Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008329.1 Hibiscus syriacus cultivar Beakdansim tig00111037_pilon, 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: 291406
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:245205 original size:23 final size:21
Alignment explanation
Indices: 245158--245207 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
245148 TTAGTATTCG
* *
245158 TTAAAAAATTAACGTTAAGTT
1 TTAAAAAATTAAAGTTAAGTA
*
245179 TTAAAAAATTAAAAGTTTAGATA
1 TTAAAAAATT-AAAGTTAAG-TA
245202 TTAAAA
1 TTAAAA
245208 TGAATCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.42
22 7 0.29
23 7 0.29
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36
Consensus pattern (21 bp):
TTAAAAAATTAAAGTTAAGTA
Found at i:248167 original size:51 final size:51
Alignment explanation
Indices: 248111--248223 Score: 217
Period size: 51 Copynumber: 2.2 Consensus size: 51
248101 GAAAATGCGC
*
248111 TATTATAAGAAGGGAAACTAAGATTACGAGAAGGTTGGGAAAAAACAGGTT
1 TATTATTAGAAGGGAAACTAAGATTACGAGAAGGTTGGGAAAAAACAGGTT
248162 TATTATTAGAAGGGAAACTAAGATTACGAGAAGGTTGGGAAAAAACAGGTT
1 TATTATTAGAAGGGAAACTAAGATTACGAGAAGGTTGGGAAAAAACAGGTT
248213 TATTATTAGAA
1 TATTATTAGAA
248224 ACACGTGTTT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.44, C:0.05, G:0.26, T:0.25
Consensus pattern (51 bp):
TATTATTAGAAGGGAAACTAAGATTACGAGAAGGTTGGGAAAAAACAGGTT
Found at i:249740 original size:20 final size:19
Alignment explanation
Indices: 249692--249742 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
249682 AAATAACCAA
* *
249692 CAAAATCGCAACGCGATCT
1 CAAATTCGCAACGCGAACT
249711 CAAATTCGCAACGCGAACT
1 CAAATTCGCAACGCGAACT
*
249730 CCAATTTCGCAAC
1 -CAAATTCGCAAC
249743 ACAGTTTCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.35, C:0.33, G:0.14, T:0.18
Consensus pattern (19 bp):
CAAATTCGCAACGCGAACT
Found at i:249777 original size:20 final size:20
Alignment explanation
Indices: 249692--249784 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
249682 AAATAACCAA
* *
249692 CAAAATCGCAACGCGATCT-
1 CAAATTCGCAACGCGATTTC
**
249711 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACGCGATTTC
* *
249731 CAATTTCGCAACAC-AGTTTC
1 CAAATTCGCAACGCGA-TTTC
*
249751 CAAATTCGCAACGCGATTTT
1 CAAATTCGCAACGCGATTTC
*
249771 CATATTCGCAACGC
1 CAAATTCGCAACGC
249785 TAATTACCAA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
19 18 0.30
20 42 0.69
21 1 0.02
ACGTcount: A:0.32, C:0.31, G:0.14, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACGCGATTTC
Found at i:249951 original size:37 final size:36
Alignment explanation
Indices: 249899--249986 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 36
249889 ATTAAAACGA
* * *
249899 AATTCACGTTGCGATAGTTGTGTTTACCTATGTCGGT
1 AATT-ACGTTGCGATAGTTATGTTGACCTATATCGGT
*
249936 AATTAGCGTTACGATAGTTATGTTGACCTATATCGGT
1 AATTA-CGTTGCGATAGTTATGTTGACCTATATCGGT
249973 AATTACGTTGCGAT
1 AATTACGTTGCGAT
249987 TTCGCAACGC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
36 9 0.20
37 36 0.80
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.39
Consensus pattern (36 bp):
AATTACGTTGCGATAGTTATGTTGACCTATATCGGT
Found at i:250146 original size:20 final size:20
Alignment explanation
Indices: 250121--250251 Score: 129
Period size: 20 Copynumber: 6.5 Consensus size: 20
250111 TCGGTAATTA
*
250121 GCGTTGTGAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
*
250141 GCGTTGTGAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
250161 GCGTTGCGAATTTGGAAAATC
1 GCGTTGCGAATTT-GAAAATC
* *
250182 ACGTTGCGAATTTGGAAA-C
1 GCGTTGCGAATTTGAAAATC
* * * **
250201 TGTGTTGCGAAATTGGAGTTC
1 -GCGTTGCGAATTTGAAAATC
*
250222 ACGTTGCGAATTTGAAAAATC
1 GCGTTGCGAATTTG-AAAATC
*
250243 GCTTTGCGA
1 GCGTTGCGA
250252 TAGTTGTGTT
Statistics
Matches: 91, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
19 1 0.01
20 60 0.66
21 30 0.33
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAATC
Found at i:250193 original size:41 final size:41
Alignment explanation
Indices: 250121--250251 Score: 142
Period size: 41 Copynumber: 3.2 Consensus size: 41
250111 TCGGTAATTA
* * *
250121 GCGTTGTGAATTT-GAAAATCGCGTTGTGAATTTGAAAATC
1 GCGTTGCGAATTTGGAAAATCACGTTGCGAATTTGAAAATC
*
250161 GCGTTGCGAATTTGGAAAATCACGTTGCGAATTTGGAAA-C
1 GCGTTGCGAATTTGGAAAATCACGTTGCGAATTTGAAAATC
* * **
250201 TGTGTTGCGAAATTGG-AGTTCACGTTGCGAATTTGAAAAATC
1 -GCGTTGCGAATTTGGAAAATCACGTTGCGAATTTG-AAAATC
*
250243 GCTTTGCGA
1 GCGTTGCGA
250252 TAGTTGTGTT
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
40 30 0.39
41 45 0.59
42 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (41 bp):
GCGTTGCGAATTTGGAAAATCACGTTGCGAATTTGAAAATC
Found at i:250308 original size:20 final size:20
Alignment explanation
Indices: 250282--250349 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
250272 GGTAATTAAC
250282 GTTGCGAATTTAAAAATCGT
1 GTTGCGAATTTAAAAATCGT
* * * *
250302 ATTGCGAATTTGAGAATCGC
1 GTTGCGAATTTAAAAATCGT
* *
250322 GTTGCGAATTTAGAAATTGT
1 GTTGCGAATTTAAAAATCGT
250342 GTTGCGAA
1 GTTGCGAA
250350 ATTGAAGTTC
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTTAAAAATCGT
Found at i:252052 original size:2 final size:2
Alignment explanation
Indices: 252045--252075 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
252035 TACATGCAAT
252045 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 T
252076 TAATAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:256584 original size:18 final size:18
Alignment explanation
Indices: 256561--256596 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
256551 ACTGACGTGG
*
256561 AGGCAATAGGAGGTTTCC
1 AGGCAATAGAAGGTTTCC
256579 AGGCAATAGAAGGTTTCC
1 AGGCAATAGAAGGTTTCC
256597 CGAAGGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (18 bp):
AGGCAATAGAAGGTTTCC
Found at i:257906 original size:122 final size:121
Alignment explanation
Indices: 257732--258653 Score: 1059
Period size: 122 Copynumber: 7.6 Consensus size: 121
257722 CCTAAACTAC
* * * *
257732 AAACTTTTAA-TTTTTTCAAAACCATATCTAACATTTAGTTTTCATTTCATTTTAGTACTTTGTC
1 AAACTTTCAATTTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTCATTTTAGTAC-TCGTC
* * * * * * *
257796 GTTAAAAAATTAACGCATTTAGTGCCTAAATTATCATTTGTGATTTGTCTTGGTACCT
65 GTTAAAAAATTAACGCGTTTAGTACCTAAACTATCATTT-TGGTCTGTTTTAGTACCT
* * * * * *
257854 AAAATTTTAATTTTTTTCAAAATCATACCTAACGTTTAG-TTTCATTTCATTTTAGTAATTGTTG
1 AAACTTTCAATTTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACTCGTCG
* ** *
257918 TTAAAAACTTATTGCGTTTAGTACCTAAACTATCAATTTTGGTCTGTTTTAATACCT
66 TTAAAAAATTAACGCGTTTAGTACCTAAACTATC-ATTTTGGTCTGTTTTAGTACCT
* * *
257975 AAACTTTTAA-GTTTTTCAAAACCATATCTAACGTTTAGTTTTCA-TTCTATTTTAGTAC-CATG
1 AAACTTTCAATTTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTC-ATTTTAGTACTC--G
*
258037 TCGTTAAAACATTAACGCGTTTAGTACCTAAACTATCAGTTTTGGTCTGTTTTAGTACCT
63 TCGTTAAAAAATTAACGCGTTTAGTACCTAAACTATCA-TTTTGGTCTGTTTTAGTACCT
* *
258097 AAACTTCCAA--TTTTTC-AAATCATACCTAACGTTTAG---T--TTTCATTTTAGTACTCGTCG
1 AAACTTTCAATTTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACTCGTCG
* * * * * *
258154 TTAAAAATTTAATGTGTTTAGTACATAAACTATCAGTTTTGGTCAGTTTTAGTATCT
66 TTAAAAAATTAACGCGTTTAGTACCTAAACTATCA-TTTTGGTCTGTTTTAGTACCT
* * *
258211 AAACTTTCAATTTTTTTCAAAACCATATCTAACATTTAGTTTTCATTTCATTTTAGTACTTTGTC
1 AAACTTTCAATTTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTCATTTTAGTAC-TCGTC
* * * *
258276 GTT-AAAAATTAACGCATTTAGTACCTAAACTATCAGTTGTGATTTGTTTT-GATACCT
65 GTTAAAAAATTAACGCGTTTAGTACCTAAACTATCA-TTTTGGTCTGTTTTAG-TACCT
* *
258333 AAACTTTCATTTTTTTTCAAAACCATATCC-AACGTTTAGTTTTCATTTCATTTTAGTACCCGTC
1 AAACTTTCAATTTTTTTCAAAACCATA-CCTAACGTTTAGTTTTCATTTCATTTTAGTACTCGTC
* * * *
258397 TTTAAAAATTTAATGCGTTTAGTACCTAAACTATCAGTTTTGGTCTATTTTAGTACCT
65 GTTAAAAAATTAACGCGTTTAGTACCTAAACTATCA-TTTTGGTCTGTTTTAGTACCT
* * * *
258455 AAACTTTCATTTTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACCACGCC
1 AAACTTTCAATTTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTCATTTTAGTA-CTCGTC
* * * *
258520 GTTAAAAAATTAACGCGTTTAGTACCTAAACTATCAATTGTGATTTGTTTTGGTACCT
65 GTTAAAAAATTAACGCGTTTAGTACCTAAACTATC-ATTTTGGTCTGTTTTAGTACCT
* * * *
258578 GAACATTC-ATTTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACCCGTCG
1 AAACTTTCAATTTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACTCGTCG
*
258642 TTAAAAACTTAA
66 TTAAAAAATTAA
258654 TGGGAGACTG
Statistics
Matches: 690, Mismatches: 85, Indels: 51
0.84 0.10 0.06
Matches are distributed among these distances:
114 63 0.09
115 10 0.01
116 10 0.01
117 18 0.03
120 47 0.07
121 100 0.14
122 349 0.51
123 92 0.13
124 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (121 bp):
AAACTTTCAATTTTTTTCAAAACCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACTCGTCG
TTAAAAAATTAACGCGTTTAGTACCTAAACTATCATTTTGGTCTGTTTTAGTACCT
Found at i:258433 original size:358 final size:361
Alignment explanation
Indices: 257743--258653 Score: 1167
Period size: 358 Copynumber: 2.5 Consensus size: 361
257733 AACTTTTAAT
* * * *
257743 TTTTTCAAAACCATATCTAACATTTAGTTTTCATTTCATTTTAGTACTTTGTCGTTAAAAAATTA
1 TTTTTCAAAATCATACCTAACGTTTAG--TT-ATTTCATTTTAGTAC-TCGTCGTTAAAAAATTA
* * * * * *
257808 ACGCATTTAGTGCCTAAATTATCATTTGTGATTTGTCTTGGTACCTAAAATTTTAATTTTTTTCA
62 ACGCGTTTAGTACCTAAACTATCATTT-TGATTTGTTTTGGTACCTAAACTTTCAATTTTTTTCA
* * ** *
257873 AAATCATACCTAACGTTTAG-TTTCATTTCATTTTAGTAATTGTTGTTAAAAACTTATTGCGTTT
126 AAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACTTGTCGTTAAAAACTTAACGCATTT
* * *
257937 AGTACCTAAACTATCAATTTTGGTCTGTTTTAATACCTAAACTTTTAAGTTTTTCAAAACCATAT
191 AGTACCTAAACTATCAATTGTGATCTGTTTTAATACCTAAACTTTCAAGTTTTTCAAAACCATAT
* *
258002 CTAACGTTTAGTTTTCATTCTATTTTAGTACCATGTCGTTAAAACATTAACGCGTTTAGTACCTA
256 CCAACGTTTAGTTTTCATTCTATTTTAGTACCACGTCGTTAAAACATTAACGCGTTTAGTACCTA
*
258067 AACTATCAGTTTTGGTCTGTTTTAGTACCTAAACTTCCA-A
321 AACTATCAGTTTTGGTCTATTTTAGTACCTAAACTTCCATA
* * *
258107 TTTTTC-AAATCATACCTAACGTTTAG-T-TTTCATTTTAGTACTCGTCGTTAAAAATTTAATGT
1 TTTTTCAAAATCATACCTAACGTTTAGTTATTTCATTTTAGTACTCGTCGTTAAAAAATTAACGC
* * ** * * *
258169 GTTTAGTACATAAACTATCAGTTTTGGTCAGTTTTAGTATCTAAACTTTCAATTTTTTTCAAAAC
66 GTTTAGTACCTAAACTATCA-TTTTGATTTGTTTTGGTACCTAAACTTTCAATTTTTTTCAAAAT
* *
258234 CATATCTAACATTTAGTTTTCATTTCATTTTAGTACTTTGTCGTTAAAAA-TTAACGCATTTAGT
130 CATACCTAACGTTTAGTTTTCATTTCATTTTAGTAC-TTGTCGTTAAAAACTTAACGCATTTAGT
* * * **
258298 ACCTAAACTATCAGTTGTGATTTGTTTTGATACCTAAACTTTCATTTTTTTTCAAAACCATATCC
194 ACCTAAACTATCAATTGTGATCTGTTTTAATACCTAAACTTTCA-AGTTTTTCAAAACCATATCC
* *
258363 AACGTTTAGTTTTCATT-TCATTTTAGTACC-CGTCTTTAAAA-ATTTAATGCGTTTAGTACCTA
258 AACGTTTAGTTTTCATTCT-ATTTTAGTACCACGTCGTTAAAACA-TTAACGCGTTTAGTACCTA
* *
258425 AACTATCAGTTTTGGTCTATTTTAGTACCTAAACTTTCATTT
321 AACTATCAGTTTTGGTCTATTTTAGTACCTAAACTTCCA-TA
* *
258467 TTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACCACGCCGTTAAAAAATTA
1 TTTTTCAAAATCATACCTAACGTTTAG--TT-ATTTCATTTTAGTA-CTCGTCGTTAAAAAATTA
* * *
258532 ACGCGTTTAGTACCTAAACTATCAATTGTGATTTGTTTTGGTACCTGAACATTC-ATTTTTTTCA
62 ACGCGTTTAGTACCTAAACTATC-ATTTTGATTTGTTTTGGTACCTAAACTTTCAATTTTTTTCA
**
258596 AAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACCCGTCGTTAAAAACTTAA
126 AAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACTTGTCGTTAAAAACTTAA
258654 TGGGAGACTG
Statistics
Matches: 469, Mismatches: 61, Indels: 32
0.83 0.11 0.06
Matches are distributed among these distances:
357 80 0.17
358 149 0.32
359 57 0.12
360 7 0.01
361 20 0.04
363 17 0.04
364 7 0.01
365 11 0.02
366 64 0.14
367 56 0.12
368 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.44
Consensus pattern (361 bp):
TTTTTCAAAATCATACCTAACGTTTAGTTATTTCATTTTAGTACTCGTCGTTAAAAAATTAACGC
GTTTAGTACCTAAACTATCATTTTGATTTGTTTTGGTACCTAAACTTTCAATTTTTTTCAAAATC
ATACCTAACGTTTAGTTTTCATTTCATTTTAGTACTTGTCGTTAAAAACTTAACGCATTTAGTAC
CTAAACTATCAATTGTGATCTGTTTTAATACCTAAACTTTCAAGTTTTTCAAAACCATATCCAAC
GTTTAGTTTTCATTCTATTTTAGTACCACGTCGTTAAAACATTAACGCGTTTAGTACCTAAACTA
TCAGTTTTGGTCTATTTTAGTACCTAAACTTCCATA
Found at i:258440 original size:244 final size:242
Alignment explanation
Indices: 257732--258655 Score: 1240
Period size: 244 Copynumber: 3.8 Consensus size: 242
257722 CCTAAACTAC
* **
257732 AAACTTTTAATTTTTTCAAAACCATATCTAACATTTAGTTTTCATTTCATTTTAGTACTTTGTCG
1 AAACTTTCAATTTTTTCAAAACCATATCTAACATTTAGTTTTCATTTCATTTTAGTACCATGTCG
* * * * * *
257797 TTAAAAAATTAACGCATTTAGTGCCTAAATTATCATTTGTGATTTGTCTTGGTACCTAAAATTTT
66 TTAAAAAATTAACGCATTTAGTACCTAAACTATCAGTTGTGATTTGTTTTGATACCT-AAACTTT
* *** *
257862 AATTTTTTTCAAAATCATACCTAACGTTTAGTTTCATTTCATTTTAGTAATTGTTGTTAAAAACT
130 CATTTTTTTCAAAATCATACCTAACGTTTAGTTTCATTTCATTTTAGTACCCGTCGTTAAAAACT
* * * *
257927 TATTGCGTTTAGTACCTAAACTATCAATTTTGGTCTGTTTTAATACCT
195 TAATGCGTTTAGTACCTAAACTATCAGTTTTGGTCAGTTTTAGTACCT
* * *
257975 AAACTTTTAAGTTTTTCAAAACCATATCTAACGTTTAGTTTTCA-TTCTATTTTAGTACCATGTC
1 AAACTTTCAATTTTTTCAAAACCATATCTAACATTTAGTTTTCATTTC-ATTTTAGTACCATGTC
* * * * *
258039 GTTAAAACATTAACGCGTTTAGTACCTAAACTATCAGTTTTGGTCTGTTTT-AGTACCTAAACTT
65 GTTAAAAAATTAACGCATTTAGTACCTAAACTATCAGTTGTGATTTGTTTTGA-TACCTAAACTT
* * * *
258103 CCA-ATTTTTC-AAATCATACCTAACGTTTAG--T--TTTCATTTTAGTACTCGTCGTTAAAAAT
129 TCATTTTTTTCAAAATCATACCTAACGTTTAGTTTCATTTCATTTTAGTACCCGTCGTTAAAAAC
* * *
258162 TTAATGTGTTTAGTACATAAACTATCAGTTTTGGTCAGTTTTAGTATCT
194 TTAATGCGTTTAGTACCTAAACTATCAGTTTTGGTCAGTTTTAGTACCT
**
258211 AAACTTTCAATTTTTTTCAAAACCATATCTAACATTTAGTTTTCATTTCATTTTAGTACTTTGTC
1 AAACTTTCAA-TTTTTTCAAAACCATATCTAACATTTAGTTTTCATTTCATTTTAGTACCATGTC
258276 GTT-AAAAATTAACGCATTTAGTACCTAAACTATCAGTTGTGATTTGTTTTGATACCTAAACTTT
65 GTTAAAAAATTAACGCATTTAGTACCTAAACTATCAGTTGTGATTTGTTTTGATACCTAAACTTT
* *
258340 CATTTTTTTTCAAAACCATATCC-AACGTTTAGTTTTCATTTCATTTTAGTACCCGTCTTTAAAA
130 CA-TTTTTTTCAAAATCATA-CCTAACGTTTAG-TTTCATTTCATTTTAGTACCCGTCGTTAAAA
*
258404 ATTTAATGCGTTTAGTACCTAAACTATCAGTTTTGGTCTA-TTTTAGTACCT
192 ACTTAATGCGTTTAGTACCTAAACTATCAGTTTTGGTC-AGTTTTAGTACCT
* * * * * *
258455 AAACTTTCATTTTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACCACGCC
1 AAACTTTCA-ATTTTTTCAAAACCATATCTAACATTTAGTTTTCATTTCATTTTAGTACCATGTC
* * * * *
258520 GTTAAAAAATTAACGCGTTTAGTACCTAAACTATCAATTGTGATTTGTTTTGGTACCTGAACATT
65 GTTAAAAAATTAACGCATTTAGTACCTAAACTATCAGTTGTGATTTGTTTTGATACCTAAACTTT
258585 CATTTTTTTCAAAATCATACCTAACGTTTAGTTTTCATTTCATTTTAGTACCCGTCGTTAAAAAC
130 CATTTTTTTCAAAATCATACCTAACGTTTAG-TTTCATTTCATTTTAGTACCCGTCGTTAAAAAC
258650 TTAATG
194 TTAATG
258656 GGAGACTGAA
Statistics
Matches: 600, Mismatches: 63, Indels: 35
0.86 0.09 0.05
Matches are distributed among these distances:
236 130 0.22
237 50 0.08
238 10 0.02
239 16 0.03
240 22 0.04
241 6 0.01
242 10 0.02
243 105 0.17
244 192 0.32
245 59 0.10
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (242 bp):
AAACTTTCAATTTTTTCAAAACCATATCTAACATTTAGTTTTCATTTCATTTTAGTACCATGTCG
TTAAAAAATTAACGCATTTAGTACCTAAACTATCAGTTGTGATTTGTTTTGATACCTAAACTTTC
ATTTTTTTCAAAATCATACCTAACGTTTAGTTTCATTTCATTTTAGTACCCGTCGTTAAAAACTT
AATGCGTTTAGTACCTAAACTATCAGTTTTGGTCAGTTTTAGTACCT
Found at i:261031 original size:2 final size:2
Alignment explanation
Indices: 261024--261067 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
261014 CTTTTTAGAA
261024 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
261066 AT
1 AT
261068 TTTAATAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:269395 original size:20 final size:20
Alignment explanation
Indices: 269370--269407 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
269360 ATTCGAATCG
269370 ATATAAAAATTAGATTATCA
1 ATATAAAAATTAGATTATCA
*
269390 ATATAAAAATTGGATTAT
1 ATATAAAAATTAGATTAT
269408 AAAAACGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.37
Consensus pattern (20 bp):
ATATAAAAATTAGATTATCA
Found at i:274542 original size:8 final size:8
Alignment explanation
Indices: 274531--274564 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
274521 ATATTTTATA
274531 TATTTAAT
1 TATTTAAT
*
274539 TATTCAAT
1 TATTTAAT
*
274547 TATTTAAC
1 TATTTAAT
274555 TATTTAAT
1 TATTTAAT
274563 TA
1 TA
274565 CTTATCCGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (8 bp):
TATTTAAT
Found at i:274924 original size:55 final size:54
Alignment explanation
Indices: 274834--274972 Score: 174
Period size: 55 Copynumber: 2.6 Consensus size: 54
274824 ATATTCGGAA
* * * *
274834 AACGAGCTCGCTCCCTCATT-TTAGGGAGTATAGAACTCGAACAATTTTCTG-C
1 AACGAGTTCACTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
*
274886 GAACGAGTTCACTCCCTCTTTCTTCGGGGAGTATAGAACTCGAACAATCTTCTGTC
1 -AACGAGTTCACTCCCTCTTTCTT-AGGGAGTATAGAACTCGAACAATCTTCTGTC
* **
274942 AACGGGTTCGTTCCCTCTTTCTTAGGGAGTA
1 AACGAGTTCACTCCCTCTTTCTTAGGGAGTA
274973 GGGACTTGAA
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
53 17 0.23
54 9 0.12
55 47 0.64
56 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (54 bp):
AACGAGTTCACTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
Found at i:275138 original size:55 final size:55
Alignment explanation
Indices: 274897--275485 Score: 744
Period size: 55 Copynumber: 10.7 Consensus size: 55
274887 AACGAGTTCA
* * * * *
274897 CTCCCTCTTTCTTCGGGGAGTAT-AGAACTCGAACAATCTTCTGTCAA-CGGGT-TCG
1 CTCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTC-ATCAATCGTGTCT-G
* * * ** * *
274952 TTCCCTCTTTCTT-AGGGAGTA-GGGACTTGAAGAATCTTCATCAATCGTGT-TG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* * * * *
275004 CTCCCTATTTCCTCAGAGAGTATAAGACCCAAACAATCTTCAACAAATCTTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATC-AATCGTGTCTG
* *
275060 CTCCCTATTTCTTCAGAGAGTATAAGACCCAAACAATCTTCATCAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* *
275115 CTCCCCA-TTCTTTCAGAGAGTATAAGACTTGAACAATCTTCATCAATCGTGTCTG
1 CTCCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
**
275170 CTCCCTATTTCCGCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* * *
275225 CTCCCTATTT-TGCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* *
275279 CTCCCTATTTCTTCAGAGAGTACAAGACTCGAACAATCTTCATCCATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* * * *
275334 CTCCATATTTCTGCAGAGAGTATAAGACTCGAACAATTTTCAACAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* * *
275389 CTCCCTATTTTTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTG
1 CTCCCTA-TTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
*
275445 CTCCCTATTTCTTCAGAGAGTATAAGACTCGATCAATCTTC
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
275486 GATTATCGTT
Statistics
Matches: 473, Mismatches: 51, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
52 15 0.03
53 25 0.05
54 76 0.16
55 259 0.55
56 98 0.21
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (55 bp):
CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
Found at i:275296 original size:164 final size:164
Alignment explanation
Indices: 274975--275485 Score: 783
Period size: 164 Copynumber: 3.1 Consensus size: 164
274965 AGGGAGTAGG
* * * * *
274975 GACTTGAAGAATCTTCATCAATCGTGT-TGCTCCCTATTTCCTCAGAGAGTATAAGACCCAAACA
1 GACTCGAACAATCTTCATCAATCGTGTCTGCTCCCTATTTCCGCAGAGAGTATAAGACTCGAACA
* * * *
275039 ATCTTCAACAAATCTTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCAAACAATCTTCATC
66 ATCTTCAAC-AATCGTGTCTGCTCCCTATTT-TTCAGAGAGTATAAGACTCGAACAATCTTCAAC
* *
275104 AATCGTGTCTGCTCCCCA-TTCTTTCAGAGAGTATAA
129 AATCGCGTCTGCTCCCTATTTC-TTCAGAGAGTATAA
*
275140 GACTTGAACAATCTTCATCAATCGTGTCTGCTCCCTATTTCCGCAGAGAGTATAAGACTCGAACA
1 GACTCGAACAATCTTCATCAATCGTGTCTGCTCCCTATTTCCGCAGAGAGTATAAGACTCGAACA
* *
275205 ATCTTCATCAATCGTGTCTGCTCCCTATTTTGCAGAGAGTATAAGACTCGAACAATCTTCAACAA
66 ATCTTCAACAATCGTGTCTGCTCCCTATTTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAA
*
275270 TCGCGTCTGCTCCCTATTTCTTCAGAGAGTACAA
131 TCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAA
* * *
275304 GACTCGAACAATCTTCATCCATCGTGTCTGCTCCATATTTCTGCAGAGAGTATAAGACTCGAACA
1 GACTCGAACAATCTTCATCAATCGTGTCTGCTCCCTATTTCCGCAGAGAGTATAAGACTCGAACA
*
275369 ATTTTCAACAATCGTGTCTGCTCCCTATTTTTTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
66 ATCTTCAACAATCGTGTCTGCTCCCTA--TTTTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
275434 AATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAA
129 AATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAA
*
275470 GACTCGATCAATCTTC
1 GACTCGAACAATCTTC
275486 GATTATCGTT
Statistics
Matches: 320, Mismatches: 22, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
164 144 0.45
165 49 0.15
166 127 0.40
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.31
Consensus pattern (164 bp):
GACTCGAACAATCTTCATCAATCGTGTCTGCTCCCTATTTCCGCAGAGAGTATAAGACTCGAACA
ATCTTCAACAATCGTGTCTGCTCCCTATTTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAA
TCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAA
Found at i:276509 original size:8 final size:8
Alignment explanation
Indices: 276487--276542 Score: 50
Period size: 7 Copynumber: 7.5 Consensus size: 8
276477 GAACCCTTCC
276487 TTTTTTCCA
1 TTTTTT-CA
276496 TTTTTTCA
1 TTTTTTCA
*
276504 TTTTTTTA
1 TTTTTTCA
*
276512 -TTATT--
1 TTTTTTCA
276517 TTTTTT-A
1 TTTTTTCA
276524 TTTTTTC-
1 TTTTTTCA
276531 TTTTTTCA
1 TTTTTTCA
276539 TTTT
1 TTTT
276543 CACTCATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
6 4 0.10
7 17 0.43
8 13 0.32
9 6 0.15
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTCA
Found at i:291160 original size:28 final size:28
Alignment explanation
Indices: 291129--291189 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
291119 ACCATTGTGT
291129 ACTTTTATTAGCGATATACTATTTTGTA
1 ACTTTTATTAGCGATATACTATTTTGTA
291157 ACTTTTATTAGCGATATACTATTTTGTA
1 ACTTTTATTAGCGATATACTATTTTGTA
291185 ACTTT
1 ACTTT
291190 CAATGTCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.51
Consensus pattern (28 bp):
ACTTTTATTAGCGATATACTATTTTGTA
Done.