Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 3 of 103
Found at i:845288 original size:30 final size:30
Alignment explanation
Indices: 845252--845314 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
845242 TTATCAAGCT
845252 GTTCCTCCTCATCCTTGGACACTGCAGTAG
1 GTTCCTCCTCATCCTTGGACACTGCAGTAG
*
845282 GTTCCTCCTCATCCTTGGACACTGCAGTTG
1 GTTCCTCCTCATCCTTGGACACTGCAGTAG
845312 GTT
1 GTT
845315 TTTCTTCCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.14, C:0.32, G:0.21, T:0.33
Consensus pattern (30 bp):
GTTCCTCCTCATCCTTGGACACTGCAGTAG
Found at i:858553 original size:2 final size:2
Alignment explanation
Indices: 858548--858575 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
858538 AAAAAATCTC
858548 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
858576 AGCTGGTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:858650 original size:2 final size:2
Alignment explanation
Indices: 858643--858670 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
858633 TTAGACTTNC
858643 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
858671 AGCTGGTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:858672 original size:95 final size:94
Alignment explanation
Indices: 858546--858735 Score: 371
Period size: 95 Copynumber: 2.0 Consensus size: 94
858536 TGAAAAAATC
858546 TCTATATATATATATATATATATATATATAAGCTGGTCAAGAGTCATGTTGACAATCATATCACA
1 TCTATATATATATATATATATATATATATAAGCTGGTCAAGAGTCATGTTGACAATCATATCACA
858611 GGATAGCTGCTTTTCCATCGTATTAGACT
66 GGATAGCTGCTTTTCCATCGTATTAGACT
858640 TNCTATATATATATATATATATATATATATAAGCTGGTCAAGAGTCATGTTGACAATCATATCAC
1 T-CTATATATATATATATATATATATATATAAGCTGGTCAAGAGTCATGTTGACAATCATATCAC
858705 AGGATAGCTGCTTTTCCATCGTATTAGACT
65 AGGATAGCTGCTTTTCCATCGTATTAGACT
858735 T
1 T
858736 TTGTGTTTTC
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
94 1 0.01
95 94 0.99
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (94 bp):
TCTATATATATATATATATATATATATATAAGCTGGTCAAGAGTCATGTTGACAATCATATCACA
GGATAGCTGCTTTTCCATCGTATTAGACT
Found at i:858964 original size:20 final size:20
Alignment explanation
Indices: 858939--859029 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 20
858929 CGTTTAACAC
858939 AATTAAATAAAAATATTTAT
1 AATTAAATAAAAATATTTAT
*
858959 AATTAAAT-ATAAT-TTTATT
1 AATTAAATAAAAATATTTA-T
* * ** *
858978 ATTTAGATTTAAA-ATCTAT
1 AATTAAATAAAAATATTTAT
*
858997 AATT--ATAAAAATAATTAT
1 AATTAAATAAAAATATTTAT
*
859015 AATAAAATAAAAATA
1 AATTAAATAAAAATA
859030 ATAATAACAT
Statistics
Matches: 53, Mismatches: 12, Indels: 12
0.69 0.16 0.16
Matches are distributed among these distances:
17 5 0.09
18 11 0.21
19 15 0.28
20 22 0.42
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (20 bp):
AATTAAATAAAAATATTTAT
Found at i:859101 original size:25 final size:24
Alignment explanation
Indices: 859042--859104 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
859032 AATAACATCA
*
859042 AATATAATAAAATTTAATATAAAT
1 AATATAATAAAATTCAATATAAAT
* * *
859066 AACATATATAAAATTCATTATCATAT
1 AATATA-ATAAAATTCAATAT-AAAT
859092 AATATAATAAAAT
1 AATATAATAAAAT
859105 ACATAATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 5 0.16
25 19 0.59
26 8 0.25
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (24 bp):
AATATAATAAAATTCAATATAAAT
Found at i:863403 original size:55 final size:54
Alignment explanation
Indices: 863319--863424 Score: 203
Period size: 55 Copynumber: 1.9 Consensus size: 54
863309 TTATTGTTTC
863319 CAACTACAGAAAAGGCACTTGCATTTCCAAATATGCCTGCTTGTGACACTNTTTT
1 CAACTACAGAAAAGGCACTTGCATTTCCAAATATGCCTGCTTGTGACACT-TTTT
863374 CAACTACAGAAAAGGCACTTGCATTTCCAAATATGCCTGCTTGTGACACTT
1 CAACTACAGAAAAGGCACTTGCATTTCCAAATATGCCTGCTTGTGACACTT
863425 CACCATCAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 1 0.02
55 50 0.98
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29
Consensus pattern (54 bp):
CAACTACAGAAAAGGCACTTGCATTTCCAAATATGCCTGCTTGTGACACTTTTT
Found at i:866156 original size:28 final size:27
Alignment explanation
Indices: 866113--866166 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
866103 AAAACAAAAC
*
866113 AAAAATAATAATAATATCAAATATAAT
1 AAAAATAATAATAATAACAAATATAAT
*
866140 AAAAATTAAT-ATAAATAACATATATAA
1 AAAAA-TAATAAT-AATAACAAATATAA
866167 AATTTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAAATAATAATAATAACAAATATAAT
Found at i:866327 original size:14 final size:14
Alignment explanation
Indices: 866294--866334 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
866284 AATTAATAAA
866294 ATTTA-TTAAAA-T
1 ATTTATTTAAAATT
*
866306 AATTATTTAAAATT
1 ATTTATTTAAAATT
*
866320 ATTTATTTAAGATT
1 ATTTATTTAAAATT
866334 A
1 A
866335 AAATAATCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 4 0.17
13 6 0.25
14 14 0.58
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
ATTTATTTAAAATT
Found at i:876434 original size:306 final size:307
Alignment explanation
Indices: 876023--876602 Score: 664
Period size: 306 Copynumber: 1.9 Consensus size: 307
876013 GGTTCTTTTT
*
876023 TTTTCATAAAAATTAAAGAGAGATAAATATTAATTGGAGAGCGAAAGAGTAATTAAGTTTAGAGA
1 TTTTCATAAAAATTAAAGAGAGATAAACATTAATTGGAGAGCGAAAGAGTAATTAAGTTTAGAGA
* * *
876088 TTAATTGAGAATATGAAATCGAGACATGGTTTTGTTTTCATATAATAATTGAT-GAGTT-TTTTC
66 TTAATTGAGAATATGAAATCGAGACATGGTTTTATTTTCATATAATAATAGATGGAGTTCTTTTA
* * * * *
876151 TTT-TTTAGTACA-AATTAAATAGAGTCAAACATTAATTAGAGA-TGAAAAGAGTAATTAAGTTC
131 TTTCTTTAGTA-ATAATTAAAGAAAGACAAACATTAATTAAAGACAGAAAA-AGTAATTAAGTT-
*** * ** * *
876213 GGATCTTAACTAAGAACTT-GAAATTGAGACATGGTTTCATCATTGTTAATAGATAATTAGTTTA
193 -GA-AAGAAC-AAGAA-TTCGAAATCGAGACATGACTTCATCATTATTAATAGATAATTAGATTA
876277 TTATCTCGTCATGATCCATGAGTGTTTTCATATAATAATTGATTTTTTTTTCAC
254 TTATCTCGTCATGATCCATGAGTGTTTTCATATAATAATTGATTTTTTTTTCAC
*
876331 TTTTCGTAAAAATT-AA-AGAG-TCAAACATTAATTAGG-GA-CGCAAAGAGTAATTAAGTTTAG
1 TTTTCATAAAAATTAAAGAGAGAT-AAACATTAATT-GGAGAGCG-AAAGAGTAATTAAGTTTAG
* ** * ** ** *
876391 AGATTAATTTATTATCTTGTCAT-GATCCATGAG-TTTATTTTCATATAATAATAGATGGGGTTC
63 AGATTAATTGAGAAT-ATGAAATCGAGACATG-GTTTTATTTTCATATAATAATAGATGGAGTTC
* *
876454 TTTTATTTCTTTAGTAATAATTAAAGAAAGACAAATATTAATTAAAGACAGAGAAAGTAATTAAG
126 TTTTATTTCTTTAGTAATAATTAAAGAAAGACAAACATTAATTAAAGACAGAAAAAGTAATTAAG
* * *
876519 TTTAAAGATCAAGAATTCGAAATCGAGACATGACTTGATCATTATTAATAGATAATTAGATTATT
191 TTGAAAGAACAAGAATTCGAAATCGAGACATGACTTCATCATTATTAATAGATAATTAGATTATT
*
876584 CTCTCGTCATGATCCATGA
256 ATCTCGTCATGATCCATGA
876603 CTTTGTTTTT
Statistics
Matches: 228, Mismatches: 33, Indels: 25
0.80 0.12 0.09
Matches are distributed among these distances:
304 2 0.01
305 67 0.29
306 76 0.33
307 14 0.06
308 21 0.09
309 44 0.19
310 4 0.02
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (307 bp):
TTTTCATAAAAATTAAAGAGAGATAAACATTAATTGGAGAGCGAAAGAGTAATTAAGTTTAGAGA
TTAATTGAGAATATGAAATCGAGACATGGTTTTATTTTCATATAATAATAGATGGAGTTCTTTTA
TTTCTTTAGTAATAATTAAAGAAAGACAAACATTAATTAAAGACAGAAAAAGTAATTAAGTTGAA
AGAACAAGAATTCGAAATCGAGACATGACTTCATCATTATTAATAGATAATTAGATTATTATCTC
GTCATGATCCATGAGTGTTTTCATATAATAATTGATTTTTTTTTCAC
Found at i:881326 original size:5 final size:5
Alignment explanation
Indices: 881293--881368 Score: 52
Period size: 5 Copynumber: 15.6 Consensus size: 5
881283 CCATCCCGAT
* * *
881293 TTTTT TTTTAA TTTT- TTTTA TTGTTA TTTTA -TTTA -TTTA ATTTA ATTTA
1 TTTTA TTTT-A TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TTTTA
* * *
881342 ATTTA ATTTA ATTT- TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
881369 GAGTGTCTAC
Statistics
Matches: 64, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
4 15 0.23
5 40 0.62
6 9 0.14
ACGTcount: A:0.24, C:0.00, G:0.01, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:881345 original size:15 final size:14
Alignment explanation
Indices: 881299--881365 Score: 62
Period size: 15 Copynumber: 4.6 Consensus size: 14
881289 CGATTTTTTT
**
881299 TTTAATTTTTTTTA
1 TTTAATTTAATTTA
* *
881313 TTGTTATTTTATTTA
1 TT-TAATTTAATTTA
881328 TTTAATTTAATTTAA
1 TTTAATTTAATTT-A
*
881343 TTTAATTTAATTTT
1 TTTAATTTAATTTA
*
881357 TTTATTTTA
1 TTTAATTTA
881366 TTTGAGTGTC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
14 19 0.42
15 26 0.58
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.72
Consensus pattern (14 bp):
TTTAATTTAATTTA
Found at i:900303 original size:219 final size:220
Alignment explanation
Indices: 899911--900374 Score: 594
Period size: 219 Copynumber: 2.1 Consensus size: 220
899901 ATAGAACATG
* * * * *
899911 TGTTATTTTGTATAAATATTGTAATTATATGATGATCGATCCCTAATTAACTTTCTAATTATATT
1 TGTTATTTTGTATAAATATTGTAATTAAACGATGATCAATCCCTAATTAACTTTCAAATTACATT
*
899976 CCACAATGACAGTTTTATTAATAAAATTTACAGTTAGATAATTAATCATGACACCTAGTCGGTCA
66 CCACAATGACAGTTTTATTAATAAAATTTACAGTTAGATAATTAATCATGACACCTAGTCGGCCA
** ** * ** * * *
900041 TTTTGCATTTAACAAAATGCTTAATAAAGATAATTGTGCACTTAAGAAATGTGCCTATATATACC
131 TTAAGCATAAAACAAAAGGCTTAATAAAGATAACCGCGCACTTAAGAAATGAGCCTAAATATACC
900106 ACACACATTATCCAAATAGAACCAA
196 ACACACATTATCCAAATAGAACCAA
* *
900131 TGTTATTTT-TATAAATATTGTAATTAAACGGTGATCAATCCCTTATTAACTTTCAAATTACATT
1 TGTTATTTTGTATAAATATTGTAATTAAACGATGATCAATCCCTAATTAACTTTCAAATTACATT
** *
900195 TGACAATGACAGTTTTATTAATAAAATTTGC-GATTAGATAATTAATCATGACA-CT-GCATCGG
66 CCACAATGACAGTTTTATTAATAAAATTTACAG-TTAGATAATTAATCATGACACCTAG--TCGG
*
900257 CCATTAAGCATAAAACAAAAGGCTTAATAAAGATAACCGCGCACTTAAGAAATGAGTCTAAATAT
128 CCATTAAGCATAAAACAAAAGGCTTAATAAAGATAACCGCGCACTTAAGAAATGAGCCTAAATAT
** ** * *
900322 ACCGTACATGTTATCTAAATAGAACTAA
193 ACCACACACATTATCCAAATAGAACCAA
* *
900350 TATTATTTTGTATTAAATAATGTAA
1 TGTTATTTTGTA-TAAATATTGTAA
900375 CTATAGGAAA
Statistics
Matches: 209, Mismatches: 30, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
217 1 0.00
218 3 0.01
219 183 0.88
220 11 0.05
221 11 0.05
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (220 bp):
TGTTATTTTGTATAAATATTGTAATTAAACGATGATCAATCCCTAATTAACTTTCAAATTACATT
CCACAATGACAGTTTTATTAATAAAATTTACAGTTAGATAATTAATCATGACACCTAGTCGGCCA
TTAAGCATAAAACAAAAGGCTTAATAAAGATAACCGCGCACTTAAGAAATGAGCCTAAATATACC
ACACACATTATCCAAATAGAACCAA
Found at i:903379 original size:2 final size:2
Alignment explanation
Indices: 903372--903415 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
903362 ATTACAATTT
903372 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
903414 TA
1 TA
903416 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:903612 original size:3 final size:3
Alignment explanation
Indices: 903604--903632 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
903594 TGGAAATAGA
903604 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
903633 CGGTGGCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:910896 original size:23 final size:21
Alignment explanation
Indices: 910861--910906 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
910851 TTTAAATTAT
*
910861 ATAATATTATAAATAAAAATA
1 ATAATATTATAAAGAAAAATA
*
910882 ATAATAATTATTAAAGAGAAATA
1 ATAAT-ATTA-TAAAGAAAAATA
910905 AT
1 AT
910907 TTTAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 4 0.19
23 12 0.57
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (21 bp):
ATAATATTATAAAGAAAAATA
Found at i:910942 original size:56 final size:56
Alignment explanation
Indices: 910843--910968 Score: 148
Period size: 56 Copynumber: 2.2 Consensus size: 56
910833 TTTTTTATTA
* *
910843 AAAATAATTTTAAATTATATAATATTATAAATAAAAATAATAATAAT-TATTAAAG
1 AAAATAATTTTAAATTATAAAATATTATAAATAAAAATAATAATAATAAATTAAAG
* * * *
910898 AGAAATAATTTTAAATT-TAAAAATATTATAAATAATATTTATAATGATAAATTAAAG
1 A-AAATAATTTTAAATTAT-AAAATATTATAAATAAAAATAATAATAATAAATTAAAG
* *
910955 ATAATTATTTTAAA
1 AAAATAATTTTAAA
910969 AAATAATTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
55 2 0.03
56 50 0.83
57 8 0.13
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (56 bp):
AAAATAATTTTAAATTATAAAATATTATAAATAAAAATAATAATAATAAATTAAAG
Found at i:911459 original size:2 final size:2
Alignment explanation
Indices: 911452--911479 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
911442 ATTTTATAAG
911452 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
911480 TTATTCTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:918419 original size:23 final size:23
Alignment explanation
Indices: 918393--918438 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
918383 ATACAATAAC
* *
918393 CTTATCCTAATATAATTAGGAAT
1 CTTATCCTAATAGAATTAAGAAT
918416 CTTATCCTAATAGAATTAAGAAT
1 CTTATCCTAATAGAATTAAGAAT
918439 TGTTATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (23 bp):
CTTATCCTAATAGAATTAAGAAT
Found at i:930965 original size:7 final size:7
Alignment explanation
Indices: 930953--930987 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
930943 ATATAGCATC
930953 ATTGCCA
1 ATTGCCA
930960 ATTGCCA
1 ATTGCCA
930967 ATTGCCA
1 ATTGCCA
*
930974 ACTGCCA
1 ATTGCCA
930981 ATTGCCA
1 ATTGCCA
930988 TCTATCTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (7 bp):
ATTGCCA
Found at i:939798 original size:62 final size:62
Alignment explanation
Indices: 939696--939816 Score: 206
Period size: 62 Copynumber: 2.0 Consensus size: 62
939686 CGATACAGCG
* *
939696 TATGCAGCTATATTTTTTGTTCCGCCATGATTTTGTGTAGTCTTTGTTTCCATTTTTTTGCT
1 TATGCAGCTATATATTTTGTTCCGCCATGATTTTGAGTAGTCTTTGTTTCCATTTTTTTGCT
* *
939758 TATGCAGCTATATATTTTGTTCTGCCATGATTTTGAGTAGTCTTTGTTTGCATTTTTTT
1 TATGCAGCTATATATTTTGTTCCGCCATGATTTTGAGTAGTCTTTGTTTCCATTTTTTT
939817 CTTTATCATA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.15, C:0.14, G:0.17, T:0.55
Consensus pattern (62 bp):
TATGCAGCTATATATTTTGTTCCGCCATGATTTTGAGTAGTCTTTGTTTCCATTTTTTTGCT
Found at i:940549 original size:22 final size:21
Alignment explanation
Indices: 940504--940552 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
940494 ATAAAATAAA
*
940504 AAATTAATCATAATAAAATTT
1 AAATTAATAATAATAAAATTT
* *
940525 AAATTAATAAATATTAATATTT
1 AAATTAAT-AATAATAAAATTT
940547 AAATTA
1 AAATTA
940553 TCTATTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATTAATAATAATAAAATTT
Found at i:940601 original size:24 final size:26
Alignment explanation
Indices: 940546--940603 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
940536 TATTAATATT
* *
940546 TAAATTATCTATTATTAATGTTTTAAA
1 TAAATAATCAATTATTAA-GTTTTAAA
*
940573 TAAATAATCAATTATTAA-TTTTCAA
1 TAAATAATCAATTATTAAGTTTTAAA
940598 -AAATAA
1 TAAATAA
940604 AATAAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 6 0.21
25 6 0.21
27 16 0.57
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (26 bp):
TAAATAATCAATTATTAAGTTTTAAA
Found at i:940809 original size:108 final size:109
Alignment explanation
Indices: 940503--940838 Score: 289
Period size: 112 Copynumber: 3.0 Consensus size: 109
940493 AATAAAATAA
* * *
940503 AAAATTAATCATAATAAAATTTAAATT-AATAAATATTAATATTTAAAT-TATCTATTATTAATG
1 AAAATTAATCATAATAATATTTAAATTAAATAAATATTAATATTTAAATATAT-AATTATTAATA
* *
940566 TTTTAAATAAATAATC-AATTATTAAT-TTTCAAAAATAAAATAAAATAA
65 TTTTAAA-AAAT--TCTAATTATTAATATTTAAAAAATAAAA-AAAA-AT
* * * * *
940614 AATAATTGATCATCATAATATTTAAATAAAAATAAAAATATTTATATTTTAAA-ATATAA--ATA
1 AA-AATTAATCATAATAATATTTAAAT-TAAAT--AAATATTAATA-TTTAAATATATAATTATT
** ** * *
940676 AATATAAT-ATGAATTATCAATTATTAATATTTTAAAAATAAAAAAAAAT
61 AATATTTTAAAAAATTCT-AATTATTAATATTTAAAAAATAAAAAAAAAT
*
940725 AAAATTAAT-ATAATAATA-TTAAATTAAATAAATGTTAATATTTAAATGAT-TAATTATTAATA
1 AAAATTAATCATAATAATATTTAAATTAAATAAATATTAATATTTAAAT-ATATAATTATTAATA
* *
940787 TTTTAAAAAATTCTAGATTATTAATATTTAAAAAATCTAATAAAAAT
65 TTTTAAAAAATTCTA-ATTATTAATATTTAAAAAAT-AAAAAAAAAT
940834 AAAAT
1 AAAAT
940839 GTCACATAAA
Statistics
Matches: 179, Mismatches: 29, Indels: 36
0.73 0.12 0.15
Matches are distributed among these distances:
104 6 0.03
105 12 0.07
106 2 0.01
107 13 0.07
108 31 0.17
109 21 0.12
110 7 0.04
111 5 0.03
112 38 0.21
113 14 0.08
114 10 0.06
116 11 0.06
117 9 0.05
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (109 bp):
AAAATTAATCATAATAATATTTAAATTAAATAAATATTAATATTTAAATATATAATTATTAATAT
TTTAAAAAATTCTAATTATTAATATTTAAAAAATAAAAAAAAAT
Found at i:942725 original size:38 final size:38
Alignment explanation
Indices: 942674--942754 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
942664 CACAGTGCTT
*
942674 GTGCATTATCACCATGGTGGGGTTGGAAAATATGGATG
1 GTGCATTATCACCATGGTGGGGCTGGAAAATATGGATG
942712 GTGCATTATCACCATGGTGGGGCTGGAAAATATGGATG
1 GTGCATTATCACCATGGTGGGGCTGGAAAATATGGATG
942750 GTGCA
1 GTGCA
942755 CATTTATGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.26, C:0.12, G:0.35, T:0.27
Consensus pattern (38 bp):
GTGCATTATCACCATGGTGGGGCTGGAAAATATGGATG
Found at i:949366 original size:13 final size:13
Alignment explanation
Indices: 949348--949374 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
949338 TATTTGATAA
949348 TTTTTTTATAAGT
1 TTTTTTTATAAGT
949361 TTTTTTTATAAGT
1 TTTTTTTATAAGT
949374 T
1 T
949375 ATAATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (13 bp):
TTTTTTTATAAGT
Found at i:949394 original size:18 final size:20
Alignment explanation
Indices: 949353--949394 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
949343 GATAATTTTT
* *
949353 TTATAAGTTTTTTTTATAAG
1 TTATAAGTTTTTATTATAAA
949373 TTATAA-TTTTTATTA-AAA
1 TTATAAGTTTTTATTATAAA
949391 TTAT
1 TTAT
949395 CATAAAAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
19 8 0.40
20 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TTATAAGTTTTTATTATAAA
Found at i:958423 original size:22 final size:23
Alignment explanation
Indices: 958395--958437 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
958385 ATTGCGATTG
958395 ATATTATA-TAGTTGAAAAAATA
1 ATATTATAGTAGTTGAAAAAATA
*
958417 ATATTATAGTATTTGAAAAAA
1 ATATTATAGTAGTTGAAAAAA
958438 ACATTACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.37
Consensus pattern (23 bp):
ATATTATAGTAGTTGAAAAAATA
Found at i:965442 original size:12 final size:12
Alignment explanation
Indices: 965427--965458 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
965417 TGTTCAGAAT
965427 GAAGATGATTTA
1 GAAGATGATTTA
*
965439 GAAGAGGATTTA
1 GAAGATGATTTA
965451 GAAGATGA
1 GAAGATGA
965459 AAAACTAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.25
Consensus pattern (12 bp):
GAAGATGATTTA
Found at i:970614 original size:14 final size:14
Alignment explanation
Indices: 970595--970624 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
970585 CAGGTAGAAA
970595 AAAAAGAAAACAAG
1 AAAAAGAAAACAAG
970609 AAAAAGAAAACAAG
1 AAAAAGAAAACAAG
970623 AA
1 AA
970625 TCTGCTAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAACAAG
Found at i:980970 original size:64 final size:63
Alignment explanation
Indices: 980871--981001 Score: 156
Period size: 64 Copynumber: 2.1 Consensus size: 63
980861 TCGAGATTTT
* * * *
980871 ATTTCATTAATATGATCAATTCTGCGCGTCCATACAAACACACAATTATATATTAAATTTAAG
1 ATTTCATTAATATAATCAATTCTGCGCATCCATACAAACACACAATTACATATTAAATTCAAG
* * * * *
980934 ATTTCATTTAATATAATCAA-TCTTGTGCATCTATACATACACACATTTACATGTTAAATTCAAG
1 ATTTCA-TTAATATAATCAATTC-TGCGCATCCATACAAACACACAATTACATATTAAATTCAAG
980998 ATTT
1 ATTT
981002 TAAATAAATT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
63 8 0.14
64 49 0.86
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (63 bp):
ATTTCATTAATATAATCAATTCTGCGCATCCATACAAACACACAATTACATATTAAATTCAAG
Found at i:1009654 original size:21 final size:21
Alignment explanation
Indices: 1009609--1009673 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
1009599 CCAAGAAGCT
* *
1009609 CTTGGTTCATCAAAGGAATAT-
1 CTTGGATCATCAAACG-ATATC
1009630 CTTGGATCATCAAACGATATC
1 CTTGGATCATCAAACGATATC
* *
1009651 CTT-GCTGCATCAAACGACATC
1 CTTGGAT-CATCAAACGATATC
1009672 CT
1 CT
1009674 CCCAGCATCA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.16
21 32 0.84
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (21 bp):
CTTGGATCATCAAACGATATC
Found at i:1009681 original size:21 final size:21
Alignment explanation
Indices: 1009637--1009684 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1009627 TATCTTGGAT
* ** *
1009637 CATCAAACGATATCCTTGCTG
1 CATCAAACGACATCCTCCCAG
1009658 CATCAAACGACATCCTCCCAG
1 CATCAAACGACATCCTCCCAG
1009679 CATCAA
1 CATCAA
1009685 GTGAAAACCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.35, G:0.10, T:0.21
Consensus pattern (21 bp):
CATCAAACGACATCCTCCCAG
Found at i:1011164 original size:2 final size:2
Alignment explanation
Indices: 1011157--1011199 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1011147 TCAGATTTAT
*
1011157 TC TC TC TC TC TC TC AC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1011199 T
1 T
1011200 AGGTAAACCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1011723 original size:3 final size:3
Alignment explanation
Indices: 1011717--1011742 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1011707 ACGATTCTTT
1011717 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1011743 TCCCTTTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1024860 original size:22 final size:22
Alignment explanation
Indices: 1024832--1024881 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
1024822 ATATCCAAAA
1024832 CAAACAACATAGGATTGGAAGT
1 CAAACAACATAGGATTGGAAGT
1024854 CAAACAACATAGGATTGGAAGT
1 CAAACAACATAGGATTGGAAGT
1024876 CAAACA
1 CAAACA
1024882 TACCTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.48, C:0.16, G:0.20, T:0.16
Consensus pattern (22 bp):
CAAACAACATAGGATTGGAAGT
Found at i:1027081 original size:16 final size:14
Alignment explanation
Indices: 1027062--1027095 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
1027052 TTAAAATATC
1027062 AATAAATTAATATAAA
1 AATAAA-TAA-ATAAA
1027078 AATAAATAAATAAA
1 AATAAATAAATAAA
1027092 AATA
1 AATA
1027096 TGTATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 3 0.17
16 6 0.33
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AATAAATAAATAAA
Found at i:1028257 original size:15 final size:15
Alignment explanation
Indices: 1028196--1028263 Score: 52
Period size: 15 Copynumber: 4.4 Consensus size: 15
1028186 TCATATATTT
1028196 TATTTTTAT-TTAT-
1 TATTTTTATATTATA
1028209 TATTATCATTATATATATA
1 TATT-T--TTATAT-TATA
* *
1028228 TATTTTTTTAATATA
1 TATTTTTATATTATA
1028243 -ATCTTTTATATTATA
1 TAT-TTTTATATTATA
1028258 TATTTT
1 TATTTT
1028264 ATTTTAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
13 4 0.09
14 3 0.07
15 17 0.40
16 10 0.23
17 1 0.02
18 4 0.09
19 4 0.09
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTTTATATTATA
Found at i:1028355 original size:33 final size:33
Alignment explanation
Indices: 1028294--1028364 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
1028284 TATTATATAA
*
1028294 ATTTTAATTTATTATATTCTATTTTATTTTAAT
1 ATTTTAATTTATTATATTATATTTTATTTTAAT
1028327 -TTTTAATTT-TTATATTATATATTTTATTTTAAT
1 ATTTTAATTTATTATA-T-TATATTTTATTTTAAT
1028360 ATTTT
1 ATTTT
1028365 TTATTTTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
31 5 0.15
32 10 0.29
33 15 0.44
34 4 0.12
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (33 bp):
ATTTTAATTTATTATATTATATTTTATTTTAAT
Found at i:1028377 original size:33 final size:34
Alignment explanation
Indices: 1028313--1028383 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 34
1028303 TATTATATTC
1028313 TATTTTATTTTAATTTTTAATTTTTATATTAT-A
1 TATTTTATTTTAATTTTTAATTTTTATATTATAA
*
1028346 TATTTTATTTTAATATTTT-TTATTTTA-ATTATAA
1 TATTTTATTTTAAT-TTTTAAT-TTTTATATTATAA
1028380 TATT
1 TATT
1028384 ATAAAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
33 20 0.59
34 14 0.41
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (34 bp):
TATTTTATTTTAATTTTTAATTTTTATATTATAA
Found at i:1028485 original size:22 final size:24
Alignment explanation
Indices: 1028457--1028508 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
1028447 TGTAATGTAA
*
1028457 TGTAATTGCATT-GATTTTAT-AC
1 TGTAATTACATTAGATTTTATAAC
* *
1028479 TGTAATTACATTATATTTTTTAAC
1 TGTAATTACATTAGATTTTATAAC
1028503 TGTAAT
1 TGTAAT
1028509 ATGATTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.44
23 6 0.24
24 8 0.32
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.52
Consensus pattern (24 bp):
TGTAATTACATTAGATTTTATAAC
Found at i:1037163 original size:7 final size:7
Alignment explanation
Indices: 1037151--1037179 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1037141 CCAAACTAAA
1037151 TGCGAGC
1 TGCGAGC
1037158 TGCGAGC
1 TGCGAGC
1037165 TGCGAGC
1 TGCGAGC
1037172 TGCGAGC
1 TGCGAGC
1037179 T
1 T
1037180 CTTTGCAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.41, T:0.17
Consensus pattern (7 bp):
TGCGAGC
Found at i:1042328 original size:17 final size:17
Alignment explanation
Indices: 1042306--1042339 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1042296 AGAAGAAAGC
1042306 AATAAAGCAGAAACATA
1 AATAAAGCAGAAACATA
**
1042323 AATAAATTAGAAACATA
1 AATAAAGCAGAAACATA
1042340 TGGTGCAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.18
Consensus pattern (17 bp):
AATAAAGCAGAAACATA
Found at i:1055985 original size:2 final size:2
Alignment explanation
Indices: 1055974--1056036 Score: 62
Period size: 2 Copynumber: 32.5 Consensus size: 2
1055964 TATTAAATTA
* *
1055974 AT AT -T AT AT AT AT AT AA AT TT GA- AT NAT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT -AT AT AT AT AT AT AT AT
1056015 AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
1056037 AAATTTGACA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
1 4 0.08
2 45 0.88
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1055992 original size:28 final size:29
Alignment explanation
Indices: 1055951--1056022 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 29
1055941 CTATTAGTTG
1055951 TTATATAT-TA-AAATATTAAATTA-ATA
1 TTATATATATATAAATATTAAATTATATA
* *
1055977 TTATATATATATAAAT-TTGAATNATATA
1 TTATATATATATAAATATTAAATTATATA
*
1056005 TTATATATATATATATAT
1 TTATATATATATAAATAT
1056023 ATATATATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
26 8 0.21
27 8 0.21
28 22 0.56
29 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
TTATATATATATAAATATTAAATTATATA
Found at i:1056308 original size:29 final size:28
Alignment explanation
Indices: 1056224--1056323 Score: 84
Period size: 29 Copynumber: 3.6 Consensus size: 28
1056214 TAAGAATTCA
* * *
1056224 ATAAAATAAAAAAATAAAGACTCAAATG
1 ATAAAATAAAAATATAAAAACTCAATTG
*
1056252 AATACAAATAAAAGA-A-AAAAACTTAATTAG
1 -ATA-AAATAAAA-ATATAAAAACTCAATT-G
*
1056282 ATAAAATAAAAATATAAACACTCAATTG
1 ATAAAATAAAAATATAAAAACTCAATTG
1056310 -T-AAA-AAAAATATAA
1 ATAAAATAAAAATATAA
1056324 TTAAAAGGGT
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
25 10 0.16
26 3 0.05
27 2 0.03
28 10 0.16
29 25 0.41
30 10 0.16
31 1 0.02
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (28 bp):
ATAAAATAAAAATATAAAAACTCAATTG
Found at i:1056367 original size:24 final size:25
Alignment explanation
Indices: 1056334--1056380 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1056324 TTAAAAGGGT
*
1056334 TTTTATTTATTATTTACTTTTACTA
1 TTTTATTTATTATTTACTCTTACTA
1056359 TTTT-TTTATTATTTACTCTTAC
1 TTTTATTTATTATTTACTCTTAC
1056381 AGTAATCAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTTATTTATTATTTACTCTTACTA
Found at i:1057990 original size:18 final size:18
Alignment explanation
Indices: 1057969--1058011 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1057959 TACACCACTT
1057969 ATAAAGAATATGGAATTC
1 ATAAAGAATATGGAATTC
1057987 ATAAAGAATATGGAATTC
1 ATAAAGAATATGGAATTC
1058005 ATAAAGA
1 ATAAAGA
1058012 GTTTAACTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (18 bp):
ATAAAGAATATGGAATTC
Found at i:1076457 original size:50 final size:50
Alignment explanation
Indices: 1076382--1076485 Score: 154
Period size: 50 Copynumber: 2.1 Consensus size: 50
1076372 TACCAAGTTA
** *
1076382 TTGTAGCACAACGGCATGGAGTTATAAACTCTGACCTTGATTAGACCTTT
1 TTGTAGCACAACGGCACAGAGTTATAAACTCTGACCTTGATTAGACCTTG
* * *
1076432 TTGTAGCACAACGGGACAGAGTTATAAACTCTGATCTTGATTGGACCTTG
1 TTGTAGCACAACGGCACAGAGTTATAAACTCTGACCTTGATTAGACCTTG
1076482 TTGT
1 TTGT
1076486 TAAAAAGGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (50 bp):
TTGTAGCACAACGGCACAGAGTTATAAACTCTGACCTTGATTAGACCTTG
Found at i:1082865 original size:17 final size:17
Alignment explanation
Indices: 1082840--1082873 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1082830 GTTCAATCGG
*
1082840 TTAATAAAAAAATAAAA
1 TTAAAAAAAAAATAAAA
1082857 TTAAAAAAAAAATAAAA
1 TTAAAAAAAAAATAAAA
1082874 AAGTTAAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
TTAAAAAAAAAATAAAA
Found at i:1086071 original size:252 final size:252
Alignment explanation
Indices: 1085551--1086708 Score: 1510
Period size: 252 Copynumber: 4.6 Consensus size: 252
1085541 ATTTTTAATT
* * * *
1085551 TTTTTAAATAAAAGATAATAAAGATCAAAATAATTATAATTTAAAGTTGACATGAAAAAGTTTTG
1 TTTTTAAATAAAAAATAATAAAGATAAAAATAATTATAATTCAAAGTTGATATGAAAAAGTTTTG
* * * *
1085616 ATGTAAAACAGTAAGAATTGACAT-AAAACTTGTAAATGTGGAATAACTAAATTTAAAATCTTAA
66 ACGTAAAATAGTAAGAATTGACGTAAAAACTTGTAAAGGTGGAATAACTAAATTTAAAATCTTAA
* * * * *
1085680 CATAAATGTATAAAGAGTTAACGTAATAAGTTAATTAAGT-AAAAAAA-TT-AATTTTAATGAAA
131 CGTAAATATGT-AAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATTTCAA-TTTAATGAAA
*
1085742 AAT-AATATTTAAATTTATATTTTCGAATTAAAAGTGTTTAACGATGTGCAAATTTTAA
194 AATAAATATTTAAATTTATATTTTCGAATTAAAAGTGTTTAACGATATGCAAATTTTAA
* * * * *
1085800 TTTTTAAATAAAAAATAATAAGGATAAAAATAATTCTAATTCAAAGTTAATATGGAAAAGTTTTA
1 TTTTTAAATAAAAAATAATAAAGATAAAAATAATTATAATTCAAAGTTGATATGAAAAAGTTTTG
*
1085865 ACGTAAAATAATAAGAATTGACGTAAAAACTTGTAAAGGTGGAATAACTAAATTTAAAATCTTAA
66 ACGTAAAATAGTAAGAATTGACGTAAAAACTTGTAAAGGTGGAATAACTAAATTTAAAATCTTAA
* *
1085930 CGTAAATATGTAAGAGTTAACGTAACAAGTTAATTAAGTAAAAAAAATTTCAATTTGATGAAAAA
131 CGTAAATATGTAAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATTTCAATTTAATGAAAAA
*
1085995 TAAATATTTAAATTTATATTTTC-AGATTAAAAGTGTTTAACTATATGCAAATTTTAA
196 TAAATATTTAAATTTATATTTTCGA-ATTAAAAGTGTTTAACGATATGCAAATTTTAA
* * *
1086052 TTTTTAAATAAACAATAAT-AAGAATAAAAATAATTATAATTCAAAATTGATATGAAAAAGTCTT
1 TTTTTAAATAAAAAATAATAAAG-ATAAAAATAATTATAATTCAAAGTTGATATGAAAAAGTTTT
* * *
1086116 GACGTAAAACAGTGAGAATTAACGTAAAAACTTGTAAAGGTGGAATAACTAAATTTAAAATCTTA
65 GACGTAAAATAGTAAGAATTGACGTAAAAACTTGTAAAGGTGGAATAACTAAATTTAAAATCTTA
* * * * * *
1086181 ACGTAAGTTTGTAAGAATTAACGTAACAAGTCAATTAAGTAAAAATAATTTCAATTTGATGCAAA
130 ACGTAAATATGTAAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATTTCAATTTAATGAAAA
* *
1086246 ATAAATATTTAAATTTATATTTTCGAATTAAAAGTGTTTAACGATGTGTAAATTTTAA
195 ATAAATATTTAAATTTATATTTTCGAATTAAAAGTGTTTAACGATATGCAAATTTTAA
* *
1086304 TTTTTAAATAAAAAATAAT-AAGA-AAAAATAATTCTAATTCAAAGTTGATATGAAAAAGCTTTG
1 TTTTTAAATAAAAAATAATAAAGATAAAAATAATTATAATTCAAAGTTGATATGAAAAAGTTTTG
* * * **
1086367 ACGTAAAATAATAAGATTTGATGTAAAAACTTGTAAATATGGAATAACTAAATTTAAAATCTTAA
66 ACGTAAAATAGTAAGAATTGACGTAAAAACTTGTAAAGGTGGAATAACTAAATTTAAAATCTTAA
* * * * * ** *
1086432 TGTAAGTGTGTAAGAGTTAACGTAACAAGTCAATTAAGTAAAGATAATTAAAATTTAATGAAAAT
131 CGTAAATATGTAAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATTTCAATTTAATGAAAAA
* **
1086497 TAAATATTTAAATTTATATTTTC-AGATTAAAAGTGTTTAATGATATATAAATTTTAA
196 TAAATATTTAAATTTATATTTTCGA-ATTAAAAGTGTTTAACGATATGCAAATTTTAA
* * * * * * *
1086554 TTTTTAAATAAAAAATAATAAAGATAATAATAATTATAGTTTAAAGTT-ACTATTAGAAGGGTTT
1 TTTTTAAATAAAAAATAATAAAGATAAAAATAATTATAATTCAAAGTTGA-TATGAAAAAGTTTT
* * * * * * * ** * *
1086618 GTCGTAAAGTTGTAAGTATTGACGTAAAATCTTATGAAGGTATAATAATTAGATTTAAAATCTTA
65 GACGTAAAATAGTAAGAATTGACGTAAAAACTTGTAAAGGTGGAATAACTAAATTTAAAATCTTA
* *
1086683 ACATAAATATATAAGAGTTAACGTAA
130 ACGTAAATATGTAAGAGTTAACGTAA
1086709 ATAAATTTTA
Statistics
Matches: 801, Mismatches: 96, Indels: 21
0.87 0.10 0.02
Matches are distributed among these distances:
249 104 0.13
250 274 0.34
251 23 0.03
252 399 0.50
253 1 0.00
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.35
Consensus pattern (252 bp):
TTTTTAAATAAAAAATAATAAAGATAAAAATAATTATAATTCAAAGTTGATATGAAAAAGTTTTG
ACGTAAAATAGTAAGAATTGACGTAAAAACTTGTAAAGGTGGAATAACTAAATTTAAAATCTTAA
CGTAAATATGTAAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATTTCAATTTAATGAAAAA
TAAATATTTAAATTTATATTTTCGAATTAAAAGTGTTTAACGATATGCAAATTTTAA
Found at i:1086645 original size:502 final size:500
Alignment explanation
Indices: 1085551--1086708 Score: 1616
Period size: 502 Copynumber: 2.3 Consensus size: 500
1085541 ATTTTTAATT
* *
1085551 TTTTTAAATAAAAGATAATAAAGATCAAAATAATTATAATTTAAAGTTGAC-ATGAAAAAGTTTT
1 TTTTTAAATAAAAAATAATAAAGAT-AAAATAATTATAATTTAAAGTTGACTATG-AAAAGGTTT
* *
1085615 GAT-GTAAAACAGTAAGAATTGACAT-AAAACTTGTAAATGTGGAATAACTAAATTTAAAATCTT
64 G-TCGTAAAACAGTAAGAATTGACGTAAAAACTTGTAAAGGTGGAATAACTAAATTTAAAATCTT
* * *
1085678 AACATAAATGTATAAAGAGTTAACGTAATAAGTTAATTAAGTAAAAAAATTAATTTTAATGAAAA
128 AACATAAATATAT-AAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAATTAATTTTAATGAAAA
1085743 ATAATATTTAAATTTATATTTTCGAATTAAAAGTGTTTAACGATGTGCAAATTTTAATTTTTAAA
192 ATAATATTTAAATTTATATTTTCGAATTAAAAGTGTTTAACGATGTGCAAATTTTAATTTTTAAA
* *
1085808 TAAAAAATAATAAGGATAAAAATAATTCTAATTCAAAGTTAATATGGAAAAGTTTTAACGTAAAA
257 TAAAAAATAATAAGGATAAAAATAATTCTAATTCAAAGTTAATATGAAAAAGCTTTAACGTAAAA
*
1085873 TAATAAGAATTGACGTAAAAACTTGTAAAGGTGGAATAACTAAATTTAAAATCTTAACGTAAATA
322 TAATAAGAATTGACGTAAAAACTTGTAAAGATGGAATAACTAAATTTAAAATCTTAACGTAAATA
* ** *
1085938 TGTAAGAGTTAACGTAACAAGTTAATTAAGTAAAAAAAATTTCAATTTGATGAAAAATAAATATT
387 TGTAAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATTAAAATTTAATGAAAAATAAATATT
*
1086003 TAAATTTATATTTTCAGATTAAAAGTGTTTAACTATATGCAAATTTTAA
452 TAAATTTATATTTTCAGATTAAAAGTGTTTAACTATATACAAATTTTAA
* * * *
1086052 TTTTTAAATAAACAATAAT-AAGAATAAAAATAATTATAATTCAAAATTGA-TATGAAAAAGTCT
1 TTTTTAAATAAAAAATAATAAAG-AT-AAAATAATTATAATTTAAAGTTGACTATGAAAAGGT-T
* * *
1086115 TGACGTAAAACAGTGAGAATTAACGTAAAAACTTGTAAAGGTGGAATAACTAAATTTAAAATCTT
63 TGTCGTAAAACAGTAAGAATTGACGTAAAAACTTGTAAAGGTGGAATAACTAAATTTAAAATCTT
* * * * * * *
1086180 AACGTAAGTTTGTAAGAATTAACGTAACAAGTCAATTAAGTAAAAATAATTTCAA-TTTGATGCA
128 AACATAAATATATAAGAGTTAACGTAACAAGTCAATTAAGTAAAAA-AA-TT-AATTTTAATGAA
*
1086244 AAATAAATATTTAAATTTATATTTTCGAATTAAAAGTGTTTAACGATGTGTAAATTTTAATTTTT
190 AAAT-AATATTTAAATTTATATTTTCGAATTAAAAGTGTTTAACGATGTGCAAATTTTAATTTTT
* *
1086309 AAATAAAAAATAATAA-GA-AAAAATAATTCTAATTCAAAGTTGATATGAAAAAGCTTTGACGTA
254 AAATAAAAAATAATAAGGATAAAAATAATTCTAATTCAAAGTTAATATGAAAAAGCTTTAACGTA
* * * *
1086372 AAATAATAAGATTTGATGTAAAAACTTGTAAATATGGAATAACTAAATTTAAAATCTTAATGTAA
319 AAATAATAAGAATTGACGTAAAAACTTGTAAAGATGGAATAACTAAATTTAAAATCTTAACGTAA
* * * * *
1086437 GTGTGTAAGAGTTAACGTAACAAGTCAATTAAGTAAAGATAATTAAAATTTAATGAAAATTAAAT
384 ATATGTAAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATTAAAATTTAATGAAAAATAAAT
*
1086502 ATTTAAATTTATATTTTCAGATTAAAAGTGTTTAA-TGATATATAAATTTTAA
449 ATTTAAATTTATATTTTCAGATTAAAAGTGTTTAACT-ATATACAAATTTTAA
* * *
1086554 TTTTTAAATAAAAAATAATAAAGATAATAATAATTATAGTTTAAAGTT-ACTATTAGAAGGGTTT
1 TTTTTAAATAAAAAATAATAAAGATAA-AATAATTATAATTTAAAGTTGACTATGA-AAAGGTTT
*** * * * * ** * *
1086618 GTCGTAAAGTTGTAAGTATTGACGTAAAATCTTATGAAGGTATAATAATTAGATTTAAAATCTTA
64 GTCGTAAAACAGTAAGAATTGACGTAAAAACTTGTAAAGGTGGAATAACTAAATTTAAAATCTTA
1086683 ACATAAATATATAAGAGTTAACGTAA
129 ACATAAATATATAAGAGTTAACGTAA
1086709 ATAAATTTTA
Statistics
Matches: 575, Mismatches: 68, Indels: 27
0.86 0.10 0.04
Matches are distributed among these distances:
500 8 0.01
501 100 0.17
502 368 0.64
503 22 0.04
504 77 0.13
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.35
Consensus pattern (500 bp):
TTTTTAAATAAAAAATAATAAAGATAAAATAATTATAATTTAAAGTTGACTATGAAAAGGTTTGT
CGTAAAACAGTAAGAATTGACGTAAAAACTTGTAAAGGTGGAATAACTAAATTTAAAATCTTAAC
ATAAATATATAAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAATTAATTTTAATGAAAAATAA
TATTTAAATTTATATTTTCGAATTAAAAGTGTTTAACGATGTGCAAATTTTAATTTTTAAATAAA
AAATAATAAGGATAAAAATAATTCTAATTCAAAGTTAATATGAAAAAGCTTTAACGTAAAATAAT
AAGAATTGACGTAAAAACTTGTAAAGATGGAATAACTAAATTTAAAATCTTAACGTAAATATGTA
AGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATTAAAATTTAATGAAAAATAAATATTTAAA
TTTATATTTTCAGATTAAAAGTGTTTAACTATATACAAATTTTAA
Found at i:1088973 original size:30 final size:30
Alignment explanation
Indices: 1088919--1088975 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1088909 AATCGAACTC
*
1088919 TTATATTTTTATTTTGAACTAAATAAATTT
1 TTATATTTTTATTTTAAACTAAATAAATTT
1088949 TTATATTTTTATTTTAAA-TCAAATAAA
1 TTATATTTTTATTTTAAACT-AAATAAA
1088976 CTTTATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (30 bp):
TTATATTTTTATTTTAAACTAAATAAATTT
Found at i:1088981 original size:29 final size:29
Alignment explanation
Indices: 1088914--1088982 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
1088904 TCTTCAATCG
*
1088914 AACTCTTATATTTTTATTTTGAACTAAATA
1 AACT-TTATATTTTTATTTTAAACTAAATA
*
1088944 AATTTTTATATTTTTATTTTAAA-TCAAATA
1 AA-CTTTATATTTTTATTTTAAACT-AAATA
1088974 AACTTTATA
1 AACTTTATA
1088983 ATTAATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 7 0.21
30 26 0.76
31 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.52
Consensus pattern (29 bp):
AACTTTATATTTTTATTTTAAACTAAATA
Found at i:1109343 original size:21 final size:21
Alignment explanation
Indices: 1109318--1109357 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1109308 GACTCATAAA
**
1109318 AAATTAAATTATATATATTAT
1 AAATTAAAAAATATATATTAT
1109339 AAATTAAAAAATATATATT
1 AAATTAAAAAATATATATT
1109358 CCCAACCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATTAAAAAATATATATTAT
Found at i:1109506 original size:18 final size:18
Alignment explanation
Indices: 1109472--1109518 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
1109462 AGTTTAATAT
1109472 ATTA-AATGAAAATTTAA
1 ATTATAATGAAAATTTAA
*
1109489 TTTATAATGTAAAA-TTAA
1 ATTATAATG-AAAATTTAA
1109507 ATTATAAATGAA
1 ATTAT-AATGAA
1109519 TAAATTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 3 0.12
18 14 0.56
19 8 0.32
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
ATTATAATGAAAATTTAA
Found at i:1115729 original size:38 final size:36
Alignment explanation
Indices: 1115682--1115775 Score: 91
Period size: 38 Copynumber: 2.5 Consensus size: 36
1115672 TAATGATGTC
1115682 GTTAAATTATAATACTGTG-ATACAGATTTAATAATAAA
1 GTTAAATTAT-ATACTGTGTATA-A-ATTTAATAATAAA
* * *
1115720 GTTAGATTATGATACTGTTGTATAAATTTAATGATACA
1 GTTAAATTAT-ATACTG-TGTATAAATTTAATAATAAA
*
1115758 GTTACATTACTATACTGT
1 GTTAAATTA-TATACTGT
1115776 TAATAATATA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
37 1 0.02
38 40 0.83
39 4 0.08
40 3 0.06
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.40
Consensus pattern (36 bp):
GTTAAATTATATACTGTGTATAAATTTAATAATAAA
Found at i:1115814 original size:15 final size:15
Alignment explanation
Indices: 1115794--1115829 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1115784 TAGAATATAA
1115794 AATTTTTCTTTTTCT
1 AATTTTTCTTTTTCT
* *
1115809 AATTTTTTTTTTTGT
1 AATTTTTCTTTTTCT
1115824 AATTTT
1 AATTTT
1115830 ACATTGACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.75
Consensus pattern (15 bp):
AATTTTTCTTTTTCT
Found at i:1118766 original size:21 final size:19
Alignment explanation
Indices: 1118736--1118776 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1118726 TTTTATTTTT
1118736 TTAATATTTATATTATAAAAA
1 TTAATATTTA-A-TATAAAAA
*
1118757 TTAATTTTTAATATAAAAA
1 TTAATATTTAATATAAAAA
1118776 T
1 T
1118777 ATTAAAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 1 0.05
21 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAATATTTAATATAAAAA
Found at i:1143830 original size:112 final size:110
Alignment explanation
Indices: 1143585--1143862 Score: 296
Period size: 111 Copynumber: 2.5 Consensus size: 110
1143575 AATGGCTTGA
* *
1143585 TCGTAACATGTCAATCGACAATCTTCCATTGAAACAAATTTTATATATAGTATAAATATAAATTA
1 TCGTTACATGTCAATCGATAATC-TCCATTGAAACAAATTTTATATATAGTATAAATATAAATTA
** * * * *
1143650 AGTATAATAAGTGAGATTTTTAACTATTAATAAACGAGAAAATGAT
65 AGTATAATAAGCAAGATTATTAACTATTAATAAAAGAGAAAATAAC
* * * *
1143696 TCGTTACGTGTCAA-CTGATAATCTCCATTTGAAACAATTTTTATATATGGTATAGATATAAATT
1 TCGTTACATGTCAATC-GATAATCTCCA-TTGAAACAAATTTTATATATAGTATAAATATAAATT
*
1143760 AAGTGTAAATGAA-CAAGATTATTAACTATTAA-AAGAAGAGAAAATAAC
64 AAGTAT-AAT-AAGCAAGATTATTAACTATTAATAA-AAGAGAAAATAAC
* * * *
1143808 TCGTTACATATCAATCGATAATCTCTC-TTCAAA-ACAATTTTATACATAATATAAA
1 TCGTTACATGTCAATCGATAATCTC-CATTGAAACA-AATTTTATATATAGTATAAA
1143863 AATGAGATAC
Statistics
Matches: 138, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
110 6 0.04
111 78 0.57
112 50 0.36
113 4 0.03
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (110 bp):
TCGTTACATGTCAATCGATAATCTCCATTGAAACAAATTTTATATATAGTATAAATATAAATTAA
GTATAATAAGCAAGATTATTAACTATTAATAAAAGAGAAAATAAC
Found at i:1158099 original size:95 final size:97
Alignment explanation
Indices: 1157965--1158152 Score: 281
Period size: 95 Copynumber: 2.0 Consensus size: 97
1157955 AGGAAGGAGA
* * * * *
1157965 TCAAAATCAAGAAAAAAAAAATGATAGAAGACATTATTGTTGATAGACAAAGTAGATAGTTTGGC
1 TCAAAATAAAGAAAAAAAAAATGACAGAAGACATCATTGTTGATAGACAAAGGAGATAGCTTGGC
*
1158030 TGTCTCTAGCAAATTTTAAGGTT-TTAACTTC
66 TGTATCTAGCAAATTTTAAGGTTATTAACTTC
* * *
1158061 TCAAAATAAAG-AAAAAAAAATTACAGAGGACATCATTGTTGGTAGACAAAGGAGATAGCTTGGC
1 TCAAAATAAAGAAAAAAAAAATGACAGAAGACATCATTGTTGATAGACAAAGGAGATAGCTTGGC
1158125 TGTATCTAGCAAATTTTAAGGTTATTAA
66 TGTATCTAGCAAATTTTAAGGTTATTAA
1158153 TTTATTTGAT
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
95 68 0.83
96 14 0.17
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.29
Consensus pattern (97 bp):
TCAAAATAAAGAAAAAAAAAATGACAGAAGACATCATTGTTGATAGACAAAGGAGATAGCTTGGC
TGTATCTAGCAAATTTTAAGGTTATTAACTTC
Found at i:1172118 original size:21 final size:22
Alignment explanation
Indices: 1172092--1172132 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1172082 TACGGTTATG
*
1172092 GACGG-ATTCAGATGAAATATC
1 GACGGAATTCAGACGAAATATC
*
1172113 GACGGAATTCTGACGAAATA
1 GACGGAATTCAGACGAAATA
1172133 AATTAATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (22 bp):
GACGGAATTCAGACGAAATATC
Found at i:1178076 original size:2 final size:2
Alignment explanation
Indices: 1178069--1178112 Score: 52
Period size: 2 Copynumber: 20.0 Consensus size: 2
1178059 TATTAATTAA
1178069 AT AT AT AT AT AT AT AT AT AT AT AT CAGT AT AT AT CAT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -A-T AT AT AT -AT AT -AT AT
1178113 GTTAATTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 31 0.82
3 6 0.16
4 1 0.03
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1178768 original size:16 final size:18
Alignment explanation
Indices: 1178733--1178770 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1178723 AAATTGTGAC
1178733 ATAATTAAAATAACATTA
1 ATAATTAAAATAACATTA
1178751 ATAATTAAAA-AA-ATTA
1 ATAATTAAAATAACATTA
1178767 ATAA
1 ATAA
1178771 ATTCATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAATTAAAATAACATTA
Found at i:1210971 original size:18 final size:19
Alignment explanation
Indices: 1210933--1210978 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1210923 AATATTTTTT
1210933 AATTA-ATTTTTATAAATA
1 AATTATATTTTTATAAATA
* *
1210951 AATTTTATTTTTGTAAA-A
1 AATTATATTTTTATAAATA
1210969 AATTATATTT
1 AATTATATTT
1210979 ATTAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
AATTATATTTTTATAAATA
Found at i:1211067 original size:40 final size:40
Alignment explanation
Indices: 1211016--1211115 Score: 175
Period size: 40 Copynumber: 2.5 Consensus size: 40
1211006 AATATTCTTA
1211016 ATTTAAAAATTAATATATTTATTTATATAATTATTAATTTT
1 ATTT-AAAATTAATATATTTATTTATATAATTATTAATTTT
*
1211057 TTTTAAAATTAATATATTTATTTATATAATTATTAATTTT
1 ATTTAAAATTAATATATTTATTTATATAATTATTAATTTT
1211097 ATTTAAAATTAATA-ATTTA
1 ATTTAAAATTAATATATTTA
1211116 ACTTTTTCTT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
39 5 0.09
40 49 0.86
41 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (40 bp):
ATTTAAAATTAATATATTTATTTATATAATTATTAATTTT
Found at i:1222259 original size:22 final size:22
Alignment explanation
Indices: 1222229--1222273 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1222219 GGGGCTGCAT
1222229 GCACCAATTAGAAAGGC-TTAA
1 GCACCAATTAGAAAGGCGTTAA
* *
1222250 GCACCTAATTGGATAGGCGTTAA
1 GCACC-AATTAGAAAGGCGTTAA
1222273 G
1 G
1222274 TCTTGGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 10 0.50
23 5 0.25
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (22 bp):
GCACCAATTAGAAAGGCGTTAA
Found at i:1223554 original size:20 final size:20
Alignment explanation
Indices: 1223529--1223708 Score: 57
Period size: 20 Copynumber: 8.8 Consensus size: 20
1223519 ACGTTATAAT
1223529 TAAAATAAAATATATTAAAA
1 TAAAATAAAATATATTAAAA
1223549 TAAAATATATAATATA--AAAA
1 TAAAATA-A-AATATATTAAAA
* ** *
1223569 T-CAA-AACTTAAATTAAAA
1 TAAAATAAAATATATTAAAA
* * *
1223587 TAAAATATAAGAAATTAAAA
1 TAAAATAAAATATATTAAAA
** * *
1223607 T-TTATATAATATAGGTAAAA
1 TAAAATAAAATATA-TTAAAA
* * * *
1223627 GAAATTAAAATAAAATATATAA
1 TAAAATAAAAT-ATAT-TAAAA
*
1223649 TATAA-AAAATATATTAAAAA
1 TAAAATAAAATATATT-AAAA
* *
1223669 TAAAAAAAAGATTATAATAAAAAA
1 TAAAATAAA-A-TAT-AT-TAAAA
1223693 TAAAAATAAAATATAT
1 T-AAAATAAAATATAT
1223709 GACATTAAAA
Statistics
Matches: 113, Mismatches: 30, Indels: 32
0.65 0.17 0.18
Matches are distributed among these distances:
16 3 0.03
17 1 0.01
18 6 0.05
19 13 0.12
20 38 0.34
21 14 0.12
22 17 0.15
23 6 0.05
24 8 0.07
25 7 0.06
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (20 bp):
TAAAATAAAATATATTAAAA
Found at i:1223671 original size:18 final size:17
Alignment explanation
Indices: 1223630--1223694 Score: 64
Period size: 18 Copynumber: 3.9 Consensus size: 17
1223620 GGTAAAAGAA
1223630 ATTAAAAT--AAAATAT
1 ATTAAAATAAAAAATAT
*
1223645 A-TAATATAAAAAATAT
1 ATTAAAATAAAAAATAT
* *
1223661 ATTAAAAATAAAAAAAAG
1 ATT-AAAATAAAAAATAT
*
1223679 ATTATAATAAAAAATA
1 ATTAAAATAAAAAATA
1223695 AAAATAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
14 5 0.12
15 1 0.03
16 8 0.20
17 12 0.30
18 14 0.35
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.28
Consensus pattern (17 bp):
ATTAAAATAAAAAATAT
Found at i:1223705 original size:18 final size:18
Alignment explanation
Indices: 1223633--1223705 Score: 51
Period size: 18 Copynumber: 3.9 Consensus size: 18
1223623 AAAAGAAATT
1223633 AAAATAAAATATATAATATAA
1 AAAATAAAA-ATA-AA-ATAA
* *
1223654 AAAAT-ATATTAAAAATAA
1 AAAATAAAAAT-AAAATAA
* * *
1223672 AAAA-AAGATTATAATAA
1 AAAATAAAAATAAAATAA
1223689 AAAATAAAAATAAAATA
1 AAAATAAAAATAAAATA
1223706 TATGACATTA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
17 10 0.24
18 21 0.50
19 3 0.07
20 3 0.07
21 5 0.12
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (18 bp):
AAAATAAAAATAAAATAA
Found at i:1237280 original size:35 final size:35
Alignment explanation
Indices: 1237234--1237302 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
1237224 AACTATGCCA
*
1237234 ATGAAATAAACACTATCACTCCATTACTTATTTAT
1 ATGAAATAAACACAATCACTCCATTACTTATTTAT
1237269 ATGAAATAAACACAATCACTCCATTACTTATTTA
1 ATGAAATAAACACAATCACTCCATTACTTATTTA
1237303 ATTATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.42, C:0.20, G:0.03, T:0.35
Consensus pattern (35 bp):
ATGAAATAAACACAATCACTCCATTACTTATTTAT
Found at i:1259584 original size:70 final size:70
Alignment explanation
Indices: 1259508--1259641 Score: 178
Period size: 70 Copynumber: 1.9 Consensus size: 70
1259498 AAAGTTGTCC
* * * * *
1259508 CTTAATAATGTAATTATTGAAAAAACAAATTTAATCCAAAAATTATGTCTTATAATATTAAAGAT
1 CTTAATAATGTAACTATTGAAAAAACAAATGTAATCCAAAAATTATATCTTATAACATGAAAGAT
1259573 TATCA
66 TATCA
* * * * *
1259578 CTTAATAATGTGACTATTGAAAAAACACATGTAATTCAAAAGTTATATTTTATAACATGAAAGA
1 CTTAATAATGTAACTATTGAAAAAACAAATGTAATCCAAAAATTATATCTTATAACATGAAAGA
1259642 GTGTATTCAA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
70 54 1.00
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.35
Consensus pattern (70 bp):
CTTAATAATGTAACTATTGAAAAAACAAATGTAATCCAAAAATTATATCTTATAACATGAAAGAT
TATCA
Found at i:1261675 original size:22 final size:22
Alignment explanation
Indices: 1261632--1261676 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1261622 GGAGAAAGCT
* *
1261632 AAAGAAATGAAAGAAATTTGCA
1 AAAGAAATCAAAGAAATGTGCA
**
1261654 AAAGAAATCAAAGTGATGTGCA
1 AAAGAAATCAAAGAAATGTGCA
1261676 A
1 A
1261677 TTAAGGTAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.18
Consensus pattern (22 bp):
AAAGAAATCAAAGAAATGTGCA
Found at i:1264608 original size:19 final size:22
Alignment explanation
Indices: 1264571--1264626 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
1264561 ATCAACTAAA
1264571 AATAATAAATATAATTTTAATT
1 AATAATAAATATAATTTTAATT
1264593 AATAAT-AAT-TAA-TTTAATTT
1 AATAATAAATATAATTTTAA-TT
1264613 AAATAA-AAATATAA
1 -AATAATAAATATAA
1264627 AAATTTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
19 5 0.17
20 5 0.17
21 11 0.37
22 9 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AATAATAAATATAATTTTAATT
Found at i:1269071 original size:27 final size:26
Alignment explanation
Indices: 1269019--1269071 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
1269009 TAATTTCTCA
** *
1269019 ATTTAAAAAATAAAATTTATTTTTTT
1 ATTTAAAAAATAAAAAATATTCTTTT
*
1269045 ATTTTAAAAATAAAAAATATTACTTTT
1 ATTTAAAAAATAAAAAATATT-CTTTT
1269072 CCTCAAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTAAAAAATAAAAAATATTCTTTT
Found at i:1276102 original size:12 final size:12
Alignment explanation
Indices: 1276081--1276123 Score: 54
Period size: 11 Copynumber: 3.6 Consensus size: 12
1276071 AAAGTTCATT
1276081 AATT-ATTTTAA
1 AATTAATTTTAA
1276092 AATTAATTTT-A
1 AATTAATTTTAA
1276103 AATTAAAATTTTAA
1 AATT--AATTTTAA
1276117 AATTAAT
1 AATTAAT
1276124 CCACATCAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
11 9 0.32
12 8 0.29
13 6 0.21
14 5 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AATTAATTTTAA
Found at i:1276114 original size:13 final size:14
Alignment explanation
Indices: 1276085--1276122 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1276075 TTCATTAATT
1276085 ATTTTAAAATT--A
1 ATTTTAAAATTAAA
1276097 ATTTT-AAATTAAA
1 ATTTTAAAATTAAA
1276110 ATTTTAAAATTAA
1 ATTTTAAAATTAA
1276123 TCCACATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.22
12 5 0.22
13 6 0.26
14 7 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTTTAAAATTAAA
Found at i:1281706 original size:14 final size:14
Alignment explanation
Indices: 1281689--1281718 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1281679 ATCAAATAAA
*
1281689 TTTTTAAATAAAAT
1 TTTTTAAAAAAAAT
1281703 TTTTTAAAAAAAAT
1 TTTTTAAAAAAAAT
1281717 TT
1 TT
1281719 AAAAAAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTTAAAAAAAAT
Found at i:1289059 original size:2 final size:2
Alignment explanation
Indices: 1289054--1289079 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1289044 ACACACACAA
1289054 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
1289080 CTAACGGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1332064 original size:13 final size:13
Alignment explanation
Indices: 1332046--1332072 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1332036 TATCTCTTTG
1332046 GAATTCAGATTAT
1 GAATTCAGATTAT
1332059 GAATTCAGATTAT
1 GAATTCAGATTAT
1332072 G
1 G
1332073 TATATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (13 bp):
GAATTCAGATTAT
Found at i:1334057 original size:48 final size:48
Alignment explanation
Indices: 1333986--1334081 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
1333976 GCAGGAAGAT
1333986 AAGCTTTGGTTATTCACTAGCAGCAGAGCAGAAGAACTCCTAAAAGGC
1 AAGCTTTGGTTATTCACTAGCAGCAGAGCAGAAGAACTCCTAAAAGGC
1334034 AAGCTTTGGTTATTCACTAGCAGCAGAGCAGAAGAACTCCTAAAAGGC
1 AAGCTTTGGTTATTCACTAGCAGCAGAGCAGAAGAACTCCTAAAAGGC
1334082 TAAGTTACAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (48 bp):
AAGCTTTGGTTATTCACTAGCAGCAGAGCAGAAGAACTCCTAAAAGGC
Found at i:1339114 original size:29 final size:30
Alignment explanation
Indices: 1339074--1339136 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
1339064 AACAGGAATC
*
1339074 CAAA-TAAGTACAGATACGATTGGGAACAT
1 CAAATTAAGTACAGATACGATTGGGAACAG
*
1339103 CAAATTAA-TACAGGTACGATTGGGAACAG
1 CAAATTAAGTACAGATACGATTGGGAACAG
1339132 CAAAT
1 CAAAT
1339137 CCCCATGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 28 0.90
30 3 0.10
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (30 bp):
CAAATTAAGTACAGATACGATTGGGAACAG
Found at i:1341475 original size:15 final size:15
Alignment explanation
Indices: 1341455--1341494 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
1341445 TGTTTGAGTT
1341455 TGAGTTTGAGTGTTG
1 TGAGTTTGAGTGTTG
1341470 TGAGTTTGAGTGTTG
1 TGAGTTTGAGTGTTG
1341485 TGAGTTTGAG
1 TGAGTTTGAG
1341495 AGTGGGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.15, C:0.00, G:0.40, T:0.45
Consensus pattern (15 bp):
TGAGTTTGAGTGTTG
Found at i:1349527 original size:3 final size:3
Alignment explanation
Indices: 1349519--1349544 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1349509 TGCATAGTTT
1349519 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1349545 TTCAATTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1350089 original size:16 final size:17
Alignment explanation
Indices: 1350049--1350094 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
1350039 AAATGATGGG
1350049 TATTTATTTTTAAACTT
1 TATTTATTTTTAAACTT
* *
1350066 T-TTAATTTTTATA-TT
1 TATTTATTTTTAAACTT
1350081 TATTTATTTATTAA
1 TATTTATTT-TTAA
1350095 TAAAGTGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
15 3 0.13
16 16 0.70
17 4 0.17
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTTATTTTTAAACTT
Found at i:1350341 original size:2 final size:2
Alignment explanation
Indices: 1350334--1350372 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1350324 TAAATTAAGA
1350334 AT AT 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 AT AT A
1350373 GTAAACAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1355184 original size:27 final size:27
Alignment explanation
Indices: 1355154--1355208 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1355144 ATCTTGCTTG
* * *
1355154 TTGTTACAAGTTAAGGCATGAATCACT
1 TTGTTACAACTCAAAGCATGAATCACT
*
1355181 TTGTTACACCTCAAAGCATGAATCACT
1 TTGTTACAACTCAAAGCATGAATCACT
1355208 T
1 T
1355209 CATCAGTAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (27 bp):
TTGTTACAACTCAAAGCATGAATCACT
Found at i:1366984 original size:2 final size:2
Alignment explanation
Indices: 1366977--1367006 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1366967 CCTTTGTTTG
1366977 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1367007 AAGGGCTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1380593 original size:12 final size:11
Alignment explanation
Indices: 1380565--1380598 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1380555 GAATTTTACA
*
1380565 TAAAAAATGAT
1 TAAAAAATAAT
1380576 TAAAAAATAAT
1 TAAAAAATAAT
1380587 TATAAAAATAAT
1 TA-AAAAATAAT
1380599 CATATTGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (11 bp):
TAAAAAATAAT
Found at i:1398030 original size:17 final size:17
Alignment explanation
Indices: 1398008--1398051 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
1397998 AATTAATTAT
1398008 ATTAAAAATATACAAAA
1 ATTAAAAATATACAAAA
* *
1398025 ATTAAAAAAATATAAAA
1 ATTAAAAATATACAAAA
*
1398042 ATAAAAAATA
1 ATTAAAAATA
1398052 ATTAATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (17 bp):
ATTAAAAATATACAAAA
Found at i:1398054 original size:27 final size:27
Alignment explanation
Indices: 1398010--1398062 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1398000 TTAATTATAT
*
1398010 TAAAAATATACAAAAATTAAAAAAATA
1 TAAAAATATAAAAAAATTAAAAAAATA
*
1398037 TAAAAATA-AAAAATAATTAATAAAAT
1 TAAAAATATAAAAA-AATTAAAAAAAT
1398063 TATTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (27 bp):
TAAAAATATAAAAAAATTAAAAAAATA
Found at i:1398235 original size:40 final size:41
Alignment explanation
Indices: 1398151--1398247 Score: 160
Period size: 40 Copynumber: 2.4 Consensus size: 41
1398141 TAATTCTTAA
*
1398151 TTATATTCTCTTATTCCTCCAACAACTATTTTTTTTTTTCAT
1 TTAT-TTCTCTTATTTCTCCAACAACTATTTTTTTTTTTCAT
*
1398193 TTATTTCTCTTATTTNTCCAACAACTA-TTTTTTTTTTCAT
1 TTATTTCTCTTATTTCTCCAACAACTATTTTTTTTTTTCAT
1398233 TTATTTCTCTTATTT
1 TTATTTCTCTTATTT
1398248 TCAATGAACG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
40 28 0.53
41 21 0.40
42 4 0.08
ACGTcount: A:0.20, C:0.19, G:0.00, T:0.61
Consensus pattern (41 bp):
TTATTTCTCTTATTTCTCCAACAACTATTTTTTTTTTTCAT
Found at i:1399162 original size:28 final size:28
Alignment explanation
Indices: 1399123--1399193 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 28
1399113 GAAAAAAAAT
1399123 TAAAAGAA-TTTAATTAT-AAAAGTTTAAA
1 TAAAA-AATTTTAATTATAAAAAG-TTAAA
1399151 TAAAAAATTTTACA-TATCAAAAAGTTAAA
1 TAAAAAATTTTA-ATTAT-AAAAAGTTAAA
*
1399180 -AAAAAATTTAAATT
1 TAAAAAATTTTAATT
1399194 TTAATTAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
27 3 0.08
28 23 0.62
29 6 0.16
30 5 0.14
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (28 bp):
TAAAAAATTTTAATTATAAAAAGTTAAA
Found at i:1401635 original size:67 final size:67
Alignment explanation
Indices: 1401552--1401690 Score: 233
Period size: 67 Copynumber: 2.1 Consensus size: 67
1401542 TCCTGAAGCC
*
1401552 TTGGAGCAATTGGGGGAAGATAGCTGAGCTAGACACAACGAACAGAGGTGTTGAGCTGCAAACGA
1 TTGGAGCAATTGGGGGAAGATAGCTGAGCTAGACACAACGAACAGAGGTGTTGAGCTACAAACGA
1401617 CA
66 CA
* * * *
1401619 TTGGAGCAATTTGGGGAAGATAGCTGAGCTAGAGACGACGAACCGAGGTGTTGAGCTACAAACGA
1 TTGGAGCAATTGGGGGAAGATAGCTGAGCTAGACACAACGAACAGAGGTGTTGAGCTACAAACGA
1401684 CA
66 CA
1401686 TTGGA
1 TTGGA
1401691 CTGAGCCCGT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.33, C:0.16, G:0.33, T:0.18
Consensus pattern (67 bp):
TTGGAGCAATTGGGGGAAGATAGCTGAGCTAGACACAACGAACAGAGGTGTTGAGCTACAAACGA
CA
Found at i:1403460 original size:33 final size:33
Alignment explanation
Indices: 1403453--1403541 Score: 115
Period size: 33 Copynumber: 2.7 Consensus size: 33
1403443 TGATGGTGGA
* * *
1403453 GGTGGAGGTGGTGGTGGTGGAGGGGGTTGTGAT
1 GGTGGTGGTGGAGGAGGTGGAGGGGGTTGTGAT
* *
1403486 GGTGGTGGTGGTGGTGGTGGAGGGGGTTGTGAT
1 GGTGGTGGTGGAGGAGGTGGAGGGGGTTGTGAT
* *
1403519 GGTGGTGGTGGTGGAGGCGGAGG
1 GGTGGTGGTGGAGGAGGTGGAGG
1403542 CGGAGGAGGT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.08, C:0.01, G:0.65, T:0.26
Consensus pattern (33 bp):
GGTGGTGGTGGAGGAGGTGGAGGGGGTTGTGAT
Found at i:1403461 original size:21 final size:21
Alignment explanation
Indices: 1403435--1403496 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
1403425 AGGAGGTGGA
*
1403435 GGAGGTTTTGATGGTGGAGGT
1 GGAGGTTGTGATGGTGGAGGT
* *
1403456 GGAGGTGGTGGTGGTGGA-G-
1 GGAGGTTGTGATGGTGGAGGT
*
1403475 GG-GGTTGTGATGGTGGTGGT
1 GGAGGTTGTGATGGTGGAGGT
1403495 GG
1 GG
1403497 TGGTGGTGGA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 12 0.36
19 3 0.09
20 3 0.09
21 15 0.45
ACGTcount: A:0.10, C:0.00, G:0.61, T:0.29
Consensus pattern (21 bp):
GGAGGTTGTGATGGTGGAGGT
Found at i:1403467 original size:3 final size:3
Alignment explanation
Indices: 1403446--1403532 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
1403436 GAGGTTTTGA
* * * * * *
1403446 TGG TGG AGG TGG AGG TGG TGG TGG TGG AGG GGG TTG TGA TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
* * * *
1403494 TGG TGG TGG TGG AGG GGG TTG TGA TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1403533 AGGCGGAGGC
Statistics
Matches: 66, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.07, C:0.00, G:0.64, T:0.29
Consensus pattern (3 bp):
TGG
Found at i:1404954 original size:15 final size:15
Alignment explanation
Indices: 1404934--1404965 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1404924 GTGACAGACG
*
1404934 TTACGTGACTTAATA
1 TTACGTGACTGAATA
1404949 TTACGTGACTGAATA
1 TTACGTGACTGAATA
1404964 TT
1 TT
1404966 TGTTGAGTAT
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:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (15 bp):
TTACGTGACTGAATA
Found at i:1404967 original size:102 final size:103
Alignment explanation
Indices: 1404743--1404971 Score: 316
Period size: 103 Copynumber: 2.2 Consensus size: 103
1404733 TTTATTTGGC
* * * * *
1404743 ATTAGGTGCCTGAATATTTATTGAGCATTGTGTGAGTTCTTTATAAGCATTACGTGACTGAATAT
1 ATTACGTGACTGAATATTTGTTGAACATTGCGTGAGTTCTTTATAAGCATTACGTGACTGAATAT
* **
1404808 ATGTTGAGCGTTGCGTGAGAGTTAATACGTGACTGAAT
66 ATGTTGAGCGTTGCGTGACAGACAATACGTGACTGAAT
* * *
1404846 ATTACCTGACTGAATATTTGTTGAACATTGCGTGAGTTTTTTATAGGCATTACGTGACTGAATAT
1 ATTACGTGACTGAATATTTGTTGAACATTGCGTGAGTTCTTTATAAGCATTACGTGACTGAATAT
* ** *
1404911 TTGTT-AGCGTTGCGTGACAGACGTTACGTGACTTAAT
66 ATGTTGAGCGTTGCGTGACAGACAATACGTGACTGAAT
1404948 ATTACGTGACTGAATATTTGTTGA
1 ATTACGTGACTGAATATTTGTTGA
1404972 GTATTACGTG
Statistics
Matches: 110, Mismatches: 16, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
102 49 0.45
103 61 0.55
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.38
Consensus pattern (103 bp):
ATTACGTGACTGAATATTTGTTGAACATTGCGTGAGTTCTTTATAAGCATTACGTGACTGAATAT
ATGTTGAGCGTTGCGTGACAGACAATACGTGACTGAAT
Found at i:1404982 original size:102 final size:103
Alignment explanation
Indices: 1404743--1405006 Score: 323
Period size: 102 Copynumber: 2.6 Consensus size: 103
1404733 TTTATTTGGC
* * * * * *
1404743 ATTAGGTGCCTGAATATTTATTGAGCATTGTGTGAGTTCTTTATAAGCATTACGTGACTGAATAT
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTATTTATAGGCATTACGTGACTGAATAT
* **
1404808 ATGTTGAGCGTTGCGTGAGAGTTAATACGTGACTGAAT
66 ATGTTGAGCGTTGCGTGACAGACAATACGTGACTGAAT
* * *
1404846 ATTACCTGACTGAATATTTGTTGAACATTGCGTGAGTTTTTTATAGGCATTACGTGACTGAATAT
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTATTTATAGGCATTACGTGACTGAATAT
* ** *
1404911 TTGTT-AGCGTTGCGTGACAGACGTTACGTGACTTAAT
66 ATGTTGAGCGTTGCGTGACAGACAATACGTGACTGAAT
* * ** * *
1404948 ATTACGTGACTGAATATTTGTTGAGTATTACGTGACCTATTTGTAGGCATTGCGTGACT
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTATTTATAGGCATTACGTGACT
1405007 TTAGCTACCT
Statistics
Matches: 137, Mismatches: 24, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
102 76 0.55
103 61 0.45
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (103 bp):
ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTATTTATAGGCATTACGTGACTGAATAT
ATGTTGAGCGTTGCGTGACAGACAATACGTGACTGAAT
Found at i:1419471 original size:162 final size:162
Alignment explanation
Indices: 1419204--1419521 Score: 566
Period size: 162 Copynumber: 2.0 Consensus size: 162
1419194 CTTATGGCTC
** *
1419204 TGGGGCCATACCACCACCTCCTTATTTTGCTTATGGTTACGGAGTCCCTCTTGCACCCCCGTATT
1 TGGGGCCATACCACCACCTCCTTATTTTGAGTATGGTTACGGAGTCCCTCTTGCACCACCGTATT
*
1419269 TTGGTCCTCATCCTCATGGCTATGGAATCCCCTCTAGCTCGGGCGGGTATAACGTCAATAGCCAT
66 TTGGTCCTCATCCTCATGGCTATGGAATCCCCTCTAGCTCGGGCAGGTATAACGTCAATAGCCAT
*
1419334 CCGCATGGTAACAGTCAAGGTCACGGTGTCTA
131 CCGCATAGTAACAGTCAAGGTCACGGTGTCTA
1419366 TGGGGCCATACCACCACCTCCTTATTTTGAGTATGGTTACGGAGTCCCTCTTGCACCACCGTATT
1 TGGGGCCATACCACCACCTCCTTATTTTGAGTATGGTTACGGAGTCCCTCTTGCACCACCGTATT
1419431 TTGGTCCTCATCCTCATGGCTATGGAAT-CCCTCCTAGCTCGGGCAGGTATAACGTCAATAGCCA
66 TTGGTCCTCATCCTCATGGCTATGGAATCCCCT-CTAGCTCGGGCAGGTATAACGTCAATAGCCA
*
1419495 TCCGCATAGTGACAGTCAAGGTCACGG
130 TCCGCATAGTAACAGTCAAGGTCACGG
1419522 AGGTTGGGGA
Statistics
Matches: 149, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
161 4 0.03
162 145 0.97
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.28
Consensus pattern (162 bp):
TGGGGCCATACCACCACCTCCTTATTTTGAGTATGGTTACGGAGTCCCTCTTGCACCACCGTATT
TTGGTCCTCATCCTCATGGCTATGGAATCCCCTCTAGCTCGGGCAGGTATAACGTCAATAGCCAT
CCGCATAGTAACAGTCAAGGTCACGGTGTCTA
Found at i:1421415 original size:60 final size:60
Alignment explanation
Indices: 1421319--1421560 Score: 276
Period size: 60 Copynumber: 4.1 Consensus size: 60
1421309 AAGCCCAGTT
* * *
1421319 CCACCACCATCACCATCAGCTCCGTATCTTTGTAATGCTTATGGCTATGGGGCCATTCCG
1 CCACCACCATCACCATCAGCTCCGTCTCTTTATAATGCTTATGGCTATGGGGCCATTCCA
*
1421379 CCACCACCATCACCATCAGCTCCGTCTCTTTATAATGCTTATGGCTATGGGGCCATTCCG
1 CCACCACCATCACCATCAGCTCCGTCTCTTTATAATGCTTATGGCTATGGGGCCATTCCA
* * * * * *
1421439 CCACCACCATCATCATCAGCTTCG-C-C-TTATTATGTTTATGGCTATGGAGCCATTCAA
1 CCACCACCATCACCATCAGCTCCGTCTCTTTATAATGCTTATGGCTATGGGGCCATTCCA
* * * * * * * * *
1421496 CCACCACCACCACCACCACCAT-CTTCGCCTTATTATGCATATGGCTATGGTGCCATTCCA
1 CCACCACCATCACCATCAGC-TCCGTCTCTTTATAATGCTTATGGCTATGGGGCCATTCCA
1421556 CCACC
1 CCACC
1421561 TCCTTATTCT
Statistics
Matches: 160, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
57 43 0.27
58 3 0.02
59 2 0.01
60 112 0.70
ACGTcount: A:0.22, C:0.36, G:0.15, T:0.28
Consensus pattern (60 bp):
CCACCACCATCACCATCAGCTCCGTCTCTTTATAATGCTTATGGCTATGGGGCCATTCCA
Found at i:1443983 original size:30 final size:30
Alignment explanation
Indices: 1443925--1443983 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
1443915 GGGTACTTCC
* *
1443925 AAATTTAACGTGGACGATTTTACGCGTATT
1 AAATTTAACGTGGACGATTCTACACGTATT
* * *
1443955 AAATTTAATGTGGATGATTCTGCACGTAT
1 AAATTTAACGTGGACGATTCTACACGTAT
1443984 CGAAAAAACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (30 bp):
AAATTTAACGTGGACGATTCTACACGTATT
Found at i:1446443 original size:17 final size:17
Alignment explanation
Indices: 1446418--1446450 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1446408 TTCAATTTGG
*
1446418 AAAACAAAAATATCAAA
1 AAAAAAAAAATATCAAA
1446435 AAAAAAAAAATATCAA
1 AAAAAAAAAATATCAA
1446451 TCAATTCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAAAAAAAATATCAAA
Found at i:1453009 original size:2 final size:2
Alignment explanation
Indices: 1453002--1453027 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1452992 AACTAAACAC
1453002 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
1453028 TACGTCCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1471207 original size:12 final size:12
Alignment explanation
Indices: 1471192--1471241 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
1471182 CCTTTTTCTC
1471192 TTTTTTTTC--T
1 TTTTTTTTCTTT
1471202 TTTTTTTTCTTT
1 TTTTTTTTCTTT
*
1471214 TTTTCTTTCTTT
1 TTTTTTTTCTTT
1471226 TTTTCTCTTTCTTT
1 TTTT-T-TTTCTTT
1471240 TT
1 TT
1471242 CTCCCAGCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 9 0.26
12 16 0.47
14 9 0.26
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:1471214 original size:18 final size:17
Alignment explanation
Indices: 1471192--1471241 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
1471182 CCTTTTTCTC
1471192 TTTTTTTTCTTTTTTTT
1 TTTTTTTTCTTTTTTTT
1471209 TCTTTTTTTCTTTCTTTTT
1 T-TTTTTTTCTTT-TTTTT
* *
1471228 TTCTCTTTCTTTTT
1 TTTTTTTTCTTTTT
1471242 CTCCCAGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 3 0.10
18 20 0.69
19 6 0.21
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTTTTTCTTTTTTTT
Found at i:1471242 original size:12 final size:11
Alignment explanation
Indices: 1471184--1471244 Score: 76
Period size: 10 Copynumber: 5.7 Consensus size: 11
1471174 CGTTTGAACC
1471184 TTTTTCTCTTT
1 TTTTTCTCTTT
1471195 TTTTTCT-TTT
1 TTTTTCTCTTT
1471205 TTTTTCT-TTT
1 TTTTTCTCTTT
1471215 TTTCTT-TC-TT
1 TTT-TTCTCTTT
1471225 TTTTTCTCTTT
1 TTTTTCTCTTT
1471236 CTTTTTCTC
1 -TTTTTCTC
1471245 CCAGCCGCTC
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
9 2 0.04
10 24 0.53
11 11 0.24
12 8 0.18
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTCTCTTT
Found at i:1471280 original size:17 final size:18
Alignment explanation
Indices: 1471259--1471325 Score: 93
Period size: 17 Copynumber: 3.7 Consensus size: 18
1471249 CCGCTCCCCT
1471259 TTTCTTCTCTCTTTCTT-
1 TTTCTTCTCTCTTTCTTC
*
1471276 TTTCTTTTCTCTTTCTTC
1 TTTCTTCTCTCTTTCTTC
1471294 TTTCTT-TCTCTTTCTTTC
1 TTTCTTCTCTCTTTC-TTC
1471312 TTTCTTTCTCTCTT
1 TTTC-TTCTCTCTT
1471326 AGCCGCCCCC
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
17 24 0.53
18 13 0.29
19 2 0.04
20 6 0.13
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTCTTCTCTCTTTCTTC
Found at i:1471292 original size:4 final size:4
Alignment explanation
Indices: 1471259--1471325 Score: 58
Period size: 4 Copynumber: 18.5 Consensus size: 4
1471249 CCGCTCCCCT
* *
1471259 TTTC -TTC TCTC TTTC -TT- TTTC TTT- TCTC TTTC -TTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
1471302 --TC TTTC TTTC TTTC TTTC TCTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TT
1471326 AGCCGCCCCC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
2 2 0.04
3 12 0.24
4 36 0.72
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:1471294 original size:28 final size:29
Alignment explanation
Indices: 1471259--1471324 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
1471249 CCGCTCCCCT
*
1471259 TTTCTTCTCTCTTTCTTTTTCTTT-TCTC
1 TTTCTTCTCTCTTTCTCTTTCTTTCTCTC
* *
1471287 TTTCTTCTTTCTTTCTCTTTCTTTCTTTC
1 TTTCTTCTCTCTTTCTCTTTCTTTCTCTC
1471316 TTTC-TCTCT
1 TTTCTTCTCT
1471325 TAGCCGCCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 26 0.79
29 7 0.21
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (29 bp):
TTTCTTCTCTCTTTCTCTTTCTTTCTCTC
Found at i:1471298 original size:79 final size:77
Alignment explanation
Indices: 1471188--1471346 Score: 196
Period size: 79 Copynumber: 2.0 Consensus size: 77
1471178 TGAACCTTTT
* * * *
1471188 TCTCTTTTTTTTCTTTTTTTTTCTTTTTTTCTTTCT-TTTTTTCTCTTTCTTTTTCTCCCAGCCG
1 TCTCTTTTTTTTCTTTTTCTTTCTTTCTTTCTTTCTCTTTCTT-TCTTTCTTTCTCTCCCAGCCG
**
1471252 CTCCCCTTTTCTTC
65 C-CCCCCCTTCTTC
**
1471266 TCTCTTTCTTTTTCTTTTCTCTTTC-TTCTTTCTTTCTCTTTCTTTCTTTCTTTCTCTCTTAGCC
1 TCTCTTT-TTTTTCTTTT-TCTTTCTTTCTTTCTTTCTCTTTCTTTCTTTCTTTCTCTCCCAGCC
1471330 GCCCCCCCTTCTTC
64 GCCCCCCCTTCTTC
1471344 TCT
1 TCT
1471347 TTCTTCTCCT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 20 0.29
79 40 0.57
80 10 0.14
ACGTcount: A:0.01, C:0.32, G:0.03, T:0.64
Consensus pattern (77 bp):
TCTCTTTTTTTTCTTTTTCTTTCTTTCTTTCTTTCTCTTTCTTTCTTTCTTTCTCTCCCAGCCGC
CCCCCCTTCTTC
Found at i:1471406 original size:14 final size:14
Alignment explanation
Indices: 1471379--1471417 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 14
1471369 TTGGCTTCTC
1471379 CTTTCTTT-TTCCT
1 CTTTCTTTCTTCCT
1471392 CTTTCTTTCTTCCT
1 CTTTCTTTCTTCCT
1471406 CATTCTCTTTCT
1 C-TT-TCTTTCT
1471418 CCTTTCTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.35
14 6 0.26
15 2 0.09
16 7 0.30
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (14 bp):
CTTTCTTTCTTCCT
Found at i:1471742 original size:14 final size:13
Alignment explanation
Indices: 1471717--1471766 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 13
1471707 GATGGATGGG
*
1471717 TTTTTATATATTT
1 TTTTTATTTATTT
1471730 TTCTTTATTTATTT
1 TT-TTTATTTATTT
*
1471744 TTTATATTATATTT
1 TTTTTATT-TATTT
1471758 TATTTTATT
1 T-TTTTATT
1471767 ATAATTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
13 7 0.23
14 18 0.58
15 6 0.19
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTATTTATTT
Found at i:1475804 original size:21 final size:21
Alignment explanation
Indices: 1475778--1475862 Score: 134
Period size: 21 Copynumber: 4.0 Consensus size: 21
1475768 CCCGTCAATG
1475778 ACTTTAGTCAGCTAACTTCAC
1 ACTTTAGTCAGCTAACTTCAC
*
1475799 ACTTTAGTCAGCTAACTTAAC
1 ACTTTAGTCAGCTAACTTCAC
* *
1475820 ACCTTAGTCAGCTAACTTCAT
1 ACTTTAGTCAGCTAACTTCAC
*
1475841 GCTTTAGTCAGCTAACTTCAC
1 ACTTTAGTCAGCTAACTTCAC
1475862 A
1 A
1475863 GATTAAGTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (21 bp):
ACTTTAGTCAGCTAACTTCAC
Found at i:1497324 original size:3 final size:3
Alignment explanation
Indices: 1497318--1497344 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1497308 AAAGATTAGA
1497318 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1497345 TTGATTTCAT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1500165 original size:27 final size:27
Alignment explanation
Indices: 1500134--1500270 Score: 112
Period size: 27 Copynumber: 5.0 Consensus size: 27
1500124 GTTTCTCTTT
* * *
1500134 TTATTATACGTTATGTTAAAAATTTAA
1 TTATTACACATTATATTAAAAATTTAA
* * * *
1500161 TTATTACACGTTATGTTAAAAAATATAG
1 TTATTACACATTATATT-AAAAATTTAA
* * * *
1500189 TTATTATACATCATATTGAAAATTTAG
1 TTATTACACATTATATTAAAAATTTAA
* * *
1500216 TTGTTACATATTATATTGAAAATTTAA
1 TTATTACACATTATATTAAAAATTTAA
** *
1500243 TTATTACACACCATATTGAAAATTTAA
1 TTATTACACATTATATTAAAAATTTAA
1500270 T
1 T
1500271 ATCTATGTCA
Statistics
Matches: 91, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
27 70 0.77
28 21 0.23
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (27 bp):
TTATTACACATTATATTAAAAATTTAA
Found at i:1500211 original size:55 final size:54
Alignment explanation
Indices: 1500134--1500270 Score: 139
Period size: 55 Copynumber: 2.5 Consensus size: 54
1500124 GTTTCTCTTT
* * * * * * *
1500134 TTATTATACGTTATGTTAAAAATTTAATTATTACACGTTATGTTAAAAAATATAG
1 TTATTATACATCATATTGAAAATTTAATTATTACACATTATATT-AAAAATATAA
* * * * *
1500189 TTATTATACATCATATTGAAAATTTAGTTGTTACATATTATATTGAAAATTTAA
1 TTATTATACATCATATTGAAAATTTAATTATTACACATTATATTAAAAATATAA
* *
1500243 TTATTACACACCATATTGAAAATTTAAT
1 TTATTATACATCATATTGAAAATTTAAT
1500271 ATCTATGTCA
Statistics
Matches: 67, Mismatches: 15, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
54 32 0.48
55 35 0.52
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (54 bp):
TTATTATACATCATATTGAAAATTTAATTATTACACATTATATTAAAAATATAA
Found at i:1501501 original size:30 final size:30
Alignment explanation
Indices: 1501437--1501502 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
1501427 TATGACAATA
*
1501437 TTAAAATGATAATTTTATTTTTTATTAATT
1 TTAAAATGATAATTTTATTTTTTATTAATG
* *
1501467 TTAAAATTATTATTTTATAATTTTT-TTAA-G
1 TTAAAATGATAATTTTAT--TTTTTATTAATG
1501497 TTAAAA
1 TTAAAA
1501503 AAAGGAAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 22 0.71
31 4 0.13
32 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (30 bp):
TTAAAATGATAATTTTATTTTTTATTAATG
Found at i:1516917 original size:13 final size:13
Alignment explanation
Indices: 1516899--1516924 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1516889 ATTTCTATTA
1516899 AGAAATTATCCAT
1 AGAAATTATCCAT
1516912 AGAAATTATCCAT
1 AGAAATTATCCAT
1516925 TGGCTATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
AGAAATTATCCAT
Done.