACTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (37 bp):
CTCATCAGGAAGACGAATTCGGTTCACTTCTCAGTAC
Done.