Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015163.1 Corchorus capsularis cultivar CVL-1 contig15184, 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: 30309
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:880 original size:322 final size:320
Alignment explanation
Indices: 1--2139 Score: 2778
Period size: 322 Copynumber: 6.6 Consensus size: 320
*
1 AGAAGCTTGAAAAGCCCATCAATCTTATTGGCGTTGAATTATATTTTTTT-TAAGTATTGTGGCA
1 AGAAGCTTGAAAAGCCCGTCAATCTTATTGGCGTTGAATTATATTTTTTTCTAAGTATTGTGGCA
* * *
65 AAAAATTGAGAAAAAAAATTTCGGGTCAGCTTTTAGTCGAAATCGTGTACAAAAATCGTCAAAAA
66 AAAAATTGAGAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGT------A-C-T-AAACA
* * *
130 TCACAG-TTTTGGTTAAAAACGCGTTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGCAA
122 TCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAA
* * *
194 ATACTCCTTGAAATATCTATATTTATCGAACAAAATCTTTGCCATACTGGATATAAGGATTTTGT
187 AGACTCCTTGAAATATCTATATTCATCGAACAAAATCTTAGCCATACTGGATATAAGGATTTT-T
*
259 TTTTCGAGCATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAAAAAATAAC
251 TTTTCGAGCATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGAAAAA-AAC
324 GATATT
315 GATATT
* * * * **
330 AGAAGGTTGAAAATCCCGTCAATCTTATTGGCGTTGAAGTATATTTTGTTAGAAGTATTGTGGCA
1 AGAAGCTTGAAAAGCCCGTCAATCTTATTGGCGTTGAATTATATTTTTTTCTAAGTATTGTGGCA
* * ** * * *
395 AAAAATTGAGAAAAAAAAATCTCTGGTTTGTTTTTAGCCGAAATCATG---T-AATATCACTGTT
66 AAAAATTGAG-AAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAAACATCACGGTT
* * * * *
456 TTTGGCTAAAAATGCGTTCCGGGGCCCGGGCTCAGTTTTGCATGATTTTTGGTGCAAAGGCTCCT
130 TTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCT
*
521 TGAAATATCTATATTCACCGAACAAAATCTTAGCCATACTGGATATAAGG-TTTTTTTTTCGAGC
195 TGAAATATCTATATTCATCGAACAAAATCTTAGCCATACTGGATATAAGGATTTTTTTTTCGAGC
*
585 ATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGTAAAAAACGATATT
260 ATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAA-TGAAAAAAACGATATT
* * * *
648 AGAAGTTTGAAAAGCCCGTCAATCTTATTCGTGTTGAATTATATTTTTTTTCTAAATATTGTGGC
1 AGAAGCTTGAAAAGCCCGTCAATCTTATTGGCGTTGAATTATA-TTTTTTTCTAAGTATTGTGGC
* *
713 AAAAAATTGAGAAGAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTAC-AAACAACACGGT
65 AAAAAATTGAGAA-AAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAAACATCACGGT
* * * *
777 TTTTGGCTAAAAACGCGTTACGGGGCCCCGGCTCAATTCTGTATGATTTTTGGCGAAAAGACTCC
129 TTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCC
* * * * * *
842 TTCAAATATCTATATTCATCGAACCAAATCTCAGCCATATTGGATATAAAGATTTGTTTTTTTGG
194 TTGAAATATCTATATTCATCGAACAAAATCTTAGCCATACTGGATATAAGGA-TT-TTTTTTTCG
* * *
907 AGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGAAAAAAAATGATTTT
257 AGCATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATG-AAAAAAACGATATT
* * *
972 AGAAGCTTGAAAAGCCCATCAATCTTATTGGAGTTGAATTATATTTTTTTTTCTATTGTAATTGT
1 AGAAGCTTGAAAAGCCCGTCAATCTTATTGGCGTTGAATTATA--TTTTTTTCTA-AGT-ATTGT
* ** *
1037 GGCAAAAAAATTGAGAAAAAAAATTTCGGGTTAGTTTTTA-CTTCGAAATTATGTACTAATCATC
62 GGC-AAAAAATTGAGAAAAAAAATTTCGGGTCAGTTTTTAGC--CGAAATCGTGTACTAAACATC
* *
1101 AACGGTTTTTGGCTAAAAACGCTGTTCCGGGGCCCCGGCTCAATTTTGCAT-AATTTTGGCGTAT
124 -ACGGTTTTTGGCTAAAAACGC-GTTCCGGGGCCCCGGCTCAATTTTGCATGATTTTTGGCGCA-
* * * * *
1165 AA-ACTACTTGAAATATCTATATTCATCAAAGAAAATCTTAGCCATACTGGATATAAAGATTTGT
186 AAGACTCCTTGAAATATCTATATTCATCGAACAAAATCTTAGCCATACTGGATATAAGGATTTTT
* *
1229 TTTCCGAGCATCTCAATCATGTTTCGATTTAATTAGAAATTAATGCGGAAAAAATGGAAAAAAAA
251 TTTTCGAGCATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAT-G---AAAAA
*
1294 AACAATATT
312 AACGATATT
** * * *
1303 AGAAGCTTGAAAAGGGCGTCAATCTTATTGTCGTTGAATTATATTTTTTTCGAAGTATT-TTGCA
1 AGAAGCTTGAAAAGCCCGTCAATCTTATTGGCGTTGAATTATATTTTTTTCTAAGTATTGTGGCA
* * * * * *
1367 AAAAATTGAG-AAAAAAACTTCGGTTCAGTTTTTAGCCGAAATTGTGCACTAACCAGCACGGTTT
66 AAAAATTGAGAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAAACATCACGGTTT
* * * * * *
1431 TTGGGTAAAAACGCGTTCCGGGGCCCGGGCTCAGTTTTCCATGATTTTTGGTGCAAAGGCTCCTT
131 TTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTT
* * *
1496 GAAATATCTATATTCACCGAACAAAATCTTAACCATACTGGATATAAGGATTTTTTTTTTCAAGC
196 GAAATATCTATATTCATCGAACAAAATCTTAGCCATACTGGATATAAGGA-TTTTTTTTTCGAGC
* * * *
1561 ATCTCAATCCTGTTTCGATTTAATTAGAAATTATTTCGAAAAAAAATGAAAAGAACGATATT
260 ATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCG-GAAAAAATGAAAAAAACGATATT
*
1623 AGAAGCTTGCAAAAGCCCGTCAATCTTATTGGCGTTGAATTATATTTTTTTCTAAGTATTGGGGC
1 AGAAGCTTG-AAAAGCCCGTCAATCTTATTGGCGTTGAATTATATTTTTTTCTAAGTATTGTGGC
* * *
1688 AAAAAATTGAGAAAAAAAAATTCGGGTCAG-TTTTAGCCGAAACCGTGTACTAACCATCACGGTT
65 AAAAAATTGAGAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAAACATCACGGTT
* * * * *
1752 TGTAGCTAAAAACGCGTTCCGGGGCCCCGACTCGATTTTCCATGATTTTTGGCGCAAAGACTCCT
130 TTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCT
* *
1817 TGAAGTATCTATATTCATTGAACAAAATCTTAGCCATACTGGATATAAGGATATTTTTTTTTTCG
195 TGAAATATCTATATTCATCGAACAAAATCTTAGCCATACTGGATATAAGG--A-TTTTTTTTTCG
* *
1882 AGTATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATG-TAAAAACGATATT
257 AGCATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGAAAAAAACGATATT
* * *
1945 AGAAGTTTGAAAAGCCCCTCAATCTTATTGGTGTTGAATTATATTTTTTTCTAAGTATTGTGGCA
1 AGAAGCTTGAAAAGCCCGTCAATCTTATTGGCGTTGAATTATATTTTTTTCTAAGTATTGTGGCA
* * * * * *
2010 AAAAATTGAGAACAAAAATTTTAGGGTAAGTTTTTAGCCGAAATCATGTACTAACCATCACGGGT
66 AAAAATTGAGAA-AAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAAACATCACGGTT
* *
2075 TTTGGCTAAAAACGCGTTCCGTGGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAAACTCCT
130 TTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCT
2140 AGGATGTGTT
Statistics
Matches: 1584, Mismatches: 186, Indels: 86
0.85 0.10 0.05
Matches are distributed among these distances:
317 49 0.03
318 67 0.04
319 167 0.11
320 22 0.01
321 138 0.09
322 365 0.23
323 179 0.11
324 136 0.09
325 72 0.05
326 5 0.00
327 32 0.02
328 79 0.05
329 62 0.04
330 104 0.07
331 107 0.07
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (320 bp):
AGAAGCTTGAAAAGCCCGTCAATCTTATTGGCGTTGAATTATATTTTTTTCTAAGTATTGTGGCA
AAAAATTGAGAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAAACATCACGGTTT
TTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTT
GAAATATCTATATTCATCGAACAAAATCTTAGCCATACTGGATATAAGGATTTTTTTTTCGAGCA
TCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGAAAAAAACGATATT
Found at i:2621 original size:3 final size:3
Alignment explanation
Indices: 2613--2696 Score: 132
Period size: 3 Copynumber: 27.3 Consensus size: 3
2603 GATTTGTATG
2613 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
2661 TTA TTA TTA TTA TATA CGTA TTA TTA TCA TTA TTA T
1 TTA TTA TTA TTA T-TA -TTA TTA TTA TTA TTA TTA T
2697 ATATATCTAC
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
3 71 0.95
4 4 0.05
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:2778 original size:2 final size:2
Alignment explanation
Indices: 2767--2796 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2757 ATATCATTAT
2767 TA TA TA -A 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 T
2797 CTACTACCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2900 original size:34 final size:32
Alignment explanation
Indices: 2857--2925 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
2847 GAAAAATGAG
*
2857 TATTTCAATTTTGGGGAGAAATCATTATTATATA
1 TATTTCAA-TTT-GGGACAAATCATTATTATATA
* *
2891 TATTTCAATTTGGGCCATATCATTATTATATA
1 TATTTCAATTTGGGACAAATCATTATTATATA
2923 TAT
1 TAT
2926 ATATATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 21 0.66
33 3 0.09
34 8 0.25
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (32 bp):
TATTTCAATTTGGGACAAATCATTATTATATA
Found at i:3209 original size:11 final size:11
Alignment explanation
Indices: 3193--3217 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3183 AGAGGTGATC
3193 GGATCACCCCT
1 GGATCACCCCT
3204 GGATCACCCCT
1 GGATCACCCCT
3215 GGA
1 GGA
3218 AGGGTGATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.40, G:0.24, T:0.16
Consensus pattern (11 bp):
GGATCACCCCT
Found at i:3981 original size:326 final size:326
Alignment explanation
Indices: 3324--6224 Score: 3429
Period size: 324 Copynumber: 9.0 Consensus size: 326
3314 CGCAACCCTA
*
3324 GAAATATCTATATTCATCGAACAAAATCTCAGTCATACTGGATATAAGGATTTG-TTTTTTCGAG
1 GAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTGTTTTTTTCGAG
* * *
3388 CAACTCAATCATGTTTCGATATAATAAGAAATTAATTCGG-AAAAATG---AAAAAAACGATATT
66 CATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGAAAAAAAAAACGATATT
* * * *
3449 AGAAGCTTGAAAAGCCCGTCAATCATATTGACATTGAATTATATTTTCTTACTAAGTATTGTGGC
131 AGAAGCTTGAAAAGCCCGTCAATCTTATTGGCGTTGAATTATATTTT-TTTCTAAGTATTGTGGC
* * *
3514 AAAAAATT-GAGGAAAAAAA-TTTCGGGTCACTTTTTAGCCG-AA-T-TGTACTAACCATCATGG
195 AAAAAATTAGA-AAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATTGTGTACTAACCATCACGG
* * * *
3574 TTTTTTTGCTAAAAATGCGTTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGTAAATACT
259 -TTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACT
3639 CCTT
323 CCTT
* * * * *
3643 AAAATATCTATATTCATCGAACCAAATCTCAGCCATATTGAATATAAGGATTTGTTTTTTTGGAG
1 GAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTGTTTTTTTCGAG
* * *
3708 CATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATGAAAAAAAAAACAATATT
66 CATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGAAAAAAAAAACGATATT
* * *
3773 AGAAGCTTGAAAATG-GCATCAATCTTATTGGCGTTGAATTATATTTTTTTTTAAGTATTGTGGC
131 AGAAGCTTGAAAA-GCCCGTCAATCTTATTGGCGTTGAATTATATTTTTTTCTAAGTATTGTGGC
* * *
3837 -AAAAATTCAGAAAAAAAAACTTTCGGGTCAGTTTTTAGCCGAAATTGTCTACTAACCATCACGA
195 AAAAAATT-AGAAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATTGTGTACTAACCATCACGG
* * **
3901 TTTTTGGCTAAAAACGCGTTCCGAGGCCCCGGCTCAATTTTGCATGATTTTTTCCGCAAAGACTC
259 TTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTC
3966 CTT
324 CTT
*
3969 CAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTT-TCTTTTTTCGA
1 GAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTGT-TTTTTTCGA
* *
4033 GCATCTCAATCATGTTTCGATTTAATTAGAAATTAATTTGGAAAAAA--AATGAAAAATAACGAT
65 GCATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGAA--AAAAAAAACGAT
* * * *
4096 ATTAGAAGCTTAAAAATCCCGTCAATCTTATT-GCTGTTGAATTATATTTTTTTCGAAGAATTGT
128 ATTAGAAGCTTGAAAAGCCCGTCAATCTTATTGGC-GTTGAATTATATTTTTTTCTAAGTATTGT
* * * * *
4160 GGCAAAAAATT-GAGAATAAATATTTTTGGGTCAGTTTTTAGCCGAAATCGTGTA-TTA-CATCA
192 GGCAAAAAATTAGA-AAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATTGTGTACTAACCATCA
* *
4222 CGGTTTTT-GCTAAAAACACGTTCCAGGGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGA
256 CGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGA
4286 CTCCTT
321 CTCCTT
* * *
4292 CAAATATCTATACTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTT-ATTTTTTCGAG
1 GAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTGTTTTTTTCGAG
* **
4356 CATCTTAATCATGTTTCGAAATAATTAGAAATTAATTCGGAAAAAA--AAGAAAAAAAACGATAT
66 CATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGAA-AAAAAAAACGATAT
* * * ** * * *
4419 TAGAAGATTCAAAAAGCCCGTAAATCTTATTTTCATTTAATTATATTTTATTTTTCTAATTATTG
130 TAGAAGCTT-GAAAAGCCCGTCAATCTTATTGGCGTTGAATTATA--TT-TTTTTCTAAGTATTG
* * *
4484 TGGCAAAAAATTA-AGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATTATATACTAACCATCA
191 TGGCAAAAAATTAGAAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATTGTGTACTAACCATCA
* * ***
4548 CGGTTTTTGGCTAAAAACGCATTCCGGGGCCACGACTCAATTTTGCATGATTTTTTATGCAAAGA
256 CGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGA
4613 CTCCTT
321 CTCCTT
* * * * *
4619 GTAATATCTATATTCATAGAAGC-AAATCTCAGCCATATTGGATATAAGGATTTCTTTTTTTGGA
1 GAAATATCTATATTCATCGAA-CAAAATCTCAGCCATACTGGATATAAGGATTTGTTTTTTTCGA
* **
4683 GCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTC-GAACAAAA--AATGTAAAAAACGAT
65 GCATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGGAA-AAAATGAA-AAAAAAAACGAT
* * * *
4745 ATTAGAAGCTTGAAAAGCCCTTCAATCTTATTGGCGTTAAATTATATCTTTTTCTAAGAATTGTG
128 ATTAGAAGCTTGAAAAGCCCGTCAATCTTATTGGCGTTGAATTATATTTTTTTCTAAGTATTGTG
* ** * ** * *
4810 GCAAAAAATT-GAAAAAAAAAATTTCATGTCAGTTTTTAGCTGAAATCATGTACTAACCATGATG
193 GCAAAAAATTAGAAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATTGTGTACTAACCATCACG
* * * * *
4874 GTTTTTGGCTAAAAACGCGTTCCGTGGCCCCGGCTCAATTTTGTATGATTTTTTGCGCAAAAAAC
258 GTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGC-AAAGAC
*
4939 TCCTA
322 TCCTT
* *
4944 GAAATATCTATATTTATCGAACAAAATCTCAGCCATACTAGATATAAGGATTTG-TTTTTTCGAG
1 GAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTGTTTTTTTCGAG
* * *
5008 CATCTCAATCATGTTTCGATATAATAAGAAATTAATTCGGAAAAAAATGAAAAAAAAAAACGAGA
66 CATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAATG-AAAAAAAAAACGATA
* * * * *
5073 TTAGAAACTTGAAAAGCCCGTCAATCATATTGGCATTGAGTTATATTTTCTTACTAAGTATTGTG
129 TTAGAAGCTTGAAAAGCCCGTCAATCTTATTGGCGTTGAATTATATTTT-TTTCTAAGTATTGTG
* * *
5138 GCAAAAAATT-G-AGAAAAAATTTTCGGGTCACTTTTTAGCCGAAATTGTGTACTAACCTTCACG
193 GCAAAAAATTAGAAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATTGTGTACTAACCATCACG
* * * * ***
5201 GTTTTTTGCTAAAAACGGGTTTCGGGGCCCCGACTCAATTTTCCATGATTTTT-G-GC-TTTACT
258 GTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACT
5263 CCTT
323 CCTT
* * * *
5267 GAAATATCTATATTCATCGAACCAAATCTCAGCCATATTAGATATAAGGATTTGTTTTTTTGGAG
1 GAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTGTTTTTTTCGAG
* * * * *
5332 CATATCAATCTTGTATCGATTTAATTAGAATTTAATTCGGAAAAAAATG---AAAAAAACAATAT
66 CATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAATGAAAAAAAAAACGATAT
** * *
5394 TAGAAGCTTGAAAAGGGCATCAATCTTATTGGCATTGAATTATATTTTTTTCTAAGTATTGTGGC
130 TAGAAGCTTGAAAAGCCCGTCAATCTTATTGGCGTTGAATTATATTTTTTTCTAAGTATTGTGGC
* * * * *
5459 -AGAAGTT-GAGAAAAAAA-TTTCAGGTCAATTTTTAGCCGAAATTGTGTACTAACCATCACGGT
195 AAAAAATTAGAAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATTGTGTACTAACCATCACGGT
* *
5521 TTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTC-AGTTTGCATGATTTTTGACGCAAAGACTCC
260 TTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCC
5585 TCT
325 T-T
* * * * * * * *
5588 -AAATATCTATATTTAGCGAAGAAAATCTTAGCCATACAGTATATAAGGATTTCTTTTTTTCGAA
1 GAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTGTTTTTTTCGAG
* * * *
5652 AATCTCAATCATATTTCGATTTAATTAGAAATTAATTCGGAAAAAAATG--TAAAATAACGATAT
66 CATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAATGAAAAAAAAAACGATAT
* * * * *
5715 TAGAAGCTTCAAAATCCCGTCAATCTTATT-GCTGTTGAATTATATATATTTCGAAGTATTGTGG
130 TAGAAGCTTGAAAAGCCCGTCAATCTTATTGGC-GTTGAATTATATTTTTTTCTAAGTATTGTGG
** * ** * *
5779 CAAAAAAACGAGAAAAAAATATTTTTAGGTCAGTTTTTAGCCGAAATCGTGTA-TTA-CATCACG
194 C-AAAAAATTAGAAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATTGTGTACTAACCATCACG
* *
5842 GTTTTTTGCTAAAAATGCGTTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACT
258 GTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACT
*
5907 GCTT
323 CCTT
* * ** * *
5911 GAAATATCTATATTCATCGAACAAAATCTTAGTCATTTTGGATATAAGGTTTTGTTTTTTTGGAG
1 GAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTGTTTTTTTCGAG
* * *
5976 CATATCAATCTTGTTTCGATTTAATTAGAAATTAACTCGGAAAAAAATGAAAAAAAAAACGATAT
66 CATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAATGAAAAAAAAAACGATAT
* * * *
6041 TAGAAGTTTGAAAAGCCCATCAATCTTATTGGCGTTGAATTATATTTTTTTTCCTGAGTATTGCG
130 TAGAAGCTTGAAAAGCCCGTCAATCTTATTGGCGTTGAATTATA-TTTTTTT-CTAAGTATTGTG
** ** ** * *
6106 TTAAAAAATT-G--GGAAAAATTTTCCAGTCAGTTTTTAGCCAAAATCGTG---T----AT--CG
193 GCAAAAAATTAGAAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATTGTGTACTAACCATCACG
* * * *
6159 GTTTTTGGCTAAAAATGCGTTCCGGCGCCCCGGCTCAATTTTGCAAGATTTTTGGCGCAAAGACT
258 GTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACT
6224 C
323 C
6225 AGCCATGCAG
Statistics
Matches: 2221, Mismatches: 302, Indels: 120
0.84 0.11 0.05
Matches are distributed among these distances:
317 77 0.03
318 79 0.04
319 75 0.03
320 200 0.09
321 94 0.04
322 90 0.04
323 233 0.10
324 505 0.23
325 128 0.06
326 330 0.15
327 305 0.14
328 105 0.05
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (326 bp):
GAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTGTTTTTTTCGAG
CATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGAAAAAAAAAACGATATT
AGAAGCTTGAAAAGCCCGTCAATCTTATTGGCGTTGAATTATATTTTTTTCTAAGTATTGTGGCA
AAAAATTAGAAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATTGTGTACTAACCATCACGGTT
TTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCCT
T
Found at i:5797 original size:968 final size:959
Alignment explanation
Indices: 3324--7030 Score: 4470
Period size: 968 Copynumber: 3.9 Consensus size: 959
3314 CGCAACCCTA
*
3324 GAAATATCTATATTCATCGAACAAAATCTCAGTCATACTGGATATAAGGATTTGTTTTTTCGAGC
1 GAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTGTTTTTTCGAGC
*
3389 A-ACTCAATCATGTTTCGATATAATAAGAAATTAATTCGG--AAAAATG-AAAAAAACGATATTA
66 ATA-TCAATCATGTTTCGATATAATTAGAAATTAATTCGGAAAAAAATGAAAAAAAACGATATTA
* * *
3450 GAAGCTTGAAAAGCCCGTCAATCATATTGACATTGAATTATATTTTCTTACTAAGTATTGTGGCA
130 GAAGCTTGAAAAGCCCGTCAATCTTATTGGCATTGAATTATATTTT-TTTCTAAGTATTGTGGCA
* *
3515 AAAAATTGAGGAAAAAAA-TTTCGGGTCACTTTTTAGCCG-AATTG--TACTAACCATCATGGTT
194 AAAAATTGA-GAAAAAAATTTTCGGGTCAATTTTTAGCCGAAATTGTATACTAACCATCACGG-T
* * * * * *
3576 TTTTTGCTAAAAATGCGTTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGTAAATACTCC
257 TTTTGGCTAAAAACGCATTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGACGCAAAGACTCC
* *
3641 TTAAAATATCTATATTCATCGAACCAAATCTCAGCCATATTGAATATAAGGATTTGTTTTTTTGG
322 TTAAAATATCTATATTCATCGAACCAAATCTCAGCCATATTGGATATAAGGATTTCTTTTTTTGG
* * * *
3706 AGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATGAAAAAAAAAACAATA
387 AGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATG--TAAAATAACGATA
** *
3771 TTAGAAGCTTGAAAATGGCATCAATCTTATTGGCGTTGAATTATATTTTTTTTTAAGTATTGTGG
450 TTAGAAGCTTGAAAATCCCATCAATCTTATTGGCGTTGAATTATA-TTTTTTCTAAGTATTGTGG
** * * *
3836 CAAAAATTC-AGAAAAAAAAACTTTCGGGTCAGTTTTTAGCCGAAATTGTCTACTAACCATCACG
514 CAAAAAAACGAG-AAAAAAAACTTTCAGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACG
* **
3900 ATTTTTGGCTAAAAACGCGTTCCGAGGCCCCGGCTCAATTTTGCATGATTTTTTCCGCAAAGACT
578 GTTTTTGGCTAAAAACGCGTTCCG-GGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACT
* *
3965 CCTTCAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTTCTTTTTT
642 CCTTGAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGA-TTTGTTTTTT
* *
4030 CGAGCATCTCAATCATGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAAATG--AAAAATAAC
706 CGAGCATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAAATGAAAAAAAAAAC
* * * *
4093 GATATTAGAAGCTTAAAAATCCCGTCAATCTTATT-GCTGTTGAATTATATTTTTTTCGAAGAAT
770 GATATTAGAAGCTTGAAAAGCCCGTCAATCTTATTGGC-GTTGAATTATATTTTTTTCTAAGTAT
*
4157 TGTGGCAAAAAATTGAGAATAAATATTTTTGGGTCAGTTTTTAGCCGAAATCGTGTATTACATCA
834 TGTGGCAAAAAATTGAGAA-AAA-ATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTA-TAC-TCA
* *
4222 CGG-TTTTTGCTAAAAACACGTTCCAGGGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGA
895 CGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCGACTCAATTTTGCATGATTTTT-G-GC----A
4286 CTCCTT
954 CTCCTT
* * *
4292 CAAATATCTATACTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTATTTTTTCGAGC
1 GAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTGTTTTTTCGAGC
* * * *
4357 ATCTTAATCATGTTTCGAAATAATTAGAAATTAATTCGGAAAAAAAAGAAAAAAAACGATATTAG
66 ATATCAATCATGTTTCGATATAATTAGAAATTAATTCGGAAAAAAATGAAAAAAAACGATATTAG
* * * ** * *
4422 AAGATTCAAAAAGCCCGTAAATCTTATTTTCATTTAATTATATTTTATTTTTCTAATTATTGTGG
131 AAGCTT-GAAAAGCCCGTCAATCTTATTGGCATTGAATTATA--TT-TTTTTCTAAGTATTGTGG
* * *
4487 CAAAAAATTAAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATTATATACTAACCATCACGGT
192 CAAAAAATTGAGAAAAAAATTTTCGGGTCAATTTTTAGCCGAAATTGTATACTAACCATCACGGT
* * *
4552 TTTTGGCTAAAAACGCATTCCGGGGCCACGACTCAATTTTGCATGATTTTTTATGCAAAGACTCC
257 TTTTGGCTAAAAACGCATTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGACGCAAAGACTCC
** * *
4617 TTGTAATATCTATATTCATAGAAGCAAATCTCAGCCATATTGGATATAAGGATTTCTTTTTTTGG
322 TTAAAATATCTATATTCATCGAACCAAATCTCAGCCATATTGGATATAAGGATTTCTTTTTTTGG
*
4682 AGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGAACAAAAAATGTAAAA-AACGATA
387 AGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCG--GAAAAAATGTAAAATAACGATA
* * * *
4746 TTAGAAGCTTGAAAAGCCCTTCAATCTTATTGGCGTTAAATTATATCTTTTTCTAAGAATTGTGG
450 TTAGAAGCTTGAAAATCCCATCAATCTTATTGGCGTTGAATTATAT-TTTTTCTAAGTATTGTGG
** * * * * * *
4811 CAAAAAATTGA-AAAAAAAAATTTCATGTCAGTTTTTAGCTGAAATCATGTACTAACCATGATGG
514 CAAAAAAACGAGAAAAAAAACTTTCAGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGG
* * *
4875 TTTTTGGCTAAAAACGCGTTCCGTGGCCCCGGCTCAATTTTGTATGATTTTTTGCGCAAAAAACT
579 TTTTTGGCTAAAAACGCGTTCCG-GGCCCCGGCTCAATTTTGCATGATTTTTGGCGC-AAAGACT
* * *
4940 CCTAGAAATATCTATATTTATCGAACAAAATCTCAGCCATACTAGATATAAGGATTTGTTTTTTC
642 CCTTGAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTGTTTTTTC
* *
5005 GAGCATCTCAATCATGTTTCGATATAATAAGAAATTAATTCGGAAAAAAATGAAAAAAAAAAACG
707 GAGCATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATG-AAAAAAAAAACG
* * * * * *
5070 AGATTAGAAACTTGAAAAGCCCGTCAATCATATTGGCATTGAGTTATATTTTCTTACTAAGTATT
771 ATATTAGAAGCTTGAAAAGCCCGTCAATCTTATTGGCGTTGAATTATATTTT-TTTCTAAGTATT
* *
5135 GTGGCAAAAAATTGAGAAAAAATTTTCGGGTCACTTTTTAGCCGAAATTGTGTACTAACCTTCAC
835 GTGGCAAAAAATTGAGAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTA-T-A-C-TCAC
* * *
5200 GGTTTTTTGCTAAAAACGGGTTTCGGGGCCCCGACTCAATTTTCCATGATTTTTGGCTTTACTCC
896 GGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGGC---ACTCC
5265 TT
958 TT
* * * *
5267 GAAATATCTATATTCATCGAACCAAATCTCAGCCATATTAGATATAAGGATTTGTTTTTTTGGAG
1 GAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTG-TTTTTTCGAG
* * * * *
5332 CATATCAATCTTGTATCGATTTAATTAGAATTTAATTCGGAAAAAAATG-AAAAAAACAATATTA
65 CATATCAATCATGTTTCGATATAATTAGAAATTAATTCGGAAAAAAATGAAAAAAAACGATATTA
** *
5396 GAAGCTTGAAAAGGGCATCAATCTTATTGGCATTGAATTATATTTTTTTCTAAGTATTGTGGC-A
130 GAAGCTTGAAAAGCCCGTCAATCTTATTGGCATTGAATTATATTTTTTTCTAAGTATTGTGGCAA
* * * *
5460 GAAGTTGAGAAAAAAA-TTTCAGGTCAATTTTTAGCCGAAATTGTGTACTAACCATCACGGTTTT
195 AAAATTGAGAAAAAAATTTTCGGGTCAATTTTTAGCCGAAATTGTATACTAACCATCACGGTTTT
* *
5524 TGGCTAAAAACGCGTTCCGGGGCCCCGACTC-AGTTTGCATGATTTTTGACGCAAAGACTCCTCT
260 TGGCTAAAAACGCATTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGACGCAAAGACTCCT-T
* * ** * ** * * *
5588 -AAATATCTATATTTAGCGAAGAAAATCTTAGCCATACAGTATATAAGGATTTCTTTTTTTCGAA
324 AAAATATCTATATTCATCGAACCAAATCTCAGCCATATTGGATATAAGGATTTCTTTTTTTGGAG
* * *
5652 AATCTCAATCATATTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGTAAAATAACGATATTA
389 CATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAATGTAAAATAACGATATTA
* * * *
5717 GAAGCTTCAAAATCCCGTCAATCTTATT-GCTGTTGAATTATATATATTTCGAAGTATTGTGGCA
453 GAAGCTTGAAAATCCCATCAATCTTATTGGC-GTTGAATTATAT-TTTTTCTAAGTATTGTGGCA
* * *
5781 AAAAAACGAGAAAAAAATATTTTTAGGTCAGTTTTTAGCCGAAATCGTGTA-TTA-CATCACGGT
516 AAAAAACGAGAAAAAAA-ACTTTCAGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGT
* * * *
5844 TTTTTGCTAAAAATGCGTTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTGC
580 TTTTGGCTAAAAACGCGTTCC-GGGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCC
* * ** * *
5909 TTGAAATATCTATATTCATCGAACAAAATCTTAGTCATTTTGGATATAAGGTTTTGTTTTTTTGG
644 TTGAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTG-TTTTTTCG
* * *
5974 AGCATATCAATCTTGTTTCGATTTAATTAGAAATTAACTCGGAAAAAAATGAAAAAAAAAACGAT
708 AGCATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGAAAAAAAAAACGAT
* * *
6039 ATTAGAAGTTTGAAAAGCCCATCAATCTTATTGGCGTTGAATTATATTTTTTTTCCTGAGTATTG
773 ATTAGAAGCTTGAAAAGCCCGTCAATCTTATTGGCGTTGAATTATA-TTTTTTT-CTAAGTATTG
* ** * ** *
6104 CGTTAAAAAATTG-GGAAAAATTTTCCAGTCAGTTTTTAGCCAAAATCGTG--TA-T--CGGTTT
836 TGGCAAAAAATTGAGAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTATACTCACGGTTT
* * * * *
6163 TTGGCTAAAAATGCGTTCCGGCGCCCCGGCTCAATTTTGCAAGATTTTTGG-----C--
901 TTTGCTAAAAACGCGTTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCACTCCTT
* *
6215 G------C-A-A---A--G------A-CTCAGCCATGCAGGATATAAGGATTTGTTTTTTCGAGC
1 GAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTGTTTTTTCGAGC
* * * * *
6260 TTCTCATTCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGAAAAAGAAAACGATAT
66 ATATCAATCATGTTTCGATATAATTAGAAATTAATTCGG-AAAAAAATG-AAAA-AAAACGATAT
* * *
6325 TAGAAGCTTGAAAATCCTGTCAATCTTATTGGCGTTGAATTATATTTTTTTCTAAGTATTGTGGC
128 TAGAAGCTTGAAAAGCCCGTCAATCTTATTGGCATTGAATTATATTTTTTTCTAAGTATTGTGGC
* * *
6390 AAAAAATTGAGAAAAAAAATTTTCGGGTCAATTTTTCA-CCGAAATCGTATAATAACCAACACGG
193 AAAAAATTGAG-AAAAAAATTTTCGGGTCAATTTTT-AGCCGAAATTGTATACTAACCATCACGG
* * * * * *
6454 TTTTTGGTTAAAAACGCATTACGGGGCCCCGGCTCAATTCTGCATGATCTTTTG-TGCAAAAACT
256 TTTTTGGCTAAAAACGCATTCCGGGGCCCCGACTCAATTTTGCATGAT-TTTTGACGCAAAGACT
* * * * * * * *
6518 CCTTTAAATATCTATATTCTTCGAACCATATCTCCGCCATGTTGGGATATTAGAATTTGTTTTTT
320 CCTTAAAATATCTATATTCATCGAACCAAATCTCAGCCATATT-GGATATAAGGATTTCTTTTTT
* *
6583 AGGAGCATCTCAATCTTGTTTCTATTTAATTAGAAATTAATTCGG---AAA---AAAAT---GAT
384 TGGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGTAAAATAACGAT
*
6639 ATTAGAAGCTTGAAAAGT-CCATCAATCTTAGTGGCGTTGAATTATATTTTTTCTAAGTATTGTG
449 ATTAGAAGCTTGAAAA-TCCCATCAATCTTATTGGCGTTGAATTATATTTTTTCTAAGTATTGTG
* * * * *
6703 GCAAAAAAA--ATGAGAAAAAATTTTCTGGTTAGTTTTTAGCCGAAATTGTGTAC---CCATCAC
513 GCAAAAAAACGA-GAAAAAAAACTTTCAGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCAC
* * * *
6763 TGTTTTTGGCTAAAAACGCGTGCCGGTGCCCGGGCTCAATTTTGCATGATTTTTGGCGCAAAGGC
577 GGTTTTTGGCTAAAAACGCGTTCCGG-GCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGAC
*
6828 TCCTTGAAATATCTATATTCATCGAACAAAATCTCAGCAATACTGGATATAAGGATTTGTTTTTT
641 TCCTTGAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTGTTTTTT
* * *
6893 CGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAAA--AATGAAAAGAAC
706 CGAGCATCTCAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGAA-AAAAAAAAC
*
6955 GATATTAGAAGCTTGAAAAGCCCGTCAATCTTATTGGTGTTGAATTATATTTTTTTCTAAGTATT
770 GATATTAGAAGCTTGAAAAGCCCGTCAATCTTATTGGCGTTGAATTATATTTTTTTCTAAGTATT
7020 GTGGCAAAAAA
835 GTGGCAAAAAA
7031 CTTTCCAACG
Statistics
Matches: 2380, Mismatches: 304, Indels: 161
0.84 0.11 0.06
Matches are distributed among these distances:
917 16 0.01
918 9 0.00
919 53 0.02
920 8 0.00
921 47 0.02
922 113 0.05
923 30 0.01
924 7 0.00
925 24 0.01
926 42 0.02
927 47 0.02
928 32 0.01
929 6 0.00
930 3 0.00
931 68 0.03
932 11 0.00
933 7 0.00
934 69 0.03
935 50 0.02
936 60 0.03
937 1 0.00
940 1 0.00
941 1 0.00
942 1 0.00
948 1 0.00
950 1 0.00
958 49 0.02
960 1 0.00
963 1 0.00
964 1 0.00
967 156 0.07
968 414 0.17
969 84 0.04
970 48 0.02
971 39 0.02
972 31 0.01
973 17 0.01
974 221 0.09
975 237 0.10
976 268 0.11
977 51 0.02
978 54 0.02
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (959 bp):
GAAATATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTGTTTTTTCGAGC
ATATCAATCATGTTTCGATATAATTAGAAATTAATTCGGAAAAAAATGAAAAAAAACGATATTAG
AAGCTTGAAAAGCCCGTCAATCTTATTGGCATTGAATTATATTTTTTTCTAAGTATTGTGGCAAA
AAATTGAGAAAAAAATTTTCGGGTCAATTTTTAGCCGAAATTGTATACTAACCATCACGGTTTTT
GGCTAAAAACGCATTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGACGCAAAGACTCCTTAA
AATATCTATATTCATCGAACCAAATCTCAGCCATATTGGATATAAGGATTTCTTTTTTTGGAGCA
TCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGTAAAATAACGATATTAGAA
GCTTGAAAATCCCATCAATCTTATTGGCGTTGAATTATATTTTTTCTAAGTATTGTGGCAAAAAA
ACGAGAAAAAAAACTTTCAGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGG
CTAAAAACGCGTTCCGGGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAAT
ATCTATATTCATCGAACAAAATCTCAGCCATACTGGATATAAGGATTTGTTTTTTCGAGCATCTC
AATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGAAAAAAAAAACGATATTAGAAG
CTTGAAAAGCCCGTCAATCTTATTGGCGTTGAATTATATTTTTTTCTAAGTATTGTGGCAAAAAA
TTGAGAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTATACTCACGGTTTTTTGCTAAAA
ACGCGTTCCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCACTCCTT
Found at i:10004 original size:15 final size:15
Alignment explanation
Indices: 9986--10033 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
9976 TCAACCAGTT
*
9986 CCATCACCGCCACCG
1 CCATCACCGCCACCA
*
10001 CCATCTCCGCCACCA
1 CCATCACCGCCACCA
* *
10016 CCTTCACCACCACCA
1 CCATCACCGCCACCA
10031 CCA
1 CCA
10034 GCTGCCAACA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.23, C:0.60, G:0.06, T:0.10
Consensus pattern (15 bp):
CCATCACCGCCACCA
Found at i:13675 original size:28 final size:28
Alignment explanation
Indices: 13641--13698 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
13631 TTCCTTCCAA
13641 TTTATTTATTTGATATAAGCAACAATAT
1 TTTATTTATTTGATATAAGCAACAATAT
13669 TTTATTTATTTGATATAAGCAACAATAT
1 TTTATTTATTTGATATAAGCAACAATAT
13697 TT
1 TT
13699 AGAATTGGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (28 bp):
TTTATTTATTTGATATAAGCAACAATAT
Found at i:21314 original size:42 final size:41
Alignment explanation
Indices: 21255--21338 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 41
21245 TAGCTGCAAT
* *
21255 AATAGAACGCAAATCACTTGATTAAGAACAAAATTACAAAAG
1 AATAGAACGCAAATCACTTAATTAAGAACAAAA-AACAAAAG
* *
21297 AATAGCACGCAAATCACTTAATTTAGAACAAAAAACAAAAG
1 AATAGAACGCAAATCACTTAATTAAGAACAAAAAACAAAAG
21338 A
1 A
21339 GGGTATAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
41 8 0.21
42 30 0.79
ACGTcount: A:0.56, C:0.15, G:0.11, T:0.18
Consensus pattern (41 bp):
AATAGAACGCAAATCACTTAATTAAGAACAAAAAACAAAAG
Found at i:21639 original size:17 final size:19
Alignment explanation
Indices: 21601--21639 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
21591 CTCTACGGGA
21601 AAAAACCCTACGGAGAGAAG
1 AAAAACCCTAC-GAGAGAAG
21621 AAAAACCCTA-GAG-GAAG
1 AAAAACCCTACGAGAGAAG
21638 AA
1 AA
21640 TGGAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 3 0.16
20 10 0.53
ACGTcount: A:0.54, C:0.18, G:0.23, T:0.05
Consensus pattern (19 bp):
AAAAACCCTACGAGAGAAG
Done.