Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014886.1 Kokia drynarioides strain JFW-HI SEQ_129929, 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: 301427
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 1062 characters in sequence are not A, C, G, or T
Found at i:3883 original size:2 final size:2
Alignment explanation
Indices: 3878--3904 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3868 AAAAACATAA
3878 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3905 ATTATTCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7937 original size:17 final size:18
Alignment explanation
Indices: 7915--7950 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7905 TAAATGAGTT
7915 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
7932 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
7950 A
1 A
7951 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:8141 original size:14 final size:13
Alignment explanation
Indices: 8122--8159 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
8112 TAATTTAAAT
8122 TATTTATTATTTAA
1 TATTTA-TATTTAA
*
8136 TATTTAT-TTTGA
1 TATTTATATTTAA
8148 TATTTATATTTA
1 TATTTATATTTA
8160 CCAAGTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 11 0.52
13 4 0.19
14 6 0.29
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (13 bp):
TATTTATATTTAA
Found at i:15564 original size:83 final size:83
Alignment explanation
Indices: 15420--15579 Score: 198
Period size: 83 Copynumber: 1.9 Consensus size: 83
15410 TGTCTCAAAT
* *** * **
15420 TCATGTTCTTAATCATACTAACTGAATTTGGAATATATAATCATACTGAAACTCAACTAATTTAA
1 TCATGTTCTTAATCATACTAACTAAATTCAAAATATATAATCAAACAAAAACTCAACTAATTTAA
**
15485 GTATGCATTTTACTCCCC
66 GTAAACATTTTACTCCCC
*
15503 TCATGTTCTTAATCATACTATA-TAAATTCAAAATATATAATCAAACAAAAACTTGAA-TAATTT
1 TCATGTTCTTAATCATACTA-ACTAAATTCAAAATATATAATCAAACAAAAAC-TCAACTAATTT
15566 AAGTAAACATTTTA
64 AAGTAAACATTTTA
15580 TTCTCCTCGT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
83 61 0.94
84 4 0.06
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.37
Consensus pattern (83 bp):
TCATGTTCTTAATCATACTAACTAAATTCAAAATATATAATCAAACAAAAACTCAACTAATTTAA
GTAAACATTTTACTCCCC
Found at i:15947 original size:131 final size:131
Alignment explanation
Indices: 15672--15955 Score: 448
Period size: 130 Copynumber: 2.2 Consensus size: 131
15662 TTACTCTTCT
* * * *
15672 CACGATTTATAGAGTACTTGAAATCTAAACTCAGAGATTTCAAGTTCATGTTCTTAATCATGCTA
1 CACGATTTATAGAGTAATTGAAATCTAAACTCAGAGATTTCAAATTCACGTTCTTAATCATACTA
15737 ATTGAATTCGAAATATATAATCATACTGAAACTCAACTAATTTTAAGTAGAAATTTCATTCTCCT
66 ATTGAATTCGAAATATATAATCATACTGAAACTCAACTAATTTTAAGTAGAAATTTCATTCTCCT
15802 C
131 C
* *
15803 GA-GATTTATAGAGTAATTGAAATCTAAACTCTA-ATATTTCAAATTCACGTTCTTAATCATACT
1 CACGATTTATAGAGTAATTGAAATCTAAACTC-AGAGATTTCAAATTCACGTTCTTAATCATACT
* * *
15866 AATTGAATTCGAGATATAATAATCATACTGAAATTCAACTAATTTTAAGTATAAATTTCATTCTC
65 AATTGAATTCGAAATAT-ATAATCATACTGAAACTCAACTAATTTTAAGTAGAAATTTCATTCTC
15931 C-C
129 CTC
15933 CACGATTTATAGAGTAATTGAAA
1 CACGATTTATAGAGTAATTGAAA
15956 CCAAAATCCA
Statistics
Matches: 140, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
130 72 0.51
131 68 0.49
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (131 bp):
CACGATTTATAGAGTAATTGAAATCTAAACTCAGAGATTTCAAATTCACGTTCTTAATCATACTA
ATTGAATTCGAAATATATAATCATACTGAAACTCAACTAATTTTAAGTAGAAATTTCATTCTCCT
C
Found at i:17992 original size:7 final size:7
Alignment explanation
Indices: 17982--18026 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
17972 ATGTTTTGAT
17982 TTTTGGA
1 TTTTGGA
17989 TTTTGGA
1 TTTTGGA
*
17996 TTTCGGA
1 TTTTGGA
*
18003 TTTTAGA
1 TTTTGGA
**
18010 TTTTTAA
1 TTTTGGA
18017 TTTTGGA
1 TTTTGGA
18024 TTT
1 TTT
18027 GATTTTTTAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.18, C:0.02, G:0.20, T:0.60
Consensus pattern (7 bp):
TTTTGGA
Found at i:18019 original size:21 final size:19
Alignment explanation
Indices: 17995--18038 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
17985 TGGATTTTGG
17995 ATTTCGGATTTTAGATTTTTA
1 ATTTCGGA-TTT-GATTTTTA
* *
18016 ATTTTGGATTTGATTTTTT
1 ATTTCGGATTTGATTTTTA
18035 ATTT
1 ATTT
18039 ATGTTTAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.52
20 3 0.14
21 7 0.33
ACGTcount: A:0.20, C:0.02, G:0.14, T:0.64
Consensus pattern (19 bp):
ATTTCGGATTTGATTTTTA
Found at i:20748 original size:21 final size:21
Alignment explanation
Indices: 20708--20748 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20698 AAAAAATTAT
*
20708 AAAAAAATTATTGAATTATTC
1 AAAAAAATTATTGAAGTATTC
* *
20729 AAAAAATTTATTTAAGTATT
1 AAAAAAATTATTGAAGTATT
20749 GAATTATTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (21 bp):
AAAAAAATTATTGAAGTATTC
Found at i:21648 original size:14 final size:15
Alignment explanation
Indices: 21622--21651 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
21612 AAATTAAATT
21622 AGTTAACATTGTATG
1 AGTTAACATTGTATG
21637 AGTTAA-ATTGTATG
1 AGTTAACATTGTATG
21651 A
1 A
21652 CACGTCCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (15 bp):
AGTTAACATTGTATG
Found at i:24169 original size:14 final size:15
Alignment explanation
Indices: 24152--24192 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
24142 ACTTAATTTT
24152 AAAAAATTATAA-AA
1 AAAAAATTATAATAA
24166 AAAAAATTAATAATTAA
1 AAAAAATT-ATAA-TAA
24183 AAAAAATTAT
1 AAAAAATTAT
24193 TTTATGTCGC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.33
15 4 0.17
16 2 0.08
17 10 0.42
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAAATTATAATAA
Found at i:40614 original size:18 final size:19
Alignment explanation
Indices: 40575--40615 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
40565 TACTAATTTT
*
40575 TTTA-AATTTTGAATATTT
1 TTTATAATTTTGAATATTA
*
40593 TTTATAATTTTTAA-ATTA
1 TTTATAATTTTGAATATTA
40611 TTTAT
1 TTTAT
40616 TGAGGCGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTATAATTTTGAATATTA
Found at i:41430 original size:13 final size:13
Alignment explanation
Indices: 41414--41438 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41404 TGTCTGTTTT
41414 GGTAATTAAATTG
1 GGTAATTAAATTG
41427 GGTAATTAAATT
1 GGTAATTAAATT
41439 CATTTTGGCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (13 bp):
GGTAATTAAATTG
Found at i:45217 original size:28 final size:30
Alignment explanation
Indices: 45177--45251 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 30
45167 CTAAGAATAT
45177 AACTCCAACAATAATGCT-TGT-AAAAAAA
1 AACTCCAACAATAATGCTATGTAAAAAAAA
* *
45205 AACTCCAACAATAATGTTATTTCAGAAAAAAA
1 AACTCCAACAATAATGCTATGT-A-AAAAAAA
45237 AACTCCAA-AATAATG
1 AACTCCAACAATAATG
45252 GAACGAAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
28 17 0.41
29 2 0.05
31 7 0.17
32 15 0.37
ACGTcount: A:0.53, C:0.17, G:0.07, T:0.23
Consensus pattern (30 bp):
AACTCCAACAATAATGCTATGTAAAAAAAA
Found at i:58956 original size:117 final size:118
Alignment explanation
Indices: 58824--59053 Score: 286
Period size: 118 Copynumber: 2.0 Consensus size: 118
58814 TTTTGAGATT
* * * *
58824 TATTTTGCTAAAATAAATTCTGTTTTATAA-CTTTTGAATATTATTTCACAACATTT-AAAAATT
1 TATTGTGCTAAAATAAATTCTGATTTATAATCTTTTGAATATTATTTCACAAAATTTCAAAAA-A
** * *
58887 ATTTTCATAGATATTTAT-AAAAGAATAAAATTTCAAGAATTTTGAAATTGTTTA
65 AAATT-ATAAATATTTATGAAAACAATAAAATTTCAAGAATTTTGAAATTGTTTA
* * * * *
58941 TATTGTGCTAAAATAATTTTTGATTTATAATTTTTTTAATGTTATTTCACAAAATTTCAAAAAAA
1 TATTGTGCTAAAATAAATTCTGATTTATAATCTTTTGAATATTATTTCACAAAATTTCAAAAAAA
* *
59006 AATTATAAATATTTTTGAAAACAATAAAATTTCAAGAATTTTTAAATT
66 AATTATAAATATTTATGAAAACAATAAAATTTCAAGAATTTTGAAATT
59054 ATTTTGATTA
Statistics
Matches: 95, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
117 36 0.38
118 54 0.57
119 5 0.05
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (118 bp):
TATTGTGCTAAAATAAATTCTGATTTATAATCTTTTGAATATTATTTCACAAAATTTCAAAAAAA
AATTATAAATATTTATGAAAACAATAAAATTTCAAGAATTTTGAAATTGTTTA
Found at i:62394 original size:14 final size:14
Alignment explanation
Indices: 62375--62404 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
62365 AAATTCAAAT
*
62375 AAAACCCAGAATTA
1 AAAACCCAAAATTA
62389 AAAACCCAAAATTA
1 AAAACCCAAAATTA
62403 AA
1 AA
62405 GATAATTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.20, G:0.03, T:0.13
Consensus pattern (14 bp):
AAAACCCAAAATTA
Found at i:64380 original size:31 final size:32
Alignment explanation
Indices: 64342--64405 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
64332 ATTAATTTGA
*
64342 TTTTTTTAAAAAG-TTGATGGTTAAATTTAAT
1 TTTTTTTAAAAAGATTAATGGTTAAATTTAAT
*
64373 TTTTTTTAAAGAGATTAATGGTTAAATTTAAT
1 TTTTTTTAAAAAGATTAATGGTTAAATTTAAT
64405 T
1 T
64406 CAATAGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (32 bp):
TTTTTTTAAAAAGATTAATGGTTAAATTTAAT
Found at i:67400 original size:30 final size:28
Alignment explanation
Indices: 67366--67445 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 28
67356 TCATTAAGCA
* *
67366 CTTCAAATTTTTGGAAATTTTGATTAAAAC
1 CTTCAAATTTTT-AAAATTTTAATT-AAAC
67396 CTTCAAGAGTTTTTAAAATTTTAATTAAAC
1 CTTCAA-A-TTTTTAAAATTTTAATTAAAC
*
67426 CTTCTAAAATTTTCAAAATT
1 CTTC--AAATTTTTAAAATT
67446 CTCATTAGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
30 24 0.56
31 12 0.28
32 7 0.16
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (28 bp):
CTTCAAATTTTTAAAATTTTAATTAAAC
Found at i:70425 original size:81 final size:80
Alignment explanation
Indices: 70263--70430 Score: 187
Period size: 80 Copynumber: 2.1 Consensus size: 80
70253 ATAAATAGAG
* * * * ***
70263 AAATTAATATATTGTAAAATTGCACTTTGCTCCTCAAATGAAAAATTTTCAATTGAATCCTCTTA
1 AAATTAATATATAGTAAAATTACACTTTACTCCTAAAATGAAAAAAAATCAATTGAATCCTCTTA
70328 TAAATAAGAAAATAT
66 TAAATAAGAAAATAT
* * *
70343 AAATTAATATATAGTAAAATTACATTTTAACTCCTAAAAATGAAAAAAAATCTATT-AATCCTTT
1 AAATTAATATATAGTAAAATTACACTTT-ACTCCT-AAAATGAAAAAAAATCAATTGAATCCTCT
*
70407 TA-AAATGAAGAAATTAT
64 TATAAAT-AAGAAAATAT
*
70424 AATTTAA
1 AAATTAA
70431 CACATGATAA
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
80 29 0.40
81 29 0.40
82 15 0.21
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.36
Consensus pattern (80 bp):
AAATTAATATATAGTAAAATTACACTTTACTCCTAAAATGAAAAAAAATCAATTGAATCCTCTTA
TAAATAAGAAAATAT
Found at i:75678 original size:23 final size:24
Alignment explanation
Indices: 75644--75691 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
75634 GTTTCAATTC
75644 AATTTATATATAAAAATATT-TTA
1 AATTTATATATAAAAATATTATTA
75667 AATTTA-ATTATAAAAATATTATTA
1 AATTTATA-TATAAAAATATTATTA
75691 A
1 A
75692 TAAAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 1 0.04
23 18 0.78
24 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AATTTATATATAAAAATATTATTA
Found at i:77219 original size:3 final size:3
Alignment explanation
Indices: 77197--77251 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
77187 ACAGGTCAGT
* * * *
77197 TTC TTC ATC TTC TTC ATC TTC TTC ATC TTC TTC ATC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
77245 TTC TTC T
1 TTC TTC T
77252 GTCAATGAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.07, C:0.33, G:0.00, T:0.60
Consensus pattern (3 bp):
TTC
Found at i:77251 original size:9 final size:9
Alignment explanation
Indices: 77197--77247 Score: 93
Period size: 9 Copynumber: 5.7 Consensus size: 9
77187 ACAGGTCAGT
77197 TTCTTCATC
1 TTCTTCATC
77206 TTCTTCATC
1 TTCTTCATC
77215 TTCTTCATC
1 TTCTTCATC
77224 TTCTTCATC
1 TTCTTCATC
*
77233 TTCTTCTTC
1 TTCTTCATC
77242 TTCTTC
1 TTCTTC
77248 TTCTGTCAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.08, C:0.33, G:0.00, T:0.59
Consensus pattern (9 bp):
TTCTTCATC
Found at i:82441 original size:21 final size:23
Alignment explanation
Indices: 82408--82449 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
82398 CACAATACCA
82408 TTAACAATGTCTTTCA-TATCTG
1 TTAACAATGTCTTTCAGTATCTG
*
82430 TTAA-AATTTCTTTCAGTATC
1 TTAACAATGTCTTTCAGTATC
82450 CATGATTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.48
Consensus pattern (23 bp):
TTAACAATGTCTTTCAGTATCTG
Found at i:88922 original size:21 final size:20
Alignment explanation
Indices: 88890--88941 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
88880 TCGAAAACTC
* *
88890 TCAATTTTTTTTTTTACAAT
1 TCAATATTTTTTTCTACAAT
*
88910 TCAATACTTTTTTTCTATAAT
1 TCAATA-TTTTTTTCTACAAT
88931 TCAATATTTTT
1 TCAATATTTTT
88942 ATTCATGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.62
Consensus pattern (20 bp):
TCAATATTTTTTTCTACAAT
Found at i:103703 original size:3 final size:3
Alignment explanation
Indices: 103697--103721 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
103687 AATGTGAACT
103697 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
103722 CATCCGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:110249 original size:21 final size:21
Alignment explanation
Indices: 110225--110294 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
110215 CAAATGTTTG
110225 TATAGTGTGTAACGTTGATTA
1 TATAGTGTGTAACGTTGATTA
* ** *
110246 TATAGATCCTGT-ACGAAGGATTG
1 TATAG-T-GTGTAACG-TTGATTA
*
110269 TGTAGTGTGTAACGTTGATTA
1 TATAGTGTGTAACGTTGATTA
110290 TATAG
1 TATAG
110295 ATCCTGTATG
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
21 16 0.46
22 8 0.23
23 11 0.31
ACGTcount: A:0.29, C:0.07, G:0.26, T:0.39
Consensus pattern (21 bp):
TATAGTGTGTAACGTTGATTA
Found at i:110267 original size:23 final size:23
Alignment explanation
Indices: 110241--110309 Score: 54
Period size: 23 Copynumber: 3.1 Consensus size: 23
110231 GTGTAACGTT
110241 GATTATATAGATCCTGTACGAAG
1 GATTATATAGATCCTGTACGAAG
* * * **
110264 GATTGTGTAG-T-GTGTAACG-TT
1 GATTATATAGATCCTGT-ACGAAG
*
110285 GATTATATAGATCCTGTATGAAG
1 GATTATATAGATCCTGTACGAAG
110308 GA
1 GA
110310 GTAAAAATAG
Statistics
Matches: 31, Mismatches: 11, Indels: 8
0.62 0.22 0.16
Matches are distributed among these distances:
21 11 0.35
22 7 0.23
23 13 0.42
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35
Consensus pattern (23 bp):
GATTATATAGATCCTGTACGAAG
Found at i:110290 original size:44 final size:44
Alignment explanation
Indices: 110222--110309 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
110212 TCACAAATGT
110222 TTGTATAGTGTGTAACGTTGATTATATAGATCCTGTACGAAGGA
1 TTGTATAGTGTGTAACGTTGATTATATAGATCCTGTACGAAGGA
* *
110266 TTGTGTAGTGTGTAACGTTGATTATATAGATCCTGTATGAAGGA
1 TTGTATAGTGTGTAACGTTGATTATATAGATCCTGTACGAAGGA
110310 GTAAAAATAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (44 bp):
TTGTATAGTGTGTAACGTTGATTATATAGATCCTGTACGAAGGA
Found at i:116290 original size:27 final size:27
Alignment explanation
Indices: 116260--116335 Score: 125
Period size: 27 Copynumber: 2.8 Consensus size: 27
116250 TGGATATGGA
*
116260 TATCCACCTCCCCCACCGGGGTATGCG
1 TATCCTCCTCCCCCACCGGGGTATGCG
*
116287 TATCCTCCTCCCCCACCAGGGTATGCG
1 TATCCTCCTCCCCCACCGGGGTATGCG
116314 TATCCTCCTCCCCCACCAGGGG
1 TATCCTCCTCCCCCACC-GGGG
116336 CTTATGGGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
27 42 0.93
28 3 0.07
ACGTcount: A:0.14, C:0.46, G:0.20, T:0.20
Consensus pattern (27 bp):
TATCCTCCTCCCCCACCGGGGTATGCG
Found at i:116718 original size:3 final size:3
Alignment explanation
Indices: 116710--116755 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
116700 TCTTTTATAA
116710 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
116756 GATTTTGGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:128393 original size:22 final size:22
Alignment explanation
Indices: 128376--128420 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
128366 ATAATTGAGC
128376 GTAAGAGCCAAATGAATTGAAA
1 GTAAGAGCCAAATGAATTGAAA
*
128398 GTGAGAGCCAAATGAATTGAAA
1 GTAAGAGCCAAATGAATTGAAA
128420 G
1 G
128421 GTTCATGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.09, G:0.27, T:0.18
Consensus pattern (22 bp):
GTAAGAGCCAAATGAATTGAAA
Found at i:133336 original size:10 final size:10
Alignment explanation
Indices: 133321--133346 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
133311 TTTGCAAATT
133321 AAAAAAGAAA
1 AAAAAAGAAA
133331 AAAAAAGAAA
1 AAAAAAGAAA
133341 AAAAAA
1 AAAAAA
133347 ATAAAAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:133347 original size:16 final size:17
Alignment explanation
Indices: 133321--133355 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
133311 TTTGCAAATT
133321 AAAAAAGAAAAAAAAAG
1 AAAAAAGAAAAAAAAAG
*
133338 AAAAAA-AAAATAAAAG
1 AAAAAAGAAAAAAAAAG
133354 AA
1 AA
133356 GCTTAAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.89, C:0.00, G:0.09, T:0.03
Consensus pattern (17 bp):
AAAAAAGAAAAAAAAAG
Found at i:135521 original size:28 final size:28
Alignment explanation
Indices: 135462--135521 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
135452 TATATATATT
*
135462 TTTATAATTTTTAAGATTAAATTGAAAT
1 TTTATAATTTTTAAGATTAAATTGAAAC
*
135490 TTTATTATTTTTATAG-TTAAATT-ATAAC
1 TTTATAATTTTTA-AGATTAAATTGA-AAC
135518 TTTA
1 TTTA
135522 CCATGTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.04
28 25 0.89
29 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (28 bp):
TTTATAATTTTTAAGATTAAATTGAAAC
Found at i:135892 original size:3 final size:3
Alignment explanation
Indices: 135884--135915 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
135874 ATTTAATAAC
135884 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
135916 ATTTCTCTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:137524 original size:12 final size:12
Alignment explanation
Indices: 137485--137525 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
137475 AAACCAGAGA
137485 ATATATACATAC
1 ATATATACATAC
*
137497 ATACATACATAC
1 ATATATACATAC
* *
137509 ATATATATATAT
1 ATATATACATAC
137521 ATATA
1 ATATA
137526 GCAAATTCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (12 bp):
ATATATACATAC
Found at i:137525 original size:8 final size:8
Alignment explanation
Indices: 137485--137523 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
137475 AAACCAGAGA
137485 ATATATAC
1 ATATATAC
*
137493 ATACATAC
1 ATATATAC
*
137501 ATACATAC
1 ATATATAC
*
137509 ATATATAT
1 ATATATAC
137517 ATATATA
1 ATATATA
137524 TAGCAAATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATATAC
Found at i:140107 original size:2 final size:2
Alignment explanation
Indices: 140100--140125 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
140090 TTAAAACATA
140100 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
140126 TTATGAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:156036 original size:7 final size:7
Alignment explanation
Indices: 156026--156059 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
156016 TTCAAAAATG
156026 AAAAAGA
1 AAAAAGA
156033 AAAAA-A
1 AAAAAGA
156039 AAAAAGA
1 AAAAAGA
156046 AAAAAGA
1 AAAAAGA
156053 AAAAAGA
1 AAAAAGA
156060 CTTTAAGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:156042 original size:13 final size:14
Alignment explanation
Indices: 156026--156059 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
156016 TTCAAAAATG
156026 AAAAAGAAAAAA-A
1 AAAAAGAAAAAAGA
156039 AAAAAGAAAAAAGA
1 AAAAAGAAAAAAGA
156053 AAAAAGA
1 AAAAAGA
156060 CTTTAAGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAGA
Found at i:159380 original size:31 final size:31
Alignment explanation
Indices: 159330--159398 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
159320 AAAAAACAAC
* *
159330 AATTTAA-TTTTTTTGAAATATTAATAA-TTA
1 AATTTAACTCTTTTTAAAATATTAA-AAGTTA
159360 AATTTAACTCTTTTTAAAATATTAAAAGTTA
1 AATTTAACTCTTTTTAAAATATTAAAAGTTA
159391 AA-TTAACT
1 AATTTAACT
159399 AAAAAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 15 0.43
31 20 0.57
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (31 bp):
AATTTAACTCTTTTTAAAATATTAAAAGTTA
Found at i:168303 original size:22 final size:21
Alignment explanation
Indices: 168278--168327 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
168268 TCATATATTA
168278 TAAATTATATATTTTTTATAAT
1 TAAATTA-ATATTTTTTATAAT
* *
168300 TAAACTTAATGTTTTTTATTAT
1 TAAA-TTAATATTTTTTATAAT
*
168322 TTAATT
1 TAAATT
168328 TGAATTTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 19 0.79
23 3 0.12
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TAAATTAATATTTTTTATAAT
Found at i:169150 original size:21 final size:23
Alignment explanation
Indices: 169114--169156 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
169104 TTCTTGAAAA
169114 ATATTTATATTAATTTTAATTTC
1 ATATTTATATTAATTTTAATTTC
169137 ATATTTA-A-TAATTTTAATTT
1 ATATTTATATTAATTTTAATTT
169157 TTCATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.60
22 1 0.05
23 7 0.35
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
ATATTTATATTAATTTTAATTTC
Found at i:172647 original size:17 final size:17
Alignment explanation
Indices: 172622--172658 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
172612 ACCAACTTAT
*
172622 TGGATAATAAGTGTGGG
1 TGGAGAATAAGTGTGGG
172639 TGGAGAATAAGTGTGGG
1 TGGAGAATAAGTGTGGG
172656 TGG
1 TGG
172659 TTTGTTAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.46, T:0.27
Consensus pattern (17 bp):
TGGAGAATAAGTGTGGG
Found at i:176095 original size:163 final size:163
Alignment explanation
Indices: 175852--176178 Score: 654
Period size: 163 Copynumber: 2.0 Consensus size: 163
175842 CAAGGCAAAG
175852 ACATCCTGGAATTTTCTTTAGATGCTTCAGTATAGTTTAACTTTTTTCCCCTCAATAAATATATA
1 ACATCCTGGAATTTTCTTTAGATGCTTCAGTATAGTTTAACTTTTTTCCCCTCAATAAATATATA
175917 TACATACAAATATTTAACATATTTCTCAATATATACTTGTTATTTTGGACTAGCATTTTTCTTCT
66 TACATACAAATATTTAACATATTTCTCAATATATACTTGTTATTTTGGACTAGCATTTTTCTTCT
175982 AAAGCTCAAATGACTTTTATCAAATGATTAGTT
131 AAAGCTCAAATGACTTTTATCAAATGATTAGTT
176015 ACATCCTGGAATTTTCTTTAGATGCTTCAGTATAGTTTAACTTTTTTCCCCTCAATAAATATATA
1 ACATCCTGGAATTTTCTTTAGATGCTTCAGTATAGTTTAACTTTTTTCCCCTCAATAAATATATA
176080 TACATACAAATATTTAACATATTTCTCAATATATACTTGTTATTTTGGACTAGCATTTTTCTTCT
66 TACATACAAATATTTAACATATTTCTCAATATATACTTGTTATTTTGGACTAGCATTTTTCTTCT
176145 AAAGCTCAAATGACTTTTATCAAATGATTAGTT
131 AAAGCTCAAATGACTTTTATCAAATGATTAGTT
176178 A
1 A
176179 AAAACACTTG
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
163 164 1.00
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (163 bp):
ACATCCTGGAATTTTCTTTAGATGCTTCAGTATAGTTTAACTTTTTTCCCCTCAATAAATATATA
TACATACAAATATTTAACATATTTCTCAATATATACTTGTTATTTTGGACTAGCATTTTTCTTCT
AAAGCTCAAATGACTTTTATCAAATGATTAGTT
Found at i:181535 original size:17 final size:16
Alignment explanation
Indices: 181506--181539 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
181496 AATAGAATTT
181506 TTAAAATAATATTATA
1 TTAAAATAATATTATA
*
181522 TTAAATATATTATTATA
1 TTAAA-ATAATATTATA
181539 T
1 T
181540 GATACATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAAATAATATTATA
Found at i:188354 original size:17 final size:17
Alignment explanation
Indices: 188320--188353 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
188310 AATTTTTTAA
*
188320 TAAAATTTTTATAATTT
1 TAAAAATTTTATAATTT
188337 TAAAAATTTTAT-ATTT
1 TAAAAATTTTATAATTT
188353 T
1 T
188354 TTATTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAAAAATTTTATAATTT
Found at i:195933 original size:22 final size:22
Alignment explanation
Indices: 195903--195947 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
195893 TAAATTTAGT
*
195903 AACCCTTCTCACATCATTGAGC
1 AACCCTTCTCACATCATTAAGC
* * *
195925 AACCTTTCTTAGATCATTAAGC
1 AACCCTTCTCACATCATTAAGC
195947 A
1 A
195948 TGTATATTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.29, G:0.09, T:0.31
Consensus pattern (22 bp):
AACCCTTCTCACATCATTAAGC
Found at i:197955 original size:9 final size:9
Alignment explanation
Indices: 197941--197978 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
197931 AGTGTCAAGC
197941 AATATTTTT
1 AATATTTTT
197950 AATATTTTT
1 AATATTTTT
*
197959 ATAAATTTTT
1 A-ATATTTTT
197969 AAT-TTTTT
1 AATATTTTT
197977 AA
1 AA
197979 ATGTATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 7 0.27
9 11 0.42
10 8 0.31
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
AATATTTTT
Found at i:201481 original size:44 final size:42
Alignment explanation
Indices: 201432--201570 Score: 125
Period size: 44 Copynumber: 3.2 Consensus size: 42
201422 ACGGAGGAAG
* *
201432 AATTTTGTTGTGTTCCCATAGCCTAGTGATAGATTTTATTTGCA
1 AATTTTGTTGTGTTCCCA-AGCC-AGTGACAGATTTTATTTACA
* * *
201476 AATTTTGTTGTGTACTCACAATCCAGTGACAGGTTTTATTTACA
1 AATTTTGTTGTGT--TCCCAAGCCAGTGACAGATTTTATTTACA
* * * * * *
201520 AATTTTGTTGTGTACCCACAATCCAATGGCAGAATTTATCTACA
1 AATTTTGTTGTGT-TCC-CAAGCCAGTGACAGATTTTATTTACA
201564 AATTTTG
1 AATTTTG
201571 CTGTATCCAT
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
43 1 0.01
44 71 0.90
45 3 0.04
46 4 0.05
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (42 bp):
AATTTTGTTGTGTTCCCAAGCCAGTGACAGATTTTATTTACA
Found at i:201954 original size:24 final size:24
Alignment explanation
Indices: 201905--201954 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
201895 GAACTTATGC
*
201905 TTTTTTTTACTGTTTTGTCATTAT
1 TTTTTTTTACTGTTTTGTCATCAT
*
201929 TTTTTTTTATTGTTTTG-CTATCAT
1 TTTTTTTTACTGTTTTGTC-ATCAT
201953 TT
1 TT
201955 CTCTATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.12, C:0.08, G:0.08, T:0.72
Consensus pattern (24 bp):
TTTTTTTTACTGTTTTGTCATCAT
Found at i:202532 original size:21 final size:21
Alignment explanation
Indices: 202506--202546 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
202496 AACCCCATAT
*
202506 ATAATGTAATATTGAATTTGG
1 ATAATGTAATATTAAATTTGG
202527 ATAATGTAATATTAAATTTG
1 ATAATGTAATATTAAATTTG
202547 ACGAAACTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (21 bp):
ATAATGTAATATTAAATTTGG
Found at i:204628 original size:1 final size:1
Alignment explanation
Indices: 204624--204649 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
204614 TTTTTAATTT
204624 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
204650 CTTAAACTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:204847 original size:17 final size:18
Alignment explanation
Indices: 204827--204860 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
204817 AATTAATTTT
*
204827 TTAAATTAAAT-GAAAAA
1 TTAAAATAAATCGAAAAA
204844 TTAAAATAAATCGAAAA
1 TTAAAATAAATCGAAAA
204861 TTTACATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (18 bp):
TTAAAATAAATCGAAAAA
Found at i:218222 original size:16 final size:17
Alignment explanation
Indices: 218201--218233 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
218191 GAAAAACTAA
218201 ATTTAA-TATTTACGAT
1 ATTTAAGTATTTACGAT
218217 ATTTAATGTATTTACGA
1 ATTTAA-GTATTTACGA
218234 AAGGTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (17 bp):
ATTTAAGTATTTACGAT
Found at i:219731 original size:23 final size:23
Alignment explanation
Indices: 219703--219797 Score: 131
Period size: 23 Copynumber: 4.2 Consensus size: 23
219693 AACAGGAAGT
*
219703 ACACACAGTGC-AATCCAGTAGGC
1 ACACACAGCGCAAAT-CAGTAGGC
*
219726 ACACACAGTGC-AATCAGTAGGC
1 ACACACAGCGCAAATCAGTAGGC
*
219748 ACACATAGCGCAAATCAGTAGGC
1 ACACACAGCGCAAATCAGTAGGC
*
219771 ACACATAGCGCAAATCAGTAGGC
1 ACACACAGCGCAAATCAGTAGGC
219794 ACAC
1 ACAC
219798 GAAGTGCGAA
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
22 17 0.25
23 52 0.75
ACGTcount: A:0.38, C:0.28, G:0.21, T:0.13
Consensus pattern (23 bp):
ACACACAGCGCAAATCAGTAGGC
Found at i:219812 original size:23 final size:22
Alignment explanation
Indices: 219703--219836 Score: 128
Period size: 23 Copynumber: 5.9 Consensus size: 22
219693 AACAGGAAGT
* *
219703 ACACACAGTGCAATCCAGTAGGC
1 ACACATAGTGCAA-ACAGTAGGC
* *
219726 ACACACAGTGCAATCAGTAGGC
1 ACACATAGTGCAAACAGTAGGC
*
219748 ACACATAGCGCAAATCAGTAGGC
1 ACACATAGTGCAAA-CAGTAGGC
*
219771 ACACATAGCGCAAATCAGTAGGC
1 ACACATAGTGCAAA-CAGTAGGC
*
219794 ACACGA-AGTGCGAAACAGTAAGC
1 ACAC-ATAGTGC-AAACAGTAGGC
219817 ACACGA-AGTGCGAAACAGTA
1 ACAC-ATAGTGC-AAACAGTA
219837 AGCGCGCTAG
Statistics
Matches: 102, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
22 19 0.19
23 79 0.77
24 4 0.04
ACGTcount: A:0.40, C:0.25, G:0.23, T:0.12
Consensus pattern (22 bp):
ACACATAGTGCAAACAGTAGGC
Found at i:226973 original size:23 final size:22
Alignment explanation
Indices: 226941--227043 Score: 100
Period size: 23 Copynumber: 4.5 Consensus size: 22
226931 GCTGGGGAAA
*
226941 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
226963 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
** * *
226986 CAGTAGGTGCACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
*
227009 CAGTAGGCACACGA-AGTGCAAAA
1 CAGTAGGCACAC-ACAGTGC-AAT
*
227032 CAGTAAGCACAC
1 CAGTAGGCACAC
227044 GAAGTGCGAA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
22 15 0.22
23 52 0.76
24 1 0.01
ACGTcount: A:0.39, C:0.26, G:0.22, T:0.13
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:227044 original size:23 final size:23
Alignment explanation
Indices: 226938--227062 Score: 94
Period size: 23 Copynumber: 5.5 Consensus size: 23
226928 AGTGCTGGGG
226938 AAACAGTAAGCACACACAGTGCA
1 AAACAGTAAGCACACACAGTGCA
** *
226961 ATCCAGTAGGCACACACAGTGC-
1 AAACAGTAAGCACACACAGTGCA
* * ** * *
226983 AATCAGTAGGTGCACATAGCGCA
1 AAACAGTAAGCACACACAGTGCA
* *
227006 AATCAGTAGGCACACGA-AGTGCA
1 AAACAGTAAGCACAC-ACAGTGCA
*
227029 AAACAGTAAGCACACGA-AGTGCG
1 AAACAGTAAGCACAC-ACAGTGCA
*
227052 AAACAATAAGC
1 AAACAGTAAGC
227063 GCTAGCGTTC
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
22 16 0.19
23 67 0.80
24 1 0.01
ACGTcount: A:0.42, C:0.24, G:0.22, T:0.12
Consensus pattern (23 bp):
AAACAGTAAGCACACACAGTGCA
Found at i:233868 original size:15 final size:14
Alignment explanation
Indices: 233839--233877 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
233829 ACCACCCATA
233839 TTTTTTTTTC-ATG
1 TTTTTTTTTCTATG
233852 TTTTTTTTTCTATTG
1 TTTTTTTTTCTA-TG
*
233867 TTTCTTTTTCT
1 TTTTTTTTTCT
233878 TTTCTACTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.43
14 1 0.04
15 12 0.52
ACGTcount: A:0.05, C:0.10, G:0.05, T:0.79
Consensus pattern (14 bp):
TTTTTTTTTCTATG
Found at i:234038 original size:6 final size:6
Alignment explanation
Indices: 234023--234051 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
234013 CACTAAAACC
234023 CTTTTT -TTTTT CTTTTT CTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
234052 TGCTACTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
CTTTTT
Found at i:241179 original size:6 final size:6
Alignment explanation
Indices: 241168--241203 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
241158 ACCCGTACAT
241168 ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA
1 ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA
241204 CCGGTATAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (6 bp):
ACAAAA
Found at i:253387 original size:58 final size:56
Alignment explanation
Indices: 253270--253394 Score: 144
Period size: 58 Copynumber: 2.2 Consensus size: 56
253260 ATATTTAAAA
* * *
253270 AAATTTAATTTAATAATTATCTTAATAGTATTCTATTAATTTAATAAGATTTAATATT
1 AAATTTAATCTAATAATTATCTTAATAGTATTATATTAATTTAAT-A-ATTAAATATT
* *
253328 AAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAAT-ATTAAAGTGATT
1 AAATTTAATCTAATAATTATCTTAAT-AGTATTATATTAATTTAATAATTAAA-T-ATT
*
253386 AAGTTTAAT
1 AAATTTAAT
253395 ATAGTTAAAC
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
56 5 0.09
57 1 0.02
58 34 0.59
59 18 0.31
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (56 bp):
AAATTTAATCTAATAATTATCTTAATAGTATTATATTAATTTAATAATTAAATATT
Found at i:255530 original size:28 final size:29
Alignment explanation
Indices: 255499--255559 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
255489 AAAATGCAAT
* *
255499 TTTTGGATAC-CCAGGGGCAAAACGGTAA
1 TTTTGGACACTCCAGGGGCAAAACAGTAA
* * *
255527 TTTTGTACACTTCAGGGGCAAAATAGTAA
1 TTTTGGACACTCCAGGGGCAAAACAGTAA
255556 TTTT
1 TTTT
255560 TGGAGGTTCG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (29 bp):
TTTTGGACACTCCAGGGGCAAAACAGTAA
Found at i:255577 original size:29 final size:29
Alignment explanation
Indices: 255541--255823 Score: 93
Period size: 29 Copynumber: 9.8 Consensus size: 29
255531 GTACACTTCA
*
255541 GGGG-CAAAATAGTAATTTTTGGAGGTTC
1 GGGGTCAAAATAGTAATTTTTGGAAGTTC
*
255569 GGGGTCAAAA-ATGGAATTTTTGGACA-TTC
1 GGGGTCAAAATA-GTAATTTTTGGA-AGTTC
* *
255598 GAGAGT-AAAATGGTAATTTTTGGAAAGTTC
1 G-GGGTCAAAATAGTAATTTTTGG-AAGTTC
* * * * * * *
255628 AGGATCAAAAAAGAAATTTTTAGATATTTG
1 GGGGTCAAAATAGTAATTTTTGGA-AGTTC
* * * * *
255658 GGGGT-AAAATGGTAATTTCTGAAAATTT
1 GGGGTCAAAATAGTAATTTTTGGAAGTTC
** * *
255686 TAGGTCAAAA-AATGAATTTTTGGAAGTTTA
1 GGGGTCAAAATAGT-AATTTTTGGAAG-TTC
* * * * *
255716 AGGGTAAAAAT-GTAATTTTTGAAAAATTT
1 GGGGTCAAAATAGTAATTTTTG-GAAGTTC
* * *
255745 AGGGTTAAAA-ATGTAATTTTTGAAAGTTC
1 GGGGTCAAAATA-GTAATTTTTGGAAGTTC
* * *
255774 AAGGGT-AAAAT-GTGATTTTTGGAAAGTTT
1 -GGGGTCAAAATAGTAATTTTTGG-AAGTTC
* *
255803 GAGGTTAAAAT-GTAATTTTTG
1 GGGGTCAAAATAGTAATTTTTG
255824 TAAAGTTTAA
Statistics
Matches: 187, Mismatches: 48, Indels: 39
0.68 0.18 0.14
Matches are distributed among these distances:
28 24 0.13
29 110 0.59
30 53 0.28
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.36
Consensus pattern (29 bp):
GGGGTCAAAATAGTAATTTTTGGAAGTTC
Found at i:255646 original size:59 final size:57
Alignment explanation
Indices: 255537--255868 Score: 208
Period size: 59 Copynumber: 5.7 Consensus size: 57
255527 TTTTGTACAC
* * * * *
255537 TTCAGGGGCAAAATAGTAATTTTTGG-AGGTTCGGGGTCAAAAATGGAATTTTTGGACA-
1 TTCAAGGGTAAAAT-GTAATTTTTGGAAAGTTCAGGGTCAAAAA-AGAATTTTTGGA-AG
* * * *
255595 TTCGAGAGTAAAATGGTAATTTTTGGAAAGTTCAGGATCAAAAAAGAAATTTTTAGATA-
1 TTCAAGGGTAAAAT-GTAATTTTTGGAAAGTTCAGGGTCAAAAAAG-AATTTTTGGA-AG
*** * * * *
255654 TTTGGGGGTAAAATGGTAATTTCTGAAAATTTTA-GGTCAAAAAATGAATTTTTGGAAG
1 TTCAAGGGTAAAAT-GTAATTTTTGGAAAGTTCAGGGTCAAAAAA-GAATTTTTGGAAG
* * * * * * *
255712 TTTAAGGGTAAAAATGTAATTTTTGAAAAATTTAGGGTTAAAAATGTAATTTTTGAAAG
1 TTCAAGGGT-AAAATGTAATTTTTGGAAAGTTCAGGGTCAAAAAAG-AATTTTTGGAAG
* * * * *
255771 TTCAAGGGTAAAATGTGATTTTTGGAAAGTT-TGAGGT-TAAAATGTAATTTTTGTAAAG
1 TTCAAGGGTAAAATGTAATTTTTGGAAAGTTCAG-GGTCAAAAAAG-AATTTTTG-GAAG
* * * *
255829 TTTAAGGGTTAGAATGTGATTTTTGGAAAGTTTAGGGTCA
1 TTCAAGGG-TAAAATGTAATTTTTGGAAAGTTCAGGGTCA
255869 GAAATGTACT
Statistics
Matches: 225, Mismatches: 37, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
57 17 0.08
58 98 0.44
59 109 0.48
60 1 0.00
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (57 bp):
TTCAAGGGTAAAATGTAATTTTTGGAAAGTTCAGGGTCAAAAAAGAATTTTTGGAAG
Found at i:255721 original size:58 final size:57
Alignment explanation
Indices: 255571--255892 Score: 247
Period size: 59 Copynumber: 5.5 Consensus size: 57
255561 GGAGGTTCGG
* ** * * * *
255571 GGTCAAAAATGGAATTTTTGGACA-TTCGAGAGTAAAATGGTAATTTTTGGAAAGTTCA
1 GGTCAAAAATGTAATTTTTGGA-AGTTTAAGGGTAAAAT-GTAATTTTTGAAAATTTTA
* * * ** *
255629 GGATCAAAAAAGAAATTTTTAGATA-TTTGGGGGTAAAATGGTAATTTCTGAAAATTTTA
1 GG-TCAAAAATGTAATTTTTGGA-AGTTTAAGGGTAAAAT-GTAATTTTTGAAAATTTTA
*
255688 GGTCAAAAAATG-AATTTTTGGAAGTTTAAGGGTAAAAATGTAATTTTTGAAAAATTTA
1 GGTC-AAAAATGTAATTTTTGGAAGTTTAAGGGT-AAAATGTAATTTTTGAAAATTTTA
* * * * * *
255746 GGGTTAAAAATGTAATTTTTGAAAGTTCAAGGGTAAAATGTGATTTTTGGAAAGTTTGA
1 -GGTCAAAAATGTAATTTTTGGAAGTTTAAGGGTAAAATGTAATTTTT-GAAAATTTTA
* * * * * *
255805 GGT-TAAAATGTAATTTTTGTAAAGTTTAAGGGTTAGAATGTGATTTTTGGAAAGTTTA
1 GGTCAAAAATGTAATTTTTG-GAAGTTTAAGGG-TAAAATGTAATTTTTGAAAATTTTA
* *
255863 GGGTCAGAAATGTACTTTTTGGATAGTTTA
1 -GGTCAAAAATGTAATTTTTGGA-AGTTTA
255893 GGGACTTTTT
Statistics
Matches: 217, Mismatches: 35, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
57 16 0.07
58 77 0.35
59 105 0.48
60 19 0.09
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (57 bp):
GGTCAAAAATGTAATTTTTGGAAGTTTAAGGGTAAAATGTAATTTTTGAAAATTTTA
Found at i:255755 original size:117 final size:115
Alignment explanation
Indices: 255571--255868 Score: 280
Period size: 117 Copynumber: 2.5 Consensus size: 115
255561 GGAGGTTCGG
** * * *
255571 GGTCAAAAATGGAATTTTTGGACA-TTCGAGAGTAAAATGGTAATTTTTGGAAAGTTCAGGATCA
1 GGTCAAAAAT-GAATTTTTGGA-AGTTTAAGGGTAAAAT-GTAATTTTTGGAAAGTTTAGGGTCA
* *** *
255635 AAAAAGAAATTTTTAGATA-TTTGGGGGTAAAATGGTAATTTCT-GAAAATTTTA
63 AAAAAGAAATTTTT-GAAAGTTCAAGGGTAAAAT-GTAATTTCTGGAAAATTTGA
* * *
255688 GGTCAAAAAATGAATTTTTGGAAGTTTAAGGGTAAAAATGTAATTTTTGAAAAATTTAGGGTTAA
1 GGTC-AAAAATGAATTTTTGGAAGTTTAAGGGT-AAAATGTAATTTTTGGAAAGTTTAGGGTCAA
* * * * *
255753 AAATGTAATTTTTGAAAGTTCAAGGGTAAAATGTGATTTTTGGAAAGTTTGA
64 AAAAGAAATTTTTGAAAGTTCAAGGGTAAAATGTAATTTCTGGAAAATTTGA
* * * *
255805 GGT-TAAAATGTAATTTTTGTAAAGTTTAAGGGTTAGAATGTGATTTTTGGAAAGTTTAGGGTCA
1 GGTCAAAAATG-AATTTTTG-GAAGTTTAAGGG-TAAAATGTAATTTTTGGAAAGTTTAGGGTCA
255869 GAAATGTACT
Statistics
Matches: 148, Mismatches: 25, Indels: 16
0.78 0.13 0.08
Matches are distributed among these distances:
115 6 0.04
116 19 0.13
117 111 0.75
118 12 0.08
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (115 bp):
GGTCAAAAATGAATTTTTGGAAGTTTAAGGGTAAAATGTAATTTTTGGAAAGTTTAGGGTCAAAA
AAGAAATTTTTGAAAGTTCAAGGGTAAAATGTAATTTCTGGAAAATTTGA
Found at i:255845 original size:30 final size:30
Alignment explanation
Indices: 255694--255892 Score: 223
Period size: 30 Copynumber: 6.8 Consensus size: 30
255684 TTTAGGTCAA
*
255694 AAAATG-AATTTTTGG-AAGTTTAAGGGTA
1 AAAATGTAATTTTTGGAAAGTTTAAGGGTT
* *
255722 AAAATGTAATTTTTGAAAAATTT-AGGGTT
1 AAAATGTAATTTTTGGAAAGTTTAAGGGTT
*
255751 AAAAATGTAATTTTT-GAAAGTTCAAGGG-T
1 -AAAATGTAATTTTTGGAAAGTTTAAGGGTT
* *
255780 AAAATGTGATTTTTGGAAAGTTTGA-GGTT
1 AAAATGTAATTTTTGGAAAGTTTAAGGGTT
*
255809 AAAATGTAATTTTTGTAAAGTTTAAGGGTT
1 AAAATGTAATTTTTGGAAAGTTTAAGGGTT
* * *
255839 AGAATGTGATTTTTGGAAAGTTT-AGGGTC
1 AAAATGTAATTTTTGGAAAGTTTAAGGGTT
* *
255868 AGAAATGTACTTTTTGGATAGTTTA
1 A-AAATGTAATTTTTGGAAAGTTTA
255893 GGGACTTTTT
Statistics
Matches: 142, Mismatches: 20, Indels: 15
0.80 0.11 0.08
Matches are distributed among these distances:
28 21 0.15
29 56 0.39
30 65 0.46
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.40
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAGTTTAAGGGTT
Found at i:255893 original size:30 final size:29
Alignment explanation
Indices: 255603--255895 Score: 222
Period size: 30 Copynumber: 10.0 Consensus size: 29
255593 CATTCGAGAG
* *
255603 TAAAATGGTAATTTTTGGAAAGTTCAGGAT
1 TAAAAT-GTAATTTTTGGAAAGTTTAGGGT
* * * * * * *
255633 CAAAAAAGAAATTTTTAGATA-TTTGGGGG
1 -TAAAATGTAATTTTTGGAAAGTTTAGGGT
* * *
255662 TAAAATGGTAATTTCTGAAAATTTTA-GGT
1 TAAAAT-GTAATTTTTGGAAAGTTTAGGGT
*
255691 CAAAAAATG-AATTTTTGG-AAGTTTAAGGGT
1 --TAAAATGTAATTTTTGGAAAGTTT-AGGGT
* * *
255721 AAAAATGTAATTTTTGAAAAATTTAGGGT
1 TAAAATGTAATTTTTGGAAAGTTTAGGGT
*
255750 TAAAAATGTAATTTTT-GAAAGTTCAAGGG-
1 T-AAAATGTAATTTTTGGAAAGTT-TAGGGT
*
255779 TAAAATGTGATTTTTGGAAAGTTT-GAGGT
1 TAAAATGTAATTTTTGGAAAGTTTAG-GGT
*
255808 TAAAATGTAATTTTTGTAAAGTTTAAGGGT
1 TAAAATGTAATTTTTGGAAAGTTT-AGGGT
* *
255838 TAGAATGTGATTTTTGGAAAGTTTAGGGT
1 TAAAATGTAATTTTTGGAAAGTTTAGGGT
* * *
255867 CAGAAATGTACTTTTTGGATAGTTTAGGG
1 TA-AAATGTAATTTTTGGAAAGTTTAGGG
255896 ACTTTTTAGG
Statistics
Matches: 206, Mismatches: 40, Indels: 33
0.74 0.14 0.12
Matches are distributed among these distances:
27 1 0.00
28 31 0.15
29 77 0.37
30 87 0.42
31 10 0.05
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.38
Consensus pattern (29 bp):
TAAAATGTAATTTTTGGAAAGTTTAGGGT
Found at i:257790 original size:17 final size:16
Alignment explanation
Indices: 257768--257842 Score: 78
Period size: 17 Copynumber: 4.4 Consensus size: 16
257758 AAATTTAAAC
*
257768 TTAAATTTATAATAAGT
1 TTAAATTTAAAATAA-T
*
257785 TTAAATTTCAAATAATT
1 TTAAATTTAAAATAA-T
**
257802 TTAAACCTAAAATAAAT
1 TTAAATTTAAAAT-AAT
257819 TTAAATTTAAAATGAAT
1 TTAAATTTAAAAT-AAT
257836 TTAAATT
1 TTAAATT
257843 CTATTGGGCT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
17 46 0.96
18 2 0.04
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.43
Consensus pattern (16 bp):
TTAAATTTAAAATAAT
Found at i:260218 original size:41 final size:41
Alignment explanation
Indices: 260149--260317 Score: 236
Period size: 41 Copynumber: 4.1 Consensus size: 41
260139 TTGGTGTTTA
* * *
260149 AAAGGAAGACTCATGTCTTGAGAA-GAGCATGAGATTATATT
1 AAAGGAAGACTCGTGACTCGA-AATGAGCATGAGATTATATT
*
260190 AAAGGAAGACTTGTGACTCGAAATGAGCATGAGATTATATT
1 AAAGGAAGACTCGTGACTCGAAATGAGCATGAGATTATATT
*
260231 AAAGGAAGACTCGTGACTCGAAATAAGCATGAGATTATATT
1 AAAGGAAGACTCGTGACTCGAAATGAGCATGAGATTATATT
**
260272 AAAGGAAGACTCGT--CTCGGGATGAGCATGAGATTATATTT
1 AAAGGAAGACTCGTGACTCGAAATGAGCATGAGATTATA-TT
260312 AAAGGA
1 AAAGGA
260318 TGACGTATGA
Statistics
Matches: 117, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
39 20 0.17
40 10 0.09
41 87 0.74
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (41 bp):
AAAGGAAGACTCGTGACTCGAAATGAGCATGAGATTATATT
Found at i:260346 original size:80 final size:81
Alignment explanation
Indices: 260149--260360 Score: 229
Period size: 82 Copynumber: 2.6 Consensus size: 81
260139 TTGGTGTTTA
* * *
260149 AAAGGAAGACTCATGTCTTGAGA-AGAGCATGAGATTATATTAAAGGAAGACTTGTGACTCGAAA
1 AAAGGAAGACTCATGACTCGA-ATAGAGCATGAGATTATATTAAAGGAAGACTCGT-ACTCGAAA
260213 TGAGCATGAGATTATATT
64 TGAGCATGAGATTATATT
* **
260231 AAAGGAAGACTCGTGACTCGAAATA-AGCATGAGATTATATTAAAGGAAGACTCGT-CTCGGGAT
1 AAAGGAAGACTCATGACTCG-AATAGAGCATGAGATTATATTAAAGGAAGACTCGTACTCGAAAT
260294 GAGCATGAGATTATATTT
65 GAGCATGAGATTATA-TT
* * * * *
260312 AAAGGATGACGT-ATGACTTG-GTAGAGCATAAGATTGT-TTAAAAGGAAGA
1 AAAGGAAGAC-TCATGACTCGAATAGAGCATGAGATTATATT-AAAGGAAGA
260361 TCTACGACTC
Statistics
Matches: 112, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
79 4 0.04
80 41 0.37
81 17 0.15
82 48 0.43
83 2 0.02
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.26
Consensus pattern (81 bp):
AAAGGAAGACTCATGACTCGAATAGAGCATGAGATTATATTAAAGGAAGACTCGTACTCGAAATG
AGCATGAGATTATATT
Found at i:264442 original size:2 final size:2
Alignment explanation
Indices: 264435--264466 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
264425 TCAAACAGAG
264435 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
264467 GAAACAACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:278051 original size:17 final size:18
Alignment explanation
Indices: 278011--278052 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
278001 GTCATTTTAG
* *
278011 TTTTTTATTTAATTTTTG
1 TTTTTTATTTAATTCTTA
*
278029 TCTTTT-TTTAATTCTTA
1 TTTTTTATTTAATTCTTA
278046 TTTTTTA
1 TTTTTTA
278053 ATGTCTATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTTTATTTAATTCTTA
Found at i:282878 original size:8 final size:9
Alignment explanation
Indices: 282857--282886 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
282847 ACACAAAAAG
282857 AAAAATTAT
1 AAAAATTAT
282866 AAAAATTAT
1 AAAAATTAT
*
282875 AAAAATTTT
1 AAAAATTAT
282884 AAA
1 AAA
282887 TCTTAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:284949 original size:41 final size:40
Alignment explanation
Indices: 284872--284954 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 40
284862 AAATACACTT
284872 AAAAATATTAAAACAATATAAAAACAACAAACAAATTAAA
1 AAAAATATTAAAACAATATAAAAACAACAAACAAATTAAA
* *
284912 AAAAATATTAAAACAAT-TCGTAAAACAACAAACAAATTGAA
1 AAAAATATTAAAACAATAT--AAAAACAACAAACAAATTAAA
284953 AA
1 AA
284955 TATAATAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
39 1 0.03
40 17 0.44
41 21 0.54
ACGTcount: A:0.69, C:0.11, G:0.02, T:0.18
Consensus pattern (40 bp):
AAAAATATTAAAACAATATAAAAACAACAAACAAATTAAA
Found at i:285054 original size:20 final size:22
Alignment explanation
Indices: 285029--285072 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
285019 CAAAAGTTCT
285029 ATAAT-AT-CCAAATAATATTA
1 ATAATAATGCCAAATAATATTA
285049 ATAATAGATGCCAAATAATATTA
1 ATAATA-ATGCCAAATAATATTA
285072 A
1 A
285073 AAAGAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.24
22 2 0.10
23 14 0.67
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.32
Consensus pattern (22 bp):
ATAATAATGCCAAATAATATTA
Found at i:285087 original size:23 final size:23
Alignment explanation
Indices: 285038--285089 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
285028 TATAATATCC
*
285038 AAATAATATTAATAATAGATGCC
1 AAATAATATTAATAATAGATGCA
285061 AAATAATATTAA-AA-AGAATAGCA
1 AAATAATATTAATAATAG-AT-GCA
285084 AAATAA
1 AAATAA
285090 CATAAACAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 2 0.08
22 4 0.15
23 20 0.77
ACGTcount: A:0.62, C:0.06, G:0.08, T:0.25
Consensus pattern (23 bp):
AAATAATATTAATAATAGATGCA
Found at i:285128 original size:11 final size:11
Alignment explanation
Indices: 285114--285217 Score: 57
Period size: 11 Copynumber: 9.4 Consensus size: 11
285104 AAACAACAAT
285114 AAAACAGCACC
1 AAAACAGCACC
* *
285125 AAAACATC-CA
1 AAAACAGCACC
*
285135 AAAACAGCACTG
1 AAAACAGCAC-C
* * *
285147 AAAATAGTACT
1 AAAACAGCACC
* *
285158 AAAATAGAACC
1 AAAACAGCACC
*
285169 AAAAACAGTACC
1 -AAAACAGCACC
*
285181 AAAACTGCACC
1 AAAACAGCACC
* * *
285192 AAAAAAACATC
1 AAAACAGCACC
*
285203 AAATCAGCACC
1 AAAACAGCACC
285214 AAAA
1 AAAA
285218 ACAACCTGCA
Statistics
Matches: 68, Mismatches: 22, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
10 8 0.12
11 43 0.63
12 17 0.25
ACGTcount: A:0.58, C:0.25, G:0.08, T:0.10
Consensus pattern (11 bp):
AAAACAGCACC
Found at i:286081 original size:47 final size:47
Alignment explanation
Indices: 286012--286120 Score: 218
Period size: 47 Copynumber: 2.3 Consensus size: 47
286002 GCATTTCACT
286012 AAACTTAGAAGCATTAAATATTATTTCATCTTACCCATCGAATATTC
1 AAACTTAGAAGCATTAAATATTATTTCATCTTACCCATCGAATATTC
286059 AAACTTAGAAGCATTAAATATTATTTCATCTTACCCATCGAATATTC
1 AAACTTAGAAGCATTAAATATTATTTCATCTTACCCATCGAATATTC
286106 AAACTTAGAAGCATT
1 AAACTTAGAAGCATT
286121 CAAAAATTCG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 62 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.35
Consensus pattern (47 bp):
AAACTTAGAAGCATTAAATATTATTTCATCTTACCCATCGAATATTC
Found at i:288604 original size:2 final size:2
Alignment explanation
Indices: 288599--288632 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
288589 TTAAAAAATA
288599 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
288633 TGTTTTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:289102 original size:21 final size:22
Alignment explanation
Indices: 289070--289120 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
289060 TTAATAAATC
*
289070 TTTTAA-ATTTT-AAAAATTAT
1 TTTTAATATTTTAAAAAATAAT
289090 TTTTAATATTTTAAAAAATAAT
1 TTTTAATATTTTAAAAAATAAT
*
289112 TTTTTATAT
1 TTTTAATAT
289121 ATGCTGATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 6 0.22
21 5 0.19
22 16 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAATATTTTAAAAAATAAT
Found at i:289253 original size:20 final size:20
Alignment explanation
Indices: 289213--289264 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
289203 AAATAATTTG
**
289213 ATAAAAAATATAAATTTAAAA
1 ATAAAAAAT-TAAATAAAAAA
289234 ATAAAAAATTAAATAAAAAA
1 ATAAAAAATTAAATAAAAAA
*
289254 CTAAAATAATT
1 ATAAAA-AATT
289265 TTTTTTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
ATAAAAAATTAAATAAAAAA
Found at i:291975 original size:2 final size:2
Alignment explanation
Indices: 291968--291999 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
291958 CTATATCATT
*
291968 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
292000 GACAAACTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:296555 original size:21 final size:21
Alignment explanation
Indices: 296530--296569 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
296520 TCACATAAAT
296530 CTAAAAATA-TTATATAAAACC
1 CTAAAAA-AGTTATATAAAACC
296551 CTAAAAAAGTTATATAAAA
1 CTAAAAAAGTTATATAAAA
296570 TCTATAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.60, C:0.10, G:0.03, T:0.28
Consensus pattern (21 bp):
CTAAAAAAGTTATATAAAACC
Found at i:297557 original size:4 final size:4
Alignment explanation
Indices: 297544--297594 Score: 77
Period size: 4 Copynumber: 12.8 Consensus size: 4
297534 AAAAATGATG
*
297544 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAAA
297592 GAA
1 GAA
297595 GAAGGAAGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 3 0.07
4 37 0.86
5 3 0.07
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:301330 original size:5 final size:5
Alignment explanation
Indices: 301320--301357 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
301310 TTCTTTTATC
301320 TATTT TATTT TA--T TATTT TATTT TATTT T-TTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT T
301358 TTTAGTATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 3 0.10
4 4 0.13
5 23 0.77
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TATTT
Found at i:301333 original size:22 final size:22
Alignment explanation
Indices: 301294--301361 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
301284 TAAGTCCTTC
** *
301294 ATTCTATATTTTGCTATTCTTTT
1 ATTCTAT-TTTTTTTATTATTTT
301317 A-TCTATTTTATTTTATTATTTT
1 ATTCTATTTT-TTTTATTATTTT
* *
301339 ATTTTATTTTTTTTATTTTTTT
1 ATTCTATTTTTTTTATTATTTT
301361 A
1 A
301362 GTATGTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
21 3 0.08
22 27 0.71
23 8 0.21
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (22 bp):
ATTCTATTTTTTTTATTATTTT
Found at i:301338 original size:13 final size:13
Alignment explanation
Indices: 301313--301357 Score: 63
Period size: 14 Copynumber: 3.3 Consensus size: 13
301303 TTTGCTATTC
301313 TTTTATCTATTTTA
1 TTTTAT-TATTTTA
301327 TTTTATTATTTTA
1 TTTTATTATTTTA
*
301340 TTTTATTTTTTTTA
1 TTTTA-TTATTTTA
301354 TTTT
1 TTTT
301358 TTTAGTATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.41
14 17 0.59
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTATTTTA
Found at i:301370 original size:27 final size:27
Alignment explanation
Indices: 301313--301371 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
301303 TTTGCTATTC
* *
301313 TTTTATCTATTTTATTTTATTATTTTA
1 TTTTATCTATTTTATTTTATTAGTATA
* * * *
301340 TTTTATTTTTTTTATTTTTTTAGTATG
1 TTTTATCTATTTTATTTTATTAGTATA
301367 TTTTA
1 TTTTA
301372 AATCTTTTAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.02, G:0.03, T:0.76
Consensus pattern (27 bp):
TTTTATCTATTTTATTTTATTAGTATA
Done.