Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020406.1 Corchorus olitorius cultivar O-4 contig20439, 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: 231827
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:816 original size:334 final size:332
Alignment explanation
Indices: 1--1182 Score: 1722
Period size: 334 Copynumber: 3.6 Consensus size: 332
*
1 CTAAAATTTTGCAAAAATTGACCTGAAAGATTTTTTCCACAATCTTTGGCCAAAACACTTATAGA
1 CTAAAATTTTGCAAAAATTGACCCGAAAG-TTTTTTCCACAATCTTTGGCCAAAACACTTATAGA
* * * *
66 ATATGTATAATTTAACGCCAAAAATATTGAAGGGTTTTTAACGCTTCTAATATCAATTTTCCAAT
65 ATATGTATAATTCAACGCCAAAAAGATTGAAGGGTTTTTAACGCTTCTAATATCGATTTTCCTAT
* *
131 ATCTTTCCGAACTAATTTCTGATTAAATCGAAACATGATTCTGATGCTCGTAAAATCAAATCCGT
130 ATCTTTCCGAATTAATTTCTGATTAAATCGAAACATGATTCTGATGCTCGTAAAATCAAATCCTT
* * * * *
196 AAATCCAATTTGGCTTAGATCTGGTTAGATGAATATAGATATGTCAAGTAGTCTTGGGGCCAAAT
195 AAATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGATATGTCAAGGAGTCTCGGGGCCAAAA
* * ** * *
261 ATCATTGAAAACTTAGCCGGAAATCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
260 ATCATTGAAAACTAAGCGGGGCA-CCGGAACGCGTTTATAGCCAAAAACCGTAATGGTTAGTACA
326 CGATTTCGG
324 CGATTTCGG
* * *
335 CTAAAATTTTGCAAAATTTGACCCGAAACTTTTTTCCACAATCTTTGGCCAAAACACTAATAGAA
1 CTAAAATTTTGCAAAAATTGACCCGAAAGTTTTTTCCACAATCTTTGGCCAAAACACTTATAGAA
* *
400 TATGTATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGATTTTCCTAAA
66 TATGTATAATTCAACGCCAAAAAGATTGAAGGGTTTTTAACGCTTCTAATATCGATTTTCCTATA
* * * *
465 TGTTTCCGAAATAATTTCTGCTTAAATCGAAACATGATTCTGATGCTCGTAAGATCAAATCCTTA
131 TCTTTCCGAATTAATTTCTGATTAAATCGAAACATGATTCTGATGCTCGTAAAATCAAATCCTTA
* *
530 AATCCAATTAGGCTGAGATTTGGTTATATGAATATAGATATGTCAAGGAGTCTCGGGGCCAAAAA
196 AATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGATATGTCAAGGAGTCTCGGGGCCAAAAA
* *
595 TCATTGAAAACTAAGTCGGGGCACCGGAACGCGTTTATAGCCAAAAACCGTAATGATTAGTACAT
261 TCATTGAAAACTAAG-CGGGGCACCGGAACGCGTTTATAGCCAAAAACCGTAATGGTTAGTACAC
660 GATTTTCGG
325 GA-TTTCGG
*
669 CTAAAATTTTGCAAAAATTGACCCGAAAGTTTTTTCCACAATCTTTGGCCAAAACACTTACAGAA
1 CTAAAATTTTGCAAAAATTGACCCGAAAGTTTTTTCCACAATCTTTGGCCAAAACACTTATAGAA
* *
734 TATGTATAATTCAATGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGATTTTCCTATA
66 TATGTATAATTCAACGCCAAAAAGATTGAAGGGTTTTTAACGCTTCTAATATCGATTTTCCTATA
**
799 TCTTTCCGAATTAATTTCTGATTAAATCGAAACATGATTCTGATGCTCACAAAATCAAATCCTTA
131 TCTTTCCGAATTAATTTCTGATTAAATCGAAACATGATTCTGATGCTCGTAAAATCAAATCCTTA
* *
864 AATCCAATTTGGCTGAGATTTGGTTAGATGAAGATAGATATGTCAAGGACTCTCGGGGCCAAAAA
196 AATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGATATGTCAAGGAGTCTCGGGGCCAAAAA
* * * *
929 TCATTGAAAAGTAAGCCGGGGCCCCGGAACGTGTTTATAGCCAAAAACCATAATGGTTAGTACAC
261 TCATTGAAAACTAAG-CGGGGCACCGGAACGCGTTTATAGCCAAAAACCGTAATGGTTAGTACAC
994 GATTTCGG
325 GATTTCGG
* * * * * * *
1002 CTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATA-AA
1 CTAAAATTTTGCAAAAATTGACCCGAAAGTTTTTTCCACAATCTTTGGCCAAAACACTTATAGAA
* ** * *** * * * * *
1066 AACATATAATTCGATATCAAAAAAATTGAAGGGCTCTTAACGCTTCTAATATTGTTTTTCCTAT-
66 TATGTATAATTCAACGCCAAAAAGATTGAAGGGTTTTTAACGCTTCTAATATCGATTTTCCTATA
* * *
1130 T-TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
131 TCTTTCCGAATTAATTTCTGATTAAATCGAAACATGATTCTGATGCTCGTAAAA
1183 AATAAATAAT
Statistics
Matches: 768, Mismatches: 78, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
330 47 0.06
331 1 0.00
332 54 0.07
333 326 0.42
334 340 0.44
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (332 bp):
CTAAAATTTTGCAAAAATTGACCCGAAAGTTTTTTCCACAATCTTTGGCCAAAACACTTATAGAA
TATGTATAATTCAACGCCAAAAAGATTGAAGGGTTTTTAACGCTTCTAATATCGATTTTCCTATA
TCTTTCCGAATTAATTTCTGATTAAATCGAAACATGATTCTGATGCTCGTAAAATCAAATCCTTA
AATCCAATTTGGCTGAGATTTGGTTAGATGAATATAGATATGTCAAGGAGTCTCGGGGCCAAAAA
TCATTGAAAACTAAGCGGGGCACCGGAACGCGTTTATAGCCAAAAACCGTAATGGTTAGTACACG
ATTTCGG
Found at i:1353 original size:2 final size:2
Alignment explanation
Indices: 1346--1376 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1336 GGTTAGATGA
1346 AT AT AT 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
1377 AGGAGTCTTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1873 original size:332 final size:332
Alignment explanation
Indices: 1455--2140 Score: 901
Period size: 333 Copynumber: 2.1 Consensus size: 332
1445 GATTTCGGCT
* * * *
1455 AAAATTGACCCGAAAGATTTTTCCACAATTTTTCGCCAAAACACTAATAGAATGTGTATAATTCA
1 AAAATTGACCCGAAAG-TTTTTCCACAATCTTTCGCCAAAACACTAATAGAATATATATAATACA
* * * *
1520 ACGACAAAAAGATTGAAGGG-TTTTCACGCTTCTAATATCGATTTTCCCAAATGTTTCTAAATTT
65 ACGACAAAAAGATTAAAGGGTTTTTCACGCTTCCAATATCGATTTTCCCAAATGTTTCCAAATTA
* * * * * * *
1584 ATTTCTGATTAAATCGAAACATGATTCTGATGCTCGTAAATTGAAATCCTTACATCCAATTTGGC
130 ATTTATGATTAAACCGAAACACGATTCTGATGATCGTAAAATCAAATCCTTAAATCCAATTTGGC
* * * *
1649 TGAGATTTGGTTAGATGAATATAGATATATCAAGGAGTCTCGGGGCCAAAAATAATT-ATAAACT
195 AGAGATTTGGTTACATCAATATAGATATATCAAGGAGTCTCGGGGACAAAAATAATTGA-AAACT
* * * * *
1713 AAGCCGGGGCCCCGGAACGCGTTTATAGCCAAAAATCGTAATGGTTAGTATAAGATTTTGGCTAA
259 AAGCAGGGGCCCCGGAACGCGTTTATAGCCAAAAACCGTAATGGTAAGTACAAGATTTCGGCTAA
1778 AATATTG-A
324 AATATTGCA
* * *
1786 AGAAATTGACCCGAAAGTTGTTTCCATAATCTTTGGCCAAAACACTTATAGAATATATATAATAC
1 A-AAATTGACCCGAAAGTT-TTTCCACAATCTTTCGCCAAAACACTAATAGAATATATATAATAC
* * * * *
1851 AATGCCAAAAAGATTAAAGGGTTTTTCACGCTTCCAATATCGATTTTCCTATATGTTTCCGAATT
64 AACGACAAAAAGATTAAAGGGTTTTTCACGCTTCCAATATCGATTTTCCCAAATGTTTCCAAATT
* * *
1916 AATTTATGATTTAACCGAAACACGATTTTGATGATCGTAAAATCAAATCCTTAAATCCCATTTGG
129 AATTTATGATTAAACCGAAACACGATTCTGATGATCGTAAAATCAAATCCTTAAATCCAATTTGG
* * * *
1981 CAGAGATTTGGTTACTTCAATATAGATATGTTAAGGAGTCTCGGGGACAAAAATCATTGAAAACT
194 CAGAGATTTGGTTACATCAATATAGATATATCAAGGAGTCTCGGGGACAAAAATAATTGAAAACT
* * * *
2046 GAGCAGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTACACGATTTCGGCTAA
259 AAGCAGGGGCCCCGGAACGCGTTTATAGCCAAAAACCGTAATGGTAAGTACAAGATTTCGGCTAA
*
2111 AATTTTGCA
324 AATATTGCA
* *
2120 AAAATTGAGCTGAAAGTTTTT
1 AAAATTGACCCGAAAGTTTTT
2141 TGCGACAAAA
Statistics
Matches: 304, Mismatches: 46, Indels: 9
0.85 0.13 0.03
Matches are distributed among these distances:
331 3 0.01
332 74 0.24
333 224 0.74
334 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31
Consensus pattern (332 bp):
AAAATTGACCCGAAAGTTTTTCCACAATCTTTCGCCAAAACACTAATAGAATATATATAATACAA
CGACAAAAAGATTAAAGGGTTTTTCACGCTTCCAATATCGATTTTCCCAAATGTTTCCAAATTAA
TTTATGATTAAACCGAAACACGATTCTGATGATCGTAAAATCAAATCCTTAAATCCAATTTGGCA
GAGATTTGGTTACATCAATATAGATATATCAAGGAGTCTCGGGGACAAAAATAATTGAAAACTAA
GCAGGGGCCCCGGAACGCGTTTATAGCCAAAAACCGTAATGGTAAGTACAAGATTTCGGCTAAAA
TATTGCA
Found at i:2425 original size:288 final size:290
Alignment explanation
Indices: 1856--2429 Score: 821
Period size: 290 Copynumber: 2.0 Consensus size: 290
1846 AATACAATGC
* *
1856 CAAAAAGATTAAAGGGTTTTTCACGCTTCCAATATCGATTTTCCTATATGTTTCCGAATTAATTT
1 CAAAAAGATTAAAGGGTATTTCACGCTTCCAATATCGATTTTCCTATATCTTTCCGAATTAATTT
* * * *
1921 ATGATTTAACCGAAACACGATTTTGATGATCGTAAAATCAAATCCTTAAATCCCATTTGGCAGAG
66 ATGATTAAACCGAAACACAATTCTGATGACCGTAAAATCAAATCCTTAAATCCCATTTGGCAGAG
* * * *
1986 ATTTGGTTACTTCAATATAGATATGTTAAGGAGTCTCGGGGACAAAAATCATTGAAAACTGAGCA
131 ATTTGGTTACATCAATATAGATATGTCAAGGAGTCTCCGGGACAAAAATCATTGAAAACTAAGCA
* * * *
2051 GGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTACACGATTTCGGCTAAAATTT
196 GGGGCCCCGGAACGCGTTTATAGCAAAAAACCGTAATGATAAGTACACGATTTCGGCTAAAATTT
* *
2116 TGCAAAAATTGAGCTGAAAGTTTTTTGCGA
261 TGCAAAAATTGACCCGAAAGTTTTTTGCGA
* **
2146 CAAAAAGATTGAAGGGTATTTCACGCTTCGGATATCGATTTTCCTATATCTTTCCGAATTAATTT
1 CAAAAAGATTAAAGGGTATTTCACGCTTCCAATATCGATTTTCCTATATCTTTCCGAATTAATTT
* * * ** * * **
2211 CTGATTAAATCGAAACATAATTCTGATTCCCGTAAATTCAAATCCTTAAATCCGATTTGGTTGAG
66 ATGATTAAACCGAAACACAATTCTGATGACCGTAAAATCAAATCCTTAAATCCCATTTGGCAGAG
* * *
2276 -TTTGGTTAGATGAATATAGATATGTCAAGGAGTC-CCGGGCCAAAAATCATTGAAAACTAAGTC
131 ATTTGGTTACATCAATATAGATATGTCAAGGAGTCTCCGGGACAAAAATCATTGAAAACTAAG-C
* *
2339 -GGGGCCCCGGAACGCGTTTATAGCAAAAAATCGTAATGATTAGTACACGATTTCGGCTAAAATT
195 AGGGGCCCCGGAACGCGTTTATAGCAAAAAACCGTAATGATAAGTACACGATTTCGGCTAAAATT
2403 TTGCAAAAATTGACCCGAAAGTTTTTT
260 TTGCAAAAATTGACCCGAAAGTTTTTT
2430 CCACAATCTT
Statistics
Matches: 250, Mismatches: 33, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
288 107 0.43
289 31 0.12
290 112 0.45
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (290 bp):
CAAAAAGATTAAAGGGTATTTCACGCTTCCAATATCGATTTTCCTATATCTTTCCGAATTAATTT
ATGATTAAACCGAAACACAATTCTGATGACCGTAAAATCAAATCCTTAAATCCCATTTGGCAGAG
ATTTGGTTACATCAATATAGATATGTCAAGGAGTCTCCGGGACAAAAATCATTGAAAACTAAGCA
GGGGCCCCGGAACGCGTTTATAGCAAAAAACCGTAATGATAAGTACACGATTTCGGCTAAAATTT
TGCAAAAATTGACCCGAAAGTTTTTTGCGA
Found at i:3257 original size:330 final size:326
Alignment explanation
Indices: 2146--3923 Score: 1435
Period size: 319 Copynumber: 5.4 Consensus size: 326
2136 TTTTTTGCGA
** *
2146 CAAAAAGATTGAAGGG-TATTTCACGCTTCGGATATC-GATTTTCCTATATCTT-TCCGAATTAA
1 CAAAAAGATTGAAGGGCT-TTTCACGCTTCTAATATCTG-TTTTCCTAT-T-TTCT-CAAATTAA
* * * * * ** * * **
2208 TTTCTGATTAAATCGAAACATAATTCTGATTCCCGTAAATTCAAATCCTTAAATCCGATTTGGTT
61 TTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACT
* * * *
2273 GAG-TTTGGTTAGATGAATATAGATATGTCAAGGAGTCCCGGGCCAAAAATCATTG-AAAACTAA
126 GAGATTTGGTTAGATGAAAATAAATATATCAAGGAGT-CTGGGCCAAAAATCA-TGCAAAACTAA
* * * * * * *
2336 GTCGGGGCCCCGGAACGCGTTTATAGCAAAAAATCGTAATGATTAGTACACGATTTCGGCTAAAA
189 G-CCGAGCCCCGGAACGCATTTTTAGCCAAAAACCATAATG-TTAGTACACGATTTCGGCTAAAA
* * * * * * * * *
2401 TTTTGCAAAAATTGACCCGAAAGTTTTTTCCACAATCTTTGGCCAAAACACTTATAGAATATATA
252 TTTTGCAAAAATTGACCCGAAAG-ATTTTACTCAATTTTTAGCCAAAATACTCATAAAAAATATA
*
2466 TAATTCAACGC
316 TAATTCAACAC
* * *
2477 CAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATC-GATTTTCCTATATCTT-TCCGATTTAAT
1 CAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCTG-TTTTCCTAT-T-TTCT-CAAATTAAT
* * * * * * ** * * *
2540 TTTTGATTAAATCGAAACATAATTCTGATGCCCATAAATTCAAATCCTTAAGTCCAATTTGGCTG
62 TTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTG
* * * * *
2605 AGATTTGGTTAGATTAATATAGATATGTCAAGGAGTCTCGGGGCCAAAAATCATTG-AAAACTGA
127 AGATTTGGTTAGATGAAAATAAATATATCAAGGAGTCT--GGGCCAAAAATCA-TGCAAAACTAA
* * *
2669 GCCGGAGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATG---GTACACGATTTCGGC-----
189 GCC-GA-GCCCCGGAACGCATTTTTAGCCAAAAACCATAATGTTAGTACACGATTTCGGCTAAAA
* * * * * * ** * *
2726 ---T---AAAATTGACCCGAAAGATTTTTCCACAATCTTTGGCCAAAACACTAATAGTATATGTA
252 TTTTGCAAAAATTGACCCGAAAGA-TTTTACTCAATTTTTAGCCAAAATACTCATAAAAAATATA
*
2785 TAATTCAACGC
316 TAATTCAACAC
* * *
2796 CAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATC-GATTTTCCTAAATGGTTC-CGAATTAAT
1 CAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCTG-TTTTCCT--AT-TTTCTCAAATTAAT
* * * * *
2859 TTCTGATTAAATCGAAACATGATTCTGATGCTCGTAAAATCAAATCCTTAAATCCAATTTGGCTG
62 TTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTG
* * *
2924 AGATTTGGTTAGATGAAAATAGATATGTCAAGGACTCTCAGGGCCAAAAATCATTG-AAAACTAA
127 AGATTTGGTTAGATGAAAATAAATATATCAAGGAGTCT--GGGCCAAAAATCA-TGCAAAACTAA
* * *
2988 GCCGGGGCCCCGGAACGTATTTATAGCCAAAAACCATAATGGTTAGTACACGATTTCGGCTAAAA
189 GCC-GAGCCCCGGAACGCATTTTTAGCCAAAAACCATAAT-GTTAGTACACGATTTCGGCTAAAA
* *
3053 TTTTGCAAAAAATTGACCCGAAAGATATTTACTCAATTTTTTGCTAAAATACTCAT-AAAAATAT
252 TTTTGC-AAAAATTGACCCGAAAGAT-TTTACTCAATTTTTAGCCAAAATACTCATAAAAAATAT
* * *
3117 ATAATTCGATAT
315 ATAATTCAACAC
* *
3129 CAAAAAG-TTGAAGGGCTTTTAACGCTTCTAATAT-TGTTTTCCTATTTTCTCGGAATTAATTTC
1 CAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCTGTTTTCCTATTTTCTC-AAATTAATTTC
* * *
3192 TAATTAAATCGAAACAAGATTCAGATGGTCGTAAAAACAAATCCTTAAATCTAATGTGACTGAGA
65 TAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAGA
* * * *
3257 TTTGGTTAGATGAATATAAATATTTCAAGGAGTCTTGGCACAAAAAATCATGCAAAACTGAGCCG
130 TTTGGTTAGATGAAAATAAATATATCAAGGAGTCTGGGC-C-AAAAATCATGCAAAACTAAGCCG
* * * * * * *
3322 AGCCCCGGAAAGCATTTTTAGCCGAAAACCGTGATAGTCAGTTCACGGTTTCGGCT-AAATTTTG
193 AGCCCCGGAACGCATTTTTAGCCAAAAACCATAAT-GTTAGTACACGATTTCGGCTAAAATTTTG
* * * * *
3386 TAAAAATTGACCCGAATGATTTTTCCTC-ATTTTCTAGCGAAAATACTCATAAAAAATAAATAAT
257 CAAAAATTGACCCGAAAGA-TTTTACTCAATTTT-TAGCCAAAATACTCATAAAAAATATATAAT
*
3450 TTAACAC
320 TCAACAC
* *** * * *
3457 CAAAAAAATTGAAACCCATTTTCACGCTTCTAATATCGTTTTTTTCTATTTTATTTCAAAGTTAA
1 CAAAAAGATTGAAGGGC-TTTTCACGCTTCTAATATC-TGTTTTCCTA-TTT-TCTCAAA-TTAA
* * * * ** * * *
3522 TTTCTGATTAAATCGAAATAGGATTTAGAAACTCGTACAAACAAATCCTTAAATACAATGTGGCT
61 TTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACT
* * **
3587 GAGAATTGGTTAGATGAATATATATTTATATATATATTAAGGAGTCTTGGCGTAAAAAAATCATG
126 GAGATTTGGTTAGATG-A-A-A-A--TA-A-ATATATCAAGGAGTC-TGG-G-CCAAAAATCATG
* * * ** ** * *
3652 CAAAACTGAA-CTAGAGCCCCGGAACGCGTTTTTAACCAAAAAAAACCATGATGGTACAC-ATTT
180 CAAAACT-AAGC-CGAGCCCCGGAACGCATTTTTAGCCAAAAACCATAATGTTAGTACACGATTT
* * * * *
3715 CGGCTAAAATTTTACAAAAATTGACCTGAAATATTTTTCTCAATTTTTAGCCACAATACTCATAA
243 CGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTACTCAATTTTTAGCCAAAATACTCATAA
*
3780 AAAATATATAATTCAACGC
308 AAAATATATAATTCAACAC
** ** * * *
3799 CAAAAAGATTGAAGATCTTCCCACGCTTCTAATATCGGTTTTCCTTTTTGTTTTCAAATTAATTT
1 CAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCTGTTTTCC-TATT-TTCTCAAATTAATTT
* *
3864 CTAATTAAATTGAAACATGATTCAAATGCTCGTAAAAA-AAATCCTTAAATCCAATGTGAC
64 CTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGAC
3924 ACGATTTCGG
Statistics
Matches: 1217, Mismatches: 170, Indels: 113
0.81 0.11 0.08
Matches are distributed among these distances:
318 29 0.02
319 241 0.20
320 2 0.00
321 2 0.00
322 16 0.01
326 5 0.00
327 37 0.03
328 36 0.03
329 58 0.05
330 150 0.12
331 127 0.10
332 68 0.06
333 50 0.04
334 146 0.12
335 1 0.00
336 1 0.00
338 21 0.02
339 36 0.03
340 16 0.01
341 20 0.02
342 73 0.06
343 53 0.04
344 29 0.02
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (326 bp):
CAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCTGTTTTCCTATTTTCTCAAATTAATTTCT
AATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAGAT
TTGGTTAGATGAAAATAAATATATCAAGGAGTCTGGGCCAAAAATCATGCAAAACTAAGCCGAGC
CCCGGAACGCATTTTTAGCCAAAAACCATAATGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
AATTGACCCGAAAGATTTTACTCAATTTTTAGCCAAAATACTCATAAAAAATATATAATTCAACA
C
Found at i:4083 original size:215 final size:215
Alignment explanation
Indices: 3707--4117 Score: 589
Period size: 215 Copynumber: 1.9 Consensus size: 215
3697 CCATGATGGT
* * *
3707 ACACATTTCGGCTAAAATTTTACAAAAATTGACCTGAAATATTTTTCTCAATTTTTAGCCACAAT
1 ACACATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAGATTTTCCTCAATTTTTAGCCACAAT
*
3772 ACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGATCTTCCCACGCTTCTAATATCGG
66 ACTCATAAAAAATATATAATTCAACGCCAAAAAGATGGAAGATCTTCCCACGCTTCTAATATCGG
* * *
3837 TTTTCCTTTTTGTTTTCAAATTAATTTCTAATTAAATTGAAACATGATTCAAATGCTCGTAAAAA
131 TTTTCATATTTGTTTTCAAATTAATTTCTAATTAAATCGAAACATGATTCAAATGCTCGTAAAAA
3902 AAATCCTTAAATCCAATGTG
196 AAATCCTTAAATCCAATGTG
* *
3922 ACACGATTTCGGCT-AAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCCATA
1 ACAC-ATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAGAT-TTTCCTCAATTTTTAGCCACA
* *** *
3986 ATACTCAT-AAAAATATATAATTCAACGCCAAAAAGATGGAA-AGGCTTTTTGACGCTTTTAATA
64 ATACTCATAAAAAATATATAATTCAACGCCAAAAAGATGGAAGA-TC-TTCCCACGCTTCTAATA
* *
4049 TCGTTTTTCATAATTT-TTTT-AAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGT
127 TCGGTTTTCAT-ATTTGTTTTCAAATTAATTTCTAATTAAATCGAAACATGATTCAAATGCTCGT
*
4112 TAAAAA
191 AAAAAA
4118 CAAAAAAAGA
Statistics
Matches: 174, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
214 1 0.01
215 108 0.62
216 62 0.36
217 3 0.02
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.36
Consensus pattern (215 bp):
ACACATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAGATTTTCCTCAATTTTTAGCCACAAT
ACTCATAAAAAATATATAATTCAACGCCAAAAAGATGGAAGATCTTCCCACGCTTCTAATATCGG
TTTTCATATTTGTTTTCAAATTAATTTCTAATTAAATCGAAACATGATTCAAATGCTCGTAAAAA
AAATCCTTAAATCCAATGTG
Found at i:5134 original size:332 final size:331
Alignment explanation
Indices: 4345--5143 Score: 951
Period size: 332 Copynumber: 2.4 Consensus size: 331
4335 TAAAATATAT
* * * **
4345 ATTGAAGGACTTTTCACGCTTTTAACATCGTTTTTCATA-TTTTTCTGTATTAATTTTT-ATATA
1 ATTGAAGGGCTTTTCACGCTTTTAATATTGTTTTTCATATTTTTTCTAAATTAATTTTTAAT-TA
* *
4408 AATCGAAACAAGATTTAGATGCTTGTAAAAACAAAATT-TTAAATCTAATGTGGCTGAGATTTAA
65 AATCGAAACAAGATTTAGATGCTCGTAAAAAC-AAATTCTTAAATCTAATGTGGCTGAGATTTGA
* * *
4472 TTAT-ATGAATATAGGTACCTCAAGGAGTCTTGGTGCCAAAAATCATGCAAAATTGAGTCGGGGC
129 TT-TGATGAATATAGATACCTCAAGGAGTCTTGGAGCCAAAAATCATGCAAAA-TGAGTCGGGCC
* * * * **
4536 CAGAAAACGCTTTTTTATCCAAAAACTGTGATGTTTATTACACAATTTTGGCTAAAATTTTGTAA
192 CAGAAAACGATTTTTTAGCCAAAAACTGTAATGTTTAGTACACAATTTCAGCTAAAATTTTGTAA
*
4601 AAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAACTCAA
257 AAATTGACACGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAACTCAA
4666 CACCAAAAAG
322 CACCAAAAAG
* * * * *
4676 ATTGAAGGGCTTTTGATG-TTTCTAATATTGTTTTTCCTATTTTTTCCAAATTAATTTCTAATTA
1 ATTGAAGGGCTTTTCACGCTTT-TAATATTGTTTTTCATATTTTTTCTAAATTAATTTTTAATTA
* * * * *
4740 AATCGAAACAAAATTTAGATGCTCGTAAAGACAAATCCTTAAAACTAATGTGGGTGAGATTTGAT
65 AATCGAAACAAGATTTAGATGCTCGTAAAAACAAATTCTTAAATCTAATGTGGCTGAGATTTGAT
** * *
4805 TTGATGAATATAGATAGTTCAAGTAGTCTTGGAGCCAGAAATCATGC-AAA-GAG-CTGGGTCCC
130 TTGATGAATATAGATACCTCAAGGAGTCTTGGAGCCAAAAATCATGCAAAATGAGTC-GGG-CCC
* *
4867 CG-AAAC-ATATTTTTAGCCAAAAACTGTAATGGTTTGTTAGTACACGATTTCAGCTAAAATTTT
193 AGAAAACGAT-TTTTTAGCCAAAAACTGTAAT-G--T-TTAGTACACAATTTCAGCTAAAATTTT
4930 -TCAAAAATTGACACG-AA-ATATTTCTTCTCAATTTTTGGCTAAAATACTCAT-AAAAATATAT
253 GT-AAAAATTGACACGAAAGATATTTC--CTCAATTTTTGGCTAAAATACTCATAAAAAATATAT
* **
4991 AATTCAATGCCAAAAAG
315 AACTCAACACCAAAAAG
* * * *
5008 ATTGGAGGGCTTTTTACGCTTTTAATATTGTATTTCTTATTTTTTCTAAATTAATTTTTAATTAA
1 ATTGAAGGGCTTTTCACGCTTTTAATATTGTTTTTCATATTTTTTCTAAATTAATTTTTAATTAA
* ** * *
5073 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCCATGTTGCTGAGATTTGGTT
66 ATCGAAACAAGATTTAGATGCTCGTAAAAACAAATTCTTAAATCTAATGTGGCTGAGATTTGATT
*
5138 AGATGA
131 TGATGA
5144 TGTAAAGTAT
Statistics
Matches: 398, Mismatches: 54, Indels: 31
0.82 0.11 0.06
Matches are distributed among these distances:
328 2 0.01
329 29 0.07
330 7 0.02
331 44 0.11
332 251 0.63
333 65 0.16
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36
Consensus pattern (331 bp):
ATTGAAGGGCTTTTCACGCTTTTAATATTGTTTTTCATATTTTTTCTAAATTAATTTTTAATTAA
ATCGAAACAAGATTTAGATGCTCGTAAAAACAAATTCTTAAATCTAATGTGGCTGAGATTTGATT
TGATGAATATAGATACCTCAAGGAGTCTTGGAGCCAAAAATCATGCAAAATGAGTCGGGCCCAGA
AAACGATTTTTTAGCCAAAAACTGTAATGTTTAGTACACAATTTCAGCTAAAATTTTGTAAAAAT
TGACACGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAACTCAACACC
AAAAAG
Found at i:5521 original size:15 final size:16
Alignment explanation
Indices: 5503--5532 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5493 ATAAATAATA
5503 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
5518 ATATTATAATCTAAA
1 ATATTATAATCTAAA
5533 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:6137 original size:45 final size:45
Alignment explanation
Indices: 6083--6208 Score: 216
Period size: 45 Copynumber: 2.8 Consensus size: 45
6073 ATTCTACTAT
* *
6083 ATCTCTAGGTAATTCATCAAAATTAAGCGAATATTATACTCCTCC
1 ATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTCC
* *
6128 ATTTCTAGGTAATTCATCAAAATAAAGCTAATATTCTACTCCTCC
1 ATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTCC
6173 ATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
1 ATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
6209 ATTGTTGCTT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 75 1.00
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (45 bp):
ATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTCC
Found at i:8323 original size:53 final size:53
Alignment explanation
Indices: 8264--8365 Score: 186
Period size: 53 Copynumber: 1.9 Consensus size: 53
8254 AACCAAGCAA
*
8264 ATCCTAAATATTTGAATCTTAATAAAAAGATTGAGCTTTCACCAACAAAATAT
1 ATCCTAAATATTTGAATCTTAATAAAAAGATTGAACTTTCACCAACAAAATAT
*
8317 ATCCTAAATATTTGAATCTTAATAAAAAGATTGAACTTTCACTAACAAA
1 ATCCTAAATATTTGAATCTTAATAAAAAGATTGAACTTTCACCAACAAA
8366 TTGTAAGTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (53 bp):
ATCCTAAATATTTGAATCTTAATAAAAAGATTGAACTTTCACCAACAAAATAT
Found at i:10858 original size:3 final size:3
Alignment explanation
Indices: 10850--10890 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
10840 TGGGAAGAGT
*
10850 TTA TTA TTAA TTA TTA TCA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
10891 GATGATATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 28 0.82
4 6 0.18
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:17194 original size:2 final size:2
Alignment explanation
Indices: 17187--17218 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
17177 TAATATTTAG
*
17187 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17219 CTACTATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:31253 original size:21 final size:21
Alignment explanation
Indices: 31229--31271 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
31219 ATGATCATAC
31229 AAATGAACAAAATTT-TCCAAA
1 AAATGAA-AAAATTTCTCCAAA
*
31250 AAATGAAAAAGTTTCTCCAAA
1 AAATGAAAAAATTTCTCCAAA
31271 A
1 A
31272 GGCTCGCCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.56, C:0.14, G:0.07, T:0.23
Consensus pattern (21 bp):
AAATGAAAAAATTTCTCCAAA
Found at i:35320 original size:36 final size:32
Alignment explanation
Indices: 35250--35315 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
35240 CAATCCATCC
35250 ATTCTTATATTTCTTAAAACTTGAATAAATAA
1 ATTCTTATATTTCTTAAAACTTGAATAAATAA
35282 ATTCTTATATTTCTTAAAACTTGAATAAATAA
1 ATTCTTATATTTCTTAAAACTTGAATAAATAA
35314 AT
1 AT
35316 AAATTAAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (32 bp):
ATTCTTATATTTCTTAAAACTTGAATAAATAA
Found at i:39953 original size:12 final size:12
Alignment explanation
Indices: 39938--39962 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39928 AAAAACAAAA
39938 AAAAAAAAAGAG
1 AAAAAAAAAGAG
39950 AAAAAAAAAGAG
1 AAAAAAAAAGAG
39962 A
1 A
39963 GAAACGTCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAG
Found at i:39953 original size:14 final size:14
Alignment explanation
Indices: 39936--39966 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
39926 CCAAAAACAA
39936 AAAAAAAAAAAGAG
1 AAAAAAAAAAAGAG
*
39950 AAAAAAAAAGAGAG
1 AAAAAAAAAAAGAG
39964 AAA
1 AAA
39967 CGTCAGGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGAG
Found at i:44940 original size:3 final size:3
Alignment explanation
Indices: 44926--44955 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
44916 ATTTGGTTGC
*
44926 AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
44956 CAGGGTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:54468 original size:16 final size:16
Alignment explanation
Indices: 54449--54491 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
54439 CCGTTCGAGT
* *
54449 CCGAACCCGAAATTAC
1 CCGAATCCGAAAATAC
* *
54465 CCGAGTCTGAAAATAC
1 CCGAATCCGAAAATAC
54481 CCGAATCCGAA
1 CCGAATCCGAA
54492 CCCGATCCGA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.33, G:0.16, T:0.14
Consensus pattern (16 bp):
CCGAATCCGAAAATAC
Found at i:54496 original size:12 final size:12
Alignment explanation
Indices: 54479--54520 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
54469 GTCTGAAAAT
54479 ACCCGAATCCGA
1 ACCCGAATCCGA
54491 ACCCG-ATCCGA
1 ACCCGAATCCGA
*
54502 GA-CCGAGTCCGA
1 -ACCCGAATCCGA
54514 ACCCGAA
1 ACCCGAA
54521 ATAATTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.31, C:0.40, G:0.21, T:0.07
Consensus pattern (12 bp):
ACCCGAATCCGA
Found at i:55027 original size:31 final size:31
Alignment explanation
Indices: 54956--55027 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
54946 GTCTATCAGC
*
54956 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
54987 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
55017 GTTTTAATTTG
1 -TTTTAATTTG
55028 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:55335 original size:17 final size:17
Alignment explanation
Indices: 55313--55348 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
55303 TCAAAATCAA
55313 ACCCGAGCCCGAACCCG
1 ACCCGAGCCCGAACCCG
*
55330 ACCCGAGCCTGAACCCG
1 ACCCGAGCCCGAACCCG
55347 AC
1 AC
55349 TTAACCCGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.50, G:0.22, T:0.03
Consensus pattern (17 bp):
ACCCGAGCCCGAACCCG
Found at i:57254 original size:2 final size:2
Alignment explanation
Indices: 57247--57277 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
57237 GACCTTTATT
57247 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
57278 TAACACCCGT
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:61586 original size:1 final size:1
Alignment explanation
Indices: 61580--61604 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
61570 TTAGTAAGAG
61580 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
61605 CATAACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:62314 original size:2 final size:2
Alignment explanation
Indices: 62307--62341 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
62297 TGATTCATAA
62307 AT AT AT AT AT 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 AT AT A
62342 CACACACTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:62621 original size:12 final size:12
Alignment explanation
Indices: 62604--62628 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
62594 AGTTCCATAT
62604 AGTTCAAAAGGC
1 AGTTCAAAAGGC
62616 AGTTCAAAAGGC
1 AGTTCAAAAGGC
62628 A
1 A
62629 AAAAGGCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (12 bp):
AGTTCAAAAGGC
Found at i:63343 original size:16 final size:17
Alignment explanation
Indices: 63310--63348 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
63300 ACTAGACTCG
63310 AAACTGACTCGAAAAAAC
1 AAACTGACTC-AAAAAAC
*
63328 GAACTGACTC-AAAAAC
1 AAACTGACTCAAAAAAC
63344 AAACT
1 AAACT
63349 AAAAAAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.54, C:0.23, G:0.10, T:0.13
Consensus pattern (17 bp):
AAACTGACTCAAAAAAC
Found at i:63737 original size:47 final size:47
Alignment explanation
Indices: 63677--63768 Score: 166
Period size: 47 Copynumber: 2.0 Consensus size: 47
63667 GTAATTTTCT
*
63677 AACCTTAATTATCAGACGCATTGAAAAAATTAAAGCATTGAAAATGA
1 AACCTTAATTATCAAACGCATTGAAAAAATTAAAGCATTGAAAATGA
*
63724 AACCTTAATTATCAAACGCATTGAAAAAATTAAAGTATTGAAAAT
1 AACCTTAATTATCAAACGCATTGAAAAAATTAAAGCATTGAAAAT
63769 TTTCATTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.27
Consensus pattern (47 bp):
AACCTTAATTATCAAACGCATTGAAAAAATTAAAGCATTGAAAATGA
Found at i:72875 original size:3 final size:3
Alignment explanation
Indices: 72867--72893 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
72857 TAAGGAAATT
72867 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
72894 AAACCCTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:94215 original size:31 final size:31
Alignment explanation
Indices: 94177--94236 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
94167 TTAGAAAAAC
* *
94177 TTATTTATCCAGCTTAAGCAGGTCTCGAGAT
1 TTATTTATCCAGCTTAAACAGGTATCGAGAT
*
94208 TTATTTATCCAGTTTAAACAGGTATCGAG
1 TTATTTATCCAGCTTAAACAGGTATCGAG
94237 TTCGAGACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (31 bp):
TTATTTATCCAGCTTAAACAGGTATCGAGAT
Found at i:101050 original size:30 final size:30
Alignment explanation
Indices: 101016--101090 Score: 127
Period size: 28 Copynumber: 2.6 Consensus size: 30
101006 GTTCTCCTTC
101016 ATCTGCAATGACTATTTTTTTTGGCCACAT
1 ATCTGCAATGACTATTTTTTTTGGCCACAT
*
101046 ATCTGCAATGACTA--TTTTTTGGCTACAT
1 ATCTGCAATGACTATTTTTTTTGGCCACAT
101074 ATCTGCAATGACTATTT
1 ATCTGCAATGACTATTT
101091 ATGCAATCAG
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 27 0.64
30 15 0.36
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (30 bp):
ATCTGCAATGACTATTTTTTTTGGCCACAT
Found at i:108498 original size:31 final size:30
Alignment explanation
Indices: 108431--108503 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
108421 ATTCACTGTC
* *
108431 TTTTCTCAAAATGACCAAATAAGCCCTTTA
1 TTTTTTCAAAATGACCAAATAAGCCCTTAA
*
108461 TCTTTTTCAAAATGACTAAATAAG-CCTTCAAA
1 T-TTTTTCAAAATGACCAAATAAGCCCTT--AA
*
108493 TTTTTTTAAAA
1 TTTTTTCAAAA
108504 AAATTTTACA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 5 0.14
31 29 0.81
32 2 0.06
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38
Consensus pattern (30 bp):
TTTTTTCAAAATGACCAAATAAGCCCTTAA
Found at i:109054 original size:35 final size:35
Alignment explanation
Indices: 109008--109076 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
108998 TTAAAAATTA
* *
109008 TTCAGACAGAAATACACACTTGCGCGCACACATTG
1 TTCAGACAGAAATACACACGTACGCGCACACATTG
*
109043 TTCAGACAGAAATACACACGTACGTGCACACATT
1 TTCAGACAGAAATACACACGTACGCGCACACATT
109077 TTTATTTGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Consensus pattern (35 bp):
TTCAGACAGAAATACACACGTACGCGCACACATTG
Found at i:110187 original size:114 final size:110
Alignment explanation
Indices: 109948--110239 Score: 311
Period size: 114 Copynumber: 2.6 Consensus size: 110
109938 TTAGAAAGCG
** * * * *
109948 ATACATTCGAAGTAATCACTCGATTAGGGCCAGGTGGCACAAACAAAAAGAG--ATAGCCTTTAC
1 ATACATTCGGGGTAATCACTCGATTAGAGTCAGGTGGCACAAACAAAAAGAGAAAAAGCCCTTAC
** ** * *
110011 TCTTGCAACTTTTTTTGGCATAGACAGATTTGAATGAGGAGAGCT
66 TCTACCAACTTTTTCGGGCATAGAAAGAGTTGAATGAGGAGAGCT
* * *
110056 ATATAATCGGGGTAATCACTTGATTAGAGTCAGGTGGCACAAACAAAAAGAGACAAAAGCCCTTA
1 ATACATTCGGGGTAATCACTCGATTAGAGTCAGGTGGCACAAACAAAAAGAGA-AAAAGCCCTTA
* * * *
110121 CTCTACCAGTCTTTTTCGGGTATAGAAAAAGAGTTGAATTAGGAGATCT
65 CTCTACCA-ACTTTTTCGGGCATAG--AAAGAGTTGAATGAGGAGAGCT
* * *
110170 ATACATTCGGGGTAATCACGCGATCA-AGGTCAGGTGGCACAAACAAAAAGAGATATAAGCCCTT
1 ATACATTCGGGGTAATCACTCGATTAGA-GTCAGGTGGCACAAACAAAAAGAGA-AAAAGCCCTT
110234 ACTCTA
64 ACTCTA
110240 TACCAACCCT
Statistics
Matches: 151, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
108 45 0.30
111 14 0.09
112 12 0.08
113 1 0.01
114 79 0.52
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (110 bp):
ATACATTCGGGGTAATCACTCGATTAGAGTCAGGTGGCACAAACAAAAAGAGAAAAAGCCCTTAC
TCTACCAACTTTTTCGGGCATAGAAAGAGTTGAATGAGGAGAGCT
Found at i:113844 original size:22 final size:22
Alignment explanation
Indices: 113796--113844 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
113786 TTGCCCTTCT
*
113796 TCTCT-CTCCCCCCACTAACTC
1 TCTCTCCTCCCCCCACTAACTA
* * *
113817 TTTCTCCTCCTCCCACTCACTA
1 TCTCTCCTCCCCCCACTAACTA
113839 TCTCTC
1 TCTCTC
113845 TTCATGAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.12, C:0.53, G:0.00, T:0.35
Consensus pattern (22 bp):
TCTCTCCTCCCCCCACTAACTA
Found at i:121705 original size:15 final size:16
Alignment explanation
Indices: 121679--121709 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
121669 ATGAAAAGAC
121679 AAATTAGAGAAAAATA
1 AAATTAGAGAAAAATA
121695 AAATT-GAGAAAAATA
1 AAATTAGAGAAAAATA
121710 GAGCCACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (16 bp):
AAATTAGAGAAAAATA
Found at i:124964 original size:18 final size:17
Alignment explanation
Indices: 124943--124981 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
124933 GTGATGATGA
124943 TGATGAGAGTGATTCCAG
1 TGATGAGAG-GATTCCAG
124961 TGAT--GAGGATTCCAG
1 TGATGAGAGGATTCCAG
124976 TGATGA
1 TGATGA
124982 AGACAGTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
15 12 0.63
16 3 0.16
18 4 0.21
ACGTcount: A:0.28, C:0.10, G:0.33, T:0.28
Consensus pattern (17 bp):
TGATGAGAGGATTCCAG
Found at i:124971 original size:15 final size:15
Alignment explanation
Indices: 124953--124981 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
124943 TGATGAGAGT
124953 GATTCCAGTGATGAG
1 GATTCCAGTGATGAG
124968 GATTCCAGTGATGA
1 GATTCCAGTGATGA
124982 AGACAGTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.28
Consensus pattern (15 bp):
GATTCCAGTGATGAG
Found at i:126575 original size:52 final size:52
Alignment explanation
Indices: 126460--126673 Score: 376
Period size: 52 Copynumber: 4.1 Consensus size: 52
126450 AAAAATGAAA
*
126460 TTTGAGTAAAAAAAAAAGACCTATAATAGTTCCAATAATAATAAGGAAAAGG
1 TTTGAGTAAAAAAAAAAGACCTATAATAATTCCAATAATAATAAGGAAAAGG
126512 TTTGAGT-AAAAAAAAAGACCTATAATAATTCCAATAATAATAAGGAAAAGG
1 TTTGAGTAAAAAAAAAAGACCTATAATAATTCCAATAATAATAAGGAAAAGG
126563 TTTGAGTAAAAAAAAAAGACCTATAATAATTCCAATAATAATAAGGAAAAGG
1 TTTGAGTAAAAAAAAAAGACCTATAATAATTCCAATAATAATAAGGAAAAGG
126615 TTTGAGTAAAAAAAAAAAAAAGACCTATAATAATTCCAATAATAATAAGGAAAAGG
1 TTTGAGT----AAAAAAAAAAGACCTATAATAATTCCAATAATAATAAGGAAAAGG
126671 TTT
1 TTT
126674 TGGGAGTACT
Statistics
Matches: 156, Mismatches: 1, Indels: 6
0.96 0.01 0.04
Matches are distributed among these distances:
51 50 0.32
52 58 0.37
56 48 0.31
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (52 bp):
TTTGAGTAAAAAAAAAAGACCTATAATAATTCCAATAATAATAAGGAAAAGG
Found at i:127364 original size:97 final size:95
Alignment explanation
Indices: 127177--127629 Score: 525
Period size: 97 Copynumber: 4.7 Consensus size: 95
127167 ACATTAAGTC
* *
127177 TAAGTCTCGGTTCAAGTAGGATTCATAGCT-CATTTAACCTCGATTAATTCAAAGTCGAGTCAAG
1 TAAGTCTCGGTTCAAGTAGGATTCATAGCTACATTTAACCT-GACTAATTCAAAGTCGAGTCGAG
* * * * *
127241 TCACGTTTAACTCCCGAGTTTTGTAGCCACAT
65 TCACATTGAAC-CCAGAATTTGGTAGCCACAT
* * *
127273 TAAGTCTCGGTTCAAGTAGGATTTATAGCTACATTTGACCCTGACAAATTCAAAGTCGAGTCGAG
1 TAAGTCTCGGTTCAAGTAGGATTCATAGCTACATTT-AACCTGACTAATTCAAAGTCGAGTCGAG
** *
127338 TCACATTGAACCACAGGGTTCGGTAGCCACAT
65 TCACATTGAACC-CAGAATTTGGTAGCCACAT
*
127370 TAAGTCTCGGTTCAAGTAGGATTCATAGCTACATTTAACCCCGACTAATTCAAAGTCGAGTCGAG
1 TAAGTCTCGGTTCAAGTAGGATTCATAGCTACATTTAA-CCTGACTAATTCAAAGTCGAGTCGAG
* *
127435 TCACATTAAATACCC-GAATTTGGTAGCCACGT
65 TCACATT-GA-ACCCAGAATTTGGTAGCCACAT
** ** * * * * *
127467 TAAGTCTTAGTTCACTTAGGATTCATAGCTACATTTAACCTCGACAAATTCAATGTCAAGCCAAG
1 TAAGTCTCGGTTCAAGTAGGATTCATAGCTACATTTAACCT-GACTAATTCAAAGTCGAGTCGAG
127532 TTCACATTGAACCCCCA-AATTTGGTAGCCACAT
65 -TCACATTGAA--CCCAGAATTTGGTAGCCACAT
* * *
127565 TAAGTCTCAGTTCAAGTAGGATTCGTAGCTACATTTAATCCTAACTAATTCAAAGTCGAGTCGAG
1 TAAGTCTCGGTTCAAGTAGGATTCATAGCTACATTTAA-CCTGACTAATTCAAAGTCGAGTCGAG
127630 ACACTTTAAA
Statistics
Matches: 303, Mismatches: 42, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
96 34 0.11
97 181 0.60
98 82 0.27
99 6 0.02
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (95 bp):
TAAGTCTCGGTTCAAGTAGGATTCATAGCTACATTTAACCTGACTAATTCAAAGTCGAGTCGAGT
CACATTGAACCCAGAATTTGGTAGCCACAT
Found at i:127499 original size:194 final size:194
Alignment explanation
Indices: 127177--127639 Score: 610
Period size: 194 Copynumber: 2.4 Consensus size: 194
127167 ACATTAAGTC
* * *
127177 TAAGTCTCGGTTCAAGTAGGATTCATAGCT-CATTTAACCTCGATTAATTCAAAGTCGAGTCAAG
1 TAAGTCTCGGTTCAAGTAGGATTCATAGCTACATTTAACCCCGACTAATTCAAAGTCGAGTCGAG
* * * * *
127241 TCACGTTTAACTCCCGAGTTTTGTAGCCACATTAAGTCTCGGTTCAAGTAGGATTTATAGCTACA
66 TCAC-TTTAAATCCCGAATTTGGTAGCCACATTAAGTCTCAGTTCAAGTAGGATTCATAGCTACA
* * * * **
127306 TTTGACC-CTGACAAATTCAAAGTCGAGTCGAG-TCACATTGAA-CCACAGGGTTCGGTAGCCAC
130 TTTAACCTC-GACAAATTCAAAGTCAAGCCAAGTTCACATTGAACCCACA-AATTCGGTAGCCAC
127368 AT
193 AT
127370 TAAGTCTCGGTTCAAGTAGGATTCATAGCTACATTTAACCCCGACTAATTCAAAGTCGAGTCGAG
1 TAAGTCTCGGTTCAAGTAGGATTCATAGCTACATTTAACCCCGACTAATTCAAAGTCGAGTCGAG
* * * **
127435 TCACATTAAATACCCGAATTTGGTAGCCACGTTAAGTCTTAGTTCACTTAGGATTCATAGCTACA
66 TCACTTTAAAT-CCCGAATTTGGTAGCCACATTAAGTCTCAGTTCAAGTAGGATTCATAGCTACA
* * *
127500 TTTAACCTCGACAAATTCAATGTCAAGCCAAGTTCACATTGAACCCCCAAATTTGGTAGCCACAT
130 TTTAACCTCGACAAATTCAAAGTCAAGCCAAGTTCACATTGAACCCACAAATTCGGTAGCCACAT
* * * **
127565 TAAGTCTCAGTTCAAGTAGGATTCGTAGCTACATTTAATCCTAACTAATTCAAAGTCGAGTCGAG
1 TAAGTCTCGGTTCAAGTAGGATTCATAGCTACATTTAACCCCGACTAATTCAAAGTCGAGTCGAG
*
127630 ACACTTTAAA
66 TCACTTTAAA
127640 CCCCAAATGA
Statistics
Matches: 236, Mismatches: 29, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
193 35 0.15
194 105 0.44
195 92 0.39
196 4 0.02
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (194 bp):
TAAGTCTCGGTTCAAGTAGGATTCATAGCTACATTTAACCCCGACTAATTCAAAGTCGAGTCGAG
TCACTTTAAATCCCGAATTTGGTAGCCACATTAAGTCTCAGTTCAAGTAGGATTCATAGCTACAT
TTAACCTCGACAAATTCAAAGTCAAGCCAAGTTCACATTGAACCCACAAATTCGGTAGCCACAT
Found at i:127836 original size:58 final size:58
Alignment explanation
Indices: 127766--127883 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
127756 TTTTCTCATT
*
127766 TCTCTCAATAGTTACATTAAAGTATCGGTTCAAATTCTCCCAATAACCACATTAAGTC
1 TCTCTCAATAGTTACATTAAAATATCGGTTCAAATTCTCCCAATAACCACATTAAGTC
127824 TCTCTCAATAGTTACATTAAAATATCGGTTCAAATTCTCCCAATAACCACATTAAGTC
1 TCTCTCAATAGTTACATTAAAATATCGGTTCAAATTCTCCCAATAACCACATTAAGTC
127882 TC
1 TC
127884 AGTTCAAGTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.33
Consensus pattern (58 bp):
TCTCTCAATAGTTACATTAAAATATCGGTTCAAATTCTCCCAATAACCACATTAAGTC
Found at i:129895 original size:1 final size:1
Alignment explanation
Indices: 129889--129951 Score: 72
Period size: 1 Copynumber: 63.0 Consensus size: 1
129879 CTCCTAACAT
* ** * **
129889 AAAAAAAAAAAAAACAAAAAAAAACGAAAAAAAAACAAAAAAAAAAAACTAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
129952 CGGAAAATTC
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.90, C:0.06, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:129918 original size:24 final size:23
Alignment explanation
Indices: 129891--129951 Score: 95
Period size: 24 Copynumber: 2.6 Consensus size: 23
129881 CCTAACATAA
129891 AAAAAAAAAAAACAAAAAAAAACG
1 AAAAAAAAAAAA-AAAAAAAAACG
*
129915 AAAAAAAAACAAAAAAAAAAAACT
1 AAAAAAAAA-AAAAAAAAAAAACG
129939 AAAAAAAAAAAAA
1 AAAAAAAAAAAAA
129952 CGGAAAATTC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
23 4 0.11
24 28 0.80
25 3 0.09
ACGTcount: A:0.90, C:0.07, G:0.02, T:0.02
Consensus pattern (23 bp):
AAAAAAAAAAAAAAAAAAAAACG
Found at i:129920 original size:21 final size:21
Alignment explanation
Indices: 129894--129958 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
129884 AACATAAAAA
129894 AAAAAAAAACAAAAAAAAACG
1 AAAAAAAAACAAAAAAAAACG
129915 AAAAAAAAACAAAAAAAAA--
1 AAAAAAAAACAAAAAAAAACG
**
129934 AAACTAAAA-AAAAAAAAACG
1 AAAAAAAAACAAAAAAAAACG
*
129954 GAAAA
1 AAAAA
129959 TTCATAAAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
18 9 0.24
19 7 0.19
20 2 0.05
21 19 0.51
ACGTcount: A:0.86, C:0.08, G:0.05, T:0.02
Consensus pattern (21 bp):
AAAAAAAAACAAAAAAAAACG
Found at i:129958 original size:16 final size:15
Alignment explanation
Indices: 129890--129958 Score: 57
Period size: 15 Copynumber: 4.3 Consensus size: 15
129880 TCCTAACATA
*
129890 AAAAAAAAAAAAACAA
1 AAAAAAAAAAAAAC-G
**
129906 AAAAAAACGAAAAAAAA
1 AAAAAAA--AAAAAACG
*
129923 ACAAAAAAAAAAAACT
1 A-AAAAAAAAAAAACG
129939 AAAAAAAAAAAAACG
1 AAAAAAAAAAAAACG
*
129954 GAAAA
1 AAAAA
129959 TTCATAAAGG
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
15 17 0.38
16 14 0.31
17 2 0.04
18 12 0.27
ACGTcount: A:0.87, C:0.07, G:0.04, T:0.01
Consensus pattern (15 bp):
AAAAAAAAAAAAACG
Found at i:131704 original size:41 final size:42
Alignment explanation
Indices: 131645--131726 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 42
131635 TTTAATCAAT
* * *
131645 CAATCCAATTAAATTTTTGAATAGA-TTAGAATCTATTAACA
1 CAATCCAATTAAAATTTTGAAGAAATTTAGAATCTATTAACA
*
131686 CAATCTAATTAAAATTTTGAAGAAATTTAGAATCTATTAAC
1 CAATCCAATTAAAATTTTGAAGAAATTTAGAATCTATTAAC
131727 TAAAATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 21 0.58
42 15 0.42
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (42 bp):
CAATCCAATTAAAATTTTGAAGAAATTTAGAATCTATTAACA
Found at i:134800 original size:23 final size:24
Alignment explanation
Indices: 134744--134801 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 24
134734 TGAAATTGTA
134744 TATTAATGAGTGTGGGATAGCTCCC
1 TATTAAT-AGTGTGGGATAGCTCCC
* *
134769 TATTTATAGTTTGGGA-AGCTCCC
1 TATTAATAGTGTGGGATAGCTCCC
134792 T-TATAATAGT
1 TAT-TAATAGT
134802 AAAATATCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 1 0.03
23 14 0.48
24 8 0.28
25 6 0.21
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (24 bp):
TATTAATAGTGTGGGATAGCTCCC
Found at i:148837 original size:26 final size:26
Alignment explanation
Indices: 148808--148857 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
148798 CCTTTAACTC
148808 AAAAAACAGAGCAAAAACAGGGGACG
1 AAAAAACAGAGCAAAAACAGGGGACG
148834 AAAAAACAGAGCAAAAACAGGGGA
1 AAAAAACAGAGCAAAAACAGGGGA
148858 GGAGTGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.60, C:0.14, G:0.26, T:0.00
Consensus pattern (26 bp):
AAAAAACAGAGCAAAAACAGGGGACG
Found at i:149931 original size:16 final size:16
Alignment explanation
Indices: 149906--149939 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
149896 CCTACCAAAT
*
149906 AATAATTCTAAAACAA
1 AATAACTCTAAAACAA
*
149922 AATAACTCTAACACAA
1 AATAACTCTAAAACAA
149938 AA
1 AA
149940 AAATCCCATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.18, G:0.00, T:0.21
Consensus pattern (16 bp):
AATAACTCTAAAACAA
Found at i:152554 original size:19 final size:19
Alignment explanation
Indices: 152518--152554 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
152508 AAAGAACAAT
*
152518 GGTAAAAATATAAGATAAA
1 GGTAAAAATACAAGATAAA
*
152537 GGTAAAAATACAATATAA
1 GGTAAAAATACAAGATAA
152555 TGGGACAGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.14, T:0.22
Consensus pattern (19 bp):
GGTAAAAATACAAGATAAA
Found at i:154248 original size:20 final size:19
Alignment explanation
Indices: 154219--154259 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
154209 CAAGAGTAAG
154219 AATTTAAGGTGTGCACCAC
1 AATTTAAGGTGTGCACCAC
154238 AATTGTAAGGTGTGCACCAC
1 AATT-TAAGGTGTGCACCAC
154258 AA
1 AA
154260 GAGGGTGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (19 bp):
AATTTAAGGTGTGCACCAC
Found at i:155423 original size:13 final size:13
Alignment explanation
Indices: 155405--155429 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
155395 TATAAAGTTT
155405 GTAGTAGTAATTA
1 GTAGTAGTAATTA
155418 GTAGTAGTAATT
1 GTAGTAGTAATT
155430 TATTACTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (13 bp):
GTAGTAGTAATTA
Found at i:158566 original size:10 final size:10
Alignment explanation
Indices: 158551--158588 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
158541 TTTAGAAATA
158551 TATCTATATC
1 TATCTATATC
158561 TATCTATATC
1 TATCTATATC
158571 TAT-T-TATC
1 TATCTATATC
158579 TATACTATAT
1 TAT-CTATAT
158589 AAAAAGTACG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.28
9 1 0.04
10 14 0.56
11 3 0.12
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.53
Consensus pattern (10 bp):
TATCTATATC
Found at i:158921 original size:21 final size:22
Alignment explanation
Indices: 158897--159018 Score: 106
Period size: 22 Copynumber: 5.6 Consensus size: 22
158887 AATTTTGGAA
* *
158897 GTTATCAAAA-TTCATTGTGTG
1 GTTATCAAAATTTTATAGTGTG
*
158918 GTTA-CTAAAATTTTATAGTGCG
1 GTTATC-AAAATTTTATAGTGTG
*
158940 GTTTTCAAAATTTTATAGTGTG
1 GTTATCAAAATTTTATAGTGTG
* *
158962 GTTACCAAAATTTCATAG-GTAG
1 GTTATCAAAATTTTATAGTGT-G
* * * *
158984 GATGTTAAAATTTTATAGTGTA
1 GTTATCAAAATTTTATAGTGTG
*
159006 GTTATCACAATTT
1 GTTATCAAAATTT
159019 CATGGGATGT
Statistics
Matches: 78, Mismatches: 18, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
20 1 0.01
21 10 0.13
22 64 0.82
23 3 0.04
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (22 bp):
GTTATCAAAATTTTATAGTGTG
Found at i:159136 original size:22 final size:22
Alignment explanation
Indices: 159030--159221 Score: 104
Period size: 22 Copynumber: 8.8 Consensus size: 22
159020 ATGGGATGTT
* * *
159030 AAATTTCATAAGGAGGTTATCG
1 AAATTTCATAGGGAGATTATCA
* *
159052 AAA-TTCAT-GGGAAGGTTGTCA
1 AAATTTCATAGGG-AGATTATCA
* *
159073 AAATTTCACAGGGAGATTACCA
1 AAATTTCATAGGGAGATTATCA
**** *
159095 AAATTTCATATCCTGGTTATCA
1 AAATTTCATAGGGAGATTATCA
* *
159117 AAATTTCATAGGGCGATTATCG
1 AAATTTCATAGGGAGATTATCA
* *
159139 AAATCTT-ATATGGA-AGTTATTA
1 AAAT-TTCATAGGGAGA-TTATCA
* * *
159161 TAATTTTATAGGAAGATTATCA
1 AAATTTCATAGGGAGATTATCA
* * * *
159183 AAATTTCATAGTGTGCTTATAA
1 AAATTTCATAGGGAGATTATCA
* *
159205 AAATTACATAGTGAGAT
1 AAATTTCATAGGGAGAT
159222 AGAGTGAGCT
Statistics
Matches: 125, Mismatches: 38, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
20 2 0.02
21 18 0.14
22 99 0.79
23 6 0.05
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (22 bp):
AAATTTCATAGGGAGATTATCA
Found at i:159333 original size:22 final size:23
Alignment explanation
Indices: 159297--159351 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
159287 ATAGAGGTAA
*
159297 CAAAATTTCATAGGGAAG-TTAT
1 CAAAATTTCAGAGGGAAGATTAT
* * *
159319 CGAAATTTTAGAGGGGAGATTAT
1 CAAAATTTCAGAGGGAAGATTAT
159342 CAAAATTTCA
1 CAAAATTTCA
159352 TAGTGTGGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (23 bp):
CAAAATTTCAGAGGGAAGATTAT
Found at i:159404 original size:61 final size:60
Alignment explanation
Indices: 159323--159439 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 60
159313 AGTTATCGAA
* *
159323 ATTTTAGAGGGGAGATTATCAAAATTTCATAGTGTGGTTA-ATAAAATTTTATAATGTGGT
1 ATTTCAGAGGGGAGATTATCAAAATTTCATAGTGTGG-TAGATAAAATTTCATAATGTGGT
* * *
159383 ATTTCAGAGGGAGAGATTATCAAATTTTCATTGTGTGGTAGTTAAAATTTCATAATG
1 ATTTCAGAGGG-GAGATTATCAAAATTTCATAGTGTGGTAGATAAAATTTCATAATG
159440 AGTGTATCGA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 12 0.24
61 38 0.76
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.39
Consensus pattern (60 bp):
ATTTCAGAGGGGAGATTATCAAAATTTCATAGTGTGGTAGATAAAATTTCATAATGTGGT
Found at i:159473 original size:21 final size:22
Alignment explanation
Indices: 159426--159524 Score: 85
Period size: 22 Copynumber: 4.5 Consensus size: 22
159416 TGTGGTAGTT
* *
159426 AAAATTTCATAATGAG-TGTATC
1 AAAATTTCATAGTGAGAT-TAAC
*
159448 GAAATTT-ATAGTGAGATTAAC
1 AAAATTTCATAGTGAGATTAAC
* * * **
159469 AAAATTTGATAGTGTGGTTCTC
1 AAAATTTCATAGTGAGATTAAC
* *
159491 AAAATTTTATAGGGAGATTAAC
1 AAAATTTCATAGTGAGATTAAC
159513 AAAATTTCATAG
1 AAAATTTCATAG
159525 GTAAGTTATC
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
21 16 0.27
22 44 0.73
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.35
Consensus pattern (22 bp):
AAAATTTCATAGTGAGATTAAC
Found at i:159541 original size:44 final size:42
Alignment explanation
Indices: 159426--159541 Score: 108
Period size: 44 Copynumber: 2.6 Consensus size: 42
159416 TGTGGTAGTT
* * *
159426 AAAATTTCATA-ATGAGTGTATCGAAATTTATAGTGAGATTAAC
1 AAAATTTCATAGGT-AGT-TATCGAATTTTATAGGGAGATTAAC
* * * *
159469 AAAATTTGATAGTGTGGTTCTCAAAATTTTATAGGGAGATTAAC
1 AAAATTTCATAG-GTAGTTATC-GAATTTTATAGGGAGATTAAC
159513 AAAATTTCATAGGTAAGTTATCGTAATTT
1 AAAATTTCATAGGT-AGTTATCG-AATTT
159542 CATGGTGTAA
Statistics
Matches: 57, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
43 15 0.26
44 41 0.72
45 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (42 bp):
AAAATTTCATAGGTAGTTATCGAATTTTATAGGGAGATTAAC
Found at i:159582 original size:21 final size:21
Alignment explanation
Indices: 159556--159806 Score: 109
Period size: 22 Copynumber: 11.7 Consensus size: 21
159546 GTGTAATTAA
**
159556 TTATCAAAATTTTGTTGGGGG
1 TTATCAAAATTTCATTGGGGG
159577 TTATCAAAATTTCATTGGGGG
1 TTATCAAAATTTCATTGGGGG
* * ***
159598 TTATCAAAATTTAATAGTGTTC
1 TTATCAAAATTTCATTG-GGGG
* * *
159620 TTATCAAAATTTCGTAGGAGG
1 TTATCAAAATTTCATTGGGGG
* * *
159641 TTAACAAAAGTTT-ATAAGGAGG
1 TTATCAAAA-TTTCAT-TGGGGG
* * **
159663 TTATAAAAAATTT-ATAGGATG
1 TTAT-CAAAATTTCATTGGGGG
* **
159684 TTATCAAAATTTCATAAGATGG
1 TTATCAAAATTTCAT-TGGGGG
159706 TTATCAAAATTTCA-TGAGGTGG
1 TTATCAAAATTTCATTG-GG-GG
* * *
159728 TTTTCAAAATTTCA-T-GAGA
1 TTATCAAAATTTCATTGGGGG
* * *
159747 TTATCAAAATTTGAAATGGAGG
1 TTATCAAAATTT-CATTGGGGG
*
159769 TTATCAAAATGTT-ATAGGGAGG
1 TTATCAAAAT-TTCATTGGG-GG
*
159791 TTTATAAAAATTTCAT
1 -TTATCAAAATTTCAT
159807 AGTGAGGTAT
Statistics
Matches: 181, Mismatches: 34, Indels: 28
0.74 0.14 0.12
Matches are distributed among these distances:
19 12 0.07
20 10 0.06
21 59 0.33
22 83 0.46
23 17 0.09
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (21 bp):
TTATCAAAATTTCATTGGGGG
Found at i:159776 original size:41 final size:43
Alignment explanation
Indices: 159577--159851 Score: 162
Period size: 43 Copynumber: 6.4 Consensus size: 43
159567 TTGTTGGGGG
* * * *
159577 TTATCAAAATTTCAT-TGGGGGTTATCAAAATTTAATAG-TGTTC
1 TTATCAAAATTTCATAAGGAGGTTATCAAAATTTCATAGATG--A
* * *
159620 TTATCAAAATTTCGT-AGGAGGTTAACAAAAGTTT-ATAAGGA-GG
1 TTATCAAAATTTCATAAGGAGGTTATCAAAA-TTTCAT-A-GATGA
* * *
159663 TTATAAAAAATTT-AT-AGGATGTTATCAAAATTTCATAAGATGG
1 TTAT-CAAAATTTCATAAGGAGGTTATCAAAATTTCAT-AGATGA
* * *
159706 TTATCAAAATTTCATGAGGTGGTTTTCAAAATTTCAT-GA-GA
1 TTATCAAAATTTCATAAGGAGGTTATCAAAATTTCATAGATGA
* * *
159747 TTATCAAAATTTGA-AATGGAGGTTATCAAAATGTT-ATAGGGAGGT
1 TTATCAAAATTTCATAA-GGAGGTTATCAAAAT-TTCATA--GATGA
* * * *
159792 TTATAAAAATTTCAT-AGTGAGG-TATCACAATTTCATGATATGT
1 TTATCAAAATTTCATAAG-GAGGTTATCAAAATTTCAT-AGATGA
159835 TTATCAAAATTTCATAA
1 TTATCAAAATTTCATAA
159852 TGTGATTACC
Statistics
Matches: 187, Mismatches: 25, Indels: 39
0.75 0.10 0.16
Matches are distributed among these distances:
40 1 0.01
41 29 0.16
42 16 0.09
43 77 0.41
44 43 0.23
45 21 0.11
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (43 bp):
TTATCAAAATTTCATAAGGAGGTTATCAAAATTTCATAGATGA
Found at i:159824 original size:129 final size:127
Alignment explanation
Indices: 159575--159849 Score: 310
Period size: 129 Copynumber: 2.1 Consensus size: 127
159565 TTTTGTTGGG
* * *
159575 GGTTATCAAAATTTCATTGGGGGTTATCAAAATTTAATAGTGTTCTTATCAAAATTTCGTAGGAG
1 GGTTATCAAAATTTCA-TGGGGGTTATCAAAATTTAATAGAG-TATTATCAAAATTTCGAAGGAG
*
159640 GTTAACAAAAGTTTATAAGGAGGTTATAAAAAATTTATAGGATGTTATCAAAATTTCATAAGAT
64 GTTAACAAAAGTTTATAAGGAGGTTATAAAAAATTTATAGGATGGTATCAAAATTTCATAAGAT
* *
159704 GGTTATCAAAATTTCATGAGGTGGTTTTCAAAATTTCAT-GAG-ATTATCAAAATTT-GAAATGG
1 GGTTATCAAAATTTCATG-GG-GGTTATCAAAATTTAATAGAGTATTATCAAAATTTCG-AA-GG
* * *
159766 AGGTTATCAAAA-TGTTATAGGGAGGTT-TATAAAAATTTCATAGTGA-GGTATCACAATTTCAT
62 AGGTTAACAAAAGT-TTATAAGGAGGTTATA-AAAAATTT-ATAG-GATGGTATCAAAATTTCAT
* *
159828 GATAT
123 AAGAT
*
159833 GTTTATCAAAATTTCAT
1 GGTTATCAAAATTTCAT
159850 AATGTGATTA
Statistics
Matches: 126, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
126 1 0.01
127 16 0.13
128 35 0.28
129 57 0.45
130 17 0.13
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (127 bp):
GGTTATCAAAATTTCATGGGGGTTATCAAAATTTAATAGAGTATTATCAAAATTTCGAAGGAGGT
TAACAAAAGTTTATAAGGAGGTTATAAAAAATTTATAGGATGGTATCAAAATTTCATAAGAT
Found at i:159843 original size:107 final size:106
Alignment explanation
Indices: 159658--159849 Score: 248
Period size: 107 Copynumber: 1.8 Consensus size: 106
159648 AAGTTTATAA
* * *
159658 GGAGGTTATAAAAAATTTATAGGATGTTATCAAAATTTCATAAGATGGTTATCAAAATTTCATGA
1 GGAGGTTATAAAAAATTTATAGGAGGTTATAAAAATTTCATAAGATGGGTATCAAAATTTCATGA
*
159723 GGTGGTTTTCAAAATTTCATGAGATTATCAAAATTTGAAAT
66 GATGGTTTTCAAAATTTCATGAGATTATCAAAATTTGAAAT
* *
159764 GGAGGTTAT-CAAAATGTTATAGGGAGGTTTATAAAAATTTCAT-AG-TGAGGTATCACAATTTC
1 GGAGGTTATAAAAAAT-TTATA-GGAGG-TTATAAAAATTTCATAAGATG-GGTATCAAAATTTC
*
159826 ATGATAT-GTTTATCAAAATTTCAT
62 ATGAGATGGTTT-TCAAAATTTCAT
159850 AATGTGATTA
Statistics
Matches: 74, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
105 5 0.07
106 20 0.27
107 35 0.47
108 14 0.19
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37
Consensus pattern (106 bp):
GGAGGTTATAAAAAATTTATAGGAGGTTATAAAAATTTCATAAGATGGGTATCAAAATTTCATGA
GATGGTTTTCAAAATTTCATGAGATTATCAAAATTTGAAAT
Found at i:159936 original size:22 final size:21
Alignment explanation
Indices: 159911--159980 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
159901 GCTTACCAAC
159911 ATTTCATTGGGAGTTTATTAAA
1 ATTTCATTGGGAG-TTATTAAA
* * *
159933 ATTTCATAAGGTAGTTATCAAA
1 ATTTCAT-TGGGAGTTATTAAA
*
159955 ATTTCATTAGGTG-GTTGTTAAA
1 ATTTCATT-GG-GAGTTATTAAA
159977 ATTT
1 ATTT
159981 TTATTAGGGA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
22 34 0.89
23 4 0.11
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (21 bp):
ATTTCATTGGGAGTTATTAAA
Found at i:160095 original size:22 final size:22
Alignment explanation
Indices: 160070--160136 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
160060 TATCGTCATA
*
160070 AAAACTTTATAGTGTAATTATC
1 AAAATTTTATAGTGTAATTATC
*
160092 AAAATTTTATA-TGGAGATTATC
1 AAAATTTTATAGTGTA-ATTATC
160114 AAAATTTTATAGTGT--TTATC
1 AAAATTTTATAGTGTAATTATC
160134 AAA
1 AAA
160137 TTTCATAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 8 0.20
21 3 0.08
22 27 0.68
23 2 0.05
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (22 bp):
AAAATTTTATAGTGTAATTATC
Found at i:162470 original size:21 final size:20
Alignment explanation
Indices: 162444--162507 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 20
162434 GCTGCTCTAA
162444 TAATCTCATCTGTACAGTATC
1 TAATCTCATCTGTACAGT-TC
* *
162465 TAATCTAATCTGTACAG-TG
1 TAATCTCATCTGTACAGTTC
162484 TAATCTCATCTGTACAGTTAC
1 TAATCTCATCTGTACAGTT-C
162505 TAA
1 TAA
162508 ACAGTGTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.46
20 1 0.03
21 19 0.51
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTTC
Found at i:162589 original size:21 final size:20
Alignment explanation
Indices: 162565--162608 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
162555 TTGACACTGT
162565 TTAGCAACTGTACAGATTAGA
1 TTAGCAACTGTACAGA-TAGA
**
162586 TTAGGTACTGTACAGATAGA
1 TTAGCAACTGTACAGATAGA
162606 TTA
1 TTA
162609 TTAGAGCAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.32
Consensus pattern (20 bp):
TTAGCAACTGTACAGATAGA
Found at i:163562 original size:20 final size:20
Alignment explanation
Indices: 163537--163577 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
163527 ACAACTAGAG
163537 CTGTTCAAGGGCCGGGCTAC
1 CTGTTCAAGGGCCGGGCTAC
*
163557 CTGTTCAAGGGTCGGGCTAC
1 CTGTTCAAGGGCCGGGCTAC
163577 C
1 C
163578 CGCCCAAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.29, G:0.34, T:0.22
Consensus pattern (20 bp):
CTGTTCAAGGGCCGGGCTAC
Found at i:163585 original size:20 final size:20
Alignment explanation
Indices: 163542--163586 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
163532 TAGAGCTGTT
* **
163542 CAAGGGCCGGGCTACCTGTT
1 CAAGGGCCGGGCTACCCGCC
*
163562 CAAGGGTCGGGCTACCCGCC
1 CAAGGGCCGGGCTACCCGCC
163582 CAAGG
1 CAAGG
163587 TCGTAAGCCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.33, G:0.36, T:0.13
Consensus pattern (20 bp):
CAAGGGCCGGGCTACCCGCC
Found at i:175199 original size:11 final size:11
Alignment explanation
Indices: 175183--175208 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
175173 AGATAATTTC
175183 TTTTCTTCTAG
1 TTTTCTTCTAG
175194 TTTTCTTCTAG
1 TTTTCTTCTAG
175205 TTTT
1 TTTT
175209 TTAGGCAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:184639 original size:13 final size:13
Alignment explanation
Indices: 184620--184656 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
184610 CCACAAACGT
*
184620 AAAATTTCCCAGC
1 AAAATTTCCCAGA
*
184633 CAAATTTCCCAGA
1 AAAATTTCCCAGA
184646 AAAATTTCCCA
1 AAAATTTCCCA
184657 AACACGCACG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.30, G:0.05, T:0.24
Consensus pattern (13 bp):
AAAATTTCCCAGA
Found at i:184965 original size:64 final size:66
Alignment explanation
Indices: 184850--184978 Score: 210
Period size: 64 Copynumber: 2.0 Consensus size: 66
184840 ATCTCTAATT
*
184850 TCCTTGATAAATCTGTATAGATCTATCTATAGTTTATGTTAATTTTTGCCTTAACATTCAGATCT
1 TCCTTGATAAAACTGTATAGATCTATCTATAGTTTATGTTAATTTTTGCCTTAACATTCAGATCT
184915 A
66 A
*
184916 TCCTTGATAAAACTAG-ATAGATCTATC-A-AGTTTATGTTAATTTTTGCCTTAATATTCAGATC
1 TCCTTGATAAAACT-GTATAGATCTATCTATAGTTTATGTTAATTTTTGCCTTAACATTCAGATC
184978 T
65 T
184979 CTTTCGTAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
64 34 0.57
65 1 0.02
66 24 0.40
67 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (66 bp):
TCCTTGATAAAACTGTATAGATCTATCTATAGTTTATGTTAATTTTTGCCTTAACATTCAGATCT
A
Found at i:185074 original size:54 final size:54
Alignment explanation
Indices: 184992--185098 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
184982 TCGTAATCTC
184992 CAATTTTCTTAATAGATTTATCTAATTTATGTTACTTTTTGCTTTAACTTTCAA
1 CAATTTTCTTAATAGATTTATCTAATTTATGTTACTTTTTGCTTTAACTTTCAA
*
185046 CAATTTTCTTAATAGATTTATCTAATTTATGTTAGTTTTTGCTTTAACTTTCA
1 CAATTTTCTTAATAGATTTATCTAATTTATGTTACTTTTTGCTTTAACTTTCA
185099 GATCTCTGTC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.54
Consensus pattern (54 bp):
CAATTTTCTTAATAGATTTATCTAATTTATGTTACTTTTTGCTTTAACTTTCAA
Found at i:185224 original size:12 final size:12
Alignment explanation
Indices: 185207--185245 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
185197 AGCAGTTAGT
*
185207 GGCAGCTGGACG
1 GGCAGCTGAACG
*
185219 GGCAGCTGAACA
1 GGCAGCTGAACG
185231 GGCAGCTGAACG
1 GGCAGCTGAACG
185243 GGC
1 GGC
185246 TAGGAAAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.23, C:0.26, G:0.44, T:0.08
Consensus pattern (12 bp):
GGCAGCTGAACG
Found at i:193071 original size:17 final size:16
Alignment explanation
Indices: 193049--193080 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
193039 GTCATTACCA
193049 TTTCTTTCTTTTTTTCT
1 TTTCTTT-TTTTTTTCT
193066 TTTCTTTTTTTTTTC
1 TTTCTTTTTTTTTTC
193081 ATTCTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTCTTTTTTTTTTCT
Found at i:194260 original size:29 final size:29
Alignment explanation
Indices: 194218--194276 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
194208 TCTTGTTCTT
194218 ATGGTTAGATAAATGCATTTGAACCTAAA
1 ATGGTTAGATAAATGCATTTGAACCTAAA
*
194247 ATGGTTAGATAAATGCATTTGAATCTAAA
1 ATGGTTAGATAAATGCATTTGAACCTAAA
194276 A
1 A
194277 AATAAGGGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.32
Consensus pattern (29 bp):
ATGGTTAGATAAATGCATTTGAACCTAAA
Found at i:202971 original size:1 final size:1
Alignment explanation
Indices: 202965--203006 Score: 84
Period size: 1 Copynumber: 42.0 Consensus size: 1
202955 CGGATGGGAT
202965 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
203007 CCCTACTAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:204883 original size:26 final size:26
Alignment explanation
Indices: 204854--204907 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
204844 GAATAAATTT
*
204854 GCTTAATTATGGAGATCCAGTAGTTA
1 GCTTAATTATGGAGATCCAGGAGTTA
204880 GCTTAATTATGGAGATCCAGGAGTTA
1 GCTTAATTATGGAGATCCAGGAGTTA
204906 GC
1 GC
204908 CAAGAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (26 bp):
GCTTAATTATGGAGATCCAGGAGTTA
Found at i:212412 original size:16 final size:17
Alignment explanation
Indices: 212391--212424 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
212381 CAACGCTCAT
212391 AAAATTGTGT-ATTATG
1 AAAATTGTGTAATTATG
212407 AAAATTGTGTAATTATG
1 AAAATTGTGTAATTATG
212424 A
1 A
212425 GGTCTTAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (17 bp):
AAAATTGTGTAATTATG
Found at i:222121 original size:59 final size:59
Alignment explanation
Indices: 222049--222171 Score: 228
Period size: 59 Copynumber: 2.1 Consensus size: 59
222039 ATTTTCTTTT
222049 TCAAATTACATAAGATGCTTAGAAAGTGACCTATAACCTTACACAAAATTCCATGAGCA
1 TCAAATTACATAAGATGCTTAGAAAGTGACCTATAACCTTACACAAAATTCCATGAGCA
* *
222108 TCAAATTACATAAGATGTTTAGAAAGTGACCTATAACCTTACACAAAATTCTATGAGCA
1 TCAAATTACATAAGATGCTTAGAAAGTGACCTATAACCTTACACAAAATTCCATGAGCA
222167 TCAAA
1 TCAAA
222172 CCATAATTCC
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.27
Consensus pattern (59 bp):
TCAAATTACATAAGATGCTTAGAAAGTGACCTATAACCTTACACAAAATTCCATGAGCA
Found at i:231706 original size:2 final size:2
Alignment explanation
Indices: 231701--231731 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
231691 AACTCTAATA
231701 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
231732 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.