Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015082.1 Corchorus olitorius cultivar O-4 contig15115, 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: 34359
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:742 original size:21 final size:19
Alignment explanation
Indices: 685--742 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
675 CTGTTTAGCA
685 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* * *
704 ACTGTACAGATTAAATTAGGT
1 ACTGTACAGATGAGATTA--C
725 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
743 TTAGAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:1520 original size:25 final size:25
Alignment explanation
Indices: 1491--1550 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 25
1481 TATAATTAAC
*
1491 ATAAAGATGTATTCACATTCATATT
1 ATAAAAATGTATTCACATTCATATT
*
1516 ATAAAAAAATGTATTCATATTCATATT
1 AT--AAAAATGTATTCACATTCATATT
1543 ATAAAAAT
1 ATAAAAAT
1551 ATATACGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 8 0.26
27 23 0.74
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.38
Consensus pattern (25 bp):
ATAAAAATGTATTCACATTCATATT
Found at i:1528 original size:27 final size:27
Alignment explanation
Indices: 1497--1549 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
1487 TAACATAAAG
1497 ATGTATTCACATTCATATTATAAAAAA
1 ATGTATTCACATTCATATTATAAAAAA
*
1524 ATGTATTCATATTCATATTATAAAAA
1 ATGTATTCACATTCATATTATAAAAA
1550 TATATACGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (27 bp):
ATGTATTCACATTCATATTATAAAAAA
Found at i:4417 original size:333 final size:332
Alignment explanation
Indices: 3132--4452 Score: 1248
Period size: 333 Copynumber: 4.0 Consensus size: 332
3122 GTAAAAACAA
* * * * * *
3132 TGGCTG-GCTTTGGTTAGATGAATATAGATATTTTAAGGAGTCTCGGCGCCAAAAATCATTCAAA
1 TGGCTGAGATTTGTTTAGATGAATATAGATATCTCAAGGAGTCTCGGAGCCAAAAATCATGCAAA
** * ** * * * *
3196 ACTGAACCGGGT-CCCGGAACGCGTTTTTAGTCAAAAATCGTGATGA---TTATTACATGATTTC
66 ACTGAGTCGAGTCCCCAAAACGCGTTTTTAG-CAAAAACCGTAATGATTGTTAGTACACGATTTC
* * * * * *
3257 GGCTAAAATTTTACAAAAATTGACCCGAAAAATAAT-TACTCAATTTTTAGCTATAATACTAATA
130 GGCAAAAATTTTACAAAAATTGACCCGAAAGAT-TTCTCCTCAATTTTTGGCTAAAATACTAAT-
* *
3321 AAAAATATATAATTCAACGCGAAAAAGATTGAAGGGCTTTTGACGCTTTTAATATCGTTTTTCAT
193 AAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTGACGCTTTTAATATCGTATTTC-T
* * * * *
3386 ATTTTTTCTTAATTAATTTCTAATTAAATCGAAACAAAATTCTGATACTCGTGAAAACAAATTCT
257 ATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCTCGTAAAAACAAATTCT
*
3451 TAAATGCAATG
322 TAAATCCAATG
* * * * *
3462 TGGCTAAAATTT-TATTAGATTAATATAGATATTTTCAAGGAGTCTC-GACGCCAAAAATCATGT
1 TGGCTGAGATTTGT-TTAGATGAATATAGATA-TCTCAAGGAGTCTCGGA-GCCAAAAATCATGC
* * * * * * *
3525 ACAACTGAG-CTGA-TGCTCAGAAATGCGTTTTTAGCTAAAAA---TAGTGATGGTGT-GTAAAC
63 AAAACTGAGTC-GAGTCCCCA-AAACGCGTTTTTAGC-AAAAACCGTAATGATTGT-TAGTACAC
* * * * * *
3584 GATTTTGGCTAAAATTTTGCAAAAAAATGACCCGAAA-ATTTTTCCTCAA-TTTTGAGATAAAAT
124 GATTTCGGCAAAAATTTTAC-AAAAATTGACCCGAAAGATTTCTCCTCAATTTTTG-GCTAAAAT
* * * * * * * *
3647 ACTCAT-AATATATATAATTTAACGGCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTT
187 ACTAATAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTGACGCTTTTAATATCGTA
* * * *
3711 TTTC-ATATTTTTCTGAATTAATTT-TGAATTAAATCGAAATAAGATTCAGATGCTTGTAAAAAC
252 TTTCTAT-TTTTTCTAAATTAATTTCT-AATTAAATCGAAACAATATTCAGATGCTCGTAAAAAC
*
3774 AAATTTTTAAATCCAATG
315 AAATTCTTAAATCCAATG
* * * *
3792 TGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCAT-TGCGCAAAAAATCATGCAA
1 TGGCTGAGATTTGTTTAGATGAATATAGATATCTCAAGGAGTC-TCGGAGCCAAAAATCATGCAA
* * ** * * * * * *
3856 AACTGAGTCGGGACCCCAAAAC-TTTCTTTTATCCAAAAACTGTGATG-GTGTTATTACACTATT
65 AACTGAGTCGAGTCCCCAAAACGCGT-TTTTA-GCAAAAACCGTAATGATTGTTAGTACACGATT
*
3919 TCGGCTAAAAA-TTTATAAAAATTGACCCGAAAGTTATTTCT--TCAATTTTTGGCTAAAATACT
128 TCGGC-AAAAATTTTACAAAAATTGACCCGAAAG--ATTTCTCCTCAATTTTTGGCTAAAATACT
* *
3981 AATAAAAA-ATATATATCTCCACGCCAAAAAGATTGAAGGGCTTTTGACG-TTTCTAATGTCG-A
190 AATAAAAATATATA-AT-TCAACGCCAAAAAGATTGAAGGGCTTTTGACGCTTT-TAATATCGTA
* * * * * *
4043 TTTTCCTATTTGTCCCAAATTAATTTCTAATTAAATCGAAACAATATTTAGTTTCTCGTAAAAAC
252 -TTT-CTATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCTCGTAAAAAC
*
4108 AAATCCTTAAATCCAATG
315 AAATTCTTAAATCCAATG
* * *
4126 TGGGTGAGATTTGTTTAGATGAATATAGATA-CTCAAGTAATCTCGGAGCCAAAAATCATGCAAA
1 TGGCTGAGATTTGTTTAGATGAATATAGATATCTCAAGGAGTCTCGGAGCCAAAAATCATGCAAA
* *
4190 ATTGAGTCGAGTCCCCATAACGCGTTTTTAGACAAAAACCGTAATGATTTGTTAGTACACGATTT
66 ACTGAGTCGAGTCCCCAAAACGCGTTTTTAG-CAAAAACCGTAATGA-TTGTTAGTACACGATTT
** *
4255 CGG-AAAAATTTTGA-AAAAATTGAAACGAAAGATTTCTCCTCAATTTTTGGCTAAAATACTCAT
129 CGGCAAAAATTTT-ACAAAAATTGACCCGAAAGATTTCTCCTCAATTTTTGGCTAAAATACTAAT
* * *
4318 AAAAATATATAATTCAACACCAAAAAGATTGGAGGGCTTTTTACGCTTTTAATATCGTATTTCTT
193 AAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTGACGCTTTTAATATCGTATTTC-T
* * * *
4383 TTTTTTTCTAAATTAATTTCTTATTAAATCGAAAC-TTGATTCAGATGCTTGTAAAAACAAATTC
257 ATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAT-ATTCAGATGCTCGTAAAAACAAATTC
4447 TTAAAT
321 TTAAAT
4453 GTTGCTGAGA
Statistics
Matches: 799, Mismatches: 137, Indels: 107
0.77 0.13 0.10
Matches are distributed among these distances:
328 1 0.00
329 48 0.06
330 121 0.15
331 114 0.14
332 70 0.09
333 260 0.33
334 159 0.20
335 26 0.03
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (332 bp):
TGGCTGAGATTTGTTTAGATGAATATAGATATCTCAAGGAGTCTCGGAGCCAAAAATCATGCAAA
ACTGAGTCGAGTCCCCAAAACGCGTTTTTAGCAAAAACCGTAATGATTGTTAGTACACGATTTCG
GCAAAAATTTTACAAAAATTGACCCGAAAGATTTCTCCTCAATTTTTGGCTAAAATACTAATAAA
AATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTGACGCTTTTAATATCGTATTTCTATTT
TTTCTAAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCTCGTAAAAACAAATTCTTAAA
TCCAATG
Found at i:4852 original size:15 final size:15
Alignment explanation
Indices: 4821--4881 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
4811 TTTCATAACA
*
4821 ATAATT-AATAATTTT
1 ATAATTAAAT-ATATT
4836 ATAATTAAATATATT
1 ATAATTAAATATATT
*
4851 ATAATATAAAAATATT
1 ATAAT-TAAATATATT
* *
4867 AGAAGTAAAT-TATT
1 ATAATTAAATATATT
4881 A
1 A
4882 ATTACAATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
14 5 0.13
15 19 0.49
16 15 0.38
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:4860 original size:16 final size:15
Alignment explanation
Indices: 4821--4867 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
4811 TTTCATAACA
* *
4821 ATAATTAATAATTTT
1 ATAATTAAAAATATT
*
4836 ATAATTAAATATATT
1 ATAATTAAAAATATT
4851 ATAATATAAAAATATT
1 ATAAT-TAAAAATATT
4867 A
1 A
4868 GAAGTAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 17 0.63
16 10 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAAAAATATT
Found at i:6563 original size:2 final size:2
Alignment explanation
Indices: 6553--6582 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6543 ATATTTAGCC
6553 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6583 ACATAATAAT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10524 original size:21 final size:21
Alignment explanation
Indices: 10489--10530 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
10479 GGTGTGTGTG
*
10489 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGATTGGTTT-GTAGA
10511 TGTGA-TGATTGGTTTGTAGA
1 TGTGATTGATTGGTTTGTAGA
10531 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
TGTGATTGATTGGTTTGTAGA
Found at i:15039 original size:20 final size:20
Alignment explanation
Indices: 15014--15051 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
15004 AATGTGCCTG
15014 AGATTTGGTTAGTTAAATAT
1 AGATTTGGTTAGTTAAATAT
15034 AGATTTGGTTAGTTAAAT
1 AGATTTGGTTAGTTAAAT
15052 CGTGATGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (20 bp):
AGATTTGGTTAGTTAAATAT
Found at i:15294 original size:274 final size:276
Alignment explanation
Indices: 14776--15308 Score: 634
Period size: 274 Copynumber: 1.9 Consensus size: 276
14766 AGCAAAAAAC
* *
14776 CGTGATGGTTAGTACATGATTTCAGTTAAAATTTTGCAAAAATTGACCCAAAAGATATTTCCATA
1 CGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCAAAAGATATTTCCATA
* * * * * * * * *
14841 ATTTTTGGTTAAAAATACTCATAAAAAATATGTAATTCGACATCAAAAAGATTGGAGGGCTTTTA
66 ATATCTAGTCAAAAATACTCATAAAAAATATATAATTCGACATCAAAAAAATTGAAAGCCTTTTA
* * * * * * * *
14906 ACGCTTCTAATATTGTTTTTCTTTTTTTTTTTTCCGAATTAATTTCTAATTAAATGGAAACAAGA
131 ACGCTTCTAATATGGTTTTTCTCTATTTTATTTCCAAATTAAATTCTAATTAAATCGAAACAACA
** * *
14971 TTCAGATGTTCGTAAAAACAAATCCTTAAATCTAATGTGCCTGAGATTTGGTTAGTTAAATATAG
196 TTCAGAACTTCGTAAAAACAAATCCTTAAATCTAATGTGCCTGAGATTTGATTAGATAAATATAG
15036 ATTTGGTTAGTTAAAT
261 ATTTGGTTAGTTAAAT
* * *
15052 CGTGATGGTT-GTACACGATTTTCTGCT-AAATTTTGCAAAAATTGACCCAAAAGATTTTTCCTT
1 CGTGATGGTTAGTACACGA-TTTCAGCTAAAATTTTGCAAAAATTGACCCAAAAGATATTTCCAT
* * *
15115 GATATCTAG-CGAAAATACTCATAAAAAATGTATAATTC-A-ATGCCAAAAAAATTGAAAGCCTT
65 AATATCTAGTCAAAAATACTCATAAAAAATATATAATTCGACAT--CAAAAAAATTGAAAGCC-T
* *
15177 TTTCACGCTTCTAATATGGTTTTTC-CTATTTTATTT-CAATATTAAATTCTGATTAAATCGAAA
127 TTTAACGCTTCTAATATGGTTTTTCTCTATTTTATTTCCAA-ATTAAATTCTAATTAAATCGAAA
* * *
15240 CAACATTTAGAAACTT-GTAAAAACAAATCCTTAAATAC-AATGTGGCTGAGATTTGATTAGATG
191 CAACATTCAG-AACTTCGTAAAAACAAATCCTTAAAT-CTAATGTGCCTGAGATTTGATTAGATA
15303 AATATA
254 AATATA
15309 TAAATATTTT
Statistics
Matches: 216, Mismatches: 34, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
272 2 0.01
273 3 0.01
274 121 0.56
275 74 0.34
276 16 0.07
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (276 bp):
CGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCAAAAGATATTTCCATA
ATATCTAGTCAAAAATACTCATAAAAAATATATAATTCGACATCAAAAAAATTGAAAGCCTTTTA
ACGCTTCTAATATGGTTTTTCTCTATTTTATTTCCAAATTAAATTCTAATTAAATCGAAACAACA
TTCAGAACTTCGTAAAAACAAATCCTTAAATCTAATGTGCCTGAGATTTGATTAGATAAATATAG
ATTTGGTTAGTTAAAT
Found at i:16198 original size:329 final size:320
Alignment explanation
Indices: 15066--16553 Score: 1036
Period size: 328 Copynumber: 4.5 Consensus size: 320
15056 ATGGTTGTAC
* * * * ** * * * *
15066 ACGATTTTCTGCT-AAATTTTGCAA-AAATTGACCCAAAAGATTTTTCCTTGATATCTAGCGAAA
1 ACGA-TTTCGGCTAAAATTTTGCAAGAAA-TGAGCCAAAATATATTTCCTCAATTTTTAGCCACA
* * * * * *
15129 ATACTCATAAAAAATGTATAATTCAATGCCAAAAAAATTGAAAGCCTTTTTCACGCTTCTAATAT
64 ATACTCATAAAAAATATATAATTCAA-ACCAAAAAGATTGGAGGGC-TTTTCACGCTTCTAATAT
** * * * ** * ** *
15194 GGTTTTTCCTATTTTATTTCAATATTAAATTCTGATTAAATCGAAACAACATTTAGAAACTTGTA
127 CATTTTT-C-ATATT-TTTCAA-ATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTA
* * * * * *
15259 AAAACAAATCCTTAAATACAATGTGGCTGAGATTTGATTAGATGAATATATAAATATTTTAAGGA
188 AAAACAAATCCTTAAATCCAATGTGGATGAAATTTGATTAGAT-AA-ATATAGATGTTTCAAGGA
* * * * * *
15324 GTCTCG-CTGCCAAAAATCATGCAAAACTGACATAGGACCTCGAAATGCGTTTTTAGCAAAAAAA
251 GTCTTGAC-GCAAAAAATCATGC-AAACTAAC-CAGGGCC-CGAAACGCGTTTTTA-C-------
** * *
15388 ACAAAACCATGTTGGTAC
304 -CAAAACTGTGATGGTAA
* * * * * * *
15406 ACGGTTTCGGCTGAAATTTTACAA-AAATTGACCCAAAATATTTTTTTCTCAATTTATAGCCACA
1 ACGATTTCGGCTAAAATTTTGCAAGAAA-TGAGCCAAAATA-TATTTCCTCAATTTTTAGCCACA
* * * * *
15470 ATACTTATAAAAAATATATATTTCAAAGCCAAAAAGATTGAAGGGCTTATCACGCTTGTAATATC
64 ATACTCATAAAAAATATATAATTCAAA-CCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATC
* * * * *
15535 GTTTTTCTTAATTTTTCAATTTAATTTCTAATTAAATTGAAACATGATTCAAATGCTCGTAAAAA
128 ATTTTTCAT-ATTTTTCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAA
* * * * *
15600 CAAACCCTTAAACCCAATGTGGCT-AAGATTTGATTAGATAAATATAGATGCTTCAAGGAGTGTT
192 CAAATCCTTAAATCCAATGTGGATGAA-ATTTGATTAGATAAATATAGATGTTTCAAGGAGTCTT
* * * * *
15664 GCCACCAAAAATCATGCAAAACTAACCCGAGGCCCCAGAACGCGTTTTTACCTAAAAAACTGTGA
256 GACGCAAAAAATCATGC-AAACTAACCAG-GGCCCGA-AACGCGTTTTTACC---AAAACTGTGA
15729 TGGTAA
315 TGGTAA
* * * * * * *
15735 ATGATTTTGGCTAAAATTTTGTAAGAACTGAGCCAAAATATTTTTCCTTAATTTTAAGCCACAAT
1 ACGATTTCGGCTAAAATTTTGCAAGAAATGAGCCAAAATATATTTCCTCAATTTTTAGCCACAAT
* * * * *
15800 ACTCATAAAATATATATAATT-AAAGGCCAAAAAGATTGGAGGACTCTTCACGCTTTTAATATTA
66 ACTCATAAAAAATATATAATTCAAA--CCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCA
* * * *
15864 TTTTTCATATTTTTCTAAATGAATTTCTAATTAAATCGAAAAAAGATTCAGATGCTCGTAAAAAT
129 TTTTTCATATTTTTC-AAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAAC
* * * *
15929 AAATCCTTAAATTCAATGT-GTTGAAATTTGATTAGATGAATATAGATGTTTCAAGGAGTCTTGG
193 AAATCCTTAAATCCAATGTGGATGAAATTTGATTAGATAAATATAGATGTTTCAAGGAGTCTTGA
15993 CGCAAAAAAT-ATGCAAAGCTAAGCCAGGGTCCCGAAACGCGTTTTTAGCCAAAACTTGTGATGA
258 CGCAAAAAATCATGCAAA-CTAA-CCAGGG-CCCGAAACGCGTTTTTA-CCAAAAC-TGTGATG-
*
16057 TTATTA
317 GTA--A
* * *
16063 CACGATTTCGGCTAGAATTTTGCAA-AAATG-GACTTGAAAGT-TATTTCCTCAATTTTTAGCCA
1 -ACGATTTCGGCTAAAATTTTGCAAGAAATGAG-C--CAAAATATATTTCCTCAATTTTTAGCCA
* **
16125 CAATACTCATAAAAAATATATAATTCAACACCGAAAAGATTGGAGGGCTTTTCATTCTTCTAATA
62 CAATACTCATAAAAAATATATAATTCAA-ACCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATA
* * * *
16190 TCATTTTTCCTATTATTTTCCGAATTAATTTTTAATTAAATCGAAACATGATTTAGATGCT--TA
126 TCATTTTT-C-A-TATTTTTCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTA
*** * * * *
16253 TTTTACAAATCCTTAAATCCAATGTGGATGAGATTTGGTTAGATTAATATAGATATTTCAAGGAG
188 -AAAACAAATCCTTAAATCCAATGTGGATGAAATTTGATTAGATAAATATAGATGTTTCAAGGAG
* * *
16318 TCTCGACGCAAAAAATCATGCAACACTGAACTAGGGCCTCGAAACGTGTTTTTATCCAAAAACCA
252 TCTTGACGCAAAAAATCATGCAA-ACT-AACCAGGGCC-CGAAACGCGTTTTTA-CC-AAAA-C-
* *
16383 TGATTCGACTAACGTAC
310 TG--T-GA-T--GGTAA
* * * * * * *
16400 ACGATTTCGGTTAATATTTTACAA-AAATTTA-CGAGAAATAGT-TTTCCTCAAGTTTT-GTCTA
1 ACGATTTCGGCTAAAATTTTGCAAGAAA-TGAGCCA-AAATA-TATTTCCTCAATTTTTAG-CCA
* * * *
16461 AAATTCTCAT--AAAATATATAATTC-AACTTCAAAAATATTGGAGGACTTTTCACGCTTCTAAT
62 CAATACTCATAAAAAATATATAATTCAAAC--CAAAAAGATTGGAGGGCTTTTCACGCTTCTAAT
* *
16523 ATCGTTTTTCATATTTTTTAGAATTAATTTC
125 ATCATTTTTCATATTTTTCA-AATTAATTTC
16554 GCTTTAATAT
Statistics
Matches: 931, Mismatches: 162, Indels: 118
0.77 0.13 0.10
Matches are distributed among these distances:
324 5 0.01
325 10 0.01
326 25 0.03
327 65 0.07
328 144 0.15
329 141 0.15
330 28 0.03
331 92 0.10
332 48 0.05
333 9 0.01
334 59 0.06
335 57 0.06
336 52 0.06
337 72 0.08
338 8 0.01
339 12 0.01
340 50 0.05
341 54 0.06
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (320 bp):
ACGATTTCGGCTAAAATTTTGCAAGAAATGAGCCAAAATATATTTCCTCAATTTTTAGCCACAAT
ACTCATAAAAAATATATAATTCAAACCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATCATT
TTTCATATTTTTCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAA
TCCTTAAATCCAATGTGGATGAAATTTGATTAGATAAATATAGATGTTTCAAGGAGTCTTGACGC
AAAAAATCATGCAAACTAACCAGGGCCCGAAACGCGTTTTTACCAAAACTGTGATGGTAA
Found at i:16588 original size:38 final size:40
Alignment explanation
Indices: 16513--16590 Score: 133
Period size: 39 Copynumber: 2.0 Consensus size: 40
16503 GGACTTTTCA
*
16513 CGCTTCTAATATCGTTTTTCATATTTTTTAGAATTAATTT
1 CGCTTCTAATATAGTTTTTCATATTTTTTAGAATTAATTT
16553 CGCTT-TAATATAGTTTTTCATATTTTTT-GAATTAATTT
1 CGCTTCTAATATAGTTTTTCATATTTTTTAGAATTAATTT
16591 TTTAATTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
38 10 0.27
39 22 0.59
40 5 0.14
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.56
Consensus pattern (40 bp):
CGCTTCTAATATAGTTTTTCATATTTTTTAGAATTAATTT
Found at i:17368 original size:327 final size:323
Alignment explanation
Indices: 16556--17598 Score: 978
Period size: 327 Copynumber: 3.2 Consensus size: 323
16546 TTAATTTCGC
* * * * *
16556 TTTAATATAGTTTTTCATATTTTT-TGAATTAATTTTTTAATTAAATCGAAATAATATTCAAATG
1 TTTAATATCGTTTTTCATATTTTTCTGAATTAA-TTTCTAATTAAATCGAAAAAAGATTCAGATG
* *
16620 CTT-GTAAAAATAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATATATACATT
65 -TTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGAT--ATT
* ** *
16684 TCAAAGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGGAGCCCCGAAACGCGTTTTTCG-C
127 TC-AAGAGTCTTGACGCCAAAAATCATGCAAAACTGACCCGGA-CCCCGAAAC-ATTTTTTAGCC
** *
16748 AAAAACCCGTGATGGGTTAGTACACGATTTCAACTAAAATTTTGC-AAAATATGACCACAAA-AA
189 AAAAA-CCGTGAT-GG-T--TACACGATTTCGGCTAAAATTTTGCAAAAAT-TGACCAGAAAGAA
* * * * *
16811 ATTTTCCTCAA-TTTTTGACTAAAATACTCATGAAATATATTTAATTTAAGGCCAAAAAGATTGG
248 A-TTTCCTCAATTTTTTG-CTAAAATACTCATAAAAAATATATAATTTAACGCC-AAAATATT-G
*
16875 T-GGACTTTT-CATGCT
309 TAGGATTTTTACA--CT
* * * * * * * *
16890 TTTCATATCCTTTTTCATATTATTCTTAATTAGTTACTAATTAAATCGAAACAAGATTCAGATGC
1 TTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAAAAAGATTCAGATGT
* * *
16955 TCGTAAAAACAAATCCCTAAATGCAATGTGGCTGAGACTTGATTAGATGAATA-AGGATATCTCA
66 TCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATA-GATATTTCA
* **
17019 AGTAGT-TTTAGCGCCAAAAATCATGCAAAACTGACCCAGGACCCTAAAACAAATTTTTTAGCCA
130 AG-AGTCTTGA-CGCCAAAAATCATGCAAAACTGACCC-GGACCCCGAAAC--ATTTTTTAGCCA
* * * ** *
17083 AAAACCGTGATGGTTACACGATTTCGGTTAAAATTTTACAAAAATTTACTGGAAAGATATTTCCT
190 AAAACCGTGATGGTTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAAGAAATTTCCT
* * *
17148 CAATTTTTTGCTAAAATACTAATAAAAAAAATATAATTCAACGCCAAAATATTGTAGG-TTTTTA
255 CAATTTTTTGCTAAAATACTCATAAAAAATATATAATTTAACGCCAAAATATTGTAGGATTTTTA
17212 CACT
320 CACT
** * * * *
17216 CCTAATATCGTTTTTCCTAATTTTTCCGAATTAATTTCTAATTAAATAGAAAAAAGATTTAGATG
1 TTTAATATCGTTTTTCAT-ATTTTTCTGAATTAATTTCTAATTAAATCGAAAAAAGATTCAGATG
* * *
17281 TTCGTAAAAACAAATCCTTAAATCCAATGTTGCTGAGATTTGGTTAGATGAATATAGATATTTCA
65 TTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCA
* * * * * * * *
17346 AGCAGTCTCGACGCCCAAAATCATTCAAAACTG-CATCGGGCCCCGGAACGTGTTTTTAGCTAAA
130 AG-AGTCTTGACGCCAAAAATCATGCAAAACTGAC-CCGGACCCCGAAACAT-TTTTTAGCCAAA
* * * * * *
17410 AATCGTGATGATAATTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAGACATTTGC
192 AACCGTGATG---GTTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAAGAAATTTCC
* * * ** * * *
17475 TCAATTTTTAGCCATAATACTCATAAAAAATATATAATTTGTCGCTAAAAATATTGAAGGGCTTT
254 TCAATTTTTTGCTAAAATACTCATAAAAAATATATAATTTAACGC-CAAAATATTGTA-GG-ATT
*
17540 TTTACGCT
316 TTTACACT
*
17548 TTTAATATTGTTTTTCATATTTTTTCTGAATTAATATT-TAATTAAATCGAA
1 TTTAATATCGTTTTTCATA-TTTTTCTGAATTAAT-TTCTAATTAAATCGAA
17599 TTGAATATAG
Statistics
Matches: 580, Mismatches: 102, Indels: 56
0.79 0.14 0.08
Matches are distributed among these distances:
324 1 0.00
325 20 0.03
326 24 0.04
327 126 0.22
328 94 0.16
329 74 0.13
330 15 0.03
331 8 0.01
332 90 0.16
333 20 0.03
334 102 0.18
335 6 0.01
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (323 bp):
TTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAAAAAGATTCAGATGT
TCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAA
GAGTCTTGACGCCAAAAATCATGCAAAACTGACCCGGACCCCGAAACATTTTTTAGCCAAAAACC
GTGATGGTTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAAGAAATTTCCTCAATTT
TTTGCTAAAATACTCATAAAAAATATATAATTTAACGCCAAAATATTGTAGGATTTTTACACT
Found at i:18555 original size:335 final size:326
Alignment explanation
Indices: 17670--18584 Score: 850
Period size: 335 Copynumber: 2.8 Consensus size: 326
17660 TCGAAACACG
* * * * ** * *
17670 TTTTTAGCCAAAAACCGTG-ATGGTTAGTACACGATTTTGGCTTCAATTTTG-AAGAAAATGACC
1 TTTTTAGCCAAAAACTG-GAATGGTTATTACACGATTTCGTCTAAAATTTTGCAA-AAACTGAGC
* * * *
17733 CGAAA-ATTTTTTCCTTAATTTTTGGATAAAATACTCATAAAATATATATAATTTAATGGCAAAA
64 CGAAAGA-TTTTTCCTCAATTTTTGGCTAAAATACTCATAAAA-ATATATAA-TTAACGCCAAAA
* * * * *
17797 AGATTAGA-GG--TTTCACATTTTTAATATCGTTTT-TCATATTTTTCTAAATTAATTTCTAATT
126 AGATTGGAGGGCTTTTCACACTTATAATATCGTTTTCTTAT-TTTTTCTAAATTAATTTATAATT
* * * * *
17858 AAATCTAAACAAGATTCAGATTCTTGTAAAAA-AAATTC-TGAACTCAAATATGGCTGAGATTTG
190 AAATCGAAACAAGATTCAGATACTT-TAAAAACAAATTCTTAAATTC-AATTTGG-TGAGATTTG
* * * *
17921 ATTAGATTAATATAGATATCTCAAGGAGTCTCGGCGCCAAAAATCATGAAAAACTGAGCTGGGGC
252 ATTAGATGAATATAGATATCTCAAGGACTCTCGGAGCCAAAAATCATGAAAAACTAAGCTGGGGC
17986 CCCAGAACGC
317 CCCAGAACGC
** * ** *
17996 TTTTTTTCCAAAAACTGTAATGGTTATTACACGATTTCGTCTAAAATTTTGTTAAAATTGAGCCG
1 TTTTTAGCCAAAAACTGGAATGGTTATTACACGATTTCGTCTAAAATTTTGCAAAAACTGAGCCG
* * * *
18061 AAAGATATTTCCTCAATTTTTGACTAAAAATACTCATAAAAAATATATAACTTAACGTCATAAAG
66 AAAGATTTTTCCTCAATTTTTGGCT-AAAATACTCAT-AAAAATATATAA-TTAACGCCAAAAAG
* ** * ** * *
18126 ATTGAAGCACTTTTGA-TGTTCTAATATCGTTTTCCTT-TTTTTTCCAAATTAATTTATAATTAA
128 ATTGGAGGGCTTTTCACACTTATAATATCGTTTT-CTTATTTTTTCTAAATTAATTTATAATTAA
* * * *
18189 ATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTTGGTGAGATTTGATT
192 ATCGAAACAAGATTCAGATACT-TTAAAAACAAATTCTTAAATTCAAT-TTGGTGAGATTTGATT
* * * * ** * * * * *
18254 AGATGAATATAGATATTTCAAGTACTCTTGTAGTGAAAAATCATGCAAAATTCAATC-GGGTCCT
255 AGATGAATATAGATATCTCAAGGACTCTCGGAGCCAAAAATCATGAAAAACT-AAGCTGGGGCCC
**
18318 TGGAACGC
319 CAGAACGC
* *
18326 ATTTTTAGCCAAAAATTGCGATTGTTTGTTATTACACGATTTCGGT-TAAAATTTTGCAAAAACT
1 -TTTTTAGCCAAAAACTG-GAATG---GTTATTACACGATTTC-GTCTAAAATTTTGCAAAAACT
*
18390 GA-CATGAAAGATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAATATATAATTCAACGCCA
60 GAGC-CGAAAGATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAATATATAATT-AACGCCA
* * *
18454 AAAAGATTGGAGGGCTTTTTACACTTATAATATCGTACTTCTTATTTTTTCTAAATTAATTTTTA
123 AAAAGATTGGAGGGCTTTTCACACTTATAATATCGT-TTTCTTATTTTTTCTAAATTAATTTATA
* * * *
18519 ATTAAATCGAAACAAGATTCAGATACTTTAAAAAACAATTTTTTAAATCCAATTTTGCTGAGATT
187 ATTAAATCGAAACAAGATTCAGATACTTT-AAAAACAAATTCTTAAATTCAA-TTTGGTGAGATT
18584 T
250 T
18585 ATCATTTGGT
Statistics
Matches: 474, Mismatches: 87, Indels: 47
0.78 0.14 0.08
Matches are distributed among these distances:
326 69 0.15
327 36 0.08
328 4 0.01
329 62 0.13
330 77 0.16
331 25 0.05
332 5 0.01
333 34 0.07
334 27 0.06
335 132 0.28
336 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (326 bp):
TTTTTAGCCAAAAACTGGAATGGTTATTACACGATTTCGTCTAAAATTTTGCAAAAACTGAGCCG
AAAGATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAATATATAATTAACGCCAAAAAGATT
GGAGGGCTTTTCACACTTATAATATCGTTTTCTTATTTTTTCTAAATTAATTTATAATTAAATCG
AAACAAGATTCAGATACTTTAAAAACAAATTCTTAAATTCAATTTGGTGAGATTTGATTAGATGA
ATATAGATATCTCAAGGACTCTCGGAGCCAAAAATCATGAAAAACTAAGCTGGGGCCCCAGAACG
C
Found at i:18968 original size:15 final size:15
Alignment explanation
Indices: 18948--18980 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
18938 ATTTTATGAA
18948 TATAATT-AATAATAT
1 TATAATTAAAT-ATAT
18963 TATAATTAAATATAT
1 TATAATTAAATATAT
18978 TAT
1 TAT
18981 TATTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATAATTAAATATAT
Found at i:18983 original size:18 final size:18
Alignment explanation
Indices: 18925--19023 Score: 57
Period size: 18 Copynumber: 5.6 Consensus size: 18
18915 TCTTTACATA
18925 ATTATAATTAAA-A-ATT
1 ATTATAATTAAATATATT
* *
18941 -TTATGAATATAATTAATAAT
1 ATTAT-AAT-TAAAT-ATATT
18961 ATTATAATTAAATATATT
1 ATTATAATTAAATATATT
*
18979 ATTAT--TTAAAAATAATT
1 ATTATAATTAAATAT-ATT
* *
18996 ATTAGAAGTAAAT-TATT
1 ATTATAATTAAATATATT
*
19013 AATTACAATTA
1 -ATTATAATTA
19024 TAATGGATTA
Statistics
Matches: 63, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
15 4 0.06
16 10 0.16
17 13 0.21
18 18 0.29
19 9 0.14
20 5 0.08
21 4 0.06
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (18 bp):
ATTATAATTAAATATATT
Found at i:24737 original size:4 final size:4
Alignment explanation
Indices: 24728--24757 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
24718 CTAGATAGTG
*
24728 ATTT ATTT ATTT ATTT ATTT ATTT TTTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
24758 GGAAATAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
ATTT
Found at i:25534 original size:29 final size:29
Alignment explanation
Indices: 25491--25548 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
25481 TATTTAATAC
**
25491 TACTACTATGTGAAATTATTGGGGAAAAA
1 TACTACTATACGAAATTATTGGGGAAAAA
25520 TACTACTATACGAAATTATTGGGGAAAAA
1 TACTACTATACGAAATTATTGGGGAAAAA
25549 ACCGAATTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.29
Consensus pattern (29 bp):
TACTACTATACGAAATTATTGGGGAAAAA
Found at i:30210 original size:439 final size:438
Alignment explanation
Indices: 29281--30253 Score: 1310
Period size: 439 Copynumber: 2.2 Consensus size: 438
29271 AATAGAACAT
* * * * * *
29281 AAAAACAAAAGTC-AAAGCGTTAAATCGTCCAACCTATAATTGTAAATGATTCAATAGCATGAAA
1 AAAAATAAAAGCCGAAA-CGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAA
* * ** * *
29345 CATAAAAGTATGAGGGTCATTAAATAAATAATTCAGAAAAAAAGTATTAGTTTATGAAGACAAAA
65 CATAAAAGTATAAGGATCATTTGATGAATAATCCAGAAAAAAAGTATTAGTTTATGAAGACAAAA
* * ** * *
29410 CTTAAAAATTTCCTCTTGAATCCTCCACGAAACTCATTAATCAAATTCAACCTTCATGCCCTTAA
130 CATAAAAATTCCCTCTCAAACCCTCCACGAAACTCATTAATCAAATTCAACCTTCAGGCCCTTAA
* * *
29475 TGAAAGTCGTAGATCACACAATAACCTTCTAACCGACACTTGAACAACTTCAATCGGACAAGTGG
195 CGAAAGTCATAGATCACACAATAACCTTCTAACCGACACTTGAACAACCTCAATCGGACAAGTGG
* *
29540 ACCGAAAATTATACGATATTAAATAGACCGGCAATCGAAACCACAAAATTTAAGAAACAATTTTT
260 ACCGAAAATTATACAATATTAAATAGACCGACAATCGAAACCACAAAATTTAAGAAACAATTTTT
* ** *
29605 AGAATCAAAACATTAAAATTGACTTCTGAGTTTTTCATGAAAGTTGTAGATCATGAGATTACCTT
325 AGAATCAAAACATGAAAATTGACTTCTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTT
** * *
29670 TTAATAGACTTTTGAATCACCTTGATCGGACAAATAGAACTAAAAATAC
390 TTAATAGACACTTGAATCACCTTGATCGAACAAATAAAACTAAAAATAC
*
29719 AAAAATAAAAGCCGATACGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAAC
1 AAAAATAAAAGCCGAAACGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAAC
* * *
29784 ATAAAAGTATAAGGATCATTTGATGAATAATCCAGCAAAAAATA-TATTTGTTTATGGAGACCAA
66 ATAAAAGTATAAGGATCATTTGATGAATAATCCAG-AAAAAA-AGTATTAGTTTATGAAGACAAA
* * * *
29848 ACATAAAAATTCCCTCTCAAACCCTCCACGAAACTCATTAATCAAATTCAGCTTTCAGGTCCTTG
129 ACATAAAAATTCCCTCTCAAACCCTCCACGAAACTCATTAATCAAATTCAACCTTCAGGCCCTTA
* * * *
29913 ACGAAAGTCATTGATCACATAATAACCTTTTAACTGACACTTGAACAACCTCAATCGGACAAGTG
194 ACGAAAGTCATAGATCACACAATAACCTTCTAACCGACACTTGAACAACCTCAATCGGACAAGTG
* * * * *
29978 GATCGAAAATTATACAATATTAGATAGACCGACAATCGAGACCACAAAATTTAAGAAGCATTTTT
259 GACCGAAAATTATACAATATTAAATAGACCGACAATCGAAACCACAAAATTTAAGAAACAATTTT
* *
30043 TAGAATCGAAACATGAAAATTG-GTT-TGCAGTCCTTCATGAAAGTTGTAGATCATGAAATTACC
324 TAGAATCAAAACATGAAAATTGACTTCTG-AGTCCTTCATGAAAGTTGTAGATCATGAAATTACC
*
30106 TTTTAATAGACACTTGAATCACCTTGATCGAACAAGTAAAAC-AAAAAGTA-
388 TTTTAATAGACACTTGAATCACCTTGATCGAACAAATAAAACTAAAAA-TAC
* * * * *
30156 AAAGAATTAAAGCCGAAACGTTCAATCGTCCAACCCATAATTTGTGAGGGATTAAATAGTATAAA
1 AAA-AATAAAAGCCGAAACGTTAAATCGTCCAACCCATAA-TTGTAAAGGATTAAATAGCATAAA
* * *
30221 GCATAAAAGTATAGGGCTCATTTGATGAATAAT
64 ACATAAAAGTATAAGGATCATTTGATGAATAAT
30254 GCAATAAAAA
Statistics
Matches: 468, Mismatches: 60, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
437 10 0.02
438 190 0.41
439 267 0.57
440 1 0.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (438 bp):
AAAAATAAAAGCCGAAACGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAAC
ATAAAAGTATAAGGATCATTTGATGAATAATCCAGAAAAAAAGTATTAGTTTATGAAGACAAAAC
ATAAAAATTCCCTCTCAAACCCTCCACGAAACTCATTAATCAAATTCAACCTTCAGGCCCTTAAC
GAAAGTCATAGATCACACAATAACCTTCTAACCGACACTTGAACAACCTCAATCGGACAAGTGGA
CCGAAAATTATACAATATTAAATAGACCGACAATCGAAACCACAAAATTTAAGAAACAATTTTTA
GAATCAAAACATGAAAATTGACTTCTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTT
TAATAGACACTTGAATCACCTTGATCGAACAAATAAAACTAAAAATAC
Found at i:32010 original size:28 final size:28
Alignment explanation
Indices: 31960--32018 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
31950 CGAACCCGCT
31960 CGAAGCCGAACCCGAGACAGCCCGAGCC
1 CGAAGCCGAACCCGAGACAGCCCGAGCC
*
31988 CGAA-CCG-ACCCGAGACGGAGCCCGATCC
1 CGAAGCCGAACCCGAGAC--AGCCCGAGCC
32016 CGA
1 CGA
32019 CCCAAGCCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 9 0.32
27 3 0.11
28 16 0.57
ACGTcount: A:0.27, C:0.42, G:0.29, T:0.02
Consensus pattern (28 bp):
CGAAGCCGAACCCGAGACAGCCCGAGCC
Found at i:33315 original size:30 final size:30
Alignment explanation
Indices: 33281--33509 Score: 368
Period size: 30 Copynumber: 7.6 Consensus size: 30
33271 TACATACAAA
* *
33281 TGACACCAGAAGTTGTCATGGTCTTACAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* * *
33311 TGACACCAGAAGTTGTCATGGTCTTACAAA
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
33341 TGACACCAGAAGTTGTCATAATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
33371 TGACACCAGAAGTTGTCATGCTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
33401 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
33431 TGACACCAGAAGTTGTCATGATGTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
33461 TGACACCAGAAGTTGTCATGATGTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
33491 TGACACCAGAAGTTGTCAT
1 TGACACCAGAAGTTGTCAT
33510 ATTATATTAT
Statistics
Matches: 189, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 189 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATCTTGCAAT
Found at i:33533 original size:34 final size:31
Alignment explanation
Indices: 33490--33667 Score: 201
Period size: 34 Copynumber: 5.6 Consensus size: 31
33480 GATGTTGCAA
33490 TTGACACCAGAAGTTGTCATATTATATTATTATC
1 TTGACACCAGAAGTTGTCATA--A-ATTATTATC
33524 TTGACACCAGAAGTTGTCATGAAA--ATTA--
1 TTGACACCAGAAGTTGTCAT-AAATTATTATC
33552 TTGACACCAGAAGTTGTCATAGCAAATTATTATC
1 TTGACACCAGAAGTTGTCAT---AAATTATTATC
33586 TTGACACCAGAAGTTGTCATGAAA--ATTA--
1 TTGACACCAGAAGTTGTCAT-AAATTATTATC
33614 TTGACACCAGAAGTTGTCATAGCAAATTATTATC
1 TTGACACCAGAAGTTGTCAT---AAATTATTATC
33648 TTGACACCAGAAGTTGTCAT
1 TTGACACCAGAAGTTGTCAT
33668 GCTGAGGAAA
Statistics
Matches: 128, Mismatches: 3, Indels: 26
0.82 0.02 0.17
Matches are distributed among these distances:
28 40 0.31
30 14 0.11
32 12 0.09
33 1 0.01
34 60 0.47
35 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (31 bp):
TTGACACCAGAAGTTGTCATAAATTATTATC
Found at i:33572 original size:62 final size:62
Alignment explanation
Indices: 33460--33699 Score: 347
Period size: 62 Copynumber: 3.8 Consensus size: 62
33450 GATGTTGCAA
** ** *
33460 TTGACACCAGAAGTTGTCATG-ATGTTGCAATTGACACCAGAAGTTGTCATATTATATTATTATC
1 TTGACACCAGAAGTTGTCATGAAAATT---ATTGACACCAGAAGTTGTCATAGCAAATTATTATC
33524 TTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATAGCAAATTATTATC
1 TTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATAGCAAATTATTATC
33586 TTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATAGCAAATTATTATC
1 TTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATAGCAAATTATTATC
*
33648 TTGACACCAGAAGTTGTCATGCTGAGGAAATTATTGACACTAGAAGTTGTCA
1 TTGACACCAGAAGTTGTCA---TGA--AAATTATTGACACCAGAAGTTGTCA
33700 CCCTAAGATT
Statistics
Matches: 164, Mismatches: 6, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
62 113 0.69
64 21 0.13
65 6 0.04
67 24 0.15
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (62 bp):
TTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATAGCAAATTATTATC
Done.