Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold618
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: 46042
ACGTcount: A:0.12, C:0.05, G:0.06, T:0.11
Warning! 30488 characters in sequence are not A, C, G, or T
Found at i:2324 original size:24 final size:24
Alignment explanation
Indices: 2297--2348 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2287 TTAGTAAGTC
*
2297 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2321 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2345 AAAT
1 AAAT
2349 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2815 original size:34 final size:33
Alignment explanation
Indices: 2776--2869 Score: 91
Period size: 35 Copynumber: 2.7 Consensus size: 33
2766 GCCCATTTTT
2776 TAATAAACATTAAAAAATTATTTTAAAAATAAAA
1 TAATAAA-ATTAAAAAATTATTTTAAAAATAAAA
** * *
2810 TAATAAAAATATTTAAAAGTATTTTAAAATTAAAA
1 TAAT-AAAAT-TAAAAAATTATTTTAAAAATAAAA
*
2845 -AATAAAAATAAAAAATATATATTTA
1 TAATAAAATTAAAAAAT-TAT-TTTA
2870 TTATATTCGG
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
32 5 0.10
33 7 0.15
34 13 0.27
35 23 0.48
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (33 bp):
TAATAAAATTAAAAAATTATTTTAAAAATAAAA
Found at i:2835 original size:35 final size:34
Alignment explanation
Indices: 2789--2854 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
2779 TAAACATTAA
*
2789 AAAATTATTTTAAAAATAAAATAATAAAAATATTT
1 AAAAGTATTTTAAAAATAAAA-AATAAAAATATTT
*
2824 AAAAGTATTTTAAAATTAAAAAATAAAAATA
1 AAAAGTATTTTAAAAATAAAAAATAAAAATA
2855 AAAAATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 10 0.34
35 19 0.66
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (34 bp):
AAAAGTATTTTAAAAATAAAAAATAAAAATATTT
Found at i:4343 original size:16 final size:16
Alignment explanation
Indices: 4303--4350 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
4293 ATTAATTTTT
*
4303 ATATTTATATT-TATA
1 ATATTAATATTATATA
4318 ATATTATAATATTATATA
1 ATA-T-TAATATTATATA
*
4336 ATATTAATAATATAT
1 ATATTAATATTATAT
4351 TATGTTATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 3 0.11
16 11 0.39
17 7 0.25
18 7 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATTAATATTATATA
Found at i:4519 original size:14 final size:14
Alignment explanation
Indices: 4500--4541 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
4490 TCTACCATTA
4500 TTATATTAAATATG
1 TTATATTAAATATG
*
4514 TTATATTTATATAT-
1 TTATA-TTAAATATG
*
4528 TTATATTAAGTATG
1 TTATATTAAATATG
4542 GCATTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 6 0.26
14 10 0.43
15 7 0.30
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
TTATATTAAATATG
Found at i:4598 original size:13 final size:13
Alignment explanation
Indices: 4582--4609 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4572 ATTCGAGTCT
4582 ATAATTCATATTA
1 ATAATTCATATTA
4595 ATAATTCATATTA
1 ATAATTCATATTA
4608 AT
1 AT
4610 TATGAATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAATTCATATTA
Found at i:5041 original size:21 final size:23
Alignment explanation
Indices: 4999--5053 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
4989 TTTATTTATA
*
4999 TATTTA-ATATTCTATTCAA-TT
1 TATTTATATATTATATTCAATTT
*
5020 TATTTATATATTATA-TCTATTT
1 TATTTATATATTATATTCAATTT
5042 TATTCTATATAT
1 TATT-TATATAT
5054 ATTCTAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 9 0.31
22 13 0.45
23 7 0.24
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTTATATATTATATTCAATTT
Found at i:5097 original size:13 final size:13
Alignment explanation
Indices: 5076--5115 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
5066 TTAGTTATTT
*
5076 TTATATTTATATA
1 TTATTTTTATATA
5089 TTATTTTTATATA
1 TTATTTTTATATA
*
5102 TTA-TTATATATA
1 TTATTTTTATATA
5114 TT
1 TT
5116 TTTATTTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTATTTTTATATA
Found at i:5103 original size:21 final size:22
Alignment explanation
Indices: 5071--5120 Score: 79
Period size: 19 Copynumber: 2.4 Consensus size: 22
5061 CTATTTTAGT
5071 TATTTTTATAT-TTA-TATAT-
1 TATTTTTATATATTATTATATA
5090 TATTTTTATATATTATTATATA
1 TATTTTTATATATTATTATATA
5112 TATTTTTAT
1 TATTTTTAT
5121 TTCTATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.39
20 3 0.11
21 5 0.18
22 9 0.32
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TATTTTTATATATTATTATATA
Found at i:7564 original size:176 final size:173
Alignment explanation
Indices: 7337--7667 Score: 513
Period size: 176 Copynumber: 1.9 Consensus size: 173
7327 TTAAAAATCG
7337 CCGCAAAAAACTAAGCCAAACGACGCCGTATTATGAGCTTTCGCAAATTTAGTGGCGTTTTTTAG
1 CCGCAAAAAACTAAGCCAAACGACGCCGTATTATGAGCTTTCGCAAATTTAGTGGCGTTTTTTAG
*
7402 CAAGCGCCGCTAATGCTCAGGGCTTTTAGCGGCATTTTTGAG-AAAGCGCCGCAAAA-AGACATA
66 CAAGCGCCGCTAATGCTCAGGGCTTTT-GCGGCATTTTTG-GTAAAGCGCCGCAAAATAAAC-TA
**
7465 AGCCCAACGGTGCCATTTTCTGAGCTTTCGGGGATTTAGCGGCGCT
128 AGCCCAACGACGCCATTTTCTGAGCTTTCGGGGATTTAGCGGCGCT
* * * *
7511 CCGCAAAATAATCTAAGCCCAACGACGCCGTTTTTTGAGCTTTCGCGAATTTAGTGGCGTTTTTT
1 CCGCAAAA-AA-CTAAGCCAAACGACGCCGTATTATGAGCTTTCGCAAATTTAGTGGCGTTTTTT
* *
7576 AGGAAGCGCCGCTAATGCTCAGGGCTTTTGCGGCGTTTTTGGTAAAGCGCCGCAAAATAAACTAA
64 AGCAAGCGCCGCTAATGCTCAGGGCTTTTGCGGCATTTTTGGTAAAGCGCCGCAAAATAAACTAA
*
7641 GCCCAACGACGCCGTTTTCTGAGCTTT
129 GCCCAACGACGCCATTTTCTGAGCTTT
7668 TACGAATTTA
Statistics
Matches: 143, Mismatches: 10, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
174 9 0.06
175 54 0.38
176 80 0.56
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (173 bp):
CCGCAAAAAACTAAGCCAAACGACGCCGTATTATGAGCTTTCGCAAATTTAGTGGCGTTTTTTAG
CAAGCGCCGCTAATGCTCAGGGCTTTTGCGGCATTTTTGGTAAAGCGCCGCAAAATAAACTAAGC
CCAACGACGCCATTTTCTGAGCTTTCGGGGATTTAGCGGCGCT
Found at i:7711 original size:114 final size:114
Alignment explanation
Indices: 7511--7817 Score: 397
Period size: 114 Copynumber: 2.7 Consensus size: 114
7501 TAGCGGCGCT
* * *
7511 CCGCAAAATAATCTAAGCCCAACGACGCCGTTTTTTGAGCTTTCGCGAATTTAGTGGCGTTTTTT
1 CCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTCACGAATTTAGTGGCGTTTTTT
* * *
7576 AGGAAGCGCCGCTAATGCTCAGGGCTTTTGCGGCGTTTTTG-GTAAAGCG
66 AGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTGTGAG-AAAACG
* *
7625 CCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTTACGAATTTAGTGTCGTTTTTT
1 CCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTCACGAATTTAGTGGCGTTTTTT
*
7690 AGGATA-TGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTGTGAGAAAACG
66 AGGA-AGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTGTGAGAAAACG
* * * * * *
7739 CCGCAAAA-AGACATAAGCCCAATGACGCCGTTTTCTGAGCTTT-AGGGGGATTTAGCGGCATTT
1 CCGCAAAATAAAC-TAAGCCCAACGACGCCGTTTTCTGAGCTTTCA--CGAATTTAGTGGCGTTT
7802 TTTAGGAAAGCGCCGC
63 TTTAGG-AAGCGCCGC
7818 AAAAAAAGCA
Statistics
Matches: 169, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
113 4 0.02
114 138 0.82
115 21 0.12
116 6 0.04
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (114 bp):
CCGCAAAATAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTTCACGAATTTAGTGGCGTTTTTT
AGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTGTGAGAAAACG
Found at i:7983 original size:15 final size:15
Alignment explanation
Indices: 7963--8011 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 15
7953 GATTTAAGGT
*
7963 TTAGGGGTTAGAGGG
1 TTAGGGGTTAGAGAG
*
7978 TTAGGGGTTAGA-CG
1 TTAGGGGTTAGAGAG
*
7992 TTTGGGGTTA-AGAG
1 TTAGGGGTTAGAGAG
8006 TTAGGG
1 TTAGGG
8012 ATTTAAGGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 1 0.03
14 16 0.55
15 12 0.41
ACGTcount: A:0.20, C:0.02, G:0.47, T:0.31
Consensus pattern (15 bp):
TTAGGGGTTAGAGAG
Found at i:8219 original size:15 final size:14
Alignment explanation
Indices: 8199--8247 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
8189 CATATTTTAA
*
8199 GGTTTAGGGAGTAT
1 GGTTTAGGGACTAT
*
8213 GGGTTTAGGGATTAT
1 -GGTTTAGGGACTAT
*
8228 GGATTAGGGACTAT
1 GGTTTAGGGACTAT
8242 GGTTTA
1 GGTTTA
8248 AGGGTTAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 17 0.57
15 13 0.43
ACGTcount: A:0.22, C:0.02, G:0.39, T:0.37
Consensus pattern (14 bp):
GGTTTAGGGACTAT
Found at i:8274 original size:29 final size:28
Alignment explanation
Indices: 8245--8337 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 28
8235 GGACTATGGT
8245 TTAAGGGTTAGGACTTAAGGTTTAGGGG
1 TTAAGGGTTAGGACTTAAGGTTTAGGGG
* ** *
8273 TTAGGGGTTTAGGGGTTAGACG-TTAGGGG
1 TTAAGGG-TTAGGACTTA-AGGTTTAGGGG
* *
8302 TTAAGAGTTAGGGATTTAAGGTTTAGGGG
1 TTAAGGGTTA-GGACTTAAGGTTTAGGGG
*
8331 TTCAGGG
1 TTAAGGG
8338 GTCGAGTTAA
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
28 11 0.22
29 37 0.74
30 2 0.04
ACGTcount: A:0.23, C:0.03, G:0.42, T:0.32
Consensus pattern (28 bp):
TTAAGGGTTAGGACTTAAGGTTTAGGGG
Found at i:8278 original size:7 final size:7
Alignment explanation
Indices: 8266--8339 Score: 58
Period size: 7 Copynumber: 10.1 Consensus size: 7
8256 GACTTAAGGT
8266 TTAGGGG
1 TTAGGGG
8273 TTAGGGG
1 TTAGGGG
8280 TTTAGGGG
1 -TTAGGGG
**
8288 TTAGACG
1 TTAGGGG
8295 TTAGGGG
1 TTAGGGG
* *
8302 TTAAGAG
1 TTAGGGG
*
8309 TTAGGGAT
1 TTAGGG-G
* *
8317 TTAAGGT
1 TTAGGGG
8324 TTAGGGG
1 TTAGGGG
8331 TTCAGGGG
1 TT-AGGGG
8339 T
1 T
8340 CGAGTTAAGG
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
7 34 0.65
8 18 0.35
ACGTcount: A:0.20, C:0.03, G:0.45, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:8282 original size:36 final size:37
Alignment explanation
Indices: 8242--8328 Score: 97
Period size: 36 Copynumber: 2.4 Consensus size: 37
8232 TAGGGACTAT
* * *
8242 GGTTTAAGGGTTAGGAC-TTAAGGTTTAGGGGTTAGG
1 GGTTTAAGGGTTAGGACGTTAAGGGTTAAGAGTTAGG
* *
8278 GGTTTAGGGGTTA-GACGTTAGGGGTTAAGAGTTAGG
1 GGTTTAAGGGTTAGGACGTTAAGGGTTAAGAGTTAGG
* *
8314 GATTTAAGGTTTAGG
1 GGTTTAAGGGTTAGG
8329 GGTTCAGGGG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
35 3 0.07
36 37 0.90
37 1 0.02
ACGTcount: A:0.23, C:0.02, G:0.41, T:0.33
Consensus pattern (37 bp):
GGTTTAAGGGTTAGGACGTTAAGGGTTAAGAGTTAGG
Found at i:8283 original size:15 final size:15
Alignment explanation
Indices: 8263--8339 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
8253 TAGGACTTAA
8263 GGTTTAGGGGTTAGG
1 GGTTTAGGGGTTAGG
*
8278 GGTTTAGGGGTTAGA
1 GGTTTAGGGGTTAGG
* *
8293 CG-TTAGGGGTTAAG
1 GGTTTAGGGGTTAGG
* * *
8307 AG-TTAGGGATTTA-A
1 GGTTTAGGG-GTTAGG
8321 GGTTTAGGGGTTCAGG
1 GGTTTAGGGGTT-AGG
8337 GGT
1 GGT
8340 CGAGTTAAGG
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
14 20 0.42
15 25 0.52
16 3 0.06
ACGTcount: A:0.19, C:0.03, G:0.45, T:0.32
Consensus pattern (15 bp):
GGTTTAGGGGTTAGG
Found at i:8790 original size:136 final size:138
Alignment explanation
Indices: 8627--8878 Score: 363
Period size: 136 Copynumber: 1.8 Consensus size: 138
8617 TTTAGCATAA
* *
8627 CAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTT-ATGC-AAAATGCCG
1 CAAAACAGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTTCA--CAAAAACGCCG
8690 CAAAAGATAA-CAAATAGCGGCGTTTCTATA-AAAACGCCGCA-A-AAAATAAATCAATTTATAG
64 CAAAAGATAAGC-AATAGCGGC-TTTCTATATAAAACGCCGCAGAGAAAATAAATCAATTTATAG
8751 AAAACAAAATAG
127 AAAACAAAATAG
*
8763 CAAAACAGTGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTTCACAAAAACGCCGCA
1 CAAAACAGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTTCACAAAAACGCCGCA
* * * *
8828 AAATATAAGCAATAGCGGCTTTTTTTATAAAACGTCGCAGAGAAAATAAAT
66 AAAGATAAGCAATAGCGGCTTTCTATATAAAACGCCGCAGAGAAAATAAAT
8879 AAATAAAAAA
Statistics
Matches: 103, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
135 7 0.07
136 84 0.82
137 3 0.03
138 9 0.09
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (138 bp):
CAAAACAGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTTCACAAAAACGCCGCA
AAAGATAAGCAATAGCGGCTTTCTATATAAAACGCCGCAGAGAAAATAAATCAATTTATAGAAAA
CAAAATAG
Found at i:9115 original size:105 final size:105
Alignment explanation
Indices: 8949--9204 Score: 476
Period size: 105 Copynumber: 2.4 Consensus size: 105
8939 GCGTTTTTGT
*
8949 TAAAAATGCCGCAAAAAAGTAAATCAATTTATAAAAAACAAAATAAAAAATTTTGTGCATAGCAA
1 TAAAAACGCCGCAAAAAA-TAAATCAATTT-TAAAAAACAAAATAAAAAATTTTGTGCATAGCAA
9014 AACGGCGTCATTTTGTTCAAATTGAAGTTGTGGCGTTTTCCC
64 AACGGCGTCATTTTGTTCAAATTGAAGTTGTGGCGTTTTCCC
9056 TAAAAACGCCGCAAAAAATAAATCAATTTTAAAAAACAAAATAAAAAATTTTGTGCATAGCAAAA
1 TAAAAACGCCGCAAAAAATAAATCAATTTTAAAAAACAAAATAAAAAATTTTGTGCATAGCAAAA
9121 CGGCGTCATTTTGTTCAAATTGAAGTTGTGGCGTTTTCCC
66 CGGCGTCATTTTGTTCAAATTGAAGTTGTGGCGTTTTCCC
9161 TAAAAACGCCGCAAAAAATAAATCAATTTTAAGAAAACAAAATA
1 TAAAAACGCCGCAAAAAATAAATCAATTTTAA-AAAACAAAATA
9205 GCAAAACAGT
Statistics
Matches: 147, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
105 108 0.73
106 22 0.15
107 17 0.12
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.27
Consensus pattern (105 bp):
TAAAAACGCCGCAAAAAATAAATCAATTTTAAAAAACAAAATAAAAAATTTTGTGCATAGCAAAA
CGGCGTCATTTTGTTCAAATTGAAGTTGTGGCGTTTTCCC
Found at i:13886 original size:43 final size:42
Alignment explanation
Indices: 13834--14207 Score: 266
Period size: 43 Copynumber: 8.6 Consensus size: 42
13824 TCTGTTAAAA
* * * ** *
13834 TTAGTGGCGTTTTTAAAAAACGCACCGCTAAAGGTCATGGTCT
1 TTAGCGGCGTTTTCAAAAAA-GCGCCGCTAAAGAACATGATCT
* *** * *
13877 TTAGCGGCGTATGTGGGAAAAGCACCGCTAAAAGAACATGACCT
1 TTAGCGGCGT-TTTCAAAAAAGCGCCGCT-AAAGAACATGATCT
* ** * *
13921 TTAGTGGCGTTTGTGGAGAAAGCGCCGCCAAAGAACATGATCT
1 TTAGCGGCGTTT-TCAAAAAAGCGCCGCTAAAGAACATGATCT
*
13964 TTAGCGGCGTTTCCAAAAGAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTTCAAAA-AAGCGCCGCTAAAGAACATGATCT
* *
14007 TTAGCGGCGTTTGCAAAAAAAGCGCCGCTAAAGGACATGATCT
1 TTAGCGGCGTTTTC-AAAAAAGCGCCGCTAAAGAACATGATCT
* * * *
14050 TTAGCGGCG-TTTGAGGAATAAGCGCCGCTAAAGTACATGACCT
1 TTAGCGGCGTTTTCA--AAAAAGCGCCGCTAAAGAACATGATCT
** * * * * *
14093 TTAGCGGCGTTTGT-AGGGAATGCGCCACTAAAGACCCTGACCT
1 TTAGCGGCGTTT-TCA-AAAAAGCGCCGCTAAAGAACATGATCT
****** *
14136 TTAGCGGCGTTTTTTTTTGTAGCGCCGCTAAAGAACATGACCT
1 TTAGCGGCG-TTTTCAAAAAAGCGCCGCTAAAGAACATGATCT
*
14179 TTAGCGGCGTTTATAAAAATAAGCGCCGC
1 TTAGCGGCGTTT-TCAAAA-AAGCGCCGC
14208 AAATGTTAGC
Statistics
Matches: 266, Mismatches: 52, Indels: 25
0.78 0.15 0.07
Matches are distributed among these distances:
41 1 0.00
42 7 0.03
43 202 0.76
44 55 0.21
45 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (42 bp):
TTAGCGGCGTTTTCAAAAAAGCGCCGCTAAAGAACATGATCT
Found at i:14029 original size:86 final size:85
Alignment explanation
Indices: 13834--14207 Score: 336
Period size: 86 Copynumber: 4.3 Consensus size: 85
13824 TCTGTTAAAA
* * * * ** * ***
13834 TTAGTGGCGTTTTTAAAAAACGCACCGCTAAAGGTCATGGTCTTTAGCGGCGTATGTGGGAA-AA
1 TTAGCGGCGTTTGTAAAAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGT-T-TCAAAAGAA
*
13898 GCACCGCTAAAAGAACATGACCT
64 GCGCCGCT-AAAGAACATGACCT
* ** * *
13921 TTAGTGGCGTTTGTGGAGAAAGCGCCGCCAAAGAACATGATCTTTAGCGGCGTTTCCAAAAGAAG
1 TTAGCGGCGTTTGTAAAAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-CAAAAGAAG
*
13986 CGCCGCTAAAGAACATGATCT
65 CGCCGCTAAAGAACATGACCT
* * * * *
14007 TTAGCGGCGTTTGCAAAAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGCGTTTGAGGAATAAG
1 TTAGCGGCGTTTGTAAAAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTCA-AAAGAAG
*
14072 CGCCGCTAAAGTACATGACCT
65 CGCCGCTAAAGAACATGACCT
*** * * * * * ***** *
14093 TTAGCGGCGTTTGTAGGGAATGCGCCACTAAAGACCCTGACCTTTAGCGGCGTTTTTTTTTGTAG
1 TTAGCGGCGTTTGTAAAAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTCAAAAGAAG
14158 CGCCGCTAAAGAACATGACCT
65 CGCCGCTAAAGAACATGACCT
*
14179 TTAGCGGCGTTTATAAAAATAAGCGCCGC
1 TTAGCGGCGTTTGTAAAAA-AAGCGCCGC
14208 AAATGTTAGC
Statistics
Matches: 231, Mismatches: 51, Indels: 10
0.79 0.17 0.03
Matches are distributed among these distances:
85 2 0.01
86 167 0.72
87 62 0.27
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (85 bp):
TTAGCGGCGTTTGTAAAAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTCAAAAGAAGC
GCCGCTAAAGAACATGACCT
Found at i:14118 original size:129 final size:130
Alignment explanation
Indices: 13858--14104 Score: 327
Period size: 129 Copynumber: 1.9 Consensus size: 130
13848 AAAAAACGCA
** * * ****
13858 CCGCTAAAGGTCATGGTCTTTAGCGGCGTATGTGGGAAAAGCACCGCTAAAAGAACATGACCTTT
1 CCGCTAAAGAACATGATCTTTAGCGGCGTTTGCAAAAAAAGCACCGCTAAAAGAACATGACCTTT
* * *
13923 AGTGGCGTTTGTGGAGAAAGCGCCGCCAAAGAACATGATCTTTAGCGGCGTTTCCAAAAGAAGCG
66 AGCGGCGTTTGAGGAGAAAGCGCCGCCAAAGAACATGACCTTTAGCGGCGTTTCCAAAAGAAGCG
* * *
13988 CCGCTAAAGAACATGATCTTTAGCGGCGTTTGCAAAAAAAGCGCCGCT-AAAGGACATGATCTTT
1 CCGCTAAAGAACATGATCTTTAGCGGCGTTTGCAAAAAAAGCACCGCTAAAAGAACATGACCTTT
* *
14052 AGCGGCGTTTGAGGA-ATAAGCGCCGCTAAAGTACATGACCTTTAGCGGCGTTT
66 AGCGGCGTTTGAGGAGA-AAGCGCCGCCAAAGAACATGACCTTTAGCGGCGTTT
14105 GTAGGGAATG
Statistics
Matches: 100, Mismatches: 16, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
128 1 0.01
129 60 0.60
130 39 0.39
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (130 bp):
CCGCTAAAGAACATGATCTTTAGCGGCGTTTGCAAAAAAAGCACCGCTAAAAGAACATGACCTTT
AGCGGCGTTTGAGGAGAAAGCGCCGCCAAAGAACATGACCTTTAGCGGCGTTTCCAAAAGAAGCG
Found at i:14160 original size:129 final size:129
Alignment explanation
Indices: 13894--14190 Score: 337
Period size: 129 Copynumber: 2.3 Consensus size: 129
13884 CGTATGTGGG
* * *
13894 AAAAGCACCGCTAAAAGAACATGACCTTTAGTGGCGTTTGTGGAGAAAGCGCCGCCAAAGAACAT
1 AAAAGCGCCGCT-AAAGAACATGACCTTTAGCGGCGTTTGAGGAGAAAGCGCCGCCAAAGAACAT
* * *
13959 GATCTTTAGCGGCGTTTCCAAAAGAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGCAAA
65 GACCTTTAGCGGCGTTTCCAAAAGAAGCGCCACTAAAGAACATGACCTTTAGCGGCGTTTGCAAA
* * * *
14024 AAAAGCGCCGCTAAAGGACATGATCTTTAGCGGCGTTTGAGGA-ATAAGCGCCGCTAAAGTACAT
1 AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGAGGAGA-AAGCGCCGCCAAAGAACAT
** ** * * ****
14088 GACCTTTAGCGGCGTTT-GTAGGGAATGCGCCACTAAAGACCCTGACCTTTAGCGGCGTTTTTTT
65 GACCTTTAGCGGCGTTTCCAAAAGAA-GCGCCACTAAAGAACATGACCTTTAGCGGCGTTTGCAA
*
14152 T
129 A
***
14153 TGTAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTT
1 AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTT
14191 ATAAAAATAA
Statistics
Matches: 139, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
128 5 0.04
129 123 0.88
130 11 0.08
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.24
Consensus pattern (129 bp):
AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGAGGAGAAAGCGCCGCCAAAGAACATG
ACCTTTAGCGGCGTTTCCAAAAGAAGCGCCACTAAAGAACATGACCTTTAGCGGCGTTTGCAAA
Found at i:14480 original size:97 final size:94
Alignment explanation
Indices: 14315--14499 Score: 289
Period size: 97 Copynumber: 1.9 Consensus size: 94
14305 TGTAGTTTCT
* * *
14315 TAATATGTTGCTAATATGTCACCCCAAAGGTTATCTTTTTGTCTGTTTTATTAAAAACATTGATA
1 TAATATGTTCCTAATATGTCACCCCAAAGGTCATCTTTTTGTCTGTTTTATTAAAAACATTGACA
14380 TTTATGTTGCAAGAATTTATAAACTTTGA
66 TTTATGTTGCAAGAATTTATAAACTTTGA
* * *
14409 TAATATGTTCCTAATATGTCATCCCATAGGTCATCTTTTTTTTTTCTGTTTTATTAAAAACATTG
1 TAATATGTTCCTAATATGTCACCCCAAAGGTCATC---TTTTTGTCTGTTTTATTAAAAACATTG
14474 ACATTTATGTTGCAAGAATTTATAAA
63 ACATTTATGTTGCAAGAATTTATAAA
14500 TATTTAGGGG
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
94 31 0.38
97 51 0.62
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.45
Consensus pattern (94 bp):
TAATATGTTCCTAATATGTCACCCCAAAGGTCATCTTTTTGTCTGTTTTATTAAAAACATTGACA
TTTATGTTGCAAGAATTTATAAACTTTGA
Found at i:45311 original size:14 final size:14
Alignment explanation
Indices: 45292--45319 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
45282 TATTTACCTT
45292 CGATCAATATTATC
1 CGATCAATATTATC
45306 CGATCAATATTATC
1 CGATCAATATTATC
45320 TTTATCTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
CGATCAATATTATC
Found at i:45874 original size:23 final size:23
Alignment explanation
Indices: 45848--45893 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
45838 GGGATATTAG
45848 ATATTGACTAGTTATATACGAAC
1 ATATTGACTAGTTATATACGAAC
45871 ATATTGACTAGTTATATACGAAC
1 ATATTGACTAGTTATATACGAAC
45894 TCAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (23 bp):
ATATTGACTAGTTATATACGAAC
Done.