Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018461.1 Corchorus olitorius cultivar O-4 contig18494, 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: 246974
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1281 original size:17 final size:17
Alignment explanation
Indices: 1259--1293 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1249 TCTTTCCTTC
1259 TTTTTTCTTTTCTTTTT
1 TTTTTTCTTTTCTTTTT
1276 TTTTTTCTTTTCTTTTT
1 TTTTTTCTTTTCTTTTT
1293 T
1 T
1294 GTTCTCAGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (17 bp):
TTTTTTCTTTTCTTTTT
Found at i:1293 original size:12 final size:12
Alignment explanation
Indices: 1256--1286 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1246 TGCTCTTTCC
1256 TTCTTTTTTCTT
1 TTCTTTTTTCTT
*
1268 TTCTTTTTTTTT
1 TTCTTTTTTCTT
1280 TTCTTTT
1 TTCTTTT
1287 CTTTTTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:8082 original size:23 final size:26
Alignment explanation
Indices: 8056--8123 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
8046 ACCTTATACC
*
8056 CTTTTCTCTATTAC-CCAC-TGT-CG
1 CTTTTCTCTATTACAACACATGTACG
* *
8079 CTTTTCTCTATCACAACACATTTACG
1 CTTTTCTCTATTACAACACATGTACG
*
8105 CTTTTCTCTATTATAACAC
1 CTTTTCTCTATTACAACAC
8124 TTTTACATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 13 0.35
24 3 0.08
25 2 0.05
26 19 0.51
ACGTcount: A:0.22, C:0.31, G:0.04, T:0.43
Consensus pattern (26 bp):
CTTTTCTCTATTACAACACATGTACG
Found at i:8113 original size:26 final size:26
Alignment explanation
Indices: 8077--8129 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
8067 TACCCACTGT
8077 CGCTTTTCTCTATCACAACACATTTA
1 CGCTTTTCTCTATCACAACACATTTA
* * *
8103 CGCTTTTCTCTATTATAACACTTTTA
1 CGCTTTTCTCTATCACAACACATTTA
8129 C
1 C
8130 ATATCTACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.28, G:0.04, T:0.43
Consensus pattern (26 bp):
CGCTTTTCTCTATCACAACACATTTA
Found at i:8159 original size:41 final size:40
Alignment explanation
Indices: 8114--8212 Score: 180
Period size: 41 Copynumber: 2.4 Consensus size: 40
8104 GCTTTTCTCT
8114 ATTATAACACTTTTACATATCTACAACATTGCCATTTCTAA
1 ATTATAACACTTTTACATATCTACAACATTGCCATTTCT-A
8155 ATTATAACACTTTTACATATCTACAACATTGCCATTTCTA
1 ATTATAACACTTTTACATATCTACAACATTGCCATTTCTA
8195 ATTATAAACACTTTTACA
1 ATTAT-AACACTTTTACA
8213 CCTTTTAAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
40 6 0.11
41 51 0.89
ACGTcount: A:0.37, C:0.21, G:0.02, T:0.39
Consensus pattern (40 bp):
ATTATAACACTTTTACATATCTACAACATTGCCATTTCTA
Found at i:8269 original size:65 final size:65
Alignment explanation
Indices: 8188--8319 Score: 246
Period size: 65 Copynumber: 2.0 Consensus size: 65
8178 CAACATTGCC
*
8188 ATTTCTAATTATAAACACTTTTACACCTTTTAAAAGCATTTTAAAAAATAGTCAAAACTTACAAA
1 ATTTCTAATTATAAACACTTTTACACCTTTTAAAAACATTTTAAAAAATAGTCAAAACTTACAAA
*
8253 ATTTCTAATTATAAACACTTTTACACCTTTTAAAAACATTTTAAAAGATAGTCAAAACTTACAAA
1 ATTTCTAATTATAAACACTTTTACACCTTTTAAAAACATTTTAAAAAATAGTCAAAACTTACAAA
8318 AT
1 AT
8320 ATAACACATA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (65 bp):
ATTTCTAATTATAAACACTTTTACACCTTTTAAAAACATTTTAAAAAATAGTCAAAACTTACAAA
Found at i:9120 original size:20 final size:20
Alignment explanation
Indices: 9095--9132 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
9085 CAAAAGTATA
9095 ATTTACTCTTAAATCATTCC
1 ATTTACTCTTAAATCATTCC
9115 ATTTACTCTTAAATCATT
1 ATTTACTCTTAAATCATT
9133 TTTGCACCTT
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:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTACTCTTAAATCATTCC
Found at i:14004 original size:52 final size:52
Alignment explanation
Indices: 13945--14051 Score: 196
Period size: 52 Copynumber: 2.1 Consensus size: 52
13935 AAATTTTTGC
13945 AAATACAGATTTTCAAGTTTAATAGATATCTGTTAACGAACAGTTACCTTGA
1 AAATACAGATTTTCAAGTTTAATAGATATCTGTTAACGAACAGTTACCTTGA
* *
13997 AAATACAGTTTTTCAAGTTTAATAGATATCTGTTGACGAACAGTTACCTTGA
1 AAATACAGATTTTCAAGTTTAATAGATATCTGTTAACGAACAGTTACCTTGA
14049 AAA
1 AAA
14052 GATGTCTCTG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (52 bp):
AAATACAGATTTTCAAGTTTAATAGATATCTGTTAACGAACAGTTACCTTGA
Found at i:14992 original size:60 final size:60
Alignment explanation
Indices: 14876--15000 Score: 157
Period size: 63 Copynumber: 2.1 Consensus size: 60
14866 TTTTGCATCA
*
14876 TTTTTTAAAATTAGTTACTCAATTAAACCTGCTCTCTTTTATACATGAAAAATTGGAATTTAT
1 TTTTTTAAAATTAGTTACTCAATTAAACC-GCTCTCTTGTATACATGAAAAATTGG-ATTT-T
* * *
14939 TTTTTTTAAATTAGTTACTCAGTTACA-C-CTCTCTTGTATACAT-AAAACATTGGATTTT
1 TTTTTTAAAATTAGTTACTCAATTAAACCGCTCTCTTGTATACATGAAAA-ATTGGATTTT
14997 TTTT
1 TTTT
15001 GCCAGAGGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
58 5 0.09
59 8 0.14
60 19 0.33
62 1 0.02
63 24 0.42
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (60 bp):
TTTTTTAAAATTAGTTACTCAATTAAACCGCTCTCTTGTATACATGAAAAATTGGATTTT
Found at i:16837 original size:7 final size:7
Alignment explanation
Indices: 16825--16849 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16815 CTGTCATTCT
16825 CTCACTC
1 CTCACTC
16832 CTCACTC
1 CTCACTC
16839 CTCACTC
1 CTCACTC
16846 CTCA
1 CTCA
16850 ACCAGCTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.56, G:0.00, T:0.28
Consensus pattern (7 bp):
CTCACTC
Found at i:17443 original size:2 final size:2
Alignment explanation
Indices: 17436--17464 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17426 TAACTATCAA
17436 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17465 AAAGTACGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18391 original size:21 final size:23
Alignment explanation
Indices: 18367--18596 Score: 135
Period size: 22 Copynumber: 10.4 Consensus size: 23
18357 TTAGGAGTAC
*
18367 CAAAATTTGATAGA-AAG-TTAT
1 CAAAATTTCATAGAGAAGATTAT
* * *
18388 C-AAATCTCATTGAGTAG-TTAT
1 CAAAATTTCATAGAGAAGATTAT
*
18409 CGAAATTTCATAGAGATCAGATTAT
1 CAAAATTTCATAGAGA--AGATTAT
18434 CAAAATTT-ATA-AGAAGATTAT
1 CAAAATTTCATAGAGAAGATTAT
* * **
18455 CAAAATTTTATAGTG-TTATTAT
1 CAAAATTTCATAGAGAAGATTAT
* * *
18477 CAAAATTTCAAAGCG-AGGTTAT
1 CAAAATTTCATAGAGAAGATTAT
* *
18499 CAAAATTACATA-ATG-TGATTAT
1 CAAAATTTCATAGA-GAAGATTAT
* * * *
18521 CAAAATTTCATAGAG-GGGTCAA
1 CAAAATTTCATAGAGAAGATTAT
* *
18543 CAAAATTTTATAGAG-AGGTTAT
1 CAAAATTTCATAGAGAAGATTAT
* *
18565 CAAAATTTCATAAAG-AGGTTAT
1 CAAAATTTCATAGAGAAGATTAT
*
18587 CAAATTTTCA
1 CAAAATTTCA
18597 AAATGTGATT
Statistics
Matches: 166, Mismatches: 34, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
20 9 0.05
21 23 0.14
22 113 0.68
23 5 0.03
24 5 0.03
25 11 0.07
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (23 bp):
CAAAATTTCATAGAGAAGATTAT
Found at i:18520 original size:44 final size:45
Alignment explanation
Indices: 18428--18617 Score: 194
Period size: 44 Copynumber: 4.3 Consensus size: 45
18418 ATAGAGATCA
* * *
18428 GATTATCAAAATTT-ATAAGA-AGATTATCAAAATTTTATAGTGT
1 GATTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGT
* * *
18471 TATTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGT
* * * * *
18515 GATTATCAAAATTTCAT-AGAGGGGTCAACAAAATTTTATAGA-GA
1 GATTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATA-ATGT
* * *
18559 GGTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGT
*
18603 GATTACCAAAATTTC
1 GATTATCAAAATTTC
18618 GTAGTGGTAT
Statistics
Matches: 117, Mismatches: 24, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
43 17 0.15
44 98 0.84
45 2 0.02
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (45 bp):
GATTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGT
Found at i:18548 original size:88 final size:88
Alignment explanation
Indices: 18455--18617 Score: 229
Period size: 88 Copynumber: 1.9 Consensus size: 88
18445 AGAAGATTAT
* ** * *
18455 CAAAATTTTATAGTGTTATTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATT
1 CAAAATTTTATAGAGAGATTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATGTGATT
*
18519 ATCAAAATTTCATAGAGGGGTCAA
65 ACCAAAATTTCATAGAGGGGTCAA
* * *
18543 CAAAATTTTATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTA
1 CAAAATTTTATAGAGAGATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
18608 CCAAAATTTC
66 CCAAAATTTC
18618 GTAGTGGTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
88 63 0.97
89 2 0.03
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (88 bp):
CAAAATTTTATAGAGAGATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
CCAAAATTTCATAGAGGGGTCAA
Found at i:18613 original size:66 final size:66
Alignment explanation
Indices: 18430--18617 Score: 168
Period size: 66 Copynumber: 2.9 Consensus size: 66
18420 AGAGATCAGA
* * * * *
18430 TTATCAAAATTT-AT-AAGAAGATTATCAAAATTTT-ATAGTGTTATTATCAAAATTTCAAAGCG
1 TTATCAAAATTTCATAAAG-AGATTATC-AAATTTTCAAAATGTGATTAACAAAATTTCAAAGAG
18492 AGG
64 AGG
* * * * * * * * * *
18495 TTATCAAAATTACATAATGTGATTATCAAAATTTCATAGA-GGGGTCAACAAAATTTTATAGAGA
1 TTATCAAAATTTCATAAAGAGATTATCAAATTTTCA-AAATGTGATTAACAAAATTTCAAAGAGA
18559 GG
65 GG
* *
18561 TTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTACCAAAATTTC
1 TTATCAAAATTTCATAAAGAGATTATCAAATTTTCAAAATGTGATTAACAAAATTTC
18618 GTAGTGGTAT
Statistics
Matches: 92, Mismatches: 26, Indels: 9
0.72 0.20 0.07
Matches are distributed among these distances:
65 19 0.21
66 71 0.77
67 2 0.02
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.35
Consensus pattern (66 bp):
TTATCAAAATTTCATAAAGAGATTATCAAATTTTCAAAATGTGATTAACAAAATTTCAAAGAGAG
G
Found at i:18875 original size:23 final size:22
Alignment explanation
Indices: 18702--19227 Score: 215
Period size: 22 Copynumber: 24.3 Consensus size: 22
18692 TTATGGAGTA
* *
18702 ATCAAAATTTC--AGGCAGGAT
1 ATCAAAATTTCATAGGGAGGTT
* *
18722 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* **
18744 ATCTAAATTTCATAGGGATATT
1 ATCAAAATTTCATAGGGAGGTT
** **
18766 AAAAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
18788 -TCAAAAAATT-GTAGGGAGGTT
1 ATC-AAAATTTCATAGGGAGGTT
*
18809 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
*
18825 ATCAAGATTTCATTA-GGAGGTT
1 ATCAAAATTTCA-TAGGGAGGTT
*
18847 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* * *
18870 ATCAAAATTTTATATGAAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
*
18893 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * * *
18915 ATCACAATTTCATTGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* *
18937 ATCAAAATTTCAGAGTGA--TT
1 ATCAAAATTTCATAGGGAGGTT
* * *
18957 A-CTAACAA-TTCATATGAATGTT
1 ATC-AA-AATTTCATAGGGAGGTT
* * * ** *
18979 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
19001 ATCAATATTTCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * **
19023 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
* *
19046 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
** *
19068 ATCAAAATTTCATATTGAAGTCT
1 ATCAAAATTTCATAGGGAGGT-T
* * *
19091 -TCAAAATTCCTTAAGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
19112 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * ***
19134 A-AAAAATTTTATAAAAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * * *
19155 CTCGAAATTCCATA-GTATCGTT
1 ATCAAAATTTCATAGGGA-GGTT
* * * *
19177 ATTAAAATCTCATAGGAAGATT
1 ATCAAAATTTCATAGGGAGGTT
* * *
19199 ATCAAAATTTCATAAGGAGATC
1 ATCAAAATTTCATAGGGAGGTT
19221 ATCAAAA
1 ATCAAAA
19228 ATAGTGTAAT
Statistics
Matches: 375, Mismatches: 107, Indels: 46
0.71 0.20 0.09
Matches are distributed among these distances:
16 9 0.02
17 4 0.01
19 2 0.01
20 25 0.07
21 38 0.10
22 238 0.63
23 59 0.16
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:19056 original size:45 final size:45
Alignment explanation
Indices: 18996--19081 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
18986 TTTCATAACG
* * *
18996 TGGTTATCAATATTTCATAT-GGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATCTCATAGTGT
*
19041 TGGTTATCAAAATTTCATTGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATTTCATTGGGAAGTTATCAAAATCTCATA
19082 TTGAAGTCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 1 0.03
45 35 0.97
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (45 bp):
TGGTTATCAAAATTTCATTGGGAAGTTATCAAAATCTCATAGTGT
Found at i:19427 original size:27 final size:27
Alignment explanation
Indices: 19389--19452 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
19379 TACCATTTTT
19389 TTAAAAT-ATATTTCTAAATTA-CCATTA
1 TTAAAATAATATTT-T-AATTATCCATTA
19416 TT-AAATAATATTTTAATTATTCCATTA
1 TTAAAATAATATTTTAATTA-TCCATTA
19443 TTAAAATAAT
1 TTAAAATAAT
19453 GGAAAATTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
25 5 0.15
26 5 0.15
27 16 0.48
28 7 0.21
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (27 bp):
TTAAAATAATATTTTAATTATCCATTA
Found at i:20079 original size:5 final size:5
Alignment explanation
Indices: 20069--20106 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
20059 TTTAATGTTA
20069 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
20107 TATTGGCCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:22237 original size:21 final size:22
Alignment explanation
Indices: 22176--22239 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
22166 ACTATAGTAT
* *
22176 CAAAATATTATAGGGAGATTAA
1 CAAAATATTATAGGAAGGTTAA
* *
22198 CAAAATCTCATAGGGAAGGTT-A
1 CAAAATATTATA-GGAAGGTTAA
*
22220 CAAAATTTTATAGGAAGGTT
1 CAAAATATTATAGGAAGGTT
22240 TATTAAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
21 8 0.23
22 21 0.60
23 6 0.17
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (22 bp):
CAAAATATTATAGGAAGGTTAA
Found at i:22255 original size:23 final size:21
Alignment explanation
Indices: 22197--22255 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
22187 AGGGAGATTA
*
22197 ACAAAATCTCATAGGGAAGGTT
1 ACAAAATTTCATA-GGAAGGTT
*
22219 ACAAAATTTTATAGGAAGGTTT
1 ACAAAATTTCATAGGAAGG-TT
*
22241 ATTAAAATTTCATAG
1 A-CAAAATTTCATAG
22256 TTAGACTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 6 0.19
22 14 0.45
23 11 0.35
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.32
Consensus pattern (21 bp):
ACAAAATTTCATAGGAAGGTT
Found at i:22309 original size:21 final size:20
Alignment explanation
Indices: 22245--22311 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 20
22235 AGGTTTATTA
* *
22245 AAATTTCATAGTTAGACTATC
1 AAATTTCATAGGTA-ATTATC
* *
22266 AAAGTTTCATATGAAATTTATC
1 AAA-TTTCATAGGTAA-TTATC
22288 ACAATTTCATAGGTAATTATC
1 A-AATTTCATAGGTAATTATC
22309 AAA
1 AAA
22312 ATTTTTTATA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
20 2 0.05
21 10 0.27
22 23 0.62
23 2 0.05
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (20 bp):
AAATTTCATAGGTAATTATC
Found at i:22353 original size:22 final size:22
Alignment explanation
Indices: 22283--22361 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
22273 CATATGAAAT
* *
22283 TTATCACAATTTCATAGG-TAA
1 TTATCAAAATTTAATAGGATAA
* * **
22304 TTATCAAAATTTTTTATAGCATGG
1 TTATCAAAA--TTTAATAGGATAA
22328 TTATCAAAATTTAATAGGATAA
1 TTATCAAAATTTAATAGGATAA
22350 TTATCGAAAATT
1 TTATC-AAAATT
22362 CATAAAAATA
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
21 8 0.18
22 14 0.31
23 13 0.29
24 10 0.22
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTAATAGGATAA
Found at i:23996 original size:44 final size:45
Alignment explanation
Indices: 23911--23997 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 45
23901 TCTCCTACAA
*
23911 TCAAACACATGCAAATTAAAGAAAAAAATACAATAATATCTCTAG
1 TCAAACACATGCAAATTAAAGAAAAAAATACAACAATATCTCTAG
*
23956 TCAAACACATGGAAATTAAAG-AAAAAATACAACAATATCTCT
1 TCAAACACATGCAAATTAAAGAAAAAAATACAACAATATCTCT
23998 TGTATTATAG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 20 0.50
45 20 0.50
ACGTcount: A:0.55, C:0.16, G:0.07, T:0.22
Consensus pattern (45 bp):
TCAAACACATGCAAATTAAAGAAAAAAATACAACAATATCTCTAG
Found at i:24061 original size:63 final size:63
Alignment explanation
Indices: 23962--24086 Score: 250
Period size: 63 Copynumber: 2.0 Consensus size: 63
23952 CTAGTCAAAC
23962 ACATGGAAATTAAAGAAAAAATACAACAATATCTCTTGTATTATAGCATCCTTTCTACCTACT
1 ACATGGAAATTAAAGAAAAAATACAACAATATCTCTTGTATTATAGCATCCTTTCTACCTACT
24025 ACATGGAAATTAAAGAAAAAATACAACAATATCTCTTGTATTATAGCATCCTTTCTACCTAC
1 ACATGGAAATTAAAGAAAAAATACAACAATATCTCTTGTATTATAGCATCCTTTCTACCTAC
24087 CACCGCTTCA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (63 bp):
ACATGGAAATTAAAGAAAAAATACAACAATATCTCTTGTATTATAGCATCCTTTCTACCTACT
Found at i:24151 original size:33 final size:33
Alignment explanation
Indices: 24113--24185 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
24103 TAAGAAATTC
*
24113 GAAATTATCTCTTCCGTATGATATGGAAGATTT
1 GAAATTATCTCTTCCGTATCATATGGAAGATTT
*
24146 GAAATTATCTCTTTCGTATCATATGGAAGATTT
1 GAAATTATCTCTTCCGTATCATATGGAAGATTT
*
24179 GAGATTA
1 GAAATTA
24186 ATCCAAAGCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.40
Consensus pattern (33 bp):
GAAATTATCTCTTCCGTATCATATGGAAGATTT
Found at i:24344 original size:23 final size:23
Alignment explanation
Indices: 24314--24360 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
24304 CAAAAACTCA
24314 TTCATTGTGA-AAGGAATCCTAAT
1 TTCATTGTGATAA-GAATCCTAAT
*
24337 TTCATTGTGATAATAATCCTAAT
1 TTCATTGTGATAAGAATCCTAAT
24360 T
1 T
24361 CCAGTTCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (23 bp):
TTCATTGTGATAAGAATCCTAAT
Found at i:25013 original size:17 final size:16
Alignment explanation
Indices: 24987--25051 Score: 62
Period size: 17 Copynumber: 4.1 Consensus size: 16
24977 AAATGAAATC
* *
24987 TATATCTTTATCTTTT
1 TATATTTTTATATTTT
25003 ATATATTTTTATATTTT
1 -TATATTTTTATATTTT
*
25020 TATA--TTTATATTTA
1 TATATTTTTATATTTT
*
25034 TATATTTATTTTATTTT
1 TATATTT-TTATATTTT
25051 T
1 T
25052 TTACTATTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
14 13 0.32
16 5 0.12
17 22 0.55
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TATATTTTTATATTTT
Found at i:25017 original size:8 final size:8
Alignment explanation
Indices: 24987--25051 Score: 62
Period size: 8 Copynumber: 8.1 Consensus size: 8
24977 AAATGAAATC
*
24987 TATATCTT
1 TATATTTT
*
24995 TATCTTTT
1 TATATTTT
25003 ATATATTTT
1 -TATATTTT
25012 TATATTTT
1 TATATTTT
25020 TATA--TT
1 TATATTTT
*
25026 TATATTTA
1 TATATTTT
25034 TATATTTAT
1 TATATTT-T
*
25043 TTTATTTT
1 TATATTTT
25051 T
1 T
25052 TTACTATTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
6 6 0.13
8 28 0.60
9 13 0.28
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (8 bp):
TATATTTT
Found at i:25029 original size:14 final size:14
Alignment explanation
Indices: 25004--25047 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
24994 TTATCTTTTA
*
25004 TATATTTTTATATT
1 TATATATTTATATT
*
25018 TTTATATTTATATT
1 TATATATTTATATT
25032 TATATATTTAT-TT
1 TATATATTTATATT
25045 TAT
1 TAT
25048 TTTTTTACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 5 0.19
14 22 0.81
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATATATTTATATT
Found at i:25059 original size:20 final size:20
Alignment explanation
Indices: 25010--25047 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25000 TTTATATATT
*
25010 TTTATATTTTTATATTTATA
1 TTTATATATTTATATTTATA
25030 TTTATATATTTAT-TTTAT
1 TTTATATATTTATATTTAT
25048 TTTTTTACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATATATTTATATTTATA
Found at i:25683 original size:4 final size:4
Alignment explanation
Indices: 25674--25712 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
25664 AATACACTTG
*
25674 TATC TATC TATC TATC GATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TAT
25713 ATATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.26, C:0.23, G:0.03, T:0.49
Consensus pattern (4 bp):
TATC
Found at i:27001 original size:22 final size:22
Alignment explanation
Indices: 26976--27208 Score: 145
Period size: 22 Copynumber: 10.5 Consensus size: 22
26966 CTTGTCTGTG
*
26976 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
26998 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
27021 -GGTTATCAAAA-TTCTATAGTG-
1 TGGTTATCAAAATTTC-ATAG-GA
*
27042 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
* *
27065 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAGGA
*
27086 AGGTTATCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* * * *
27108 TGATTACCAAAATCTCATCGGA
1 TGGTTATCAAAATTTCATAGGA
* *
27130 TCAGGTTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAGGA
* * ** *
27154 AGGTTGTTGAAATTTCAT-GGTG
1 TGGTTATCAAAATTTCATAGG-A
* * **
27176 TGGTTATCACAATTTTATAAAA
1 TGGTTATCAAAATTTCATAGGA
*
27198 AGGTTATCAAA
1 TGGTTATCAAA
27209 GAGATTATCA
Statistics
Matches: 159, Mismatches: 38, Indels: 28
0.71 0.17 0.12
Matches are distributed among these distances:
21 11 0.07
22 125 0.79
23 8 0.05
24 15 0.09
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:27079 original size:66 final size:66
Alignment explanation
Indices: 26973--27208 Score: 210
Period size: 66 Copynumber: 3.5 Consensus size: 66
26963 TTTCTTGTCT
* * * *
26973 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGG-AGGTTATCAAAA-TTCT
1 GTGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATG-GGAAGGTTATCAAAATTTC-
27036 ATA
64 ATA
*
27039 GTGTGGTTACCAAAATTTCATATGGA-AGTTATCAAAATTTCATGGGAAGGTTATCAAAATTTCA
1 GTGTGGTTACCAAAATTTCATA-AGATAGTTATCAAAATTTCATGGGAAGGTTATCAAAATTTCA
27103 TA
65 TA
* * ** * * * * **
27105 GTGTGATTACCAAAATCTCATCGGATCAGGTTATTAAAATTTCTTAGGAAGGTTGTTGAAATTTC
1 GTGTGGTTACCAAAATTTCATAAGAT-A-GTTATCAAAATTTCATGGGAAGGTTATCAAAATTTC
*
27170 ATG
64 ATA
* * * *
27173 GTGTGGTTATCACAATTTTATAA-AAAGGTTATCAAA
1 GTGTGGTTACCAAAATTTCATAAGATA-GTTATCAAA
27209 GAGATTATCA
Statistics
Matches: 140, Mismatches: 24, Indels: 12
0.80 0.14 0.07
Matches are distributed among these distances:
65 5 0.04
66 80 0.57
67 7 0.05
68 48 0.34
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.37
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATGGGAAGGTTATCAAAATTTCAT
A
Found at i:27324 original size:22 final size:22
Alignment explanation
Indices: 27299--27356 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
27289 TTCTTTGGGA
27299 GGTTATCAAAATTTTTTAGTGT
1 GGTTATCAAAATTTTTTAGTGT
*
27321 GGTTATCAAAATTTTTTGGTGT
1 GGTTATCAAAATTTTTTAGTGT
27343 GGTTATCAAAATTT
1 GGTTATCAAAATTT
27357 CATATGAAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.28, C:0.05, G:0.19, T:0.48
Consensus pattern (22 bp):
GGTTATCAAAATTTTTTAGTGT
Found at i:27368 original size:22 final size:22
Alignment explanation
Indices: 27213--27622 Score: 101
Period size: 22 Copynumber: 18.6 Consensus size: 22
27203 ATCAAAGAGA
* *
27213 TTATCAAAATGTCATA-GCGAGG
1 TTATCAAAATTTCATATG-AAGG
* *
27235 TTATAAAAATTTCATATTG-TGG
1 TTATCAAAATTTCATA-TGAAGG
* * *
27257 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCATATGAAGG
* * *
27279 TTA-CTAATATTTC-TTTGGGAGG
1 TTATC-AAAATTTCATAT-GAAGG
** *
27301 TTATCAAAATTTTTTAGTG-TGG
1 TTATCAAAATTTCATA-TGAAGG
** * *
27323 TTATCAAAATTTTTTGGTG-TGG
1 TTATCAAAATTTCAT-ATGAAGG
27345 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATATGAAGG
*
27367 TTAT-AAAAGTCTCAGTTTCAT-AAGG
1 TTATCAAAA-TTTCA---T-ATGAAGG
* *
27392 AGTACCAAAA--T--TA-GAAGG
1 -TTATCAAAATTTCATATGAAGG
* *
27410 TTATC-AAATCTCATA-GAGTGG
1 TTATCAAAATTTCATATGA-AGG
*
27431 TTATCGAAATTTCATA-GAGATCGG
1 TTATCAAAATTTCATATGA-A--GG
* *
27455 ATTATCAAAATTT-ATAGGAAGA
1 -TTATCAAAATTTCATATGAAGG
* **
27477 TTATCAAATTTTCATAGTG-TTG
1 TTATCAAAATTTCATA-TGAAGG
* *
27499 TTATCAAAATTTCA-AAGCGAGG
1 TTATCAAAATTTCATATG-AAGG
* * *
27521 TTATCAAAATTACATAATG-TGA
1 TTATCAAAATTTCAT-ATGAAGG
*
27543 TTATCAAAATTTCATA-GAGGGG
1 TTATCAAAATTTCATATGA-AGG
* * *
27565 TCAACAAAATTTTATA-GAGAGG
1 TTATCAAAATTTCATATGA-AGG
*
27587 TTATCAAAATTTCATA-AAGAGG
1 TTATCAAAATTTCATATGA-AGG
*
27609 TTATCAAATTTTCA
1 TTATCAAAATTTCA
27623 AAATGTGATT
Statistics
Matches: 298, Mismatches: 54, Indels: 72
0.70 0.13 0.17
Matches are distributed among these distances:
16 3 0.01
17 3 0.01
18 6 0.02
19 1 0.00
20 6 0.02
21 29 0.10
22 209 0.70
23 4 0.01
24 11 0.04
25 18 0.06
26 4 0.01
27 4 0.01
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATATGAAGG
Found at i:27369 original size:44 final size:44
Alignment explanation
Indices: 27213--27374 Score: 129
Period size: 44 Copynumber: 3.7 Consensus size: 44
27203 ATCAAAGAGA
* * * *
27213 TTATCAAAATGTCATAGCGAGGTTATAAAAATTTCATAT--TGTGG
1 TTATCAAAATTTCATA-TGAGGTTATCAAAATTTC-TTTGGTGTGG
* * * *
27257 TTAACAAAATTTCATAAGGAGGTTA-CTAATATTTCTTTGG-GAGG
1 TTATCAAAATTTCAT-ATGAGGTTATC-AAAATTTCTTTGGTGTGG
** *
27301 TTATCAAAATTTTTTAGTGTGGTTATCAAAATTT-TTTGGTGTGG
1 TTATCAAAATTTCATA-TGAGGTTATCAAAATTTCTTTGGTGTGG
27345 TTATCAAAATTTCATATGAAGGTTAT-AAAA
1 TTATCAAAATTTCATATG-AGGTTATCAAAA
27375 GTCTCAGTTT
Statistics
Matches: 93, Mismatches: 17, Indels: 17
0.73 0.13 0.13
Matches are distributed among these distances:
43 14 0.15
44 77 0.83
45 2 0.02
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (44 bp):
TTATCAAAATTTCATATGAGGTTATCAAAATTTCTTTGGTGTGG
Found at i:27547 original size:44 final size:44
Alignment explanation
Indices: 27410--27633 Score: 156
Period size: 44 Copynumber: 5.1 Consensus size: 44
27400 AATTAGAAGG
* * * *
27410 TTATC-AAATCTCATAGAGTGGTTATCGAAATTTCATAGA-GATCGGA
1 TTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATA-ATG-T--GA
* * * *
27456 TTATCAAAATTT-ATAG-GAAGATTATCAAATTTTCATAGTGTTG-
1 TTATCAAAATTTCAAAGAG-AGGTTATCAAAATTTCATAATG-TGA
* *
27499 TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTGA
* * * * * * *
27543 TTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAGA-GAGG
1 TTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATA-ATGTGA
* *
27587 TTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGTGA
27631 TTA
1 TTA
27634 CTGAAATTTC
Statistics
Matches: 139, Mismatches: 30, Indels: 20
0.74 0.16 0.11
Matches are distributed among these distances:
43 15 0.11
44 89 0.64
45 4 0.03
46 26 0.19
47 5 0.04
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.35
Consensus pattern (44 bp):
TTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTGA
Found at i:27573 original size:66 final size:66
Alignment explanation
Indices: 27474--27622 Score: 181
Period size: 66 Copynumber: 2.3 Consensus size: 66
27464 ATTTATAGGA
* ** * * * *
27474 AGATTATCAAATTTTCATAGTGTTGTTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAAT
1 AGATTATCAAATTTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAAA
27539 G
66 G
* * * * *
27540 TGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAGAGAGGTTATCAAAATTTCATAAA
1 AGATTATCAAATTTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAAA
27605 G
66 G
*
27606 AGGTTATCAAATTTTCA
1 AGATTATCAAATTTTCA
27623 AAATGTGATT
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (66 bp):
AGATTATCAAATTTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAAA
G
Found at i:27773 original size:22 final size:22
Alignment explanation
Indices: 27728--27849 Score: 74
Period size: 22 Copynumber: 5.6 Consensus size: 22
27718 ATATGGAGTC
*
27728 ATCAAAATTTC--AGGAAGG-A
1 ATCAAAATTTCATATGAAGGTA
27747 TATCAAAATTTCATATGAAGGTA
1 -ATCAAAATTTCATATGAAGGTA
** *
27770 ATCAAAATTTCATACTTTA-GTT
1 ATCAAAATTTCATA-TGAAGGTA
* * * * *
27792 TTCAAAATTTCGTAAGAGGGTT
1 ATCAAAATTTCATATGAAGGTA
* * *
27814 ATGAAAATTTCATA-GTATGTA
1 ATCAAAATTTCATATGAAGGTA
27835 GATCAAAATTTCATA
1 -ATCAAAATTTCATA
27850 GGGAGATTGA
Statistics
Matches: 78, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
20 11 0.14
21 3 0.04
22 61 0.78
23 3 0.04
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTA
Found at i:27885 original size:22 final size:22
Alignment explanation
Indices: 27747--28323 Score: 235
Period size: 22 Copynumber: 26.4 Consensus size: 22
27737 TCAGGAAGGA
* *
27747 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATAAGGAGGT
* ***
27769 AATCAAAATTTCATACTTTA-GT
1 TATCAAAATTTCATA-AGGAGGT
* *
27791 TTTCAAAATTTCGTAA-GAGGGT
1 TATCAAAATTTCATAAGGA-GGT
* * *
27813 TATGAAAATTTCAT-AGTATGT
1 TATCAAAATTTCATAAGGAGGT
* * *
27834 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATAAGGAGGT
**
27857 TGA-CAAAATTTCATAATTAGGT
1 T-ATCAAAATTTCATAAGGAGGT
** *
27879 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAAGGAGGT
*
27901 TATCAAAA-TT--T--GTA-GT
1 TATCAAAATTTCATAAGGAGGT
*
27917 TATCAAGATTTCATAAGGAGGT
1 TATCAAAATTTCATAAGGAGGT
* * *
27939 TATCAAAATTTTATAGGGAGATT
1 TATCAAAATTTCATAAGGAG-GT
*
27962 TATCAAAATTTTAT-AGGAAGGT
1 TATCAAAATTTCATAAGG-AGGT
* *
27984 T-TACCAAATATTCATAACGAGGT
1 TAT-CAAAAT-TTCATAAGGAGGT
* * *
28007 TATCACAATTTCAT-AGTGTGAT
1 TATCAAAATTTCATAAG-GAGGT
* * * *
28029 TATCAAAATTTCAGAATGTGAT
1 TATCAAAATTTCATAAGGAGGT
*
28051 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATAAGGAGGT
* * * *
28073 TTTTAAATTTTCATAACGTA-GT
1 TATCAAAATTTCATAA-GGAGGT
* * *
28095 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATAAGGAGGT
* * *
28117 TATCAACATCTCAT-AGTGTTGGT
1 TATCAAAATTTCATAAG-G-AGGT
** *
28140 TATCAAAATTTCATTGGGAAGT
1 TATCAAAATTTCATAAGGAGGT
*
28162 TATCAAAATTTCAT-AGTGAGAT
1 TATCAAAATTTCATAAG-GAGGT
* * *
28184 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATAAGGAGGT
* *
28206 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATAAGGAGGT
** **
28228 TAAAAAAAATTT-ATAAAAAGGT
1 T-ATCAAAATTTCATAAGGAGGT
* * * * *
28250 TCTCGAAATTCCAT-AGTATCGT
1 TATCAAAATTTCATAAGGA-GGT
* *
28272 TATTAAAATTCCAT-AGGAAGGT
1 TATCAAAATTTCATAAGG-AGGT
28294 TATCAAAATTTCATAAGGAGGT
1 TATCAAAATTTCATAAGGAGGT
*
28316 CATCAAAA
1 TATCAAAA
28324 ATAGTGTAAT
Statistics
Matches: 409, Mismatches: 106, Indels: 80
0.69 0.18 0.13
Matches are distributed among these distances:
16 9 0.02
17 4 0.01
19 2 0.00
20 1 0.00
21 23 0.06
22 294 0.72
23 72 0.18
24 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TATCAAAATTTCATAAGGAGGT
Found at i:28164 original size:45 final size:45
Alignment explanation
Indices: 28093--28179 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
28083 TCATAACGTA
* * *
28093 GTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGTTG
1 GTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGTTG
* *
28138 GTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATAGTG
1 GTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATAGTG
28180 AGATCTTCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 35 0.97
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.38
Consensus pattern (45 bp):
GTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGTTG
Found at i:28653 original size:17 final size:18
Alignment explanation
Indices: 28631--28664 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28621 TGTGATTAAT
28631 AATTT-ACTTCTCATAAA
1 AATTTAACTTCTCATAAA
28648 AATTTAACTTCTCATAA
1 AATTTAACTTCTCATAA
28665 TTATTCTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTTAACTTCTCATAAA
Found at i:29264 original size:46 final size:44
Alignment explanation
Indices: 29195--29304 Score: 114
Period size: 44 Copynumber: 2.5 Consensus size: 44
29185 ACAATCAAAC
* * * * *
29195 CAAAATTACATAAAAAGATTATCAAAAAATTTCATGGTGT-GATTAT
1 CAAAATTTCATATAGAGATTATC--AAAACTTCATAGTGTAG-TTAT
*
29241 CAAAATTTCATATAGAGGTTATCAAAACTTCATAGTGTAGTTAT
1 CAAAATTTCATATAGAGATTATCAAAACTTCATAGTGTAGTTAT
**
29285 CAAACCTTCATATAGAGATT
1 CAAAATTTCATATAGAGATT
29305 GCCAAAATGT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
44 34 0.63
45 1 0.02
46 19 0.35
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.34
Consensus pattern (44 bp):
CAAAATTTCATATAGAGATTATCAAAACTTCATAGTGTAGTTAT
Found at i:29591 original size:22 final size:22
Alignment explanation
Indices: 29220--29776 Score: 148
Period size: 22 Copynumber: 25.4 Consensus size: 22
29210 AGATTATCAA
* * *
29220 AAAATTTCATGGTGTGATTATC
1 AAAATTTCATAGTGAGGTTATC
29242 AAAATTTCATA-TAGAGGTTATC
1 AAAATTTCATAGT-GAGGTTATC
*
29264 AAAACTTCATAGTGTA-GTTATC
1 AAAATTTCATAGTG-AGGTTATC
** * **
29286 AAACCTTCATA-TAGAGATTGCC
1 AAAATTTCATAGT-GAGGTTATC
* *** *
29308 AAAATGTCATAAAAAGGTTACC
1 AAAATTTCATAGTGAGGTTATC
* * *
29330 AAAATTTCTTAGGGATGTTAAT-
1 AAAATTTCATAGTGAGGTT-ATC
* *
29352 AAAATTTCATA-TGAAAGTTAAC
1 AAAATTTCATAGTG-AGGTTATC
* *
29374 AAAATTTCATAAGGAGGGAGGTTACC
1 AAAATTTCAT----AGTGAGGTTATC
*
29400 AAAA-TT--T-GT--GCTTATC
1 AAAATTTCATAGTGAGGTTATC
* * *
29416 AAAATTTCCTAGGGAGGTTAAC
1 AAAATTTCATAGTGAGGTTATC
* * *
29438 AAAATTTTATAGGGAGGTTATA
1 AAAATTTCATAGTGAGGTTATC
* * * *
29460 AAAATTTTATGGAGCGGTTATC
1 AAAATTTCATAGTGAGGTTATC
* * *
29482 GAAAA-TACATAGAGAGGATATC
1 -AAAATTTCATAGTGAGGTTATC
*
29504 ACAATTTCATTCTCATAGGGAGGTTATC
1 A-AA----ATT-TCATAGTGAGGTTATC
* * * * *
29532 GAAATTTCATGGTGTGATTATT
1 AAAATTTCATAGTGAGGTTATC
*
29554 AAGATTT--TA-TGAGGTTATC
1 AAAATTTCATAGTGAGGTTATC
*
29573 AAAATTTCATAGTGCGGTTA-C
1 AAAATTTCATAGTGAGGTTATC
* * * * *
29594 -CAATTTTATTTAGTGTGATTATT
1 AAAATTTCA--TAGTGAGGTTATC
* * **
29617 AAAATTTTATAAG-CAAATTATC
1 AAAATTTCAT-AGTGAGGTTATC
* *
29639 AAAATTTCACATTGAGGTTATC
1 AAAATTTCATAGTGAGGTTATC
* * *
29661 GAAATTTCATAGTGTGGTTACC
1 AAAATTTCATAGTGAGGTTATC
*
29683 AAAATTTCACAGTGTA-GTTATC
1 AAAATTTCATAGTG-AGGTTATC
* * *
29705 AAATTTTC--AGAGAGGTTATT
1 AAAATTTCATAGTGAGGTTATC
** * * *
29725 GGAATTTCACAATGAGGCTATC
1 AAAATTTCATAGTGAGGTTATC
* * * *
29747 AAATTTTCAAAATGTGGTTATC
1 AAAATTTCATAGTGAGGTTATC
*
29769 AATATTTC
1 AAAATTTC
29777 TACATTGGAG
Statistics
Matches: 386, Mismatches: 108, Indels: 82
0.67 0.19 0.14
Matches are distributed among these distances:
16 9 0.02
17 2 0.01
18 1 0.00
19 15 0.04
20 21 0.05
21 10 0.03
22 277 0.72
23 13 0.03
24 7 0.02
25 2 0.01
26 12 0.03
27 4 0.01
28 13 0.03
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAGTGAGGTTATC
Found at i:29689 original size:66 final size:63
Alignment explanation
Indices: 29523--29676 Score: 168
Period size: 66 Copynumber: 2.4 Consensus size: 63
29513 TTCTCATAGG
* * ** *
29523 GAGGTTATCGAAATTTCATGGTGTGATTATTAAGATTTTATGAGGTTATCAAAATTTCATAGT
1 GAGGTTATCGAAATTTCATAGTGTGATTATTAAAATTTTATGAAATTATCAAAATTTCACAGT
* * *
29586 GCGGTTA-C-CAATTTTATTTAGTGTGATTATTAAAATTTTATAAGCAAATTATCAAAATTTCAC
1 GAGGTTATCGAAATTTCA--TAGTGTGATTATTAAAATTTTAT--G-AAATTATCAAAATTTCAC
*
29649 ATT
61 AGT
29652 GAGGTTATCGAAATTTCATAGTGTG
1 GAGGTTATCGAAATTTCATAGTGTG
29677 GTTACCAAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 11
0.76 0.13 0.12
Matches are distributed among these distances:
61 6 0.08
62 1 0.01
63 27 0.38
65 1 0.01
66 30 0.42
67 1 0.01
68 6 0.08
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (63 bp):
GAGGTTATCGAAATTTCATAGTGTGATTATTAAAATTTTATGAAATTATCAAAATTTCACAGT
Found at i:30654 original size:42 final size:43
Alignment explanation
Indices: 30603--30696 Score: 122
Period size: 45 Copynumber: 2.2 Consensus size: 43
30593 AGTGCATTAC
* *
30603 CTAA-ATTCTA-CTCCATCTCTAG-GTATTTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATTA-TTCATCAAAATAAAA
30644 CTAATATTCTACTCCTCCATCTCTAGATTATTCATCAAAATAAAA
1 CTAATATTCTA--CCTCCATCTCTAGATTATTCATCAAAATAAAA
30689 CTAATATT
1 CTAATATT
30697 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 34 0.74
46 2 0.04
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.36
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATTATTCATCAAAATAAAA
Found at i:32386 original size:26 final size:26
Alignment explanation
Indices: 32352--32438 Score: 156
Period size: 26 Copynumber: 3.3 Consensus size: 26
32342 CAACACAACA
32352 GCCGCTCACTCTTCCTTACCCTCACC
1 GCCGCTCACTCTTCCTTACCCTCACC
* *
32378 GCCGGTCACTCTTCCTTACCCTCATC
1 GCCGCTCACTCTTCCTTACCCTCACC
32404 GCCGCTCACTCTTCCTTACCCTCACC
1 GCCGCTCACTCTTCCTTACCCTCACC
32430 GCCGCTCAC
1 GCCGCTCAC
32439 ACTCAAACAC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 57 1.00
ACGTcount: A:0.11, C:0.52, G:0.10, T:0.26
Consensus pattern (26 bp):
GCCGCTCACTCTTCCTTACCCTCACC
Found at i:33569 original size:26 final size:26
Alignment explanation
Indices: 33539--33589 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
33529 CAAACTATGT
**
33539 TGTTAGACCATTACATTTCATTTTCA
1 TGTTAGAAAATTACATTTCATTTTCA
*
33565 TGTTAGAAAATTACCTTTCATTTTC
1 TGTTAGAAAATTACATTTCATTTTC
33590 TTTTCTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (26 bp):
TGTTAGAAAATTACATTTCATTTTCA
Found at i:33621 original size:20 final size:20
Alignment explanation
Indices: 33596--33649 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
33586 TTTCTTTTCT
33596 ATTATGAATGTTCAGCTTGG
1 ATTATGAATGTTCAGCTTGG
33616 ATTATGAATGTTCAGCTTGG
1 ATTATGAATGTTCAGCTTGG
33636 ATTATGAATGTTCA
1 ATTATGAATGTTCA
33650 TTGTCCAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTATGAATGTTCAGCTTGG
Found at i:38018 original size:12 final size:12
Alignment explanation
Indices: 38001--38044 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
37991 GGAAGAGGGA
*
38001 GAAGAAAGTGGG
1 GAAGAAAGTGAG
38013 GAAGAAAGTGAG
1 GAAGAAAGTGAG
38025 GAAGAATTAGATGAG
1 GAAGAA--AG-TGAG
38040 GAAGA
1 GAAGA
38045 GGAAGAGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 17 0.61
14 2 0.07
15 9 0.32
ACGTcount: A:0.48, C:0.00, G:0.41, T:0.11
Consensus pattern (12 bp):
GAAGAAAGTGAG
Found at i:38741 original size:24 final size:24
Alignment explanation
Indices: 38713--38759 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
38703 AACTTTCTGT
*
38713 TTTTTGTTCAAACTTGTTGTTTTC
1 TTTTTGCTCAAACTTGTTGTTTTC
*
38737 TTTTTGCTCATACTTGTTGTTTT
1 TTTTTGCTCAAACTTGTTGTTTT
38760 TCTGAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.11, C:0.13, G:0.13, T:0.64
Consensus pattern (24 bp):
TTTTTGCTCAAACTTGTTGTTTTC
Found at i:38889 original size:26 final size:26
Alignment explanation
Indices: 38848--38898 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
38838 AAACTTACTG
*
38848 TTTTTTGTTCAAACTTGTTGTTTTTC
1 TTTTTTGCTCAAACTTGTTGTTTTTC
*
38874 TTTTTTGCTCATACTTGTTGTTTTT
1 TTTTTTGCTCAAACTTGTTGTTTTT
38899 TCTGAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.10, C:0.12, G:0.12, T:0.67
Consensus pattern (26 bp):
TTTTTTGCTCAAACTTGTTGTTTTTC
Found at i:38960 original size:139 final size:138
Alignment explanation
Indices: 38626--39021 Score: 742
Period size: 139 Copynumber: 2.9 Consensus size: 138
38616 AAGGTTAGTT
*
38626 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTTGGAGGCTAATTCTGAAACTTAATTGCT
1 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
*
38691 CAAAGTTGCTGAAACTTTCTGTTTTTTGTTCAAACTTGTTG-TTTTC-TTTTTGCTCATACTTGT
66 CAAAGTTGCTGAAACTTACTGTTTTTTGTTCAAACTTGTTGTTTTTCTTTTTTGCTCATACTTGT
38754 TGTTTTTC
131 TGTTTTTC
38762 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
1 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
38827 CAAAGTTGCTGAAACTTACTGTTTTTTGTTCAAACTTGTTGTTTTTCTTTTTTGCTCATACTTGT
66 CAAAGTTGCTGAAACTTACTGTTTTTTGTTCAAACTTGTTGTTTTTCTTTTTTGCTCATACTTGT
38892 TGTTTTTTC
131 TG-TTTTTC
38901 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
1 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
*
38966 CAAAGTTGCTGAAACTTACTGTTTTTTGTTCAAACTTGCTGTTTTTCTTTTTTGCT
66 CAAAGTTGCTGAAACTTACTGTTTTTTGTTCAAACTTGTTGTTTTTCTTTTTTGCT
39022 ATATTTCTGT
Statistics
Matches: 254, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
136 104 0.41
137 5 0.02
138 19 0.07
139 126 0.50
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (138 bp):
TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
CAAAGTTGCTGAAACTTACTGTTTTTTGTTCAAACTTGTTGTTTTTCTTTTTTGCTCATACTTGT
TGTTTTTC
Found at i:76967 original size:14 final size:13
Alignment explanation
Indices: 76948--76986 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
76938 AAATTGTAAA
76948 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
76961 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
76975 ATTTAAAAAATT
1 ATTTAAAAAATT
76987 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:77195 original size:126 final size:127
Alignment explanation
Indices: 76972--77229 Score: 346
Period size: 134 Copynumber: 2.0 Consensus size: 127
76962 ATTTAAGAAA
76972 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAAT---A
* * * *
77037 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAG-TTTTAGTTGAGTAAAACTGTAAAA
63 CA-GTATAAGGATATTAGATTTAAATAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAA
77101 G
127 G
* *
77102 TATATTTAAAAAATTCTAATATATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT
1 TATATTTAAAAAATTC---TA-ATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAAT
*
77167 -CA-TA-AA-GATATTAGATTTAAATAAATAAAATTAGAGTTTTTAGTTGAATAAAACTATAAAA
62 ACAGTATAAGGATATTAGATTTAAATAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAA
77228 G
127 G
77229 T
1 T
77230 TTAAATAATG
Statistics
Matches: 116, Mismatches: 7, Indels: 13
0.85 0.05 0.10
Matches are distributed among these distances:
126 28 0.24
127 26 0.22
128 2 0.02
130 17 0.15
133 2 0.02
134 41 0.35
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.36
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATACAG
TATAAGGATATTAGATTTAAATAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAAG
Found at i:84568 original size:22 final size:22
Alignment explanation
Indices: 84540--84969 Score: 133
Period size: 22 Copynumber: 19.7 Consensus size: 22
84530 GGGATTAAGG
*
84540 AATTTTGA-AGACCTCACTATGA
1 AATTTTGATA-ACCTCACAATGA
* *
84562 AATTTTGATAACTTCCCAATGA
1 AATTTTGATAACCTCACAATGA
* *
84584 AATTTTGATAACCAACACTATGA
1 AATTTTGATAACC-TCACAATGA
* *
84607 GATGTTGATAACCTC-CATATGA
1 AATTTTGATAACCTCACA-ATGA
* * * ***
84629 TATATTGATAACCACGTTATGA
1 AATTTTGATAACCTCACAATGA
* * *
84651 AAATTTAAAAACCTC-CATATG-
1 AATTTTGATAACCTCACA-ATGA
* * **
84672 AATTGTT-AGTAATCACACTCTGA
1 AATT-TTGA-TAACCTCACAATGA
* * *
84695 AATTTTGATAATCACACTATGA
1 AATTTTGATAACCTCACAATGA
* ***
84717 AATTGT-AGTAACCTCGTTATGA
1 AATTTTGA-TAACCTCACAATGA
*
84739 AATTTTGATAAACCTTC-CTAT-A
1 AATTTTGAT-AACC-TCACAATGA
* * *
84761 AATTTTTGATAAACCTCCCTATAA
1 AA-TTTTGAT-AACCTCACAATGA
*
84785 AATTTTGATAACCTC-CTCATGA
1 AATTTTGATAACCTCAC-AATGA
*
84807 AATCTTGATAA-CT-AC----A
1 AATTTTGATAACCTCACAATGA
* * *
84823 AATTTTGATAATCTCCCTAT-A
1 AATTTTGATAACCTCACAATGA
* **
84844 ATTTTTTGATAACCTCATTATGA
1 A-ATTTTGATAACCTCACAATGA
* * * *
84867 AATTTTGTTAATCTCCCTATGA
1 AATTTTGATAACCTCACAATGA
**
84889 AATTTTGATAACCCTC-TTATGA
1 AATTTTGATAA-CCTCACAATGA
* * *
84911 AATTTTGA-AAACTAAACTATGA
1 AATTTTGATAACCT-CACAATGA
*
84933 AATTTTGATAACCTTCA-TATGA
1 AATTTTGATAACC-TCACAATGA
*
84955 AATTTTGATATCCTC
1 AATTTTGATAACCTC
84970 CCTGAAATTT
Statistics
Matches: 316, Mismatches: 61, Indels: 63
0.72 0.14 0.14
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 2 0.01
21 16 0.05
22 214 0.68
23 64 0.20
24 6 0.02
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
AATTTTGATAACCTCACAATGA
Found at i:84885 original size:44 final size:44
Alignment explanation
Indices: 84557--84980 Score: 226
Period size: 44 Copynumber: 9.8 Consensus size: 44
84547 AAGACCTCAC
* *
84557 TATGAAATTTTGATAA-CTTCCCAATGAAATTTTGATAACCAACAC-
1 TATGAAATTTTGATAATC-TCCCTATGAAATTTTGATAACC--CTCT
* * * * * * *
84602 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCAC-GT
1 TATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACC-CTCT
* * * * * * *
84646 TATGAAAATTTAAAAACCTCCATATG-AATTGTT-AGTAATCACAC-
1 TATGAAATTTTGATAATCTCCCTATGAAATT-TTGA-TAA-CCCTCT
* * * *
84690 TCTGAAATTTTGATAATCACACTATGAAATTGT-AGTAA-CCTCGT
1 TATGAAATTTTGATAATCTCCCTATGAAATTTTGA-TAACCCTC-T
* * * *
84734 TATGAAATTTTGATAAACCTTCCTAT-AAATTTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AATCTCCCTATGAAA-TTTTGATAACCCT-CT
* * *
84780 TATAAAATTTTGATAACCT-CCTCATGAAATCTTGATAA----C-
1 TATGAAATTTTGATAATCTCCCT-ATGAAATTTTGATAACCCTCT
* *
84819 TA-CAAATTTTGATAATCTCCCTAT-AATTTTTTGATAA-CCTCAT
1 TATGAAATTTTGATAATCTCCCTATGAA-ATTTTGATAACCCTC-T
*
84862 TATGAAATTTTGTTAATCTCCCTATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCCTCT
* ** * *
84906 TATGAAATTTTGA-AAACTAAACTATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAATCT-CCCTATGAAATTTTGATAACCCTCT
84950 TATGAAATTTTGAT-ATCCTCCC--TGAAATTTT
1 TATGAAATTTTGATAAT-CTCCCTATGAAATTTT
84981 AATTACTTCA
Statistics
Matches: 298, Mismatches: 52, Indels: 61
0.73 0.13 0.15
Matches are distributed among these distances:
37 2 0.01
38 24 0.08
39 5 0.02
40 1 0.00
41 1 0.00
42 11 0.04
43 9 0.03
44 150 0.50
45 73 0.24
46 21 0.07
47 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCCTCT
Found at i:84889 original size:82 final size:84
Alignment explanation
Indices: 84738--84900 Score: 215
Period size: 82 Copynumber: 2.0 Consensus size: 84
84728 CCTCGTTATG
* *
84738 AAATTTTGATAAACCTTCCTATAAATTTTTGATAAACCTCCCTATAAAATTTTGATAACCTCCTC
1 AAATTTTGATAAACCTCCCTATAAATTTTTGATAAACCTCACTATAAAATTTTGATAACCTCCTC
84803 ATGAAATCTTGATAACTAC
66 ATGAAATCTTGATAACTAC
* * * * * *
84822 AAATTTTGAT-AATCTCCCTATAATTTTTTGAT-AACCTCATTATGAAATTTTGTTAATCTCC-C
1 AAATTTTGATAAACCTCCCTATAAATTTTTGATAAACCTCACTATAAAATTTTGATAACCTCCTC
*
84884 TATGAAATTTTGATAAC
66 -ATGAAATCTTGATAAC
84901 CCTCTTATGA
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
81 1 0.01
82 39 0.57
83 19 0.28
84 10 0.14
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (84 bp):
AAATTTTGATAAACCTCCCTATAAATTTTTGATAAACCTCACTATAAAATTTTGATAACCTCCTC
ATGAAATCTTGATAACTAC
Found at i:85227 original size:88 final size:88
Alignment explanation
Indices: 85064--85230 Score: 201
Period size: 88 Copynumber: 1.9 Consensus size: 88
85054 AGAAATACCA
* * * * * **
85064 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCCC
1 CTATGAAATTCTGATAATAACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
*
85129 TCGATAAAATTTTGTTGACCCCT
66 ACGATAAAATTTTGTTGACCCCT
* * *
85152 CTATGAAATTCTGATAATAACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAATAA
1 CTATGAAATTCTGATAATAACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACAA
* *
85216 CACTATGAAATTTTG
65 CACGATAAAATTTTG
85231 ATAATCTACC
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
88 63 0.97
89 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.40
Consensus pattern (88 bp):
CTATGAAATTCTGATAATAACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACGATAAAATTTTGTTGACCCCT
Found at i:85415 original size:22 final size:22
Alignment explanation
Indices: 85062--85502 Score: 182
Period size: 22 Copynumber: 19.9 Consensus size: 22
85052 CGAGAAATAC
* *
85062 CACTATGAAATTTTGGTAATCA
1 CACTATGAAATTTTGATAACCA
* * * *
85084 CATTTTGAAAATTTGATAACCT
1 CACTATGAAATTTTGATAACCA
** *
85106 CTTTATGAAATTTTGATAACCC
1 CACTATGAAATTTTGATAACCA
* * * * * *
85128 CTCGATAAAATTTTGTTGACCC
1 CACTATGAAATTTTGATAACCA
* * **
85150 CTCTATGAAATTCTGATAATAA
1 CACTATGAAATTTTGATAACCA
* * *
85172 CATTATGTAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
* * **
85194 CGCTTTGAAATTTTGATAATAA
1 CACTATGAAATTTTGATAACCA
*
85216 CACTATGAAATTTTGATAATCTA
1 CACTATGAAATTTTGATAA-CCA
* *
85239 C-CTAT-AAATTTTAATAATCTGA
1 CACTATGAAATTTTGATAA-C-CA
* * *
85261 TCTCTATGAAATTTCGATAATCA
1 -CACTATGAAATTTTGATAACCA
* *
85284 CTCTATGAGA-TTTGATAACC-
1 CACTATGAAATTTTGATAACCA
** * * * *
85304 TTCTATCAAATTTTGGTACTCCT
1 CACTATGAAATTTTGATA-ACCA
* *
85327 CA-TGAAATTGAGACTTTT-ATAACCTT
1 CACT---A-TGA-AATTTTGATAACC-A
85353 CA-TATGAAATTTTGATAACCA
1 CACTATGAAATTTTGATAACCA
**
85374 CACTAAAAAATTTTGATAACCA
1 CACTATGAAATTTTGATAACCA
*
85396 CACTATGAAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
* * * * *
85418 CCCCATGATATATT-AGTAACCTT
1 CACTATGAAATTTTGA-TAACC-A
* *
85441 C-TTATGAAATTTTGTTAACCA
1 CACTATGAAATTTTGATAACCA
* *
85462 CATTATGAAATTCTT-ATAACCT
1 CACTATGAAATT-TTGATAACCA
* *
85484 CGCTATGACATTTTGATAA
1 CACTATGAAATTTTGATAA
85503 TCTTTTTGAT
Statistics
Matches: 314, Mismatches: 83, Indels: 44
0.71 0.19 0.10
Matches are distributed among these distances:
20 7 0.02
21 38 0.12
22 230 0.73
23 9 0.03
24 4 0.01
25 13 0.04
26 8 0.03
27 5 0.02
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.39
Consensus pattern (22 bp):
CACTATGAAATTTTGATAACCA
Found at i:85482 original size:44 final size:43
Alignment explanation
Indices: 85175--85695 Score: 156
Period size: 44 Copynumber: 11.9 Consensus size: 43
85165 ATAATAACAT
* * * * *
85175 TATGTAATTTTGATAACCTCGCTTTGAAATTTTGATAA--TAACA
1 TATGAAATTTTGATAACCACACTATGAAATTTT-ATAACCT-TCA
* * *
85218 CTATGAAATTTTGATAATCTAC-CTAT-AAATTTTAATAATCTGATCTC
1 -TATGAAATTTTGATAA-CCACACTATGAAATTTT-ATAACCT--TC-A
* * * * *
85265 TATGAAATTTCGATAATCACTCTATGAGATTTGATAACCTTC-
1 TATGAAATTTTGATAACCACACTATGAAATTTTATAACCTTCA
* * * * *
85307 TATCAAATTTTGGTACTCCTCA-TGAAATTGAGACTTTTATAACCTTCA
1 TATGAAATTTTGATA-ACCACACT---A-TGA-AATTTTATAACCTTCA
** *
85355 TATGAAATTTTGATAACCACACTAAAAAATTTTGATAACC-ACA
1 TATGAAATTTTGATAACCACACTATGAAATTTT-ATAACCTTCA
* * * * * *
85398 CTATGAAATTTTGATAACCTCCCCATGATATATTAGTAACCTTCT
1 -TATGAAATTTTGATAACCACACTATGAAATTTTA-TAACCTTCA
* * *
85443 TATGAAATTTTGTTAACCACATTATGAAATTCTTATAACC-TCGC
1 TATGAAATTTTGATAACCACACTATGAAATT-TTATAACCTTC-A
* * *
85487 TATGACATTTTGAT-A--A-TCT-T----TTTGATAACCTTTC-
1 TATGAAATTTTGATAACCACACTATGAAATTTTATAACC-TTCA
* * * *
85521 TAT-ATAATTGTGATAACCACACAATGAAATTTCAATAACCTTCC
1 TATGA-AATTTTGATAACCACACTATGAAATTT-TATAACCTTCA
* * * *
85565 TAAGAAATTTTAATAACCTGATC-CTATGAAA-TTTAGGTAAGC-ACA
1 TATGAAATTTTGATAACC--A-CACTATGAAATTTTA--TAACCTTCA
* * *
85610 CTATGAATTTTTGATAA-CATTC-CCATGAAATTTTGATAA-GTTCCA
1 -TATGAAATTTTGATAACCA--CACTATGAAATTTT-ATAACCTT-CA
* *
85655 TATGAAATTTTGGTAACCACACTATGGAATTTTGATAACCT
1 TATGAAATTTTGATAACCACACTATGAAATTTT-ATAACCT
85696 CCTCATGAAA
Statistics
Matches: 350, Mismatches: 77, Indels: 99
0.67 0.15 0.19
Matches are distributed among these distances:
33 1 0.00
34 17 0.05
35 3 0.01
36 2 0.01
37 1 0.00
38 1 0.00
39 2 0.01
40 1 0.00
41 1 0.00
42 13 0.04
43 32 0.09
44 160 0.46
45 24 0.07
46 56 0.16
47 22 0.06
48 14 0.04
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (43 bp):
TATGAAATTTTGATAACCACACTATGAAATTTTATAACCTTCA
Found at i:85659 original size:22 final size:22
Alignment explanation
Indices: 85544--85737 Score: 96
Period size: 22 Copynumber: 8.7 Consensus size: 22
85534 TAACCACACA
** *
85544 ATGAAATTTCAATAACCTTCCT
1 ATGAAATTTTGATAACATTCCT
* * *
85566 AAGAAATTTTAATAACCTGATCCT
1 ATGAAATTTTGATAACAT--TCCT
* *
85590 ATGAAATTTAGGTAAGCA--CACT
1 ATGAAATTTTGATAA-CATTC-CT
* *
85612 ATGAATTTTTGATAACATTCCC
1 ATGAAATTTTGATAACATTCCT
*
85634 ATGAAATTTTGATAA-GTTCCAT
1 ATGAAATTTTGATAACATTCC-T
*
85656 ATGAAATTTTGGTAACCA--CACT
1 ATGAAATTTTGATAA-CATTC-CT
* *
85678 ATGGAATTTTGATAAC-CTCCT
1 ATGAAATTTTGATAACATTCCT
* * *
85699 CATGAAATTATAATAATCA-TCTT
1 -ATGAAATTTTGATAA-CATTCCT
*
85722 ACGAAATTTTGATAAC
1 ATGAAATTTTGATAAC
85738 CACACAGAAA
Statistics
Matches: 132, Mismatches: 25, Indels: 31
0.70 0.13 0.16
Matches are distributed among these distances:
21 11 0.08
22 99 0.75
23 6 0.05
24 15 0.11
25 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (22 bp):
ATGAAATTTTGATAACATTCCT
Found at i:85728 original size:66 final size:66
Alignment explanation
Indices: 85534--85742 Score: 185
Period size: 66 Copynumber: 3.1 Consensus size: 66
85524 ATAATTGTGA
* * ** * *
85534 TAACCACACAATGAAATTTCAATAACCTTCCT-AAGAAATTTTAATAACCTGATCCTATGAAATT
1 TAACCACACTATGGAATTTTGATAACC-TCCTCATGAAATTTTAATAA-CT-ATCATATGAAATT
*
85598 TAGG
63 TTGG
* * * *
85602 TAAGCACACTAT-GAATTTTTGATAACATTCC-CATGAAATTTTGATAAGT-TCCATATGAAATT
1 TAACCACACTATGGAA-TTTTGATAAC-CTCCTCATGAAATTTTAATAACTAT-CATATGAAATT
85664 TTGG
63 TTGG
* * *
85668 TAACCACACTATGGAATTTTGATAACCTCCTCATGAAATTATAATAA-TCATCTTACGAAATTTT
1 TAACCACACTATGGAATTTTGATAACCTCCTCATGAAATTTTAATAACT-ATCATATGAAATTTT
*
85732 GA
65 GG
85734 TAACCACAC
1 TAACCACAC
85743 AGAAACAAGG
Statistics
Matches: 115, Mismatches: 18, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
65 5 0.04
66 69 0.60
67 7 0.06
68 34 0.30
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (66 bp):
TAACCACACTATGGAATTTTGATAACCTCCTCATGAAATTTTAATAACTATCATATGAAATTTTG
G
Found at i:86962 original size:41 final size:41
Alignment explanation
Indices: 86905--86986 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
86895 ACAATTTAGA
86905 AATATATTTGAAAAAAAGGGTACAATTGGAAAATATAAAGT
1 AATATATTTGAAAAAAAGGGTACAATTGGAAAATATAAAGT
86946 AATATATTTGAAAAAAAGGGTACAATTGGAAAATATAAAGT
1 AATATATTTGAAAAAAAGGGTACAATTGGAAAATATAAAGT
86987 TTCCCCTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.27
Consensus pattern (41 bp):
AATATATTTGAAAAAAAGGGTACAATTGGAAAATATAAAGT
Found at i:86977 original size:19 final size:19
Alignment explanation
Indices: 86914--86978 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
86904 AAATATATTT
86914 GAAAAAAAGGGTACAATTG
1 GAAAAAAAGGGTACAATTG
* * *
86933 GAAAATATAA-AGTAATATATTT
1 GAAAA-A-AAGGGT-ACA-ATTG
86955 GAAAAAAAGGGTACAATTG
1 GAAAAAAAGGGTACAATTG
86974 GAAAA
1 GAAAA
86979 TATAAAGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
19 13 0.37
20 7 0.20
21 7 0.20
22 8 0.23
ACGTcount: A:0.55, C:0.03, G:0.20, T:0.22
Consensus pattern (19 bp):
GAAAAAAAGGGTACAATTG
Found at i:97980 original size:20 final size:20
Alignment explanation
Indices: 97955--97993 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
97945 CATATAAAAT
*
97955 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
97975 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
97994 TTTAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:100914 original size:28 final size:27
Alignment explanation
Indices: 100872--100926 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
100862 ACTGAGACTA
*
100872 GACTCGAAACTGACTCGAAAAAACAAACT
1 GACTCGAAACCGACTC--AAAAACAAACT
100901 GACTC-AAACCGACTCAAAAACAAACT
1 GACTCGAAACCGACTCAAAAACAAACT
100927 CAAATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 11 0.44
28 9 0.36
29 5 0.20
ACGTcount: A:0.49, C:0.27, G:0.11, T:0.13
Consensus pattern (27 bp):
GACTCGAAACCGACTCAAAAACAAACT
Found at i:103344 original size:22 final size:21
Alignment explanation
Indices: 103314--103393 Score: 52
Period size: 22 Copynumber: 3.7 Consensus size: 21
103304 TATTTTTATG
* *
103314 AAATATTGAAAACTACCCTATC
1 AAATTTTGAAAACTA-CCTATA
* * * *
103336 AAATTTTGATAACCATCATATG
1 AAATTTTGAAAACTA-CCTATA
* *
103358 AAATTTTGATAATTACCTATA
1 AAATTTTGAAAACTACCTATA
*
103379 AAATTGTGATAAACT
1 AAATTTTGA-AAACT
103394 CCATAAGAGA
Statistics
Matches: 44, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
21 12 0.27
22 32 0.73
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (21 bp):
AAATTTTGAAAACTACCTATA
Found at i:104322 original size:2 final size:2
Alignment explanation
Indices: 104317--104361 Score: 63
Period size: 2 Copynumber: 21.5 Consensus size: 2
104307 AAGCCACACA
*
104317 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT CAT AGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT
104361 A
1 A
104362 AAAGGCTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 35 0.90
3 4 0.10
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:106390 original size:12 final size:11
Alignment explanation
Indices: 106368--106402 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 11
106358 ATACTTTTAT
106368 ATATAATATAG
1 ATATAATATAG
106379 ATATAGATATAG
1 ATATA-ATATAG
106391 ATAT-ATATAG
1 ATATAATATAG
106401 AT
1 AT
106403 TCTAAGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.35
11 5 0.22
12 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.37
Consensus pattern (11 bp):
ATATAATATAG
Found at i:107217 original size:2 final size:2
Alignment explanation
Indices: 107210--107242 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
107200 TAATTATAGG
107210 AT AT AT AT AT AT -T 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
107243 TTGTTTGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:109860 original size:4 final size:4
Alignment explanation
Indices: 109846--109881 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
109836 TTTTTCATCT
*
109846 TTTA TTTTA TTTA TTTA TTTA TTTA TTTA TATA TTT
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
109882 GTTTTAGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:114574 original size:21 final size:21
Alignment explanation
Indices: 114550--114592 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
114540 CTTGCGTGCT
114550 TCTCAATTAGCACTTCAACAA
1 TCTCAATTAGCACTTCAACAA
* *
114571 TCTCTATTAGCTCTTCAACAA
1 TCTCAATTAGCACTTCAACAA
114592 T
1 T
114593 ATCTGGAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.35
Consensus pattern (21 bp):
TCTCAATTAGCACTTCAACAA
Found at i:117016 original size:3 final size:3
Alignment explanation
Indices: 117008--117033 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
116998 GCTTAGTTTT
117008 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
117034 GGGAACATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:119004 original size:18 final size:18
Alignment explanation
Indices: 118967--119000 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
118957 TTTTTAAGTA
118967 AAAATATAATATATAAAT
1 AAAATATAATATATAAAT
*
118985 AAAATTTAATAT-TAAA
1 AAAATATAATATATAAA
119001 ATAATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATATAATATATAAAT
Found at i:119888 original size:5 final size:6
Alignment explanation
Indices: 119874--119902 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
119864 AAGCCCAATT
119874 ATTAAA ATT-AA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
119903 CAATGTCACT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATTAAA
Found at i:119888 original size:11 final size:12
Alignment explanation
Indices: 119874--119902 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
119864 AAGCCCAATT
119874 ATTAAAATT-AA
1 ATTAAAATTAAA
119885 ATTAAAATTAAA
1 ATTAAAATTAAA
119897 ATTAAA
1 ATTAAA
119903 CAATGTCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
ATTAAAATTAAA
Found at i:127957 original size:42 final size:43
Alignment explanation
Indices: 127910--127997 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 43
127900 TTACCTAAAA
*
127910 TCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCAAATAT
1 TCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCAAATAT
* *
127952 TCTACTCCTCCATCTCTAGATAATTCATCCAAATAAAGCTAATAT
1 TCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAGCAAATAT
127997 T
1 T
127998 AATTGTTGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
42 4 0.10
45 36 0.90
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.33
Consensus pattern (43 bp):
TCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCAAATAT
Found at i:135654 original size:42 final size:45
Alignment explanation
Indices: 135603--135696 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
135593 AGTGCATTAT
135603 CTAA-ATTCTACTCCAT-C-TCTA-AG-TAATTCATCAAAATAAAG
1 CTAATATTCTACTCC-TCCATCTATAGATAATTCATCAAAATAAAG
135644 CTAATATTCTACTCCTCCATCTATAGATAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCCATCTATAGATAATTCATCAAAATAAAG
*
135689 TTAATATT
1 CTAATATT
135697 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
41 5 0.11
42 11 0.23
43 4 0.09
44 2 0.04
45 25 0.53
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.35
Consensus pattern (45 bp):
CTAATATTCTACTCCTCCATCTATAGATAATTCATCAAAATAAAG
Found at i:137314 original size:23 final size:22
Alignment explanation
Indices: 137252--137315 Score: 56
Period size: 27 Copynumber: 2.6 Consensus size: 22
137242 ATAGTCACTA
*
137252 AAAATAATATATAGTATATATAT
1 AAAA-AATATATATTATATATAT
*
137275 AATTATATATATAATATTACTATATAT
1 AA--A-AAATAT-ATATTA-TATATAT
137302 AAAAAATATATATT
1 AAAAAATATATATT
137316 TAATTATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
23 7 0.21
24 5 0.15
25 6 0.18
26 6 0.18
27 9 0.27
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
AAAAAATATATATTATATATAT
Found at i:137330 original size:15 final size:14
Alignment explanation
Indices: 137255--137329 Score: 62
Period size: 15 Copynumber: 5.0 Consensus size: 14
137245 GTCACTAAAA
137255 ATAATA-TATAGTAT
1 ATAATATTATA-TAT
137269 ATATATAATTATATAT
1 ATA-AT-ATTATATAT
137285 ATAATATTACTATAT
1 ATAATATTA-TATAT
* *
137300 ATAAAAAATATATAT
1 AT-AATATTATATAT
*
137315 TTAATTATTATATAT
1 ATAA-TATTATATAT
137330 TGATAAACCG
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
14 9 0.18
15 25 0.50
16 12 0.24
17 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (14 bp):
ATAATATTATATAT
Found at i:139978 original size:61 final size:61
Alignment explanation
Indices: 139883--140011 Score: 190
Period size: 61 Copynumber: 2.1 Consensus size: 61
139873 AAAACTCAAA
* * *
139883 TTTCAAATAATTTTTTCCATATTATGAACTAATTGAGATT-ATTCAAACTCAAAATTATCCC
1 TTTCAAATAATGTTTTCCATATTATGAACTAATTGA-ATTGATTCAAACTCAAAACTATACC
**
139944 TTTCAAATAATGTTTTCCATATTATGAACTAATTGAATTGATTCGTACTCAAAACTATACC
1 TTTCAAATAATGTTTTCCATATTATGAACTAATTGAATTGATTCAAACTCAAAACTATACC
140005 -TTCAAAT
1 TTTCAAAT
140012 GCGTGTATGA
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
60 10 0.16
61 52 0.84
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.40
Consensus pattern (61 bp):
TTTCAAATAATGTTTTCCATATTATGAACTAATTGAATTGATTCAAACTCAAAACTATACC
Found at i:148168 original size:19 final size:21
Alignment explanation
Indices: 148138--148201 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
148128 TTGACACTAT
*
148138 TTAGCAACTGTACAGATGAGA
1 TTAGCTACTGTACAGATGAGA
*
148159 TTA-C-ACTGTACAGATTAGA
1 TTAGCTACTGTACAGATGAGA
148178 TTAGCTACTGTACAGATGAGA
1 TTAGCTACTGTACAGATGAGA
148199 TTA
1 TTA
148202 TTAGAGCAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.44
20 2 0.05
21 20 0.51
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (21 bp):
TTAGCTACTGTACAGATGAGA
Found at i:148259 original size:19 final size:19
Alignment explanation
Indices: 148235--148273 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
148225 TTTGGGCCCA
*
148235 AAACAGTGATGAAACGGTT
1 AAACAGTGATGAAACAGTT
148254 AAACAGTGATGAAACAGTT
1 AAACAGTGATGAAACAGTT
148273 A
1 A
148274 CACATACACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.21
Consensus pattern (19 bp):
AAACAGTGATGAAACAGTT
Found at i:149380 original size:35 final size:35
Alignment explanation
Indices: 149333--149400 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
149323 ACAATGTCTT
*
149333 ATCCTAGAATTAATGTTAATTAATGTGGAAAGTTA
1 ATCCTAGAATTAATGTTAATTAATGGGGAAAGTTA
*
149368 ATCCTAGGATTAATGTTAATTAATGGGGAAAGT
1 ATCCTAGAATTAATGTTAATTAATGGGGAAAGT
149401 ATGAAGAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (35 bp):
ATCCTAGAATTAATGTTAATTAATGGGGAAAGTTA
Found at i:150893 original size:108 final size:108
Alignment explanation
Indices: 150703--150917 Score: 308
Period size: 108 Copynumber: 2.0 Consensus size: 108
150693 AAATGGTAGG
* **
150703 GTTGTTCCTGAAAATGAAAACTTTTTAGGCTCAAATGGAGATGAAGTGATTATGGAGAAGACCCA
1 GTTGTTCCTGAAAATGAAAACCTTTTAGGCTCAAATGGAGATGAAGTGACCATGGAGAAGACCCA
* *
150768 GTTTGGCAATTCCTCTGAGGA-AGTAAATAATGCAACTTTGGCA
66 GTTGGGCAATTCCTCTGA-GACAGCAAATAATGCAACTTTGGCA
* *
150811 GTTGTTCCTGAAGAT-AAAACCCTTTTAGGCTCAAATGGAGATGAAGTGACCATGGAGAATACCC
1 GTTGTTCCTGAAAATGAAAA-CCTTTTAGGCTCAAATGGAGATGAAGTGACCATGGAGAAGACCC
* * *
150875 AGTTGGGCAATTCTTCTGATACTGCAAATAATGCAACTTTGGC
65 AGTTGGGCAATTCCTCTGAGACAGCAAATAATGCAACTTTGGC
150918 TGGTGAAAAT
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 5 0.05
108 90 0.95
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.28
Consensus pattern (108 bp):
GTTGTTCCTGAAAATGAAAACCTTTTAGGCTCAAATGGAGATGAAGTGACCATGGAGAAGACCCA
GTTGGGCAATTCCTCTGAGACAGCAAATAATGCAACTTTGGCA
Found at i:161581 original size:17 final size:17
Alignment explanation
Indices: 161559--161591 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
161549 ACTTTTACAT
161559 CCTCCAATAATAGAATA
1 CCTCCAATAATAGAATA
161576 CCTCCAATAATAGAAT
1 CCTCCAATAATAGAAT
161592 GACACTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.24
Consensus pattern (17 bp):
CCTCCAATAATAGAATA
Found at i:163119 original size:14 final size:14
Alignment explanation
Indices: 163100--163126 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
163090 TGGTGCTTGC
163100 TATTCGATTTTTAG
1 TATTCGATTTTTAG
163114 TATTCGATTTTTA
1 TATTCGATTTTTA
163127 TGAGGGTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.11, T:0.59
Consensus pattern (14 bp):
TATTCGATTTTTAG
Found at i:166645 original size:21 final size:21
Alignment explanation
Indices: 166597--166677 Score: 83
Period size: 22 Copynumber: 3.8 Consensus size: 21
166587 ATTAATTAGG
*
166597 TTATCAAAATTTCATATGG-AGT
1 TTATCAAAATTTCATA-GGTA-A
*
166619 TTATCACAATTTCATAGGTAA
1 TTATCAAAATTTCATAGGTAA
* *
166640 TTATCAAAATTTAATAGGATAG
1 TTATCAAAATTTCATAGG-TAA
*
166662 TAATCAAAATTTCATA
1 TTATCAAAATTTCATA
166678 AAAATATTCA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
21 18 0.36
22 32 0.64
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGTAA
Found at i:168626 original size:12 final size:13
Alignment explanation
Indices: 168609--168638 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
168599 CAGAAAAGGA
168609 CAAAAAAAAAGTT
1 CAAAAAAAAAGTT
168622 CAAAAAAAAAGTT
1 CAAAAAAAAAGTT
168635 CAAA
1 CAAA
168639 TGGAGCCTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.70, C:0.10, G:0.07, T:0.13
Consensus pattern (13 bp):
CAAAAAAAAAGTT
Found at i:173163 original size:21 final size:21
Alignment explanation
Indices: 173139--173183 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
173129 TTGACACTGT
*
173139 TTAGCAACTGTACAGATTAGA
1 TTAGCAACTGTACAGATGAGA
** *
173160 TTAGGTACTGTATAGATGAGA
1 TTAGCAACTGTACAGATGAGA
173181 TTA
1 TTA
173184 TTAGAGCAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (21 bp):
TTAGCAACTGTACAGATGAGA
Found at i:181528 original size:30 final size:30
Alignment explanation
Indices: 181494--181551 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
181484 GTGGGTTGTG
181494 CTTGGTACTTTATATTGAAACTTATTAACT
1 CTTGGTACTTTATATTGAAACTTATTAACT
*
181524 CTTGGTACTTTATATTGAAATTTATTAA
1 CTTGGTACTTTATATTGAAACTTATTAA
181552 TTAACTTGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (30 bp):
CTTGGTACTTTATATTGAAACTTATTAACT
Found at i:194815 original size:7 final size:7
Alignment explanation
Indices: 194798--194829 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
194788 ACTAGACTAT
194798 TAGTA-C
1 TAGTAGC
194804 TAGTAGC
1 TAGTAGC
194811 TAGTAGC
1 TAGTAGC
194818 TAGTAGC
1 TAGTAGC
194825 -AGTAG
1 TAGTAG
194830 AAGTAGAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 10 0.40
7 15 0.60
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.28
Consensus pattern (7 bp):
TAGTAGC
Found at i:210391 original size:26 final size:26
Alignment explanation
Indices: 210338--210400 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
210328 CATGTTATAC
* *
210338 ATGAACACTACTGAATATGCAACAAT
1 ATGAACCCTACTGAATATACAACAAT
*
210364 ATGAACCCTACTGAATA-ACAAACTAT
1 ATGAACCCTACTGAATATAC-AACAAT
*
210390 ATGAATCCTAC
1 ATGAACCCTAC
210401 GGGTTATGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 1 0.03
26 31 0.97
ACGTcount: A:0.44, C:0.22, G:0.10, T:0.24
Consensus pattern (26 bp):
ATGAACCCTACTGAATATACAACAAT
Found at i:210629 original size:51 final size:50
Alignment explanation
Indices: 210532--210674 Score: 173
Period size: 51 Copynumber: 2.8 Consensus size: 50
210522 CATGGCTCCT
* *
210532 ACTAAATATGCAACTACAT-G-ATTCAATTGAATATGCAACTAAATAAACCC
1 ACTAAATATGCAACTACATGGCCTT--ACTGAATATGCAACTAAATAAACCC
*
210582 ACTAAATATGCAACTACATGGCCCTTACTGAATATGCAACTAAATAAATCC
1 ACTAAATATGCAACTACATGG-CCTTACTGAATATGCAACTAAATAAACCC
* ** *
210633 ACTGAATACACAACTACATGGCCTCTACTGATTATGCAACTA
1 ACTAAATATGCAACTACATGGCCT-TACTGAATATGCAACTA
210675 TTAAAGAATA
Statistics
Matches: 82, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
50 22 0.27
51 58 0.71
53 2 0.02
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.26
Consensus pattern (50 bp):
ACTAAATATGCAACTACATGGCCTTACTGAATATGCAACTAAATAAACCC
Found at i:210672 original size:26 final size:26
Alignment explanation
Indices: 210493--210674 Score: 99
Period size: 25 Copynumber: 7.2 Consensus size: 26
210483 CAGTCATACT
* * *
210493 ACTACATGG-CACTGCTGAATATTCA
1 ACTACATGGCCTCTACTGAATATGCA
* *
210518 ATTACATGG-CTCCTACTAAATATGCA
1 ACTACATGGCCT-CTACTGAATATGCA
** * *
210544 ACTACAT-GATTCAATTGAATATGCA
1 ACTACATGGCCTCTACTGAATATGCA
* ** *
210569 ACTAAATAAACC-C-ACTAAATATGCA
1 ACTACAT-GGCCTCTACTGAATATGCA
210594 ACTACATGGCC-CTTACTGAATATGCA
1 ACTACATGGCCTC-TACTGAATATGCA
* *** * **
210620 ACTAAAT-AAATCCACTGAATACACA
1 ACTACATGGCCTCTACTGAATATGCA
*
210645 ACTACATGGCCTCTACTGATTATGCA
1 ACTACATGGCCTCTACTGAATATGCA
210671 ACTA
1 ACTA
210675 TTAAAGAATA
Statistics
Matches: 114, Mismatches: 35, Indels: 15
0.70 0.21 0.09
Matches are distributed among these distances:
24 3 0.03
25 59 0.52
26 52 0.46
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (26 bp):
ACTACATGGCCTCTACTGAATATGCA
Found at i:211338 original size:30 final size:29
Alignment explanation
Indices: 211302--211391 Score: 101
Period size: 30 Copynumber: 3.1 Consensus size: 29
211292 TTCCCTGTTA
* *
211302 ATGCAACCATATATGCACACTACTGAATAT
1 ATGCAACTACATATGCACACTACT-AATAT
* * *
211332 ATGCAACTGCATATCCACCCTACTAA-AT
1 ATGCAACTACATATGCACACTACTAATAT
*
211360 ATACAACTACATATGCACACTACTAAATAT
1 ATGCAACTACATATGCACACTACT-AATAT
211390 AT
1 AT
211392 AACTGTTCGC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
28 22 0.45
29 4 0.08
30 23 0.47
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.27
Consensus pattern (29 bp):
ATGCAACTACATATGCACACTACTAATAT
Found at i:211372 original size:28 final size:28
Alignment explanation
Indices: 211312--211395 Score: 105
Period size: 28 Copynumber: 2.9 Consensus size: 28
211302 ATGCAACCAT
* *
211312 ATATGCACACTACTGAATATATGCAACTGC
1 ATATGCACACTACT-AA-ATATACAACTAC
* *
211342 ATATCCACCCTACTAAATATACAACTAC
1 ATATGCACACTACTAAATATACAACTAC
*
211370 ATATGCACACTACTAAATATATAACT
1 ATATGCACACTACTAAATATACAACT
211396 GTTCGCGCCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 33 0.70
29 2 0.04
30 12 0.26
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.27
Consensus pattern (28 bp):
ATATGCACACTACTAAATATACAACTAC
Found at i:211552 original size:49 final size:48
Alignment explanation
Indices: 211464--211584 Score: 165
Period size: 49 Copynumber: 2.5 Consensus size: 48
211454 AATTTTACCC
* * **
211464 AAAAATTGATAAAAAGTGCAA-TGAAAATTAAAAGATCAATTTTGTCTT
1 AAAAATTGAGAAAAAGTGCAAGT-AAAAATAAAAGATCAATTTTGTAGT
*
211512 AAAAATTGAGAAAAAGGTGCAAGTAAAAATAAAAGTTCAATTTTGTAGT
1 AAAAATTGAGAAAAA-GTGCAAGTAAAAATAAAAGATCAATTTTGTAGT
211561 AAAAATTGAGAAAAAGTGC-AGTAA
1 AAAAATTGAGAAAAAGTGCAAGTAA
211585 GAAGTAAATG
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
47 5 0.08
48 18 0.27
49 42 0.64
50 1 0.02
ACGTcount: A:0.52, C:0.05, G:0.17, T:0.26
Consensus pattern (48 bp):
AAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAGATCAATTTTGTAGT
Found at i:220839 original size:62 final size:60
Alignment explanation
Indices: 220773--220961 Score: 142
Period size: 60 Copynumber: 3.1 Consensus size: 60
220763 AGGTATGTAG
220773 TTTATTTATGGTATAGTTTCTAGTTTTGGTTGAATTCTCATTTAGATGTTTGGATATAGAGA
1 TTTATTTATGGTATAGTTTCTAG-TTTGGTTGAATTCT-ATTTAGATGTTTGGATATAGAGA
* * * * ** * * *
220835 TTTATTTGAATTGTAATGAGATT-T-GTTGGGTTTG--TT-TGTTTATTTGGTAGG-TATATAG-
1 TTTATTT--ATGGT-AT-AGTTTCTAGTTTGG-TTGAATTCTATTTAGATGTTTGGATATAGAGA
*
220893 TTTATTTATGGTATAATTTCTAGTTTGCGTTGAATTCTTATTTAGATGTTT-GAGTATAGAGA
1 TTTATTTATGGTATAGTTTCTAGTTTG-GTTGAATTC-TATTTAGATGTTTGGA-TATAGAGA
220955 TTTATTT
1 TTTATTT
220962 GAATTGTAAT
Statistics
Matches: 93, Mismatches: 19, Indels: 30
0.65 0.13 0.21
Matches are distributed among these distances:
54 3 0.03
55 3 0.03
56 11 0.12
57 1 0.01
58 9 0.10
59 7 0.08
60 17 0.18
61 7 0.08
62 16 0.17
63 4 0.04
64 8 0.09
65 3 0.03
66 4 0.04
ACGTcount: A:0.23, C:0.03, G:0.21, T:0.52
Consensus pattern (60 bp):
TTTATTTATGGTATAGTTTCTAGTTTGGTTGAATTCTATTTAGATGTTTGGATATAGAGA
Found at i:220958 original size:120 final size:120
Alignment explanation
Indices: 220745--220973 Score: 390
Period size: 120 Copynumber: 1.9 Consensus size: 120
220735 TTGTTTGTAA
* *
220745 TTTGTTTATTTATTTGGTAGGTATGTAGTTTATTTATGGTATAGTTTCTAGTTTTGGTTGAATTC
1 TTTGTTTATTTATTTGGTAGGTATATAGTTTATTTATGGTATAATTTCTAGTTTTGGTTGAATTC
220810 TCATTTAGATGTTTGGATATAGAGATTTATTTGAATTGTAATGAGATTTGTTGGG
66 TCATTTAGATGTTTGGATATAGAGATTTATTTGAATTGTAATGAGATTTGTTGGG
*
220865 TTTGTTTGTTTATTTGGTAGGTATATAGTTTATTTATGGTATAATTTCTAG-TTTGCGTTGAATT
1 TTTGTTTATTTATTTGGTAGGTATATAGTTTATTTATGGTATAATTTCTAGTTTTG-GTTGAATT
*
220929 CTTATTTAGATGTTT-GAGTATAGAGATTTATTTGAATTGTAATGA
65 CTCATTTAGATGTTTGGA-TATAGAGATTTATTTGAATTGTAATGA
220974 CTTTTTCATT
Statistics
Matches: 103, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
119 6 0.06
120 97 0.94
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.52
Consensus pattern (120 bp):
TTTGTTTATTTATTTGGTAGGTATATAGTTTATTTATGGTATAATTTCTAGTTTTGGTTGAATTC
TCATTTAGATGTTTGGATATAGAGATTTATTTGAATTGTAATGAGATTTGTTGGG
Found at i:225486 original size:21 final size:21
Alignment explanation
Indices: 225462--225502 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
225452 TCGCTGCTCT
*
225462 AATAATCTAATCTGAACAGTA
1 AATAATCTAATATGAACAGTA
*
225483 AATAATCTAATATGTACAGT
1 AATAATCTAATATGAACAGT
225503 GTAATTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (21 bp):
AATAATCTAATATGAACAGTA
Found at i:227182 original size:29 final size:31
Alignment explanation
Indices: 227147--227226 Score: 110
Period size: 29 Copynumber: 2.6 Consensus size: 31
227137 ATTGGAAAAA
*
227147 GATCAATTTAGTCCCTCCATTA-TGAAATCT
1 GATCAATTTAGTCCCTCCATTATTGAAAACT
* * *
227177 G-TCAATTTAATCCCTCTATTATTGAAAAGT
1 GATCAATTTAGTCCCTCCATTATTGAAAACT
227207 GATCAATTTAGTCCCTCCAT
1 GATCAATTTAGTCCCTCCAT
227227 GAAACGGGAC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 18 0.43
30 8 0.19
31 16 0.38
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.38
Consensus pattern (31 bp):
GATCAATTTAGTCCCTCCATTATTGAAAACT
Found at i:228319 original size:16 final size:17
Alignment explanation
Indices: 228298--228338 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
228288 TTCTAATTAA
228298 AAATT-GATTTTTTTTT
1 AAATTGGATTTTTTTTT
*
228314 AAATTGGGTTTTTTTTT
1 AAATTGGATTTTTTTTT
228331 AAAATTGG
1 -AAATTGG
228339 CCCCTTCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.23
17 10 0.45
18 7 0.32
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.59
Consensus pattern (17 bp):
AAATTGGATTTTTTTTT
Found at i:228327 original size:17 final size:18
Alignment explanation
Indices: 228305--228338 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
228295 TAAAAATTGA
228305 TTTTTTTTT-AAATTGGG
1 TTTTTTTTTAAAATTGGG
228322 TTTTTTTTTAAAATTGG
1 TTTTTTTTTAAAATTGG
228339 CCCCTTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.65
Consensus pattern (18 bp):
TTTTTTTTTAAAATTGGG
Found at i:230666 original size:29 final size:29
Alignment explanation
Indices: 230604--230666 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
230594 CCCTCTTATT
230604 TGAGGGACACTTGTCATTTTTTGGGCTGA
1 TGAGGGACACTTGTCATTTTTTGGGCTGA
* *
230633 -CAGGGACACTTGTCAATTTTTT-GGCTTA
1 TGAGGGACACTTGTC-ATTTTTTGGGCTGA
230661 TGAGGG
1 TGAGGG
230667 TCAAATGGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 18 0.62
29 11 0.38
ACGTcount: A:0.19, C:0.14, G:0.30, T:0.37
Consensus pattern (29 bp):
TGAGGGACACTTGTCATTTTTTGGGCTGA
Found at i:231223 original size:33 final size:33
Alignment explanation
Indices: 231172--231257 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
231162 AAAAAGAATC
231172 AATCAAACCTAAAA-CCCAAAATCC-AGACCTAA
1 AATCAAACCTAAAACCCCAAAA-CCTAGACCTAA
*
231204 AATGAAACCTAAAACCCCAAAACCTAGACCTAA
1 AATCAAACCTAAAACCCCAAAACCTAGACCTAA
231237 AATCAAACCTAAAACCCCAAA
1 AATCAAACCTAAAACCCCAAA
231258 TCAATTAAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
32 15 0.30
33 35 0.70
ACGTcount: A:0.53, C:0.31, G:0.03, T:0.12
Consensus pattern (33 bp):
AATCAAACCTAAAACCCCAAAACCTAGACCTAA
Found at i:231384 original size:35 final size:34
Alignment explanation
Indices: 231338--231409 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 34
231328 AACAGCCATC
231338 AATCCTTTGTTCTTGGAGCTTGTAAAAATCCCAAG
1 AATCCTTTGTTCTTGGAGCTTGTAAAAAT-CCAAG
* *
231373 AATCCTTTGTTCTTGGGGCTTGTGAAAATCCAAG
1 AATCCTTTGTTCTTGGAGCTTGTAAAAATCCAAG
231407 AAT
1 AAT
231410 TTGATATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 8 0.23
35 27 0.77
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (34 bp):
AATCCTTTGTTCTTGGAGCTTGTAAAAATCCAAG
Found at i:233546 original size:21 final size:22
Alignment explanation
Indices: 233503--233545 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
233493 TATTTTTATA
*
233503 TATTGTCTTTATGTTTCTTTTT
1 TATTGTCTTTATGTTCCTTTTT
233525 TATTGT-TTTAT-TTCCTTTTT
1 TATTGTCTTTATGTTCCTTTTT
233545 T
1 T
233546 TTTGAATGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 5 0.25
22 6 0.30
ACGTcount: A:0.09, C:0.09, G:0.07, T:0.74
Consensus pattern (22 bp):
TATTGTCTTTATGTTCCTTTTT
Found at i:234330 original size:109 final size:109
Alignment explanation
Indices: 234135--234346 Score: 336
Period size: 109 Copynumber: 1.9 Consensus size: 109
234125 ACGAGGGAAT
234135 TTAATAAACTACTCCTCTGTTTTGGGAAGTGGAGCACACGGGGTTCGATATCACAAATATCAACC
1 TTAATAAACTACTCCTCTGTTTTGGGAAGTGGAGCACACGGGGTTCGATATCACAAATATCAACC
* * *
234200 TTCGTGTCAGTCACGATCC-AAAATTATGAGTATGCAAAGCATA
66 TTCGCGTCAGTCACGAACCAAAAATTACGAGTATGCAAAGCATA
* * * *
234243 TTAATAAATTACTCCTCTGTTTTTGGGAAGTGGAGTACCCGGGGTTCGGTATCACAAATATCAAC
1 TTAATAAACTACTCCTCTG-TTTTGGGAAGTGGAGCACACGGGGTTCGATATCACAAATATCAAC
*
234308 CTTCGCGTTAGTCACGAACCAAAAATTACGAGTATGCAA
65 CTTCGCGTCAGTCACGAACCAAAAATTACGAGTATGCAA
234347 GGCACCTTAA
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
108 18 0.19
109 59 0.63
110 17 0.18
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (109 bp):
TTAATAAACTACTCCTCTGTTTTGGGAAGTGGAGCACACGGGGTTCGATATCACAAATATCAACC
TTCGCGTCAGTCACGAACCAAAAATTACGAGTATGCAAAGCATA
Found at i:244433 original size:43 final size:43
Alignment explanation
Indices: 244385--244470 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
244375 AGCAGCCATG
* *
244385 CCATTTGCAGCAGTTTCCTTCTTAGAAAATGCTGATAATTGAA
1 CCATTTGCAGCAATTTCCTTCTTAGAAAATGCAGATAATTGAA
244428 CCATTTGCAGCAATTTCCTTCTTAGAAAATGCAGATAATTGAA
1 CCATTTGCAGCAATTTCCTTCTTAGAAAATGCAGATAATTGAA
244471 ATCCAATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.34
Consensus pattern (43 bp):
CCATTTGCAGCAATTTCCTTCTTAGAAAATGCAGATAATTGAA
Done.