Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008585.1 Hibiscus syriacus cultivar Beakdansim tig00111521_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: 188024
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2221 original size:29 final size:29
Alignment explanation
Indices: 2187--2245 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2177 CCTAAATTAA
2187 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2216 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2245 T
1 T
2246 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:3235 original size:88 final size:86
Alignment explanation
Indices: 3136--3320 Score: 334
Period size: 88 Copynumber: 2.1 Consensus size: 86
3126 TTATTTTTCA
3136 GAGCATTTTAGCCTCTAATGTTTTAATTTTGGGCAAAAATATCTCCAATGTTTGACTAAATAGTA
1 GAGCATTTTAGCCTCTAATGTTTTAATTTTGGGCAAAAATATCTCCAAT-TTTGACTAAATAGTA
3201 ACTTTGACTCTTATTTTCTATTG
65 ACTTTGACTCTTA-TTTCTATTG
**
3224 GAGCATTTTAGCCTCTAATGTTTTAATTTTGGTTAAAAATATCTCCAATTTTGACTAAATAGTAA
1 GAGCATTTTAGCCTCTAATGTTTTAATTTTGGGCAAAAATATCTCCAATTTTGACTAAATAGTAA
3289 CTTTGACTCTTATTTCTATTG
66 CTTTGACTCTTATTTCTATTG
3310 GAGCATTTTAG
1 GAGCATTTTAG
3321 TCTCAACGTT
Statistics
Matches: 95, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
86 20 0.21
87 28 0.29
88 47 0.49
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.44
Consensus pattern (86 bp):
GAGCATTTTAGCCTCTAATGTTTTAATTTTGGGCAAAAATATCTCCAATTTTGACTAAATAGTAA
CTTTGACTCTTATTTCTATTG
Found at i:3432 original size:88 final size:84
Alignment explanation
Indices: 3185--3435 Score: 236
Period size: 88 Copynumber: 2.9 Consensus size: 84
3175 TATCTCCAAT
* * *
3185 GTTTGACTAAATAGTAACTTTGACTCTTATTTTCTATTGGAGCATTTTAGCCTCTAATGTTTTAA
1 GTTTGACTAAATAGTAACTTT-ACTCTTA-TTTCTATTGGAGCATTTTAGCC-CCAACGTTTCAA
** ** * **
3250 TTTTGGTTAAAAATATCTCCAA-
63 TTTAAGACAAAAA-ATTTATAAC
* * * *
3272 TTTTGACTAAATAGTAACTTTGACTCTTATTTCTATTGGAGCATTTTAGTCTCAACGTTTCAGTT
1 GTTTGACTAAATAGTAACTTT-ACTCTTATTTCTATTGGAGCATTTTAGCCCCAACGTTTCAATT
3337 TAAGACAAAAAATTTATAAC
65 TAAGACAAAAAATTTATAAC
* * *
3357 GTTTGACTAAATAGTAAC-TTATCTCTTATTCTTTTTTATTTGAGCATTTTTGCCCCAACGTTTC
1 GTTTGACTAAATAGTAACTTTA-CTCTTA----TTTCTATTGGAGCATTTTAGCCCCAACGTTTC
*
3421 AATTTAGGACAAAAA
61 AATTTAAGACAAAAA
3436 TAACACTCTT
Statistics
Matches: 136, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
83 1 0.01
84 13 0.10
85 33 0.24
86 21 0.15
87 28 0.21
88 40 0.29
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (84 bp):
GTTTGACTAAATAGTAACTTTACTCTTATTTCTATTGGAGCATTTTAGCCCCAACGTTTCAATTT
AAGACAAAAAATTTATAAC
Found at i:4931 original size:31 final size:31
Alignment explanation
Indices: 4885--4957 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
4875 TAAACTATTC
*
4885 ATATGACCACTTAACTATAGGATTGTTGTAG
1 ATATGACCACCTAACTATAGGATTGTTGTAG
*
4916 ATATAACCACCTAACTATAGGATTGTTGTAG
1 ATATGACCACCTAACTATAGGATTGTTGTAG
4947 ATATGACCACC
1 ATATGACCACC
4958 ATACTTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (31 bp):
ATATGACCACCTAACTATAGGATTGTTGTAG
Found at i:8461 original size:13 final size:13
Alignment explanation
Indices: 8434--8471 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
8424 TACATACAAC
**
8434 AAAATAAATTGAT
1 AAAATAAATAAAT
8447 AAAATAAATAAAT
1 AAAATAAATAAAT
8460 -AAATAAATAAAT
1 AAAATAAATAAAT
8472 CGAATATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:10527 original size:3 final size:3
Alignment explanation
Indices: 10519--10577 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
10509 TAAGCAAAAT
10519 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
10567 ATA ATA ATA AT
1 ATA ATA ATA AT
10578 TACAATTAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:11151 original size:129 final size:129
Alignment explanation
Indices: 10786--11639 Score: 1460
Period size: 129 Copynumber: 6.6 Consensus size: 129
10776 CGTCTAAGGG
* * * * * * * *
10786 TGACATGGTTCCTACGTGATGAGGAAATCTGGTCAAGGG-TTGACACTGCTCATACGTGATAAAG
1 TGACACGGCTCCTACATGATGAGGAGATCTGGTC-TGGGAATGACACGGCTCATACGTGATGAAG
* * *
10850 AGTTCTTGGCCATCTTAAGGTGATAACACAGTTCCTACGTGATGAGGACGGCTGGTTATCTACGG
65 AGTTC-TGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGG
10915 T
129 T
*
10916 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGAATGACACGGCTCATACGTGATGAAG
1 TGACACGGCTCCTACATGATGAGGAGATCTGGTCT-GGGAATGACACGGCTCATACGTGATGAAG
10981 AGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
65 AGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
*
11046 TGACACGGCTCCTATATGATGAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACATGATGAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGA
11111 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
66 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
11175 TGACACGGCTCCTACATGATGAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACATGATGAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGA
* *
11240 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTAAGTTATGAGGACGGCTGGTTATCTATGGT
66 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
*
11304 TGACACGACTCCTACATGATGAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACATGATGAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGA
11369 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
66 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
11433 TGACACGGCTCCTACATGATGAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACATGATGAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGA
11498 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
66 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
* * * * *
11562 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAAGA
1 TGACACGGCTCCTACATGATGAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGA
*
11627 CG-GCTGGCCATCT
66 -GTTCTGGCCATCT
11640 TTAGGAGTTA
Statistics
Matches: 696, Mismatches: 25, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
129 544 0.78
130 125 0.18
131 27 0.04
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (129 bp):
TGACACGGCTCCTACATGATGAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGA
GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
Found at i:11692 original size:28 final size:28
Alignment explanation
Indices: 11652--11748 Score: 83
Period size: 28 Copynumber: 3.4 Consensus size: 28
11642 AGGAGTTATG
* *
11652 GTTTCAAGAGAAACCA-AATTAAAGATTT
1 GTTTCAAAAGAAA-CAGAATCAAAGATTT
*
11680 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGAATCAAAGATTT
*
11708 GTTTCAAGAA-AAACA-AGCTCAAAGATAATGT
1 GTTTCAA-AAGAAACAGA-ATCAAAGAT--T-T
11739 GTTTCAAAAG
1 GTTTCAAAAG
11749 CAACTGTCTC
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
27 3 0.05
28 43 0.73
29 2 0.03
30 3 0.05
31 8 0.14
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.26
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGAATCAAAGATTT
Found at i:11745 original size:31 final size:28
Alignment explanation
Indices: 11672--11748 Score: 95
Period size: 28 Copynumber: 2.6 Consensus size: 28
11662 AAACCAAATT
11672 AAAGATTTGTTTCAAAAGAAACAGACTC
1 AAAGATTTGTTTCAAAAGAAACAGACTC
11700 AAAGATTTGTTTCAAGAA-AAACA-AGCTC
1 AAAGATTTGTTTCAA-AAGAAACAGA-CTC
11728 AAAGATAATGTGTTTCAAAAG
1 AAAGAT--T-TGTTTCAAAAG
11749 CAACTGTCTC
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
27 1 0.02
28 29 0.67
29 2 0.05
30 3 0.07
31 8 0.19
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.26
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAGACTC
Found at i:11939 original size:66 final size:64
Alignment explanation
Indices: 11750--11939 Score: 159
Period size: 66 Copynumber: 2.9 Consensus size: 64
11740 TTTCAAAAGC
** * *
11750 AACTGTCTCGAAAGAGACAAAATTCATTTCAAATGAAAC-AACTCAAAAGATG-ACGTTTAAAGG
1 AACTGTCTC-AAAGAGACAAAATTCATTTCAAGGGAAACGATCTC-AAAGATGTATGTTTAAAGG
11813 G
64 G
* * ** * * * * * * *
11814 AATTGTCTCAAGCGAGACAAAATTTGTTTTTAAGGGAAACGTTCTCAAATATCTGTGTTTCATGG
1 AACTGTCTCAA-AGAGACAAAA-TTCATTTCAAGGGAAACGATCTCAAAGATGTATGTTTAAAGG
11879 G
64 G
* *
11880 AAACTGTCTCAAATGAGACAAAATTCATTTCGAGGGAAACGATCTCAAAGATGTTTGTTT
1 -AACTGTCTCAAA-GAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGTATGTTT
11940 TGTTTCAAGG
Statistics
Matches: 95, Mismatches: 25, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
63 2 0.02
64 17 0.18
65 17 0.18
66 40 0.42
67 19 0.20
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (64 bp):
AACTGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGTATGTTTAAAGGG
Found at i:12477 original size:130 final size:130
Alignment explanation
Indices: 12131--12496 Score: 336
Period size: 129 Copynumber: 2.8 Consensus size: 130
12121 GTATCTTAGT
*
12131 GAGACAAAATTTTGTTTCCAAA-GAAACAGACTC--AGATTTTTCTTCAAAAGAAACTGT-TTTA
1 GAGACAAAATTTTGTTT-CAAAGGAAACAGACTCAAAGATTTTT-TTCAAAAGAAATTGTCTTTA
* * * * * *
12192 AGGGATAAAACCTTGTTTCCAGAGAAACAAACTCAAAGATGATCTTGTTTTAAAAGAAAATGTTT
64 AGAGATAAAA-TTTGTTTCCAAAGAAACAAACTCAAAGATGATCATGTTTCAAAAGAAAATGTCT
*
12257 TAA
128 CAA
* * **** * * * **
12260 GAGACAAAA-TTCGTTTCAAGGGAAAC-GACTCAAAGATGACATTGAAAGGAAATTGTCTCATGC
1 GAGACAAAATTTTGTTTCAAAGGAAACAGACTCAAAGATTTTTTTCAAAAGAAATTGTCT-TTAA
* * * * * * **
12323 GAGACAAAATTTGTTT-TAATAGAAACGATCTCAAAGGTGGGT-AT-TTTCAAAAGAAGTTGTCT
65 GAGATAAAATTTGTTTCCAA-AGAAACAAACTCAAAGAT-GATCATGTTTCAAAAGAAAATGTCT
*
12385 CGA
128 CAA
*
12388 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTCTTTAAG
1 GAGACAAAATTTTGTTTCAAAGGAAACAGACTCAAAGATTTTTTTCAAAAGAAATTGTCTTTAAG
12453 AGATAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATGGATCA
66 AGATAAAA-TTTGTTTCCAAAGAAACAAACTCAAAGAT-GATCA
12497 CATCTCAAGT
Statistics
Matches: 179, Mismatches: 46, Indels: 22
0.72 0.19 0.09
Matches are distributed among these distances:
127 8 0.04
128 48 0.27
129 60 0.34
130 60 0.34
131 3 0.02
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (130 bp):
GAGACAAAATTTTGTTTCAAAGGAAACAGACTCAAAGATTTTTTTCAAAAGAAATTGTCTTTAAG
AGATAAAATTTGTTTCCAAAGAAACAAACTCAAAGATGATCATGTTTCAAAAGAAAATGTCTCAA
Found at i:12603 original size:118 final size:119
Alignment explanation
Indices: 12388--12609 Score: 263
Period size: 118 Copynumber: 1.9 Consensus size: 119
12378 GTTGTCTCGA
* *
12388 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTCTTTAAG
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTTCAAG
* *
12453 AGATAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATGGATCACATCTCAAGT
66 AGACAAAATTATGTTTCCAAAGAAACAAACTCAAAGATGGATCACATCTCAAGT
* * * **
12507 GAGACCAAA-TTTGTTTCAAATGAAACAATCTCAAA-AGTTAGTTTTTCATTAGAAACTGTC-TC
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGA-TT--TTTTTCAAAAGAAACTGTCTTC
* ** * *
12569 AAGAGACAACA-TATGTTTTTAAAGAAATAGACTCAAAGATG
63 AAGAGACAAAATTATGTTTCCAAAGAAACAAACTCAAAGATG
12610 ATTTTGTTAA
Statistics
Matches: 86, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
117 1 0.01
118 51 0.59
119 18 0.21
120 16 0.19
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (119 bp):
GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTTCAAG
AGACAAAATTATGTTTCCAAAGAAACAAACTCAAAGATGGATCACATCTCAAGT
Found at i:12829 original size:67 final size:67
Alignment explanation
Indices: 12721--13167 Score: 712
Period size: 67 Copynumber: 6.7 Consensus size: 67
12711 AGAAAAACAG
*
12721 ATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACA
1 ATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACA
12786 AA
66 AA
*
12788 ATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAAAGACA
1 ATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACA
12853 AA
66 AA
12855 ATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACA
1 ATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACA
12920 AA
66 AA
12922 ATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACA
1 ATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACA
12987 AA
66 AA
*
12989 ATTTGGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACA
1 ATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACA
13054 AA
66 AA
* * *
13056 ATTTTGTTTCTTCAAAGAAACAAACTCAAAGATTTTT-TTT---ACGAAATTGTCTCAAGAGAGA
1 ATTTTGTTTC--CAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
13117 CAAA
64 CAAA
* * *
13121 ACTTTGTTT-CAAA-ATACATAGACTCAAA-ATTTTT-TTCTCACAAGAAA
1 ATTTTGTTTCCAAAGAAACA-A-ACTCAAAGATTTTTGTT-TCAAAAGAAA
13168 CAACTCAAAA
Statistics
Matches: 361, Mismatches: 11, Indels: 17
0.93 0.03 0.04
Matches are distributed among these distances:
61 4 0.01
62 13 0.04
63 8 0.02
65 30 0.08
66 5 0.01
67 273 0.76
68 3 0.01
69 25 0.07
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.32
Consensus pattern (67 bp):
ATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACA
AA
Found at i:13213 original size:31 final size:28
Alignment explanation
Indices: 13142--13216 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 28
13132 AAATACATAG
*
13142 ACTCAAAATTTTTTTCTCACAAGAAACA
1 ACTCAAAATTTTTTTCTCAAAAGAAACA
*
13170 ACTCAAAAATTTTTATAT-TCAAAAGGAACA
1 ACTC-AAAATTTTT-T-TCTCAAAAGAAACA
13200 TACTCAAAGATTTTTTT
1 -ACTCAAA-ATTTTTTT
13217 TACGAAATTG
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
28 4 0.10
29 10 0.25
30 15 0.38
31 11 0.28
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (28 bp):
ACTCAAAATTTTTTTCTCAAAAGAAACA
Found at i:13278 original size:26 final size:25
Alignment explanation
Indices: 13239--13302 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 25
13229 TCAAGAGAGA
* *
13239 CAAAACTTTGTTTCAAAAGACATAGACT
1 CAAAA-TTT-TTTCAAAAGAAACA-ACT
*
13267 CAAAATTTTTTCACAAGAAACAACT
1 CAAAATTTTTTCAAAAGAAACAACT
*
13292 CAAAAATTTTT
1 CAAAATTTTTT
13303 ATATTCAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 13 0.41
26 11 0.34
27 3 0.09
28 5 0.16
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.31
Consensus pattern (25 bp):
CAAAATTTTTTCAAAAGAAACAACT
Found at i:13320 original size:119 final size:121
Alignment explanation
Indices: 13069--13364 Score: 470
Period size: 122 Copynumber: 2.4 Consensus size: 121
13059 TTGTTTCTTC
* *
13069 AAAGAAACAAACTCAAAGATTTTTTTTACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAA
1 AAAGGAACATACTCAAAGATTTTTTTTACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAA
*
13134 ATACATAGACTCAAAATTTTTTTCTCACAAGAAACAACTCAAAAATTTTTATATTCA
66 AGACATAGACTCAAAA-TTTTTTCTCACAAGAAACAACTCAAAAATTTTTATATTCA
13191 AAAGGAACATACTCAAAGATTTTTTTTACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAA
1 AAAGGAACATACTCAAAGATTTTTTTTACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAA
13256 AGACATAGACTCAAAA-TTTTT-TCACAAGAAACAACTCAAAAATTTTTATATTCA
66 AGACATAGACTCAAAATTTTTTCTCACAAGAAACAACTCAAAAATTTTTATATTCA
* ** * **
13310 AAATGAACATACTCAAAGATTTGTTTCAAGAGAAACCGTCTCAAGAGAGACAAAA
1 AAAGGAACATACTCAAAGATTT-TTTTTA-CGAAATTGTCTCAAGAGAGACAAAA
13365 ATCATTTTAA
Statistics
Matches: 163, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
119 54 0.33
120 9 0.06
121 22 0.13
122 78 0.48
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (121 bp):
AAAGGAACATACTCAAAGATTTTTTTTACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAA
AGACATAGACTCAAAATTTTTTCTCACAAGAAACAACTCAAAAATTTTTATATTCA
Found at i:13657 original size:21 final size:21
Alignment explanation
Indices: 13596--13657 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
13586 GGTGGAAAAA
*
13596 TGTCTCAAGCGAGACATAATT
1 TGTCTCAAGCGAGACAAAATT
* * * *
13617 TGTTTTAA---AGA-GAAAGT
1 TGTCTCAAGCGAGACAAAATT
13634 TGTCTCAAGCGAGACAAAATT
1 TGTCTCAAGCGAGACAAAATT
13655 TGT
1 TGT
13658 TTTTAAGAAA
Statistics
Matches: 28, Mismatches: 9, Indels: 8
0.62 0.20 0.18
Matches are distributed among these distances:
17 9 0.32
18 3 0.11
20 3 0.11
21 13 0.46
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (21 bp):
TGTCTCAAGCGAGACAAAATT
Found at i:13674 original size:36 final size:36
Alignment explanation
Indices: 13590--13698 Score: 119
Period size: 38 Copynumber: 2.9 Consensus size: 36
13580 AAAATTGGTG
* *
13590 GAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAA
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAA
*
13626 GAGAAAGTTGTCTCAAGCGAGACAAAATTTGTTTTTAA
1 GA-AAA-ATGTCTCAAGCGAGACAAAATTTGTTTTTAA
* * * * *
13664 GAAAACTGTCTCTAGTGAGACGACACTTTGTTTTT
1 GAAAAATGTCTCAAGCGAGAC-AAAATTTGTTTTT
13699 TTTTTTAATA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
36 15 0.24
37 17 0.27
38 30 0.48
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (36 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAA
Found at i:21223 original size:3 final size:3
Alignment explanation
Indices: 21215--21240 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
21205 TAAGCAAAAT
21215 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
21241 TACAATTAGA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:21536 original size:18 final size:18
Alignment explanation
Indices: 21510--21556 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
21500 AATTTAATAT
*
21510 CTATCTGTAAACGGATGA
1 CTATTTGTAAACGGATGA
*
21528 CTATTTGTAAAATGGATGA
1 CTATTTGT-AAACGGATGA
21547 CTATTTGTAA
1 CTATTTGTAA
21557 CTAATTATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (18 bp):
CTATTTGTAAACGGATGA
Found at i:22125 original size:30 final size:29
Alignment explanation
Indices: 22082--22202 Score: 136
Period size: 29 Copynumber: 4.1 Consensus size: 29
22072 AATTGGATAA
** *
22082 TTATCTTTCTGACTTTCACATTTAGTATTATT
1 TTAT-TTT-TGACTTTCACATTTAGT-GGAAT
* *
22114 TTATTTTTGACTTTCACGTTCAGTGGAAT
1 TTATTTTTGACTTTCACATTTAGTGGAAT
22143 TTATTTTTGACTTTCACATTTAGTGGAAT
1 TTATTTTTGACTTTCACATTTAGTGGAAT
***
22172 TTATTTTTGAC-AAAACATTTAGTGGAAT
1 TTATTTTTGACTTTCACATTTAGTGGAAT
22200 TTA
1 TTA
22203 AAACCGCTAT
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.22
29 40 0.51
30 15 0.19
31 3 0.04
32 4 0.05
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (29 bp):
TTATTTTTGACTTTCACATTTAGTGGAAT
Found at i:24865 original size:31 final size:31
Alignment explanation
Indices: 24830--24915 Score: 154
Period size: 31 Copynumber: 2.8 Consensus size: 31
24820 ATCCAGTTAC
24830 AACACATGACATAAATTATGATGAAACCCTA
1 AACACATGACATAAATTATGATGAAACCCTA
*
24861 AACACATGACATAAATTATGATAAAACCCTA
1 AACACATGACATAAATTATGATGAAACCCTA
*
24892 AACACATAACATAAATTATGATGA
1 AACACATGACATAAATTATGATGA
24916 GGAATCCCAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.23
Consensus pattern (31 bp):
AACACATGACATAAATTATGATGAAACCCTA
Found at i:26942 original size:12 final size:12
Alignment explanation
Indices: 26905--26961 Score: 55
Period size: 12 Copynumber: 4.7 Consensus size: 12
26895 AGCCTTCTGT
26905 CCCACCCCACCGC
1 CCCACCCCACC-C
26918 CCCATCCCC-CCC
1 CCCA-CCCCACCC
26930 CCCACCCCA-CC
1 CCCACCCCACCC
*
26941 CCCATCCCCATCC
1 CCCA-CCCCACCC
*
26954 CCAACCCC
1 CCCACCCC
26962 TGCACCTCTG
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
11 10 0.26
12 14 0.36
13 11 0.28
14 4 0.10
ACGTcount: A:0.16, C:0.77, G:0.02, T:0.05
Consensus pattern (12 bp):
CCCACCCCACCC
Found at i:28440 original size:46 final size:46
Alignment explanation
Indices: 28390--28479 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 46
28380 TATTTGAAAC
*
28390 TAAAAATGGAGA-GAGACAAATATCTTATTTGATCAATATTTAAAGT
1 TAAAAATGGA-ACGAGACAAAGATCTTATTTGATCAATATTTAAAGT
* * * * *
28436 TAAAATTTGAACGGGATAAAGATCTTATTTGATTAATATTTAAA
1 TAAAAATGGAACGAGACAAAGATCTTATTTGATCAATATTTAAA
28480 CTAAAAAGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
45 1 0.03
46 36 0.97
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (46 bp):
TAAAAATGGAACGAGACAAAGATCTTATTTGATCAATATTTAAAGT
Found at i:38566 original size:5 final size:5
Alignment explanation
Indices: 38556--38581 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
38546 TTCCCTCCAA
38556 TCCTC TCCTC TCCTC TCCTC TCCTC T
1 TCCTC TCCTC TCCTC TCCTC TCCTC T
38582 ATCTCTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (5 bp):
TCCTC
Found at i:44892 original size:3 final size:3
Alignment explanation
Indices: 44884--44942 Score: 84
Period size: 3 Copynumber: 20.0 Consensus size: 3
44874 TTTTTTATCG
** *
44884 TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TA TTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44931 TTA TTA TTA TTA
1 TTA TTA TTA TTA
44943 ATTTACAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:52868 original size:4 final size:4
Alignment explanation
Indices: 52859--52904 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
52849 GATCGAGAAA
*
52859 ACAT ACAT ACAT ACAT ACAT AAAT AC-- ACAT ACAT ACAT A-AT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
52904 A
1 A
52905 AAATTTGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 3 0.08
4 32 0.86
ACGTcount: A:0.54, C:0.22, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:52890 original size:18 final size:17
Alignment explanation
Indices: 52867--52902 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
52857 AAACATACAT
52867 ACATACATACATAAATAC
1 ACATACATACAT-AATAC
52885 ACATACATACATAATAC
1 ACATACATACATAATAC
52902 A
1 A
52903 TAAAATTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (17 bp):
ACATACATACATAATAC
Found at i:53603 original size:29 final size:29
Alignment explanation
Indices: 53565--53719 Score: 228
Period size: 29 Copynumber: 5.5 Consensus size: 29
53555 TTTCTCTTAA
*
53565 AAAAATCTTTGAGTTGGTTCCTTTTAAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTAAAT
53594 AAAAATCTTTGAGTTTGTTCCTTTTAAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTAAAT
53623 AAAAATCTTTGAGTTTGTTCCTTTTAAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTAAAT
* *
53652 AAAAATCTTGGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTAAAT
* * *
53681 AAATATCTTTGAG-TTGTTTCTTTT---G
1 AAAAATCTTTGAGTTTGTTCCTTTTAAAT
53706 AAAAATCTTTGAGT
1 AAAAATCTTTGAGT
53720 CTATTTATTC
Statistics
Matches: 117, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
25 12 0.10
28 10 0.09
29 95 0.81
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.47
Consensus pattern (29 bp):
AAAAATCTTTGAGTTTGTTCCTTTTAAAT
Found at i:53934 original size:131 final size:130
Alignment explanation
Indices: 53784--54175 Score: 732
Period size: 131 Copynumber: 3.0 Consensus size: 130
53774 AAAAAAATCT
53784 TTGAGATAGTTTCTTTTAAAACAAAAATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTA
1 TTGAGATAGTTTCTTTTAAAACAAAAATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTA
*
53849 TTAAAGACAATTTCTCTTGAAAAAAATCTTTGAGTTTGTTT-CTTTGGAAACAAAATTTTGTCTC
66 TTAAAGACAATTTCTTTTG-AAAAAATCTTTGAGTTTGTTTCCTTT-GAAACAAAATTTTGTCTC
53913 TC
129 TC
53915 TTGAGATAGTTTCTTTTAAAACAAAAATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTA
1 TTGAGATAGTTTCTTTTAAAACAAAAATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTA
53980 TTAAAGACAATTTCTTTTGAAAAAATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTC
66 TTAAAGACAATTTCTTTTGAAAAAATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTC
*
54045 TTAAGATAGTTTCTTTTAAAACAAAAATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTA
1 TTGAGATAGTTTCTTTTAAAACAAAAATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTA
54110 TTAAAGACAATTTCTTTTGGAAAAAATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCT
66 TTAAAGACAATTTCTTTT-GAAAAAATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCT
54175 C
130 C
54176 GAGACAACTT
Statistics
Matches: 257, Mismatches: 2, Indels: 4
0.98 0.01 0.02
Matches are distributed among these distances:
130 123 0.48
131 134 0.52
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (130 bp):
TTGAGATAGTTTCTTTTAAAACAAAAATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTA
TTAAAGACAATTTCTTTTGAAAAAATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTC
Found at i:54375 original size:15 final size:15
Alignment explanation
Indices: 54352--54395 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
54342 TTTTGAGTCG
*
54352 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
54367 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
54382 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
54396 AGATCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:55259 original size:128 final size:129
Alignment explanation
Indices: 54810--55257 Score: 819
Period size: 129 Copynumber: 3.5 Consensus size: 129
54800 CCAGTCGTCC
* * *
54810 TCATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAAC
1 TCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCTTCATCACGTATGAGCCGTGTCAAC
54874 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
65 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
54939 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
55004 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
*
55068 TCATCACGTATGAGTCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTC-ACC
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
*
55132 CTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
*
55196 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCA
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCA
55258 CCTTTAGACG
Statistics
Matches: 310, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
128 125 0.40
129 180 0.58
130 5 0.02
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (129 bp):
TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
Found at i:55285 original size:257 final size:258
Alignment explanation
Indices: 54825--55288 Score: 801
Period size: 257 Copynumber: 1.8 Consensus size: 258
54815 ATGTAGGAAC
54825 CGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCG
1 CGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCG
54890 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCC
66 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCC
* * **
54955 GTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGT
131 GTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGAGAACCAAACGT
55020 CCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGT
196 CCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGT
*
55083 CGTGTCATTCCCC-GACCAGATCTCTTCATCACGTATGAGCCGTGTC-ACCCTAGATAACCAGCC
1 CGTGTCA-TCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCC
55146 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGC
65 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGC
* *
55211 CGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTC-ACCTTTAGACGACCCAAA
130 CGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACC-ATAGA-GAACCAAA
*
55275 C-TCTTCATCACGTA
193 CGTCCTCATCACGTA
55289 TGAGCAGTGT
Statistics
Matches: 195, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
256 3 0.02
257 142 0.73
258 45 0.23
259 5 0.03
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (258 bp):
CGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCG
TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCC
GTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGAGAACCAAACGT
CCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGT
Found at i:55462 original size:3 final size:3
Alignment explanation
Indices: 55454--55509 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
55444 TTTTTTATCG
**
55454 TTA TTA TTA TTA TTA TTA TTA TCG TTA -TA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
55501 TTA TTA TTA
1 TTA TTA TTA
55510 ATTTACAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:62664 original size:29 final size:29
Alignment explanation
Indices: 62630--62703 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
62620 ATGATTCTAA
62630 TATAAAATATTAATTTTAA-C-TAAATTT
1 TATAAAATATTAATTTTAATCATAAATTT
62657 TAGTTAAAATATTAA-TTTAATTCATAAATTT
1 TA--TAAAATATTAATTTTAA-TCATAAATTT
*
62688 TATAAAATATCAATTT
1 TATAAAATATTAATTT
62704 GATCTCTTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
27 2 0.05
28 5 0.12
29 21 0.52
30 3 0.08
31 9 0.22
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (29 bp):
TATAAAATATTAATTTTAATCATAAATTT
Found at i:64225 original size:27 final size:27
Alignment explanation
Indices: 64168--64227 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
64158 ACATCAAAGG
* * * *
64168 AACATGTTCATGAATGTTAAATAAATG
1 AACATGTTCATAAATGCTAAAGAAATA
64195 AACATGTTCATAAATGCTAAACGAAA-A
1 AACATGTTCATAAATGCTAAA-GAAATA
64222 AACATG
1 AACATG
64228 AACACCTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 25 0.89
28 3 0.11
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (27 bp):
AACATGTTCATAAATGCTAAAGAAATA
Found at i:64791 original size:31 final size:30
Alignment explanation
Indices: 64747--64816 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
64737 TTTTTTCGTC
* *
64747 AAATTCAAATATCAAAATAATATTTTATCT
1 AAATTTAAATATCAAAATAATATTTCATCT
* *
64777 GAAATTTAATTATCAAAATGATATTTCATCT
1 -AAATTTAAATATCAAAATAATATTTCATCT
64808 AAAGTTTAA
1 AAA-TTTAA
64817 GACTCAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 3 0.09
31 31 0.91
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (30 bp):
AAATTTAAATATCAAAATAATATTTCATCT
Found at i:64824 original size:31 final size:31
Alignment explanation
Indices: 64757--64824 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
64747 AAATTCAAAT
* *
64757 ATCAAAATAATATTTTATCTGAAATTTAATT
1 ATCAAAATAATATTTCATCTGAAATTTAATG
*
64788 ATCAAAATGATATTTCATCT-AAAGTTTAA-G
1 ATCAAAATAATATTTCATCTGAAA-TTTAATG
64818 ACTCAAA
1 A-TCAAA
64825 TTAAAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (31 bp):
ATCAAAATAATATTTCATCTGAAATTTAATG
Found at i:70309 original size:32 final size:31
Alignment explanation
Indices: 70204--70314 Score: 108
Period size: 30 Copynumber: 3.7 Consensus size: 31
70194 GAATTCGAAT
* ** *
70204 TTTTTTAAAAGT-ATCAACCAAGTCCTTAAA
1 TTTTTTAAAAATAATCAATTAAGTCCTCAAA
70234 TTTTTT--AAA-AATCAATTAAG-CCTTCAAA
1 TTTTTTAAAAATAATCAATTAAGTCC-TCAAA
* *
70262 -CTTTTAAAAAGAATCAATTAAGTCCTCAAA
1 TTTTTTAAAAATAATCAATTAAGTCCTCAAA
70292 TTTTTTTAAAAATAATCAATTAA
1 -TTTTTTAAAAATAATCAATTAA
70315 ACATATATAT
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
27 6 0.09
28 14 0.21
29 3 0.05
30 22 0.33
31 2 0.03
32 19 0.29
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.38
Consensus pattern (31 bp):
TTTTTTAAAAATAATCAATTAAGTCCTCAAA
Found at i:74384 original size:2 final size:2
Alignment explanation
Indices: 74365--74433 Score: 52
Period size: 2 Copynumber: 34.0 Consensus size: 2
74355 TTATTATTAT
* * *
74365 TA TA TA TGA TG TA CA TA TA TA TA TA TA TA TA TA TA T- TT TCA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
* *
74408 T- TG TT TCA TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA
74434 ATGTAGAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
1 2 0.04
2 49 0.89
3 4 0.07
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:75770 original size:134 final size:134
Alignment explanation
Indices: 75522--75770 Score: 340
Period size: 134 Copynumber: 1.9 Consensus size: 134
75512 AATTCAGGCA
*
75522 ATTCTGAAGCAAGCTAGAATGAGCAAATACAAATATGATCAGGCTCTTAGGAAAACATAGTTTGA
1 ATTCAGAAGCAAGCTAGAATGAGCAAATACAAATATGA-CAGGCTCTTAGGAAAACATAGTTTGA
* * ** *
75587 TTTCGTCATAAGCGTGATTCGGAGCATTGCGCTTACTGTAAGTATGCCCGGTGATGCATTTCAAA
65 TTTCGTCATAAGCGTCATTCAGAGCATCCCGCTTACTGTAAGTACGCCCGGTGATGCATTTCAAA
75652 AAGTG
130 AAGTG
* * * * *
75657 ATTCAGAAGCATA-CTAGAATGAGTACATACATATATG-CAGAGTTCTTGGGAAAACATAGTTTG
1 ATTCAGAAGCA-AGCTAGAATGAGCAAATACAAATATGACAG-GCTCTTAGGAAAACATAGTTTG
* *
75720 GTTTTGTCATAAGCGTCATTCAGAGCATCCCGCTTACTGTAAGTACGCCCG
64 ATTTCGTCATAAGCGTCATTCAGAGCATCCCGCTTACTGTAAGTACGCCCG
75771 ATTATGCGTT
Statistics
Matches: 99, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
133 3 0.03
134 64 0.65
135 31 0.31
136 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (134 bp):
ATTCAGAAGCAAGCTAGAATGAGCAAATACAAATATGACAGGCTCTTAGGAAAACATAGTTTGAT
TTCGTCATAAGCGTCATTCAGAGCATCCCGCTTACTGTAAGTACGCCCGGTGATGCATTTCAAAA
AGTG
Found at i:84728 original size:16 final size:17
Alignment explanation
Indices: 84701--84734 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
84691 TATCGCCGAC
84701 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
84718 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
84734 C
1 C
84735 ATGAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:92922 original size:21 final size:22
Alignment explanation
Indices: 92896--92976 Score: 78
Period size: 21 Copynumber: 3.8 Consensus size: 22
92886 CAGAACCCCA
*
92896 GGGGGGTATCGATTCCCCT-AT
1 GGGGGGAATCGATTCCCCTCAT
* *
92917 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGATTCCCC-TCAT
* *
92940 AGGGGGAATCGGTT-CCCTCAT
1 GGGGGGAATCGATTCCCCTCAT
*
92961 -GGGGGTATCGATTCCC
1 GGGGGGAATCGATTCCC
92977 TCTGTACCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 11 0.22
21 21 0.42
22 4 0.08
23 14 0.28
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.25
Consensus pattern (22 bp):
GGGGGGAATCGATTCCCCTCAT
Found at i:92970 original size:20 final size:21
Alignment explanation
Indices: 92897--92978 Score: 69
Period size: 20 Copynumber: 3.9 Consensus size: 21
92887 AGAACCCCAG
* *
92897 GGGGGTATCGATTCCC-CTAT
1 GGGGGAATCGATTCCCTCAAT
* *
92917 GGGGGGAATCGGTTCCCCTTCAAA
1 -GGGGGAATCGATT-CCC-TCAAT
*
92941 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGATTCCCTCAAT
*
92961 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
92979 TGTACCAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 17 0.33
21 13 0.25
22 6 0.12
23 13 0.25
24 2 0.04
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.26
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTCAAT
Found at i:95321 original size:30 final size:30
Alignment explanation
Indices: 95281--95464 Score: 359
Period size: 30 Copynumber: 6.1 Consensus size: 30
95271 AAAGGACCTA
95281 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
95311 TCCGGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
95341 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
95371 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
95401 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
95431 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
95461 TCCA
1 TCCA
95465 TATGTTCCTT
Statistics
Matches: 152, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 152 1.00
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.23
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:95513 original size:31 final size:30
Alignment explanation
Indices: 95453--95517 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
95443 AAAGATCCTC
**
95453 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCAAAGAACATA
*
95483 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCAAAGAACATA
95514 GGTA
1 GGTA
95518 GTTCTTTGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 4 0.13
31 22 0.73
32 4 0.13
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCAAAGAACATA
Found at i:95785 original size:20 final size:20
Alignment explanation
Indices: 95760--95860 Score: 92
Period size: 20 Copynumber: 5.3 Consensus size: 20
95750 TTCATATTCT
95760 TTCTTATGTCCATTTCATAC
1 TTCTTATGTCCATTTCATAC
*
95780 TTCTTAT-TTCATATTC-T--
1 TTCTTATGTCCAT-TTCATAC
*
95797 TTCTTATGTCCTTTTCATAC
1 TTCTTATGTCCATTTCATAC
*
95817 TTCTTAT-TTCATATTC-T--
1 TTCTTATGTCCAT-TTCATAC
*
95834 TTCTTATGTCCTTTTCATAC
1 TTCTTATGTCCATTTCATAC
95854 TTCTTAT
1 TTCTTAT
95861 TTCATATTCT
Statistics
Matches: 64, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
17 20 0.31
18 8 0.12
19 9 0.14
20 27 0.42
ACGTcount: A:0.17, C:0.22, G:0.03, T:0.58
Consensus pattern (20 bp):
TTCTTATGTCCATTTCATAC
Found at i:95789 original size:37 final size:37
Alignment explanation
Indices: 95747--95871 Score: 241
Period size: 37 Copynumber: 3.4 Consensus size: 37
95737 ATATTCTGTA
*
95747 TATTTCATATTCTTTCTTATGTCCATTTCATACTTCT
1 TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
95784 TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
1 TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
95821 TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
1 TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
95858 TATTTCATATTCTT
1 TATTTCATATTCTT
95872 ATGAAATCAT
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 87 1.00
ACGTcount: A:0.18, C:0.21, G:0.02, T:0.59
Consensus pattern (37 bp):
TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
Found at i:95812 original size:13 final size:12
Alignment explanation
Indices: 95749--95869 Score: 56
Period size: 13 Copynumber: 9.8 Consensus size: 12
95739 ATTCTGTATA
95749 TTTCATATT-C-
1 TTTCATATTCCT
* *
95759 TTTCTTATGTCCA
1 TTTCATAT-TCCT
*
95772 TTTCATACTTCTT
1 TTTCATA-TTCCT
95785 ATTTCATATT-C-
1 -TTTCATATTCCT
*
95796 TTTCTTATGTCCT
1 TTTCATAT-TCCT
*
95809 TTTCATACTTCTT
1 TTTCATA-TTCCT
95822 ATTTCATATT-C-
1 -TTTCATATTCCT
*
95833 TTTCTTATGTCCT
1 TTTCATAT-TCCT
*
95846 TTTCATACTTCTT
1 TTTCATA-TTCCT
95859 ATTTCATATTC
1 -TTTCATATTC
95870 TTATGAAATC
Statistics
Matches: 84, Mismatches: 12, Indels: 27
0.68 0.10 0.22
Matches are distributed among these distances:
10 21 0.25
11 3 0.04
12 3 0.04
13 33 0.39
14 24 0.29
ACGTcount: A:0.17, C:0.21, G:0.02, T:0.59
Consensus pattern (12 bp):
TTTCATATTCCT
Found at i:95872 original size:13 final size:13
Alignment explanation
Indices: 95771--95873 Score: 69
Period size: 13 Copynumber: 8.2 Consensus size: 13
95761 TCTTATGTCC
95771 ATTTCATACTTCTT
1 ATTTCATA-TTCTT
95785 ATTTCATATTCTT
1 ATTTCATATTCTT
* *
95798 -TCTT-AT-GTCCT
1 AT-TTCATATTCTT
95809 -TTTCATACTTCTT
1 ATTTCATA-TTCTT
95822 ATTTCATATTCTT
1 ATTTCATATTCTT
* *
95835 -TCTT-AT-GTCCT
1 AT-TTCATATTCTT
95846 -TTTCATACTTCTT
1 ATTTCATA-TTCTT
95859 ATTTCATATTCTT
1 ATTTCATATTCTT
95872 AT
1 AT
95874 GAAATCATAT
Statistics
Matches: 71, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
10 4 0.06
11 12 0.17
12 6 0.08
13 27 0.38
14 22 0.31
ACGTcount: A:0.18, C:0.20, G:0.02, T:0.59
Consensus pattern (13 bp):
ATTTCATATTCTT
Found at i:96476 original size:19 final size:20
Alignment explanation
Indices: 96439--96476 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
96429 TTTTTTATTA
*
96439 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
96459 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
96477 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:103728 original size:31 final size:31
Alignment explanation
Indices: 103692--103774 Score: 82
Period size: 30 Copynumber: 2.7 Consensus size: 31
103682 CAACCCTAAA
103692 TTTAGATAAAATATTAATTTTATCCTT-ACAC
1 TTTAGATAAAATATTAATTTTATCCTTGA-AC
** * *
103723 TTTAGA-AAAATACAAAATTAATCCTTGAAC
1 TTTAGATAAAATATTAATTTTATCCTTGAAC
*
103753 TTCAGATAAAATATCT-ATTTTA
1 TTTAGATAAAATAT-TAATTTTA
103775 AAATGATTAG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
30 23 0.57
31 17 0.43
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (31 bp):
TTTAGATAAAATATTAATTTTATCCTTGAAC
Found at i:107631 original size:16 final size:16
Alignment explanation
Indices: 107610--107640 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
107600 AGTGCATTAG
*
107610 ACTCGAGTACGAGTGC
1 ACTCGACTACGAGTGC
107626 ACTCGACTACGAGTG
1 ACTCGACTACGAGTG
107641 ACACATATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (16 bp):
ACTCGACTACGAGTGC
Found at i:107633 original size:21 final size:20
Alignment explanation
Indices: 107589--107639 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
107579 GTAGCACTTC
*
107589 ACTCGTAGTCGAGTGCATTAG
1 ACTCG-AGTCGAGTGCACTAG
*
107610 ACTCGAGTACGAGTGCACTCG
1 ACTCGAGT-CGAGTGCACTAG
107631 ACTACGAGT
1 ACT-CGAGT
107640 GACACATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 3 0.12
21 18 0.69
22 5 0.19
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (20 bp):
ACTCGAGTCGAGTGCACTAG
Found at i:109841 original size:22 final size:24
Alignment explanation
Indices: 109813--109856 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
109803 TCGACCCGGA
109813 TCAGAAAAT-A-AAATAAAAAAAC
1 TCAGAAAATAACAAATAAAAAAAC
*
109835 TCAGAAATTAACAAATAAAAAA
1 TCAGAAAATAACAAATAAAAAA
109857 GAAATTAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 1 0.05
24 10 0.53
ACGTcount: A:0.70, C:0.09, G:0.05, T:0.16
Consensus pattern (24 bp):
TCAGAAAATAACAAATAAAAAAAC
Found at i:113336 original size:2 final size:2
Alignment explanation
Indices: 113329--113379 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
113319 TTACTCTAAT
113329 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
113371 TA TA TA TA T
1 TA TA TA TA T
113380 TTTACATTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:124269 original size:20 final size:20
Alignment explanation
Indices: 124244--124294 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
124234 CATCTTCTAC
124244 TTTTTATTCTTATTTCTTCA
1 TTTTTATTCTTATTTCTTCA
*
124264 TTTTTATTCTTTTTTCTTCA
1 TTTTTATTCTTATTTCTTCA
124284 TTTTTATTCTT
1 TTTTTATTCTT
124295 CTTCAAAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTATTCTTATTTCTTCA
Found at i:126280 original size:23 final size:23
Alignment explanation
Indices: 126254--126299 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
126244 AAAACGTGTC
*
126254 ATTCAATAGCGAAAATGAGTTTT
1 ATTCAATAGAGAAAATGAGTTTT
* **
126277 ATTCGATAGAGACGATGAGTTTT
1 ATTCAATAGAGAAAATGAGTTTT
126300 TTTAAAGGCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.35
Consensus pattern (23 bp):
ATTCAATAGAGAAAATGAGTTTT
Found at i:134122 original size:31 final size:31
Alignment explanation
Indices: 134087--134236 Score: 192
Period size: 31 Copynumber: 4.8 Consensus size: 31
134077 ATATATTGAT
* *
134087 CACTAATATTATCGATTTATAATAAATTGGC
1 CACTAACATTATCGATTTATAACAAATTGGC
**
134118 CACTAACATTATCGATTTATAACAAATCAGC
1 CACTAACATTATCGATTTATAACAAATTGGC
* * * *
134149 CATTAATATTATTGATTTATAACAAATTGAC
1 CACTAACATTATCGATTTATAACAAATTGGC
* *
134180 CACTAACATTGTCGATTTATAACAAATTGGT
1 CACTAACATTATCGATTTATAACAAATTGGC
* *
134211 AAATAACATTATCGATTTATAACAAA
1 CACTAACATTATCGATTTATAACAAA
134237 CCGTTAATAT
Statistics
Matches: 100, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 100 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (31 bp):
CACTAACATTATCGATTTATAACAAATTGGC
Found at i:139465 original size:21 final size:23
Alignment explanation
Indices: 139417--139467 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
139407 ATTCCCCTGT
139417 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
139440 AGGGGGAATCGGTT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
139461 GGGGGGA
1 GGGGGGA
139468 TCGATTTCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 10 0.38
22 3 0.12
23 13 0.50
ACGTcount: A:0.20, C:0.22, G:0.41, T:0.18
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:139476 original size:21 final size:22
Alignment explanation
Indices: 139395--139473 Score: 74
Period size: 21 Copynumber: 3.7 Consensus size: 22
139385 CCAGAACCCC
* *
139395 AGGGGGGTATCGATTCCCCT-G
1 AGGGGGGAATCGATTCCCCTCA
* *
139416 TGGGGGGAATCGGTTCCCCTTCA
1 AGGGGGGAATCGATTCCCC-TCA
* *
139439 AAGGGGGAATCGGTT-CCCTCA
1 AGGGGGGAATCGATTCCCCTCA
139460 AGGGGGG-ATCGATT
1 AGGGGGGAATCGATT
139474 TCCTCTGCAC
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
20 6 0.12
21 25 0.52
22 4 0.08
23 13 0.27
ACGTcount: A:0.18, C:0.22, G:0.38, T:0.23
Consensus pattern (22 bp):
AGGGGGGAATCGATTCCCCTCA
Found at i:139478 original size:20 final size:20
Alignment explanation
Indices: 139418--139478 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
139408 TTCCCCTGTG
*
139418 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATT-CCC-TC-AA
*
139441 GGGGGAATCGGTTCCCTCAA
1 GGGGGAATCGATTCCCTCAA
* *
139461 GGGGGGATCGATTTCCTC
1 GGGGGAATCGATTCCCTC
139479 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.18, C:0.25, G:0.34, T:0.23
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAA
Found at i:142483 original size:2 final size:2
Alignment explanation
Indices: 142476--142500 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
142466 ATGCATCATG
142476 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
142501 CCCTATTTTA
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:145338 original size:6 final size:6
Alignment explanation
Indices: 145327--145386 Score: 79
Period size: 6 Copynumber: 9.8 Consensus size: 6
145317 AATCGTTCAA
145327 CCTCCC CCT-CC CCT-CC CCTCCCTC CTCTCCC CCTCCC CCTCCC CCTCCC
1 CCTCCC CCTCCC CCTCCC CCT-CC-C C-CTCCC CCTCCC CCTCCC CCTCCC
145376 CCTCCC CCTCC
1 CCTCCC CCTCC
145387 ACTTTCTCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.20
6 31 0.62
7 3 0.06
8 4 0.08
9 2 0.04
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (6 bp):
CCTCCC
Found at i:146733 original size:18 final size:19
Alignment explanation
Indices: 146710--146752 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
146700 CAGTAATCAT
146710 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
146728 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGTAATCTTAC
146748 ATTCC
1 ATTCC
146753 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.13
19 4 0.17
20 16 0.70
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.37
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:146740 original size:20 final size:20
Alignment explanation
Indices: 146715--146752 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
146705 ATCATATTCC
146715 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
146735 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
146753 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:146924 original size:6 final size:6
Alignment explanation
Indices: 146913--147812 Score: 1504
Period size: 6 Copynumber: 156.7 Consensus size: 6
146903 GCAAAAGGAA
146913 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
146961 AT-AAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT-AAT AT-AAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
147006 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT-AA-
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
147052 ATAAA- ATAAAT ATAAAT AT-AAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
147098 AT-AA- ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT-AA- ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
147142 ATAAAT ATAAAT AT-AAT AT-AAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
147188 ATAAAT AT-AAT A-ATAAT ATAAAT ATAAAT ATAAAT ATAAAT AT-AAT
1 ATAAAT ATAAAT ATA-AAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
147234 ATAAAT AT-AAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
147281 ATAAAT AT-AA- ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT-AA-
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
147325 ATAAAT AT-AAT ATAAAT ATAAAT AT-AAT ATAAAT AT-AAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
147370 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
147418 ATAAAT AT-AAT ATAAAT ATAAAT ATAAAT AT-AA- ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
147463 ATAAAT AT-AAT ATAAAT ATAAAT AT--AT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
147508 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT-AA- ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
147554 ATAAAT AT-AA- ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
147600 A-AAAT ATAAAT ATAAAT AT-AAT AT-AAT ATAAAT ATAAAT A-AAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
147644 ATAAAT AT-AA- ATAAA- ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
147689 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
147737 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
147785 ATAAAT ATAAAT ATAAAT ATAAAT ATAA
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAA
147813 TAATAATAAA
Statistics
Matches: 857, Mismatches: 0, Indels: 74
0.92 0.00 0.08
Matches are distributed among these distances:
4 22 0.03
5 135 0.16
6 699 0.82
7 1 0.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATAAAT
Found at i:161011 original size:12 final size:12
Alignment explanation
Indices: 160994--161027 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
160984 TTAGGAACTT
160994 ACCAACGGCGCC
1 ACCAACGGCGCC
*
161006 ACCAACTGCGCC
1 ACCAACGGCGCC
*
161018 TCCAACGGCG
1 ACCAACGGCG
161028 ACTCCGGCGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.47, G:0.24, T:0.06
Consensus pattern (12 bp):
ACCAACGGCGCC
Found at i:161239 original size:2 final size:2
Alignment explanation
Indices: 161232--161264 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
161222 TATAAATTAA
161232 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 A
161265 GAATTACAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:161609 original size:24 final size:25
Alignment explanation
Indices: 161572--161618 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
161562 TTATTATTAA
*
161572 TTTAATTTTAAAAATATTTTTTTGT
1 TTTAATTTTAAAAATATATTTTTGT
161597 TTTAA-TTTAAAAATATATTTTT
1 TTTAATTTTAAAAATATATTTTT
161619 AAAAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTAATTTTAAAAATATATTTTTGT
Found at i:161625 original size:15 final size:16
Alignment explanation
Indices: 161605--161635 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
161595 GTTTTAATTT
161605 AAAAATATAT-TTTTA
1 AAAAATATATATTTTA
161620 AAAAATATATATTTTA
1 AAAAATATATATTTTA
161636 TTCTTATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAAATATATATTTTA
Found at i:161664 original size:31 final size:33
Alignment explanation
Indices: 161621--161704 Score: 104
Period size: 32 Copynumber: 2.6 Consensus size: 33
161611 ATATTTTTAA
* *
161621 AAAATATATATTTTATTCTTA-TGTAATTTTTT
1 AAAATATATATTTTATTCTTATTGTAACTTTTC
*
161653 AAAA-ATATATTTTATTAC-TATTTTAACTTTTC
1 AAAATATATATTTTATT-CTTATTGTAACTTTTC
161685 AAAATATATATTTTA-TCTTA
1 AAAATATATATTTTATTCTTA
161705 ATTTACTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
31 15 0.33
32 20 0.44
33 10 0.22
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (33 bp):
AAAATATATATTTTATTCTTATTGTAACTTTTC
Found at i:161832 original size:28 final size:29
Alignment explanation
Indices: 161789--161873 Score: 100
Period size: 28 Copynumber: 2.9 Consensus size: 29
161779 AACATAAAAT
* *
161789 ATATATTTTTATATTAAAATAAAAATAAA
1 ATATATTTTTAAATTAATATAAAAATAAA
* *
161818 ATAT-TTTTTAAATTAATTTAATAATAAA
1 ATATATTTTTAAATTAATATAAAAATAAA
* *
161846 ATATATTTAATAAGTTAATATAAAAATA
1 ATATATTT-TTAAATTAATATAAAAATA
161874 TTTTTTAAAG
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
28 24 0.52
29 7 0.15
30 15 0.33
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (29 bp):
ATATATTTTTAAATTAATATAAAAATAAA
Found at i:164297 original size:5 final size:5
Alignment explanation
Indices: 164287--164314 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
164277 TTTGAAAAAT
164287 CTCTC CTCTC CTCTC CTCTC CTCTC CTC
1 CTCTC CTCTC CTCTC CTCTC CTCTC CTC
164315 CCCTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (5 bp):
CTCTC
Found at i:164853 original size:19 final size:20
Alignment explanation
Indices: 164831--164869 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
164821 TTCATTTTAA
164831 ATCTCAAATTCT-TTTTTCG
1 ATCTCAAATTCTATTTTTCG
* *
164850 ATCTCGAATTTTATTTTTCG
1 ATCTCAAATTCTATTTTTCG
164870 TTTCTCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.21, C:0.18, G:0.08, T:0.54
Consensus pattern (20 bp):
ATCTCAAATTCTATTTTTCG
Found at i:167477 original size:22 final size:23
Alignment explanation
Indices: 167449--167498 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
167439 AGTAACATAC
*
167449 CACAAAAGCGGAGAAAAA-ATGT
1 CACAAAAGCAGAGAAAAATATGT
*
167471 CACAAAAGCATAGAAAAATATGT
1 CACAAAAGCAGAGAAAAATATGT
167494 CACAA
1 CACAA
167499 TGACATGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.56, C:0.16, G:0.16, T:0.12
Consensus pattern (23 bp):
CACAAAAGCAGAGAAAAATATGT
Found at i:180005 original size:41 final size:41
Alignment explanation
Indices: 179948--180029 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
179938 AAGTGAGTAC
179948 TTATCAGTTCAACTTTGGTACATTAGTGTATCAATGTTCAG
1 TTATCAGTTCAACTTTGGTACATTAGTGTATCAATGTTCAG
* *
179989 TTATCAGTTCGACTTTGGTACATTTGTGTATCAATGTTCAG
1 TTATCAGTTCAACTTTGGTACATTAGTGTATCAATGTTCAG
180030 CACCGTTGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (41 bp):
TTATCAGTTCAACTTTGGTACATTAGTGTATCAATGTTCAG
Found at i:181950 original size:71 final size:71
Alignment explanation
Indices: 181875--182015 Score: 183
Period size: 71 Copynumber: 2.0 Consensus size: 71
181865 GAATTAATTG
* * * * * * * * *
181875 CTCTTTTAACTTGAGGAAGTGAGACTTTGAATGAATCGTTTCTCCAACTTGACATGGTGAGAGAT
1 CTCTTTTAACATGAGGAAATAAGACTTTGAATGAATCGCTCCTCCAAATTGAAATGATGAGAAAT
181940 GTCTTA
66 GTCTTA
* *
181946 CTCTTTTAACATGAGGAAATAATACTTTTAATGAATCGCTCCTCCAAATTGAAATGATGAGAAAT
1 CTCTTTTAACATGAGGAAATAAGACTTTGAATGAATCGCTCCTCCAAATTGAAATGATGAGAAAT
182011 GTCTT
66 GTCTT
182016 GCTCCATTAC
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
71 59 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (71 bp):
CTCTTTTAACATGAGGAAATAAGACTTTGAATGAATCGCTCCTCCAAATTGAAATGATGAGAAAT
GTCTTA
Found at i:183769 original size:18 final size:18
Alignment explanation
Indices: 183746--183780 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
183736 TTGCAATATT
*
183746 AATATTATTAATTAATTC
1 AATATTAATAATTAATTC
*
183764 AATATTAATATTTAATT
1 AATATTAATAATTAATT
183781 TTTATTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
AATATTAATAATTAATTC
Done.