Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019690.1 Corchorus olitorius cultivar O-4 contig19723, 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: 55031
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:16 original size:2 final size:2
Alignment explanation
Indices: 5--42 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
1 ATAC
5 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43 TGAATAAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1216 original size:68 final size:66
Alignment explanation
Indices: 1107--1234 Score: 195
Period size: 68 Copynumber: 1.9 Consensus size: 66
1097 TGACGTCACG
* **
1107 AGCTAATTCAATATCAACTCATTAAGTAAAAATCTAAAAAAAGAGAGGAAAATGGTAAATTACCT
1 AGCTAATTCAATATCAACTCAATAAGTAAAAATCTAAAAAAA-A-AGGAAAATAATAAATTACCT
1172 ATC
64 ATC
1175 AGCTAATTCAATATCAACTCAATAAGT-AAAATCTTAAAAAAAAAGGAAAATAATAAATTA
1 AGCTAATTCAATATCAACTCAATAAGTAAAAATC-TAAAAAAAAAGGAAAATAATAAATTA
1235 ACCATCTTGA
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
66 15 0.27
67 7 0.12
68 34 0.61
ACGTcount: A:0.54, C:0.12, G:0.09, T:0.25
Consensus pattern (66 bp):
AGCTAATTCAATATCAACTCAATAAGTAAAAATCTAAAAAAAAAGGAAAATAATAAATTACCTAT
C
Found at i:2597 original size:18 final size:18
Alignment explanation
Indices: 2574--2639 Score: 71
Period size: 18 Copynumber: 3.5 Consensus size: 18
2564 GATAAGATAA
2574 GCACGGAGCTTAGTTGTT
1 GCACGGAGCTTAGTTGTT
* *
2592 GCACGGAGC-AAGTTGAGATAA
1 GCACGGAGCTTAGTT--G-T-T
2613 GCACGGAGCTTAGTTGTT
1 GCACGGAGCTTAGTTGTT
2631 GCACGGAGC
1 GCACGGAGC
2640 AAATTTGAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
17 4 0.10
18 18 0.46
19 2 0.05
20 2 0.05
21 9 0.23
22 4 0.10
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (18 bp):
GCACGGAGCTTAGTTGTT
Found at i:2622 original size:39 final size:40
Alignment explanation
Indices: 2568--2652 Score: 154
Period size: 39 Copynumber: 2.1 Consensus size: 40
2558 GCCTGAGATA
2568 AGATAAGCACGGAGCTTAGTTGTTGCACGGAGC-AAGTTG
1 AGATAAGCACGGAGCTTAGTTGTTGCACGGAGCAAAGTTG
*
2607 AGATAAGCACGGAGCTTAGTTGTTGCACGGAGCAAATTTG
1 AGATAAGCACGGAGCTTAGTTGTTGCACGGAGCAAAGTTG
2647 AGATAA
1 AGATAA
2653 CGAGACGGAC
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 33 0.75
40 11 0.25
ACGTcount: A:0.32, C:0.14, G:0.31, T:0.24
Consensus pattern (40 bp):
AGATAAGCACGGAGCTTAGTTGTTGCACGGAGCAAAGTTG
Found at i:2760 original size:24 final size:25
Alignment explanation
Indices: 2706--2768 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
2696 CTGCAGAGGA
2706 TGGCGCAGGGCCT-ATGAGAGAAAAG
1 TGGCGCAGGGCCTGATGAGAG-AAAG
2731 TGGCGCAGGGCCTGAATGAG-G-AAG
1 TGGCGCAGGGCCTG-ATGAGAGAAAG
2755 TGGCGCAGGGCCTG
1 TGGCGCAGGGCCTG
2769 GAGAAAGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
24 17 0.47
25 13 0.36
26 1 0.03
27 5 0.14
ACGTcount: A:0.24, C:0.19, G:0.44, T:0.13
Consensus pattern (25 bp):
TGGCGCAGGGCCTGATGAGAGAAAG
Found at i:6973 original size:3 final size:3
Alignment explanation
Indices: 6965--6996 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
6955 GTGGACAATA
6965 TAT TAT TAT TAT TAT TAT TAAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT T
6997 GCTGTCTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:16811 original size:1 final size:1
Alignment explanation
Indices: 16805--16830 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
16795 CACAAATCTG
16805 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
16831 GCATAATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19158 original size:27 final size:28
Alignment explanation
Indices: 19127--19184 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
19117 ACTTGTAACG
* *
19127 TTTGGACGTTTTGCC-CTTAAACTTCAA
1 TTTGGACATTTTGCCTCCTAAACTTCAA
19154 TTTGGACATTTTGCCTCCTAAACTTCAA
1 TTTGGACATTTTGCCTCCTAAACTTCAA
19182 TTT
1 TTT
19185 TGGGATGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.43
Consensus pattern (28 bp):
TTTGGACATTTTGCCTCCTAAACTTCAA
Found at i:19355 original size:29 final size:29
Alignment explanation
Indices: 19283--19357 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
19273 TAGGTTGAAT
*
19283 GGGCAAAACGTCCTAAAATTGAAGTTCAAG
1 GGGCAAAACGTCC-AAAATTGAAATTCAAG
**
19313 GGGCAAAATTTCCAAAATTGAAATTC-AG
1 GGGCAAAACGTCCAAAATTGAAATTCAAG
*
19341 GGAGTAAAACGTCCAAA
1 GG-GCAAAACGTCCAAA
19358 CGCTACAAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 4 0.11
29 23 0.61
30 11 0.29
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (29 bp):
GGGCAAAACGTCCAAAATTGAAATTCAAG
Found at i:21325 original size:30 final size:28
Alignment explanation
Indices: 21289--21366 Score: 77
Period size: 30 Copynumber: 2.7 Consensus size: 28
21279 TCTGAAAAGT
*
21289 TTTAGGGGCAAACTGTCCTGAATTTGGAAA
1 TTTAGGGGCAAAATGTCCT-AATTT-GAAA
* *
21319 TTTAGGGAGCAAATTGTCAC-AATTTGAAG
1 TTTAGGG-GCAAAATGTC-CTAATTTGAAA
*
21348 TCTAGGGGCAAAATGTCCT
1 TTTAGGGGCAAAATGTCCT
21367 TGGCGCGTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.02
28 9 0.22
29 9 0.22
30 12 0.29
31 9 0.22
32 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (28 bp):
TTTAGGGGCAAAATGTCCTAATTTGAAA
Found at i:22614 original size:15 final size:15
Alignment explanation
Indices: 22584--22631 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
22574 AAGCAAAAGG
22584 GGAAAAAATAAAGAAA
1 GGAAAAAA-AAAGAAA
*
22600 GGAAAAAAAATGAAA
1 GGAAAAAAAAAGAAA
*
22615 GGAAAAAGAAAGGAAA
1 GGAAAAA-AAAAGAAA
22631 G
1 G
22632 TTGGTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 13 0.45
16 16 0.55
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04
Consensus pattern (15 bp):
GGAAAAAAAAAGAAA
Found at i:23000 original size:18 final size:18
Alignment explanation
Indices: 22973--23007 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
22963 TATTCCCCTT
22973 AATTAAAAAAGAAATGTA
1 AATTAAAAAAGAAATGTA
*
22991 AATTAGAAAAGAAATGT
1 AATTAAAAAAGAAATGT
23008 TATTTTCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.23
Consensus pattern (18 bp):
AATTAAAAAAGAAATGTA
Found at i:34944 original size:43 final size:43
Alignment explanation
Indices: 34883--34967 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
34873 ATACTCAGAA
34883 TCTTTCAAGGAAGAGTTTCGCCGTCCAGCTCTGTCAAATCTGT
1 TCTTTCAAGGAAGAGTTTCGCCGTCCAGCTCTGTCAAATCTGT
*
34926 TCTTTCAAGGAAGAGTTTCGCCGTCTAGCTCTGTCAAATCTG
1 TCTTTCAAGGAAGAGTTTCGCCGTCCAGCTCTGTCAAATCTG
34968 CTGCTTCTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (43 bp):
TCTTTCAAGGAAGAGTTTCGCCGTCCAGCTCTGTCAAATCTGT
Found at i:35120 original size:15 final size:15
Alignment explanation
Indices: 35100--35132 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
35090 CAGGAAACTT
35100 TCCTTTTATCTTACA
1 TCCTTTTATCTTACA
35115 TCCTTTTATCTTACA
1 TCCTTTTATCTTACA
35130 TCC
1 TCC
35133 ACAAATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.30, G:0.00, T:0.52
Consensus pattern (15 bp):
TCCTTTTATCTTACA
Found at i:37529 original size:39 final size:39
Alignment explanation
Indices: 37486--37567 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
37476 TAATGGAGAG
*
37486 GGAGGAGAGTTGAGGAGGGATGATATCGGAAATGGACTT
1 GGAGGAGAGTTGAGGAGGAATGATATCGGAAATGGACTT
*
37525 GGAGGAGAGTTGAGGAGGAATGATATCGGTAATGGACTT
1 GGAGGAGAGTTGAGGAGGAATGATATCGGAAATGGACTT
37564 GGAG
1 GGAG
37568 AAGTTTTGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.30, C:0.05, G:0.44, T:0.21
Consensus pattern (39 bp):
GGAGGAGAGTTGAGGAGGAATGATATCGGAAATGGACTT
Found at i:49326 original size:185 final size:185
Alignment explanation
Indices: 48779--49918 Score: 1341
Period size: 185 Copynumber: 6.1 Consensus size: 185
48769 ACTTAACTAT
* *
48779 AGATGCAAGTTCTGGAGGAGGAAATGTCAAAATGGTAAGCCCGTGATGAATAGTCTGTACCAATT
1 AGATACAAGTTCTGGAGGAGGAAATGTCAAAATGGTAAGCCCATGATGAATAGTCTGTACCAATT
* *
48844 ATCATGTTGTTAAAATTTAAATATCAATTAATAAAATAAGGAATTCATCATTTAAATAAACAGAC
66 ATAATGTTGTTAAAATTTAAATATCAATTAATGAAATAAGGAATTCATCATTTAAATAAACAGAC
*
48909 ATAGTAACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTAAAGTAC
131 ATGGTAACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTAAAGTAC
* * * *
48964 GGATATAAGTTTTGGAGGAGGAAATGTCAAAATGGTAAGCCCATGATGAATGGTCTGTACCAATT
1 AGATACAAGTTCTGGAGGAGGAAATGTCAAAATGGTAAGCCCATGATGAATAGTCTGTACCAATT
* **
49029 ATAATATTGTTAAAATTTAAAATATATCAACAAATGAAATAAGGAATTCATCATTTAAATAAACA
66 ATAATGTTGTTAAAATTT--AA-ATATCAATTAATGAAATAAGGAATTCATCATTTAAATAAACA
49094 GACATGGTAACCGTTAC-GATAAAATTGTCATATTATCATGACTACATATGTAAAGTAC
128 GACATGGTAACCGTTACAG-TAAAATTGTCATATTATCATGACTACATATGTAAAGTAC
* * *
49152 ATATACAAGTTCTGGAGGAGGAAATGTCAAAATGGTAAG-CCATGATGAATAATTTGTACCAATT
1 AGATACAAGTTCTGGAGGAGGAAATGTCAAAATGGTAAGCCCATGATGAATAGTCTGTACCAATT
* * * * *
49216 ATTCATGTTGTTAAAATATAAATATCAATTACTGAAATAAAGAATTCATCATTTAAATAAACATA
66 A-TAATGTTGTTAAAATTTAAATATCAATTAATGAAATAAGGAATTCATCATTTAAATAAACAGA
* *
49281 CACGGTAACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTCAAGTAC
130 CATGGTAACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTAAAGTAC
* * * * * *
49337 AGATATAAGTTTTGGAGGAGTAAATGTCAAAATGGTAAGCCCATAATGAATGGCCTGTACCAATT
1 AGATACAAGTTCTGGAGGAGGAAATGTCAAAATGGTAAGCCCATGATGAATAGTCTGTACCAATT
* * * *
49402 ATAATATTGTTAAAATTTAAATATCAACTAAAGAAATAAGGAATTCATCATTTAAATAAACAAAC
66 ATAATGTTGTTAAAATTTAAATATCAATTAATGAAATAAGGAATTCATCATTTAAATAAACAGAC
* * * * * ** * * * * * * *
49467 AAT-TTTATCGTAACGGTTACCA-TGTCTGTTTATTTTCCCTAAATAGCAGACATGGTAACCGTT
131 -ATGGTAACCGTTACAG-TAAAATTGTC---ATATTAT-CATGACTA-C--ATAT-GTAA-AG-T
49530 AC
184 AC
* * * * * ** * * * ** *
49532 -GGTAGAA-TTGT-CA-TATTATCATGACTACATAT-GTAAAGTACAT-AT-ACA-AGTTCTGGA
1 AGATACAAGTTCTGGAGGAGGA-AATGTC-A-AAATGGT-AAGCCCATGATGA-ATAG-TCTGTA
** * *
49589 GGAATTATCATGTTGTTAAAATTTAAATATCAATTACTGAAATAAGGAATTCATCATTTAAATAA
60 CCAATTATAATGTTGTTAAAATTTAAATATCAATTAATGAAATAAGGAATTCATCATTTAAATAA
49654 ACAGACATGGTAACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTAAAGTAC
125 ACAGACATGGTAACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTAAAGTAC
* * * *
49715 AGATATAAGTTTTGGAGGAGTAAATGTCAAAATGGTAAGCCCATGATGAATGGTCTGTACCAATT
1 AGATACAAGTTCTGGAGGAGGAAATGTCAAAATGGTAAGCCCATGATGAATAGTCTGTACCAATT
*
49780 ATAATGTTGTTAAAATTTAAATATCAATTACTGAAATAAGGAATTCATCATTTAAATAAACAGAC
66 ATAATGTTGTTAAAATTTAAATATCAATTAATGAAATAAGGAATTCATCATTTAAATAAACAGAC
* * *
49845 ATGGTAACTGTTACAATAAAATTGTCATATTATCATGACTACATATATAAAGTAC
131 ATGGTAACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTAAAGTAC
*
49900 ATATACAAGTTCTGGAGGA
1 AGATACAAGTTCTGGAGGA
49919 ATTATCATGT
Statistics
Matches: 800, Mismatches: 120, Indels: 70
0.81 0.12 0.07
Matches are distributed among these distances:
183 3 0.00
184 15 0.02
185 423 0.53
186 38 0.05
187 29 0.04
188 149 0.19
189 10 0.01
190 6 0.01
191 3 0.00
192 15 0.02
193 91 0.11
194 15 0.02
195 3 0.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.31
Consensus pattern (185 bp):
AGATACAAGTTCTGGAGGAGGAAATGTCAAAATGGTAAGCCCATGATGAATAGTCTGTACCAATT
ATAATGTTGTTAAAATTTAAATATCAATTAATGAAATAAGGAATTCATCATTTAAATAAACAGAC
ATGGTAACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTAAAGTAC
Found at i:49702 original size:378 final size:368
Alignment explanation
Indices: 48784--49916 Score: 1401
Period size: 378 Copynumber: 3.0 Consensus size: 368
48774 ACTATAGATG
* * * * * * * *
48784 CAAGTTCTGGAGGAGGAAATGTCAAAATGGTAAGCCCGTGATGAATAGTCTGTACCAATTATCAT
1 CAAGTTCTGGAGAAGCAAATATCAAAATGGTAAG-ACATGATGAATAATTTGGACCAATTATCAT
* * *
48849 GTTGTTAAAATTTAAATATCAATTAATAAAATAAGGAATTCATCATTTAAATAAACAGACATAGT
65 GTTGTTAAAATTTAAATATCAATTACTGAAATAAGGAATTCATCATTTAAATAAACAGACATGGT
*
48914 AACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTAAAGTACGGATATAAGTTTTGG
130 AACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTAAAGTACAGATATAAGTTTTGG
*
48979 AGGAGGAAATGTCAAAATGGTAAGCCCATGATGAATGGTCTGTACCAATTATAATATTGTTAAAA
195 AGGAGTAAATGTCAAAATGGTAAGCCCATGATGAATGGTCTGTACCAATTATAATATTGTTAAAA
*
49044 TTTAAAATATATCAAC-AAATGAAATAAGGAATTCATCATTTAAATAAACAGACATGGTAACCGT
260 TTT--AA-ATATCAACTAAA-GAAATAAGGAATTCATCATTTAAATAAACAAACATGGTAACCGT
* * *
49108 TACGATAAAATTGTCATATTATCATGACTACATATGTAAAGTACATATA
321 AACGATAAAATTGTCATATTATCATCACTAAATATG-AAAGTACATATA
* * * * *
49157 CAAGTTCTGGAGGAGGAAATGTCAAAATGGTAAGCCATGATGAATAATTTGTACCAATTATTCAT
1 CAAGTTCTGGAGAAGCAAATATCAAAATGGTAAGACATGATGAATAATTTGGACCAATTA-TCAT
* * * *
49222 GTTGTTAAAATATAAATATCAATTACTGAAATAAAGAATTCATCATTTAAATAAACATACACGGT
65 GTTGTTAAAATTTAAATATCAATTACTGAAATAAGGAATTCATCATTTAAATAAACAGACATGGT
*
49287 AACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTCAAGTACAGATATAAGTTTTGG
130 AACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTAAAGTACAGATATAAGTTTTGG
* *
49352 AGGAGTAAATGTCAAAATGGTAAGCCCATAATGAATGGCCTGTACCAATTATAATATTGTTAAAA
195 AGGAGTAAATGTCAAAATGGTAAGCCCATGATGAATGGTCTGTACCAATTATAATATTGTTAAAA
* * *
49417 TTTAAATATCAACTAAAGAAATAAGGAATTCATCATTTAAATAAACAAACAAT-TTTATCGTAAC
260 TTTAAATATCAACTAAAGAAATAAGGAATTCATCATTTAAATAAACAAAC-ATGGTAACCGTAAC
* ** * ** * * *
49481 GGTTACCA-TGTC-TGTTTATTTTCCCTAAATA-G-CAG-ACATGGTA
324 -GATAAAATTGTCAT-ATTATCATCACTAAATATGAAAGTACAT-ATA
* * * *
49524 -ACCGTTAC-GGTAGAATTGTCATATTATCATGACTACATATGTAAAGTACAT-AT-ACA-AGTT
1 CA-AGTT-CTGG-AGAA--G-CA-AATATCA--A--A-AT-GGT-AAG-ACATGATGA-ATAATT
**
49584 CTGGAGGAATTATCATGTTGTTAAAATTTAAATATCAATTACTGAAATAAGGAATTCATCATTTA
50 -TGGACCAATTATCATGTTGTTAAAATTTAAATATCAATTACTGAAATAAGGAATTCATCATTTA
49649 AATAAACAGACATGGTAACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTAAAGTA
114 AATAAACAGACATGGTAACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTAAAGTA
49714 CAGATATAAGTTTTGGAGGAGTAAATGTCAAAATGGTAAGCCCATGATGAATGGTCTGTACCAAT
179 CAGATATAAGTTTTGGAGGAGTAAATGTCAAAATGGTAAGCCCATGATGAATGGTCTGTACCAAT
* * ** *
49779 TATAATGTTGTTAAAATTTAAATATCAATTACTGAAATAAGGAATTCATCATTTAAATAAACAGA
244 TATAATATTGTTAAAATTTAAATATCAACTAAAGAAATAAGGAATTCATCATTTAAATAAACAAA
* * * *
49844 CATGGTAACTGTTACAATAAAATTGTCATATTATCATGACTACATATAT-AAAGTACATATA
309 CATGGTAACCGTAACGATAAAATTGTCATATTATCATCACTA-A-ATATGAAAGTACATATA
49905 CAAGTTCTGGAG
1 CAAGTTCTGGAG
49917 GAATTATCAT
Statistics
Matches: 656, Mismatches: 71, Indels: 59
0.83 0.09 0.08
Matches are distributed among these distances:
366 5 0.01
367 9 0.01
368 4 0.01
369 2 0.00
370 63 0.10
371 12 0.02
372 28 0.04
373 224 0.34
374 1 0.00
376 1 0.00
377 7 0.01
378 261 0.40
379 16 0.02
380 9 0.01
381 9 0.01
382 5 0.01
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (368 bp):
CAAGTTCTGGAGAAGCAAATATCAAAATGGTAAGACATGATGAATAATTTGGACCAATTATCATG
TTGTTAAAATTTAAATATCAATTACTGAAATAAGGAATTCATCATTTAAATAAACAGACATGGTA
ACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTAAAGTACAGATATAAGTTTTGGA
GGAGTAAATGTCAAAATGGTAAGCCCATGATGAATGGTCTGTACCAATTATAATATTGTTAAAAT
TTAAATATCAACTAAAGAAATAAGGAATTCATCATTTAAATAAACAAACATGGTAACCGTAACGA
TAAAATTGTCATATTATCATCACTAAATATGAAAGTACATATA
Found at i:50203 original size:328 final size:327
Alignment explanation
Indices: 49513--50246 Score: 1272
Period size: 328 Copynumber: 2.2 Consensus size: 327
49503 CCCTAAATAG
* *
49513 CAGACATGGTAACCGTTACGGTAGAATTGTCATATTATCATGACTACATATGTAAAGTACATATA
1 CAGACATGGTAACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTAAAGTACATATA
* *
49578 CAAGTTCTGGAGGAATTATCATGTTGTTAAAATTTAAATATCAATTACTGAAATAAGGAATTCAT
66 CAAGTTCTGGAGGAATTATCATGTTGTTAAAAATTAAATATCAATTACTGAAATAAAGAATTCAT
* *
49643 CATTTAAATAAACAGACATGGTAACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGT
131 CATTTAAATAAACAGACATGGTAACCGTTACAATAAAATTGTCATATTATCATGAATACATATGT
* * *
49708 AAAGTACAGATATAAGTTTTGGAGGAGTAAATGTCAAAATGGTAAGCCCATGATGAATGGTCTGT
196 AAAGTACAAATACAAGTTTTGGAGGAGTAAATGTCAAAATGGTAAGCCCATGATGAATGATCTGT
* *
49773 ACCAATTATAATGTTGTTAAAATTTAAATATCAATTACTGAAATAAGGAATTCATCATTTAAATA
261 ACCAATTATAATGTTGTTAAAATTTAAATATCAACTACTGAAATAAGGAATTCATCACTTAAATA
49838 AA
326 AA
* * *
49840 CAGACATGGTAACTGTTACAATAAAATTGTCATATTATCATGACTACATATATAAAGTACATATA
1 CAGACATGGTAACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTAAAGTACATATA
49905 CAAGTTCTGGAGGAATTATCATGTTGTTAAAAATTAAATATCAATTACTGAAATAAAGAATTCAT
66 CAAGTTCTGGAGGAATTATCATGTTGTTAAAAATTAAATATCAATTACTGAAATAAAGAATTCAT
49970 CATTTAAATAAACAGACATGGTAACCGTTACAATAAAATTGTCATATTATCATGAAATACATATG
131 CATTTAAATAAACAGACATGGTAACCGTTACAATAAAATTGTCATATTATCATG-AATACATATG
*
50035 TAAAGTACAAATACAAGTTTTTGAGGAGTAAATGTCAAAATGGTAAGCCCATGATGAATGATCTG
195 TAAAGTACAAATACAAGTTTTGGAGGAGTAAATGTCAAAATGGTAAGCCCATGATGAATGATCTG
*
50100 TACTAATTATAATGTTGTTAAAATTTAAATATCAACTACTGAAATAAGGAATTCATCACTTAAAT
260 TACCAATTATAATGTTGTTAAAATTTAAATATCAACTACTGAAATAAGGAATTCATCACTTAAAT
50165 AAA
325 AAA
* *
50168 CCA-ACATGGTAACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTAATGTACAGAT
1 -CAGACATGGTAACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTAAAGTACATAT
*
50232 ACAAGTTTTGGAGGA
65 ACAAGTTCTGGAGGA
50247 GTAAATGTCA
Statistics
Matches: 383, Mismatches: 22, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
327 176 0.46
328 205 0.54
329 2 0.01
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (327 bp):
CAGACATGGTAACCGTTACAGTAAAATTGTCATATTATCATGACTACATATGTAAAGTACATATA
CAAGTTCTGGAGGAATTATCATGTTGTTAAAAATTAAATATCAATTACTGAAATAAAGAATTCAT
CATTTAAATAAACAGACATGGTAACCGTTACAATAAAATTGTCATATTATCATGAATACATATGT
AAAGTACAAATACAAGTTTTGGAGGAGTAAATGTCAAAATGGTAAGCCCATGATGAATGATCTGT
ACCAATTATAATGTTGTTAAAATTTAAATATCAACTACTGAAATAAGGAATTCATCACTTAAATA
AA
Found at i:50321 original size:185 final size:187
Alignment explanation
Indices: 49918--50358 Score: 683
Period size: 185 Copynumber: 2.4 Consensus size: 187
49908 GTTCTGGAGG
* * *
49918 AATTATCATGTTGTTAAAAATTAAATATCAATTACTGAAATAAAGAATTCATCATTTAAATAAA-
1 AATTATAATGTTGTTAAAATTTAAATATCAACTACTGAAATAAAGAATTCATCATTTAAATAAAC
49982 CAGACATGGTAACCGTTACAATAAAATTGTCATATTATCATGAAATACATATGTAAAGTACAAAT
66 CAGACATGGTAACCGTTACAATAAAATTGTCATATTATCATGAAATACATATGTAAAGTACAAAT
* * *
50047 ACAAGTTTTTGAGGAGTAAATGTCAAAATGGTAAGCCCATGATGAATGATCTGTACT
131 ACAAGTTTTGGAGGAGTAAATGTCAAAATGGTAAGCCCATGATGAATGATCTATACC
* *
50104 AATTATAATGTTGTTAAAATTTAAATATCAACTACTGAAATAAGGAATTCATCACTTAAATAAAC
1 AATTATAATGTTGTTAAAATTTAAATATCAACTACTGAAATAAAGAATTCATCATTTAAATAAAC
* * * *
50169 CA-ACATGGTAACCGTTACAGTAAAATTGTCATATTATCATG-ACTACATATGTAATGTACAGAT
66 CAGACATGGTAACCGTTACAATAAAATTGTCATATTATCATGAAATACATATGTAAAGTACAAAT
* * *
50232 ACAAGTTTTGGAGGAGTAAATGTCAAAATGGTAAGTCCATGATGAATGGTTTATACC
131 ACAAGTTTTGGAGGAGTAAATGTCAAAATGGTAAGCCCATGATGAATGATCTATACC
* * * *
50289 AATTATAATGTTGTTAAACTTTTAAGATCAACTAATGAAATAAAGAATTCATCATTTAAATAAA-
1 AATTATAATGTTGTTAAAATTTAAATATCAACTACTGAAATAAAGAATTCATCATTTAAATAAAC
50353 CAGACA
66 CAGACA
50359 ATTTTATCGC
Statistics
Matches: 232, Mismatches: 21, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
184 2 0.01
185 131 0.56
186 97 0.42
187 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (187 bp):
AATTATAATGTTGTTAAAATTTAAATATCAACTACTGAAATAAAGAATTCATCATTTAAATAAAC
CAGACATGGTAACCGTTACAATAAAATTGTCATATTATCATGAAATACATATGTAAAGTACAAAT
ACAAGTTTTGGAGGAGTAAATGTCAAAATGGTAAGCCCATGATGAATGATCTATACC
Found at i:51165 original size:237 final size:237
Alignment explanation
Indices: 50734--51188 Score: 705
Period size: 237 Copynumber: 1.9 Consensus size: 237
50724 ATGTCTGTTT
* *
50734 TTACCATGTCTATTTATTTTCCCTAAATAAACAGACATGATAATCATTACGGTAAAATTGTCATA
1 TTACCATATCTATTTATTTTCCCTAAATAAACAGACATGATAACCATTACGGTAAAATTGTCATA
50799 TTATCATGACTACATATGTAAAGTACATATACAAGTTCTGGAGGAGTAAATGTCAAAATGGTAAG
66 TTATCATGACTACATATGTAAAGTACATATACAAGTTCTGGAGGAGTAAATGTCAAAATGGTAAG
*
50864 CCCATAATGAATGGCCTGTACCAATTATAATATTGTTAAAATTTAAATATCAACTAAAGAAATAA
131 CCCATAATGAATAGCCTGTACCAATTATAATATTGTTAAAATTTAAATATCAACTAAAGAAATAA
*
50929 GGAATTCATCATTTAAATAAACAAACAATTTTATCGTAACGG
196 AGAATTCATCATTTAAATAAACAAACAATTTTATCGTAACGG
* * * *
50971 TTACCATATCTGTTTATTTTCCCTAAATAAGCAGACATGGTAACCGTTACGGTAAAATTGTCATA
1 TTACCATATCTATTTATTTTCCCTAAATAAACAGACATGATAACCATTACGGTAAAATTGTCATA
*
51036 TTATCATGACTACATATGTAAAGTACATATACAAGTTCTGGAGGAAG-AAATTTCAAAATGGTAA
66 TTATCATGACTACATATGTAAAGTACATATACAAGTTCTGGAGG-AGTAAATGTCAAAATGGTAA
** * * ** * * * * *
51100 GCCTGTGATGAATAGTCTGTATTAATTATCATGTTGTTAAAATTTAAATCTCAATTAATGAAATA
130 GCCCATAATGAATAGCCTGTACCAATTATAATATTGTTAAAATTTAAATATCAACTAAAGAAATA
*
51165 AAGATTTCATCATTTAAATAAACA
195 AAGAATTCATCATTTAAATAAACA
51189 GACATGGTAA
Statistics
Matches: 196, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
237 194 0.99
238 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (237 bp):
TTACCATATCTATTTATTTTCCCTAAATAAACAGACATGATAACCATTACGGTAAAATTGTCATA
TTATCATGACTACATATGTAAAGTACATATACAAGTTCTGGAGGAGTAAATGTCAAAATGGTAAG
CCCATAATGAATAGCCTGTACCAATTATAATATTGTTAAAATTTAAATATCAACTAAAGAAATAA
AGAATTCATCATTTAAATAAACAAACAATTTTATCGTAACGG
Found at i:51479 original size:159 final size:157
Alignment explanation
Indices: 51181--51494 Score: 513
Period size: 159 Copynumber: 2.0 Consensus size: 157
51171 TCATCATTTA
*
51181 AATAAACAGACATGGTAACCGTTACGGTAAAGTTATCATATTATCATGACTACATATATAAAGTA
1 AATAAACAGACATGATAACCGTTACGGTAAAGTTATCATATTATCATGACTACATATATAAAGTA
* * * *
51246 CTATACAAGTTCTGGAGGAATTATCATGTTGTTAAAATTTAAATATTAATTACTGAAGTAAGGAA
66 CTATACAAGTTCTGGAGAAATTACCATGTTGTTAAAATTTAAATATTAATTAATGAAATAAGGAA
* *
51311 TTCATCATTTAAATAAACAGACATGGT
131 TTCACCATTTAAAAAAACAGACATGGT
* *
51338 AATAAACAGACATGATAACCGTTACGGTAGAA-TTGTCATATTATCATGACTACATATGTAAAGT
1 AATAAACAGACATGATAACCGTTACGGTA-AAGTTATCATATTATCATGACTACATATATAAAGT
51402 ACATATACAAAGTTCTGGAGAAATTACCATGTTGTTAAAATTTAAATATTAATTAATGAAATAAG
65 AC-TATAC-AAGTTCTGGAGAAATTACCATGTTGTTAAAATTTAAATATTAATTAATGAAATAAG
51467 GAATTCACCATTTAAAAAAACAGACATG
128 GAATTCACCATTTAAAAAAACAGACATG
51495 ATAACCCTTA
Statistics
Matches: 145, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
157 60 0.41
158 7 0.05
159 78 0.54
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (157 bp):
AATAAACAGACATGATAACCGTTACGGTAAAGTTATCATATTATCATGACTACATATATAAAGTA
CTATACAAGTTCTGGAGAAATTACCATGTTGTTAAAATTTAAATATTAATTAATGAAATAAGGAA
TTCACCATTTAAAAAAACAGACATGGT
Found at i:51925 original size:184 final size:184
Alignment explanation
Indices: 51597--51933 Score: 505
Period size: 184 Copynumber: 1.8 Consensus size: 184
51587 AATTCTAGAG
* * * * *
51597 GAGGAAATGTCAAGATGATAAGCCATGATGAATAGTCTGTATCAATTATCATGTTGTTAAAATTT
1 GAGGAAATGTCAAAATGATAAGCCATGATGAATAGTCTGTACCAATTATAATGTTATAAAAATTT
* * * * * *
51662 AAATATCAATTAATGAAATAATAAATTCATCATTTTAAAAAAAGGACATGGTAACTGTTACAGTA
66 AAATATCAATTAATAAAATAAGAAATTCATCATTTTAAAAAAAAGACATGATAACCGTTACAATA
51727 AAATTGTAATATTATCATGACTACTTATGTAAAGTACAGATATAAGTTATGGAT
131 AAATTGTAATATTATCATGACTACTTATGTAAAGTACAGATATAAGTTATGGAT
* * *
51781 GAGGAAATGTCAAAATGGTAAGCCATGATGAATGGTCTGTACCAATTTTAATGTTATAAAAATTT
1 GAGGAAATGTCAAAATGATAAGCCATGATGAATAGTCTGTACCAATTATAATGTTATAAAAATTT
*
51846 AAATATCAATTAATAAAATAAGGAATTCATCA-TTTAAAAAAACAGACATGATAACCGTTACAAT
66 AAATATCAATTAATAAAATAAGAAATTCATCATTTTAAAAAAA-AGACATGATAACCGTTACAAT
* *
51910 AACATTGTCATATTATCATGACTA
130 AAAATTGTAATATTATCATGACTA
51934 TATGTATAAT
Statistics
Matches: 135, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
183 10 0.07
184 125 0.93
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.32
Consensus pattern (184 bp):
GAGGAAATGTCAAAATGATAAGCCATGATGAATAGTCTGTACCAATTATAATGTTATAAAAATTT
AAATATCAATTAATAAAATAAGAAATTCATCATTTTAAAAAAAAGACATGATAACCGTTACAATA
AAATTGTAATATTATCATGACTACTTATGTAAAGTACAGATATAAGTTATGGAT
Found at i:54430 original size:21 final size:21
Alignment explanation
Indices: 54392--54431 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54382 ATGAGATTAC
* *
54392 ACTGTACAGATTAGATTATGT
1 ACTGTACAGATAAAATTATGT
54413 ACTGTACAGATAAAATTAT
1 ACTGTACAGATAAAATTAT
54432 TAGAGCAGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
ACTGTACAGATAAAATTATGT
Done.