Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014372.1 Kokia drynarioides strain JFW-HI SEQ_129409, 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: 40412
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Warning! 209 characters in sequence are not A, C, G, or T
Found at i:333 original size:11 final size:11
Alignment explanation
Indices: 317--348 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
307 GTTTTTTTAT
317 ATTAATTAATA
1 ATTAATTAATA
328 ATTAATTAATA
1 ATTAATTAATA
339 ATTAA-TAATA
1 ATTAATTAATA
349 TTATTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTAATTAATA
Found at i:360 original size:18 final size:17
Alignment explanation
Indices: 316--363 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
306 TGTTTTTTTA
316 TATTAATTAATAATTAAT
1 TATT-ATTAATAATTAAT
* *
334 TAATAATTAATAATATTAT
1 T-ATTATTAATAAT-TAAT
353 TATTATTAATA
1 TATTATTAATA
364 TCGAAACATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTATTAATAATTAAT
Found at i:455 original size:18 final size:19
Alignment explanation
Indices: 434--475 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
424 ATTAGTGTTA
*
434 TTATTAATATTAA-AACAG
1 TTATTAATATTAATAAAAG
452 TTATTAATATTAATAAAAG
1 TTATTAATATTAATAAAAG
471 TTATT
1 TTATT
476 GAAACGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (19 bp):
TTATTAATATTAATAAAAG
Found at i:468 original size:21 final size:21
Alignment explanation
Indices: 430--469 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
420 GGTCATTAGT
* *
430 GTTATTATTAATATTAAAACA
1 GTTATTAATAATAATAAAACA
*
451 GTTATTAATATTAATAAAA
1 GTTATTAATAATAATAAAA
470 GTTATTGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (21 bp):
GTTATTAATAATAATAAAACA
Found at i:1140 original size:18 final size:18
Alignment explanation
Indices: 1114--1229 Score: 139
Period size: 17 Copynumber: 6.6 Consensus size: 18
1104 TTATTTATTT
*
1114 TAAACTTTAAATTTGAAAA
1 TAAA-TTTAAATTTTAAAA
* * * *
1133 TAATTTTAAA-CTCAAAT
1 TAAATTTAAATTTTAAAA
1150 TAAATTTAAATTTTAAAA
1 TAAATTTAAATTTTAAAA
1168 TAAATTTAAA-TTTAAAA
1 TAAATTTAAATTTTAAAA
*
1185 TAAATTTAAATTTTTAAA
1 TAAATTTAAATTTTAAAA
*
1203 CAAATTT-AATTTTAAAA
1 TAAATTTAAATTTTAAAA
1220 TAAATTTAAA
1 TAAATTTAAA
1230 GGGAGTATGG
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
17 45 0.55
18 34 0.41
19 3 0.04
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (18 bp):
TAAATTTAAATTTTAAAA
Found at i:1158 original size:35 final size:35
Alignment explanation
Indices: 1113--1229 Score: 117
Period size: 35 Copynumber: 3.3 Consensus size: 35
1103 TTTATTTATT
*
1113 TTAAACTTTAAATTTGAAAATAATTTTAAACTCAAA
1 TTAAA-TTTAAATTTGAAAATAAATTTAAACTCAAA
* * *
1149 TTAAATTTAAATTTTAAAATAAATTTAAATTTAAA
1 TTAAATTTAAATTTGAAAATAAATTTAAACTCAAA
* ** * ** *
1184 ATAAATTTAAATTTTTAAACAAATTTAATTTTAAA
1 TTAAATTTAAATTTGAAAATAAATTTAAACTCAAA
*
1219 ATAAATTTAAA
1 TTAAATTTAAA
1230 GGGAGTATGG
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 68 0.93
36 5 0.07
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (35 bp):
TTAAATTTAAATTTGAAAATAAATTTAAACTCAAA
Found at i:1161 original size:24 final size:24
Alignment explanation
Indices: 1134--1183 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1124 ATTTGAAAAT
*
1134 AATTTTAAACTCAAA-TTAAATTTA
1 AATTTTAAAAT-AAATTTAAATTTA
1158 AATTTTAAAATAAATTTAAATTTA
1 AATTTTAAAATAAATTTAAATTTA
1182 AA
1 AA
1184 ATAAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
AATTTTAAAATAAATTTAAATTTA
Found at i:1229 original size:6 final size:6
Alignment explanation
Indices: 1112--1197 Score: 63
Period size: 6 Copynumber: 14.5 Consensus size: 6
1102 TTTTATTTAT
* * * *
1112 TTTAAA CTTTAAA TTTGAAA -ATAAT TTTAAA CTCAAA -TTAAA TTTAAA
1 TTTAAA -TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
1160 TTTTAAA -ATAAA TTTAAA TTTAAA -ATAAA TTTAAA TTT
1 -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
1198 TTAAACAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
5 14 0.23
6 33 0.53
7 15 0.24
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:2050 original size:218 final size:218
Alignment explanation
Indices: 1666--2453 Score: 1281
Period size: 218 Copynumber: 3.6 Consensus size: 218
1656 TTGTATCTCC
* * * * * * * *
1666 TCAGGGAGCTAACCGCTTTATTGCTTTGACCTGCTTCTCAGTGTCTCATCAGGAAGTTGGGGTTT
1 TCAGGAAGCTAACCGTTTTATTACTTTGACTTGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTC
* * * * * * * *
1731 GAAGATTTGCTCACATCG-GACGTGAGTTTGATTTGGTCTTTTTCACGGTATCTCATCGGGAAGA
66 GAAGATTTGCTCATACCGAG-CGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGA
** * * *
1795 TGACTGCGTCATCTGTTTCAATTCGCTTCTCTGTATCTTATCAGGAAGACGAATTTGGTCCACTT
130 TGACCACGTCGTCTGTTTCAATTCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTT
*
1860 CTCCGTACCTCATCAGGAAGATGG
195 CTCCATACCTCATCAGGAAGATGG
*
1884 TCAGGAAGCTAACCGTTTTATTACTTTGACTTGCTTCTCAGTATCTCATCAAGAAGCTGTGGTTC
1 TCAGGAAGCTAACCGTTTTATTACTTTGACTTGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTC
* * *
1949 GAAGATTTGCTCATATCGAGCGTGGGTTTAGTTTGGTTTTCTTCTCAGTATCTCATCAGGAAGAT
66 GAAGATTTGCTCATACCGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGAT
2014 GACCACGTCGTCTGTTTCAATTCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTC
131 GACCACGTCGTCTGTTTCAATTCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTC
*
2079 TCCATACCTCATCAGGAAAATGG
196 TCCATACCTCATCAGGAAGATGG
*
2102 TCAGAAAGCTAACCGTTTTATTACTTTGACTTGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTC
1 TCAGGAAGCTAACCGTTTTATTACTTTGACTTGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTC
2167 GAAGATTTGCTCATACCGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGAT
66 GAAGATTTGCTCATACCGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGAT
*
2232 GACCACGTCGTCTGTTTCAATTCGCTTCTCTGTATCTCATCAAGAAGATGAATTTGGTCCACTTC
131 GACCACGTCGTCTGTTTCAATTCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTC
2297 TCCATACCTCATCAGGAAGATGG
196 TCCATACCTCATCAGGAAGATGG
* *
2320 TCAGGAAGCTAATCGTTTTATTACTTTGACTTGCTTCTCAGTATCTCATTAGGAAGCTGTGGTTC
1 TCAGGAAGCTAACCGTTTTATTACTTTGACTTGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTC
2385 GAAGATTTGCTCATACCGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGAT
66 GAAGATTTGCTCATACCGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGAT
2450 GACC
131 GACC
2454 NNNNNNNNNN
Statistics
Matches: 534, Mismatches: 35, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
218 533 1.00
219 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (218 bp):
TCAGGAAGCTAACCGTTTTATTACTTTGACTTGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTC
GAAGATTTGCTCATACCGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGAT
GACCACGTCGTCTGTTTCAATTCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTC
TCCATACCTCATCAGGAAGATGG
Found at i:3084 original size:218 final size:217
Alignment explanation
Indices: 2788--3419 Score: 1001
Period size: 201 Copynumber: 3.0 Consensus size: 217
2778 NNNNNNNNNN
2788 AATTCGCTTCTCTGTATCTCATCAGAGAGACGAATTTGGTCCACTTCTCCATACCTCATCAGGAA
1 AATTCGCTTCTCTGTATCTCATCAGAGAGACGAATTTGGTCCACTTCTCCATACCTCATCAGGAA
2853 GATGGTCAGGAAGCTAACCATTTTATTACTTTGACTTGCTTCTCAGTATCTCATCAGGAAGCTGT
66 GATGGTCAGGAAGCTAACC-TTTTATTACTTTGACTTGCTTCTCAGTATCTCATCAGGAAGCTGT
* *
2918 GGTTCGAAGATTTGCTCATACCGAGCGTAGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATTAGG
130 GGTTCGAAGATTTGCTCATACCGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGG
2983 AAGATGACCACGTCGTTTGTTTC
195 AAGATGACCACGTCGTTTGTTTC
*
3006 AATTCGCTTCTCTGTATCTCATCA-AGAAGACGAATTTGGTCCACTTCTCCATACCTCATCAAGA
1 AATTCGCTTCTCTGTATCTCATCAGAG-AGACGAATTTGGTCCACTTCTCCATACCTCATCAGGA
* * *
3070 ATATAGTTAGGAAGCTAA-C--------C---G---T-CTTCTCAGTATCTCATCAGGAAGCTGT
65 AGATGGTCAGGAAGCTAACCTTTTATTACTTTGACTTGCTTCTCAGTATCTCATCAGGAAGCTGT
* * *
3119 GGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGGTTTGGTCTTCTTCTTAGTATCTCATCAGG
130 GGTTCGAAGATTTGCTCATACCGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGG
*
3184 AAGATGACCACGTCGTCTGTTTC
195 AAGATGACCACGTCGTTTGTTTC
3207 AATTCGCTTCTCTGTATCTCATCAGAGAGACGAATTTGGTCCACTTCTCCATACCTCATCAGGAA
1 AATTCGCTTCTCTGTATCTCATCAGAGAGACGAATTTGGTCCACTTCTCCATACCTCATCAGGAA
3272 GATGGTCAGGAAGCTAACCGTTTTATTACTTTGACTTGCTTCTCAGTATCTCATCAGGAAGCTGT
66 GATGGTCAGGAAGCTAACC-TTTTATTACTTTGACTTGCTTCTCAGTATCTCATCAGGAAGCTGT
*
3337 GGTTCGAAGATTTGCTCATGCCGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGG
130 GGTTCGAAGATTTGCTCATACCGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGG
* *
3402 AAGGTGACCGCGTCGTTT
195 AAGATGACCACGTCGTTT
3420 TGTTGGATAA
Statistics
Matches: 374, Mismatches: 21, Indels: 38
0.86 0.05 0.09
Matches are distributed among these distances:
201 184 0.49
202 4 0.01
205 1 0.00
208 1 0.00
211 1 0.00
214 1 0.00
217 4 0.01
218 178 0.48
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.34
Consensus pattern (217 bp):
AATTCGCTTCTCTGTATCTCATCAGAGAGACGAATTTGGTCCACTTCTCCATACCTCATCAGGAA
GATGGTCAGGAAGCTAACCTTTTATTACTTTGACTTGCTTCTCAGTATCTCATCAGGAAGCTGTG
GTTCGAAGATTTGCTCATACCGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGGA
AGATGACCACGTCGTTTGTTTC
Found at i:3418 original size:419 final size:420
Alignment explanation
Indices: 2504--3419 Score: 1242
Period size: 429 Copynumber: 2.2 Consensus size: 420
2494 NNNNNNNNNN
2504 TCATACCGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGTCG
1 TCATACCGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGTCG
* *
2569 TCTGTTTCAATTCGCTTCTTTGTATCTCATCAGAGAGACGAATTTGGTCCACTTCTCCATACCTC
66 TTTGTTTCAATTCGCTTCTCTGTATCTCATCAGAGAGACGAATTTGGTCCACTTCTCCATACCTC
* * *
2634 ATCAGGAAGATGGTCAGGAAGCTAACCGTCTTCTCGGTATCTCATCAGGAAGCTGTGGTTCGAAG
131 ATCAAGAAGATAGTCAGGAAGCTAACCGTCTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAG
*****************
2699 ATTTGCTCACATCGAGCGTGGGTTTGGTTTGGTCTTCTTNNNNNNNNNNNNNNNNNNNNNNNNNN
196 ATTTGCTCACATCGAGCGTGGGTTTGGTTTGGTCTTCTT---------ACTTAGTATCTCATCAG
************************
2764 NNNNNNNNNNNNNNNNNNNNNNNNAATTCGCTTCTCTGTATCTCATCAGAGAGACGAATTTGGTC
252 GAAGATGACCACGTCGTCTGTTTCAATTCGCTTCTCTGTATCTCATCAGAGAGACGAATTTGGTC
2829 CACTTCTCCATACCTCATCAGGAAGATGGTCAGGAAGCTAACCATTTTATTACTTTGACTTGCTT
317 CACTTCTCCATACCTCATCAGGAAGATGGTCAGGAAGCTAACCATTTTATTACTTTGACTTGCTT
2894 CTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGC
382 CTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGC
* *
2933 TCATACCGAGCGTAGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATTAGGAAGATGACCACGTCG
1 TCATACCGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGTCG
2998 TTTGTTTCAATTCGCTTCTCTGTATCTCATCA-AGAAGACGAATTTGGTCCACTTCTCCATACCT
66 TTTGTTTCAATTCGCTTCTCTGTATCTCATCAGAG-AGACGAATTTGGTCCACTTCTCCATACCT
* *
3062 CATCAAGAATATAGTTAGGAAGCTAACCGTCTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAA
130 CATCAAGAAGATAGTCAGGAAGCTAACCGTCTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAA
3127 GATTTGCTCACATCGAGCGTGGGTTTGGTTTGGTCTTCTT-CTTAGTATCTCATCAGGAAGATGA
195 GATTTGCTCACATCGAGCGTGGGTTTGGTTTGGTCTTCTTACTTAGTATCTCATCAGGAAGATGA
3191 CCACGTCGTCTGTTTCAATTCGCTTCTCTGTATCTCATCAGAGAGACGAATTTGGTCCACTTCTC
260 CCACGTCGTCTGTTTCAATTCGCTTCTCTGTATCTCATCAGAGAGACGAATTTGGTCCACTTCTC
*
3256 CATACCTCATCAGGAAGATGGTCAGGAAGCTAACCGTTTTATTACTTTGACTTGCTTCTCAGTAT
325 CATACCTCATCAGGAAGATGGTCAGGAAGCTAACCATTTTATTACTTTGACTTGCTTCTCAGTAT
3321 CTCATCAGGAAGCTGTGGTTCGAAGATTTGC
390 CTCATCAGGAAGCTGTGGTTCGAAGATTTGC
* * *
3352 TCATGCCGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGGTGACCGCGTCG
1 TCATACCGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGTCG
3417 TTT
66 TTT
3420 TGTTGGATAA
Statistics
Matches: 431, Mismatches: 55, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
419 207 0.48
428 2 0.00
429 222 0.52
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.32
Consensus pattern (420 bp):
TCATACCGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGTCG
TTTGTTTCAATTCGCTTCTCTGTATCTCATCAGAGAGACGAATTTGGTCCACTTCTCCATACCTC
ATCAAGAAGATAGTCAGGAAGCTAACCGTCTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAG
ATTTGCTCACATCGAGCGTGGGTTTGGTTTGGTCTTCTTACTTAGTATCTCATCAGGAAGATGAC
CACGTCGTCTGTTTCAATTCGCTTCTCTGTATCTCATCAGAGAGACGAATTTGGTCCACTTCTCC
ATACCTCATCAGGAAGATGGTCAGGAAGCTAACCATTTTATTACTTTGACTTGCTTCTCAGTATC
TCATCAGGAAGCTGTGGTTCGAAGATTTGC
Found at i:14860 original size:96 final size:96
Alignment explanation
Indices: 14676--14867 Score: 219
Period size: 96 Copynumber: 2.0 Consensus size: 96
14666 CTTTTGCGAA
* ** *
14676 AAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGTAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGAAATATTTCA
* ** *
14741 GAATCGAAGATAAGGGTACATTGCCTCGATT
66 GAACCGAAGATAAAAGAACATTGCCTCGATT
* * * *
14772 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTTGTGAGTTAAGGCGCAAAT-TTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCG-AAATATTTC
*
14836 -GAAACCCGAA-ATAAAAGAATATTGCCTCGATT
65 AG-AA-CCGAAGATAAAAGAACATTGCCTCGATT
14868 TTAAAGTTTT
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
95 1 0.01
96 72 0.90
97 7 0.09
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGAAATATTTCA
GAACCGAAGATAAAAGAACATTGCCTCGATT
Found at i:15209 original size:30 final size:29
Alignment explanation
Indices: 15173--15329 Score: 169
Period size: 30 Copynumber: 5.3 Consensus size: 29
15163 TAAATTGGTA
15173 ATTTTTGGAAGGTTCGGGGTCAAAAATGGG
1 ATTTTTGGAAGGTTCGGGGT-AAAAATGGG
* *
15203 ATTTTTGGAA-GTTCGGGGGT-GAAATGGTA
1 ATTTTTGGAAGGTTC-GGGGTAAAAATGG-G
*
15232 ATTTTTGGAAGGTTCGAGGTTAAAAATGGG
1 ATTTTTGGAAGGTTCG-GGGTAAAAATGGG
* **
15262 ATTTTTGGAA-GTTCGGGGGT-GAAATGATA
1 ATTTTTGGAAGGTTC-GGGGTAAAAATG-GG
15291 ATTTTTGGAAGGTTCGGGGTCAAAAATGGG
1 ATTTTTGGAAGGTTCGGGGT-AAAAATGGG
15321 ATTTTTGGA
1 ATTTTTGGA
15330 TAATCTAGGG
Statistics
Matches: 105, Mismatches: 12, Indels: 20
0.77 0.09 0.15
Matches are distributed among these distances:
28 11 0.10
29 37 0.35
30 46 0.44
31 11 0.10
ACGTcount: A:0.27, C:0.04, G:0.35, T:0.34
Consensus pattern (29 bp):
ATTTTTGGAAGGTTCGGGGTAAAAATGGG
Found at i:15222 original size:59 final size:59
Alignment explanation
Indices: 15158--15329 Score: 301
Period size: 59 Copynumber: 2.9 Consensus size: 59
15148 TCAAACATTG
15158 GGGGGT-AAATTGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
1 GGGGGTGAAA-TGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
* *
15217 GGGGGTGAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTC
1 GGGGGTGAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
*
15276 GGGGGTGAAATGATAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGA
1 GGGGGTGAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGA
15330 TAATCTAGGG
Statistics
Matches: 107, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
59 104 0.97
60 3 0.03
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (59 bp):
GGGGGTGAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
Found at i:16127 original size:8 final size:7
Alignment explanation
Indices: 16100--16125 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16090 TCTCCCTTTT
16100 AAAAACA
1 AAAAACA
16107 AAAAACA
1 AAAAACA
16114 AAAAACA
1 AAAAACA
16121 AAAAA
1 AAAAA
16126 ACGGATCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:16422 original size:11 final size:11
Alignment explanation
Indices: 16406--16450 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
16396 GTTTTTTTTA
16406 TATTAATTAAT
1 TATTAATTAAT
16417 TATTAATTAAT
1 TATTAATTAAT
*
16428 AATT-ATTAA-
1 TATTAATTAAT
16437 TATT-ATT-AT
1 TATTAATTAAT
16446 TATTA
1 TATTA
16451 TTATCGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 1 0.03
9 10 0.33
10 5 0.17
11 14 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTAATTAAT
Found at i:16423 original size:7 final size:7
Alignment explanation
Indices: 16411--16453 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
16401 TTTTATATTA
16411 ATTAATT
1 ATTAATT
16418 ATTAATT
1 ATTAATT
*
16425 AATAATT
1 ATTAATT
16432 ATTAA-T
1 ATTAATT
16438 ATT-ATT
1 ATTAATT
16444 ATT-ATT
1 ATTAATT
16450 ATTA
1 ATTA
16454 TCGAAACATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 14 0.44
7 17 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATTAATT
Found at i:16450 original size:18 final size:21
Alignment explanation
Indices: 16412--16453 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 21
16402 TTTATATTAA
*
16412 TTAATTATTAATTAATAATTA
1 TTAATTATTAATTAATTATTA
16433 TTAA-TATT-ATT-ATTATTA
1 TTAATTATTAATTAATTATTA
16451 TTA
1 TTA
16454 TCGAAACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 9 0.45
19 3 0.15
20 4 0.20
21 4 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATTATTAATTAATTATTA
Found at i:16545 original size:18 final size:19
Alignment explanation
Indices: 16524--16565 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
16514 ATTAGTGTTA
*
16524 TTATTAATATTAA-AACAG
1 TTATTAATATTAATAAAAG
16542 TTATTAATATTAATAAAAG
1 TTATTAATATTAATAAAAG
16561 TTATT
1 TTATT
16566 GAAACGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (19 bp):
TTATTAATATTAATAAAAG
Found at i:16558 original size:21 final size:21
Alignment explanation
Indices: 16520--16559 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16510 GGTCATTAGT
* *
16520 GTTATTATTAATATTAAAACA
1 GTTATTAATAATAATAAAACA
*
16541 GTTATTAATATTAATAAAA
1 GTTATTAATAATAATAAAA
16560 GTTATTGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (21 bp):
GTTATTAATAATAATAAAACA
Found at i:17229 original size:18 final size:18
Alignment explanation
Indices: 17203--17318 Score: 121
Period size: 17 Copynumber: 6.6 Consensus size: 18
17193 TTATTTATTT
*
17203 TAAACTTTAAATTTGAAAA
1 TAAA-TTTAAATTTTAAAA
* * * *
17222 TAATTTTAAA-CTCAAAT
1 TAAATTTAAATTTTAAAA
17239 TAAATTTAAATTTTAAAA
1 TAAATTTAAATTTTAAAA
*
17257 CAAATTTAAA-TTTAAAA
1 TAAATTTAAATTTTAAAA
* *
17274 TAATTTTAAATTTTTAAA
1 TAAATTTAAATTTTAAAA
*
17292 CAAATTT-AATTTTAAAA
1 TAAATTTAAATTTTAAAA
17309 TAAATTTAAA
1 TAAATTTAAA
17319 GGGAGTATGG
Statistics
Matches: 78, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
17 43 0.55
18 32 0.41
19 3 0.04
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (18 bp):
TAAATTTAAATTTTAAAA
Found at i:17247 original size:35 final size:35
Alignment explanation
Indices: 17202--17318 Score: 108
Period size: 35 Copynumber: 3.3 Consensus size: 35
17192 TTTATTTATT
* *
17202 TTAAACTTTAAATTTGAAAATAATTTTAAACTCAAA
1 TTAAA-TTTAAATTTGAAAACAAATTTAAACTCAAA
* * *
17238 TTAAATTTAAATTTTAAAACAAATTTAAATTTAAA
1 TTAAATTTAAATTTGAAAACAAATTTAAACTCAAA
* * ** ** *
17273 ATAATTTTAAATTTTTAAACAAATTTAATTTTAAA
1 TTAAATTTAAATTTGAAAACAAATTTAAACTCAAA
*
17308 ATAAATTTAAA
1 TTAAATTTAAA
17319 GGGAGTATGG
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 66 0.93
36 5 0.07
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (35 bp):
TTAAATTTAAATTTGAAAACAAATTTAAACTCAAA
Found at i:17250 original size:24 final size:24
Alignment explanation
Indices: 17223--17272 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
17213 ATTTGAAAAT
*
17223 AATTTTAAACTCAAA-TTAAATTTA
1 AATTTTAAA-ACAAATTTAAATTTA
17247 AATTTTAAAACAAATTTAAATTTA
1 AATTTTAAAACAAATTTAAATTTA
17271 AA
1 AA
17273 ATAATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (24 bp):
AATTTTAAAACAAATTTAAATTTA
Found at i:17652 original size:16 final size:17
Alignment explanation
Indices: 17631--17663 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17621 GGCTTCTTTT
17631 ATTTTG-AGTTAATTCA
1 ATTTTGAAGTTAATTCA
*
17647 ATTTTGAATTTAATTCA
1 ATTTTGAAGTTAATTCA
17664 TAACACATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (17 bp):
ATTTTGAAGTTAATTCA
Found at i:28078 original size:30 final size:30
Alignment explanation
Indices: 28039--28102 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
28029 TAAATTGTTA
*
28039 GTGACAAAATTA-AAAAATATT-ATAGTTTG
1 GTGACAAAA-TAGAAAAATATTAATAGTTGG
*
28068 GTGACCAAAATAGAAACATATTAATAGTTGG
1 GTGA-CAAAATAGAAAAATATTAATAGTTGG
28099 GTGA
1 GTGA
28103 TTAACGGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 6 0.20
30 13 0.43
31 11 0.37
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.30
Consensus pattern (30 bp):
GTGACAAAATAGAAAAATATTAATAGTTGG
Found at i:28823 original size:22 final size:22
Alignment explanation
Indices: 28798--28840 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28788 ATCAGCTATT
* *
28798 TTGCTACTGTTTTGTTATTATA
1 TTGCCACTATTTTGTTATTATA
*
28820 TTGCCACTATTTTGTTGTTAT
1 TTGCCACTATTTTGTTATTAT
28841 TGTTTGAGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.58
Consensus pattern (22 bp):
TTGCCACTATTTTGTTATTATA
Found at i:28888 original size:18 final size:19
Alignment explanation
Indices: 28849--28889 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
28839 ATTGTTTGAG
*
28849 TATTGTATAATTTTTATTT
1 TATTGTATAATTTTTATAT
28868 TATTGT-TAA-TTTTACTAT
1 TATTGTATAATTTTTA-TAT
28886 TATT
1 TATT
28890 TTAGAGATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (19 bp):
TATTGTATAATTTTTATAT
Found at i:30323 original size:23 final size:23
Alignment explanation
Indices: 30297--30340 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
30287 TTATTAACTT
30297 AATCCAAACTAAAAAATTATTTA
1 AATCCAAACTAAAAAATTATTTA
* * *
30320 AATCTAAACTCACAAATTATT
1 AATCCAAACTAAAAAATTATT
30341 CGAAACACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (23 bp):
AATCCAAACTAAAAAATTATTTA
Found at i:31854 original size:22 final size:23
Alignment explanation
Indices: 31811--31858 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
31801 AATAAAATAC
*
31811 AAAAATTAAATTTCAAATTTTAA
1 AAAAATTAAATTTCAAACTTTAA
* *
31834 AAAAATTATATTT-AACCTTTAA
1 AAAAATTAAATTTCAAACTTTAA
31856 AAA
1 AAA
31859 GTAATACATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAAATTAAATTTCAAACTTTAA
Found at i:35551 original size:206 final size:203
Alignment explanation
Indices: 35042--35574 Score: 687
Period size: 206 Copynumber: 2.6 Consensus size: 203
35032 CGTGGAAGCA
* * *
35042 TTTTTCAAAAAAGCGTCCACGTGAAAGCGTTTTTGCGCACGAGAAGGTGACCATTGGGAGAAAAC
1 TTTTTCAAAAAAGCGTCCACGTGGAAGCGTTTTTGCGCAAGAGAAGGTGACCATTGGGGGAAAAC
* * *
35107 ACGGGCAAAAGAGCATCCACATGAGGGCTTTTTTGAAAAAAAACCCTTCCACATCAATGCGCTTT
66 ACGGGCAAAAGAGCGTCCACATGAGAGCTTTTTTG---AAAAACGCTTCCACATC-A-GCGCTTT
* * *
35172 TGCCTGACACAGCGAAAAAAGCTTACGTGAAAGCATTTTTCTGATTTATTTCCTGAAAAGCATGC
126 TACCTGACACAACGAAAAAAGCTTACGTGAAAGCATTTTTCTAATTTATTTCCTGAAAAGCATGC
*
35237 TTACGTGGAAGTG
191 TTACGTGAAAGTG
*
35250 TTTTTCAAAAAAGCGTCCACGTGGAAGTGTTTTTGCGCACA-AGAAGGTGACCATTGGGGGAAAA
1 TTTTTCAAAAAAGCGTCCACGTGGAAGCGTTTTTGCGCA-AGAGAAGGTGACCATTGGGGGAAAA
* *
35314 CACAGGTAAAAGAGCGTCCACATGAGAGCTTTTTTGAAAAACGCTTCCACATCAGCGCTCTTTAC
65 CACGGGCAAAAGAGCGTCCACATGAGAGCTTTTTTGAAAAACGCTTCCACATCAGCGCT-TTTAC
* * *
35379 TTGACACAACGAAAAAAAGCTTACGTGGAAGCATTTTTCTAATTTA-TTCCTTGAAAAGCGTG-T
129 CTGACACAACG-AAAAAAGCTTACGTGAAAGCATTTTTCTAATTTATTTCC-TGAAAAGCATGCT
*
35442 TGATGTGAAAGTG
192 T-ACGTGAAAGTG
* * * * * *
35455 TTTTTTAAAAAAAGTGTTCATGTGGAAGCGTTTTTGCGCAAGAGAAGGTGATCGTTGGGGGAAAA
1 -TTTTTCAAAAAAGCGTCCACGTGGAAGCGTTTTTGCGCAAGAGAAGGTGACCATTGGGGGAAAA
* ** *
35520 CATGGGCAAAATCGCGTCCACATTG-GAGCTTTTTTGAAAAACGCTTTCACATCAG
65 CACGGGCAAAAGAGCGTCCACA-TGAGAGCTTTTTTGAAAAACGCTTCCACATCAG
35575 TGCGTTTTTG
Statistics
Matches: 287, Mismatches: 30, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
203 5 0.02
204 20 0.07
205 68 0.24
206 101 0.35
207 2 0.01
208 91 0.32
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (203 bp):
TTTTTCAAAAAAGCGTCCACGTGGAAGCGTTTTTGCGCAAGAGAAGGTGACCATTGGGGGAAAAC
ACGGGCAAAAGAGCGTCCACATGAGAGCTTTTTTGAAAAACGCTTCCACATCAGCGCTTTTACCT
GACACAACGAAAAAAGCTTACGTGAAAGCATTTTTCTAATTTATTTCCTGAAAAGCATGCTTACG
TGAAAGTG
Done.