Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000867.1 Hibiscus syriacus cultivar Beakdansim tig00001674_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: 604573
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 2 of 3
Found at i:304031 original size:26 final size:24
Alignment explanation
Indices: 304001--304071 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 24
303991 CAAGGTGGAA
304001 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
* * * *
304025 AGGGAATGTTTTAA-G-ATCGAA-A-
1 A--GAATATTTCAAGGTCTCAAAGAG
304047 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
304071 A
1 A
304072 TAAAATGTCA
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
20 9 0.27
21 1 0.03
22 5 0.15
23 2 0.06
24 6 0.18
25 1 0.03
26 9 0.27
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (24 bp):
AGAATATTTCAAGGTCTCAAAGAG
Found at i:306360 original size:31 final size:32
Alignment explanation
Indices: 306304--306365 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
306294 TGACAAAATG
306304 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
306336 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
306366 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:308317 original size:29 final size:29
Alignment explanation
Indices: 308285--308344 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
308275 TGGTAATAAT
* * *
308285 AAATTAAAGGGCTAAAACAGAAAAATAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
* *
308314 AAATTAAAAGACTAAAATAGCAAAACAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
308343 AA
1 AA
308345 CGTAGGGACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.65, C:0.08, G:0.13, T:0.13
Consensus pattern (29 bp):
AAATTAAAAGACTAAAACAGAAAAACAGA
Found at i:309964 original size:3 final size:3
Alignment explanation
Indices: 309945--309992 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
309935 ATGTAAAATG
*
309945 TAA TAT TAA TAA T-A TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
309990 TAA
1 TAA
309993 CGATAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 6 0.15
3 34 0.85
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:309998 original size:23 final size:22
Alignment explanation
Indices: 309951--309998 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
309941 AATGTAATAT
*
309951 TAATAATATAATAAAATAATAA
1 TAATAATATAATAAAATAACAA
*
309973 TAATAATAATAATAAAATAACGA
1 TAATAAT-ATAATAAAATAACAA
309996 TAA
1 TAA
309999 AAAACCCGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (22 bp):
TAATAATATAATAAAATAACAA
Found at i:316454 original size:3 final size:3
Alignment explanation
Indices: 316443--316506 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
316433 GTTTTTTTCG
** *
316443 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
316488 TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
316507 CAAATTTTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:316484 original size:32 final size:32
Alignment explanation
Indices: 316440--316504 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
316430 CGGGTTTTTT
*
316440 TCGTTATTTTATTATTATTATTATTA-TTATTA
1 TCGTTATCTTATTATT-TTATTATTATTTATTA
316472 TCGTTATCTTATTATTTTATTATTATTTATTA
1 TCGTTATCTTATTATTTTATTATTATTTATTA
316504 T
1 T
316505 TACAAATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 9 0.29
32 22 0.71
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (32 bp):
TCGTTATCTTATTATTTTATTATTATTTATTA
Found at i:322259 original size:13 final size:13
Alignment explanation
Indices: 322241--322267 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
322231 TCGACAGTAC
322241 GCACAACGATGGA
1 GCACAACGATGGA
322254 GCACAACGATGGA
1 GCACAACGATGGA
322267 G
1 G
322268 GGATGTTGCA
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:0.22, G:0.33, T:0.07
Consensus pattern (13 bp):
GCACAACGATGGA
Found at i:323143 original size:26 final size:25
Alignment explanation
Indices: 323114--323191 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 25
323104 AATTTTTGAC
323114 ATTCTATCTCTTTGAGACCTTGAAAT
1 ATTCT-TCTCTTTGAGACCTTGAAAT
* *
323140 A---TTCT-TTT-CGACCTTGAAAC
1 ATTCTTCTCTTTGAGACCTTGAAAT
* *
323160 GTTCCCTCTCTTTGAGACCTTGAAAT
1 ATT-CTTCTCTTTGAGACCTTGAAAT
323186 ATTCTT
1 ATTCTT
323192 TCCACCTTGA
Statistics
Matches: 38, Mismatches: 8, Indels: 13
0.64 0.14 0.22
Matches are distributed among these distances:
20 10 0.26
21 3 0.08
22 3 0.08
23 1 0.03
24 3 0.08
25 5 0.13
26 13 0.34
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (25 bp):
ATTCTTCTCTTTGAGACCTTGAAAT
Found at i:325009 original size:4 final size:4
Alignment explanation
Indices: 325000--325034 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
324990 TCGAGAAAAG
325000 TACA TACA TACA TACA TACA TAC- -ACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA T
325035 GATACATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
4 27 0.93
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:325026 original size:22 final size:21
Alignment explanation
Indices: 325001--325042 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
324991 CGAGAAAAGT
325001 ACATACATACATACATACATAC
1 ACATACATACAT-CATACATAC
*
325023 ACATACATACATGATACATA
1 ACATACATACATCATACATA
325043 AAATTGGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.24
Consensus pattern (21 bp):
ACATACATACATCATACATAC
Found at i:325633 original size:36 final size:36
Alignment explanation
Indices: 325581--325698 Score: 150
Period size: 36 Copynumber: 3.3 Consensus size: 36
325571 TGAGAATTTT
* *
325581 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTTC
1 AAAACAAA-TTTTGTCTCGATTGAGACAATTTCTTTA
* *
325618 AAAGCAAATTTTGTCTCGATTGAGACAGCTTTC--TA
1 AAAACAAATTTTGTCTCGATTGAGACA-ATTTCTTTA
* *
325653 AAAACAAATTTTGTCTCGTTTGAGACAATTTCTTGA
1 AAAACAAATTTTGTCTCGATTGAGACAATTTCTTTA
325689 AAAACAAATT
1 AAAACAAATT
325699 CCGCCTCACT
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
34 4 0.06
35 26 0.37
36 29 0.41
37 11 0.16
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGATTGAGACAATTTCTTTA
Found at i:325714 original size:71 final size:72
Alignment explanation
Indices: 325581--325715 Score: 175
Period size: 71 Copynumber: 1.9 Consensus size: 72
325571 TGAGAATTTT
** * ** * *
325581 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTTCAAAGCAAATTTTGTCTCGATTGAGACAG
1 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTGAAAAACAAATTCCGCCTCGATGGAGACAG
325646 CTTTCTA
66 CTTTCTA
*
325653 AAAACAAA-TTTTGTCTCGTTTGAGACAATTTCTTGAAAAACAAATTCCGCCTC-ACTGGAGACA
1 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTGAAAAACAAATTCCGCCTCGA-TGGAGACA
325716 TTTTTCATTG
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
70 1 0.02
71 45 0.83
72 8 0.15
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (72 bp):
AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTGAAAAACAAATTCCGCCTCGATGGAGACAG
CTTTCTA
Found at i:325867 original size:34 final size:36
Alignment explanation
Indices: 325788--325880 Score: 118
Period size: 36 Copynumber: 2.6 Consensus size: 36
325778 ATCGTTTTCT
* *
325788 CAAACTTTGTCTCGCTTGAGACAATTTCTCTAAAAA
1 CAAATTTTGTCTCGCTTGAGACAATATCTCTAAAAA
** * *
325824 CAAATTTTGTCTCATTTGAGACTATATCT-T-AAAG
1 CAAATTTTGTCTCGCTTGAGACAATATCTCTAAAAA
325858 CAAATTTTGTCTCGCTTGAGACA
1 CAAATTTTGTCTCGCTTGAGACA
325881 TCATTTTCTC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
34 23 0.48
35 1 0.02
36 24 0.50
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (36 bp):
CAAATTTTGTCTCGCTTGAGACAATATCTCTAAAAA
Found at i:326163 original size:27 final size:27
Alignment explanation
Indices: 326122--326341 Score: 264
Period size: 27 Copynumber: 7.9 Consensus size: 27
326112 TCTTGAGACA
326122 GTTTCTCTTGAAAAAAATCTTTGAGTTT
1 GTTTCTCTTG-AAAAAATCTTTGAGTTT
*
326150 GTTTCTCTTGAAAAAATCTTTGAGTTA
1 GTTTCTCTTGAAAAAATCTTTGAGTTT
326177 GTTTCTCTTGAAAAAAAAATCTTTGAGTTT
1 GTTTCTCTTG---AAAAAATCTTTGAGTTT
*
326207 GTTTCTCTGGAAAAAATCTTTGAGTTT
1 GTTTCTCTTGAAAAAATCTTTGAGTTT
*
326234 GTTCCTCTTGAAAAAATCTTTGAGTTT
1 GTTTCTCTTGAAAAAATCTTTGAGTTT
* * * *
326261 GCTCCTTTTGAATAAAAATCTTGGAGTTT
1 GTTTCTCTTG-A-AAAAATCTTTGAGTTT
* *
326290 GTTCCTTTTGAATAAATATCTTTGAG-TT
1 GTTTCTCTTGAA-AAA-ATCTTTGAGTTT
*
326318 GTTTCTTTTG-AAAAATCTTTGAGT
1 GTTTCTCTTGAAAAAATCTTTGAGT
326342 CTATTTATTT
Statistics
Matches: 173, Mismatches: 11, Indels: 18
0.86 0.05 0.09
Matches are distributed among these distances:
25 9 0.05
26 3 0.02
27 78 0.45
28 26 0.15
29 32 0.18
30 25 0.14
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (27 bp):
GTTTCTCTTGAAAAAATCTTTGAGTTT
Found at i:326211 original size:57 final size:55
Alignment explanation
Indices: 326121--326341 Score: 268
Period size: 57 Copynumber: 4.0 Consensus size: 55
326111 CTCTTGAGAC
*
326121 AGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTTCTCTTGAAAAAATCTTTGAGTT
1 AGTTCCTCTTGAAAAAAATCTTTGAGTTTGTTTCTCTTGAAAAAATCTTTGAGTT
* *
326176 AGTTTCTCTTGAAAAAAAAATCTTTGAGTTTGTTTCTCTGGAAAAAATCTTTGAGTT
1 AGTTCCTCTTG--AAAAAAATCTTTGAGTTTGTTTCTCTTGAAAAAATCTTTGAGTT
* * * * *
326233 TGTTCCTCTTG-AAAAAATCTTTGAGTTTGCTCCTTTTGAATAAAAATCTTGGAGTT
1 AGTTCCTCTTGAAAAAAATCTTTGAGTTTGTTTCTCTTG-A-AAAAATCTTTGAGTT
* * * *
326289 TGTTCCTTTTGAATAAATATCTTTGAG-TTGTTTCTTTTG-AAAAATCTTTGAGT
1 AGTTCCTCTTGAA-AAAAATCTTTGAGTTTGTTTCTCTTGAAAAAATCTTTGAGT
326342 CTATTTATTT
Statistics
Matches: 147, Mismatches: 13, Indels: 13
0.85 0.08 0.08
Matches are distributed among these distances:
54 36 0.24
55 12 0.08
56 24 0.16
57 63 0.43
58 12 0.08
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (55 bp):
AGTTCCTCTTGAAAAAAATCTTTGAGTTTGTTTCTCTTGAAAAAATCTTTGAGTT
Found at i:326236 original size:84 final size:83
Alignment explanation
Indices: 326122--326341 Score: 282
Period size: 84 Copynumber: 2.6 Consensus size: 83
326112 TCTTGAGACA
* * *
326122 GTTTCTCTTGAAAAAAATCTTTGAGTTTGTTTCTCTTGAAAAAATCTTTGAGTTAGTTTCTCTTG
1 GTTTCTC-TGGAAAAAATCTTTGAGTTTGTTTCTCTTGAAAAAATCTTTGAGTTAGCTCCTCTTG
*
326187 AAAAAAAAATCTTTGAGTTT
65 -AAAAAAAATCTTGGAGTTT
* * *
326207 GTTTCTCTGGAAAAAATCTTTGAGTTTGTTCCTCTTGAAAAAATCTTTGAGTTTGCTCCTTTTGA
1 GTTTCTCTGGAAAAAATCTTTGAGTTTGTTTCTCTTGAAAAAATCTTTGAGTTAGCTCCTCTTGA
*
326272 ATAAAAATCTTGGAGTTT
66 AAAAAAATCTTGGAGTTT
* * * *
326290 GTTCCTTTTGAATAAATATCTTTGAG-TTGTTTCTTTTG-AAAAATCTTTGAGT
1 GTTTCTCTGGAA-AAA-ATCTTTGAGTTTGTTTCTCTTGAAAAAATCTTTGAGT
326342 CTATTTATTT
Statistics
Matches: 120, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
83 40 0.33
84 64 0.53
85 16 0.13
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (83 bp):
GTTTCTCTGGAAAAAATCTTTGAGTTTGTTTCTCTTGAAAAAATCTTTGAGTTAGCTCCTCTTGA
AAAAAAATCTTGGAGTTT
Found at i:326474 original size:28 final size:28
Alignment explanation
Indices: 326443--326510 Score: 102
Period size: 28 Copynumber: 2.5 Consensus size: 28
326433 ATTTTGTGAA
*
326443 AAAAAAATCTTTGAGATTGTTTCTTTTG
1 AAAAAAATCTTTGAGATTGTTTCTTTGG
*
326471 AAAAAAATCTTTGAGTTTGTTTCTTTGG
1 AAAAAAATCTTTGAGATTGTTTCTTTGG
*
326499 AAACAAAT-TTTG
1 AAAAAAATCTTTG
326511 TCTCTCTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 4 0.11
28 33 0.89
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (28 bp):
AAAAAAATCTTTGAGATTGTTTCTTTGG
Found at i:326559 original size:94 final size:93
Alignment explanation
Indices: 326405--326577 Score: 242
Period size: 94 Copynumber: 1.8 Consensus size: 93
326395 CTTTGAGTCT
* *
326405 GAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAAAATCTTTGAGATTGTTTCTTTT
1 GAAACAAAGTTTTGTCTCTCTTAAGACAATTTTGTGAAAAAAAAATCTTTGAGATTGTTTCTTTG
326470 GAAA-AAAATCTTTGAGTTTGTTTCTTTG
66 GAAACAAAAT-TTTGAGTTTGTTTCTTTG
* * * * *
326498 GAAACAAA-TTTTGTCTCTCTTAAGATAGTTTCTTTTAAAACAAAAATCTTTGAGTTTGTTTCTT
1 GAAACAAAGTTTTGTCTCTCTTAAGACAATTT-TGTGAAAA-AAAAATCTTTGAGATTGTTTCTT
326562 TGGAAACAAAATTTTG
64 TGGAAACAAAATTTTG
326578 TCTATCTTAA
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
92 20 0.29
93 14 0.20
94 31 0.44
95 5 0.07
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.43
Consensus pattern (93 bp):
GAAACAAAGTTTTGTCTCTCTTAAGACAATTTTGTGAAAAAAAAATCTTTGAGATTGTTTCTTTG
GAAACAAAATTTTGAGTTTGTTTCTTTG
Found at i:326588 original size:67 final size:64
Alignment explanation
Indices: 326456--326720 Score: 268
Period size: 66 Copynumber: 4.1 Consensus size: 64
326446 AAAATCTTTG
* *
326456 AGATTGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAATTTTGTCTCTCTTA
1 AGATAGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAATTTTGTCTATCTTA
*
326520 AGATAGTTTCTTTTAAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTATCT
1 AGATAGTTTCTTTT-GAA-AAAAATCTTTGAGTTTGTTTCTTTGGAAAC-AAATTTTGTCTATCT
326585 TA
63 TA
* * * * ** * * *
326587 AGATAATTTCTTTTGAAAAAAATCTTTGAATCTGTTTCTCTT-AAAATGAATTTTGTATCTCTTG
1 AGATAGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCT-TTGGAAACAAATTTTGTCTATCTTA
* ** * *
326651 AGACAGTTTCTAATGAAAAACTAA-CTTTTGAGATTGTTTCATTT-GAAACAAATTTGGTCTCA-
1 AGATAGTTTCTTTTGAAAAA--AATC-TTTGAGTTTGTTTC-TTTGGAAACAAATTTTGTCT-AT
326713 CTTA
61 CTTA
326717 AGAT
1 AGAT
326721 GTGATCAATC
Statistics
Matches: 164, Mismatches: 28, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
64 42 0.26
65 26 0.16
66 66 0.40
67 30 0.18
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (64 bp):
AGATAGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAATTTTGTCTATCTTA
Found at i:326606 original size:131 final size:125
Alignment explanation
Indices: 326462--326831 Score: 348
Period size: 131 Copynumber: 2.9 Consensus size: 125
326452 TTTGAGATTG
* *
326462 TTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAATTTTGTCTCTCTTAAGATAGT
1 TTTCTTTTGAAAAAAATCTTTGAGTCTGTTTCTTT-GAAACAAATTTTGTCTCTCTTAAGACAGT
326527 TTCTTTTAAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCT-ATCTTAAGAT
65 TTCTTTTAAAA-AAAAATCTTTGAGTTTGTTTCTTT-GAAACAAAATTTTGTCTCA-CTTAAG--
326591 AA
125 -A
* * ** * *
326593 TTTCTTTTGAAAAAAATCTTTGAATCTGTTTCTCTTAAAATGAATTTTGTATCTCTTGAGACAGT
1 TTTCTTTTGAAAAAAATCTTTGAGTCTGTTTCT-TTGAAACAAATTTTGTCTCTCTTAAGACAGT
* * ** * *
326658 TTCTAATGAAAAACTAA-CTTTTGAGATTGTTTCATTTGAAAC-AAATTTGGTCTCACTTAAGA
65 TTCT-TTTAAAAAAAAATC-TTTGAGTTTGTTTC-TTTGAAACAAAATTTTGTCTCACTTAAGA
* ** * * *
326720 -----TGTG--ATCAATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCT-TAAAGACAA
1 TTTCTTTTGAAAAAAATCTTTGAGTCTGTTTC-TTTGAAAC-AAATTTTGTCTCTCTTAAGACAG
*
326777 TTTCTTTTGAAAAAAAATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC
64 TTTCTTTTAAAAAAAAATCTTTGAGTTTGTTT-CTTTGAAACAAAATTTTGTCTC
326832 TCGAGACAAC
Statistics
Matches: 196, Mismatches: 33, Indels: 31
0.75 0.13 0.12
Matches are distributed among these distances:
119 27 0.14
120 47 0.24
121 11 0.06
122 3 0.02
127 1 0.01
130 17 0.09
131 80 0.41
132 10 0.05
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (125 bp):
TTTCTTTTGAAAAAAATCTTTGAGTCTGTTTCTTTGAAACAAATTTTGTCTCTCTTAAGACAGTT
TCTTTTAAAAAAAAATCTTTGAGTTTGTTTCTTTGAAACAAAATTTTGTCTCACTTAAGA
Found at i:326808 original size:65 final size:64
Alignment explanation
Indices: 326727--326853 Score: 191
Period size: 65 Copynumber: 2.0 Consensus size: 64
326717 AGATGTGATC
* *
326727 AATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 AATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTC-TAAAGACAACTTCTTTTGAAAAAA
* * **
326792 AATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 AATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAA
326854 TACCCACATT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
64 19 0.34
65 37 0.66
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (64 bp):
AATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAAAA
Found at i:326824 original size:120 final size:120
Alignment explanation
Indices: 326607--326831 Score: 276
Period size: 120 Copynumber: 1.9 Consensus size: 120
326597 TTTTGAAAAA
** * * *
326607 AATCTTTGAATCTGTTTCTCTTAAAATGAATTTTGTATCTCTTGAGACAGTTTCTAATGAAAAAC
1 AATCTTTGAATCTGTTTCTCTTAAAACAAAATTTGTATCTCTTAAGACAATTTCTAATGAAAAAC
*
326672 TAACTTTTGAGATTGTTTCATTTGAAACAAATTTGGTCTCACTTAAGATGTGATC
66 AAACTTTTGAGATTGTTTCATTTGAAACAAATTTGGTCTCACTTAAGATGTGATC
* * * **
326727 AATCTTTGAGTCTGTTTCTTTTGAAACAAAATTT-TATCTCTTAAAGACAATTTCTTTTGAAAAA
1 AATCTTTGAATCTGTTTCTCTTAAAACAAAATTTGTATCTCTT-AAGACAATTTCTAATGAAAAA
* * *
326791 -AAA-TCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC
65 CAAACT-TTTGAGATTGTTTCATTTGAAAC-AAATTTGGTCTC
326832 TCGAGACAAC
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
118 1 0.01
119 31 0.35
120 56 0.64
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.43
Consensus pattern (120 bp):
AATCTTTGAATCTGTTTCTCTTAAAACAAAATTTGTATCTCTTAAGACAATTTCTAATGAAAAAC
AAACTTTTGAGATTGTTTCATTTGAAACAAATTTGGTCTCACTTAAGATGTGATC
Found at i:326898 original size:40 final size:40
Alignment explanation
Indices: 326835--326914 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
326825 TTGTCTCTCG
326835 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
* *
326875 AGACAATTTCTTTT-AAAACTACCCACCTTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAA-TACCCACATTTGAGATCGTTT
326915 CTATTAAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 4 0.11
40 33 0.89
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (40 bp):
AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
Found at i:327459 original size:27 final size:28
Alignment explanation
Indices: 327429--327509 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
327419 GAAACACATT
327429 ATCTTTGAG-CTTGTTT-TCTTGAAACAA
1 ATCTTTGAGTC-TGTTTCTCTTGAAACAA
*
327456 ATCTTTGAGTCTGTTTCTTTTGAAACAA
1 ATCTTTGAGTCTGTTTCTCTTGAAACAA
* *
327484 ATCTTT-AATTTGGTTTCTCTTGAAAC
1 ATCTTTGAGTCT-GTTTCTCTTGAAAC
327510 CATAACTCCT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 17 0.36
28 30 0.64
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.47
Consensus pattern (28 bp):
ATCTTTGAGTCTGTTTCTCTTGAAACAA
Found at i:327487 original size:28 final size:28
Alignment explanation
Indices: 327414--327489 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 28
327404 GAGACAGTTG
327414 CTTTTGAAACACATTATCTTTGAGCTTGTTT
1 CTTTTGAAACA-A--ATCTTTGAGCTTGTTT
*
327445 -TCTTGAAACAAATCTTTGAG-TCTGTTT
1 CTTTTGAAACAAATCTTTGAGCT-TGTTT
327472 CTTTTGAAACAAATCTTT
1 CTTTTGAAACAAATCTTT
327490 AATTTGGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 1 0.02
27 14 0.34
28 16 0.39
29 1 0.02
30 9 0.22
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGCTTGTTT
Found at i:327596 original size:40 final size:40
Alignment explanation
Indices: 327538--327851 Score: 186
Period size: 40 Copynumber: 7.4 Consensus size: 40
327528 CCATCCGTCT
*
327538 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCC
1 TCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCC
* * * * *
327578 TCATCACGTAGGAGCCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGATCTCC
* * * *
327624 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGATTTCC
1 TCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCC
* * * *
327664 TCATCACGTAGGAACTGGGTCA-CCCTTAGATAACCAG-CCGTCC
1 TCATCACGTAGGAACCGTGTCATCCC-CAG---ACCAGATC-TCC
* * * *
327707 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGACCTCT
1 TCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGATCTCC
* * * *
327753 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGATTTCC
1 TCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCC
* *
327793 TCATCACGTAGGAACCGGGTCA-CCCCTAGATAACCAG-CCGTCC
1 TCATCACGTAGGAACCGTGTCATCCCC-AG---ACCAGATC-TCC
327836 TCATCACGTAGGAACC
1 TCATCACGTAGGAACC
327852 TAGTTATCAC
Statistics
Matches: 212, Mismatches: 39, Indels: 43
0.72 0.13 0.15
Matches are distributed among these distances:
39 7 0.03
40 74 0.35
41 2 0.01
43 59 0.28
44 1 0.00
45 6 0.03
46 61 0.29
47 2 0.01
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.24
Consensus pattern (40 bp):
TCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCC
Found at i:327639 original size:46 final size:46
Alignment explanation
Indices: 327568--327772 Score: 178
Period size: 46 Copynumber: 4.7 Consensus size: 46
327558 CATCCCCAGA
*
327568 CCAGATCTCCTCATCACGTAGGAGCCGTGTTATCACCTTTAGATGG
1 CCAGACCTCCTCATCACGTAGGAGCCGTGTTATCACCTTTAGATGG
* * * * *
327614 CCAGAACTCTTCATCACGTATGAGCCGTGTCATC-CC-CT-GA---
1 CCAGACCTCCTCATCACGTAGGAGCCGTGTTATCACCTTTAGATGG
** * ** * **
327654 CCAGATTTCCTCATCACGTAGGA-AC-TG-GGTCACCCTTAGATAA
1 CCAGACCTCCTCATCACGTAGGAGCCGTGTTATCACCTTTAGATGG
*
327697 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
1 CCAGACC-TCCTCATCACGTAGGAGCCGTGTTATCACCTTTAGATGG
* *
327743 CCAGACCTCTTCATCACGTATGAGCCGTGT
1 CCAGACCTCCTCATCACGTAGGAGCCGTGT
327773 CATCCCCTGA
Statistics
Matches: 124, Mismatches: 24, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
37 2 0.02
38 4 0.03
39 2 0.02
40 21 0.17
43 22 0.18
44 2 0.02
45 4 0.03
46 65 0.52
47 2 0.02
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (46 bp):
CCAGACCTCCTCATCACGTAGGAGCCGTGTTATCACCTTTAGATGG
Found at i:327667 original size:86 final size:86
Alignment explanation
Indices: 327535--327972 Score: 289
Period size: 86 Copynumber: 5.1 Consensus size: 86
327525 TGGCCATCCG
* *
327535 TCTTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTTA
1 TCTTCATCACGTAGGAACCGTGTCATCCCCTGACCAGATCTCCTCATCACGTAGGAGCCGTGTTA
* *
327600 TCACCTTTAGATGGCCAGAAC
66 TCACCCTTAGATGACCAGAAC
* * * * **
327621 TCTTCATCACGTATGAGCCGTGTCATCCCCTGACCAGATTTCCTCATCACGTAGGA-AC-TG-GG
1 TCTTCATCACGTAGGAACCGTGTCATCCCCTGACCAGATCTCCTCATCACGTAGGAGCCGTGTTA
* *
327683 TCACCCTTAGATAACCAG-CC
66 TCACCCTTAGATGACCAGAAC
* * * * * *
327703 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGACCTCTTCATCACGTATGAGC
1 -TCTTCATCACGTAGGAACCGTGTCATC-CC-CT-GA---CCAGATCTCCTCATCACGTAGGAGC
* **
327768 CGTGTCATC-CCC-----TGACCAGATT
59 CGTGTTATCACCCTTAGATGACCAGAAC
* * * *
327790 TCCTCATCACGTAGGAACCGGGTCA-CCCCTAGATAACCAG-CCGTCCTCATCACGTAGGAACC-
1 TCTTCATCACGTAGGAACCGTGTCATCCCCT-G---ACCAGATC-TCCTCATCACGTAGGAGCCG
327852 TAGTTATCACCCTTCCTAAAGATGACCAGAAC
61 T-GTTATCACCC-T--T--AGATGACCAGAAC
* * * * * **
327884 TCTTCGTCACGTATGAGCCGTGTCATCCCCCGA-CAGATTTTTTCATCACGTAGGAGCCGTG---
1 TCTTCATCACGTAGGAACCGTGTCATCCCCTGACCAGATCTCCTCATCACGTAGGAGCCGTGTTA
* *
327945 TCGCCCTTAGATGACCAGACC
66 TCACCCTTAGATGACCAGAAC
327966 TCTTCAT
1 TCTTCAT
327973 TGCGTATGAG
Statistics
Matches: 272, Mismatches: 50, Indels: 64
0.70 0.13 0.17
Matches are distributed among these distances:
82 22 0.08
83 66 0.24
84 10 0.04
85 3 0.01
86 84 0.31
87 5 0.02
89 19 0.07
90 21 0.08
91 7 0.03
92 2 0.01
94 29 0.11
95 4 0.01
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.26
Consensus pattern (86 bp):
TCTTCATCACGTAGGAACCGTGTCATCCCCTGACCAGATCTCCTCATCACGTAGGAGCCGTGTTA
TCACCCTTAGATGACCAGAAC
Found at i:327708 original size:43 final size:43
Alignment explanation
Indices: 327661--327851 Score: 176
Period size: 43 Copynumber: 4.4 Consensus size: 43
327651 TGACCAGATT
* *
327661 TCCTCATCACGTAGGAACTGGGTCACCCTTAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGGGTCACCCCTAGATAACCAGCCG
* ** **
327704 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGACC-
1 TCCTCATCACGTAGGAACCG-G--GTCACCCCTAGATAACCAG-CCG
* * * * ***
327750 TCTTCATCACGTATGAGCCGTGTCATCCCCT-G---ACCAGATT
1 TCCTCATCACGTAGGAACCGGGTCA-CCCCTAGATAACCAGCCG
327790 TCCTCATCACGTAGGAACCGGGTCACCCCTAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGGGTCACCCCTAGATAACCAGCCG
327833 TCCTCATCACGTAGGAACC
1 TCCTCATCACGTAGGAACC
327852 TAGTTATCAC
Statistics
Matches: 116, Mismatches: 22, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
39 5 0.04
40 26 0.22
43 47 0.41
44 4 0.03
46 32 0.28
47 2 0.02
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.23
Consensus pattern (43 bp):
TCCTCATCACGTAGGAACCGGGTCACCCCTAGATAACCAGCCG
Found at i:327797 original size:129 final size:129
Alignment explanation
Indices: 327575--327962 Score: 591
Period size: 129 Copynumber: 3.0 Consensus size: 129
327565 AGACCAGATC
*
327575 TCCTCATCACGTAGGAGCCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCC
1 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCC
*
327640 GTGTCATCCCCTGACCAGATTTCCTCATCACGTAGGAACTGGGTCACCCTTAGATAACCAGCCG
66 GTGTCATCCCCTGACCAGATTTCCTCATCACGTAGGAACCGGGTCACCCTTAGATAACCAGCCG
*
327704 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGACCTCTTCATCACGTATGAGCC
1 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCC
*
327769 GTGTCATCCCCTGACCAGATTTCCTCATCACGTAGGAACCGGGTCACCCCTAGATAACCAGCCG
66 GTGTCATCCCCTGACCAGATTTCCTCATCACGTAGGAACCGGGTCACCCTTAGATAACCAGCCG
* *
327833 TCCTCATCACGTAGGAACC-TAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCGTCACGTA
1 TCCTCATCACGTAGGAACCGT-GTTATCA-CCTT--T--AGATGGCCAGAACTCTTCATCACGTA
* ** * * * *
327897 TGAGCCGTGTCATCCCCCGA-CAGATTTTTTCATCACGTAGGAGCCGTGTCGCCCTTAGATGACC
60 TGAGCCGTGTCATCCCCTGACCAGATTTCCTCATCACGTAGGAACCGGGTCACCCTTAGATAACC
327961 AG
125 AG
327963 ACCTCTTCAT
Statistics
Matches: 238, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
128 1 0.00
129 151 0.63
130 4 0.02
132 1 0.00
133 39 0.16
134 42 0.18
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (129 bp):
TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCC
GTGTCATCCCCTGACCAGATTTCCTCATCACGTAGGAACCGGGTCACCCTTAGATAACCAGCCG
Found at i:328156 original size:3 final size:3
Alignment explanation
Indices: 328145--328208 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
328135 GTTTTTTTCG
** *
328145 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
328190 TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
328209 CAAATTTTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:328186 original size:32 final size:32
Alignment explanation
Indices: 328142--328206 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
328132 CGGGTTTTTT
*
328142 TCGTTATTTTATTATTATTATTATTA-TTATTA
1 TCGTTATCTTATTATT-TTATTATTATTTATTA
328174 TCGTTATCTTATTATTTTATTATTATTTATTA
1 TCGTTATCTTATTATTTTATTATTATTTATTA
328206 T
1 T
328207 TACAAATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 9 0.29
32 22 0.71
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (32 bp):
TCGTTATCTTATTATTTTATTATTATTTATTA
Found at i:336790 original size:17 final size:17
Alignment explanation
Indices: 336764--336801 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
336754 ACAAGGAATG
*
336764 AAAGTTCTTGTGGAGCA
1 AAAGTCCTTGTGGAGCA
336781 AAAGTCCTTGTGGAGCA
1 AAAGTCCTTGTGGAGCA
336798 AAAG
1 AAAG
336802 CTACTTCCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.24
Consensus pattern (17 bp):
AAAGTCCTTGTGGAGCA
Found at i:343855 original size:57 final size:57
Alignment explanation
Indices: 343761--343871 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 57
343751 GTTTTGTAAC
* * *
343761 TTATAATTCTCAAGTGAAACAATGATGTAAAGTCTTATAAATAAATAGACTTGTCAT
1 TTATAATTCTCAAGTAAAACAATGAAGTAAAGGCTTATAAATAAATAGACTTGTCAT
* * * *
343818 TTATGATTCTCAAGTAAAACAATGAAGTAGAGGCTTATAAATTAATAGATTTGT
1 TTATAATTCTCAAGTAAAACAATGAAGTAAAGGCTTATAAATAAATAGACTTGT
343872 AAAACGGATG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.35
Consensus pattern (57 bp):
TTATAATTCTCAAGTAAAACAATGAAGTAAAGGCTTATAAATAAATAGACTTGTCAT
Found at i:350153 original size:23 final size:23
Alignment explanation
Indices: 350123--350230 Score: 152
Period size: 23 Copynumber: 4.9 Consensus size: 23
350113 CTGAATGATT
*
350123 CAGTGCTGACTGATTCAGCAAAA
1 CAGTGCTGAATGATTCAGCAAAA
350146 CAGTGCTGAATGATTCAGCAAAA
1 CAGTGCTGAATGATTCAGCAAAA
**
350169 CAGTGCTGAATGATT---C-ATT
1 CAGTGCTGAATGATTCAGCAAAA
350188 CAGTGCTGAATGATTCAGCAAAA
1 CAGTGCTGAATGATTCAGCAAAA
*
350211 CAGTGTTGAATGATTCAGCA
1 CAGTGCTGAATGATTCAGCA
350231 CAGAAATACA
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
19 16 0.21
20 1 0.01
22 1 0.01
23 57 0.76
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (23 bp):
CAGTGCTGAATGATTCAGCAAAA
Found at i:350203 original size:42 final size:42
Alignment explanation
Indices: 350146--350227 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
350136 TTCAGCAAAA
350146 CAGTGCTGAATGATTCAGCAAAACAGTGCTGAATGATTCATT
1 CAGTGCTGAATGATTCAGCAAAACAGTGCTGAATGATTCATT
*
350188 CAGTGCTGAATGATTCAGCAAAACAGTGTTGAATGATTCA
1 CAGTGCTGAATGATTCAGCAAAACAGTGCTGAATGATTCA
350228 GCACAGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (42 bp):
CAGTGCTGAATGATTCAGCAAAACAGTGCTGAATGATTCATT
Found at i:350255 original size:65 final size:61
Alignment explanation
Indices: 350112--350230 Score: 166
Period size: 65 Copynumber: 1.9 Consensus size: 61
350102 GTTTCGCACC
* *
350112 TCTGAATGATTCAGTGCTGACTGATTCAGCAAAACAGTGCTGAATGATTCAGCAAAACAGT
1 TCTGAATAATTCAGTGCTGAATGATTCAGCAAAACAGTGCTGAATGATTCAGCAAAACAGT
* *
350173 GCTGAATGATTCATTCAGTGCTGAATGATTCAGCAAAACAGTGTTGAATGATTCAGCA
1 TCTGAAT-A---ATTCAGTGCTGAATGATTCAGCAAAACAGTGCTGAATGATTCAGCA
350231 CAGAAATACA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
61 6 0.12
65 44 0.88
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.28
Consensus pattern (61 bp):
TCTGAATAATTCAGTGCTGAATGATTCAGCAAAACAGTGCTGAATGATTCAGCAAAACAGT
Found at i:350326 original size:16 final size:16
Alignment explanation
Indices: 350301--350426 Score: 132
Period size: 16 Copynumber: 8.1 Consensus size: 16
350291 ATTCATACAG
*
350301 AGCATCTGAATCATTC
1 AGCATTTGAATCATTC
350317 AGCATTTGAATCATTC
1 AGCATTTGAATCATTC
* **
350333 AACGCTT-AATCATTC
1 AGCATTTGAATCATTC
*
350348 AGCATTTAAATCATTC
1 AGCATTTGAATCATTC
* **
350364 AACGCTT-AATCATTC
1 AGCATTTGAATCATTC
350379 AGCATTTGAATCATTC
1 AGCATTTGAATCATTC
* **
350395 AACGCTT-AATCATTC
1 AGCATTTGAATCATTC
350410 AGCATTTGAATCATTC
1 AGCATTTGAATCATTC
350426 A
1 A
350427 ACGCTTAATC
Statistics
Matches: 88, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
15 36 0.41
16 52 0.59
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (16 bp):
AGCATTTGAATCATTC
Found at i:350345 original size:15 final size:15
Alignment explanation
Indices: 350325--350440 Score: 124
Period size: 15 Copynumber: 7.5 Consensus size: 15
350315 TCAGCATTTG
350325 AATCATTCAACGCTT
1 AATCATTCAACGCTT
* **
350340 AATCATTCAGCATTT
1 AATCATTCAACGCTT
350355 AAATCATTCAACGCTT
1 -AATCATTCAACGCTT
* **
350371 AATCATTCAGCATTT
1 AATCATTCAACGCTT
350386 GAATCATTCAACGCTT
1 -AATCATTCAACGCTT
* **
350402 AATCATTCAGCATTT
1 AATCATTCAACGCTT
350417 GAATCATTCAACGCTT
1 -AATCATTCAACGCTT
350433 AATCATTC
1 AATCATTC
350441 TTAAGTAAAC
Statistics
Matches: 80, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
15 44 0.55
16 36 0.45
ACGTcount: A:0.34, C:0.23, G:0.08, T:0.35
Consensus pattern (15 bp):
AATCATTCAACGCTT
Found at i:350346 original size:31 final size:31
Alignment explanation
Indices: 350309--350440 Score: 255
Period size: 31 Copynumber: 4.3 Consensus size: 31
350299 AGAGCATCTG
350309 AATCATTCAGCATTTGAATCATTCAACGCTT
1 AATCATTCAGCATTTGAATCATTCAACGCTT
*
350340 AATCATTCAGCATTTAAATCATTCAACGCTT
1 AATCATTCAGCATTTGAATCATTCAACGCTT
350371 AATCATTCAGCATTTGAATCATTCAACGCTT
1 AATCATTCAGCATTTGAATCATTCAACGCTT
350402 AATCATTCAGCATTTGAATCATTCAACGCTT
1 AATCATTCAGCATTTGAATCATTCAACGCTT
350433 AATCATTC
1 AATCATTC
350441 TTAAGTAAAC
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 99 1.00
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (31 bp):
AATCATTCAGCATTTGAATCATTCAACGCTT
Found at i:358469 original size:17 final size:17
Alignment explanation
Indices: 358437--358476 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
358427 CAATTCACAA
*
358437 TTAATT-TAAATGATAT
1 TTAATTATAAATAATAT
358453 TTAATTATAAATAATAT
1 TTAATTATAAATAATAT
*
358470 CTAATTA
1 TTAATTA
358477 ATTTGATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TTAATTATAAATAATAT
Found at i:358542 original size:11 final size:11
Alignment explanation
Indices: 358526--358553 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
358516 AATATTGATT
358526 TGGATTTTAAA
1 TGGATTTTAAA
358537 TGGATTTTAAA
1 TGGATTTTAAA
358548 TGGATT
1 TGGATT
358554 GGGCTTGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.46
Consensus pattern (11 bp):
TGGATTTTAAA
Found at i:370319 original size:22 final size:22
Alignment explanation
Indices: 370278--370319 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
370268 AGTACCACCC
* **
370278 AATATTAATATTTTCGATAAAA
1 AATAATAATATTTTAAATAAAA
370300 AATAATAATATTTTAAATAA
1 AATAATAATATTTTAAATAA
370320 CACTTTACAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
AATAATAATATTTTAAATAAAA
Found at i:371635 original size:44 final size:44
Alignment explanation
Indices: 371568--371651 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
371558 GATAAACTTG
*
371568 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGGAA
1 TTTTTATTTATTTTGTTTATTAATGTTTTTATTTAATTATGGAA
371612 TTTTTATTTATTTTGTTTATTAATGTTTTTATTTAATTAT
1 TTTTTATTTATTTTGTTTATTAATGTTTTTATTTAATTAT
371652 TGGACCCAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.23, C:0.01, G:0.07, T:0.69
Consensus pattern (44 bp):
TTTTTATTTATTTTGTTTATTAATGTTTTTATTTAATTATGGAA
Found at i:374344 original size:29 final size:29
Alignment explanation
Indices: 374302--374388 Score: 129
Period size: 29 Copynumber: 3.0 Consensus size: 29
374292 GTCCCGGGGG
*
374302 TAGGTCGCCATGCACGCCCGGCGACCTAC
1 TAGGTCGCCATGCACGCCCAGCGACCTAC
**
374331 TAGGTCGCCATGCACGCCCAGCGACCTGG
1 TAGGTCGCCATGCACGCCCAGCGACCTAC
* *
374360 TAGGTCGCCATGCATGCCCTGCGACCTAC
1 TAGGTCGCCATGCACGCCCAGCGACCTAC
374389 CAGCACCTCC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.17, C:0.39, G:0.28, T:0.16
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCCAGCGACCTAC
Found at i:374404 original size:10 final size:10
Alignment explanation
Indices: 374397--374479 Score: 75
Period size: 10 Copynumber: 8.3 Consensus size: 10
374387 ACCAGCACCT
374397 CCATGCACGC
1 CCATGCACGC
374407 CCATGCACGC
1 CCATGCACGC
*
374417 CCA-ACGAC-C
1 CCATGC-ACGC
374426 TCCATGCACGC
1 -CCATGCACGC
*
374437 CCAGGCACGC
1 CCATGCACGC
*
374447 CCA-ACGAC-C
1 CCATGC-ACGC
374456 TCCATGCACGC
1 -CCATGCACGC
374467 CCATGCACGC
1 CCATGCACGC
374477 CCA
1 CCA
374480 ACGACCTCCA
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
9 4 0.07
10 52 0.87
11 4 0.07
ACGTcount: A:0.23, C:0.51, G:0.18, T:0.08
Consensus pattern (10 bp):
CCATGCACGC
Found at i:374411 original size:40 final size:40
Alignment explanation
Indices: 374367--374449 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
374357 TGGTAGGTCG
* ** *
374367 CCATGCATGCCCTGCGACCTACCA-GCAC-CTCCATGCACGC
1 CCATGCACGCCCAACGACCT-CCATGCACGC-CCAGGCACGC
374407 CCATGCACGCCCAACGACCTCCATGCACGCCCAGGCACGC
1 CCATGCACGCCCAACGACCTCCATGCACGCCCAGGCACGC
374447 CCA
1 CCA
374450 ACGACCTCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
39 3 0.08
40 33 0.89
41 1 0.03
ACGTcount: A:0.22, C:0.49, G:0.18, T:0.11
Consensus pattern (40 bp):
CCATGCACGCCCAACGACCTCCATGCACGCCCAGGCACGC
Found at i:374427 original size:30 final size:30
Alignment explanation
Indices: 374393--374499 Score: 205
Period size: 30 Copynumber: 3.6 Consensus size: 30
374383 ACCTACCAGC
374393 ACCTCCATGCACGCCCATGCACGCCCAACG
1 ACCTCCATGCACGCCCATGCACGCCCAACG
*
374423 ACCTCCATGCACGCCCAGGCACGCCCAACG
1 ACCTCCATGCACGCCCATGCACGCCCAACG
374453 ACCTCCATGCACGCCCATGCACGCCCAACG
1 ACCTCCATGCACGCCCATGCACGCCCAACG
374483 ACCTCCATGCACGCCCA
1 ACCTCCATGCACGCCCA
374500 GCTCGCCAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 75 1.00
ACGTcount: A:0.23, C:0.50, G:0.17, T:0.09
Consensus pattern (30 bp):
ACCTCCATGCACGCCCATGCACGCCCAACG
Found at i:375163 original size:21 final size:21
Alignment explanation
Indices: 375138--375181 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
375128 AATTTAGTTA
375138 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
375159 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
375180 AT
1 AT
375182 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:378341 original size:14 final size:14
Alignment explanation
Indices: 378324--379269 Score: 332
Period size: 14 Copynumber: 68.3 Consensus size: 14
378314 GATGATTTAG
*
378324 TAATGATTTGATAA
1 TAATGATTTAATAA
*
378338 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
378350 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
378364 TAATTATTTAGT--
1 TAATGATTTAATAA
* **
378376 T-ATTATTTAGGAA
1 TAATGATTTAATAA
378389 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
378399 TAATGATTTAATAC
1 TAATGATTTAATAA
378413 TAATGATTTAATAATTTA
1 TAATGATTTAAT-A---A
*
378431 GTAATGATTTAATAC
1 -TAATGATTTAATAA
378446 TAATGATTTAATAA
1 TAATGATTTAATAA
*
378460 TTTAGTGATGATTTAATAC
1 --TA---ATGATTTAATAA
378479 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
378490 TAATGATTTAATAC
1 TAATGATTTAATAA
378504 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
378515 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
378531 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
378550 TAATGATTTGATAA
1 TAATGATTTAATAA
*
378564 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
378576 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
378590 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
378602 T-ATTATTTAGTAA
1 TAATGATTTAATAA
378615 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
378625 TAATGATTTAATAC
1 TAATGATTTAATAA
378639 TAATGATTTAATAATTTA
1 TAATGATTTAAT-A---A
*
378657 GTAATGATTTAATAC
1 -TAATGATTTAATAA
378672 TAATGATTTAATAA
1 TAATGATTTAATAA
*
378686 TTTAGTGATGATTTAATAC
1 --TA---ATGATTTAATAA
378705 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
378716 TAATGATTTAATAC
1 TAATGATTTAATAA
378730 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
378741 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
378757 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
378776 TAATGATTTGATAA
1 TAATGATTTAATAA
*
378790 TAATCATTATAATAA
1 TAATGATT-TAATAA
*
378805 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
378817 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
378831 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
378843 T-ATTATTTAGTAA
1 TAATGATTTAATAA
378856 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
378866 TAATGATTTAATAC
1 TAATGATTTAATAA
*
378880 TAATGATTTAATAC
1 TAATGATTTAATAA
378894 TAATGATTTAATAA
1 TAATGATTTAATAA
*
378908 TTTAGTGATGATTTAATAC
1 --TA---ATGATTTAATAA
378927 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
378938 TAATGATTTAATAC
1 TAATGATTTAATAA
378952 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
378963 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
378979 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
* *
378998 TAATAATTTGATAA
1 TAATGATTTAATAA
* *
379012 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
379024 TAATGATTTGATAA
1 TAATGATTTAATAA
*
379038 TAATCA-TT-ATAA
1 TAATGATTTAATAA
* *
379050 AAATGATTTAGTAA
1 TAATGATTTAATAA
*
379064 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
379076 AAATGA-TT--TAA
1 TAATGATTTAATAA
*
379087 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
379103 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
**
379122 TAATGATTTGTTAA
1 TAATGATTTAATAA
*
379136 TAATTA-TT-ATAA
1 TAATGATTTAATAA
*
379148 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
379162 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
379174 T-ATTATTTAGTAA
1 TAATGATTTAATAA
*
379187 T--T-ATTT-ATAG
1 TAATGATTTAATAA
*
379197 TAATGATTTAATAC
1 TAATGATTTAATAA
*
379211 TAATAATTTAATAA
1 TAATGATTTAATAA
379225 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
379236 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
379252 TAATGATTTAATAC
1 TAATGATTTAATAA
379266 TAAT
1 TAAT
379270 AATAATGATT
Statistics
Matches: 727, Mismatches: 93, Indels: 224
0.70 0.09 0.21
Matches are distributed among these distances:
10 14 0.02
11 120 0.17
12 88 0.12
13 59 0.08
14 249 0.34
15 27 0.04
16 58 0.08
17 6 0.01
18 6 0.01
19 92 0.13
20 8 0.01
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:378437 original size:19 final size:19
Alignment explanation
Indices: 378413--378477 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
378403 GATTTAATAC
378413 TAATGATTTAATAATTTAG
1 TAATGATTTAATAATTTAG
*
378432 TAATGA-TT--TAA--TAC
1 TAATGATTTAATAATTTAG
378446 TAATGATTTAATAATTTAG
1 TAATGATTTAATAATTTAG
*
378465 TGATGATTTAATA
1 TAATGATTTAATA
378478 CTAATGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 8 0.21
15 2 0.05
16 3 0.08
17 3 0.08
18 2 0.05
19 20 0.53
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.46
Consensus pattern (19 bp):
TAATGATTTAATAATTTAG
Found at i:378441 original size:33 final size:33
Alignment explanation
Indices: 378399--378493 Score: 181
Period size: 33 Copynumber: 2.9 Consensus size: 33
378389 TTATTTATAA
378399 TAATGATTTAATACTAATGATTTAATAATTTAG
1 TAATGATTTAATACTAATGATTTAATAATTTAG
378432 TAATGATTTAATACTAATGATTTAATAATTTAG
1 TAATGATTTAATACTAATGATTTAATAATTTAG
*
378465 TGATGATTTAATACTAATGATTTAATAAT
1 TAATGATTTAATACTAATGATTTAATAAT
378494 GATTTAATAC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (33 bp):
TAATGATTTAATACTAATGATTTAATAATTTAG
Found at i:378663 original size:19 final size:19
Alignment explanation
Indices: 378639--378703 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
378629 GATTTAATAC
378639 TAATGATTTAATAATTTAG
1 TAATGATTTAATAATTTAG
*
378658 TAATGA-TT--TAA--TAC
1 TAATGATTTAATAATTTAG
378672 TAATGATTTAATAATTTAG
1 TAATGATTTAATAATTTAG
*
378691 TGATGATTTAATA
1 TAATGATTTAATA
378704 CTAATGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 8 0.21
15 2 0.05
16 3 0.08
17 3 0.08
18 2 0.05
19 20 0.53
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.46
Consensus pattern (19 bp):
TAATGATTTAATAATTTAG
Found at i:378667 original size:33 final size:33
Alignment explanation
Indices: 378625--378719 Score: 181
Period size: 33 Copynumber: 2.9 Consensus size: 33
378615 TTATTTATAA
378625 TAATGATTTAATACTAATGATTTAATAATTTAG
1 TAATGATTTAATACTAATGATTTAATAATTTAG
378658 TAATGATTTAATACTAATGATTTAATAATTTAG
1 TAATGATTTAATACTAATGATTTAATAATTTAG
*
378691 TGATGATTTAATACTAATGATTTAATAAT
1 TAATGATTTAATACTAATGATTTAATAAT
378720 GATTTAATAC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (33 bp):
TAATGATTTAATACTAATGATTTAATAATTTAG
Found at i:378673 original size:226 final size:226
Alignment explanation
Indices: 378279--379088 Score: 1298
Period size: 226 Copynumber: 3.6 Consensus size: 226
378269 TCATTATAAA
**
378279 AATGATTTAATAATGATTTAAATAAGTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
1 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
*
378344 TTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGGAATTATTTATAATAATGATTTA
66 TTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTATTTATAATAATGATTTA
378409 ATACTAATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTAATAATTTAGTGATGATTT
131 ATACTAATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTAATAATTTAGTGATGATTT
378474 AATACTAATGATTTAATAATGATTTAATACT
196 AATACTAATGATTTAATAATGATTTAATACT
378505 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
1 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
378570 TTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTATTTATAATAATGATTTA
66 TTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTATTTATAATAATGATTTA
378635 ATACTAATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTAATAATTTAGTGATGATTT
131 ATACTAATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTAATAATTTAGTGATGATTT
378700 AATACTAATGATTTAATAATGATTTAATACT
196 AATACTAATGATTTAATAATGATTTAATACT
378731 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
1 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
* * * *
378796 TTATAATAATAATCATTATAATAATGATTTTA-TAATAATTATTTAGTTATTATTTAGTAAT--T
66 TTATAATAATGAT-TTTATAATAATTA-TTTAGT--T-ATTATTTAGTAATTATTTA-TAATAAT
* *
378858 -ATTT-ATAATAATGA-TT--TAA--TACTAATGATTTAATACTAATGATTTAATAATTTAGTGA
125 GATTTAATACTAATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTAATAATTTAGTGA
378916 TGATTTAATACTAATGATTTAATAATGATTTAATACT
190 TGATTTAATACTAATGATTTAATAATGATTTAATACT
*
378953 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATAATTTGATAATAATCA
1 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
* * * *** * * *
379018 TTATAGTAATGATTTGATAATAATCATTATAAAAATGATTTAGTAATAATCATTATAAAAATGAT
66 TTATAATAATGATTTTATAATAATTATT-TAGTTATTATTTAGTAATTAT--TTATAATAATGAT
379083 TTAATA
128 TTAATA
379089 ATGATTTAAA
Statistics
Matches: 549, Mismatches: 21, Indels: 30
0.92 0.04 0.05
Matches are distributed among these distances:
219 13 0.02
220 5 0.01
221 15 0.03
222 151 0.28
223 4 0.01
224 6 0.01
226 302 0.55
227 21 0.04
228 8 0.01
229 2 0.00
230 18 0.03
231 4 0.01
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.46
Consensus pattern (226 bp):
AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
TTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTATTTATAATAATGATTTA
ATACTAATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTAATAATTTAGTGATGATTT
AATACTAATGATTTAATAATGATTTAATACT
Found at i:378806 original size:15 final size:15
Alignment explanation
Indices: 378786--378834 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
378776 TAATGATTTG
378786 ATAATAATCATTATA
1 ATAATAATCATTATA
378801 ATAATAATCATTATA
1 ATAATAATCATTATA
* *
378816 ATAATGAT-TTTATA
1 ATAATAATCATTATA
378830 ATAAT
1 ATAAT
378835 TATTTAGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 10 0.31
15 22 0.69
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (15 bp):
ATAATAATCATTATA
Found at i:379024 original size:26 final size:26
Alignment explanation
Indices: 378995--379239 Score: 138
Period size: 26 Copynumber: 9.7 Consensus size: 26
378985 TTTGATGATT
*
378995 TAGTAATAATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
379021 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
**
379047 TAAAAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
379073 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
379095 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
* *
379119 TAGTAATGATTTGTTAATAATTATTA
1 TAGTAATGATTTGATAATAATCATTA
* * *
379145 TAATAATGATTTTATAATAATTATT-
1 TAGTAATGATTTGATAATAATCATTA
* * *
379170 TAGTTATTATTT-AGTAATTAT--TTA
1 TAGTAATGATTTGA-TAATAATCATTA
* * *
379194 TAGTAATGATTTAATACTAATAATTTAA
1 TAGTAATGATTTGATAATAATCA-TT-A
* *
379222 TAATAATGATTTAATAAT
1 TAGTAATGATTTGATAAT
379240 GATTTAAATA
Statistics
Matches: 178, Mismatches: 24, Indels: 32
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.01
20 5 0.03
22 3 0.02
23 13 0.07
24 25 0.14
25 25 0.14
26 82 0.46
27 7 0.04
28 17 0.10
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.46
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:379221 original size:124 final size:122
Alignment explanation
Indices: 378928--379209 Score: 386
Period size: 124 Copynumber: 2.3 Consensus size: 122
378918 ATTTAATACT
* * *
378928 AATGATTTAATAATGATTTAATACTAATGATTTAATAATGATTTAAATATTTAATGATTTGATGA
1 AATGATTTAGTAATAATTT-ATAATAATGATTTAATAATGATTTAAATATTTAATGATTTGATGA
*
378993 TTTAGTAATAATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAAA
65 TTTAGTAATAATTTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAAA
*
379051 AATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
1 AATGATTTAGTAATAAT--TTATAATAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
* * * * * **
379116 ATTTAGTAATGATTTGTTAATAATTATTATAATAATGATTTTATAATAATTATT-TAGT
64 ATTTAGTAATAATTTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAAA
* * * *
379174 TATTATTTAGTAATTATTTATAGTAATGATTTAATA
1 AATGATTTAGTAATAATTTATAATAATGATTTAATA
379210 CTAATAATTT
Statistics
Matches: 140, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
121 17 0.12
123 31 0.22
124 90 0.64
125 2 0.01
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (122 bp):
AATGATTTAGTAATAATTTATAATAATGATTTAATAATGATTTAAATATTTAATGATTTGATGAT
TTAGTAATAATTTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAAA
Found at i:379277 original size:20 final size:20
Alignment explanation
Indices: 379233--379288 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
379223 AATAATGATT
379233 TAATAATGATTTAA-A-T-A
1 TAATAATGATTTAATACTAA
*
379250 T-TTAATGATTTAATACTAA
1 TAATAATGATTTAATACTAA
*
379269 TAATAATGATTTGATACTAA
1 TAATAATGATTTAATACTAA
379289 AAATCATTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 11 0.34
17 2 0.06
18 1 0.03
19 2 0.06
20 16 0.50
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (20 bp):
TAATAATGATTTAATACTAA
Found at i:379278 original size:75 final size:72
Alignment explanation
Indices: 378524--379288 Score: 227
Period size: 75 Copynumber: 10.6 Consensus size: 72
378514 ATAATGATTT
* * * * * *
378524 AAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA-TTATAATAATGATTTTAT
1 AAATATTTAATGATTTAAT-ATATAATAATGATTTAATACTAATAATTTATAATAATGA--TT-T
*
378588 AATAATTATTT
62 AATAATGATTT
* * * * *
378599 AGTTATTATTTAGT-AATT-ATTTATAATAATGATTTAATACTAATGA-TT-TAAT-A--ATTTA
1 A---AATATTTAATGATTTAATATATAATAATGATTTAATACTAATAATTTATAATAATGATTTA
*
378657 GTAATGATTT
63 ATAATGATTT
* * * * *
378667 -AATA-CTAATGATTTAATAATTTAGTGATGATTTAATACTAATGA-TT-TAATAATGATTTAAT
1 AAATATTTAATGATTTAAT-ATATAATAATGATTTAATACTAATAATTTATAATAATGATTT-A-
378728 ACTAATGATTT
63 A-TAATGATTT
* * * *
378739 --A-A--TAATGATTTAA-ATAT-TTAATGATTTGATGATTTAGTAATGATTTGATAATAATCAT
1 AAATATTTAATGATTTAATATATAATAATGATTT-A--A--TACTAATAATTT-ATAATAATGAT
*
378797 TATAATAATAATCATT
60 T-TAATAATGAT--TT
* * * * * * *
378813 --ATA-ATAATGATTTTATA-ATAATTATTTAGTTATTATTTAGTAATTATTTATAATAATGATT
1 AAATATTTAATGATTTAATATATAA-TA-AT-GAT-TTA-ATACTAATAATTTATAATAATGATT
378874 TAATACTAATGATTT
61 T-A-A-TAATGATTT
* * * * *
378889 -AATA-CTAATGATTTAATAATTTAGTGATGATTTAATACTAATGA-TT-TAATAATGATTTAAT
1 AAATATTTAATGATTTAAT-ATATAATAATGATTTAATACTAATAATTTATAATAATGATTT-A-
378950 ACTAATGATTT
63 A-TAATGATTT
* * *
378961 --A-A--TAATGATTTAA-ATAT-TTAATGATTTGATGATTTAGTAATAATTTGATAATAATCAT
1 AAATATTTAATGATTTAATATATAATAATGATTT-A--A--TACTAATAATTT-ATAATAATGAT
*
379019 TATAGTAATGATTT
60 T-TAATAATGATTT
* * * * * * *
379033 -GATA-ATAATCA--T--TATA-AA-AATGATTTAGTAATAATCA-TTATAAAAATGATTTAATA
1 AAATATTTAATGATTTAATATATAATAATGATTTAATACTAATAATTTATAATAATGATTTAATA
379089 ATGATTT
66 ATGATTT
* * * ** * *
379096 AAATATTTAATGATTTGATGATTTAGTAATGATTTGTTAATAATTA-TTATAATAATGATTTTAT
1 AAATATTTAATGATTTAAT-ATATAATAATGATTTAATACTAATAATTTATAATAATGA--TT-T
*
379160 AATAATTATTT
62 AATAATGATTT
* * * * *
379171 AGTTATTATTTAGT-AATT-ATTTATAGTAATGATTTAATACTAATAATTTAATAATAATGATTT
1 A---AATATTTAATGATTTAATATATAATAATGATTTAATACTAATAATTT-ATAATAATGATTT
379234 AATAATGATTT
62 AATAATGATTT
*
379245 AAATATTTAATGATTTAATACTAATAATAATGATTTGATACTAA
1 AAATATTTAATGATTTAATA-T-ATAATAATGATTTAATACTAA
379289 AAATCATTGT
Statistics
Matches: 532, Mismatches: 86, Indels: 144
0.70 0.11 0.19
Matches are distributed among these distances:
63 14 0.03
64 19 0.04
65 9 0.02
66 51 0.10
67 10 0.02
68 10 0.02
69 31 0.06
70 6 0.01
71 35 0.07
72 87 0.16
73 8 0.02
74 52 0.10
75 88 0.17
76 34 0.06
77 44 0.08
78 26 0.05
79 3 0.01
80 3 0.01
81 2 0.00
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (72 bp):
AAATATTTAATGATTTAATATATAATAATGATTTAATACTAATAATTTATAATAATGATTTAATA
ATGATTT
Found at i:381458 original size:15 final size:14
Alignment explanation
Indices: 381433--381463 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
381423 TTCAACACAA
381433 AACTTTAATATAAT
1 AACTTTAATATAAT
381447 AACTTATAATATAAT
1 AACTT-TAATATAAT
381462 AA
1 AA
381464 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:381471 original size:16 final size:16
Alignment explanation
Indices: 381438--381484 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
381428 CACAAAACTT
*
381438 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
381453 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
381469 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
381485 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:381599 original size:32 final size:33
Alignment explanation
Indices: 381525--381605 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
381515 CCAAACCCTT
*
381525 AAAC-AACTAATAAAATATTTTTTATATAACTA
1 AAACTAACTAATAAACTATTTTTTATATAACTA
381557 AAACTAACTAATAAACTATTTTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTTTTT-A-TATAACTA
*
381590 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
381606 TACTAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
32 15 0.34
33 22 0.50
34 2 0.05
35 5 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.38
Consensus pattern (33 bp):
AAACTAACTAATAAACTATTTTTTATATAACTA
Found at i:381736 original size:45 final size:48
Alignment explanation
Indices: 381646--381736 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 48
381636 CAACAAACAA
381646 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
1 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
*
381694 ATATAAC-TAACTA-TTAAC-AA-AACAAACTAATT-AATTATTTTTT
1 ATATAACTTAACTATTTAACTAACAA-AAACTAATTAAATAATTTTTT
381737 AACTATATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
44 12 0.29
45 11 0.27
46 5 0.12
47 6 0.15
48 7 0.17
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (48 bp):
ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
Found at i:381805 original size:41 final size:40
Alignment explanation
Indices: 381717--381805 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
381707 TTAACAAAAC
* *
381717 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
381758 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
381799 AAACTAA
1 AAACTAA
381806 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:381870 original size:16 final size:18
Alignment explanation
Indices: 381841--381879 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
381831 ACTAATTAAC
*
381841 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
381859 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
381875 ATTTA
1 ATTTA
381880 CCTTATCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:381928 original size:16 final size:17
Alignment explanation
Indices: 381904--381935 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
381894 CTTCTTCTTA
381904 CTTTCCTTTCTTTCTCC
1 CTTTCCTTTCTTTCTCC
381921 CTTT-CTTTCTTTCTC
1 CTTTCCTTTCTTTCTC
381936 GGCTGCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (17 bp):
CTTTCCTTTCTTTCTCC
Found at i:382237 original size:29 final size:29
Alignment explanation
Indices: 382195--382260 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
382185 GTGACGCCGG
**
382195 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCCAGACTACAT
*
382224 GGCGACCTACAAGGTCGCCCAGACTGCAT
1 GGCGACCTACAAGGTCGCCCAGACTACAT
382253 GGCGACCT
1 GGCGACCT
382261 CTCCATTGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.23, C:0.33, G:0.30, T:0.14
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCCAGACTACAT
Found at i:382288 original size:32 final size:32
Alignment explanation
Indices: 382247--382328 Score: 164
Period size: 32 Copynumber: 2.6 Consensus size: 32
382237 GTCGCCCAGA
382247 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
382279 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
382311 CTGCATGGCGACCTCTCC
1 CTGCATGGCGACCTCTCC
382329 TCGTATAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.10, C:0.37, G:0.27, T:0.27
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
Found at i:382406 original size:20 final size:20
Alignment explanation
Indices: 382383--382427 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
382373 TATATGGCTT
382383 GTATGGCTCGTATGTCACCC
1 GTATGGCTCGTATGTCACCC
*
382403 GTATGGCTCGTATGTCTCCC
1 GTATGGCTCGTATGTCACCC
382423 GTATG
1 GTATG
382428 TCGCCTGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.13, C:0.27, G:0.27, T:0.33
Consensus pattern (20 bp):
GTATGGCTCGTATGTCACCC
Found at i:382470 original size:29 final size:29
Alignment explanation
Indices: 382428--382487 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
382418 CTCCCGTATG
*
382428 TCGCCTGGATTGCATGGCGTCCTACAAGA
1 TCGCCTGGATTGCATGGCATCCTACAAGA
*
382457 TCGCCTGGATTGCATGGCATCCTACGAGA
1 TCGCCTGGATTGCATGGCATCCTACAAGA
382486 TC
1 TC
382488 ACTGTAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.20, C:0.28, G:0.27, T:0.25
Consensus pattern (29 bp):
TCGCCTGGATTGCATGGCATCCTACAAGA
Found at i:385291 original size:3 final size:3
Alignment explanation
Indices: 385283--385313 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
385273 TCCACTATTC
385283 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
385314 CTCTGGTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:386191 original size:24 final size:24
Alignment explanation
Indices: 386147--386195 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
386137 ACTGTCTCAA
*
386147 CATCCCCAATAGAAGACTTGGAAC
1 CATCCCCAATACAAGACTTGGAAC
*
386171 CATCTCCCAATACAAG-TTTGGAAC
1 CATC-CCCAATACAAGACTTGGAAC
386195 C
1 C
386196 TTCAATGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.35, C:0.31, G:0.14, T:0.20
Consensus pattern (24 bp):
CATCCCCAATACAAGACTTGGAAC
Found at i:388036 original size:26 final size:26
Alignment explanation
Indices: 387989--388038 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
387979 GGATAAATTC
*
387989 ATAAAATTTTAAGTAGAAAAAAACTT
1 ATAAAATTTTAAGGAGAAAAAAACTT
* *
388015 ATAAAATTTTAAGGATACAAAAAC
1 ATAAAATTTTAAGGAGAAAAAAAC
388039 ATATTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (26 bp):
ATAAAATTTTAAGGAGAAAAAAACTT
Found at i:388868 original size:12 final size:12
Alignment explanation
Indices: 388851--388875 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
388841 ACCTTACCTC
388851 ATTATATATGAG
1 ATTATATATGAG
388863 ATTATATATGAG
1 ATTATATATGAG
388875 A
1 A
388876 ACAAGGACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (12 bp):
ATTATATATGAG
Found at i:394638 original size:2 final size:2
Alignment explanation
Indices: 394631--394655 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
394621 AAAATGAAAT
394631 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
394656 GAGTTAACGA
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:399143 original size:20 final size:18
Alignment explanation
Indices: 399120--399163 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
399110 TTATTGATCT
399120 ATTATAAAATGATCATTAAA
1 ATTATAAAAT-ATCA-TAAA
*
399140 ATTATTAAACTATCATAAA
1 ATTA-TAAAATATCATAAA
399159 ATTAT
1 ATTAT
399164 CTCAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 1 0.05
19 8 0.36
20 8 0.36
21 5 0.23
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (18 bp):
ATTATAAAATATCATAAA
Found at i:399145 original size:31 final size:32
Alignment explanation
Indices: 399099--399160 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
399089 TGGTAAGGTA
* * *
399099 ATCATAAAAACTTATTGATCTATTATAAAATG
1 ATCATAAAAACTTATTAAACTATCATAAAATG
*
399131 ATCATTAAAA-TTATTAAACTATCATAAAAT
1 ATCATAAAAACTTATTAAACTATCATAAAAT
399161 TATCTCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.37
Consensus pattern (32 bp):
ATCATAAAAACTTATTAAACTATCATAAAATG
Found at i:402236 original size:3 final size:3
Alignment explanation
Indices: 402228--402267 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
402218 TGGCCTTCAT
402228 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
402268 GCATCTTATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:408661 original size:64 final size:63
Alignment explanation
Indices: 408576--408736 Score: 207
Period size: 64 Copynumber: 2.5 Consensus size: 63
408566 TTGTTTAAGG
* *
408576 TGCATCGATGCACATGAAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATATGAAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * * * *
408640 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATATGAAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
*
408704 TGCATCGATGCATGATGTAGTGCATCGATGCAT
1 TGCATCGATGCAT-ATGAAGTGCATCGATGCAT
408737 ACCTCCATTA
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 61 0.72
65 23 0.27
66 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATATGAAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:409382 original size:103 final size:103
Alignment explanation
Indices: 409203--409420 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
409193 GTAGAGGGTC
* *
409203 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGCCTGGTGAGACACATAC
409268 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* * *
409306 TATGTGGTTCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAGGCCTGGTGAGACATATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGCCTGGTGAGACACATAC
409371 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
409409 TATGTGGTCCTT
1 TATGTGGTCCTT
409421 ATGGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGCCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:409472 original size:23 final size:23
Alignment explanation
Indices: 409437--409499 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
409427 ATTATTATAT
*
409437 GGCACTACAGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
409460 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
409483 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
409500 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:415599 original size:64 final size:63
Alignment explanation
Indices: 415514--415674 Score: 164
Period size: 64 Copynumber: 2.5 Consensus size: 63
415504 TTGTTTAAGG
* * * *
415514 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTAA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTAA
* * * *
415578 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTAA
* * *
415642 TACATCGATACAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
415675 ACCTCCATTA
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
63 1 0.01
64 59 0.72
65 21 0.26
66 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTAA
Found at i:416314 original size:103 final size:103
Alignment explanation
Indices: 416135--416360 Score: 427
Period size: 103 Copynumber: 2.2 Consensus size: 103
416125 GTAGAGGGTC
*
416135 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACATATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
416200 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
416238 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
416303 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
416341 TATGTGGTCCTT-ATGGACAT
1 TATGTGGTCCTTCA-GGACAT
416361 TATTATATGG
Statistics
Matches: 121, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
102 1 0.01
103 120 0.99
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:416402 original size:23 final size:23
Alignment explanation
Indices: 416369--416431 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
416359 ATTATTATAT
*
416369 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACAC
* *
416392 GGCACTCCGGTGCAATTCTACAT
1 GGCACTACGGTGCAATTCTACAC
416415 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
416432 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACAC
Found at i:421977 original size:31 final size:31
Alignment explanation
Indices: 421923--421989 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
421913 TGTAATAAAA
*
421923 TCCCCCAACATTTAGTCCATTTGCAAAATGG
1 TCCCCCAACATTTAGTACATTTGCAAAATGG
* ** *
421954 TCCCCCAACATTTATTATGTTTGCAATATGG
1 TCCCCCAACATTTAGTACATTTGCAAAATGG
421985 TCCCC
1 TCCCC
421990 GACCATTTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.33
Consensus pattern (31 bp):
TCCCCCAACATTTAGTACATTTGCAAAATGG
Found at i:429925 original size:18 final size:19
Alignment explanation
Indices: 429904--429978 Score: 68
Period size: 18 Copynumber: 4.0 Consensus size: 19
429894 TTCGTTTTGC
429904 AAAAAAACCGG-TTTTTTT
1 AAAAAAACCGGATTTTTTT
*
429922 AAAAAAACCGGATTTTTTCGG
1 AAAAAAACCGGATTTTTT--T
* *
429943 ATAAAAATCCAG-TTTTTTT
1 A-AAAAAACCGGATTTTTTT
429962 --AAAAACCGGATTTTTTT
1 AAAAAAACCGGATTTTTTT
429979 CCGGATAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
16 7 0.15
17 7 0.15
18 11 0.24
19 6 0.13
21 7 0.15
22 8 0.17
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (19 bp):
AAAAAAACCGGATTTTTTT
Found at i:429968 original size:38 final size:41
Alignment explanation
Indices: 429905--430000 Score: 144
Period size: 40 Copynumber: 2.4 Consensus size: 41
429895 TCGTTTTGCA
*
429905 AAAAAACCGGTTTTTTTAAAAAAACCGGA-TTTTTT-CGGAT
1 AAAAAACCAGTTTTTTT-AAAAAACCGGATTTTTTTCCGGAT
*
429945 AAAAATCCAGTTTTTTT-AAAAACCGGATTTTTTTCCGGAT
1 AAAAAACCAGTTTTTTTAAAAAACCGGATTTTTTTCCGGAT
429985 AAAAAACCAGTTTTTT
1 AAAAAACCAGTTTTTT
430001 ATCCGGTTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
38 10 0.20
39 6 0.12
40 35 0.69
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (41 bp):
AAAAAACCAGTTTTTTTAAAAAACCGGATTTTTTTCCGGAT
Found at i:429992 original size:24 final size:26
Alignment explanation
Indices: 429962--430072 Score: 115
Period size: 26 Copynumber: 4.4 Consensus size: 26
429952 CAGTTTTTTT
429962 AAAAACCGGATTTTTT-TCCGG-AT-A
1 AAAAACCGG-TTTTTTATCCGGTATGA
* *
429986 AAAAACCAGTTTTTTATCCGGTTTGA
1 AAAAACCGGTTTTTTATCCGGTATGA
*
430012 AAAAACCGGTTTTTTATCCGGTTTGAA
1 AAAAACCGGTTTTTTATCCGGTATG-A
* * *
430039 AAAAATCGGTTTTTAATCCTGTA--A
1 AAAAACCGGTTTTTTATCCGGTATGA
430063 AAAAACCGGT
1 AAAAACCGGT
430073 CGTTCAATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
23 6 0.08
24 23 0.31
25 1 0.01
26 25 0.33
27 20 0.27
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (26 bp):
AAAAACCGGTTTTTTATCCGGTATGA
Found at i:430057 original size:27 final size:26
Alignment explanation
Indices: 429962--430057 Score: 117
Period size: 26 Copynumber: 3.7 Consensus size: 26
429952 CAGTTTTTTT
*
429962 AAAAACCGGATTTTTT-TCCGG-AT-A
1 AAAAACCGG-TTTTTTATCCGGTTTGA
*
429986 AAAAACCAGTTTTTTATCCGGTTTGA
1 AAAAACCGGTTTTTTATCCGGTTTGA
430012 AAAAACCGGTTTTTTATCCGGTTTGAA
1 AAAAACCGGTTTTTTATCCGGTTTG-A
* *
430039 AAAAATCGGTTTTTAATCC
1 AAAAACCGGTTTTTTATCC
430058 TGTAAAAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.10
24 13 0.21
25 1 0.02
26 25 0.40
27 18 0.29
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (26 bp):
AAAAACCGGTTTTTTATCCGGTTTGA
Found at i:433580 original size:23 final size:24
Alignment explanation
Indices: 433549--433597 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
433539 AAAAATAACA
* *
433549 TGGTGGCATGCACTG-TTTTTTGC
1 TGGTAGCATACACTGCTTTTTTGC
433572 TGGTAGCATACACTGCTTTTTTGC
1 TGGTAGCATACACTGCTTTTTTGC
433596 TG
1 TG
433598 ACGCAGAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.12, C:0.18, G:0.27, T:0.43
Consensus pattern (24 bp):
TGGTAGCATACACTGCTTTTTTGC
Found at i:446409 original size:58 final size:58
Alignment explanation
Indices: 446327--446436 Score: 168
Period size: 58 Copynumber: 1.9 Consensus size: 58
446317 TTAAATGACC
*
446327 GTGTTAATCGGGAATGTCTAAGGAAAGACAGCCTAATATAAGGCTAAGAAAAATGTAT
1 GTGTTAACCGGGAATGTCTAAGGAAAGACAGCCTAATATAAGGCTAAGAAAAATGTAT
* **
446385 GTGTTAACCAGGG-ATGTCTAAGGAAAGACAGGCTAATATAAGTTTAAGAAAA
1 GTGTTAACC-GGGAATGTCTAAGGAAAGACAGCCTAATATAAGGCTAAGAAAA
446437 GACGCTACCA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
58 44 0.94
59 3 0.06
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.24
Consensus pattern (58 bp):
GTGTTAACCGGGAATGTCTAAGGAAAGACAGCCTAATATAAGGCTAAGAAAAATGTAT
Found at i:455428 original size:51 final size:52
Alignment explanation
Indices: 455352--455456 Score: 167
Period size: 51 Copynumber: 2.0 Consensus size: 52
455342 AAAATTTAAC
* * *
455352 AAAGATATATTTTATGAAACACATCTTCCTCC-TTTTGTCATACAATAATAT
1 AAAGATATATTTTATAAAACACATCTTACTCCTTTTTGTCATACAAGAATAT
*
455403 AAAGATATATTTTATAAAACACATCTTACTCCTTTTTTTCATACAAGAATAT
1 AAAGATATATTTTATAAAACACATCTTACTCCTTTTTGTCATACAAGAATAT
455455 AA
1 AA
455457 GAATAAGACG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
51 30 0.61
52 19 0.39
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.39
Consensus pattern (52 bp):
AAAGATATATTTTATAAAACACATCTTACTCCTTTTTGTCATACAAGAATAT
Found at i:458795 original size:25 final size:22
Alignment explanation
Indices: 458766--458811 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
458756 TTTTTAACTC
458766 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
458791 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
458812 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:459858 original size:9 final size:9
Alignment explanation
Indices: 459844--459870 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
459834 AAGTATGGGT
459844 AGAAATATC
1 AGAAATATC
459853 AGAAATATC
1 AGAAATATC
459862 AGAAATATC
1 AGAAATATC
459871 CGAGTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (9 bp):
AGAAATATC
Found at i:462494 original size:10 final size:10
Alignment explanation
Indices: 462481--462528 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
462471 AAATTTTAGC
462481 TTTTTTGGCT
1 TTTTTTGGCT
462491 TTTTTTGGCTT
1 TTTTTTGGC-T
*
462502 TTTTTTGCCT
1 TTTTTTGGCT
*
462512 TGTTTTTTG-T
1 T-TTTTTGGCT
462522 TTTTTTG
1 TTTTTTG
462529 AAAAAAATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
9 5 0.16
10 13 0.41
11 14 0.44
ACGTcount: A:0.00, C:0.08, G:0.17, T:0.75
Consensus pattern (10 bp):
TTTTTTGGCT
Found at i:462495 original size:11 final size:11
Alignment explanation
Indices: 462481--462520 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
462471 AAATTTTAGC
462481 TTTTTTGGC-T
1 TTTTTTGGCTT
462491 TTTTTTGGCTT
1 TTTTTTGGCTT
*
462502 TTTTTTGCCTT
1 TTTTTTGGCTT
462513 GTTTTTTG
1 -TTTTTTG
462521 TTTTTTTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 9 0.33
11 11 0.41
12 7 0.26
ACGTcount: A:0.00, C:0.10, G:0.17, T:0.72
Consensus pattern (11 bp):
TTTTTTGGCTT
Found at i:462505 original size:21 final size:21
Alignment explanation
Indices: 462481--462527 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
462471 AAATTTTAGC
*
462481 TTTTTTGGCTT-TTTTTGGCTT
1 TTTTTTGCCTTGTTTTTGG-TT
*
462502 TTTTTTGCCTTGTTTTTTGTT
1 TTTTTTGCCTTGTTTTTGGTT
462523 TTTTT
1 TTTTT
462528 GAAAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.00, C:0.09, G:0.15, T:0.77
Consensus pattern (21 bp):
TTTTTTGCCTTGTTTTTGGTT
Found at i:463396 original size:25 final size:22
Alignment explanation
Indices: 463367--463412 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
463357 TTTTTAACCC
463367 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
463392 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
463413 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:467981 original size:25 final size:22
Alignment explanation
Indices: 467952--467997 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
467942 TTTTTAACCC
467952 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
467977 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
467998 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:470582 original size:16 final size:16
Alignment explanation
Indices: 470558--470599 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
470548 AACAAACATA
*
470558 AAAAAACATTTCCATT
1 AAAAAACATATCCATT
*
470574 AAGAAACATATCCATT
1 AAAAAACATATCCATT
470590 AAAAAACATA
1 AAAAAACATA
470600 ATAAAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (16 bp):
AAAAAACATATCCATT
Found at i:472778 original size:3 final size:3
Alignment explanation
Indices: 472770--472803 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
472760 ATAATTTAAC
*
472770 ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
472804 AAGAAATGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:474393 original size:35 final size:35
Alignment explanation
Indices: 474347--474415 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
474337 CTTGAGCTCG
*
474347 GATTGATAACAATTAACGCCCTTAGCAACTTCTCA
1 GATTGATAACAATTAACACCCTTAGCAACTTCTCA
*
474382 GATTGATAACAATTAACACCCTTAGCAGCTTCTC
1 GATTGATAACAATTAACACCCTTAGCAACTTCTC
474416 TTAGATTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (35 bp):
GATTGATAACAATTAACACCCTTAGCAACTTCTCA
Found at i:476768 original size:27 final size:27
Alignment explanation
Indices: 476730--476788 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
476720 TTCAAATCTA
476730 TCTTGAGTTGATGAAGGGGATTTTGAT
1 TCTTGAGTTGATGAAGGGGATTTTGAT
476757 TCTTGAGTTGATGAAGGGGATTTTGAT
1 TCTTGAGTTGATGAAGGGGATTTTGAT
476784 TCTTG
1 TCTTG
476789 TGTTTTAGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.20, C:0.05, G:0.32, T:0.42
Consensus pattern (27 bp):
TCTTGAGTTGATGAAGGGGATTTTGAT
Found at i:477088 original size:23 final size:23
Alignment explanation
Indices: 477061--477110 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
477051 TTATTGGAAA
477061 TATGATAAAGGTTATTTAGTAAT
1 TATGATAAAGGTTATTTAGTAAT
*
477084 TATGATGAAGGTTATTTAGTAAT
1 TATGATAAAGGTTATTTAGTAAT
477107 TATG
1 TATG
477111 GAATGAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (23 bp):
TATGATAAAGGTTATTTAGTAAT
Found at i:481568 original size:44 final size:46
Alignment explanation
Indices: 481520--481629 Score: 127
Period size: 47 Copynumber: 2.4 Consensus size: 46
481510 GTAACCATGC
*
481520 AAATAAGCTTATGAGCTTACGGAA-T-AATGGCAAGTA-TATAGGAA
1 AAATAAGCTTACGAGCTTACGGAATTAAATGGCAAGTATTATA-GAA
* * * * *
481564 AAATAAGCTTACGAGTTTATGGAATTTAAATGGTAAGTATTTTAGTA
1 AAATAAGCTTACGAGCTTACGGAA-TTAAATGGCAAGTATTATAGAA
481611 AAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTA
481630 TGGGATAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
44 21 0.38
46 1 0.02
47 30 0.55
48 3 0.05
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTACGGAATTAAATGGCAAGTATTATAGAA
Found at i:484387 original size:18 final size:17
Alignment explanation
Indices: 484364--484432 Score: 68
Period size: 18 Copynumber: 3.9 Consensus size: 17
484354 AATATATATT
484364 ATAAGAAGAAGAAAAAAC
1 ATAAGAAGAA-AAAAAAC
*
484382 ATAAGAAGAAAAAAAAT
1 ATAAGAAGAAAAAAAAC
* *
484399 AGAAAAAGAAAATGAAAAC
1 ATAAGAAGAAAA--AAAAC
*
484418 -GAAGAAGAAAAAAAA
1 ATAAGAAGAAAAAAAA
484433 TGAAAACGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
16 4 0.09
17 16 0.36
18 20 0.45
19 4 0.09
ACGTcount: A:0.75, C:0.03, G:0.16, T:0.06
Consensus pattern (17 bp):
ATAAGAAGAAAAAAAAC
Found at i:484410 original size:6 final size:6
Alignment explanation
Indices: 484387--484463 Score: 54
Period size: 6 Copynumber: 13.3 Consensus size: 6
484377 AAAACATAAG
* * * *
484387 AAGAAA AA-AAA TAGAAA AAGAAA ATGAAA ACGAAG AAG-AA AA-AAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
* * *
484432 ATGAAA ACGAGA AAG-AA AAGAAA AAGAGAA AA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGA-AA AA
484464 AAATGAGAGA
Statistics
Matches: 54, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
5 14 0.26
6 36 0.67
7 4 0.07
ACGTcount: A:0.75, C:0.03, G:0.18, T:0.04
Consensus pattern (6 bp):
AAGAAA
Found at i:484432 original size:22 final size:23
Alignment explanation
Indices: 484402--484455 Score: 85
Period size: 22 Copynumber: 2.4 Consensus size: 23
484392 AAAAAATAGA
484402 AAAAGAAAATGAAAACGA-AGAAG
1 AAAAGAAAATGAAAACGAGA-AAG
484425 AAAA-AAAATGAAAACGAGAAAG
1 AAAAGAAAATGAAAACGAGAAAG
484447 AAAAGAAAA
1 AAAAGAAAA
484456 AGAGAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.74, C:0.04, G:0.19, T:0.04
Consensus pattern (23 bp):
AAAAGAAAATGAAAACGAGAAAG
Found at i:484438 original size:34 final size:33
Alignment explanation
Indices: 484384--484469 Score: 111
Period size: 34 Copynumber: 2.5 Consensus size: 33
484374 GAAAAAACAT
484384 AAGAAGAAAAAAAATAGAAAAAGA-AAATGAAAACG
1 AAGAAGAAAAAAAAT-GAAAAAGAGAAA-GAAAA-G
*
484419 AAGAAGAAAAAAAATGAAAACGAGAAAGAAAAG
1 AAGAAGAAAAAAAATGAAAAAGAGAAAGAAAAG
*
484452 AAAAAGAGAAAAAAATGA
1 AAGAAGA-AAAAAAATGA
484470 GAGATGAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
33 7 0.15
34 22 0.47
35 18 0.38
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (33 bp):
AAGAAGAAAAAAAATGAAAAAGAGAAAGAAAAG
Found at i:484454 original size:51 final size:50
Alignment explanation
Indices: 484368--484485 Score: 127
Period size: 51 Copynumber: 2.3 Consensus size: 50
484358 TATATTATAA
*
484368 GAAGAAGAAAAAACAT-AAGAAGAAAAAAAATAGAAAAAGA-AAATGAAAAC
1 GAAGAAGAAAAAAAATGAAGAAGAAAAAAAATAGAAAAAGAGAAA--AAAAC
* *
484418 GAAGAAGAAAAAAAATGAA-AACGAGAAAGAAA-AGAAAAAGAGAAAAAAAT
1 GAAGAAGAAAAAAAATGAAGAA-GA-AAAAAAATAGAAAAAGAGAAAAAAAC
*
484468 GAGAGATGAAAAAAAATG
1 GA-AGAAGAAAAAAAATG
484486 TTTCACTTGT
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
50 23 0.39
51 27 0.46
52 9 0.15
ACGTcount: A:0.72, C:0.03, G:0.19, T:0.06
Consensus pattern (50 bp):
GAAGAAGAAAAAAAATGAAGAAGAAAAAAAATAGAAAAAGAGAAAAAAAC
Found at i:488700 original size:47 final size:45
Alignment explanation
Indices: 488606--488731 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
488596 GTAACCATGC
* * *
488606 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * **
488650 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGTTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
*
488697 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
488732 AGATTTTATA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 22 0.31
45 11 0.15
46 1 0.01
47 37 0.52
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:490117 original size:15 final size:15
Alignment explanation
Indices: 490097--490127 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
490087 CAACAAATAG
490097 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
490112 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
490127 A
1 A
490128 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:494896 original size:3 final size:3
Alignment explanation
Indices: 494888--494913 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
494878 CAAGTGGGGA
494888 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
494914 GTTATTTTTC
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:496529 original size:15 final size:15
Alignment explanation
Indices: 496506--496536 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
496496 TTATATTATA
*
496506 GAGATAGAGAATATT
1 GAGAGAGAGAATATT
496521 GAGAGAGAGAATATT
1 GAGAGAGAGAATATT
496536 G
1 G
496537 TTTTCATCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.23
Consensus pattern (15 bp):
GAGAGAGAGAATATT
Found at i:500103 original size:8 final size:8
Alignment explanation
Indices: 500090--500121 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
500080 TCATCATGTA
500090 TTATGAAT
1 TTATGAAT
500098 TTATGAAT
1 TTATGAAT
500106 TTATGAAT
1 TTATGAAT
*
500114 TGATGAAT
1 TTATGAAT
500122 GTGACACTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (8 bp):
TTATGAAT
Found at i:502222 original size:29 final size:29
Alignment explanation
Indices: 502180--502263 Score: 116
Period size: 29 Copynumber: 2.9 Consensus size: 29
502170 GTGAAGCCGT
* *
502180 AGGTTGTCGTGCACTCCGGGCGACCAAGG
1 AGGTCGTCATGCACTCCGGGCGACCAAGG
*
502209 AGGTCGTCATGCACTCCGGGCGACCAAGT
1 AGGTCGTCATGCACTCCGGGCGACCAAGG
* *
502238 ATGTCGCCATGCACTCCGGGC-ACCAA
1 AGGTCGTCATGCACTCCGGGCGACCAA
502264 TAAACCGAGC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 5 0.10
29 45 0.90
ACGTcount: A:0.20, C:0.32, G:0.31, T:0.17
Consensus pattern (29 bp):
AGGTCGTCATGCACTCCGGGCGACCAAGG
Found at i:502858 original size:28 final size:30
Alignment explanation
Indices: 502818--502879 Score: 110
Period size: 28 Copynumber: 2.1 Consensus size: 30
502808 AATTTAGTTA
502818 ATTAGTTTGTTAGTTTAAG-T-TATATTAT
1 ATTAGTTTGTTAGTTTAAGTTATATATTAT
502846 ATTAGTTTGTTAGTTTAAGTTATATATTAT
1 ATTAGTTTGTTAGTTTAAGTTATATATTAT
502876 ATTA
1 ATTA
502880 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (30 bp):
ATTAGTTTGTTAGTTTAAGTTATATATTAT
Found at i:503378 original size:15 final size:16
Alignment explanation
Indices: 503352--503381 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
503342 AGATAATTTA
503352 TGTTTAAAAAATATTG
1 TGTTTAAAAAATATTG
503368 TGTTT-AAAAATATT
1 TGTTTAAAAAATATT
503382 TAGTAAAACA
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:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (16 bp):
TGTTTAAAAAATATTG
Done.