Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014228.1 Corchorus olitorius cultivar O-4 contig14261, 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: 4687
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.35
Found at i:90 original size:30 final size:30
Alignment explanation
Indices: 22--117 Score: 138
Period size: 31 Copynumber: 3.1 Consensus size: 30
12 ACTAAATCTA
* *
22 AAAAAAATTCTCTTATATTTTTCTTTTGGGC
1 AAAAAAA-TCCCTTATATTTTTCTTTTGGAC
*
53 AAAAAAAATCCCTTATGTTTTTCTTTTGGAC
1 -AAAAAAATCCCTTATATTTTTCTTTTGGAC
84 AAAAAAATCCCTTATATTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATATTTTTCTTTT-GGAC
115 AAA
1 AAA
118 TCAGTCCCTT
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
30 25 0.42
31 27 0.46
32 7 0.12
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (30 bp):
AAAAAAATCCCTTATATTTTTCTTTTGGAC
Found at i:128 original size:31 final size:31
Alignment explanation
Indices: 22--117 Score: 142
Period size: 30 Copynumber: 3.1 Consensus size: 31
12 ACTAAATCTA
*
22 AAAAAAATTCTCTTATATTTTTCTTTTGGG-C
1 AAAAAAA-TCCCTTATATTTTTCTTTTGGGAC
*
53 AAAAAAAATCCCTTATGTTTTTCTTTT-GGAC
1 -AAAAAAATCCCTTATATTTTTCTTTTGGGAC
84 AAAAAAATCCCTTATATTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATATTTTTCTTTTGGGAC
115 AAA
1 AAA
118 TCAGTCCCTT
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
30 27 0.46
31 25 0.42
32 7 0.12
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (31 bp):
AAAAAAATCCCTTATATTTTTCTTTTGGGAC
Found at i:283 original size:29 final size:30
Alignment explanation
Indices: 241--314 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
231 CTCATTTTTG
* *
241 AAACGTAAGGGATTAATTTGT-CCTGAAA-A
1 AAACATAAGGGATTAATTTGTACC-AAAACA
*
270 AAACATAAGGGATTATTTTGTACCAAAAGCA
1 AAACATAAGGGATTAATTTGTACCAAAA-CA
301 AAACATAAGGGATT
1 AAACATAAGGGATT
315 TTTTGGGTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 22 0.56
30 2 0.05
31 15 0.38
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.26
Consensus pattern (30 bp):
AAACATAAGGGATTAATTTGTACCAAAACA
Found at i:1005 original size:333 final size:331
Alignment explanation
Indices: 334--3207 Score: 3476
Period size: 336 Copynumber: 8.5 Consensus size: 331
324 TTTAGCCTAT
*
334 ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACCAGTATC
1 ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACGAGTATC
* *
399 TGAATCTTGTATCGATTTAATTAGAAATAAATTCAGAAAAAAATAGAAAAACGATATTAGAAGCG
66 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCA-AAAAAAATGGAAAAACGATATTAGAAGCG
* * *
464 TGAAAAACCCTTCATTGTTTTTGGCGTTGAATTATATAATTTTTTTGAGTATTGTGGCACAAAAT
130 TGAAAAACCCTTCATTGTTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAAT
*
529 TGGGGAAAAACTTTTCGGGTCAGTTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACTATCT
195 TGGGGAAAAACTTTTCGGGTCAG-TTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATC-
* * * *
594 TA-GGTTTTGGCTAAAAACGCGTTTCGGGTCTCTGGCTCAATTTTGCATGATATTTGGAAGAAAG
258 -ACGGTTTTGGCTAAAAACGCGTTTCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGAAGAAAG
658 ACTCCTCG-A
322 ACTCCTCGAA
* * * *
667 ATATATATATTCATCTAATGAAATCTTAACCACAATGGATTTAAGGATTTAATTTTACTAGTATC
1 ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACGAGTATC
* *
732 TGAATCATGTTTCGATTTAATTAGAAATAAATTTCTAAAAAAAATAGAAAAACGATATTAGAAGC
66 TGAATCTTGTTTCGATTTAATTAGAAATAAA-TTC-AAAAAAAATGGAAAAACGATATTAGAAGC
* * *
797 GTGAAAACCCCTTCATTGTTTTAGGCGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAA
129 GTGAAAAACCCTTCATTGTTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAA
* *
862 TT-GGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTATACTAACCATTA
194 TTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCA
** * *
926 CGGGTTTTGGCTAAAAACGCGTTTCGGGGTTCTGGCTTAGTTTTGCATGATTTTTGGAAGAATGA
259 C-GGTTTTGGCTAAAAACGCGTTTCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGAAGAAAGA
991 CTCCTCGAA
323 CTCCTCGAA
* * * *
1000 ATATATATATTCATTTAATCATATCTTAGCCACAATGGATTTAAGGATTTATTTTTACTAGGATC
1 ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACGAGTATC
* * *
1065 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGCAAAAAATAGAAAAACGATATTAGAAGCA
66 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCA-AAAAAAATGGAAAAACGATATTAGAAGCG
* * *
1130 TGAAAAACCCTTCATT-CTTTTGGCGTTGAATTATATGATTTTTTTGAGTATTGTGGCAAAAAGT
130 TGAAAAACCCTTCATTGTTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAAT
* * **
1194 TGGGGAAATACTTTTCGGGTCAGTTATTTTGCAAAATTTTCGCCAAAATCGTGTACTAACCATCA
195 TGGGGAAAAACTTTTCGGGTCAGTT-TTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCA
* * * ** ** *
1259 CGATTTGTAGCTAAAAACGCGTTTCGAGGCCCTATCTCAGTTTTGCATGA-TTTTACACAG-AAT
259 CGGTTT-TGGCTAAAAACGCGTTTCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGA-AGAAAG
* *
1322 ACTCGGTGTTGAA
322 ACTC---CTCGAA
* * * *
1335 TTATATGATTTTTCTGAGTATTCATCTAACCAAAATCTCAGCCACAATGGATTTACGGATTTGTT
1 --ATAT-A------T-A-TATTCATCTAATC-AAATCTTAGCCACAATGGATTTAAGGATTTATT
* * * ** *
1400 TTTACGAGCATCTGAATCTTGTTTCGATTAAATTAGAAATAAATTCGGAAAAATTTGGAGAAACG
54 TTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-AAAAAAAATGGAAAAACG
* ** * **
1465 ATATTAGAAGCGTGAAAAACCCTAT-AATACTTTTGGCGTTGAATTATATGATTATAATGAGTAT
118 ATATTAGAAGCGTGAAAAACCCT-TCATTGTTTTTGGCGTTGAATTATATGATTTTTCTGAGTAT
*
1529 TGTGGCAAAAAATTTGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTG
182 TGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTG
*
1594 TACTAACCATCACGGGTTTTGGCTAAAAACGCGTTTCGGGGCTCTGGCTCAGTTTTGCATGATTT
247 TACTAACCATCAC-GGTTTTGGCTAAAAACGCGTTTCGGGGCCCTGGCTCAGTTTTGCATGATTT
*
1659 TTGGAAGAAAAACTCCTCGAA
311 TTGGAAGAAAGACTCCTCGAA
*
1680 ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACCAGTATC
1 ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACGAGTATC
* ** *
1745 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAATTAAAAAAAGCGATATTAGAGGC
66 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCA-AAAAAAATGGAAAAA-CGATATTAGAAGC
* * * *
1810 GTGAAAACCCCGTCATTGTTTTTGGTGTTGAATTATATGATTTTTCTGAGTATTGTGGCTAAAAA
129 GTGAAAAACCCTTCATTGTTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAA
* * ** *
1875 TTGGGGAAAAACTTTTCGGGTCAGTTTTTATGCAAAACTTTCGCCAAAATCGTGTACAAACCATC
194 TTGGGGAAAAACTTTTCGGGTCAGTTTTT-TGCAAAATTTTAGCTGAAATCGTGTACTAACCATC
* * * ** **
1940 ACGATTTGTAGCTAAAAACGCGTTTCGAGGCCCTATCTCAGTTTTGCATGA-TTTTACACAG-AA
258 ACGGTTT-TGGCTAAAAACGCGTTTCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGA-AGAAA
* * *
2003 TACTCGGTGTTGAA
321 GACTC---CTCGAA
* * * *
2017 TTATATGATTTTTCTGAGTATTCATCTAACCAAAATCTCAGCCACAATGGATTT-ACGAGTTTTT
1 --ATAT-A------T-A-TATTCATCTAATC-AAATCTTAGCCACAATGGATTTAAGGA-TTTAT
*
2081 TTTTACGAGTATCTGAATCTTGTTTCGATTAAATTAGAAATAAATTCAGAAAAAAATGGAAAAAC
53 TTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCA-AAAAAAATGGAAAAAC
* *
2146 GATATTAGAAGCGTGAAAAACCCTTCATTGTTTTTGGCATTGAACTATATGATTTTTCTGAGTAT
117 GATATTAGAAGCGTGAAAAACCCTTCATTGTTTTTGGCGTTGAATTATATGATTTTTCTGAGTAT
* *
2211 TGTGGCAAAAAATTGGTGAAAAACTTTTCGGGTCAGTTTTTTTGCAAAATTTTAG-TCGAAATCA
182 TGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAG-TTTTTTGCAAAATTTTAGCT-GAAATCG
* * * * *
2275 TGTACTAACCATCACGG-TTTGGCTAAAAATGCGTTTCGGGGCCTTGACTTAGTTTTGCATGAAT
245 TGTACTAACCATCACGGTTTTGGCTAAAAACGCGTTTCGGGGCCCTGGCTCAGTTTTGCATGATT
* * *
2339 TTTGGCAGAATGACTTCTCGAA
310 TTTGGAAGAAAGACTCCTCGAA
* *
2361 ATACATATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTACGGATTTATTTTTACGAGTA
1 ATATATATATTCATCTAATCAAATCT-T-AGCCACAATGGATTTAAGGATTTATTTTTACGAGTA
* * ***
2426 TCTGAATCTTGTTTCGATTTAATTAGAAATGTATTGTGGGCAAAAAA-GGAAAAACGATATTAGA
64 TCTGAATCTTGTTTCGATTTAATTAGAAAT-AAAT-T-CAAAAAAAATGGAAAAACGATATTAGA
* ** * * ** *
2490 AGCGTTAAAAACCCTAAAATATTTTTGGCAATGAATTATATGATTTTTCCGAGTATTGTGGCAAA
126 AGCGTGAAAAACCCTTCATTGTTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAA
* * *
2555 AAATTGGGGAAAATCTTTTCGGGTCAGCTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCA
191 AAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCA
* * * * *
2620 TTACGGTTTTTGGCTGAAAACGCGTTTCGGGGCCCTGGCTCAGATTTGCATGATTTCTGGCAGAA
256 TCACGG-TTTTGGCTAAAAACGCGTTTCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGAAGAA
*
2685 AGACTTCTCGAA
320 AGACTCCTCGAA
* *
2697 ATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTACGGATTTATTTTTACGAGTA
1 ATATATATATTCATCTAATCAAATCT-T-AGCCACAATGGATTTAAGGATTTATTTTTACGAGTA
* * ***
2762 TTTGAATCTTGTTTCGATTTAATTAGAAATGTAATGTGGCAAAAAATGGAAAAACGATATTAGAA
64 TCTGAATCTTGTTTCGATTTAATTAGAAAT-AAAT-TCAAAAAAAATGGAAAAACGATATTAGAA
* * *
2827 GCGTGAAAAA-CATTAAAATT-TTTTTGGCGTTCAATTATATGATTTTTCTGAGTATTGTGGCAA
127 GCGTGAAAAACCCTT--CATTGTTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAA
* *
2890 AAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATAGTGTTCTAACC
190 AAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACC
* * * * *
2955 ATCACGGTTTTTGGCTAAAAACGCGTTTTGGGGCCTTGGTTCAGTTTTGCATGACTTTTGGCAGA
255 ATCACGG-TTTTGGCTAAAAACGCGTTTCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGAAGA
*
3020 AAGACGCCTCGAA
319 AAGACTCCTCGAA
* * * * * * * * *
3033 ATGTCTGTATTCATCGAACCAAAATCTCAGCCACAATGGATTTACGGATTTGTTTTTACGAGCAT
1 ATATATATATTCATCTAATC-AAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACGAGTAT
* * ***
3098 CTGAATCTTGTTTCGATTAAATTAGAAATAAATTCGGAAAATTTTGGAAAAACGATATTAGAAGC
65 CTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-AAAAAAAATGGAAAAACGATATTAGAAGC
* * ** *
3163 ATGAAAAACCCTAT-AATACTTTTGGTGTTGAATTATATGATTTTT
129 GTGAAAAACCCT-TCATTGTTTTTGGCGTTGAATTATATGATTTTT
3208 TGAAAAATTT
Statistics
Matches: 2214, Mismatches: 253, Indels: 147
0.85 0.10 0.06
Matches are distributed among these distances:
330 1 0.00
331 45 0.02
332 188 0.08
333 374 0.17
334 372 0.17
335 257 0.12
336 377 0.17
337 17 0.01
338 1 0.00
339 4 0.00
340 1 0.00
341 1 0.00
342 4 0.00
343 4 0.00
344 5 0.00
345 5 0.00
346 50 0.02
347 196 0.09
348 223 0.10
349 89 0.04
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (331 bp):
ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACGAGTATC
TGAATCTTGTTTCGATTTAATTAGAAATAAATTCAAAAAAAATGGAAAAACGATATTAGAAGCGT
GAAAAACCCTTCATTGTTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAATT
GGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACG
GTTTTGGCTAAAAACGCGTTTCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGAAGAAAGACTC
CTCGAA
Found at i:1876 original size:334 final size:331
Alignment explanation
Indices: 334--3207 Score: 3450
Period size: 333 Copynumber: 8.5 Consensus size: 331
324 TTTAGCCTAT
*
334 ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACCAGTATC
1 ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACGAGTATC
* *
399 TGAATCTTGTATCGATTTAATTAGAAATAAATTCAGAAAAAAATAGAAAAACGATATTAGAAGCG
66 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCAG-AAAAAATGGAAAAACGATATTAGAAGCG
* *
464 TGAAAAACCCTTCATTGTTTTTGGCGTTGAATTATATAATTTTTTTGAGTATTGTGGCACAAAAT
130 TGAAAAACCCTTCATTGTTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCA-AAAAT
* *
529 TGGGGAAAAACTTTTCGGGTCAGTTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACTATCT
194 TGGGGAAAAACTTTTCGGGTCAG-TTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCA
** * * *
594 TAGGTTTTGGCTAAAAACGCGTTTCGGGTCTCTGGCTCAATTTTGCATGATATTTGGAAGAAAGA
258 CGGGTTTTGGCTAAAAACGCGTTTCGGGGCTCTGGCTCAGTTTTGCATGATTTTTGGAAGAAAGA
659 CTCCTCG-A
323 CTCCTCGAA
* * * *
667 ATATATATATTCATCTAATGAAATCTTAACCACAATGGATTTAAGGATTTAATTTTACTAGTATC
1 ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACGAGTATC
* * *
732 TGAATCATGTTTCGATTTAATTAGAAATAAATTTCTAAAAAAAATAGAAAAACGATATTAGAAGC
66 TGAATCTTGTTTCGATTTAATTAGAAATAAA-TTC-AGAAAAAATGGAAAAACGATATTAGAAGC
* * *
797 GTGAAAACCCCTTCATTGTTTTAGGCGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAA
129 GTGAAAAACCCTTCATTGTTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGC-AAAAA
* *
862 TT-GGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTATACTAACCATTA
193 TTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCA
* * *
926 CGGGTTTTGGCTAAAAACGCGTTTCGGGGTTCTGGCTTAGTTTTGCATGATTTTTGGAAGAATGA
258 CGGGTTTTGGCTAAAAACGCGTTTCGGGGCTCTGGCTCAGTTTTGCATGATTTTTGGAAGAAAGA
991 CTCCTCGAA
323 CTCCTCGAA
* * * *
1000 ATATATATATTCATTTAATCATATCTTAGCCACAATGGATTTAAGGATTTATTTTTACTAGGATC
1 ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACGAGTATC
* *
1065 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGCAAAAAATAGAAAAACGATATTAGAAGCA
66 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCAG-AAAAAATGGAAAAACGATATTAGAAGCG
* *
1130 TGAAAAACCCTTCATT-CTTTTGGCGTTGAATTATATGATTTTTTTGAGTATTGTGGCAAAAAGT
130 TGAAAAACCCTTCATTGTTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAA-T
* * **
1194 TGGGGAAATACTTTTCGGGTCAGTTATTTTGCAAAATTTTCGCCAAAATCGTGTACTAACCATCA
194 TGGGGAAAAACTTTTCGGGTCAGTT-TTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCA
* * * * ** **
1259 C-GATTTGTAGCTAAAAACGCGTTTCGAGGCCCTATCTCAGTTTTGCATGA-TTTTACACAG-AA
258 CGGGTTT-TGGCTAAAAACGCGTTTCGGGGCTCTGGCTCAGTTTTGCATGATTTTTGGA-AGAAA
* * *
1321 TACTCGGTGTTGAA
321 GACTC---CTCGAA
* * * *
1335 TTATATGATTTTTCTGAGTATTCATCTAACCAAAATCTCAGCCACAATGGATTTACGGATTTGTT
1 --ATAT-A------T-A-TATTCATCTAATC-AAATCTTAGCCACAATGGATTTAAGGATTTATT
* * * * *
1400 TTTACGAGCATCTGAATCTTGTTTCGATTAAATTAGAAATAAATTCGGAAAAATTTGGAGAAACG
54 TTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAA-ATGGAAAAACG
* ** * **
1465 ATATTAGAAGCGTGAAAAACCCTAT-AATACTTTTGGCGTTGAATTATATGATTATAATGAGTAT
118 ATATTAGAAGCGTGAAAAACCCT-TCATTGTTTTTGGCGTTGAATTATATGATTTTTCTGAGTAT
*
1529 TGTGGCAAAAAATTTGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTG
182 TGTGGC-AAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTG
1594 TACTAACCATCACGGGTTTTGGCTAAAAACGCGTTTCGGGGCTCTGGCTCAGTTTTGCATGATTT
246 TACTAACCATCACGGGTTTTGGCTAAAAACGCGTTTCGGGGCTCTGGCTCAGTTTTGCATGATTT
*
1659 TTGGAAGAAAAACTCCTCGAA
311 TTGGAAGAAAGACTCCTCGAA
*
1680 ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACCAGTATC
1 ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACGAGTATC
** *
1745 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAATTAAAAAAAGCGATATTAGAGGC
66 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAA-TGGAAAAA-CGATATTAGAAGC
* * *
1810 GTGAAAACCCCGTCATTGTTTTTGGTGTTGAATTATATGATTTTTCTGAGTATTGTGGCTAAAAA
129 GTGAAAAACCCTTCATTGTTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGC-AAAAA
* * ** *
1875 TTGGGGAAAAACTTTTCGGGTCAGTTTTTATGCAAAACTTTCGCCAAAATCGTGTACAAACCATC
193 TTGGGGAAAAACTTTTCGGGTCAGTTTTT-TGCAAAATTTTAGCTGAAATCGTGTACTAACCATC
* * * * ** **
1940 AC-GATTTGTAGCTAAAAACGCGTTTCGAGGCCCTATCTCAGTTTTGCATGA-TTTTACACAG-A
257 ACGGGTTT-TGGCTAAAAACGCGTTTCGGGGCTCTGGCTCAGTTTTGCATGATTTTTGGA-AGAA
* * *
2002 ATACTCGGTGTTGAA
320 AGACTC---CTCGAA
* * * *
2017 TTATATGATTTTTCTGAGTATTCATCTAACCAAAATCTCAGCCACAATGGATTT-ACGAGTTTTT
1 --ATAT-A------T-A-TATTCATCTAATC-AAATCTTAGCCACAATGGATTTAAGGA-TTTAT
*
2081 TTTTACGAGTATCTGAATCTTGTTTCGATTAAATTAGAAATAAATTCAGAAAAAAATGGAAAAAC
53 TTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAG-AAAAAATGGAAAAAC
* *
2146 GATATTAGAAGCGTGAAAAACCCTTCATTGTTTTTGGCATTGAACTATATGATTTTTCTGAGTAT
117 GATATTAGAAGCGTGAAAAACCCTTCATTGTTTTTGGCGTTGAATTATATGATTTTTCTGAGTAT
* *
2211 TGTGGCAAAAAATTGGTGAAAAACTTTTCGGGTCAGTTTTTTTGCAAAATTTTAG-TCGAAATCA
182 TGTGGC-AAAAATTGGGGAAAAACTTTTCGGGTCAG-TTTTTTGCAAAATTTTAGCT-GAAATCG
* * *
2275 TGTACTAACCATCAC-GG-TTTGGCTAAAAATGCGTTTCGGGGC-CTTGACTTAGTTTTGCATGA
244 TGTACTAACCATCACGGGTTTTGGCTAAAAACGCGTTTCGGGGCTC-TGGCTCAGTTTTGCATGA
* * * *
2337 ATTTTGGCAGAATGACTTCTCGAA
308 TTTTTGGAAGAAAGACTCCTCGAA
* *
2361 ATACATATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTACGGATTTATTTTTACGAGTA
1 ATATATATATTCATCTAATCAAATCT-T-AGCCACAATGGATTTAAGGATTTATTTTTACGAGTA
* * **
2426 TCTGAATCTTGTTTCGATTTAATTAGAAATGTATTGTGGGCAAAAAA-GGAAAAACGATATTAGA
64 TCTGAATCTTGTTTCGATTTAATTAGAAAT-AAAT-TCAG-AAAAAATGGAAAAACGATATTAGA
* ** * * ** *
2490 AGCGTTAAAAACCCTAAAATATTTTTGGCAATGAATTATATGATTTTTCCGAGTATTGTGGCAAA
126 AGCGTGAAAAACCCTTCATTGTTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGC-AA
* * *
2555 AAATTGGGGAAAATCTTTTCGGGTCAGCTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCA
190 AAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCA
* * * * * * *
2620 TTACGGTTTTTGGCTGAAAACGCGTTTCGGGGCCCTGGCTCAGATTTGCATGATTTCTGGCAGAA
255 TCACGGGTTTTGGCTAAAAACGCGTTTCGGGGCTCTGGCTCAGTTTTGCATGATTTTTGGAAGAA
*
2685 AGACTTCTCGAA
320 AGACTCCTCGAA
* *
2697 ATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTACGGATTTATTTTTACGAGTA
1 ATATATATATTCATCTAATCAAATCT-T-AGCCACAATGGATTTAAGGATTTATTTTTACGAGTA
* * *
2762 TTTGAATCTTGTTTCGATTTAATTAGAAATGTAATGT-GGCAAAAAATGGAAAAACGATATTAGA
64 TCTGAATCTTGTTTCGATTTAATTAGAAAT-AAAT-TCAG-AAAAAATGGAAAAACGATATTAGA
* * *
2826 AGCGTGAAAAA-CATTAAAATT-TTTTTGGCGTTCAATTATATGATTTTTCTGAGTATTGTGGCA
126 AGCGTGAAAAACCCTT--CATTGTTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGC-
* *
2889 AAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATAGTGTTCTAAC
188 AAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAAC
* * * * *
2954 CATCACGGTTTTTGGCTAAAAACGCGTTTTGGGGC-CTTGGTTCAGTTTTGCATGACTTTTGGCA
253 CATCACGGGTTTTGGCTAAAAACGCGTTTCGGGGCTC-TGGCTCAGTTTTGCATGATTTTTGGAA
*
3018 GAAAGACGCCTCGAA
317 GAAAGACTCCTCGAA
* * * * * * * * *
3033 ATGTCTGTATTCATCGAACCAAAATCTCAGCCACAATGGATTTACGGATTTGTTTTTACGAGCAT
1 ATATATATATTCATCTAATC-AAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACGAGTAT
* * **
3098 CTGAATCTTGTTTCGATTAAATTAGAAATAAATTCGGAAAATTTTGGAAAAACGATATTAGAAGC
65 CTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAA-AATGGAAAAACGATATTAGAAGC
* * ** *
3163 ATGAAAAACCCTAT-AATACTTTTGGTGTTGAATTATATGATTTTT
129 GTGAAAAACCCT-TCATTGTTTTTGGCGTTGAATTATATGATTTTT
3208 TGAAAAATTT
Statistics
Matches: 2216, Mismatches: 246, Indels: 157
0.85 0.09 0.06
Matches are distributed among these distances:
330 5 0.00
331 40 0.02
332 188 0.08
333 378 0.17
334 366 0.17
335 260 0.12
336 376 0.17
337 18 0.01
338 1 0.00
339 4 0.00
340 1 0.00
341 1 0.00
342 4 0.00
343 4 0.00
344 5 0.00
345 6 0.00
346 54 0.02
347 193 0.09
348 218 0.10
349 88 0.04
350 6 0.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (331 bp):
ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACGAGTATC
TGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAATGGAAAAACGATATTAGAAGCGT
GAAAAACCCTTCATTGTTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAATTG
GGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGG
GTTTTGGCTAAAAACGCGTTTCGGGGCTCTGGCTCAGTTTTGCATGATTTTTGGAAGAAAGACTC
CTCGAA
Found at i:2108 original size:682 final size:664
Alignment explanation
Indices: 334--3207 Score: 3645
Period size: 682 Copynumber: 4.3 Consensus size: 664
324 TTTAGCCTAT
334 ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACCAGTATC
1 ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACCAGTATC
*
399 TGAATCTTGTATCGATTTAATTAGAAATAAATTCAGAAAAAAATAGAAAAACGATATTAGAAGCG
66 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCAG-AAAAAATAGAAAAACGATATTAGAAGCG
* * *
464 TGAAAAACCCTTCATTGTTTTTGGCGTTGAATTATATAATTTTTTTGAGTATTGTGGCACAAAAT
130 TGAAAAACCC-TCATTATTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCA-AAAAT
** *
529 TGGGGAAAAACTTTTCGGGTCAGTTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACTATCT
193 TGGGGAAAAACTTTTCGGGTCAG-TTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATC-
* * * * * **
594 TA-GGTTT-TGGCTAAAAACGCGTTTCG-GGTCTCTGGCTCAATTTTGCATGATATTTGGA-AGA
256 -ACGATTTGTAGCTAAAAACGCGTTTCGAGG-CCCTAGCTCAGTTTTGCATGAT-TTTACACAGA
** * * *
655 AAGACTC-CTCGAATATA--TATATTCATCTAA-TGAAATCTTAACCACAATGGATTTAAGGATT
318 AAGACTCTCTCGAATATATCTATATTCATCTAACCAAAATCTCAGCCACAATGGATTTACGGATT
* * * * ** *
716 TAATTTTACTAGTATCTGAATCATGTTTCGATTTAATTAGAAATAAATTTCTAAAAAAAATAGAA
383 TATTTTTACGAGTATCTGAATCTTGTTTCGATTAAATTAGAAATAAA-TTCGGAAAAAAATGGAA
* * * *
781 AAACGATATTAGAAGCGTGAAAACCCCTTCATTGTTTTAGGCGTTGAATTATATAATTTTTCTGA
447 AAACGATATTAGAAGCGTGAAAAACCCTTAATT-TTTTTGGCGTTGAATTATATGATTTTTCTGA
846 GTATTGTGGCAAAAAATTGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATC
511 GTATTGTGGCAAAAAATTGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATC
* * * *
911 GTATACTAACCATTACGGGTTTTGGCTAAAAACGCGTTTCGGGG-TTCTGGCTTAGTTTTGCATG
576 GTGTACTAACCATCACGGGTTTTGGCTAAAAACGCGTTTCGGGGCCT-TGGCTCAGTTTTGCATG
*
975 ATTTTTGGAAGAATGACTCCTCGAA
640 ATTTTTGGAAGAAAGACTCCTCGAA
* * * *
1000 ATATATATATTCATTTAATCATATCTTAGCCACAATGGATTTAAGGATTTATTTTTACTAGGATC
1 ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACCAGTATC
*
1065 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGCAAAAAATAGAAAAACGATATTAGAAGCA
66 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCAG-AAAAAATAGAAAAACGATATTAGAAGCG
* *
1130 TGAAAAACCCTTCATT-CTTTTGGCGTTGAATTATATGATTTTTTTGAGTATTGTGGCAAAAAGT
130 TGAAAAACCC-TCATTATTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAA-T
* *
1194 TGGGGAAATACTTTTCGGGTCAGTTATTTTGCAAAATTTTCGCCAAAATCGTGTACTAACCATCA
193 TGGGGAAAAACTTTTCGGGTCAGTT-TTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCA
* *
1259 CGATTTGTAGCTAAAAACGCGTTTCGAGGCCCTATCTCAGTTTTGCATGATTTTACACAG-AATA
257 CGATTTGTAGCTAAAAACGCGTTTCGAGGCCCTAGCTCAGTTTTGCATGATTTTACACAGAAAGA
* *
1323 CTCGGTGTTGAATTATATGATTTTTCTGAGTATTCATCTAACCAAAATCTCAGCCACAATGGATT
322 CTC--TCTCG-A--ATAT-A----TCT-A-TATTCATCTAACCAAAATCTCAGCCACAATGGATT
* *
1388 TACGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTAAATTAGAAATAAATTCGGAAAAA
375 TACGGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTAAATTAGAAATAAATTCGGAAAAA
** * **
1453 TTTGGAGAAACGATATTAGAAGCGTGAAAAACCCTATAATACTTTTGGCGTTGAATTATATGATT
440 AATGGAAAAACGATATTAGAAGCGTGAAAAACCCT-TAATTTTTTTGGCGTTGAATTATATGATT
* **
1518 ATAATGAGTATTGTGGCAAAAAATTTGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAG
504 TTTCTGAGTATTGTGGCAAAAAA-TTGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAG
1583 CTGAAATCGTGTACTAACCATCACGGGTTTTGGCTAAAAACGCGTTTCGGGG-CTCTGGCTCAGT
568 CTGAAATCGTGTACTAACCATCACGGGTTTTGGCTAAAAACGCGTTTCGGGGCCT-TGGCTCAGT
*
1647 TTTGCATGATTTTTGGAAGAAAAACTCCTCGAA
632 TTTGCATGATTTTTGGAAGAAAGACTCCTCGAA
1680 ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACCAGTATC
1 ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACCAGTATC
* *
1745 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAATTAAAAAAAGCGATATTAGAGGC
66 TGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAA-TAGAAAAA-CGATATTAGAAGC
* * *
1810 GTGAAAACCCCGTCATTGTTTTTGGTGTTGAATTATATGATTTTTCTGAGTATTGTGGCTAAAAA
129 GTGAAAAACCC-TCATTATTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGC-AAAAA
* * *
1875 TTGGGGAAAAACTTTTCGGGTCAGTTTTTATGCAAAACTTTCGCCAAAATCGTGTACAAACCATC
192 TTGGGGAAAAACTTTTCGGGTCAGTTTTT-TGCAAAATTTTAGCCAAAATCGTGTACTAACCATC
* *
1940 ACGATTTGTAGCTAAAAACGCGTTTCGAGGCCCTATCTCAGTTTTGCATGATTTTACACAG-AAT
256 ACGATTTGTAGCTAAAAACGCGTTTCGAGGCCCTAGCTCAGTTTTGCATGATTTTACACAGAAAG
* *
2004 ACTCGGTGTTGAATTATATGATTTTTCTGAGTATTCATCTAACCAAAATCTCAGCCACAATGGAT
321 ACTC--TCTCG-A--ATAT-A----TCT-A-TATTCATCTAACCAAAATCTCAGCCACAATGGAT
* *
2069 TTAC-GAGTTTTTTTTTACGAGTATCTGAATCTTGTTTCGATTAAATTAGAAATAAATTCAGAAA
374 TTACGGA-TTTATTTTTACGAGTATCTGAATCTTGTTTCGATTAAATTAGAAATAAATTCGGAAA
* * *
2133 AAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCATTGTTTTTGGCATTGAACTATATGA
438 AAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTAATT-TTTTTGGCGTTGAATTATATGA
2198 TTTTTCTGAGTATTGTGGCAAAAAATTGGTGAAAAACTTTTCGGGTCAGTTTTTTTGCAAAATTT
502 TTTTTCTGAGTATTGTGGCAAAAAATTGG-GAAAAACTTTTCGGGTCAG-TTTTTTGCAAAATTT
* * * *
2263 TAG-TCGAAATCATGTACTAACCATCAC-GG-TTTGGCTAAAAATGCGTTTCGGGGCCTTGACTT
565 TAGCT-GAAATCGTGTACTAACCATCACGGGTTTTGGCTAAAAACGCGTTTCGGGGCCTTGGCTC
* * * *
2325 AGTTTTGCATGAATTTTGGCAGAATGACTTCTCGAA
629 AGTTTTGCATGATTTTTGGAAGAAAGACTCCTCGAA
* * *
2361 ATACATATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTACGGATTTATTTTTACGAGTA
1 ATATATATATTCATCTAATCAAATCT-T-AGCCACAATGGATTTAAGGATTTATTTTTACCAGTA
* * ** *
2426 TCTGAATCTTGTTTCGATTTAATTAGAAATGTATTGTGGGCAAAAAA-GGAAAAACGATATTAGA
64 TCTGAATCTTGTTTCGATTTAATTAGAAAT-AAAT-TCAG-AAAAAATAGAAAAACGATATTAGA
* * * ** *
2490 AGCGTTAAAAACCCTAAAATATTTTTGGCAATGAATTATATGATTTTTCCGAGTATTGTGGCAAA
126 AGCGTGAAAAACCCT-CATTATTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGC-AA
* * *
2555 AAATTGGGGAAAATCTTTTCGGGTCAGCTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCA
189 AAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCA
* * * * * * * * **
2620 TTACGGTTTTTGGCTGAAAACGCGTTTCGGGGCCCTGGCTCAGATTTGCATGATTTCT-GGCAGA
254 TCACGATTTGTAGCTAAAAACGCGTTTCGAGGCCCTAGCTCAGTTTTGCATGATTT-TACACAGA
* *
2684 AAGACT-TCTCGAA-ATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTACGGAT
318 AAGACTCTCTCGAATATATCTATATTCATCTAACCAAA-ATCTCAGCCACAATGGATTTACGGAT
* * * *
2747 TTATTTTTACGAGTATTTGAATCTTGTTTCGATTTAATTAGAAATGTAATGT-GGCAAAAAATGG
382 TTATTTTTACGAGTATCTGAATCTTGTTTCGATTAAATTAGAAAT-AAAT-TCGGAAAAAAATGG
* *
2811 AAAAACGATATTAGAAGCGTGAAAAA-CATTAAAATTTTTTTGGCGTTCAATTATATGATTTTTC
445 AAAAACGATATTAGAAGCGTGAAAAACCCTT--AATTTTTTTGGCGTTGAATTATATGATTTTTC
2875 TGAGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGA
508 TGAGTATTGTGGCAAAAAATT-GGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGA
* * * * *
2940 AATAGTGTTCTAACCATCACGGTTTTTGGCTAAAAACGCGTTTTGGGGCCTTGGTTCAGTTTTGC
572 AATCGTGTACTAACCATCACGGGTTTTGGCTAAAAACGCGTTTCGGGGCCTTGGCTCAGTTTTGC
* * *
3005 ATGACTTTTGGCAGAAAGACGCCTCGAA
637 ATGATTTTTGGAAGAAAGACTCCTCGAA
* * * * * * * * * *
3033 ATGTCTGTATTCATCGAACCAAAATCTCAGCCACAATGGATTTACGGATTTGTTTTTACGAGCAT
1 ATATATATATTCATCTAATC-AAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACCAGTAT
* * ** *
3098 CTGAATCTTGTTTCGATTAAATTAGAAATAAATTCGGAAAATTTTGGAAAAACGATATTAGAAGC
65 CTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAA-AATAGAAAAACGATATTAGAAGC
* * *
3163 ATGAAAAACCCT-ATAATACTTTTGGTGTTGAATTATATGATTTTT
129 GTGAAAAACCCTCAT--TATTTTTGGCGTTGAATTATATGATTTTT
3208 TGAAAAATTT
Statistics
Matches: 1967, Mismatches: 183, Indels: 112
0.87 0.08 0.05
Matches are distributed among these distances:
663 1 0.00
664 20 0.01
665 135 0.07
666 141 0.07
667 2 0.00
668 6 0.00
669 18 0.01
670 166 0.08
671 175 0.09
672 80 0.04
673 6 0.00
675 1 0.00
676 2 0.00
677 2 0.00
678 1 0.00
679 97 0.05
680 309 0.16
681 121 0.06
682 463 0.24
683 206 0.10
684 7 0.00
685 2 0.00
686 6 0.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (664 bp):
ATATATATATTCATCTAATCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACCAGTATC
TGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAATAGAAAAACGATATTAGAAGCGT
GAAAAACCCTCATTATTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAATTGG
GGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCACGAT
TTGTAGCTAAAAACGCGTTTCGAGGCCCTAGCTCAGTTTTGCATGATTTTACACAGAAAGACTCT
CTCGAATATATCTATATTCATCTAACCAAAATCTCAGCCACAATGGATTTACGGATTTATTTTTA
CGAGTATCTGAATCTTGTTTCGATTAAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATAT
TAGAAGCGTGAAAAACCCTTAATTTTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGC
AAAAAATTGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAAC
CATCACGGGTTTTGGCTAAAAACGCGTTTCGGGGCCTTGGCTCAGTTTTGCATGATTTTTGGAAG
AAAGACTCCTCGAA
Found at i:3432 original size:286 final size:285
Alignment explanation
Indices: 2918--3494 Score: 960
Period size: 286 Copynumber: 2.0 Consensus size: 285
2908 TTCGGGTCAG
* * * *
2918 TTTTTTGCAAAATTTTAGCTGAAATAGTGTTCTAACCATCACGGTTTTTGGCTAAAAACGCGTTT
1 TTTTTTGAAAAATTTTAGCTGAAATAGTGTTCTAACCATCACAGTTTTTCGCAAAAAACGCGTTT
* * * * * *
2983 TGGGGCCTTGGTTCAGTTTTGCATGACTTTTGGCAGAAAGACGCCTCGAAATGTCTGTATTCATC
66 CGGGGCCCTGATTCAGTTTTGCATGACTTTTGGCAGAAAAAAGCCTCGAAATATCTGTATTCATC
*
3048 GAACCAAAATCTCAGCCACAATGGATTTACGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCG
131 GAACCAAAATCTCAGCCACAATGGATTTACGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCG
3113 ATTAAATTAGAAATAAATTCGGAAAATTTTGGAAAAACGATATTAGAAGCA-TGAAAAACCCTAT
196 ATTAAATTAGAAATAAATTCGGAAAATTTTGGAAAAACGATATTAGAAG-AGTGAAAAACCCTAT
* *
3177 AATACTTTTGGTGTTGAATTATATGA
260 AATACTTTTGGCGTTAAATTATATGA
*
3203 TTTTTTGAAAAATTTTAGCTGAAATAGTGTTCTAACCTTCACAGTTTTTCGCAAAAAACGCGTTT
1 TTTTTTGAAAAATTTTAGCTGAAATAGTGTTCTAACCATCACAGTTTTTCGCAAAAAACGCGTTT
3268 CGGGGCCCTGATTCAGTTTTGCATGACTTTTGGCAGAAAAAAAGCCTCGAAATATCTGTATTCAT
66 CGGGGCCCTGATTCAGTTTTGCATGACTTTTGGCAG-AAAAAAGCCTCGAAATATCTGTATTCAT
*
3333 CTAACCAAAATCTCAGCCACAATGGATTTACGGATTTGTTTTTACAAGCATCTGAATCTTGTTTC
130 CGAACCAAAATCTCAGCCACAATGGATTTACGGATTTGTTTTTACAAGCATCTGAATCTTGTTTC
* *
3398 GATTAAATTAGAAATAAATTTGGTAAAA-TTTGGAAAAACGATATTAGAAGAGTGAAAAACTCTA
195 GATTAAATTAGAAATAAATTCGG-AAAATTTTGGAAAAACGATATTAGAAGAGTGAAAAACCCTA
3462 TAATACTTTTGGCGTTAAATTATATGA
259 TAATACTTTTGGCGTTAAATTATATGA
3489 TTTTTT
1 TTTTTT
3495 TGAGTATTGT
Statistics
Matches: 272, Mismatches: 17, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
285 94 0.35
286 174 0.64
287 4 0.01
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (285 bp):
TTTTTTGAAAAATTTTAGCTGAAATAGTGTTCTAACCATCACAGTTTTTCGCAAAAAACGCGTTT
CGGGGCCCTGATTCAGTTTTGCATGACTTTTGGCAGAAAAAAGCCTCGAAATATCTGTATTCATC
GAACCAAAATCTCAGCCACAATGGATTTACGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCG
ATTAAATTAGAAATAAATTCGGAAAATTTTGGAAAAACGATATTAGAAGAGTGAAAAACCCTATA
ATACTTTTGGCGTTAAATTATATGA
Found at i:4227 original size:334 final size:334
Alignment explanation
Indices: 3203--4685 Score: 1531
Period size: 334 Copynumber: 4.4 Consensus size: 334
3193 AATTATATGA
* * * * * * *
3203 TTTTTTGAAAAATTTTAGCTGAAATAGTGTTCTAACCTTCACAGTTTTTCG-CAAAAAACGCGTT
1 TTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGATTTT-GACTAAAAACGCGTT
* * * * ** *
3267 TCGGGGCCCTGATTCAGTTTTGCATGACTTTTGGCAGAAAAAAAGCCTCGAAATATCTGTATTCA
65 TCGAGGCCCTGACTCAGTTTTGCATGATTTTTGGCAG-AAAGACTCCTCGAAATATCTATATTCA
* * *
3332 TCTAACCAAAATCTCAGCCACAATGGATTTACGGATTTGTTTTTACAAGCATCTGAATCTTGTTT
129 TCTAATC-AAATCTCAGCCACAATGGATTTACGGATTTATTTTTACGAGCATCTGAATCTTGTTT
** ** * * *
3397 CGATTAAATTAGAAATAAATT-TGGTAAAATTTGGAAAAACGATATTAGAAGAGTGAAAAACTCT
193 CGATTAAATTAGAAATAAATTCTGAAAAAAAATGGAAAAACGAAATTAGAAGCGTGAAAAACCCT
* * *
3461 ATAATACTTTTGGCGTTAAATTATATGATTTTTTTGAGTATTGTGGCAGAAAATTGGGGAAAAAC
258 ATAATACTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAATTGGGGAAAAAC
3526 TTTTCGGGTCAG
323 TTTTCGGGTCAG
* * ** *
3538 TTTTTTTGGAAAATTTTTGCAAAAATCGTGTACTAACCATCAC-GA-TTTGTAGCTAAAAATGCG
1 -TTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGATTTTG-A-CTAAAAACGCG
* * * * *
3601 TTTCGAGGTCCC--ACCTCAGTTTTGCATGA-TTTT-ACACAGAGTACTTGGCGTTGAATTATAT
63 TTTCGAGG-CCCTGA-CTCAGTTTTGCATGATTTTTGGCAGAAAG-AC-T--CCTCG-A--A-AT
* * *
3662 GATTTTTCTGAGTATTCATCTAACCAAAATCTCAGCCAGAATGGATTTACGGATTTGTTTTTACG
118 -A----TCT-A-TATTCATCTAATC-AAATCTCAGCCACAATGGATTTACGGATTTATTTTTACG
* * * * *
3727 AGCATCTGAATCTTGTTTCGATTAAATTAGAAACAAATTC-G-GAAAAATTGGGAGAAACGATAT
175 AGCATCTGAATCTTGTTTCGATTAAATTAGAAATAAATTCTGAAAAAAAAT-GGAAAAACGAAAT
* * * ** *
3790 TAGAAGCGTTAAAAACCCTATAATACTTTTGGCGTTGAATTACATGATTATAATTAGTATTGTGG
239 TAGAAGCGTGAAAAACCCTATAATACTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGG
* *
3855 CAAAAAATTAGGGAAAAACTTTTCGGGTCTG
304 CAAAAAATTGGGGAAAAACTTTTCGGGTCAG
3886 TTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGATTTTGACTAAAAACGCGTTT
1 TTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGATTTTGACTAAAAACGCGTTT
* * * * *
3951 CGGGGCTCTGGCTCAGTTTTGCATGATTTTTGGAAGAAAGACTCCTCGAAATATATATATTCATC
66 CGAGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTCGAAATATCTATATTCATC
* * * * * *
4016 TAATCAAATCTTAGCCACAATGGATTTAAGGGTTTATTTTTATGAGTATCTGAATCTTATTTCGA
131 TAATCAAATCTCAGCCACAATGGATTTACGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGA
* * * *
4081 TTTAATTAGAAATAAATTCAGAAAAAAAAT-GAAACAACGAAATGAGAAGCGTGAAAAACCCTTT
196 TTAAATTAGAAATAAATTCTGAAAAAAAATGGAAA-AACGAAATTAGAAGCGTGAAAAACCCTAT
* ** * * *
4145 ATTGTTTTTGGCGTTGAACTATATG-TTTTGTCTGAGTATTGTGGCAAAAAATTGTGGAAAACCT
260 AATACTTTTGGCGTTGAATTATATGATTTT-TCTGAGTATTGTGGCAAAAAATTGGGGAAAAACT
*
4209 TTTCGGGACAG
324 TTTCGGGTCAG
* *
4220 TTTTTTGCAAAATTTTAG-TCGAAATCGTGTACTAACCATCACGG--TTTGGCTAAAAATGCGTT
1 TTTTTTGCAAAATTTTAGCT-GAAATCGTGTACTAACCATCACGGATTTTGACTAAAAACGCGTT
* * *
4282 TCGTGGCCCTGACTCAGTTTTGCATGTTTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCAT
65 TCGAGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTCGAAATATCTATATTCAT
* * * *
4347 TTAATCAAATCTTTCAGCCACATTGGATTTACGGATTTATTTTTACGAGTATCTGATTCTTGTTT
130 CTAATCAAATC--TCAGCCACAATGGATTTACGGATTTATTTTTACGAGCATCTGAATCTTGTTT
* * ** * ** * *
4412 CGATTTAATTAGAATTGTATTGTGGCAAAAAATGGAAAAACGAAATTAGAAGCGTGAAAGACCAT
193 CGATTAAATTAGAAATAAATTCTGAAAAAAAATGGAAAAACGAAATTAGAAGCGTGAAAAACCCT
* * * * * * *
4477 AAAATATTTTTAGCATTGAATTATATGATTTTTCAGAGTATTGTGGCAAAAAATTGGGGAACATC
258 ATAATACTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAATTGGGGAAAAAC
*
4542 TTTTCGGGTTAG
323 TTTTCGGGTCAG
* * * * * * *
4554 CTTTTTGCAAAATTTTAACCGAAATAGTG----------CACGGTTTTTGGCTGAAAACGCGTTT
1 TTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGATTTTGACTAAAAACGCGTTT
* *
4609 CGAGGCCCTGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATC
66 CGAGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTCGAAATATCTATATTCATC
4674 TAATCAAATCTC
131 TAATCAAATCTC
4686 TC
Statistics
Matches: 971, Mismatches: 136, Indels: 92
0.81 0.11 0.08
Matches are distributed among these distances:
324 7 0.01
326 88 0.09
332 84 0.09
333 79 0.08
334 321 0.33
335 21 0.02
336 67 0.07
337 6 0.01
338 1 0.00
340 2 0.00
341 4 0.00
342 2 0.00
344 1 0.00
345 3 0.00
346 5 0.01
347 77 0.08
348 195 0.20
349 8 0.01
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.35
Consensus pattern (334 bp):
TTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGATTTTGACTAAAAACGCGTTT
CGAGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTCGAAATATCTATATTCATC
TAATCAAATCTCAGCCACAATGGATTTACGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGA
TTAAATTAGAAATAAATTCTGAAAAAAAATGGAAAAACGAAATTAGAAGCGTGAAAAACCCTATA
ATACTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAATTGGGGAAAAACTTT
TCGGGTCAG
Done.