Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008115.1 Hibiscus syriacus cultivar Beakdansim tig00110654_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 308958
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:1720 original size:15 final size:15
Alignment explanation
Indices: 1700--1738 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1690 ATTAGAGCTC
1700 AGGAGGAGAATGAGG
1 AGGAGGAGAATGAGG
1715 AGGAGGAGAATGAGG
1 AGGAGGAGAATGAGG
*
1730 AGGAAGAGA
1 AGGAGGAGA
1739 GTAGATGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.51, T:0.05
Consensus pattern (15 bp):
AGGAGGAGAATGAGG
Found at i:14437 original size:21 final size:23
Alignment explanation
Indices: 14390--14445 Score: 80
Period size: 21 Copynumber: 2.5 Consensus size: 23
14380 TAATGTTGAA
*
14390 TCATTCAGCAGTGTGTTGCTATT
1 TCATTCAGCAGTGTGTTGATATT
*
14413 TCATTCAGCAGT-T-TTGATGTT
1 TCATTCAGCAGTGTGTTGATATT
14434 TCATTCAGCAGT
1 TCATTCAGCAGT
14446 CTTCATTCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 18 0.58
22 1 0.03
23 12 0.39
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.43
Consensus pattern (23 bp):
TCATTCAGCAGTGTGTTGATATT
Found at i:16317 original size:36 final size:36
Alignment explanation
Indices: 16245--16320 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
16235 GATTACCATC
*
16245 CCGTCACCGTTTAGCATAAATAGTTTTTCCCTGTCT
1 CCGTCACCGTTTAGCATAAAGAGTTTTTCCCTGTCT
* *
16281 CCGTCCCCTTTTAGCATAAACGA-TTTTCTCCC-GTCT
1 CCGTCACCGTTTAGCATAAA-GAGTTTT-TCCCTGTCT
16317 CCGT
1 CCGT
16321 TTAATTCGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 30 0.86
37 5 0.14
ACGTcount: A:0.17, C:0.33, G:0.13, T:0.37
Consensus pattern (36 bp):
CCGTCACCGTTTAGCATAAAGAGTTTTTCCCTGTCT
Found at i:21409 original size:119 final size:122
Alignment explanation
Indices: 21275--21511 Score: 453
Period size: 120 Copynumber: 2.0 Consensus size: 122
21265 AAAATTCTAA
21275 AAAAAATATTAAAAAAAACCCTAATATTCTTA-GGGTAAAGTATACAAATGGTGTCACGACTATG
1 AAAAAATATTAAAAAAAACCCTAATATTCTTATGGGTAAAGTATACAAATGGTGTCACGACTATG
21339 GTACTATTTTATTAAGTCATTTGACTACTAAAAG-TAT-AAATGATCACTCGATTCT
66 GTACTATTTTATTAAGTCATTTGACTACTAAAAGTTATAAAATGATCACTCGATTCT
21394 AAAAAATATTAAAAAAAACCCTAATATTCTTATGGGTAAAGTATACAAATGGTGTCACGACTATG
1 AAAAAATATTAAAAAAAACCCTAATATTCTTATGGGTAAAGTATACAAATGGTGTCACGACTATG
21459 GTACTATTTTATTAAGTCATTTGACTACTAAAAGTTATAAAATGATCACTCGA
66 GTACTATTTTATTAAGTCATTTGACTACTAAAAGTTATAAAATGATCACTCGA
21512 CTATTCATTA
Statistics
Matches: 115, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
119 32 0.28
120 66 0.57
121 3 0.03
122 14 0.12
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (122 bp):
AAAAAATATTAAAAAAAACCCTAATATTCTTATGGGTAAAGTATACAAATGGTGTCACGACTATG
GTACTATTTTATTAAGTCATTTGACTACTAAAAGTTATAAAATGATCACTCGATTCT
Found at i:22704 original size:16 final size:16
Alignment explanation
Indices: 22683--22719 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
22673 AATGTAGCAA
22683 AGGAGTTGAGAGGATT
1 AGGAGTTGAGAGGATT
22699 AGGAGTTGAGAGGATT
1 AGGAGTTGAGAGGATT
22715 AGGAG
1 AGGAG
22720 CTCCCGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.46, T:0.22
Consensus pattern (16 bp):
AGGAGTTGAGAGGATT
Found at i:24796 original size:73 final size:73
Alignment explanation
Indices: 24711--24855 Score: 272
Period size: 73 Copynumber: 2.0 Consensus size: 73
24701 TTTACCCTTT
24711 TACTTCTCATTCACTTATTAATTCATCCTACACCAACATCTTTTAATTAATTCATTCACTTTTCA
1 TACTTCTCATTCACTTATTAATTCATCCTACACCAACATCTTTTAATTAATTCATTCACTTTTCA
24776 ATTTATTC
66 ATTTATTC
* *
24784 TACTTCTCATTCACTTATTAATTTATCCTACACCAACATCTTTTAATTAATTCCTTCACTTTTCA
1 TACTTCTCATTCACTTATTAATTCATCCTACACCAACATCTTTTAATTAATTCATTCACTTTTCA
24849 ATTTATT
66 ATTTATT
24856 TAATTTGGTC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (73 bp):
TACTTCTCATTCACTTATTAATTCATCCTACACCAACATCTTTTAATTAATTCATTCACTTTTCA
ATTTATTC
Found at i:26231 original size:2 final size:2
Alignment explanation
Indices: 26224--26251 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
26214 CCTTTTTGCA
26224 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
26252 GAGAAAATTG
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:34047 original size:30 final size:29
Alignment explanation
Indices: 34011--34070 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 29
34001 ACAGTGGAAG
34011 ATCGAATATTATCTCTTCAGGTATTTTCTT
1 ATCGAATATTATCTCTTCAGGTA-TTTCTT
34041 ATCGAATATTATCTCTTCAGGTATTTCTT
1 ATCGAATATTATCTCTTCAGGTATTTCTT
34070 A
1 A
34071 CTTGTAGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.48
Consensus pattern (29 bp):
ATCGAATATTATCTCTTCAGGTATTTCTT
Found at i:51036 original size:46 final size:43
Alignment explanation
Indices: 50931--51263 Score: 204
Period size: 46 Copynumber: 7.4 Consensus size: 43
50921 TCATCCCCCG
* * * * * *
50931 GACCAGATCTCTTTATCACGTATGAGCCGTGTCAACCATAGAT
1 GACCAGACCTCTTCATCACGTAGGAACCGTGTCACCCTTAGAT
*
50974 AACCAG-CCGTCTTCATCACGTAGGAACCGTGTTATCACCCTTAGAT
1 GACCAGACC-TCTTCATCACGTAGGAACCGTG---TCACCCTTAGAT
* * * * *
51020 GGCCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCTTAGGAT
1 GACCAGACCTCTTCATCACGTAGGAACCGTGTCACCCTTA-GAT
* * * *
51064 AACCAG-CCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGAT
1 GACCAGACC-TCTTCATCACGTAGGAACC--G-TGTCACCCTTAGAT
* * * * * *
51110 GGCCAGATCTCTTCATCACGTAAGAGCCGTGTCAACATTAGGAT
1 GACCAGACCTCTTCATCACGTAGGAACCGTGTCACCCTTA-GAT
* * *
51154 AACCAG-CCGTCCTCATCACGTAGGAACCGAGTTATCACCCTTCCTAAAGAT
1 GACCAGACC-TCTTCATCACGTAGGAACC--G-TGTCACCC-T--T--AGAT
** * * *
51205 GACCAGATTTCCTCATCACGTAGGAGCCGTGTCACCCTTAGAC
1 GACCAGACCTCTTCATCACGTAGGAACCGTGTCACCCTTAGAT
51248 GACCAGACCTCTTCAT
1 GACCAGACCTCTTCAT
51264 TGCGTACGAG
Statistics
Matches: 219, Mismatches: 49, Indels: 44
0.70 0.16 0.14
Matches are distributed among these distances:
42 1 0.00
43 58 0.26
44 47 0.21
45 1 0.00
46 59 0.27
47 16 0.07
48 8 0.04
49 1 0.00
50 1 0.00
51 26 0.12
52 1 0.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.25
Consensus pattern (43 bp):
GACCAGACCTCTTCATCACGTAGGAACCGTGTCACCCTTAGAT
Found at i:51097 original size:90 final size:90
Alignment explanation
Indices: 50933--51245 Score: 450
Period size: 90 Copynumber: 3.4 Consensus size: 90
50923 ATCCCCCGGA
* * * *
50933 CCAGATCTCTTTATCACGTATGAGCCGTGTCAACCATA-GATAACCAGCCGTCTTCATCACGTAG
1 CCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCTTAGGATAACCAGCCGTCCTCATCACGTAG
*
50997 GAACCGTGTTATCACCCTTAGATGG
66 GAACCATGTTATCACCCTTAGATGG
51022 CCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCTTAGGATAACCAGCCGTCCTCATCACGTAG
1 CCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCTTAGGATAACCAGCCGTCCTCATCACGTAG
*
51087 GAACCATGTTATCACCTTTAGATGG
66 GAACCATGTTATCACCCTTAGATGG
*
51112 CCAGATCTCTTCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTAG
1 CCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCTTAGGATAACCAGCCGTCCTCATCACGTAG
*
51177 GAACCGA-GTTATCACCCTTCCTAAAGATGA
66 GAACC-ATGTTATCACCC-T--T--AGATGG
* * * *
51207 CCAGATTTCCTCATCACGTAGGAGCCGTGTCACCCTTAG
1 CCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCTTAG
51246 ACGACCAGAC
Statistics
Matches: 203, Mismatches: 14, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
89 35 0.17
90 126 0.62
91 2 0.01
93 1 0.00
95 39 0.19
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (90 bp):
CCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCTTAGGATAACCAGCCGTCCTCATCACGTAG
GAACCATGTTATCACCCTTAGATGG
Found at i:54262 original size:23 final size:23
Alignment explanation
Indices: 54214--54262 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
54204 ATTAAAGTCA
* *
54214 TAATTGTTTTTAAAAATAATATT
1 TAATTGTTTTTAAAAAAAATAGT
*
54237 TAATTG-TTTTACAAAAAAATGGT
1 TAATTGTTTTTA-AAAAAAATAGT
54260 TAA
1 TAA
54263 GACACCCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (23 bp):
TAATTGTTTTTAAAAAAAATAGT
Found at i:56625 original size:2 final size:2
Alignment explanation
Indices: 56618--56646 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
56608 GTTTTATTGA
56618 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 A
56647 AATGCTCTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59844 original size:300 final size:294
Alignment explanation
Indices: 58723--59888 Score: 1175
Period size: 302 Copynumber: 3.9 Consensus size: 294
58713 GCCCTTAGCT
* * * *
58723 GTATGTTTTGATTGCCTTGTAATCTCCTAACATG-CTCGTATTTAGAATCCTTGATTTTTATTAG
1 GTATGTTTTGATTGCCTTGGAA-CGCATAACCTGTC-CGTATTTAGAATCCTTGATTTTTATTAG
* * * * * *
58787 TTGTTAGGAAGCTCTGCGTGACTTTGAAGTCGTTAATGCGTGTGAAAGGCCAATAGATGAGTAAT
64 TTGTTAGGAAGCTCTACGTGGCTTTGAAGTCGTT-GTGTGTGTGAAAGGCCAATAAATGAATAAT
** * *
58852 ATATCCGGAAATGATGTGAAGCAACCGAAAAGAACATGGAATTTCAATGTTACCACGTG-GAGAG
128 ATATCCGGAAATGATGTGAAATAACCGAAGAGAACATGGAATTTCAATGTTACCACATGAG-GAG
* * ** *
58916 GGATCTTGCTGGTGGTTCATTCCTCTTTTCCAGAAAACTCGTGCCCTAAAAGAAGATAATTACTA
192 AGATCTTGCTGGTGGTTCATTTCTCTTTTCCAGAAAACTCGTGCCCTAAAAGATCATAACTACTA
* * *
58981 TCTTTAAACGTCATTTGTATGAAACT-TGCTCCCTTTAGTC
257 TCTTT-AACGTTACTTGTATGAAACTGTGCT--CTTTTGTC
* * * * * * * *
59021 ATATGTTTTGATTGCCTTGGAATCACCTAACCTTTTCATATTTAGAATCCTCGACTTTTATTAGT
1 GTATGTTTTGATTGCCTTGGAA-CGCATAACCTGTCCGTATTTAGAATCCTTGATTTTTATTAGT
* * * *
59086 TGTTAGGAAGCTCTACATGGTTTTGAAGT-GTCAGTGTGTGTGAAGGGCCAATAAATGAATAATA
65 TGTTAGGAAGCTCTACGTGGCTTTGAAGTCGT-TGTGTGTGTGAAAGGCCAATAAATGAATAATA
* * * * *
59150 TATCCGGAATTGATGTGAAATAGCCGAAGAGAACATGAAATTTCAATGTTACCACGTGGGGGAGA
129 TATCCGGAAATGATGTGAAATAACCGAAGAGAACATGGAATTTCAATGTTACCACAT-GAGGAGA
* * *
59215 GATCTTTCTGGTGGTTGGTCATTTTCTCTTTTCCAGAAAACTCGTGCCCTAAAAGATCGTAACTG
193 GATCTTGCTGGTGG-T--TCA-TTTCTCTTTTCCAGAAAACTCGTGCCCTAAAAGATCATAACTA
* * ** *
59280 CGATCTTTATACGTTACTTGTATGGCATGTGTGCCCTTTTGTC
254 CTATCTTTA-ACGTTACTTGTAT-GAAACTGTGCTCTTTTGTC
* * *
59323 GTATTTTTTCGATTGCCTTGGAATGCATAACCTGTCTGTATTTAGAATCCTTGA-TTTTAGTATA
1 GTATGTTTT-GATTGCCTTGGAACGCATAACCTGTCCGTATTTAGAATCCTTGATTTTTA-T-TA
* * *
59387 -TT-TTTGGAAGCTCTACGTGGCTTTGAAGTCGTTGGAGTGTGTGAAAGGACAATAAATGAATAA
63 GTTGTTAGGAAGCTCTACGTGGCTTTGAAGTCGTT-GTGTGTGTGAAAGGCCAATAAATGAATAA
* * * * * **
59450 TATACCCGAAAATGATGTCAAATAACCAAAGAGAACGTGGAATTTTGATGTTACCACATG-GGAG
127 TATATCCGGAAATGATGTGAAATAACCGAAGAGAACATGGAATTTCAATGTTACCACATGAGGAG
* * *
59514 AGATCTTTTTGGTGGTGGTTCATTTTCTCTTTTCCAGAAAACCCGTGTCCTAAAAGATCATAACT
192 AGATC---TTGCTGGTGGTTCA-TTTCTCTTTTCCAGAAAACTCGTGCCCTAAAAGATCATAACT
* *
59579 ACTATCTTTGAACATTACTTGTATGATACATGTGCTCTTTTGTC
253 ACTATCTTT-AACGTTACTTGTATGAAAC-TGTGCTCTTTTGTC
** * *
59623 GTATGTTTTGATTGCCTTGGAACCGTTTCACCTGTCCGTATTTAGAATCCTTGATTTTTATTGGT
1 GTATGTTTTGATTGCCTTGGAA-CGCATAACCTGTCCGTATTTAGAATCCTTGATTTTTATTAGT
* * * *
59688 TGTTAGGAATCTCCACGTGCCTTTGAAGTCGTCAGTGTGTGTGTGTGAAGGGCCAATAAATGAAT
65 TGTTAGGAAGCTCTACGTGGCTTTGAA---GTC-GT-TGTGTGTGTGAAAGGCCAATAAATGAAT
** * * *
59753 AATATATCTTGAAATGATGTGAAATAACCGATGAGAACATGGGATTTCAATGTTACCACAT-ATG
125 AATATATCCGGAAATGATGTGAAATAACCGAAGAGAACATGGAATTTCAATGTTACCACATGAGG
* * * ** * * * *
59817 AGAGATATTGCTGGTAGTTCA-TTCTCTTATCTGGAAAA-TTGTGGCCTAAAAGATGATAATTAC
190 AGAGATCTTGCTGGTGGTTCATTTCTCTTTTCCAGAAAACTCGTGCCCTAAAAGATCATAACTAC
*
59880 TATCCTTAA
255 TATCTTTAA
59889 TCGTCATGTG
Statistics
Matches: 717, Mismatches: 120, Indels: 62
0.80 0.13 0.07
Matches are distributed among these distances:
297 79 0.11
298 99 0.14
299 43 0.06
300 135 0.19
301 61 0.09
302 184 0.26
303 26 0.04
304 6 0.01
305 83 0.12
306 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (294 bp):
GTATGTTTTGATTGCCTTGGAACGCATAACCTGTCCGTATTTAGAATCCTTGATTTTTATTAGTT
GTTAGGAAGCTCTACGTGGCTTTGAAGTCGTTGTGTGTGTGAAAGGCCAATAAATGAATAATATA
TCCGGAAATGATGTGAAATAACCGAAGAGAACATGGAATTTCAATGTTACCACATGAGGAGAGAT
CTTGCTGGTGGTTCATTTCTCTTTTCCAGAAAACTCGTGCCCTAAAAGATCATAACTACTATCTT
TAACGTTACTTGTATGAAACTGTGCTCTTTTGTC
Found at i:66533 original size:29 final size:29
Alignment explanation
Indices: 66490--66599 Score: 184
Period size: 29 Copynumber: 3.8 Consensus size: 29
66480 TTTGAGTTAT
*
66490 GAAATGAAACGTTAGACACTAAACTAGAAC
1 GAAAT-AAATGTTAGACACTAAACTAGAAC
*
66520 GAAATAAATGTTAGGCACTAAACTAGAAC
1 GAAATAAATGTTAGACACTAAACTAGAAC
66549 GAAATAAATGTTAGACACTAAACTAGAAC
1 GAAATAAATGTTAGACACTAAACTAGAAC
*
66578 GAAATAAATGTTAGGCACTAAA
1 GAAATAAATGTTAGACACTAAA
66600 ACCAAAGGCA
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 71 0.93
30 5 0.07
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (29 bp):
GAAATAAATGTTAGACACTAAACTAGAAC
Found at i:70314 original size:20 final size:16
Alignment explanation
Indices: 70271--70305 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
70261 CATAAGCAAA
70271 TCACAATCCGAGCACG
1 TCACAATCCGAGCACG
70287 TCACAATCCGAGCACG
1 TCACAATCCGAGCACG
70303 TCA
1 TCA
70306 GAAACAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.37, G:0.17, T:0.14
Consensus pattern (16 bp):
TCACAATCCGAGCACG
Found at i:71238 original size:291 final size:291
Alignment explanation
Indices: 70708--71266 Score: 811
Period size: 291 Copynumber: 1.9 Consensus size: 291
70698 ATTTTCTGAC
* * *
70708 TCCAATTATGTATAACTGGAGCACGACCGACAAGTTTTATGATTCAACCCGGTCGTCATTGCTAG
1 TCCAATTATGTATAACTCGAGCACGACCGACAAGTTTTAAGATTCAACCCGCTCGTCATTGCTAG
* * *
70773 ATTTTCAATGCTAAAGCTACACCAGACAGCAGCAAAGAAACTGATCATCTTCAAACACTATTAGC
66 ATTTTCAATGCTAAAGCGACACCAGACAGCAGCAAAGAAACTAATCATCTTCAAACACCATTAGC
* ** * * * *
70838 TGCTCCTAGTATCCAATCCAAGTTATGCACAAATCAAGCACATTCAGCAAGTTTAAGATTCAACC
131 AGCTCAAAGTATCAAATCCAAGTTATGCACAAATCAAGCACACTCAACAAGTTTAAAATTCAACC
* * *
70903 CGTCATTGCTAGATTTTCAATGCCTATGGTAGCAGGGAAGAAACTAAT-TCTTCTCGAACGCCAT
196 CATCATTGCTAGATTTTCAATGCCAATGGTAGCAGGGAAGAAACTAATAT-GTCTCGAACGCCAT
70967 TAGCAGCTCAAAGTTTCAGATTAGTTTCAGGT
260 TAGCAGCTCAAAGTTTCAGATTAGTTTCAGGT
* * *
70999 TCCAATTATGTATAAGTCGAGCACGATCGACAAGTTTTAAGATTCAACTCGCTCGTCATTGCTAG
1 TCCAATTATGTATAACTCGAGCACGACCGACAAGTTTTAAGATTCAACCCGCTCGTCATTGCTAG
* *
71064 ATTTTCAATGCTAAAGCGACACCAGACAGTAGCAAAGAAACTAATCATCTTCAAACACCATTGGC
66 ATTTTCAATGCTAAAGCGACACCAGACAGCAGCAAAGAAACTAATCATCTTCAAACACCATTAGC
* * *
71129 AGCTCAAAGTATCAAATTCC-AGTTATGCATATATCGAGCACACTCAACAAGTTTAAAATTCAAC
131 AGCTCAAAGTATCAAA-TCCAAGTTATGCACAAATCAAGCACACTCAACAAGTTTAAAATTCAAC
** *
71193 TTATC-TGTGCTAGATTTTCAATGCCAATGGTAGTAGAGG-AGAAACTAATATGTCTCGAACGCC
195 CCATCAT-TGCTAGATTTTCAATGCCAATGGTAGCAG-GGAAGAAACTAATATGTCTCGAACGCC
71256 ATTAGCAGCTC
258 ATTAGCAGCTC
71267 GAATTTTCGG
Statistics
Matches: 237, Mismatches: 27, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
290 1 0.00
291 230 0.97
292 6 0.03
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (291 bp):
TCCAATTATGTATAACTCGAGCACGACCGACAAGTTTTAAGATTCAACCCGCTCGTCATTGCTAG
ATTTTCAATGCTAAAGCGACACCAGACAGCAGCAAAGAAACTAATCATCTTCAAACACCATTAGC
AGCTCAAAGTATCAAATCCAAGTTATGCACAAATCAAGCACACTCAACAAGTTTAAAATTCAACC
CATCATTGCTAGATTTTCAATGCCAATGGTAGCAGGGAAGAAACTAATATGTCTCGAACGCCATT
AGCAGCTCAAAGTTTCAGATTAGTTTCAGGT
Found at i:71672 original size:2 final size:2
Alignment explanation
Indices: 71665--71713 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
71655 GCAAACTAAC
71665 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71707 AT AT AT A
1 AT AT AT A
71714 CTCCCAAGCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:74299 original size:53 final size:53
Alignment explanation
Indices: 74227--74384 Score: 309
Period size: 53 Copynumber: 3.0 Consensus size: 53
74217 AATAATTAAA
74227 TCCTTCTAATATCAAAGATATTCTAATCCCATACTTAAACTATTCATAATCCT
1 TCCTTCTAATATCAAAGATATTCTAATCCCATACTTAAACTATTCATAATCCT
74280 TCCTTCTAATATCAAAGATATTCTAATCCCATACTTAAACTATTCATAATCCT
1 TCCTTCTAATATCAAAGATATTCTAATCCCATACTTAAACTATTCATAATCCT
74333 TCCTTCTAATATCAAAGATATTCTAATCCCATACTT-AACTATTCATAATCCT
1 TCCTTCTAATATCAAAGATATTCTAATCCCATACTTAAACTATTCATAATCCT
74385 CCCGAACGTA
Statistics
Matches: 105, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 16 0.15
53 89 0.85
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (53 bp):
TCCTTCTAATATCAAAGATATTCTAATCCCATACTTAAACTATTCATAATCCT
Found at i:78497 original size:16 final size:16
Alignment explanation
Indices: 78476--78546 Score: 73
Period size: 16 Copynumber: 4.8 Consensus size: 16
78466 ATTTTTTATA
78476 ATTATATTAAAATAAT
1 ATTATATTAAAATAAT
78492 ATTATATTAAAATAAT
1 ATTATATTAAAATAAT
* *
78508 AATATA-TCAAAT-AT
1 ATTATATTAAAATAAT
*
78522 A-T-TA--AAAATAAA
1 ATTATATTAAAATAAT
78534 ATTATATTAAAAT
1 ATTATATTAAAAT
78547 TATCTAGAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
11 4 0.09
12 4 0.09
13 2 0.04
14 5 0.11
15 5 0.11
16 26 0.57
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTATATTAAAATAAT
Found at i:79899 original size:85 final size:85
Alignment explanation
Indices: 79756--79941 Score: 345
Period size: 85 Copynumber: 2.2 Consensus size: 85
79746 CGAATATAGT
79756 TGTATTTTTAAATATTTTAGCCACCTCCCTTACAAAATAAAAACCAACCCAAATGCATTATTTTT
1 TGTATTTTTAAATATTTTAGCCACCTCCCTTACAAAATAAAAACCAACCCAAATGCATTATTTTT
79821 TTATATTAAAATTAATTGAA
66 TTATATTAAAATTAATTGAA
79841 TGTATTTTTAAATATTTTAGCCACCTCCCTTACAAAATAAAAACCAACCCAAATGCATTATTTTT
1 TGTATTTTTAAATATTTTAGCCACCTCCCTTACAAAATAAAAACCAACCCAAATGCATTATTTTT
79906 TTATATTAAAATTAATTGAA
66 TTATATTAAAATTAATTGAA
*
79926 TATATGCTTTTAAATA
1 TGTAT--TTTTAAATA
79942 CTCATGTATT
Statistics
Matches: 98, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
85 89 0.91
87 9 0.09
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.40
Consensus pattern (85 bp):
TGTATTTTTAAATATTTTAGCCACCTCCCTTACAAAATAAAAACCAACCCAAATGCATTATTTTT
TTATATTAAAATTAATTGAA
Found at i:80420 original size:31 final size:31
Alignment explanation
Indices: 80384--80461 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
80374 AAAGATAACG
* *
80384 AGTGACTATTTTGTTACAAATCGATAATGTT
1 AGTGACCATTTTGTTACAAATCGATAATATT
*
80415 GGTGACCATTTTGTTACAAATCGATAATATT
1 AGTGACCATTTTGTTACAAATCGATAATATT
*
80446 AGTGACCAATTTGTTA
1 AGTGACCATTTTGTTA
80462 TTTTTAAAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.40
Consensus pattern (31 bp):
AGTGACCATTTTGTTACAAATCGATAATATT
Found at i:83526 original size:22 final size:22
Alignment explanation
Indices: 83492--83546 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
83482 AAAATATATT
*
83492 TATTAATAATTTTAATGATATAA
1 TATT-ATATTTTTAATGATATAA
* *
83515 TATTATATTTTTAGTGTTATAA
1 TATTATATTTTTAATGATATAA
*
83537 TATTGTATTT
1 TATTATATTT
83547 AGTTATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.56
Consensus pattern (22 bp):
TATTATATTTTTAATGATATAA
Found at i:83682 original size:8 final size:8
Alignment explanation
Indices: 83669--83693 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
83659 TAACTAATAT
83669 ATTTTAAA
1 ATTTTAAA
83677 ATTTTAAA
1 ATTTTAAA
83685 ATTTTAAA
1 ATTTTAAA
83693 A
1 A
83694 ATAATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTTTAAA
Found at i:88438 original size:16 final size:16
Alignment explanation
Indices: 88408--88447 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
88398 GAGAATATTT
* *
88408 TGTATGATATTTATGTG
1 TGTAT-ATATATATGTA
88425 TGTATATATATATGTA
1 TGTATATATATATGTA
88441 TGTATAT
1 TGTATAT
88448 GTGTAGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (16 bp):
TGTATATATATATGTA
Found at i:97938 original size:4 final size:4
Alignment explanation
Indices: 97931--97956 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
97921 AAAATATATA
97931 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
97957 TATTAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:98498 original size:2 final size:2
Alignment explanation
Indices: 98491--98521 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
98481 TATAATATCC
98491 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
98522 ATTGCAATAA
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:100735 original size:2 final size:2
Alignment explanation
Indices: 100728--100796 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
100718 ACGTATATGC
100728 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
100770 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 A
100797 CATGAACACA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:112558 original size:14 final size:15
Alignment explanation
Indices: 112539--112567 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
112529 GTTCTGTTTA
112539 AATTTTAAA-AATAT
1 AATTTTAAATAATAT
112553 AATTTTAAATAATAT
1 AATTTTAAATAATAT
112568 TTTATTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTAAATAATAT
Found at i:113381 original size:32 final size:31
Alignment explanation
Indices: 113335--113430 Score: 86
Period size: 32 Copynumber: 3.0 Consensus size: 31
113325 CCCAAACCAA
* * *
113335 AAATCAACCGATCCGATATTGACCCGACCCG
1 AAATCAATCAATCCGGTATTGACCCGACCCG
* * * *
113366 AAATCTAATTAATCCGGTATT-ATCTCAACCCAA
1 AAATC-AATCAATCCGGTATTGA-CCCGACCC-G
*
113399 AAATCAATCAATCTGGTATTGACCCGACCCG
1 AAATCAATCAATCCGGTATTGACCCGACCCG
113430 A
1 A
113431 TATTGACCGA
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
31 7 0.14
32 36 0.73
33 6 0.12
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.23
Consensus pattern (31 bp):
AAATCAATCAATCCGGTATTGACCCGACCCG
Found at i:114398 original size:58 final size:58
Alignment explanation
Indices: 114328--114445 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
114318 TTAAAGACGG
114328 AACACGTGTACTTCTGATGGTGTCTACCATGAAATTTTTTGTGCTCACTCCGAAATAT
1 AACACGTGTACTTCTGATGGTGTCTACCATGAAATTTTTTGTGCTCACTCCGAAATAT
114386 AACACGTGTACTTCTGATGGTGTCTACCATGAAATTTTTTGTGCTCACTCCGAAATAT
1 AACACGTGTACTTCTGATGGTGTCTACCATGAAATTTTTTGTGCTCACTCCGAAATAT
114444 AA
1 AA
114446 GTTTTCTTCG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (58 bp):
AACACGTGTACTTCTGATGGTGTCTACCATGAAATTTTTTGTGCTCACTCCGAAATAT
Found at i:117790 original size:14 final size:16
Alignment explanation
Indices: 117771--117817 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
117761 TTTATCTTAA
117771 AATATAT-AT-TATTT
1 AATATATAATATATTT
117785 AATATATAATATATTT
1 AATATATAATATATTT
* *
117801 AATATTTAATATTTTT
1 AATATATAATATATTT
117817 A
1 A
117818 GCTAATTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 7 0.24
15 2 0.07
16 20 0.69
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATATATAATATATTT
Found at i:123950 original size:156 final size:158
Alignment explanation
Indices: 123708--124102 Score: 537
Period size: 156 Copynumber: 2.5 Consensus size: 158
123698 TCAACATTCT
* * * * *
123708 TTCAATTTC-TCCTTTATTTTAAGTTCGTATTTTACCAAATTTGAACCACGTGCTCATAAATCAT
1 TTCAA-TTCATCCTTTATTTTAAGTCCATCTTTTACCAAATTTGAACCACATGCTCATAAACCAT
* * * *
123772 CGTAAAATACATATGTATTTTCAACTCCTCATTTT-GTTAACAAATTTTTTATTTTTCAATTTAG
65 AGTAGAATACATATGTACTTTCAACTCCTC-TTTTCGATAACAAATTTTTTATTTTTCAATTTAG
*
123836 T-CCTTAATTTTTCATATTTTT-TTATTTC
129 TCCCTTAATATTTCATATTTTTCTTATTTC
* *
123864 TTCAATTCATCCTTTATTTTAAGTCCATCTTTTACCAAATTTAAACCACATGCTCATAAACCATT
1 TTCAATTCATCCTTTATTTTAAGTCCATCTTTTACCAAATTTGAACCACATGCTCATAAACCATA
* * *
123929 GTAGAATACATATGTACTTTCAATTCCTCTTTTCGATAATAATTTTTTTATTTTTCAATTTAGTC
66 GTAGAATACATATGTACTTTCAACTCCTCTTTTCGATAACAAATTTTTTATTTTTCAATTTAGTC
123994 CCTTAATATTTCATATTTTTCTTATTTC
131 CCTTAATATTTCATATTTTTCTTATTTC
** * * * *
124022 TTCAATTCATTATTTATTTTAAGTCCATCTTTTACCAAATTTGAATCACATACTCATATACCACA
1 TTCAATTCATCCTTTATTTTAAGTCCATCTTTTACCAAATTTGAACCACATGCTCATAAACCATA
* *
124087 ATAGAATACCTATGTA
66 GTAGAATACATATGTA
124103 ACTTCAATTC
Statistics
Matches: 211, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
155 7 0.03
156 107 0.51
157 19 0.09
158 78 0.37
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.47
Consensus pattern (158 bp):
TTCAATTCATCCTTTATTTTAAGTCCATCTTTTACCAAATTTGAACCACATGCTCATAAACCATA
GTAGAATACATATGTACTTTCAACTCCTCTTTTCGATAACAAATTTTTTATTTTTCAATTTAGTC
CCTTAATATTTCATATTTTTCTTATTTC
Found at i:124170 original size:158 final size:155
Alignment explanation
Indices: 123720--124170 Score: 455
Period size: 156 Copynumber: 2.9 Consensus size: 155
123710 CAATTTCTCC
* * * * * * * * *
123720 TTTATTTTAAGTTCGTATTTTACCAAATTTGAACCACGTGCTCATAAATCATC-GTAAAATACAT
1 TTTATTTTAAGTCCATCTTTTACCAAATTTAAACCACATACTCATAAACCA-CAATAGAATACAT
* * * * *
123784 ATGTATTTTCAACTCCTCATTTT-GTTAACAAATTTTTTATTTTTCAATTTAGT-CCTTAATTTT
65 ATGTACTTTCAATTCCT-ATTTTCGATAATAATTTTTTTATTTTTCAATTTAGTCCCTTAA-TTT
* *
123847 TCATATTTTTTTATTTCTTCAATTCATCC
128 TCAT-TTTTCTTATTTCTTCAATTCATCA
* ***
123876 TTTATTTTAAGTCCATCTTTTACCAAATTTAAACCACATGCTCATAAACCATTGTAGAATACATA
1 TTTATTTTAAGTCCATCTTTTACCAAATTTAAACCACATACTCATAAACCACAATAGAATACATA
*
123941 TGTACTTTCAATTCCTCTTTTCGATAATAATTTTTTTATTTTTCAATTTAGTCCCTTAATATTTC
66 TGTACTTTCAATTCCTATTTTCGATAATAATTTTTTTATTTTTCAATTTAGTCCCTTAAT-TTTC
*
124006 ATATTTTTCTTATTTCTTCAATTCATTA
130 --ATTTTTCTTATTTCTTCAATTCATCA
* * * *
124034 TTTATTTTAAGTCCATCTTTTACCAAATTTGAATCACATACTCATATACCACAATAGAATACCTA
1 TTTATTTTAAGTCCATCTTTTACCAAATTTAAACCACATACTCATAAACCACAATAGAATACATA
* ** * *
124099 TGTAAC-TTCAATTCTTAATTTTTTACTAA-AATTGTATTTTCTTTTT-TATTTAGTCCCTTAAC
66 TGT-ACTTTCAATTCCT-ATTTTCGA-TAATAATT-T-TTTTATTTTTCAATTTAGTCCCTTAA-
*
124161 TTTGCATTTT
125 TTTTCATTTT
124171 ACTCAATTTG
Statistics
Matches: 251, Mismatches: 32, Indels: 22
0.82 0.10 0.07
Matches are distributed among these distances:
155 4 0.02
156 98 0.39
157 10 0.04
158 95 0.38
159 13 0.05
160 21 0.08
161 10 0.04
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (155 bp):
TTTATTTTAAGTCCATCTTTTACCAAATTTAAACCACATACTCATAAACCACAATAGAATACATA
TGTACTTTCAATTCCTATTTTCGATAATAATTTTTTTATTTTTCAATTTAGTCCCTTAATTTTCA
TTTTTCTTATTTCTTCAATTCATCA
Found at i:124362 original size:2 final size:2
Alignment explanation
Indices: 124355--124380 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
124345 TGTTAAAAGA
124355 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
124381 GATTAGAGAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:127595 original size:3 final size:3
Alignment explanation
Indices: 127587--127648 Score: 90
Period size: 3 Copynumber: 21.0 Consensus size: 3
127577 TTTTTTATCG
**
127587 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
127634 CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
127649 ATTTACAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:134215 original size:27 final size:27
Alignment explanation
Indices: 134185--134237 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
134175 ATTAAATTTG
*
134185 ATATTTTACTATT-TTATAATTAATTAT
1 ATATATTACTATTATTA-AATTAATTAT
*
134212 ATATATTATTATTATTAAATTAATTA
1 ATATATTACTATTATTAAATTAATTA
134238 ATTAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
ATATATTACTATTATTAAATTAATTAT
Found at i:137717 original size:6 final size:6
Alignment explanation
Indices: 137706--137731 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
137696 AAAAAAGTGA
137706 ACCTCC ACCTCC ACCTCC ACCTCC AC
1 ACCTCC ACCTCC ACCTCC ACCTCC AC
137732 GGGCGCCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.65, G:0.00, T:0.15
Consensus pattern (6 bp):
ACCTCC
Found at i:138803 original size:2 final size:2
Alignment explanation
Indices: 138796--138844 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
138786 TTACAATTAT
138796 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
138838 TA TA TA T
1 TA TA TA T
138845 TTAATATTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:139276 original size:17 final size:17
Alignment explanation
Indices: 139254--139294 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
139244 CGTTTCTTAA
139254 AAATTTTAAATTATTTT
1 AAATTTTAAATTATTTT
* *
139271 AAATTTTAGATTTTTTT
1 AAATTTTAAATTATTTT
*
139288 ATATTTT
1 AAATTTT
139295 TTATTGAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
AAATTTTAAATTATTTT
Found at i:141533 original size:30 final size:29
Alignment explanation
Indices: 141480--141537 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
141470 AATATATATT
141480 TTTTGTTATTTTTATTATTTTTTTACTTTC
1 TTTTGTTATTTTTATTATTTTTTT-CTTTC
141510 TTTTGTTATTTTCT-TT-TTCTTTTTCTTT
1 TTTTGTTATTTT-TATTATT-TTTTTCTTT
141538 TCTTGGTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 6 0.23
30 19 0.73
31 1 0.04
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (29 bp):
TTTTGTTATTTTTATTATTTTTTTCTTTC
Found at i:142020 original size:22 final size:23
Alignment explanation
Indices: 141991--142034 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
141981 TGTCACGTCC
141991 AAATTTTT-AAAA-AATATTTTT
1 AAATTTTTAAAAATAATATTTTT
142012 AAATGTTTTAAAAATAATATTTT
1 AAAT-TTTTAAAAATAATATTTT
142035 ATTTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 4 0.20
23 4 0.20
24 8 0.40
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
AAATTTTTAAAAATAATATTTTT
Found at i:142486 original size:177 final size:175
Alignment explanation
Indices: 142253--142580 Score: 523
Period size: 177 Copynumber: 1.9 Consensus size: 175
142243 TATATATATA
* * * * *
142253 TATATATAAATAAGTTAATTATCCCGCTAGTCATTGAACTTTAGTCTATTTATTGATTTTGTCAT
1 TATATATAAAAAAGTAAATTATCCCCCTAGTCATTGAACCTTAGTCTATGTATTGATTTTGTCAT
* * *
142318 TGAACTTTAAAATACTTCAATTTTGTCACTAAACTTTTAACATTGTCTTTTTTTGTTATTGGATC
66 TGAACTTTAAAAGACTTCAATTTTGTCACTAAACTTTTAACATTG--TTTTTTT-TTACTGGACC
* *
142383 ATTAAATCATTAACAACCTAATGACTATCAATTATGATGAACATTATT
128 ATTAAATCAGTAACAACCGAATGACTATCAATTATGATGAACATTATT
142431 TATATA-AAAAAAGTAAATTATCCCCCTAGTCATTGAACCTTAGTCTATGTATTGATTTTGTCAT
1 TATATATAAAAAAGTAAATTATCCCCCTAGTCATTGAACCTTAGTCTATGTATTGATTTTGTCAT
*
142495 TGAACTTTAAAAGGCTTCAATTTTGTCACTAAACTTTTAACATTGTTTTTTTTTACTGGACCATT
66 TGAACTTTAAAAGACTTCAATTTTGTCACTAAACTTTTAACATTGTTTTTTTTTACTGGACCATT
142560 AAATCAGTAACAACCGAATGA
131 AAATCAGTAACAACCGAATGA
142581 ATCAATAGTT
Statistics
Matches: 139, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
174 30 0.22
175 7 0.05
177 96 0.69
178 6 0.04
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.42
Consensus pattern (175 bp):
TATATATAAAAAAGTAAATTATCCCCCTAGTCATTGAACCTTAGTCTATGTATTGATTTTGTCAT
TGAACTTTAAAAGACTTCAATTTTGTCACTAAACTTTTAACATTGTTTTTTTTTACTGGACCATT
AAATCAGTAACAACCGAATGACTATCAATTATGATGAACATTATT
Found at i:148089 original size:84 final size:84
Alignment explanation
Indices: 147939--148107 Score: 266
Period size: 84 Copynumber: 2.0 Consensus size: 84
147929 GCGATTCTCC
* *
147939 AAAAGCGCAATGCGAATTTCATTTTCGCAACGCTAATTACCTATATCGGTAATTAGCGTTGAGAA
1 AAAACCGCAACGCGAATTTCATTTTCGCAACGCTAATTACCTATATCGGTAATTAGCGTTGAGAA
*
148004 ATTCAAGTTGTGAATTTGG
66 ATTCAAGTTGCGAATTTGG
** *
148023 AAAACCGCAACGCGAATTTTGTTTTCGCAACGCTAATTACCTATATCGGTAATTAGCGTTGCGAA
1 AAAACCGCAACGCGAATTTCATTTTCGCAACGCTAATTACCTATATCGGTAATTAGCGTTGAGAA
* *
148088 ATTCGAGTTGCGAGTTTGG
66 ATTCAAGTTGCGAATTTGG
148107 A
1 A
148108 GAATTCGCGT
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 77 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (84 bp):
AAAACCGCAACGCGAATTTCATTTTCGCAACGCTAATTACCTATATCGGTAATTAGCGTTGAGAA
ATTCAAGTTGCGAATTTGG
Found at i:148155 original size:40 final size:40
Alignment explanation
Indices: 148110--148205 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
148100 AGTTTGGAGA
* * *
148110 ATTCGCGTTGTGATTTACATATTATCGTTGCGCTTTACCT
1 ATTCGCGTTGTGAATTACATATTATCGTTGCGATTTAACT
148150 ATTCGCGTTGTGAATTACATATTATCGTTGCGATTTAACT
1 ATTCGCGTTGTGAATTACATATTATCGTTGCGATTTAACT
*
148190 ATTCGCGTTGCGAATT
1 ATTCGCGTTGTGAATT
148206 TGACTTTCGC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.43
Consensus pattern (40 bp):
ATTCGCGTTGTGAATTACATATTATCGTTGCGATTTAACT
Found at i:148192 original size:20 final size:19
Alignment explanation
Indices: 148110--148225 Score: 99
Period size: 20 Copynumber: 5.8 Consensus size: 19
148100 AGTTTGGAGA
*
148110 ATTCGCGTTGTGATTTACAT
1 ATTCGCGTTGCGATTTAC-T
** *
148130 ATTATCGTTGCGCTTTACCT
1 ATTCGCGTTGCGATTTA-CT
* *
148150 ATTCGCGTTGTGAATTACAT
1 ATTCGCGTTGCGATTTAC-T
**
148170 ATTATCGTTGCGATTTAACT
1 ATTCGCGTTGCGATTT-ACT
148190 ATTCGCGTTGCGAATTTGACT
1 ATTCGCGTTGCG-ATTT-ACT
148211 -TTCGCGTTGCGATTT
1 ATTCGCGTTGCGATTT
148226 TGGAACCTGT
Statistics
Matches: 76, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
19 5 0.07
20 61 0.80
21 10 0.13
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.43
Consensus pattern (19 bp):
ATTCGCGTTGCGATTTACT
Found at i:149577 original size:7 final size:7
Alignment explanation
Indices: 149565--149596 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
149555 TCACAAACGA
149565 TCACCAT
1 TCACCAT
149572 TCACCAT
1 TCACCAT
149579 TCACCAT
1 TCACCAT
149586 TCACCAT
1 TCACCAT
149593 TCAC
1 TCAC
149597 AAACAAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.44, G:0.00, T:0.28
Consensus pattern (7 bp):
TCACCAT
Found at i:151124 original size:14 final size:14
Alignment explanation
Indices: 151105--151166 Score: 74
Period size: 14 Copynumber: 4.6 Consensus size: 14
151095 TTTTTACCTC
151105 AACCCTAAACTCTA
1 AACCCTAAACTCTA
* *
151119 AACCCTACACCCTA
1 AACCCTAAACTCTA
151133 AA-CCTAAACTCTA
1 AACCCTAAACTCTA
* *
151146 AATCCTAAACT-TT
1 AACCCTAAACTCTA
151159 AACCCTAA
1 AACCCTAA
151167 TAAAAAATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
13 19 0.46
14 22 0.54
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (14 bp):
AACCCTAAACTCTA
Found at i:151165 original size:27 final size:27
Alignment explanation
Indices: 151105--151166 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
151095 TTTTTACCTC
*
151105 AACCCTAAACTCTAAACCCTACACCCT
1 AACCCTAAACTCTAAACCCTAAACCCT
* * **
151132 AAACCTAAACTCTAAATCCTAAACTTT
1 AACCCTAAACTCTAAACCCTAAACCCT
151159 AACCCTAA
1 AACCCTAA
151167 TAAAAAATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (27 bp):
AACCCTAAACTCTAAACCCTAAACCCT
Found at i:151166 original size:20 final size:20
Alignment explanation
Indices: 151105--151166 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
151095 TTTTTACCTC
151105 AACCCTAAACTCTAAACCCTA
1 AACCCTAAACT-TAAACCCTA
* * *
151126 CACCCTAAACCTAAACTCTA
1 AACCCTAAACTTAAACCCTA
* *
151146 AATCCTAAACTTTAACCCTA
1 AACCCTAAACTTAAACCCTA
151166 A
1 A
151167 TAAAAAATAT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
20 24 0.73
21 9 0.27
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (20 bp):
AACCCTAAACTTAAACCCTA
Found at i:151596 original size:4 final size:4
Alignment explanation
Indices: 151587--151632 Score: 65
Period size: 4 Copynumber: 11.2 Consensus size: 4
151577 CCTTCACTCG
* *
151587 TATT TATT TATT TATT TATT TATT TAAAT TATT TAAT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T-ATT TATT TATT TATT TATT T
151633 GGCTTTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
4 34 0.92
5 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (4 bp):
TATT
Found at i:158658 original size:28 final size:27
Alignment explanation
Indices: 158606--158659 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
158596 TTTATTTTTA
*
158606 TTCCCTAAAATTTATAAATTTAAATTT
1 TTCCCTAAAATTTATAAATTCAAATTT
*
158633 TTCCCTTAAAATTCTAT-AGTTCAAATT
1 TTCCC-TAAAATT-TATAAATTCAAATT
158660 CATCTTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.22
28 15 0.65
29 3 0.13
ACGTcount: A:0.37, C:0.15, G:0.02, T:0.46
Consensus pattern (27 bp):
TTCCCTAAAATTTATAAATTCAAATTT
Found at i:159455 original size:32 final size:32
Alignment explanation
Indices: 159418--159480 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
159408 AATCGTCCCT
159418 GACATGAGTACAGGATAAGTATAATTTGAGTG
1 GACATGAGTACAGGATAAGTATAATTTGAGTG
159450 GACATGAGTACAGGATAAGTATAATTTGAGT
1 GACATGAGTACAGGATAAGTATAATTTGAGT
159481 ATATGTTGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.06, G:0.27, T:0.29
Consensus pattern (32 bp):
GACATGAGTACAGGATAAGTATAATTTGAGTG
Found at i:168095 original size:23 final size:23
Alignment explanation
Indices: 168068--168113 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
168058 TATAAACTTT
*
168068 TATAAGAT-GAAATAAATTATTAA
1 TATAAAATAGAAATAAA-TATTAA
*
168091 TATAAAATATAAATAAATATTAA
1 TATAAAATAGAAATAAATATTAA
168114 AATTATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (23 bp):
TATAAAATAGAAATAAATATTAA
Found at i:168127 original size:23 final size:24
Alignment explanation
Indices: 168077--168127 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
168067 TTATAAGATG
* *
168077 AAATAAATTATTAATATAAAATAT
1 AAATAAATTATTAAAATAAAATAA
* *
168101 AAATAAA-TATTAAAATTATATAA
1 AAATAAATTATTAAAATAAAATAA
168124 AAAT
1 AAAT
168128 TGAAAAGTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATAAATTATTAAAATAAAATAA
Found at i:174977 original size:6 final size:6
Alignment explanation
Indices: 174966--175019 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
174956 GACACGTATT
174966 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
175012 ACC-CG ACC
1 ACCACG ACC
175020 CGAGACGGGA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.31
6 33 0.69
ACGTcount: A:0.30, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:179133 original size:31 final size:31
Alignment explanation
Indices: 179092--179176 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
179082 TTAATCATTT
179092 AATTCTAGATAAAATATTAATTTGACACTTAA
1 AATT-TAGATAAAATATTAATTTGACACTTAA
* *
179124 AATTTAGATAAAATATTAATATGACTCTTAA
1 AATTTAGATAAAATATTAATTTGACACTTAA
* *
179155 AATATAAATAAAATATTAATTT
1 AATTTAGATAAAATATTAATTT
179177 AATCCCTGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 44 0.92
32 4 0.08
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.39
Consensus pattern (31 bp):
AATTTAGATAAAATATTAATTTGACACTTAA
Found at i:180127 original size:21 final size:21
Alignment explanation
Indices: 180101--180141 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
180091 TCAAAAATAT
*
180101 TAAAAATATTAATATTTTAAG
1 TAAAAATAATAATATTTTAAG
180122 TAAAAATAATAATATTTTAA
1 TAAAAATAATAATATTTTAA
180142 ATATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAG
Found at i:181231 original size:30 final size:31
Alignment explanation
Indices: 181177--181234 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
181167 TTGAACTTTA
* *
181177 ATTTGACTCGTGAATTTTAGATAAAATATTG
1 ATTTGACTCGTAAATTTCAGATAAAATATTG
*
181208 ATTTGACTC-TAAATTTCATATAAAATA
1 ATTTGACTCGTAAATTTCAGATAAAATA
181235 CTAATTTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (31 bp):
ATTTGACTCGTAAATTTCAGATAAAATATTG
Found at i:181536 original size:29 final size:31
Alignment explanation
Indices: 181468--181542 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 31
181458 GGATCCAAGA
* *
181468 GTCAAATTAATGTTTTTATATAACATTTAAGT
1 GTCAAATTAAT-ATTTTATATAACATTTAAAT
* *
181500 GTTAAATTAATATTTTATATAA-GTTTAAAT
1 GTCAAATTAATATTTTATATAACATTTAAAT
181530 -TCAAATTAATATT
1 GTCAAATTAATATT
181543 CTATCTATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 12 0.32
30 6 0.16
31 10 0.26
32 10 0.26
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (31 bp):
GTCAAATTAATATTTTATATAACATTTAAAT
Found at i:184234 original size:164 final size:166
Alignment explanation
Indices: 183961--184298 Score: 653
Period size: 164 Copynumber: 2.0 Consensus size: 166
183951 GAGTATCCTG
183961 AGAACATTGTATATCATTTGTACCCTCAGTCCCGACTTCTTAGTTTTATACCCTTTTAAGCCTTG
1 AGAACATTGTATATCATTTGTACCCTCAGTCCCGACTTCTTAGTTTTATACCCTTTTAAGCCTTG
184026 AGATGCTTTTATGGTCCTTGTTCTTTACAGCAAACATCTATTTATCATTTTCCTCTATAGACACT
66 AGATGCTTTTATGGTCCTTGTTCTTTACAGCAAACATCTATTTATCATTTTCCTCTATAGACACT
184091 GACCTAATTATCTAAAATGGAGCTGCAAGAAAGAGA
131 GACCTAATTATCTAAAATGGAGCTGCAAGAAAGAGA
184127 AGAACATTGTATATCATTTGTA-CCTCA-TCCCGACTTCTTAGTTTTATACCCTTTTAAGCCTTG
1 AGAACATTGTATATCATTTGTACCCTCAGTCCCGACTTCTTAGTTTTATACCCTTTTAAGCCTTG
184190 AGATGCTTTTATGGTCCTTGTTCTTTACAGCAAACATCTATTTATCATTTTCCTCTATAGACACT
66 AGATGCTTTTATGGTCCTTGTTCTTTACAGCAAACATCTATTTATCATTTTCCTCTATAGACACT
184255 GACCTAATTATCTAAAATGGAGCTGCAAGAAAGAGA
131 GACCTAATTATCTAAAATGGAGCTGCAAGAAAGAGA
*
184291 AGTACATT
1 AGAACATT
184299 AAATATGGAT
Statistics
Matches: 171, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
164 144 0.84
165 5 0.03
166 22 0.13
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (166 bp):
AGAACATTGTATATCATTTGTACCCTCAGTCCCGACTTCTTAGTTTTATACCCTTTTAAGCCTTG
AGATGCTTTTATGGTCCTTGTTCTTTACAGCAAACATCTATTTATCATTTTCCTCTATAGACACT
GACCTAATTATCTAAAATGGAGCTGCAAGAAAGAGA
Found at i:192592 original size:2 final size:2
Alignment explanation
Indices: 192585--192609 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
192575 ATTTATGAAT
192585 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 T
192610 GTCGACACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:193863 original size:16 final size:16
Alignment explanation
Indices: 193826--193879 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
193816 AACTTAATTG
*
193826 AAATAATTAAAACA-A
1 AAATAATAAAAACATA
193841 AAGATAATAAAAACATA
1 AA-ATAATAAAAACATA
193858 AAATAA-AATAAACATA
1 AAATAATAA-AAACATA
193874 AAATAA
1 AAATAA
193880 AGACATAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
15 4 0.11
16 28 0.80
17 3 0.09
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.19
Consensus pattern (16 bp):
AAATAATAAAAACATA
Found at i:193997 original size:51 final size:50
Alignment explanation
Indices: 193915--194020 Score: 135
Period size: 51 Copynumber: 2.1 Consensus size: 50
193905 AATAATGATG
193915 AAAATACAAGAAAATAAAAGTTAGTAACTAAATAAGAAATAAAAAGTGACC
1 AAAATACAAGAAAATAAAAGTTAGTAACTAAATAAGAAATAAAAAGTGA-C
* * * *
193966 AAAATACAA-AAATTAAAA-TAATAGTAGCTAAATCAGAAATTAAAAGTGAC
1 AAAATACAAGAAAATAAAAGT--TAGTAACTAAATAAGAAATAAAAAGTGAC
194016 AAAAT
1 AAAAT
194021 TAAAATAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
49 1 0.02
50 14 0.29
51 34 0.69
ACGTcount: A:0.62, C:0.08, G:0.10, T:0.20
Consensus pattern (50 bp):
AAAATACAAGAAAATAAAAGTTAGTAACTAAATAAGAAATAAAAAGTGAC
Found at i:195207 original size:42 final size:42
Alignment explanation
Indices: 195148--195408 Score: 164
Period size: 42 Copynumber: 5.6 Consensus size: 42
195138 TGTTTGATGA
* *
195148 TGCTGATCCAAATCCGTATGCGATGGATGAGCCAAGTATTGG
1 TGCTGATCCAACTCCGTATGTGATGGATGAGCCAAGTATTGG
* *
195190 TGCTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATATTGATG
1 TGCTGATCCAACTCCGTATGTGATGG-AT-GAGC--CAA-G----TATTG--G
* *
195243 ATGGTGATCCAACTCCGTATGTGATGGATGAGCCAAGCATTGG
1 -TGCTGATCCAACTCCGTATGTGATGGATGAGCCAAGTATTGG
* * *
195286 TGTTGTTCCAACTCCGTATGTGATGGAATCAAG-CAAGAATGACAATGTTGATG
1 TGCTGATCCAACTCCGTATGTGATGG-AT-GAGCCAAG--T----A--TTG--G
* * *
195339 ATGCTGATCCAACTCCGTATATAATGGATGAGCCAAGCATTGG
1 -TGCTGATCCAACTCCGTATGTGATGGATGAGCCAAGTATTGG
* *
195382 TGCTGTTCCAACTCAGTATGTGATGGA
1 TGCTGATCCAACTCCGTATGTGATGGA
195409 ATCGAGCAAG
Statistics
Matches: 171, Mismatches: 22, Indels: 52
0.70 0.09 0.21
Matches are distributed among these distances:
42 70 0.41
43 10 0.06
44 6 0.04
45 7 0.04
46 2 0.01
47 2 0.01
49 2 0.01
50 2 0.01
51 8 0.05
52 6 0.04
53 10 0.06
54 46 0.27
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (42 bp):
TGCTGATCCAACTCCGTATGTGATGGATGAGCCAAGTATTGG
Found at i:195263 original size:54 final size:51
Alignment explanation
Indices: 195184--195427 Score: 200
Period size: 42 Copynumber: 5.0 Consensus size: 51
195174 ATGAGCCAAG
*
195184 TATTGGTGCTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAA
1 TATTGGTGCTGATCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAA
* *
195235 TATTGATGATGGTGATCCAACTCCGTATGTGATGG-AT-GAGC--CAA-G-C--
1 TATTG--G-TGCTGATCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAA
* * *
195281 -ATTGGTGTTGTTCCAACTCCGTATGTGATGGAATCAAGCAAGAATGACAA
1 TATTGGTGCTGATCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAA
* * * *
195331 TGTTGATGATGCTGATCCAACTCCGTATATAATGG-AT-GAGC--CAA-G-C--
1 TATTG--G-TGCTGATCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAA
* *
195377 -ATTGGTGCTGTTCCAACTCAGTATGTGATGGAATCGAGCAAGAATGACAA
1 TATTGGTGCTGATCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAA
195427 T
1 T
195428 GTGATGCTAA
Statistics
Matches: 149, Mismatches: 20, Indels: 48
0.69 0.09 0.22
Matches are distributed among these distances:
42 46 0.31
43 6 0.04
44 7 0.05
45 7 0.05
46 4 0.03
47 2 0.01
48 4 0.03
49 2 0.01
50 4 0.03
51 8 0.05
52 7 0.05
53 6 0.04
54 46 0.31
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (51 bp):
TATTGGTGCTGATCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAA
Found at i:195287 original size:96 final size:96
Alignment explanation
Indices: 194998--195433 Score: 680
Period size: 96 Copynumber: 4.6 Consensus size: 96
194988 AGTAAGGTGT
* * *
194998 TGCTGATT-CAACTCCATATGCGAT-GAATCGAGCGAGAATGACAATGTTGATGATGCTGATCCA
1 TGCTG-TTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTGATGATGCTGATCCA
*
195061 ACTCCGTATGTGATGGATGAGCCAAGTATTGG
65 ACTCCGTATGTGATGGATGAGCCAAGCATTGG
* * *
195093 TACTGTTCCAACTCCGTATGTTATGAAATCGAGCAAGAATGACAATGTTTGATGATGCTGATCCA
1 TGCTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATG-TTGATGATGCTGATCCA
* * *
195158 AATCCGTATGCGATGGATGAGCCAAGTATTGG
65 ACTCCGTATGTGATGGATGAGCCAAGCATTGG
* *
195190 TGCTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATATTGATGATGGTGATCCAA
1 TGCTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTGATGATGCTGATCCAA
195255 CTCCGTATGTGATGGATGAGCCAAGCATTGG
66 CTCCGTATGTGATGGATGAGCCAAGCATTGG
* *
195286 TGTTGTTCCAACTCCGTATGTGATGGAATCAAGCAAGAATGACAATGTTGATGATGCTGATCCAA
1 TGCTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTGATGATGCTGATCCAA
* *
195351 CTCCGTATATAATGGATGAGCCAAGCATTGG
66 CTCCGTATGTGATGGATGAGCCAAGCATTGG
*
195382 TGCTGTTCCAACTCAGTATGTGATGGAATCGAGCAAGAATGACAATG-TGATG
1 TGCTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTGATG
195434 CTAATCTACC
Statistics
Matches: 313, Mismatches: 25, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
94 2 0.01
95 22 0.07
96 199 0.64
97 90 0.29
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.28
Consensus pattern (96 bp):
TGCTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTGATGATGCTGATCCAA
CTCCGTATGTGATGGATGAGCCAAGCATTGG
Found at i:195622 original size:91 final size:90
Alignment explanation
Indices: 195465--195771 Score: 445
Period size: 91 Copynumber: 3.4 Consensus size: 90
195455 TAGAATCGAA
*
195465 CCAAGGTTGAACAAGTTCTTCTCATTATGAGCTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
195530 ATGAACTCTCTACTGGAAATGTTGAG
66 ATGAACTCT-TACTGGAAATGTTGAG
* *
195556 CTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATTAGTTCTTCTCATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
* * * *
195621 ATGAACTATTCACTGGAAATCTTTAA
66 ATGAACTCTT-ACTGGAAATGTTGAG
* * * * *
195647 CCAATGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGACGAGTTCTTATTATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
**
195712 ATGAACTCTT-CGTTGGAAATGCAGAG
66 ATGAACTCTTAC--TGGAAATGTTGAG
195738 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTT
195772 ATGAGTTATT
Statistics
Matches: 192, Mismatches: 21, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
89 1 0.01
90 1 0.01
91 190 0.99
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (90 bp):
CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
ATGAACTCTTACTGGAAATGTTGAG
Found at i:195795 original size:76 final size:76
Alignment explanation
Indices: 195709--195849 Score: 212
Period size: 76 Copynumber: 1.9 Consensus size: 76
195699 AGTTCTTATT
* * * * *
195709 ATTATGAACTCTTCGTTGGAAATGC-AGAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTA
1 ATTATGAACTCTCCATTCGAAAT-CTAGAACCAAAGTTGAACAAGTTCTTCTCATTATGAACTTA
195773 TGAGTTATTCTC
65 TGAGTTATTCTC
*
195785 ATTATGAACTCTCCATTCGAAATCTTGAACCAAAGTTGAACAAGTTCTTCTCATTATGAACTTAT
1 ATTATGAACTCTCCATTCGAAATCTAGAACCAAAGTTGAACAAGTTCTTCTCATTATGAACTTAT
195850 TCTCCCTCCG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
75 1 0.02
76 57 0.98
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (76 bp):
ATTATGAACTCTCCATTCGAAATCTAGAACCAAAGTTGAACAAGTTCTTCTCATTATGAACTTAT
GAGTTATTCTC
Found at i:196467 original size:67 final size:68
Alignment explanation
Indices: 196280--196483 Score: 213
Period size: 66 Copynumber: 3.1 Consensus size: 68
196270 CTTGTTTCAA
* ** * * *
196280 TCAAAGTTTTTGTGTTTCAAGAGAAACTAACTCTAGGGAGACAAAATTTAG-TTCAAGGGAAACG
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTAGTTTCAAGAGAAACG
196344 ATC
66 ATC
** * *
196347 TCAAAGA-TCGGTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCA-TTTCAAGAGAAAC-
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTAGTTTCAAGAGAAACG
*
196409 ATAT
66 AT-C
* * * *
196413 TCAAAGATTTTGTGTTTTAAGAGAAACTGTCTCAAGTGAGA-AAAATTTTGTTTCAAGAAAAACT
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTAGTTTCAAGAGAAAC-
196477 G-TC
65 GATC
196480 TCAA
1 TCAA
196484 GAGAGACAAA
Statistics
Matches: 111, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
65 2 0.02
66 58 0.52
67 50 0.45
68 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (68 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTAGTTTCAAGAGAAACG
ATC
Found at i:196476 original size:36 final size:37
Alignment explanation
Indices: 196425--196494 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 37
196415 AAAGATTTTG
* * *
196425 TGTTTTAAGAGAAACTGTCTCAAGTGAGA-AAAATTT
1 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATTT
196461 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAA
1 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAA
196495 CTCGTATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 26 0.87
37 4 0.13
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (37 bp):
TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATTT
Found at i:197748 original size:96 final size:96
Alignment explanation
Indices: 197637--198048 Score: 603
Period size: 96 Copynumber: 4.3 Consensus size: 96
197627 CATATACGAT
* *
197637 GAATCGAGCGAGAATGACAATGTTGATGATGCTGATCCAACTCTGTATGTGATGGATGAGCCAAG
1 GAATCGAGCAAGAATGACAATGTTGATGATGCTGATCCAACTCCGTATGTGATGGATGAGCCAAG
* * * * *
197702 TATTTGTGTTGTTCCAACTCCGTATGTTATA
66 CATTGGTGCTGTTCCAACTCCGTATGTGATG
* * * *
197733 AAATCGAGCAAGAATGACAATGTTTGATGTTGCTGATCCAAATCTGTATGCT-ATGGATGAGCCA
1 GAATCGAGCAAGAATGACAATG-TTGATGATGCTGATCCAACTCCGTATG-TGATGGATGAGCCA
* *
197797 AGTATTGGTGTTGTTCCAACTCCGTATGTGATG
64 AGCATTGGTGCTGTTCCAACTCCGTATGTGATG
* * *
197830 GAATCGAGCAAGAATGACAATATTAATGATGATGATCCAACTCCGTATGTGATGGATGAGCCAAG
1 GAATCGAGCAAGAATGACAATGTTGATGATGCTGATCCAACTCCGTATGTGATGGATGAGCCAAG
*
197895 CAATGGTGCTGTTCCAACTCCGTATGTGATG
66 CATTGGTGCTGTTCCAACTCCGTATGTGATG
* *
197926 GAATCAAGCAAGAATGACAATGTTGATGATGCTGATCCAACTCCGTATATGATGGATGAGCCAAG
1 GAATCGAGCAAGAATGACAATGTTGATGATGCTGATCCAACTCCGTATGTGATGGATGAGCCAAG
* *
197991 CATTGGTGCTATTCCAACTCAGTATGTGATG
66 CATTGGTGCTGTTCCAACTCCGTATGTGATG
198022 GAATCGAGCAAGAATGACAATG-TGATG
1 GAATCGAGCAAGAATGACAATGTTGATG
198049 CTAATCTACC
Statistics
Matches: 287, Mismatches: 26, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
95 6 0.02
96 193 0.67
97 87 0.30
98 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (96 bp):
GAATCGAGCAAGAATGACAATGTTGATGATGCTGATCCAACTCCGTATGTGATGGATGAGCCAAG
CATTGGTGCTGTTCCAACTCCGTATGTGATG
Found at i:197831 original size:42 final size:42
Alignment explanation
Indices: 197785--198023 Score: 120
Period size: 42 Copynumber: 5.1 Consensus size: 42
197775 TCTGTATGCT
*
197785 ATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCGTATGTG
1 ATGGATGAGCCAAGTATTGGTGATGTTCCAACTCCGTATGTG
* * *
197827 ATGGAATCGAGCAAGAATGACAATATTAATGATGATGATCCAACTCCGTATGTG
1 ATGG-AT-GAGC--CAA-G----TA-T--TGGTGATGTTCCAACTCCGTATGTG
* * *
197881 ATGGATGAGCCAAGCAATGGTGCTGTTCCAACTCCGTATGTG
1 ATGGATGAGCCAAGTATTGGTGATGTTCCAACTCCGTATGTG
* * *
197923 ATGGAATCAAG-CAAGAATGACAATGTTGATGATGCTGATCCAACTCCGTATATG
1 ATGG-AT-GAGCCAAG--T----A--TTGGTGATG-T--TCCAACTCCGTATGTG
* * * *
197977 ATGGATGAGCCAAGCATTGGTGCTATTCCAACTCAGTATGTG
1 ATGGATGAGCCAAGTATTGGTGATGTTCCAACTCCGTATGTG
198019 ATGGA
1 ATGGA
198024 ATCGAGCAAG
Statistics
Matches: 148, Mismatches: 23, Indels: 52
0.66 0.10 0.23
Matches are distributed among these distances:
42 49 0.33
43 8 0.05
44 7 0.05
45 7 0.05
46 2 0.01
47 2 0.01
49 2 0.01
50 2 0.01
51 8 0.05
52 8 0.05
53 8 0.05
54 45 0.30
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.28
Consensus pattern (42 bp):
ATGGATGAGCCAAGTATTGGTGATGTTCCAACTCCGTATGTG
Found at i:198237 original size:91 final size:91
Alignment explanation
Indices: 198077--198526 Score: 677
Period size: 91 Copynumber: 4.9 Consensus size: 91
198067 TGATAGAATC
* *
198077 GAACCAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTC
1 GAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTCTTCTC
*
198142 ATTATGAACTCTCCACTGGAAATGTT
66 ATTATGAACTCTCCACTGGAAATCTT
* *
198168 GAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTCTTCTC
1 GAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTCTTCTC
* *
198233 ATTATGAACTATTCACTGGAAATCTT
66 ATTATGAACTCTCCACTGGAAATCTT
* * * *
198259 TAACCAATGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGAACGAGTTCTTCTC
1 GAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTCTTCTC
* * *
198324 ATTATGAACTCTTCGCTGGAAATGC-A
66 ATTATGAACTCTCCACTGGAAAT-CTT
* * *
198350 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTC
1 GAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTCTTCTC
*
198415 ATTATGAACTCTCCATTGGAAATCTT
66 ATTATGAACTCTCCACTGGAAATCTT
* * * *
198441 GAACCAAAGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATTGGACGAGTTCTTCTT
1 GAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTCTTCTC
*
198506 ATTATGAACTCTCCGCTGGAA
66 ATTATGAACTCTCCACTGGAA
198527 TAATGATTGG
Statistics
Matches: 321, Mismatches: 36, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
90 1 0.00
91 319 0.99
92 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (91 bp):
GAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTCTTCTC
ATTATGAACTCTCCACTGGAAATCTT
Found at i:199050 original size:36 final size:36
Alignment explanation
Indices: 199000--199643 Score: 463
Period size: 36 Copynumber: 17.8 Consensus size: 36
198990 CAAAGATCGG
*
199000 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
* * * ***
199036 TATTTCAAGAGAAACATAT-TC-A-A-AG---ATTTT
1 TGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAACT
* * * * **
199066 GTGTTTTAAGAGAAAATGTCTCAAGCGAGACAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
** * *
199103 TGTTTCAAGAAAAACTGTCTCAAGAAAGTCAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
* *
199139 CGTTTCAAGGGAAACTGTCTCAGGAGAGAC-AAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
* *
199174 CGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
* *
199210 CGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
* * * * *
199246 CGTTTCAAGGGAAATTATCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
199282 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
* * *
199318 CGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAACC
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
* * * *
199354 TGTTTCAAGGGGAACTGTCTCAAGTGAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
** ***
199390 TGTTTCAAGGGAAACAATCTC-A-A-AGA-TTGA--
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
* *
199420 TGTTTCAAGGGAAACTGCCTCAAGAGAGATAAAATCTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-C-T
* * * *
199458 CTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-C-T
* * * *
199497 CTGTTTCAAGGGAAACTATCTCAAGCGGGATAAAATCTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-C-T
* * * *
199536 CTGTTTCAAGAGAAACTATCTTAAGCA-AGATAAAATCTT
1 -TGTTTCAAGGGAAACTGTCTCAAG-AGAGACAAAA-C-T
** * * * *
199575 ATGTTTCTTGAGAAACTATCTCAAGCGAGATAAAATCTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-C-T
* *
199614 CTGTTTCAAGGGAAACTATCTCAAGCGAGA
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGA
199644 TACAATCTTC
Statistics
Matches: 506, Mismatches: 81, Indels: 39
0.81 0.13 0.06
Matches are distributed among these distances:
30 23 0.05
31 15 0.03
32 3 0.01
33 8 0.02
34 4 0.01
35 35 0.07
36 248 0.49
37 6 0.01
39 164 0.32
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
Found at i:199059 original size:66 final size:69
Alignment explanation
Indices: 198933--199125 Score: 202
Period size: 67 Copynumber: 2.9 Consensus size: 69
198923 CAAAGTTTTT
** * * * *
198933 GTGTTTCAAGAGAAACTAACTCCAGGGAGACAAAATTTAGTTCAAG-GGAA-ATGATCTCAAAGA
1 GTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACATGATCTCAAAGA
198996 -TCG
66 TTCG
*
198999 GTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACAT-AT-TCAAAGA
1 GTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACATGATCTCAAAGA
**
199062 TTTT
66 TTCG
* * * * * *
199066 GTGTTTTAAGAGAAAATGTCTCAAGCGAGACAAATTTTGTTTCAAGAAAAAC-TG-TCTCAA
1 GTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACATGATCTCAA
199126 GAAAGTCAAA
Statistics
Matches: 106, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
66 49 0.46
67 55 0.52
68 2 0.02
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.27
Consensus pattern (69 bp):
GTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACATGATCTCAAAGA
TTCG
Found at i:199218 original size:21 final size:19
Alignment explanation
Indices: 199110--199362 Score: 68
Period size: 21 Copynumber: 13.9 Consensus size: 19
199100 TTTTGTTTCA
*
199110 AGAAAAACTGTCTCAAGAA
1 AGAAAAACTGTCTCAAGAG
* *
199129 AGTCAAAACTCGTTTCAAG-G
1 AG-AAAAACT-GTCTCAAGAG
*
199149 -G--AAACTGTCTCAGGAG
1 AGAAAAACTGTCTCAAGAG
* *
199165 AGACAAACTCGT-TTAA-AG
1 AGAAAAACT-GTCTCAAGAG
*
199183 -G-GAAACTGTCTCAAGAG
1 AGAAAAACTGTCTCAAGAG
*
199200 AGACAAAACTCGTTTCAAG-G
1 AGA-AAAACT-GTCTCAAGAG
199220 -G--AAACTGTCTCAAGAG
1 AGAAAAACTGTCTCAAGAG
*
199236 AGATAAAACTCGTTTCAAG-G
1 AGA-AAAACT-GTCTCAAGAG
* * *
199256 -G--AAATTATCTCAAGGG
1 AGAAAAACTGTCTCAAGAG
* *
199272 AGACAAAATTTGTTTCAAG-G
1 AGA-AAAA-CTGTCTCAAGAG
199292 -G--AAACTGTCTCAAGAG
1 AGAAAAACTGTCTCAAGAG
*
199308 AGACAAAACTCGTTTCAAG-G
1 AGA-AAAACT-GTCTCAAGAG
*
199328 -G--AAACTGTCTCAAGAA
1 AGAAAAACTGTCTCAAGAG
*
199344 AGACAAAACCTGTTTCAAG
1 AGA-AAAA-CTGTCTCAAG
199363 GGGAACTGTC
Statistics
Matches: 173, Mismatches: 24, Indels: 72
0.64 0.09 0.27
Matches are distributed among these distances:
15 36 0.21
16 34 0.20
17 8 0.05
18 3 0.02
19 14 0.08
20 33 0.19
21 45 0.26
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (19 bp):
AGAAAAACTGTCTCAAGAG
Found at i:199474 original size:39 final size:39
Alignment explanation
Indices: 199420--199654 Score: 353
Period size: 39 Copynumber: 6.0 Consensus size: 39
199410 CAAAGATTGA
** *
199420 TGTTTCAAGGGAAACTGCCTCAAGAGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
*
199459 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
*
199498 TGTTTCAAGGGAAACTATCTCAAGCGGGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * * *
199537 TGTTTCAAGAGAAACTATCTTAAGCAAGATAAAATCTTA
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
** *
199576 TGTTTCTTGAGAAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
*
199615 TGTTTCAAGGGAAACTATCTCAAGCGAGATACAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
199654 T
1 T
199655 TTAAAAACAA
Statistics
Matches: 176, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 176 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (39 bp):
TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
Found at i:199814 original size:75 final size:77
Alignment explanation
Indices: 199657--199819 Score: 233
Period size: 75 Copynumber: 2.1 Consensus size: 77
199647 AATCTTCTTT
* * *
199657 AAAAACAATCTTTGAGTGAAATGAAATGTATTCTTTCGAGTAAAAACTGTCTCAAGAGAGACAAA
1 AAAAACAATCTATGAGTCAAATGAAATGTATTCTTTCGAGTAAAAACAGTCTCAAGAGAGACAAA
*
199722 TCTTGTTATAAG
66 TCTCGTTATAAG
* *
199734 AAAAACAATC-ATGAGTCAAATGAAATGTCTTCTTTCGAGT-AAAACAGTCTCAAGTGAGACAAA
1 AAAAACAATCTATGAGTCAAATGAAATGTATTCTTTCGAGTAAAAACAGTCTCAAGAGAGACAAA
*
199797 GTC-CGTTTTAAG
66 -TCTCGTTATAAG
199809 AAAAACAATCT
1 AAAAACAATCT
199820 CCAATGAGAT
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
75 38 0.49
76 29 0.38
77 10 0.13
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (77 bp):
AAAAACAATCTATGAGTCAAATGAAATGTATTCTTTCGAGTAAAAACAGTCTCAAGAGAGACAAA
TCTCGTTATAAG
Found at i:201199 original size:17 final size:19
Alignment explanation
Indices: 201172--201210 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
201162 AATTTTTTTA
201172 TTTATGTTTTTTTTAT-TT
1 TTTATGTTTTTTTTATCTT
201190 TTTATG-TTTTTTTATCTT
1 TTTATGTTTTTTTTATCTT
201208 TTT
1 TTT
201211 CCTTTTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.10, C:0.03, G:0.05, T:0.82
Consensus pattern (19 bp):
TTTATGTTTTTTTTATCTT
Found at i:204828 original size:18 final size:16
Alignment explanation
Indices: 204786--204822 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
204776 AACTTAATTG
*
204786 AAATAATTAAAACA-A
1 AAATAATAAAAACATA
204801 AAATAATAAAAACATA
1 AAATAATAAAAACATA
204817 AAATAA
1 AAATAA
204823 AATAAAGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (16 bp):
AAATAATAAAAACATA
Found at i:204945 original size:51 final size:51
Alignment explanation
Indices: 204841--204968 Score: 140
Period size: 51 Copynumber: 2.5 Consensus size: 51
204831 CATAATTGCA
* *
204841 TAAATATA-AAATAATAA-TGACGAAAATACAAGAAAATAAAAGTTAGTAAC
1 TAAATA-AGAAATAAAAAGTGACCAAAATACAAGAAAATAAAAGTTAGTAAC
* *
204891 TAAATAAGAAATAAAAAGTGACCAAAATACAA-AAATTAAAA-TAATAGTAGC
1 TAAATAAGAAATAAAAAGTGACCAAAATACAAGAAAATAAAAGT--TAGTAAC
* *
204942 TAAATCAGAAATTAAAAGTGA-CAAAAT
1 TAAATAAGAAATAAAAAGTGACCAAAAT
204969 TAAAATAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
49 2 0.03
50 28 0.41
51 38 0.56
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (51 bp):
TAAATAAGAAATAAAAAGTGACCAAAATACAAGAAAATAAAAGTTAGTAAC
Found at i:204983 original size:51 final size:51
Alignment explanation
Indices: 204841--204983 Score: 127
Period size: 51 Copynumber: 2.8 Consensus size: 51
204831 CATAATTGCA
* * *
204841 TAAATATA-AAATAATAA-TGACGAAAATACAAGAAAATAAAAGT--TAGTAAC
1 TAAATA-AGAAATAAAAAGTGACCAAAATACAA-AAAA-AAAAATAATAGTAAC
** *
204891 TAAATAAGAAATAAAAAGTGACCAAAATACAAAAATTAAAATAATAGTAGC
1 TAAATAAGAAATAAAAAGTGACCAAAATACAAAAAAAAAAATAATAGTAAC
* *
204942 TAAATCAGAAATTAAAAGTGA-CAAAATTA-AAATAAAAAAAAT
1 TAAATAAGAAATAAAAAGTGACCAAAA-TACAAA-AAAAAAAAT
204984 CAGCATGCAT
Statistics
Matches: 77, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
49 5 0.06
50 25 0.32
51 47 0.61
ACGTcount: A:0.64, C:0.06, G:0.09, T:0.21
Consensus pattern (51 bp):
TAAATAAGAAATAAAAAGTGACCAAAATACAAAAAAAAAAATAATAGTAAC
Found at i:207265 original size:18 final size:18
Alignment explanation
Indices: 207244--207286 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
207234 GACGAACGGT
207244 CACCCATCCGTCACCGAC
1 CACCCATCCGTCACCGAC
207262 CACCCATCCGTCACCGAC
1 CACCCATCCGTCACCGAC
207280 CACCCAT
1 CACCCAT
207287 TGATCAATTT
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:0.23, C:0.56, G:0.09, T:0.12
Consensus pattern (18 bp):
CACCCATCCGTCACCGAC
Found at i:207702 original size:3 final size:3
Alignment explanation
Indices: 207694--207727 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
207684 GTATCAAGCC
*
207694 TAA TAA TAA TAA TAC TAA TAA TAA TAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
207728 GGTGAGGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:207713 original size:15 final size:15
Alignment explanation
Indices: 207693--207722 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
207683 TGTATCAAGC
207693 CTAATAATAATAATA
1 CTAATAATAATAATA
207708 CTAATAATAATAATA
1 CTAATAATAATAATA
207723 AAATAGGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (15 bp):
CTAATAATAATAATA
Found at i:210847 original size:15 final size:16
Alignment explanation
Indices: 210821--210850 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
210811 TTATAAATAT
210821 AATAATATTTTAAAAA
1 AATAATATTTTAAAAA
210837 AATAA-ATTTTAAAA
1 AATAATATTTTAAAA
210851 TCACCAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATAATATTTTAAAAA
Found at i:211469 original size:21 final size:21
Alignment explanation
Indices: 211445--211484 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
211435 ACACTTTACC
*
211445 AAAAATATTAATATTTTAAGT
1 AAAAATAATAATATTTTAAGT
211466 AAAAATAATAATATTTTAA
1 AAAAATAATAATATTTTAA
211485 ATACCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAGT
Found at i:211678 original size:31 final size:31
Alignment explanation
Indices: 211643--211720 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
211633 CAGTTACGTC
211643 GGGGACCATATTGCAAACAGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
* *
211674 GGGGACCATATTGAAAATAGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
*
211705 GGGGACTATATTGCAA
1 GGGGACCATATTGCAA
211721 GTTTTAAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATGTTG
Found at i:218493 original size:2 final size:2
Alignment explanation
Indices: 218486--218544 Score: 109
Period size: 2 Copynumber: 29.0 Consensus size: 2
218476 TTATCGCTAA
218486 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
218528 AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT -AT AT
218545 TTTTATATTA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 54 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:219170 original size:2 final size:2
Alignment explanation
Indices: 219130--219154 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
219120 ATTTATTTCT
219130 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 T
219155 TCACTTAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:220084 original size:26 final size:26
Alignment explanation
Indices: 220049--220112 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
220039 TAAATATAAG
* *
220049 ATTATTCCTTTCTTATAATATCCTAT
1 ATTATACCTTTCCTATAATATCCTAT
220075 ATTATACCTTTCCTATAATATCCTAT
1 ATTATACCTTTCCTATAATATCCTAT
*
220101 ATTATACATTTC
1 ATTATACCTTTC
220113 ATAACGTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTATACCTTTCCTATAATATCCTAT
Found at i:221243 original size:23 final size:23
Alignment explanation
Indices: 221217--221277 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
221207 CTCGTATAAA
221217 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
221240 TGCACCGAAATGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
221263 TGCACTGAAGTGCCA
1 TGCACCGAAGTGCCA
221278 TATAAAATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:223834 original size:21 final size:22
Alignment explanation
Indices: 223810--223855 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
223800 TAATAACTTT
223810 TGTTTT-TTATTTAAT-TTTTTG
1 TGTTTTATT-TTTAATATTTTTG
223831 TGTTTTAATTTTTAATATTTTTG
1 TGTTTT-ATTTTTAATATTTTTG
223854 TG
1 TG
223856 AACATTGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 6 0.27
22 6 0.27
23 10 0.45
ACGTcount: A:0.17, C:0.00, G:0.11, T:0.72
Consensus pattern (22 bp):
TGTTTTATTTTTAATATTTTTG
Found at i:224754 original size:32 final size:32
Alignment explanation
Indices: 224718--224781 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
224708 ATGGTGTTGC
224718 ATGAAACTGATCTGGTAATCAGATGATGGTAT
1 ATGAAACTGATCTGGTAATCAGATGATGGTAT
224750 ATGAAACTGATCTGGTAATCAGATGATGGTAT
1 ATGAAACTGATCTGGTAATCAGATGATGGTAT
224782 GATATGGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.31
Consensus pattern (32 bp):
ATGAAACTGATCTGGTAATCAGATGATGGTAT
Found at i:224776 original size:16 final size:16
Alignment explanation
Indices: 224725--224776 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
224715 TGCATGAAAC
224725 TGATCTGGTAATCAGA
1 TGATCTGGTAATCAGA
* *
224741 TGA--TGGTATATGAAA
1 TGATCTGGTA-ATCAGA
224756 CTGATCTGGTAATCAGA
1 -TGATCTGGTAATCAGA
224773 TGAT
1 TGAT
224777 GGTATGATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
14 5 0.18
15 4 0.14
16 10 0.36
17 4 0.14
18 5 0.18
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.33
Consensus pattern (16 bp):
TGATCTGGTAATCAGA
Found at i:225926 original size:30 final size:30
Alignment explanation
Indices: 225890--225988 Score: 121
Period size: 30 Copynumber: 3.3 Consensus size: 30
225880 ATAAATTTTG
* *
225890 AAAGTTTAGTGACC-AAAGTATGAAGTTTAA
1 AAAGTTTAGGGACCAAAAGTAT-AATTTTAA
* *
225920 AAAGTTTAGGGACCAAAAGGATAATTTTTA
1 AAAGTTTAGGGACCAAAAGTATAATTTTAA
* *
225950 AAAGTATAGGGACCAAAAGTCTAATTTTAA
1 AAAGTTTAGGGACCAAAAGTATAATTTTAA
225980 AAA-TTTAGG
1 AAAGTTTAGG
225989 TGTCTTGACC
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
29 5 0.08
30 48 0.81
31 6 0.10
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.29
Consensus pattern (30 bp):
AAAGTTTAGGGACCAAAAGTATAATTTTAA
Found at i:225979 original size:60 final size:58
Alignment explanation
Indices: 225866--225988 Score: 140
Period size: 60 Copynumber: 2.1 Consensus size: 58
225856 CAAATTTTGG
* * * *
225866 TTAGTGACCAAAACATAAATTTTGAAAGTTTAGTGACCAAAGTATGAAGTTTAAAAAGT
1 TTAGGGACCAAAACATAAATTTTAAAAGTATAGGGACCAAAGTATGAAGTTTAAAAA-T
* * * *
225925 TTAGGGACCAAAAGGATAATTTTTAAAAGTATAGGGACCAAAAGTCT-AATTTTAAAAAT
1 TTAGGGACCAAAA-CATAAATTTTAAAAGTATAGGGACC-AAAGTATGAAGTTTAAAAAT
225984 TTAGG
1 TTAGG
225989 TGTCTTGACC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 18 0.33
60 30 0.56
61 6 0.11
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (58 bp):
TTAGGGACCAAAACATAAATTTTAAAAGTATAGGGACCAAAGTATGAAGTTTAAAAAT
Found at i:225988 original size:29 final size:29
Alignment explanation
Indices: 225866--225988 Score: 106
Period size: 29 Copynumber: 4.2 Consensus size: 29
225856 CAAATTTTGG
* * * *
225866 TTAGTGACCAAAA-CATAAATTTTGAAAGT
1 TTAGGGACCAAAAGTAT-AATTTTAAAAAT
* *
225895 TTAGTGACC-AAAGTATGAAGTTTAAAAAGT
1 TTAGGGACCAAAAGTAT-AATTTTAAAAA-T
* *
225925 TTAGGGACCAAAAGGATAATTTTTAAAAGT
1 TTAGGGACCAAAAGTATAA-TTTTAAAAAT
* *
225955 ATAGGGACCAAAAGTCTAATTTTAAAAAT
1 TTAGGGACCAAAAGTATAATTTTAAAAAT
225984 TTAGG
1 TTAGG
225989 TGTCTTGACC
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
28 3 0.04
29 32 0.42
30 28 0.37
31 13 0.17
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (29 bp):
TTAGGGACCAAAAGTATAATTTTAAAAAT
Found at i:228890 original size:19 final size:19
Alignment explanation
Indices: 228866--228915 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
228856 TACATTGGGC
228866 TATGAATCTGAAGTAAAGT
1 TATGAATCTGAAGTAAAGT
* *
228885 TATGAATCTAAATTAAAGT
1 TATGAATCTGAAGTAAAGT
**
228904 TACAAATCTGAA
1 TATGAATCTGAA
228916 AGTGAATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (19 bp):
TATGAATCTGAAGTAAAGT
Found at i:229937 original size:28 final size:28
Alignment explanation
Indices: 229897--229968 Score: 117
Period size: 28 Copynumber: 2.6 Consensus size: 28
229887 CCGTCGTTGC
* *
229897 TTTCAAGCACTAACTCAACGGCATAACG
1 TTTCAAGCACTAACTCAAAGACATAACG
229925 TTTCAAGCACTAACTCAAAGACATAACG
1 TTTCAAGCACTAACTCAAAGACATAACG
*
229953 TTTCAAGCACTGACTC
1 TTTCAAGCACTAACTC
229969 GACAGTATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.24
Consensus pattern (28 bp):
TTTCAAGCACTAACTCAAAGACATAACG
Found at i:229978 original size:28 final size:27
Alignment explanation
Indices: 229897--229978 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 27
229887 CCGTCGTTGC
*
229897 TTTCAAGCACTAACTCAACGGCATAACG
1 TTTCAAGCACTAACTC-ACAGCATAACG
*
229925 TTTCAAGCACTAACTCAAAGACATAACG
1 TTTCAAGCACTAACTCACAG-CATAACG
* *
229953 TTTCAAGCACTGACTCGACAGTATAA
1 TTTCAAGCACTAACTC-ACAGCATAA
229979 TGTAGACAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
27 2 0.04
28 42 0.89
29 3 0.06
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (27 bp):
TTTCAAGCACTAACTCACAGCATAACG
Found at i:231157 original size:21 final size:21
Alignment explanation
Indices: 231133--231173 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
231123 AAATCTTAAA
*
231133 TTAAATGATAATGAATATTAG
1 TTAAATGATAATGAACATTAG
231154 TTAAATGATAATGAACATTA
1 TTAAATGATAATGAACATTA
231174 ATCTCAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (21 bp):
TTAAATGATAATGAACATTAG
Found at i:234748 original size:21 final size:23
Alignment explanation
Indices: 234706--234749 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
234696 GCCACAATGG
*
234706 TTAATGTTTGGATTTTTTTGAAA
1 TTAATGTTTGGATTTATTTGAAA
234729 TTAATGTTT-GA-TTATTTGAAA
1 TTAATGTTTGGATTTATTTGAAA
234750 AAGTCTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
23 9 0.45
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (23 bp):
TTAATGTTTGGATTTATTTGAAA
Found at i:235204 original size:24 final size:24
Alignment explanation
Indices: 235168--235216 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
235158 AGTCGATAAA
*
235168 ATTAATATAATTATATATTTAATT
1 ATTAATATAATTATACATTTAATT
* * *
235192 ATTATTATTATTATACATTTTATT
1 ATTAATATAATTATACATTTAATT
235216 A
1 A
235217 ATTTATCCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTAATATAATTATACATTTAATT
Found at i:235675 original size:2 final size:2
Alignment explanation
Indices: 235668--235726 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
235658 TCCCGATTTC
235668 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
235710 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
235727 CATAAACCAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:238825 original size:44 final size:44
Alignment explanation
Indices: 238762--238849 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
238752 TCCCAAGCTC
238762 TGCACCAAAAGAGTTTTGAAAGCAATGACATCCGAAACGAGAGA
1 TGCACCAAAAGAGTTTTGAAAGCAATGACATCCGAAACGAGAGA
238806 TGCACCAAAAGAGTTTTGAAAGCAATGACATCCGAAACGAGAGA
1 TGCACCAAAAGAGTTTTGAAAGCAATGACATCCGAAACGAGAGA
238850 CGTGATGAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (44 bp):
TGCACCAAAAGAGTTTTGAAAGCAATGACATCCGAAACGAGAGA
Found at i:248691 original size:21 final size:21
Alignment explanation
Indices: 248661--248708 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
248651 TAATTTTCAA
*
248661 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
248682 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
248703 ACATTG
1 ACATTG
248709 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:252386 original size:315 final size:315
Alignment explanation
Indices: 251814--252442 Score: 1186
Period size: 315 Copynumber: 2.0 Consensus size: 315
251804 GATCCTCCTG
*
251814 AGACAGGTTCATAATGATGGAACCATTCTCTTCTTGAGGTCATGTGATATGTTGCTCCCGAATCA
1 AGACAGGTTCATAATGATGGAACAATTCTCTTCTTGAGGTCATGTGATATGTTGCTCCCGAATCA
* *
251879 ATGAGCCATATATCTGCAAATCGTTTTCTTCCTTCCACGGTGGTTGACGCTTCACAGCATAGAGC
66 ATGAGCCATATATATGCAAATCATTTTCTTCCTTCCACGGTGGTTGACGCTTCACAGCATAGAGC
251944 ATCTCCATCATCTGAAGTGTTTGCGATATTGCCTTGTGGATTGGAGTTTTTATTTAGACTCCAAC
131 ATCTCCATCATCTGAAGTGTTTGCGATATTGCCTTGTGGATTGGAGTTTTTATTTAGACTCCAAC
252009 AATCCTTCTTCAAGTGACCATTCTTTCCACAGTTGTAACACTTTAAATTCTTCTTGCTTTTCGAC
196 AATCCTTCTTCAAGTGACCATTCTTTCCACAGTTGTAACACTTTAAATTCTTCTTGCTTTTCGAC
252074 TTCGATCTACCATGTTTGTGACTGCTGCTTTGGCCACGTTCTGTTGATCTCCCTA
261 TTCGATCTACCATGTTTGTGACTGCTGCTTTGGCCACGTTCTGTTGATCTCCCTA
252129 AGACAGGTTCATAATGATGGAACAATTCTCTTCTTGAGGTCATGTGATATGTTGCTCCCGAATCA
1 AGACAGGTTCATAATGATGGAACAATTCTCTTCTTGAGGTCATGTGATATGTTGCTCCCGAATCA
**
252194 ATGATTCATATATATGCAAATCATTTTCTTCCTTCCACGGTGGTTGACGCTTCACAGCATAGAGC
66 ATGAGCCATATATATGCAAATCATTTTCTTCCTTCCACGGTGGTTGACGCTTCACAGCATAGAGC
*
252259 ATCTCCATCATCTGAAGTGTTTGCGGTATTGCCTTGTGGATTGGAGTTTTTATTTAGACTCCAAC
131 ATCTCCATCATCTGAAGTGTTTGCGATATTGCCTTGTGGATTGGAGTTTTTATTTAGACTCCAAC
* *
252324 AATCCTTCTTCAAGTGACCCTTCTTTCCATAGTTGTAACACTTTAAATTCTTCTTGCTTTTCGAC
196 AATCCTTCTTCAAGTGACCATTCTTTCCACAGTTGTAACACTTTAAATTCTTCTTGCTTTTCGAC
252389 TTCGATCTACCATGTTTGTGACTGCTGCTTTGGCCACGTTCTGTTGATCTCCCT
261 TTCGATCTACCATGTTTGTGACTGCTGCTTTGGCCACGTTCTGTTGATCTCCCT
252443 CTCATCGTTG
Statistics
Matches: 306, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
315 306 1.00
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (315 bp):
AGACAGGTTCATAATGATGGAACAATTCTCTTCTTGAGGTCATGTGATATGTTGCTCCCGAATCA
ATGAGCCATATATATGCAAATCATTTTCTTCCTTCCACGGTGGTTGACGCTTCACAGCATAGAGC
ATCTCCATCATCTGAAGTGTTTGCGATATTGCCTTGTGGATTGGAGTTTTTATTTAGACTCCAAC
AATCCTTCTTCAAGTGACCATTCTTTCCACAGTTGTAACACTTTAAATTCTTCTTGCTTTTCGAC
TTCGATCTACCATGTTTGTGACTGCTGCTTTGGCCACGTTCTGTTGATCTCCCTA
Found at i:253665 original size:21 final size:21
Alignment explanation
Indices: 253635--253682 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
253625 TAATTTTCAA
253635 ACATTATTGCACCTAATTTTG
1 ACATTATTGCACCTAATTTTG
*
253656 ACATTGTTGCACCTAATTTTG
1 ACATTATTGCACCTAATTTTG
253677 ACATTA
1 ACATTA
253683 CAATATTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (21 bp):
ACATTATTGCACCTAATTTTG
Found at i:256087 original size:22 final size:22
Alignment explanation
Indices: 256049--256093 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
256039 CGCTTTGTAA
*
256049 TATTTTAATAAATTTTAATAAT
1 TATTTTAATAAATTTTAAAAAT
*
256071 TATTTT-ATAACTATTTAAAAAT
1 TATTTTAATAAAT-TTTAAAAAT
256093 T
1 T
256094 TTAATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTTTAATAAATTTTAAAAAT
Found at i:256093 original size:31 final size:32
Alignment explanation
Indices: 256052--256112 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
256042 TTTGTAATAT
256052 TTTAATAAATTTTAATAATTATTTTATAACTA
1 TTTAATAAATTTTAATAATTATTTTATAACTA
*
256084 TTTAA-AAATTTTAATTATTATTTTATAAC
1 TTTAATAAATTTTAATAATTATTTTATAAC
256113 CTTCTACTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (32 bp):
TTTAATAAATTTTAATAATTATTTTATAACTA
Found at i:259929 original size:22 final size:23
Alignment explanation
Indices: 259865--259931 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
259855 TTAATATTTT
** *
259865 TAATTAATTAATTAAAATAAAAT
1 TAATTAATTAATTAATTTAAAAA
*
259888 TAATTGA-TAATTAAATTTAAAAA
1 TAATTAATTAATT-AATTTAAAAA
259911 TAATT-ATTAATTAATTTAAAA
1 TAATTAATTAATTAATTTAAAA
259932 TCTAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
22 15 0.39
23 23 0.61
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (23 bp):
TAATTAATTAATTAATTTAAAAA
Found at i:262464 original size:33 final size:33
Alignment explanation
Indices: 262427--262498 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
262417 TATCGTCGTA
262427 TACTTTATGAATCAACAATGACTTCATTTTATT
1 TACTTTATGAATCAACAATGACTTCATTTTATT
*
262460 TACTTTATGAATCAACATTGACTTCATTTTATT
1 TACTTTATGAATCAACAATGACTTCATTTTATT
262493 T-CTTTA
1 TACTTTA
262499 ACTTAATTAC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 5 0.13
33 33 0.87
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.49
Consensus pattern (33 bp):
TACTTTATGAATCAACAATGACTTCATTTTATT
Found at i:263162 original size:82 final size:82
Alignment explanation
Indices: 263025--263204 Score: 324
Period size: 82 Copynumber: 2.2 Consensus size: 82
263015 CTCTGCAACA
* *
263025 AAAGCACCATATCAACTCAGTGTAACTAGAAAGCTTCGTCTGCATAAAGTTTCTAGATGCCAAAA
1 AAAGCACCATATCAACTCAGTATAACTAGAAAGCTTCGTCTACATAAAGTTTCTAGATGCCAAAA
263090 CATAAAGCTAGTCTACC
66 CATAAAGCTAGTCTACC
*
263107 AAAGCACCTTATCAACTCAGTATAACTAGAAAGCTTCGTCTACATAAAGTTTCTAGATGCCAAAA
1 AAAGCACCATATCAACTCAGTATAACTAGAAAGCTTCGTCTACATAAAGTTTCTAGATGCCAAAA
263172 CATAAAGCTAGTCTACC
66 CATAAAGCTAGTCTACC
*
263189 AAAGCATCATATCAAC
1 AAAGCACCATATCAAC
263205 GAAATTATTG
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 93 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.24
Consensus pattern (82 bp):
AAAGCACCATATCAACTCAGTATAACTAGAAAGCTTCGTCTACATAAAGTTTCTAGATGCCAAAA
CATAAAGCTAGTCTACC
Found at i:265249 original size:41 final size:42
Alignment explanation
Indices: 265203--265282 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
265193 TTTGTTGTAA
265203 CGTAGGAAGAGT-ACGTAAATACACGAACCAATTTATTTAAG
1 CGTAGGAAGAGTAACGTAAATACACGAACCAATTTATTTAAG
*
265244 CGTAGGAAGAGTAACGTAAATACACGAATCAATTTATTT
1 CGTAGGAAGAGTAACGTAAATACACGAACCAATTTATTT
265283 CAATGATTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
41 12 0.32
42 25 0.68
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (42 bp):
CGTAGGAAGAGTAACGTAAATACACGAACCAATTTATTTAAG
Found at i:268834 original size:2 final size:2
Alignment explanation
Indices: 268827--268863 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
268817 AAGTTAAATA
268827 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 A
268864 AAATATTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:274400 original size:14 final size:14
Alignment explanation
Indices: 274381--274416 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
274371 TCCACGCGCT
274381 TTTTGCCTTGTTTA
1 TTTTGCCTTGTTTA
274395 TTTTGCCTTGTTTA
1 TTTTGCCTTGTTTA
274409 TTTTGCCT
1 TTTTGCCT
274417 CTTACCTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.06, C:0.17, G:0.14, T:0.64
Consensus pattern (14 bp):
TTTTGCCTTGTTTA
Found at i:280520 original size:2 final size:2
Alignment explanation
Indices: 280513--280545 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
280503 GGTGAGATTC
280513 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
280546 GTTTCTACGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:287475 original size:23 final size:24
Alignment explanation
Indices: 287440--287489 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
287430 TATCTTAGTG
*
287440 TATAAATACTTAAATTTATAATAT
1 TATAAATACTTAAATTTAAAATAT
* * *
287464 TATATATA-TTAACTTTAAAATTT
1 TATAAATACTTAAATTTAAAATAT
287487 TAT
1 TAT
287490 CTTAACTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (24 bp):
TATAAATACTTAAATTTAAAATAT
Found at i:288179 original size:31 final size:31
Alignment explanation
Indices: 288144--288211 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
288134 TGATGATCAC
**
288144 ATCTTAATTAAATAAAAATGAAAGTGACCAT
1 ATCTTAATTAAATAAAAACAAAAGTGACCAT
*
288175 ATCTTAATTAAATAAAAACAAAAGTGATCAT
1 ATCTTAATTAAATAAAAACAAAAGTGACCAT
288206 ATCTTA
1 ATCTTA
288212 TGTTTTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.07, T:0.31
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACAAAAGTGACCAT
Done.