Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016357.1 Corchorus olitorius cultivar O-4 contig16390, 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: 76786
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:18045 original size:9 final size:9
Alignment explanation
Indices: 18031--18088 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
18021 TTACACCCAC
*
18031 CTTCATCTT
1 CTTCATCAT
18040 CTTCATCAT
1 CTTCATCAT
*
18049 CATCATCA-
1 CTTCATCAT
*
18057 C--CTTCAT
1 CTTCATCAT
18064 CTTCATCAT
1 CTTCATCAT
* *
18073 CATCATCAC
1 CTTCATCAT
18082 CTTCATC
1 CTTCATC
18089 TTCATCAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
6 4 0.10
7 1 0.03
8 1 0.03
9 33 0.85
ACGTcount: A:0.22, C:0.38, G:0.00, T:0.40
Consensus pattern (9 bp):
CTTCATCAT
Found at i:18048 original size:3 final size:3
Alignment explanation
Indices: 18042--18095 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
18032 TTCATCTTCT
* * * * * *
18042 TCA TCA TCA TCA TCA CCT TCA TCT TCA TCA TCA TCA TCA CCT TCA TCT
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
18090 TCA TCA
1 TCA TCA
18096 ATGTCAGATC
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.26, C:0.37, G:0.00, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:18071 original size:24 final size:24
Alignment explanation
Indices: 18039--18095 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
18029 ACCTTCATCT
18039 TCTTCATCATCATCATCACCTTCA
1 TCTTCATCATCATCATCACCTTCA
18063 TCTTCATCATCATCATCACCTTCA
1 TCTTCATCATCATCATCACCTTCA
18087 TCTTCATCA
1 TCTTCATCA
18096 ATGTCAGATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.37, G:0.00, T:0.39
Consensus pattern (24 bp):
TCTTCATCATCATCATCACCTTCA
Found at i:18088 original size:18 final size:18
Alignment explanation
Indices: 18040--18074 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18030 CCTTCATCTT
18040 CTTCATCATCATCATCAC
1 CTTCATCATCATCATCAC
*
18058 CTTCATCTTCATCATCA
1 CTTCATCATCATCATCA
18075 TCATCACCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.00, T:0.37
Consensus pattern (18 bp):
CTTCATCATCATCATCAC
Found at i:20038 original size:17 final size:18
Alignment explanation
Indices: 20007--20042 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
19997 CAGTAAAAAA
20007 AAGACATTGAACACAAAC
1 AAGACATTGAACACAAAC
20025 AAGACATT-AACACAAAC
1 AAGACATTGAACACAAAC
20042 A
1 A
20043 CTGACTCTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.58, C:0.22, G:0.08, T:0.11
Consensus pattern (18 bp):
AAGACATTGAACACAAAC
Found at i:24541 original size:54 final size:54
Alignment explanation
Indices: 24477--24583 Score: 196
Period size: 54 Copynumber: 2.0 Consensus size: 54
24467 AGGTATTTTC
24477 CAACAAATGATGCCCAAACTCTTTATAATCAAATACCCAGTAATCAATTCTGAG
1 CAACAAATGATGCCCAAACTCTTTATAATCAAATACCCAGTAATCAATTCTGAG
* *
24531 CAACAAATGATGGCCGAACTCTTTATAATCAAATACCCAGTAATCAATTCTGA
1 CAACAAATGATGCCCAAACTCTTTATAATCAAATACCCAGTAATCAATTCTGA
24584 ACAAAATTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.26
Consensus pattern (54 bp):
CAACAAATGATGCCCAAACTCTTTATAATCAAATACCCAGTAATCAATTCTGAG
Found at i:33205 original size:31 final size:32
Alignment explanation
Indices: 33155--33217 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 32
33145 AATGCCATGC
*
33155 TGGACCAAAAATGCCACGTGGCAATGACACAT
1 TGGACCAAAAAGGCCACGTGGCAATGACACAT
*
33187 TGGACC-AAAAGGCCACGTGGCAATGCCACAT
1 TGGACCAAAAAGGCCACGTGGCAATGACACAT
33218 CAAACCAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 23 0.79
32 6 0.21
ACGTcount: A:0.35, C:0.27, G:0.24, T:0.14
Consensus pattern (32 bp):
TGGACCAAAAAGGCCACGTGGCAATGACACAT
Found at i:33225 original size:31 final size:31
Alignment explanation
Indices: 33162--33225 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
33152 TGCTGGACCA
* ***
33162 AAAATGCCACGTGGCAATGACACATTGGACC
1 AAAAGGCCACGTGGCAATGACACATCAAACC
*
33193 AAAAGGCCACGTGGCAATGCCACATCAAACC
1 AAAAGGCCACGTGGCAATGACACATCAAACC
33224 AA
1 AA
33226 GATGCTGACG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.28, G:0.20, T:0.12
Consensus pattern (31 bp):
AAAAGGCCACGTGGCAATGACACATCAAACC
Found at i:35935 original size:97 final size:97
Alignment explanation
Indices: 35765--35943 Score: 277
Period size: 97 Copynumber: 1.8 Consensus size: 97
35755 CAATTATTTG
* * * *
35765 ACCATCAAAAGGGAACACTTTTATTGGCTCTTTCTTTCTTCCTTTTTTCTACAAACAATAAAACA
1 ACCATCAAAAGAGAACACATTTATAGGCTCGTTCTTTCTTCCTTTTTTCTACAAACAATAAAACA
*
35830 ACGTTAAACCAACAATATAAACCTCTAATCAC
66 ACGCTAAACCAACAATATAAACCTCTAATCAC
* * *
35862 ACCATCAAAAGAGAACACATTTGTAGGCTCGTTCTTTCTTTCTTTTTTCTACAAACAGTAAAACA
1 ACCATCAAAAGAGAACACATTTATAGGCTCGTTCTTTCTTCCTTTTTTCTACAAACAATAAAACA
*
35927 ACGCTAAACTAACAATA
66 ACGCTAAACCAACAATA
35944 AACCTAGCAA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
97 73 1.00
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.31
Consensus pattern (97 bp):
ACCATCAAAAGAGAACACATTTATAGGCTCGTTCTTTCTTCCTTTTTTCTACAAACAATAAAACA
ACGCTAAACCAACAATATAAACCTCTAATCAC
Found at i:40572 original size:20 final size:20
Alignment explanation
Indices: 40547--40587 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
40537 GGCTTATATC
40547 AAGAAAAATGAATTGATGCT
1 AAGAAAAATGAATTGATGCT
40567 AAGAAAAATGAATTGATGCT
1 AAGAAAAATGAATTGATGCT
40587 A
1 A
40588 TTGCTATCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.20, T:0.24
Consensus pattern (20 bp):
AAGAAAAATGAATTGATGCT
Found at i:52003 original size:63 final size:63
Alignment explanation
Indices: 51904--52030 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
51894 ATCTACCAAA
*
51904 TAATGACACGTGTTCTTTTTTAGTTTTTAATGTTATTCCTTGTTTGTCTAGTTAAATTAAATT
1 TAATGACACGTGTTCTTTTTTAGTTTTTAATGTTATTCCTTGTTTGCCTAGTTAAATTAAATT
51967 TAATGACACGTGTTCTTTTTTAGTTTTTAATGTTATTCCTTGTTTGCCTAGTTAAATTAAATT
1 TAATGACACGTGTTCTTTTTTAGTTTTTAATGTTATTCCTTGTTTGCCTAGTTAAATTAAATT
52030 T
1 T
52031 TATATTTTCA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.24, C:0.10, G:0.13, T:0.54
Consensus pattern (63 bp):
TAATGACACGTGTTCTTTTTTAGTTTTTAATGTTATTCCTTGTTTGCCTAGTTAAATTAAATT
Found at i:57146 original size:37 final size:38
Alignment explanation
Indices: 57096--57174 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 38
57086 ATATAATTAT
* *
57096 TCATAAAGTTATGTCTATTTGGAAAGACATG-TGTTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGATGTTGA
57133 TCATAAAGTTATGTCTATATGAAAAGACATGCATGTTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATG-ATGTTGA
57172 TCA
1 TCA
57175 AGTATATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 29 0.76
39 9 0.24
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (38 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGATGTTGA
Found at i:63019 original size:324 final size:320
Alignment explanation
Indices: 61984--64570 Score: 2084
Period size: 324 Copynumber: 8.1 Consensus size: 320
61974 CATATTTTTT
* * * * *
61984 GAATTAATTTTTAATTAAATCGAAACAAGATTTAAATACTCGTAAAAACAAATCATTAAATCCAA
1 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
* * * * * ** *
62049 TATGCCTGGGATTTGATTAAAT-AATATAGATATTTGC-AGGAGTCTCGGC-GCCAAAAATCAGG
66 TGTGGCTGAGATTTGGTTAGATGAATATAGATATTT-CAAGGAGTCT-TTCTGCCAAAAATCATG
* * * ** * * * * *
62111 TAAAATTGAGCCGGGGCTTGTAACGCGTTTTTAGGCAAAAACC---AT-GATA-TGCATGATTTC
129 CAAAATTGAGTCGGGCCCCGAAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTC
* * * * * * * *
62171 GGCTAAAAACTGACTCGAAAAATTTTTCCTCAAGTTCTTGCCACAATACTCAAAAAAAATATATG
194 GGCTAAAAACTGACCCCAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATA
* ** * * ***
62236 ATTCAACACCAAAAAGATTGACGGGCTTTTCAAGCTTTTAATATCGTTTTTC-CAATTTTTCC
259 ATTCAACGCCAAAAAGATT-AAAGGCTTTTCACGCTTCTAATATCGTTTTTCTTTTTTTTTCC
* * *
62298 GAATTAATTTCTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAA
1 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
** * * * *
62363 TGTAACTGAGATTTGGTTCGATGAATATAAATATTTCAATGAGTCTTTGTGCCAAAAATCATGCA
66 TGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCA
* * * **
62428 AAATTGAATCAGGGCTCCGGAATACG--TTTTTAGCAAAAAACTATGATGGTTAGTACAATGATT
131 AAATTGAGTC-GGGC-CCCGAA-ACGCATTTTTAGCCAAAAACCGTGATGGTTAGTAC-ATGATT
* * * *
62491 TCGGCTAAAATTTTGTAAAAATTGA-CCCAAATTTTTTTTCTCAATTCTTTGCCACAATACTTAG
192 TCGGC----------TAAAAACTGACCCCAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAG
* * * * *
62555 AAAAAATATATAATTCAACG-TAAAAAAAATGAAGGGTTGTTCACGCTTCTAATATCGTTTTTCA
247 AAAAAATATATAATTCAACGCCAAAAAGATTAAAGGCTT-TTCACGCTTCTAATATCGTTTTTC-
* *
62619 ATTTTTTTCCC
310 TTTTTTTTTCC
* * * *
62630 AAATTTATTTCTAATTAAATCGAAAGAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAA
1 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
*
62695 TGTGGCTGAGATTTGGTTAGATGAATAT-GAATATTTCAAGGAGTTTTTCTGCCAAAAATCATGC
66 TGTGGCTGAGATTTGGTTAGATGAATATAG-ATATTTCAAGGAGTCTTTCTGCCAAAAATCATGC
* * * * *
62759 AAAACTGAGCCAGGGCCCCGAAACGCATTTTTAACCCAAAAACCGTGATGGTTACTACACGATTT
130 AAAATTGAGTC-GGGCCCCGAAACGCATTTTT-AGCCAAAAACCGTGATGGTTAGTACATGATTT
* * * * *
62824 CGGCTAAAAACTGACCCCAGAAATTTTTTTCTGAATTTTTTACCATAATACTTAGAAATAATATA
193 CGGCTAAAAACTGACCCCA-AAATTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATA
** * *
62889 TAATTCAACTTCAAAAAGATTAATAGGCTTTTCGCGCTTCTAATATCATTTTTCTTTTTTTTTCC
257 TAATTCAACGCCAAAAAGATTAA-AGGCTTTTCACGCTTCTAATATCGTTTTTCTTTTTTTTTCC
* * * * * *
62954 AAATTAATTTGTAATTAAATCGAAACAAGATTTATATGCTCGTAAAAAAAAATCCTTATATCCAA
1 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
* * * * *
63019 TGTGGCTGATATTTGATTAAATGAATTTAGATATTTCAAGGAGTCTTTGC-GCCAAAAATCATGT
66 TGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CTGCCAAAAATCATGC
* * * * * * *
63083 AAAATTGAGCCGGGGCTCCGGAACGCGTTTTTGGCCAAAAATCGTGATGGTTTGTACATGATTTC
130 AAAATTGAGTC-GGGCCCCGAAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTC
* *
63148 GGCTAAAATTTTGCAATAACTGACCCGAAAATTTTTTCCTCAATTTTTTGCCACAATACTCAGAA
194 GGCT---A------AA-AACTGACCCCAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAGAA
* *
63213 AAAATATATAATTCAACGCCAATAAA-ATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTC--
249 AAAATATATAATTCAACGCCAA-AAAGATT-AAAGGCTTTTCACGCTTCTAATATCGTTTTTCTT
**
63275 CATTTTTCC
312 TTTTTTTCC
* * * * *
63284 GAATTTATTT-TCAGTTAATTCGAAACACGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCA
1 GAATTAATTTCT-AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCA
* * * *
63348 ATGTTGCTGAGATGTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGC
65 ATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGC
* * *** * * * * * **
63413 AAAATTGAGTCGAGACCCTGAAACATGTTTTTGGCAAAAAACTGAGATGGTTAATACCCGATTTC
130 AAAATTGAGTCG-GGCCCCGAAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTC
* * * *
63478 GGCTAAAAACTGACCCAAAAATTTTCTTCTTAATTTTTTGCCACAATACTCATAAAAAATATATA
194 GGCTAAAAACTGACCCCAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATA
* * * * * * * *
63543 ATTCAATGCCAAAAAGATTGAAGGGTTTTTTACGCTTCTTATAACATTTTTCTTTTTCTTTTTTT
259 ATTCAACGCCAAAAAGATT-AAAGGCTTTTCACGCTTCTAATATCGTTTTTC--TTT-TTTTTTC
63608 C
320 C
* * * *
63609 GAATTTAGTTCTAATTAAA-CGAAACAAGATTCAGATGCTTGTAAAAAGAAATCCTTAAATCCAA
1 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
* *
63673 TGTGGCTAAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCA
66 TGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCA
* * * ** * * * * *
63738 AAACTGAGTC---CCTCGAAATGGGTATTTAGCCCAAAAACTGTGATGATTAATACATGATTTCT
131 AAATTGAGTCGGGCCCCGAAACGCATTTTTAG-CCAAAAACCGTGATGGTTAGTACATGATTTCG
* * * * *
63800 GCTAAAAACGGACCCGGAAAATTTTTCTTCTAAAATTTTTGCCGCAATACTCAG-AAAAATATAT
195 GCTAAAAACTGACCC-CAAAATTTTT-TTCTCAATTTTTTGCCACAATACTCAGAAAAAATATAT
*** * * * **
63864 AATTCAACGCC------ATGGCAGGCATTTCACGCTTCTAAAATTGTTTTTC-CATTTTTTCC
258 AATTCAACGCCAAAAAGATTAAAGGCTTTTCACGCTTCTAATATCGTTTTTCTTTTTTTTTCC
* * *
63920 GAATTAATTTCTAACTAAATCGAAACAAGATTCATATGCTCGTAAAAACAAATCCTTATATCCAA
1 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
* *
63985 TGTGG-T---CTTT-G--AGAT---T-T-G--A-TTCAA-GATGTCTTTGC-GCCAAAAATTATG
66 TGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGA-GTCTTT-CTGCCAAAAATCATG
* * * * * ** * * * * *
64033 AAAAATTAAGTCGGCGCTCCGGAATGCATTTTTAGGAAAAAACCGTCACGATTTCGGCTA-A-AA
129 CAAAATTGAGTCGG-GCCCCGAAACGCATTTTTAGCCAAAAACCGTGATG-GTT-AG-TACATGA
* * * * * *
64096 TTT-TGC-AAAAACTGACCCGAAAAGTTTTTTATCGATTTTTTGCCAGAATACTCA-AAAAAATA
190 TTTCGGCTAAAAACTGACCCCAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATA
* * * * *
64158 TATATTATTTAACGCCAAAAA-AATGAAGGCTTTTTCACGTTTCTAATATCATTTTTCCATTTTT
255 TATA--ATTCAACGCCAAAAAGATTAAAGGC-TTTTCACGCTTCTAATATCGTTTTT-C-TTTTT
*
64222 TTTTCT
315 TTTTCC
* * *
64228 GAATTTATTTCTAATTAAATCGAAACAAGAATT-AGATGCTCGTAAAAACATATCCTTAAATCAA
1 GAATTAATTTCTAATTAAATCGAAACAAG-ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCA
* * * * *
64292 ATGTGGCTGAGATTTCGTTACATGAATATAGATATTTCAAGGAGTCTGTATGCCAAAAACCATGC
65 ATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGC
* * * * * * ** * *
64357 AGAACTGATTTGTGGCCCTG-AACGCGTTTTTTTTTCCAAAATA--GTGATGGATAGTACACGAT
130 AAAATTGAGTCG-GGCCCCGAAACGC--ATTTTTAGCCAAAA-ACCGTGATGGTTAGTACATGAT
* * * *
64419 TTCGGGTAAAAA-TGACACGAAAATTTTTTACTCAA-TTTTTGCCATCAATACTCAG-AAAAATA
191 TTCGGCTAAAAACTGACCCCAAAATTTTTTTCTCAATTTTTTGCCA-CAATACTCAGAAAAAATA
** * * *
64481 TATAATTCAATACCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCG----T-TTTTATTTT
255 TATAATTCAACGCCAAAAAGATT-AAAGGCTTTTCACGCTTCTAATATCGTTTTTCTTTTTTTTT
64541 CC
319 CC
* *
64543 GAATTAATTTCTAATCAAATCAAAACAA
1 GAATTAATTTCTAATTAAATCGAAACAA
64571 CACGATTTCG
Statistics
Matches: 1826, Mismatches: 335, Indels: 223
0.77 0.14 0.09
Matches are distributed among these distances:
296 2 0.00
297 63 0.03
298 11 0.01
299 20 0.01
300 14 0.01
301 20 0.01
302 2 0.00
303 2 0.00
304 6 0.00
305 24 0.01
306 1 0.00
307 1 0.00
308 70 0.04
309 4 0.00
311 24 0.01
312 49 0.03
313 1 0.00
314 73 0.04
315 98 0.05
316 18 0.01
317 3 0.00
318 5 0.00
319 6 0.00
320 114 0.06
321 58 0.03
322 87 0.05
323 135 0.07
324 321 0.18
325 53 0.03
326 7 0.00
327 1 0.00
329 6 0.00
330 200 0.11
331 52 0.03
332 240 0.13
333 35 0.02
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (320 bp):
GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
TGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCA
AAATTGAGTCGGGCCCCGAAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTCGG
CTAAAAACTGACCCCAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAT
TCAACGCCAAAAAGATTAAAGGCTTTTCACGCTTCTAATATCGTTTTTCTTTTTTTTTCC
Found at i:63675 original size:654 final size:638
Alignment explanation
Indices: 61977--64570 Score: 2229
Period size: 654 Copynumber: 4.1 Consensus size: 638
61967 TTTGTTTCAT
* * * * *
61977 ATTTTTT--GAATTAATTTT-TAATTAAATCGAAACAAGATTTAAATACTCGTAAAAACAAATCA
1 ATTTTTTCCGAATTTATTTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
* * * * * ****
62039 TTAAATCCAAT-ATGCCTGGGATTTGATTAAAT-AATATAGATATTTGC-AGGAGTCTCGGCGCC
66 TTAAATCCAATGTTG-CTGAGATCTGGTTAGATGAATAT-GATATTT-CAAGGAGTCTTTATGCC
* * * * ** * * * *
62101 AAAAATCAGGTAAAATTGAGCCG-GGGCTTGTAACGCGTTTTTAGGCAAAAACCATGATAT-G--
128 AAAAATCATGCAAAATTGAGTCGAGGCCCCG-AA-ACATTTTTAGGCAAAAAAC-TGAGATGGTT
* * * * *
62162 CAT---GATTTCGGCTAAAAACTGACTCGAAAAATTTTTCCTCAAGTTCTTGCCACAATACTCAA
190 AATACCGATTTCGGCTAAAAACTGAC-CCAAAAATTTTTTCTCAATTTTTTGCCACAATACTC-A
* * * * * *
62224 AAAAAATATATGATTCAACACCAAAAAGATTGACGGGCTTTTCAAGCTTTTAATATCGTTTTTC-
253 AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTCT
*** * *
62288 CAATTTTTCCGAATTAATTTCTAATTAAATCAAAATAAGATTCAGATGCTCGTAAAAACAAATCC
318 TTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
* ** * * * *
62353 TTATATCCAATGTAACTGAGATTTGGTTCGATGAATATAAATATTTCAATGAGTCTTTGTGCCAA
383 TTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAA
* ** * ** * * *
62418 AAATCATGCAAAATTGAATCAGGGCTCCGGAATACGTTTTTAG-CAAAAAACTATGATGGTTAGT
448 AAATCATGCAAAACTGAGCCGGGGCTCCGGAACGCGTTTTTGGCCAAAAATCTGTGATGGTTAGT
* * *
62482 ACAATGATTTCGGCTAAAATTTTGTAAAAATTGACCC-AAATTTTTTTTCTCAATTCTTTGCCAC
513 AC-ATGATTTCGGC----------TAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCAC
* ** * *
62546 AATACTTAGAAAAAATATATAATTCAACGTAAAAAAAATGAAGGGTTGTTCACGCTTCTAATATC
567 AATACTCAG-AAAAATATATAATTCAACGCCAAAAAATTGAAGGGTTTTTCACGCTTCTAATATC
*
62611 GTTTTTCA
631 GTTTTTCC
* *
62619 ATTTTTTTCCCAAATTTA-TTTCTAATTAAATCGAAAGAAGATTCAGATGCTCGTAAAAACAAAT
1 A-TTTTTT-CCGAATTTATTTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
* * * * *
62683 TCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATGAATATTTCAAGGAGTTTTTCTGCC
64 CCTTAAATCCAATGTTGCTGAGATCTGGTTAGATGAATATG-ATATTTCAAGGAGTCTTTATGCC
* * ** * * *
62748 AAAAATCATGCAAAACTGAG-CCAGGGCCCCGAAACGCATTTTTAACCCAAAAACCGTGATGGTT
128 AAAAATCATGCAAAATTGAGTCGA-GGCCCCGAAA--CATTTTTAGGCAAAAAACTGAGATGGTT
* * * * * *
62812 ACTACACGATTTCGGCTAAAAACTGACCCCAGAAATTTTTTTCTGAATTTTTTACCATAATACTT
190 AATAC-CGATTTCGGCTAAAAACTGA-CCCA-AAAATTTTTTCTCAATTTTTTGCCACAATACTC
* ** * *
62877 AGAAATAATATATAATTCAACTTCAAAAAGATT-AATAGGCTTTTCGCGCTTCTAATATCATTTT
252 A-AAAAAATATATAATTCAACGCCAAAAAGATTGAA-GGGCTTTTCACGCTTCTAATATCATTTT
* * * * *
62941 TCTTTTTTTTTCCAAATTAATTTGTAATTAAATCGAAACAAGATTTATATGCTCGTAAAAAAAAA
315 TCTTTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
* * * * *
63006 TCCTTATATCCAATGTGGCTGATATTTGATTAAATGAATTTAGATATTTCAAGGAGTCTTTGCGC
380 TCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGC
* *
63071 CAAAAATCATGTAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTGGCCAAAAATC-GTGATGGTT
445 CAAAAATCATGCAAAACTGAGCCGGGGCTCCGGAACGCGTTTTTGGCCAAAAATCTGTGATGGTT
* *
63135 TGTACATGATTTCGGCTAAAATTTTGCAATAACTGACCCGAAAATTTTTTCCTCAATTTTTTGCC
510 AGTACATGATTTCGGCT---A------AA-AACTGACCCGAAAATTTTTTTCTCAATTTTTTGCC
63200 ACAATACTCAGAAAAAATATATAATTCAACGCCAATAAAATTGAAGGGTTTTTCACGCTTCTAAT
565 ACAATACTCAG-AAAAATATATAATTCAACGCCAA-AAAATTGAAGGGTTTTTCACGCTTCTAAT
63265 ATCGTTTTTCC
628 ATCGTTTTTCC
* * * *
63276 A-TTTTTCCGAATTTATTTTC-AGTTAATTCGAAACACGATTTAGATGCTCGTAAAAACAAATCC
1 ATTTTTTCCGAATTTATTTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
*
63339 TTAAATCCAATGTTGCTGAGATGTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAA
66 TTAAATCCAATGTTGCTGAGATCTGGTTAGATGAATAT-GATATTTCAAGGAGTCTTTATGCCAA
* * * *
63404 AAACCATGCAAAATTGAGTCGAGACCCTGAAACATGTTTTTGGCAAAAAACTGAGATGGTTAATA
130 AAATCATGCAAAATTGAGTCGAGGCCCCGAAACAT-TTTTAGGCAAAAAACTGAGATGGTTAATA
*
63469 CCCGATTTCGGCTAAAAACTGACCCAAAAATTTTCTTCTTAATTTTTTGCCACAATACTCATAAA
194 -CCGATTTCGGCTAAAAACTGACCCAAAAATTTT-TTCTCAATTTTTTGCCACAATACTCA-AAA
* * * * *
63534 AAATATATAATTCAATGCCAAAAAGATTGAAGGGTTTTTTACGCTTCTTATAACATTTTTCTTTT
256 AAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTC--TT
* * * * *
63599 TCTTTTTTTCGAATTTAGTTCTAATTAAA-CGAAACAAGATTCAGATGCTTGTAAAAAGAAATCC
319 T-TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
* *
63663 TTAAATCCAATGTGGCTAAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CTGCCA
383 TTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGC-GCCA
* * * * * *
63727 AAAATCATGCAAAACTGAGTCC----CT-CGAAATGGGTATTTAGCCCAAAAA-CTGTGATGATT
447 AAAATCATGCAAAACTGAG-CCGGGGCTCCGGAACGCGT-TTTTGGCCAAAAATCTGTGATGGTT
* * * * * *
63786 AATACATGATTTCTGCTAAAAACGGACCCGGAAAATTTTTCTTCTAAAATTTTTGCCGCAATACT
510 AGTACATGATTTCGGCTAAAAACTGACCC-GAAAATTTTT-TTCTCAATTTTTTGCCACAATACT
* * ** * *
63851 CAGAAAAATATATAATTCAACGCC-----ATGGCA-GGCATTTCACGCTTCTAAAATTGTTTTTC
573 CAGAAAAATATATAATTCAACGCCAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTC
63910 C
638 C
* * *
63911 ATTTTTTCCGAA-TTAATTTCTAACTAAATCGAAACAAGATTCATATGCTCGTAAAAACAAATCC
1 ATTTTTTCCGAATTTATTTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
* * **
63975 TTATATCCAA---TG-TG-G-TCT--TT-GA-G-ATTTG--A-TTCAA-GATGTCTTTGCGCCAA
66 TTAAATCCAATGTTGCTGAGATCTGGTTAGATGAATATGATATTTCAAGGA-GTCTTTATGCCAA
* * * * * *
64025 AAATTATGAAAAATTAAGTCG-GCGCTCCGGAATGCATTTTTAGG-AAAAAACCGTCACGATTTC
130 AAATCATGCAAAATTGAGTCGAG-GC-CCCGAA-ACATTTTTAGGCAAAAAA-C-TGA-GA--T-
* * * * * *
64088 GGCTAA-A---ATTT-TGC-AAAAACTGACCCGAAAAGTTTTTTATCGATTTTTTGCCAGAATAC
186 GGTTAATACCGATTTCGGCTAAAAACTGACCC-AAAAATTTTTTCTCAATTTTTTGCCACAATAC
* * *
64147 TCAAAAAAATATATATTATTTAACGCCAAAAA-AATGAA-GGCTTTTTCACGTTTCTAATATCAT
250 TCAAAAAAATATATA--ATTCAACGCCAAAAAGATTGAAGGGC-TTTTCACGCTTCTAATATCAT
* *
64210 TTTTCCATTTTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGAATT-AGATGCTCGTAAA
312 TTTT-C-TTTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG-ATTCAGATGCTCGTAAA
* * * *
64274 AACATATCCTTAAATCAAATGTGGCTGAGATTTCGTTACATGAATATAGATATTTCAAGGAGTCT
374 AACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCT
* ** * * *** * * ** *
64339 GTATGCCAAAAACCATGCAGAACTGATTTGTGGC-CCTGAACGCGTTTTTTTTTCC-AAAAT-AG
439 TTGCGCCAAAAATCATGCAAAACTGAGCCGGGGCTCCGGAACGCG--TTTTTGGCCAAAAATCTG
* * * * *
64401 TGATGGATAGTACACGATTTCGGGTAAAAA-TGACACGAAAATTTTTTACTCAA-TTTTTGCCAT
502 TGATGGTTAGTACATGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCA-
**
64464 CAATACTCAGAAAAATATATAATTCAATACCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATAT
566 CAATACTCAGAAAAATATATAATTCAACGCCAAAAA-ATTGAAGGGTTTTTCACGCTTCTAATAT
64529 CGTTTTT--
630 CGTTTTTCC
* * *
64536 A--TTTTCCGAA-TTAATTTCTAATCAAATCAAAACAA
1 ATTTTTTCCGAATTTATTTTCTAATTAAATCGAAACAA
64571 CACGATTTCG
Statistics
Matches: 1606, Mismatches: 256, Indels: 199
0.78 0.12 0.10
Matches are distributed among these distances:
619 46 0.03
620 200 0.12
621 77 0.05
622 21 0.01
623 71 0.04
624 8 0.00
625 5 0.00
626 7 0.00
627 31 0.02
628 2 0.00
630 2 0.00
631 1 0.00
632 2 0.00
633 2 0.00
635 34 0.02
636 60 0.04
641 8 0.00
642 34 0.02
643 29 0.02
645 4 0.00
646 71 0.04
647 44 0.03
648 20 0.01
650 9 0.01
651 42 0.03
652 80 0.05
653 45 0.03
654 261 0.16
655 133 0.08
656 212 0.13
657 45 0.03
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (638 bp):
ATTTTTTCCGAATTTATTTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
TTAAATCCAATGTTGCTGAGATCTGGTTAGATGAATATGATATTTCAAGGAGTCTTTATGCCAAA
AATCATGCAAAATTGAGTCGAGGCCCCGAAACATTTTTAGGCAAAAAACTGAGATGGTTAATACC
GATTTCGGCTAAAAACTGACCCAAAAATTTTTTCTCAATTTTTTGCCACAATACTCAAAAAAATA
TATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTCTTTTTTTTT
CCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
AATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATG
CAAAACTGAGCCGGGGCTCCGGAACGCGTTTTTGGCCAAAAATCTGTGATGGTTAGTACATGATT
TCGGCTAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAATATAT
AATTCAACGCCAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCC
Found at i:67991 original size:5 final size:5
Alignment explanation
Indices: 67983--68014 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
67973 TACAGTATAG
67983 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TA
68015 GTAAGACTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.19, T:0.22
Consensus pattern (5 bp):
TAAGA
Found at i:73517 original size:15 final size:15
Alignment explanation
Indices: 73497--73528 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
73487 GATAACACAT
*
73497 CTTACTATCTTATTA
1 CTTACTATCTTACTA
73512 CTTACTATCTTACTA
1 CTTACTATCTTACTA
73527 CT
1 CT
73529 CCCTCAGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (15 bp):
CTTACTATCTTACTA
Found at i:73608 original size:14 final size:15
Alignment explanation
Indices: 73589--73624 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
73579 GACCTTTAAT
73589 TATAAAAA-AAATTA
1 TATAAAAATAAATTA
73603 TATAAAAATAAATTA
1 TATAAAAATAAATTA
73618 TATAAAA
1 TATAAAA
73625 TTATGTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TATAAAAATAAATTA
Found at i:73625 original size:14 final size:14
Alignment explanation
Indices: 73586--73625 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
73576 TTTGACCTTT
73586 AATTATA-AAAA-A
1 AATTATATAAAATA
73598 AATTATATAAAAATA
1 AATTATAT-AAAATA
73613 AATTATATAAAAT
1 AATTATATAAAAT
73626 TATGTTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.28
14 9 0.36
15 9 0.36
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATTATATAAAATA
Found at i:73899 original size:26 final size:27
Alignment explanation
Indices: 73863--73919 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
73853 TTTTAAAAAG
*
73863 TATTCTTTTTAG-TCATTTAACTTTTT
1 TATTCTTTTTAGATCATTCAACTTTTT
* *
73889 TATTTTTTTTAGATGATTCAACTTTTT
1 TATTCTTTTTAGATCATTCAACTTTTT
73916 TATT
1 TATT
73920 AATATTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.65
Consensus pattern (27 bp):
TATTCTTTTTAGATCATTCAACTTTTT
Found at i:75127 original size:327 final size:320
Alignment explanation
Indices: 74386--75099 Score: 864
Period size: 322 Copynumber: 2.2 Consensus size: 320
74376 TTAGCACTGG
* * * * * * *
74386 CTCAGTTTTGCATGATTTTTGACG-TAA-ACTCCTTGAAATATCTATATTCATCGAACAAAATCC
1 CTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTAGAAATATCTATATTCATCAAACCAAATCT
* ** * * *
74449 CAGCCACGTTCGATTTAAGTATTTGTTTTTGCGAGGCATCTGAATCTTGTTTCAATTTAATTAAA
66 CAGCCA--TTGGAAATAAGAATTTGTTTTTACGAGGCATCTGAATCTAGTTTCAATTTAATTAAA
* * * *
74514 AATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTGGCG
129 AATTAATTCGGAAAAAAATGAAAAAACGATATTAAAAGCGTGAAAAGACCATCAATCTTTTGGCG
*** *
74579 TTGAATTATATATTTTTTCGGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTTCGATCAATTT
194 TTGAATTATATATTTTTTCGGAGTATTGTGGCAAAAAATTGAGAAAAAAAAACTACGATCAATTT
*
74644 TTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCCGAGCCCCGA
259 TTAGCCGAAATAGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCCGAGCCCCGA
* *
74706 CTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGT
1 CTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTAGAAATATCTATATTCATCAAACCAAATCT
* * *
74771 CAGCCACATTGGATATAAGAATTTGTTTTTACGA-GCATCTGAATCTAGTTTCGATTTAATTAGA
66 CAG-C-CATTGGAAATAAGAATTTGTTTTTACGAGGCATCTGAATCTAGTTTCAATTTAATTAAA
*
74835 AATTAATTCGGAAAAAAATTGAAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGG
129 AATTAATTCGGAAAAAAA-TGAAAAAACGATATTAAAAGCGTGAAAAGACCATCAATC-TTTTGG
* * * ** *
74900 TGTTGAATTATAT-TTCTTTTCTGAGTATTGTGGCAAAAAGTTTTGAAAAAAAAACTACGGGTCA
192 CGTTGAATTATATATT-TTTTCGGAGTATTGTGGCAAAAAATTGAGAAAAAAAAACTAC-GATCA
* * ** ** *
74964 GTTTTTAGCTGAAAATAGTGTACTAACCATCATGGTTTTTGGGCTAAAAACGCGTTTCGGGGGCC
255 ATTTTTAGCCG-AAATAGTGTACTAACCATCACAGTTTTT-GGCTAAAAACGCG-TTCCCGAGCC
*
75029 CCGG
317 CCGA
* * * *
75033 CTTAGTTTTGCATGATTTTTGGCAG-AAAGACTCCTAGAAATATCTATATTGATCTAACC-AATC
1 CTCAATTTTGCATGATTTTTGGC-GCAAAGACTCCTAGAAATATCTATATTCATCAAACCAAATC
75096 TCAG
65 TCAG
75100 GTTTGCCGAA
Statistics
Matches: 338, Mismatches: 44, Indels: 18
0.85 0.11 0.05
Matches are distributed among these distances:
320 22 0.07
321 47 0.14
322 93 0.28
323 53 0.16
324 15 0.04
325 25 0.07
326 20 0.06
327 62 0.18
328 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (320 bp):
CTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTAGAAATATCTATATTCATCAAACCAAATCT
CAGCCATTGGAAATAAGAATTTGTTTTTACGAGGCATCTGAATCTAGTTTCAATTTAATTAAAAA
TTAATTCGGAAAAAAATGAAAAAACGATATTAAAAGCGTGAAAAGACCATCAATCTTTTGGCGTT
GAATTATATATTTTTTCGGAGTATTGTGGCAAAAAATTGAGAAAAAAAAACTACGATCAATTTTT
AGCCGAAATAGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCCGAGCCCCGA
Found at i:75714 original size:322 final size:322
Alignment explanation
Indices: 75124--75880 Score: 894
Period size: 322 Copynumber: 2.3 Consensus size: 322
75114 TTTTTTTTGT
* * * *
75124 TTTTGCATGATTTTTGACGTAAATACTCCTTAAAATATCTATATTCATCGAACAAAATCCCAGCC
1 TTTTGCATGATTTTTGGCG-AAAGACTCCTTGAAATATCTATATTCATCAAACAAAATCCCAGCC
* * **
75189 ACATTCGATTTAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAACTAA
65 ACATTCGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTAATTCAATTTAATTAAAAACTAA
* ** *
75254 TTCGGAAAAAAATGAAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAA
130 TTCGGAAAAAAATGAAAAAACGATATTAAAAGCGTGAAAAGAACATCAATCTTTTTGGCGTTGAA
**
75319 TTATATATTTTTTCTGAGTATTGTGGCAAAAAATTAAGAAAAAACTTTTCCGATAAGTTTATAAC
195 TTATATATTTTTTCTGAGTATTGTGGCAAAAAATTAAGAAAAAAC-AATCCGATAAGTTTATAAC
*
75384 CGAAATCGTGTGCTAACCATCACGGTTTTT-GGCTAAAAACGCG-TTCCCGAGCCCCGACTCAA
259 CGAAATCGTGTACTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCCCGAGCCCCGACTCAA
**
75446 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATAT-ATCAAA-ACAAATGTCAG
1 TTTTGCATGATTTTTGGCG-AAAGACTCCTTGAAATATCTATAT-TCATCAAACA-AAATCCCAG
* * * * * * *
75509 TCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGATTCTTAATTCGATTTAGTTAGAAATT
63 CCACATTCGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTAATTCAATTTAATTAAAAACT
* * * * *
75574 AATTCGGAAAAAATTGGAAAAATGATGTTAAAAGCGTGAAAAGAACATCAATCTTTTTGGTGTTG
128 AATTCGGAAAAAAATGAAAAAACGATATTAAAAGCGTGAAAAGAACATCAATCTTTTTGGCGTTG
* * * * * *
75639 AATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTCAGGAAAAAA-AATCGGGTCAGTTTTTA
193 AATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT-AAGAAAAAACAATCCGATAAGTTTATA
* * ** * *
75703 GCCGAAAATCGTGTACTAACCATCATGGTTTTTGGGCTAAAAACGCGTTTCGGGGGCCCCGGCTC
257 ACCG-AAATCGTGTACTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCCCGAGCCCCGACTC
*
75768 AG
321 AA
* * * * *
75770 TTTTGAATGATTTTTGGCAGAAAGACTCCGTGAAATATCTATTTTCATCGAAGCAATCTCAGGCT
1 TTTTGCATGATTTTTGGC-GAAAGACTCCTTGAAATATCTATATTCATC-AAACAA----A--AT
* * *
75835 CTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
58 CCCAGCCACATTCGATATAAGGATTTGTTTTTACGAGCATCTGAAT
75881 ATTGCGTTGA
Statistics
Matches: 366, Mismatches: 53, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
321 15 0.04
322 224 0.61
323 23 0.06
324 56 0.15
325 4 0.01
326 1 0.00
329 1 0.00
331 42 0.11
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (322 bp):
TTTTGCATGATTTTTGGCGAAAGACTCCTTGAAATATCTATATTCATCAAACAAAATCCCAGCCA
CATTCGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTAATTCAATTTAATTAAAAACTAAT
TCGGAAAAAAATGAAAAAACGATATTAAAAGCGTGAAAAGAACATCAATCTTTTTGGCGTTGAAT
TATATATTTTTTCTGAGTATTGTGGCAAAAAATTAAGAAAAAACAATCCGATAAGTTTATAACCG
AAATCGTGTACTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCCCGAGCCCCGACTCAA
Found at i:76617 original size:323 final size:321
Alignment explanation
Indices: 75927--76786 Score: 1305
Period size: 323 Copynumber: 2.7 Consensus size: 321
75917 TTTTTTTTGT
* * * * * * **
75927 TTTTGCATGATTTTTGACGTAAATACTCCTTGAAATATCTATATACATCGAACAAAATCCCAGCC
1 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATATCAGCC
* ** * *
75992 ACGTACGATTTAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATT-AAAATTAA
66 ACATTGGATATAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAA
*
76056 TTCGG-AAAAAATGGAAAAATGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGCA
131 TTCGGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGTGTTG-A
*
76120 TTATATATTATTTCTGAGTATTGTGGCAAAAATTGAGAAAAAACTTTTCCGATCAGTTTTTAGCC
195 TTATATATTTTTTCTGAGTATTGTGGCAAAAATTGAGAAAAAACTTTTCCGATCAGTTTTTAGCC
* *
76185 GAAATCGTGTATTTACCATCACGGTTTTTGGCTAAAAAACGTGTTCCCGAGCCCTGACTCAA
260 GAAATCGTGTATTTACCATCACGGTTTTTGGCTAAAAAACGCGTTCCCGAGCCCCGACTCAA
*
76247 TTTTGCATGATTTTTTGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATATCAGCC
1 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATATCAGCC
76312 ACATTGGATATAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAA
66 ACATTGGATATAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAA
*
76377 TTCGGAAAAAAATGGAAAAATGATATTAGTAGCGTGAAAAGCCCGTCAATCTTTTTGGTGTTGAT
131 TTCGGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGTGTTGA-
*
76442 TTATATATTTTTTCTGAGTATTGTGGCAAAAATTGAGAAAAAAACATTTTTCTGATCAGTTTTTA
195 TTATATATTTTTTCTGAGTATTGTGGCAAAAATTGAG-AAAAAAC--TTTTCCGATCAGTTTTTA
76507 GCCGAAATCGTGTA-TT-CCATCACGGTTTTTGGCTAAAAAACGCGTTCCCGAGCCCCGACTCAA
257 GCCGAAATCGTGTATTTACCATCACGGTTTTTGGCTAAAAAACGCGTTCCCGAGCCCCGACTCAA
* * * *
76570 TTTTGCATGATTTTTGGCGCAAAGATTCCTTGAAATATCTTTATTCATCAAACCAAATGTCAACC
1 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATATCAGCC
* * ** * * *
76635 ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGATTCTTAATTCGATTTAGTTAGAAATTAA
66 ACATTGGATATAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAA
* * * ** *
76700 TTCGGAAAAAATTGGAAAAATGATGTTAAAAGCGTGAAAAGAACATCAATCTTTTTGGTGTTGAA
131 TTCGGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGTGTTG-A
76765 TTATATATTTTTTCTGAGTATT
195 TTATATATTTTTTCTGAGTATT
Statistics
Matches: 494, Mismatches: 39, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
320 107 0.22
321 14 0.03
322 91 0.18
323 248 0.50
324 3 0.01
325 31 0.06
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (321 bp):
TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATATCAGCC
ACATTGGATATAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAA
TTCGGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGTGTTGAT
TATATATTTTTTCTGAGTATTGTGGCAAAAATTGAGAAAAAACTTTTCCGATCAGTTTTTAGCCG
AAATCGTGTATTTACCATCACGGTTTTTGGCTAAAAAACGCGTTCCCGAGCCCCGACTCAA
Done.