Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009605.1 Hibiscus syriacus cultivar Beakdansim tig00116989_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9158330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 35
Found at i:215669 original size:21 final size:21
Alignment explanation
Indices: 215643--215682 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
215633 GTTAGGAGCT
*
215643 TAGGTGTATCGGTACACTCTC
1 TAGGTGTATCGATACACTCTC
215664 TAGGTGTATCGATACACTC
1 TAGGTGTATCGATACACTC
215683 AGTGTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.33
Consensus pattern (21 bp):
TAGGTGTATCGATACACTCTC
Found at i:216887 original size:25 final size:25
Alignment explanation
Indices: 216853--216904 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
216843 ATCTATGTCG
216853 CACATGAGTTCTTCAAGCTCTGGAT
1 CACATGAGTTCTTCAAGCTCTGGAT
216878 CACATGAGTTCTTCAAGCTCTGGAT
1 CACATGAGTTCTTCAAGCTCTGGAT
216903 CA
1 CA
216905 TCGTCTGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (25 bp):
CACATGAGTTCTTCAAGCTCTGGAT
Found at i:218748 original size:20 final size:21
Alignment explanation
Indices: 218723--218761 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
218713 TTTAGGAGCT
218723 TAGGTGTATCG-TACACTCTC
1 TAGGTGTATCGATACACTCTC
218743 TAGGTGTATCGATACACTC
1 TAGGTGTATCGATACACTC
218762 AATGTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (21 bp):
TAGGTGTATCGATACACTCTC
Found at i:220163 original size:36 final size:36
Alignment explanation
Indices: 220071--220165 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 36
220061 CAAGATTCCT
*
220071 AAAAAATCCAACTATTTATTTCCTTTTACAAAATAGG
1 AAAAAAT-CAACGATTTATTTCCTTTTACAAAATAGG
*
220108 AAAATAATCAAATGA-TTATTTCCTTTTACAAACA-A-G
1 AAAA-AATC-AACGATTTATTTCCTTTTACAAA-ATAGG
220144 AAATAAATCAACGATTTATTTC
1 AAA-AAATCAACGATTTATTTC
220166 GATTTATTTC
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
35 4 0.08
36 15 0.30
37 24 0.48
38 7 0.14
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (36 bp):
AAAAAATCAACGATTTATTTCCTTTTACAAAATAGG
Found at i:220222 original size:59 final size:56
Alignment explanation
Indices: 220130--220242 Score: 199
Period size: 59 Copynumber: 2.0 Consensus size: 56
220120 TGATTATTTC
220130 CTTTTACAAACAAGAAATAAATCAACGATTTATTTCGATTTATTTCCTTTTTACTT
1 CTTTTACAAACAAGAAATAAATCAACGATTTATTTCGATTTATTTCCTTTTTACTT
220186 CTTTTACAAAACAAGAAAATAAATCAAACGATTTATTTCGATTTATTTCCTTTTTAC
1 CTTTTAC-AAACAAG-AAATAAATC-AACGATTTATTTCGATTTATTTCCTTTTTAC
220243 AAAATAAGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
56 7 0.13
57 7 0.13
58 9 0.17
59 31 0.57
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.42
Consensus pattern (56 bp):
CTTTTACAAACAAGAAATAAATCAACGATTTATTTCGATTTATTTCCTTTTTACTT
Found at i:220293 original size:39 final size:39
Alignment explanation
Indices: 220224--220360 Score: 157
Period size: 39 Copynumber: 3.5 Consensus size: 39
220214 CGATTTATTT
*
220224 CGATTTATTTCCTTTTTACAAAATAAGAAACTAAATCCAA
1 CGATTTATTTCC-TTTTACAAAATAGGAAACTAAATCCAA
* * ***
220264 CGAGTTATTTCCTTTTACAAATTAGGAAACTAAATTTTA
1 CGATTTATTTCCTTTTACAAAATAGGAAACTAAATCCAA
* ** * *
220303 TGATTTATTTAATTTTTCAAAATAGGAAAATAAATCCAA
1 CGATTTATTTCCTTTTACAAAATAGGAAACTAAATCCAA
*
220342 CGATTTATTTTCTTTTACA
1 CGATTTATTTCCTTTTACA
220361 TAAGAATCAT
Statistics
Matches: 77, Mismatches: 20, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
39 66 0.86
40 11 0.14
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (39 bp):
CGATTTATTTCCTTTTACAAAATAGGAAACTAAATCCAA
Found at i:220541 original size:94 final size:89
Alignment explanation
Indices: 220315--220552 Score: 230
Period size: 91 Copynumber: 2.6 Consensus size: 89
220305 ATTTATTTAA
* * * * ***
220315 TTTTTCAAAATAGGAAAATAAATCCAACGATTTATTTTCTTTTAC-ATAAGAATCATACAAGATT
1 TTTTTCAAAAAAGGAAAATATATTCAACGATTTA-TTCCTTTTACAAT-AGAATC-TGTGAGATT
**
220379 ATTAAGAAAATAAATTATCGATTTATT
63 ATTAAGAAAATAAATTATAAATTTATT
* *
220406 TTTTTCAAAAAAGGAAAATATATTCTACGATTTATTCCTTTTACAAATCAGAATCTGTGAGATTC
1 TTTTTCAAAAAAGGAAAATATATTCAACGATTTATTCCTTTTAC-AAT-AGAATCTGTGAGATTA
220471 TTAAGAAAATAAATTCA-AAATTTTATT
64 TTAAGAAAATAAATT-ATAAA-TTTATT
* * * *
220498 TTCTTTTACAAAAATGAAAATA-ATTCAACGGTTTCTTTCCTTTTACAATAGAATC
1 TT-TTTCA-AAAAAGGAAAATATATTCAACGATTT-ATTCCTTTTACAATAGAATC
220553 ATATAAGAAA
Statistics
Matches: 123, Mismatches: 17, Indels: 13
0.80 0.11 0.08
Matches are distributed among these distances:
90 9 0.07
91 52 0.42
92 23 0.19
93 17 0.14
94 22 0.18
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (89 bp):
TTTTTCAAAAAAGGAAAATATATTCAACGATTTATTCCTTTTACAATAGAATCTGTGAGATTATT
AAGAAAATAAATTATAAATTTATT
Found at i:220635 original size:30 final size:28
Alignment explanation
Indices: 220592--220677 Score: 78
Period size: 26 Copynumber: 3.1 Consensus size: 28
220582 TATTATTCAA
220592 TATTTC-C-AAAAATAAATTTAACAATT
1 TATTTCTCAAAAAATAAATTTAACAATT
220618 TATTTCTTCAACAAAATAGAA--T--C-ATT
1 TATTTC-TCAA-AAAATA-AATTTAACAATT
220644 TAATATTCTCAAAAAATAAATTTAACAATT
1 T-AT-TTCTCAAAAAATAAATTTAACAATT
220674 TATT
1 TATT
220678 AAATTTTACA
Statistics
Matches: 48, Mismatches: 0, Indels: 22
0.69 0.00 0.31
Matches are distributed among these distances:
25 2 0.04
26 16 0.33
27 8 0.17
28 5 0.10
29 5 0.10
30 10 0.21
31 2 0.04
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.40
Consensus pattern (28 bp):
TATTTCTCAAAAAATAAATTTAACAATT
Found at i:220659 original size:56 final size:55
Alignment explanation
Indices: 220590--220736 Score: 206
Period size: 56 Copynumber: 2.6 Consensus size: 55
220580 TTTATTATTC
* *
220590 AATATT-TCCAAAAATAAATTTAACAATTTATTTCTTCAACAAAATAGAATCATTT
1 AATATTCTCAAAAAATAAATTTAACAATTTATTTATTCAACAAAATAGAATCA-TT
* **
220645 AATATTCTCAAAAAATAAATTTAACAATTTATTAAATTTTACAAAATAGAATCATT
1 AATATTCTCAAAAAATAAATTTAACAATTTATT-TATTCAACAAAATAGAATCATT
*
220701 AAAATTCTCAAGAAAATAAATTTAACAATTTATTTA
1 AATATTCTCAA-AAAATAAATTTAACAATTTATTTA
220737 ATTTTAAAGG
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
55 6 0.07
56 38 0.46
57 38 0.46
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.37
Consensus pattern (55 bp):
AATATTCTCAAAAAATAAATTTAACAATTTATTTATTCAACAAAATAGAATCATT
Found at i:220717 original size:57 final size:56
Alignment explanation
Indices: 220600--220958 Score: 224
Period size: 57 Copynumber: 6.4 Consensus size: 56
220590 AATATTTCCA
** ** *
220600 AAAATAAATTTAACAATTTATTTCTTCAACAAAATAGAATCATTTAATATTCTCAA-
1 AAAATAAATTTAACAATTTATTAATTTTACAAAATAGAATCA-TTAAAATTCTCAAG
220656 AAAATAAATTTAACAATTTATTAAATTTTACAAAATAGAATCATTAAAATTCTCAAG
1 AAAATAAATTTAACAATTTATT-AATTTTACAAAATAGAATCATTAAAATTCTCAAG
* * * **
220713 AAAATAAATTTAACAATTTATTTAATTTTA-AAGGATAAAATCATCCACGATTCTCAAG
1 AAAATAAATTTAACAATTTA-TTAATTTTACAA-AATAGAATCAT-TAAAATTCTCAAG
** * * * * *
220771 AAAATAAATTCGATAATTTATT-TTTCTTACAAAGTTA-AATTATTCAAGATT-TCCAAG
1 AAAATAAATTTAACAATTTATTAATT-TTACAAA-ATAGAATCATT-AAAATTCT-CAAG
* * * *
220828 GAAAT--A--CAACAATTT-TT--TTCCTTACAAAGTAGAATCATTAAGATTCTCAAG
1 AAAATAAATTTAACAATTTATTAATT--TTACAAAATAGAATCATTAAAATTCTCAAG
* * * * * *
220879 GAAATAAATTCAACAATCTATT--TTCCTTACAAAGTTAGAATCATTTAAGATTCTAAAG
1 AAAATAAATTTAACAATTTATTAATT--TTACAAA-ATAGAATCA-TTAAAATTCTCAAG
* *
220937 GAAATAAATTTAACAATCTATT
1 AAAATAAATTTAACAATTTATT
220959 TTCCTTAGAA
Statistics
Matches: 255, Mismatches: 28, Indels: 38
0.79 0.09 0.12
Matches are distributed among these distances:
51 19 0.07
52 17 0.07
53 8 0.03
55 9 0.04
56 52 0.20
57 83 0.33
58 67 0.26
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.36
Consensus pattern (56 bp):
AAAATAAATTTAACAATTTATTAATTTTACAAAATAGAATCATTAAAATTCTCAAG
Found at i:220938 original size:58 final size:57
Alignment explanation
Indices: 220601--220979 Score: 313
Period size: 58 Copynumber: 6.7 Consensus size: 57
220591 ATATTTCCAA
* *
220601 AAATAAATTTAACAATTTA-TTTCTTCAACAAA-ATAGAATCATTTAATATTCTCAA-A
1 AAATAAATTTAACAATTTATTTTCTT--ACAAAGATAGAATCATTTAAGATTCTCAAGG
* *
220657 AAATAAATTTAACAATTTATTAAATT-TTACAAA-ATAGAATCA-TTAAAATTCTCAAGA
1 AAATAAATTTAACAATTTATT---TTCTTACAAAGATAGAATCATTTAAGATTCTCAAGG
* * * ** * *
220714 AAATAAATTTAACAATTTATTTAATTTTA-AAGGATAAAATCATCCACGATTCTCAAGA
1 AAATAAATTTAACAATTTATTT--TCTTACAAAGATAGAATCATTTAAGATTCTCAAGG
** * * * *
220772 AAATAAATTCGATAATTTATTTTTCTTACAAAGTTA-AATTATTCAAGATT-TCCAAGG
1 AAATAAATTTAACAATTTA-TTTTCTTACAAAGATAGAATCATTTAAGATTCT-CAAGG
*
220829 AAAT--A--CAACAATTT-TTTTCCTTACAAAG-TAGAATCA-TTAAGATTCTCAAGG
1 AAATAAATTTAACAATTTATTTT-CTTACAAAGATAGAATCATTTAAGATTCTCAAGG
* * * *
220880 AAATAAATTCAACAATCTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTAAAGG
1 AAATAAATTTAACAATTTATTTT-CTTACAAAGATAGAATCATTTAAGATTCTCAAGG
* * *
220938 AAATAAATTTAACAATCTATTTTCCTTAGAAAGTTAGAATCA
1 AAATAAATTTAACAATTTATTTT-CTTACAAAGATAGAATCA
220980 ACGCAAAATT
Statistics
Matches: 275, Mismatches: 25, Indels: 44
0.80 0.07 0.13
Matches are distributed among these distances:
51 22 0.08
52 14 0.05
53 8 0.03
54 1 0.00
55 9 0.03
56 49 0.18
57 79 0.29
58 86 0.31
59 5 0.02
60 2 0.01
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (57 bp):
AAATAAATTTAACAATTTATTTTCTTACAAAGATAGAATCATTTAAGATTCTCAAGG
Found at i:221191 original size:44 final size:43
Alignment explanation
Indices: 221128--221241 Score: 140
Period size: 44 Copynumber: 2.6 Consensus size: 43
221118 TTAATCCTTC
** *
221128 AATTTTAC-CAATCCAATAATCAAAAGAACTAATCCTTTGATTTT
1 AATTTT-CGCAATCCAATAATCAAAAGAACTAATAATTTG-GTTT
*
221172 AATTTTCGCAATCCAATAATCGAAAGGAACTAATAATTTGGTTT
1 AATTTTCGCAATCCAATAATC-AAAAGAACTAATAATTTGGTTT
* *
221216 AATTTTGGCAATACAATAATCAAAAG
1 AATTTTCGCAATCCAATAATCAAAAG
221242 TCTTGGTTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
43 5 0.08
44 41 0.67
45 15 0.25
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (43 bp):
AATTTTCGCAATCCAATAATCAAAAGAACTAATAATTTGGTTT
Found at i:224088 original size:197 final size:197
Alignment explanation
Indices: 223753--224146 Score: 788
Period size: 197 Copynumber: 2.0 Consensus size: 197
223743 CGATGCATAA
223753 GCTTCTGATCGATTGCAATTTTGATACTTAATGCTTCAATTTTCAATCGAGTTTGACTTCGGGTT
1 GCTTCTGATCGATTGCAATTTTGATACTTAATGCTTCAATTTTCAATCGAGTTTGACTTCGGGTT
223818 GATTCACTGAGTTGGGCAATCTTTTATAAGAAATAAACATGTTGGGGCAATGGAGAGTTCAGTCA
66 GATTCACTGAGTTGGGCAATCTTTTATAAGAAATAAACATGTTGGGGCAATGGAGAGTTCAGTCA
223883 ATGGTGACGGTTTCTCGCAGTTACAGAGCTATGGGGACAGTAGCGAGGAAGAGCTATCTGTGTTG
131 ATGGTGACGGTTTCTCGCAGTTACAGAGCTATGGGGACAGTAGCGAGGAAGAGCTATCTGTGTTG
223948 CC
196 CC
223950 GCTTCTGATCGATTGCAATTTTGATACTTAATGCTTCAATTTTCAATCGAGTTTGACTTCGGGTT
1 GCTTCTGATCGATTGCAATTTTGATACTTAATGCTTCAATTTTCAATCGAGTTTGACTTCGGGTT
224015 GATTCACTGAGTTGGGCAATCTTTTATAAGAAATAAACATGTTGGGGCAATGGAGAGTTCAGTCA
66 GATTCACTGAGTTGGGCAATCTTTTATAAGAAATAAACATGTTGGGGCAATGGAGAGTTCAGTCA
224080 ATGGTGACGGTTTCTCGCAGTTACAGAGCTATGGGGACAGTAGCGAGGAAGAGCTATCTGTGTTG
131 ATGGTGACGGTTTCTCGCAGTTACAGAGCTATGGGGACAGTAGCGAGGAAGAGCTATCTGTGTTG
224145 CC
196 CC
224147 ACGTCATTCT
Statistics
Matches: 197, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
197 197 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.32
Consensus pattern (197 bp):
GCTTCTGATCGATTGCAATTTTGATACTTAATGCTTCAATTTTCAATCGAGTTTGACTTCGGGTT
GATTCACTGAGTTGGGCAATCTTTTATAAGAAATAAACATGTTGGGGCAATGGAGAGTTCAGTCA
ATGGTGACGGTTTCTCGCAGTTACAGAGCTATGGGGACAGTAGCGAGGAAGAGCTATCTGTGTTG
CC
Found at i:225309 original size:25 final size:23
Alignment explanation
Indices: 225287--225341 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
225277 GTTGTTCGTT
225287 TTTGTGTTCGTTTACTACGTTCG
1 TTTGTGTTCGTTTACTACGTTCG
225310 TTTGTGTTCGTTTACT---TTCG
1 TTTGTGTTCGTTTACTACGTTCG
*
225330 TTTATGTTCGTT
1 TTTGTGTTCGTT
225342 ATCATTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 15 0.48
23 16 0.52
ACGTcount: A:0.07, C:0.15, G:0.20, T:0.58
Consensus pattern (23 bp):
TTTGTGTTCGTTTACTACGTTCG
Found at i:225320 original size:10 final size:10
Alignment explanation
Indices: 225291--225341 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
225281 TTCGTTTTTG
225291 TGTTCGTTTA
1 TGTTCGTTTA
*
225301 CTACGTTCGTTTG
1 -T--GTTCGTTTA
225314 TGTTCGTTTA
1 TGTTCGTTTA
225324 CT-TTCGTTTA
1 -TGTTCGTTTA
225334 TGTTCGTT
1 TGTTCGTT
225342 ATCATTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
9 1 0.03
10 22 0.65
11 2 0.06
12 1 0.03
13 8 0.24
ACGTcount: A:0.08, C:0.16, G:0.20, T:0.57
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:226056 original size:77 final size:77
Alignment explanation
Indices: 225965--226113 Score: 280
Period size: 77 Copynumber: 1.9 Consensus size: 77
225955 ATTTTAATAG
225965 TTGGTTTATTAGTCATGTATGCTTACATTTGATTCAAAATCAATGAATTGTTTCATTTTATCAGA
1 TTGGTTTATTAGTCATGTATGCTTACATTTGATTCAAAATCAATGAATTGTTTCATTTTATCAGA
226030 AAAACAAGTTAA
66 AAAACAAGTTAA
* *
226042 TTGGTTTATTAGTCATGTCTGCTTACATTTGATTCAAAATCAATGAATTGTTTCATTTTATTAGA
1 TTGGTTTATTAGTCATGTATGCTTACATTTGATTCAAAATCAATGAATTGTTTCATTTTATCAGA
226107 AAAACAA
66 AAAACAA
226114 TAAGTTAATT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 70 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (77 bp):
TTGGTTTATTAGTCATGTATGCTTACATTTGATTCAAAATCAATGAATTGTTTCATTTTATCAGA
AAAACAAGTTAA
Found at i:226917 original size:2 final size:2
Alignment explanation
Indices: 226910--226949 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
226900 GCAAGATCCC
226910 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
226950 TGAAAAGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:229534 original size:2 final size:2
Alignment explanation
Indices: 229527--229563 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
229517 TATTAAAGAA
229527 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
229564 ATAATAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:230070 original size:35 final size:35
Alignment explanation
Indices: 230031--230107 Score: 145
Period size: 35 Copynumber: 2.2 Consensus size: 35
230021 CTAAAAAACC
230031 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
230066 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
*
230101 CTCTTTT
1 CTATTTT
230108 TTTACTGAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:231048 original size:106 final size:106
Alignment explanation
Indices: 230853--231289 Score: 667
Period size: 106 Copynumber: 4.1 Consensus size: 106
230843 TCCAAGTAGG
* * * * * * * * *
230853 TTGTATTGTTTCGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGAAAATT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATT
*
230918 GTTTGTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAAC
66 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
* *
230959 TTGTGTTGTCTCGAGTCCAATATCCTTAGCTGTGAAGTTGAAATTGGTTATGAAATTGGGAAATT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATT
*
231024 GTTTGTTGACAACCAGCTGTCCCTTCGTTGTGAAGTTGAAC
66 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
**
231065 TTGTGTTGTCTCGAGTCCAATGCCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATT
231130 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
66 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
* * * * *
231171 TTGTGTTATCTTGAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATT
* * *
231236 GTTTGTTTACAACCAGTCGTCCCTTCCTTGTGAAGTTGAAC
66 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
231277 TTGTGTTGTCTCG
1 TTGTGTTGTCTCG
231290 GGTGGCGCGA
Statistics
Matches: 303, Mismatches: 28, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 303 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (106 bp):
TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATT
GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
Found at i:231951 original size:36 final size:36
Alignment explanation
Indices: 231903--231995 Score: 98
Period size: 36 Copynumber: 2.6 Consensus size: 36
231893 TTGTTTCATG
* * * *
231903 AGAAACAGTCTCAAGGGAGACAAAATTTTGTTTAAGA
1 AGAAACTGTCTCAAGGGAGACAAAACTTAGTTCAA-A
* *
231940 A-AAACTGTCTCAAGAGAGACGAAACTTAGTTCAAA
1 AGAAACTGTCTCAAGGGAGACAAAACTTAGTTCAAA
*
231975 AGAAATTGTCTCACAGGGAGA
1 AGAAACTGTCTCA-AGGGAGA
231996 TGAAATTAGT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
35 2 0.04
36 37 0.80
37 7 0.15
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.22
Consensus pattern (36 bp):
AGAAACTGTCTCAAGGGAGACAAAACTTAGTTCAAA
Found at i:232194 original size:36 final size:38
Alignment explanation
Indices: 232134--232210 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 38
232124 GAAACAATTT
*
232134 CAAAGTTTTTTTTCCAAGGAAAACTGTCTCAAGAGAGA
1 CAAAGTTTTGTTTCCAAGGAAAACTGTCTCAAGAGAGA
*
232172 CAAAG-TTTGTTT-CAAGGGAAACTGTCTCAAGAGAGA
1 CAAAGTTTTGTTTCCAAGGAAAACTGTCTCAAGAGAGA
232208 CAA
1 CAA
232211 TGGTGAGAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 26 0.70
37 6 0.16
38 5 0.14
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.26
Consensus pattern (38 bp):
CAAAGTTTTGTTTCCAAGGAAAACTGTCTCAAGAGAGA
Found at i:232722 original size:17 final size:18
Alignment explanation
Indices: 232690--232724 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
232680 TGTTAAATCC
*
232690 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
232708 CCAAAAATG-CCCAATAT
1 CCAAAAATGCCCCAATAT
232725 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.43, C:0.31, G:0.09, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:238153 original size:15 final size:15
Alignment explanation
Indices: 238133--238161 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
238123 GGAAAAACAA
238133 AATATATATATATAT
1 AATATATATATATAT
238148 AATATATATATATA
1 AATATATATATATA
238162 CATCAAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATATATATATAT
Found at i:238154 original size:13 final size:13
Alignment explanation
Indices: 238136--238161 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
238126 AAAACAAAAT
238136 ATATATATATATA
1 ATATATATATATA
238149 ATATATATATATA
1 ATATATATATATA
238162 CATCAAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:239075 original size:35 final size:35
Alignment explanation
Indices: 239029--239104 Score: 145
Period size: 35 Copynumber: 2.2 Consensus size: 35
239019 CTAAAAAACC
239029 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
239064 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
239099 CT-TTTT
1 CTATTTT
239105 GGTTACATGA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 4 0.10
35 37 0.90
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:239850 original size:12 final size:12
Alignment explanation
Indices: 239833--239859 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
239823 CATGTACTAG
239833 TAAAAAATCAAA
1 TAAAAAATCAAA
239845 TAAAAAATCAAA
1 TAAAAAATCAAA
239857 TAA
1 TAA
239860 TGTCGAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (12 bp):
TAAAAAATCAAA
Found at i:241581 original size:16 final size:17
Alignment explanation
Indices: 241552--241584 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
241542 AAAAATAGTG
241552 AACATTAGTATATTTTA
1 AACATTAGTATATTTTA
241569 AACATTA-TATATTTTA
1 AACATTAGTATATTTTA
241585 TTAGGATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (17 bp):
AACATTAGTATATTTTA
Found at i:242892 original size:3 final size:3
Alignment explanation
Indices: 242884--242978 Score: 97
Period size: 3 Copynumber: 32.7 Consensus size: 3
242874 GTAATATTTG
* * * * *
242884 TAA TAA TAA TAA TAA TAA TAA -CA CAA CAA CAA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* **
242931 T-A TGA TAA TAA TAA TTG TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
242977 TA
1 TA
242979 TTTATTGGAC
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
2 5 0.06
3 76 0.94
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:242940 original size:20 final size:20
Alignment explanation
Indices: 242917--242978 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
242907 CAACAACAAC
*
242917 AATAATAATAATAATATGAT
1 AATAATAATAATAATATAAT
**
242937 AATAATAATTGTAATATAAT
1 AATAATAATAATAATATAAT
242957 AATAATAATAATAATAATAAT
1 AATAATAATAATAAT-ATAAT
242978 A
1 A
242979 TTTATTGGAC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
20 30 0.83
21 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
AATAATAATAATAATATAAT
Found at i:243263 original size:20 final size:20
Alignment explanation
Indices: 243235--243288 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
243225 AAAACATCCT
*
243235 ACCCTGAGGTTTTACAAATC
1 ACCCGGAGGTTTTACAAATC
* *
243255 ACCCGGAGGATTTACAAATT
1 ACCCGGAGGTTTTACAAATC
243275 ACCCGGAGGTTTTA
1 ACCCGGAGGTTTTA
243289 ATTTTCTAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (20 bp):
ACCCGGAGGTTTTACAAATC
Found at i:243317 original size:119 final size:119
Alignment explanation
Indices: 243106--243387 Score: 456
Period size: 119 Copynumber: 2.4 Consensus size: 119
243096 AATTGAAGTA
* * * *
243106 AAAACATCATACCCAGAGGTTTTACAGATGACCCGGAGGTTTTATAAATCAACCGGAGGATTTAA
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATCAACCGGAGGATTTAA
*
243171 TTTTCTAGAACATTAAATGAGAAACTTTGATAATCGTTTTCTCATTTTCATGCG
66 TTTTCTAGAACATTAAATGAGAAACTTTGATAATCGCTTTCTCATTTTCATGCG
* * * * *
243225 AAAACATCCTACCCTGAGGTTTTACAAATCACCCGGAGGATTTACAAATTACCCGGAGGTTTTAA
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATCAACCGGAGGATTTAA
*
243290 TTTTCTAGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATGCG
66 TTTTCTAGAACATTAAATGAGAAACTTTGATAATCGCTTTCTCATTTTCATGCG
*
243344 AAAACATCCTACCCTGAGGTTTTACAGATGACCCAGAGGATTTA
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGATTTA
243388 ATTTTCTTGA
Statistics
Matches: 149, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
119 149 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Consensus pattern (119 bp):
AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGATTTACAAATCAACCGGAGGATTTAA
TTTTCTAGAACATTAAATGAGAAACTTTGATAATCGCTTTCTCATTTTCATGCG
Found at i:243436 original size:99 final size:99
Alignment explanation
Indices: 243255--243684 Score: 734
Period size: 99 Copynumber: 4.3 Consensus size: 99
243245 TTTACAAATC
* * * * * *
243255 ACCCGGAGGATTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGG
1 ACCCTGAGGTTTTACAGATGACCCAGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGG
*
243320 TAATCGCTTTCTCATTTTCATGCGAAAACATCCT
66 TAATCACTTTCTCATTTTCATGCGAAAACATCCT
*
243354 ACCCTGAGGTTTTACAGATGACCCAGAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTTGG
1 ACCCTGAGGTTTTACAGATGACCCAGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGG
243419 TAATCACTTTCTCATTTTCATGCGAAAACATCCT
66 TAATCACTTTCTCATTTTCATGCGAAAACATCCT
*
243453 ACCCTGAGGTTTTACAGATGACCCAGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGG
1 ACCCTGAGGTTTTACAGATGACCCAGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGG
* *
243518 TAATCGCTTTCTCATTTTCATGCAAAAACATCCT
66 TAATCACTTTCTCATTTTCATGCGAAAACATCCT
* *
243552 ACCCTGAGGTTTTACAGATGACCCGGAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTTGG
1 ACCCTGAGGTTTTACAGATGACCCAGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGG
*
243617 TAATCACTTTCTCATTTTCATGCTAAAACATCCT
66 TAATCACTTTCTCATTTTCATGCGAAAACATCCT
243651 ACCCTGAGGTTTTACAGATGACCCAGAGGATTTA
1 ACCCTGAGGTTTTACAGATGACCCAGAGGATTTA
243685 CAAATTTGTG
Statistics
Matches: 313, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
99 313 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (99 bp):
ACCCTGAGGTTTTACAGATGACCCAGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGG
TAATCACTTTCTCATTTTCATGCGAAAACATCCT
Found at i:250965 original size:46 final size:47
Alignment explanation
Indices: 250902--250994 Score: 120
Period size: 46 Copynumber: 2.0 Consensus size: 47
250892 ATATAAAAAT
* * *
250902 CCTAACTTCATACTTTCTAGTTC-CATGC-TTTGTTTGGAAAAATAAA
1 CCTAACCTCATACTTTCTAGTTCACATACATTTGTTCGG-AAAATAAA
250948 CCTAACCTCATGA-TTTCTAGTTCACATACATTTGTTCGGAAAATAAA
1 CCTAACCTCAT-ACTTTCTAGTTCACATACATTTGTTCGGAAAATAAA
250995 GTAATATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
46 20 0.49
47 13 0.32
48 8 0.20
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (47 bp):
CCTAACCTCATACTTTCTAGTTCACATACATTTGTTCGGAAAATAAA
Found at i:253208 original size:16 final size:17
Alignment explanation
Indices: 253175--253208 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
253165 AAAACTAGTG
*
253175 AACATTAGTATATTTTA
1 AACATTAGTATATATTA
253192 AACATTA-TATATATTA
1 AACATTAGTATATATTA
253208 A
1 A
253209 TAGGATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (17 bp):
AACATTAGTATATATTA
Found at i:253356 original size:17 final size:19
Alignment explanation
Indices: 253320--253357 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
253310 ATAACCAAAA
*
253320 TAAAAATATATGATTAAAT
1 TAAAAAAATATGATTAAAT
253339 TAAAAAAATAT-A-TAAAT
1 TAAAAAAATATGATTAAAT
253356 TA
1 TA
253358 TTGGTCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 1 0.06
19 10 0.56
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
TAAAAAAATATGATTAAAT
Found at i:253834 original size:12 final size:12
Alignment explanation
Indices: 253817--253850 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
253807 CACCGTCGAG
*
253817 CACTATTCTGGC
1 CACTATTCCGGC
*
253829 CACTATTCCGGT
1 CACTATTCCGGC
253841 CACTATTCCG
1 CACTATTCCG
253851 ATTACTATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.35, G:0.15, T:0.32
Consensus pattern (12 bp):
CACTATTCCGGC
Found at i:254570 original size:3 final size:3
Alignment explanation
Indices: 254562--254604 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
254552 GTAATATTTG
*
254562 TAA TAA TAA TAA TAA TAA TAA CT-G TAA T-A TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA
254605 TATTATTGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 3 0.09
3 31 0.89
4 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:255986 original size:12 final size:12
Alignment explanation
Indices: 255971--255995 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
255961 ATTCACTTTA
255971 TTTATTTGATTT
1 TTTATTTGATTT
255983 TTTATTTGATTT
1 TTTATTTGATTT
255995 T
1 T
255996 ATTTTTCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTATTTGATTT
Found at i:255999 original size:17 final size:16
Alignment explanation
Indices: 255967--256012 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
255957 TATTATTCAC
*
255967 TTTATTTATTTGATTT
1 TTTATTTATTTTATTT
255983 TTTATTTGATTTTATTT
1 TTTATTT-ATTTTATTT
*
256000 TTCATTTAATTTT
1 TTTATTT-ATTTT
256013 TTTACATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (16 bp):
TTTATTTATTTTATTT
Found at i:256376 original size:22 final size:21
Alignment explanation
Indices: 256327--256377 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
256317 CTTTTTTACT
256327 TTTTTTATTTTTTTGTATATA
1 TTTTTTATTTTTTTGTATATA
** * *
256348 TACTTTATTTTTGTTTTATTTA
1 TTTTTTATTTTT-TTGTATATA
256370 TTTTTTAT
1 TTTTTTAT
256378 AACAATTATT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (21 bp):
TTTTTTATTTTTTTGTATATA
Found at i:256458 original size:47 final size:47
Alignment explanation
Indices: 256407--256499 Score: 120
Period size: 47 Copynumber: 2.0 Consensus size: 47
256397 ATTTTTTGTA
*
256407 TTTGTTTTTA-TTTTTT-A-TGTTCATTCTTATTTATTTATTTTATTTCT
1 TTTG-TTTTAGTTTTTTAATTGTTAATT-TT-TTTATTTATTTTATTTCT
*
256454 TTTGTTTTAGTTTTTTAATTGTTAATTTTTTTATTTTTTTTATTTC
1 TTTGTTTTAGTTTTTTAATTGTTAATTTTTTTATTTATTTTATTTC
256500 CTCATTATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
46 5 0.12
47 26 0.63
48 3 0.07
49 7 0.17
ACGTcount: A:0.15, C:0.04, G:0.05, T:0.75
Consensus pattern (47 bp):
TTTGTTTTAGTTTTTTAATTGTTAATTTTTTTATTTATTTTATTTCT
Found at i:259392 original size:98 final size:94
Alignment explanation
Indices: 259133--259392 Score: 308
Period size: 95 Copynumber: 2.7 Consensus size: 94
259123 AGATTATAAT
* * * * * *
259133 ATTATATATATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTCAAACGCCCCGACTTTA
1 ATTATA-ATATACAATAAA-CTTAAGTTATCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
259198 TGGATAAGATTCAGCTAGCCTGATAATGGTA
64 TGGATAAGATTCAGCTAGCCTGATAATGGTA
* * *
259229 ATTATAATATACAATAAAGCTTGAGTTTTCCCTCTAGAGTAATTGGTTAAACGCCCCGGCTTTAT
1 ATTATAATATACAATAAA-CTTAAGTTATCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
* *
259294 GGATAATATTCAGCTAGCCTGATAAAT-GTG
65 GGATAAGATTCAGCTAGCCTGAT-AATGGTA
* *
259324 ATTATAGTATCTATACAATGATA-TTAAGTTATCCCTCTAGAGCAATTGTTTAAACGCCCCGGCT
1 ATTATA--A--TATACAAT-AAACTTAAGTTATCCCTCTAGAGCAATTGGTTAAACGCCCCGGCT
259388 TTATG
61 TTATG
259393 CATTCAGCTA
Statistics
Matches: 145, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
95 83 0.57
96 9 0.06
97 1 0.01
98 42 0.29
99 8 0.06
100 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (94 bp):
ATTATAATATACAATAAACTTAAGTTATCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATG
GATAAGATTCAGCTAGCCTGATAATGGTA
Found at i:260664 original size:84 final size:84
Alignment explanation
Indices: 260514--262085 Score: 1791
Period size: 84 Copynumber: 18.7 Consensus size: 84
260504 GAAACTATTG
* * * * *
260514 GCAGCATAACTCAAGGCTAGAAGGGTTATCTACTAACAAAAGACCTTCGAGTTTGATTACAGTCA
1 GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
** *
260579 GCTTAAAGGCACAACACTT
66 GCTCCAAGGCACAACATTT
** * * * *
260598 GCAGCATAACTCAAGGAGAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTTGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
*
260663 GCTCCAAGGCACATCATTT
66 GCTCCAAGGCACAACATTT
** * * * *
260682 GCATTATAACTCAAGGCTAGAAGGGTTATCTGCTAACAAAAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
*
260747 GCTCCAAGGCACATCATTT
66 GCTCCAAGGCACAACATTT
* * * *
260766 GCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
*
260831 GCTCAAAGGCACAACATTT
66 GCTCCAAGGCACAACATTT
* * * * * * * * * * *
260850 GCAGCATAGCTAAAGGCGATAAGGGTTATCTACCAACAAAAGACCATCGAGTTCAACTACGCTTA
1 GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* *
260915 GCTCCAAGGCATATCATTT
66 GCTCCAAGGCACAACATTT
* * *
260934 GCAACATATCTCAAGGCTAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
*
260999 GCTCAAAGGCACAACATTT
66 GCTCCAAGGCACAACATTT
* * *
261018 GCAGCATAGCTCAAGTCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
*
261083 GCTCCAAGACACAACATTT
66 GCTCCAAGGCACAACATTT
* * * * * * *
261102 GTAGCATAGCTCAAGGCGAGAAAGGCTATCTTCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
*
261167 GCTCCAAGGCACATCATTT
66 GCTCCAAGGCACAACATTT
* * * * * * * *
261186 GCAACATAACTTAAGGCTAGAAGGGATATTTTCCAAAAAAAGACCTTCGAGTTTGATTACAATCA
1 GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * *
261251 ACTCAAAGGCACAAAATTT
66 GCTCCAAGGCACAACATTT
* * * * * *
261270 GCAGCATAGCTCAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTTGGTTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
*
261335 GCTCAAAGGCACAACATTT
66 GCTCCAAGGCACAACATTT
* * * * * * *
261354 GTAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAATAATAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* *
261419 GCTCTAAGGCACATCATTT
66 GCTCCAAGGCACAACATTT
* ** ** * * * * * *
261438 GTAATATAGGTGAAGGCTAGAAGGGCTATTTGCCAAAAAAAAGACATTCGAGTTTGATTACACTT
1 GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCC-AACAAAAGACCTTCGAGTTCGATTACACTC
* *
261503 AGCTCAAAGGCACAATATTT
65 AGCTCCAAGGCACAACATTT
* * * * * * *
261523 GTAGCATAGCTCAAGGCGAAAAGGGCTATCTGCCAACAAAAGACCTCCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
*
261588 GCTCCAAGGCACATCATTT
66 GCTCCAAGGCACAACATTT
* * * * * * *
261607 ACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTTGACTACGCTCG
1 GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* *
261672 GCTCCAAGGCATATCATTT
66 GCTCCAAGGCACAACATTT
* * * * * * *
261691 GCAACATATCTCAAGGCTAGAAGGGTTATTTGCCAACAAAATACCTTCAAGTTCGAGTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
*
261756 GCTCTAAGGCACAACATTT
66 GCTCCAAGGCACAACATTT
* * * *
261775 GTAGCATAACTCAAGGCTAGAAGGGGTATCTACCAACAAAAGACCTTCGAGTTTGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
*
261840 GCTCAAAGGCA-AATCATTT
66 GCTCCAAGGCACAA-CATTT
* * * *
261859 GCAGCATAACTCAAGGCTAGAAGGGTTATCGGCCAACACAAGACCTTCGAGTTCAATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
261924 GCTCCAAGGCACAACATTT
66 GCTCCAAGGCACAACATTT
* * *
261943 GCAGCATAACTCAAAGCTAGAAGGGTTATCTGCCAACACAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * *
262008 ACT-CAATTGCACATCAAATTT
66 GCTCCAA-GGCACA--ACATTT
* * * * * * *
262029 ACAGTATAACTCAAGGCGAAAAGGGTTATCTGTCAA-TAAAGACCTTCGAGTTCGATT
1 GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATT
262086 CTATTCAGCT
Statistics
Matches: 1271, Mismatches: 211, Indels: 11
0.85 0.14 0.01
Matches are distributed among these distances:
83 5 0.00
84 1143 0.90
85 88 0.07
86 35 0.03
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (84 bp):
GCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
GCTCCAAGGCACAACATTT
Found at i:260974 original size:252 final size:252
Alignment explanation
Indices: 260514--262098 Score: 2028
Period size: 252 Copynumber: 6.3 Consensus size: 252
260504 GAAACTATTG
* * * * * * *
260514 GCAGCATAACTCAAGGCTAGAAGGGTTATCTACTAACAAAAGACCTTCGAGTTTGATTACAGTCA
1 GCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * *
260579 GCTTAAAGGCACAACACTTGCAGCATAACTCAAGGAGAGAAGGGCTATTTGCCAACAAAAGACCT
66 GCTCAAAGGCACAACATTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCT
* **
260644 TCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCATTATAACTCAAGGCTAGAAGGGTT
131 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTT
* * * * * *
260709 ATCTGCTAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
196 ATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAACATTT
* *
260766 GCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * * * *
260831 GCTCAAAGGCACAACATTTGCAGCATAGCTAAAGGCGATAAGGGTTATCTACCAACAAAAGACCA
66 GCTCAAAGGCACAACATTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCT
* * * * *
260896 TCGAGTTCAACTACGCTTAGCTCCAAGGCATATCATTTGCAACATATCTCAAGGCTAGAAGGGCT
131 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTT
260961 ATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAACATTT
196 ATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAACATTT
*
261018 GCAGCATAGCTCAAGTCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * * * *
261083 GCTCCAAGACACAACATTTGTAGCATAGCTCAAGGCGAGAAAGGCTATCTTCCAACAAAAGACCT
66 GCTCAAAGGCACAACATTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCT
* *
261148 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTTAAGGCTAGAAGGGAT
131 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTT
* * * * * *
261213 ATTTTCCAAAAAAAGACCTTCGAGTTTGATTACAATCAACTCAAAGGCACAAAATTT
196 ATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAACATTT
* * * * *
261270 GCAGCATAGCTCAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTTGGTTACACTCA
1 GCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * *
261335 GCTCAAAGGCACAACATTTGTAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAATAATAGACCT
66 GCTCAAAGGCACAACATTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCT
* * * ** * *
261400 TCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGTAATATAGGTGAAGGCTAGAAGGGCT
131 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTT
* * * * *
261465 ATTTGCCAAAAAAAAGACATTCGAGTTTGATTACACTTAGCTCAAAGGCACAATATTT
196 ATTTGCC-AACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAACATTT
* * * *
261523 GTAGCATAGCTCAAGGCGAA-AAGGGCTATCTGCCAACAAAAGACCTCCGAGTTCGACTACGCTC
1 GCAGCATAGCTCAAGGC-AAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTC
* * * * * *
261587 AGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAATAAAAGACC
65 AGCTCAAAGGCACAACATTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACC
* * * *
261652 TTCGAGTTTGACTACGCTCGGCTCCAAGGCATATCATTTGCAACATATCTCAAGGCTAGAAGGGT
130 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGT
* * * *
261717 TATTTGCCAACAAAATACCTTCAAGTTCGAGTACACTCAGCTCTAAGGCACAACATTT
195 TATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAACATTT
* * * * * *
261775 GTAGCATAACTCAAGGCTAGAAGGGGTATCTACCAACAAAAGACCTTCGAGTTTGATTACACTCA
1 GCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * *
261840 GCTCAAAGGCA-AATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCGGCCAACACAAGACC
66 GCTCAAAGGCACAA-CATTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACC
* * * * * *
261904 TTCGAGTTCAATTACACTCAGCTCCAAGGCACAACATTTGCAGCATAACTCAAAGCTAGAAGGGT
130 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGT
* * * ** *
261969 TATCTGCCAACACAAGACCTTCGAGTTCGATTACACTCAACTCAATTGCACATCAAATTT
195 TATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACA--ACATTT
* * * * * * *
262029 ACAGTATAACTCAAGGCGAA-AAGGGTTATCTGTCAA-TAAAGACCTTCGAGTTCGATT-CTATT
1 GCAGCATAGCTCAAGGC-AAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTAC-ACT
262091 CAGCTCAA
64 CAGCTCAA
262099 GGACATGTTA
Statistics
Matches: 1165, Mismatches: 160, Indels: 15
0.87 0.12 0.01
Matches are distributed among these distances:
251 2 0.00
252 882 0.76
253 247 0.21
254 33 0.03
255 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (252 bp):
GCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
GCTCAAAGGCACAACATTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCT
TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTT
ATTTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAACATTT
Found at i:264012 original size:29 final size:29
Alignment explanation
Indices: 263955--264017 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
263945 CACGTACATA
*
263955 TATTTTCTTTATTATTCACTTTATTTATT
1 TATTTTCTTTATTATTCACTTTATGTATT
*
263984 TATTTTCTTTTATTTTTTCA-TTTA-GTATT
1 TATTTTC-TTTA-TTATTCACTTTATGTATT
264013 T-TTTT
1 TATTTT
264018 ACATTTTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 4 0.13
29 12 0.40
30 8 0.27
31 6 0.20
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (29 bp):
TATTTTCTTTATTATTCACTTTATGTATT
Found at i:264189 original size:18 final size:17
Alignment explanation
Indices: 264113--264192 Score: 56
Period size: 17 Copynumber: 4.6 Consensus size: 17
264103 ATATTTTACT
*
264113 TTATTTTATT-ATTATA
1 TTATTTTATTGTTTATA
* *
264129 TTATTATTATT-TTTGTT
1 TTATT-TTATTGTTTATA
*
264146 TTGTTTTTATGTGTTTATA
1 TT-ATTTTAT-TGTTTATA
* *
264165 TTGTTTTATTGTTTTTA
1 TTATTTTATTGTTTATA
264182 CTTATTTTATT
1 -TTATTTTATT
264193 AAATATTATA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
16 5 0.10
17 21 0.42
18 18 0.36
19 6 0.12
ACGTcount: A:0.19, C:0.01, G:0.07, T:0.72
Consensus pattern (17 bp):
TTATTTTATTGTTTATA
Found at i:264340 original size:16 final size:17
Alignment explanation
Indices: 264319--264356 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
264309 GATTGGTAGA
264319 TTTTTTA-TCTTTTTAT
1 TTTTTTATTCTTTTTAT
*
264335 TTTTTTATTTTTTTTAT
1 TTTTTTATTCTTTTTAT
264352 TTTTT
1 TTTTT
264357 GTGCATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.87
Consensus pattern (17 bp):
TTTTTTATTCTTTTTAT
Found at i:264348 original size:8 final size:8
Alignment explanation
Indices: 264319--264356 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
264309 GATTGGTAGA
264319 TTTTTTAT
1 TTTTTTAT
*
264327 CTTTTTAT
1 TTTTTTAT
264335 TTTTTTATT
1 TTTTTTA-T
264344 TTTTTTAT
1 TTTTTTAT
264352 TTTTT
1 TTTTT
264357 GTGCATATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 19 0.70
9 8 0.30
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTAT
Found at i:265215 original size:16 final size:16
Alignment explanation
Indices: 265194--265224 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
265184 TATGTTGTGA
265194 GTTCTAGAATAGTTTT
1 GTTCTAGAATAGTTTT
265210 GTTCTAGAATAGTTT
1 GTTCTAGAATAGTTT
265225 GTTAGCTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.48
Consensus pattern (16 bp):
GTTCTAGAATAGTTTT
Found at i:270699 original size:38 final size:37
Alignment explanation
Indices: 270615--270858 Score: 96
Period size: 37 Copynumber: 6.4 Consensus size: 37
270605 ATATATAATA
* *
270615 ATATAATATAGTTTTTTAAAACATTTTCGAAAAACGT
1 ATATAATATAGTTTTTGAAAACATTTTCGAAAAACAT
*
270652 ATA-ACATATAGTTTTTAGAAAACGGTTATT-G-AAAACAT
1 ATATA-ATATAGTTTTT-GAAAAC-ATT-TTCGAAAAACAT
* * * *
270690 ATATAATATA-TACTTTTAAAAAAAATCAATTTTTTG-AATATAT
1 ATATAATATAGT--TTTT---GAAAA-C-A-TTTTCGAAAAACAT
* * *
270733 ATATTATATAG-TTTTGAAAACATTTTTTTGAAAATATAT
1 ATATAATATAGTTTTTGAAAACA--TTTTCGAAAA-ACAT
* *
270772 ATATTATATAAG-TTTTGAAAACATTTTTCG-AAAATAT
1 ATATAATAT-AGTTTTTGAAAACA-TTTTCGAAAAACAT
* *
270809 ATATAATATA-TAGTTTTG-AAACATTTTTG-AAAATAT
1 ATATAATATAGT--TTTTGAAAACATTTTCGAAAAACAT
* *
270845 ATATTACATAGTTT
1 ATATAATATAGTTT
270859 GTATAGTTTT
Statistics
Matches: 170, Mismatches: 16, Indels: 44
0.74 0.07 0.19
Matches are distributed among these distances:
35 2 0.01
36 23 0.14
37 41 0.24
38 33 0.19
39 27 0.16
40 15 0.09
41 9 0.05
42 3 0.02
43 17 0.10
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (37 bp):
ATATAATATAGTTTTTGAAAACATTTTCGAAAAACAT
Found at i:270741 original size:41 final size:38
Alignment explanation
Indices: 270688--270964 Score: 152
Period size: 39 Copynumber: 7.0 Consensus size: 38
270678 TATTGAAAAC
*
270688 ATATATAATATATACTTTTAAAAAAAATCAATTTTTTG-AAT
1 ATATATATTATATACTTTT---AAAAA-CAATTTTTTGAAAT
* * *
270729 ATATATATTATATAGTTTTGAAAACATTTTTTTGAAAAT
1 ATATATATTATATACTTTTAAAAACAATTTTTTG-AAAT
* * *
270768 ATATATATTATATAAGTTTTGAAAAC-ATTTTTCGAAAAT
1 ATATATATTATAT-ACTTTTAAAAACAATTTTTTG-AAAT
* * *
270807 ATATATAATATATAGTTTT-GAAAC-A-TTTTTGAAAATAT
1 ATATATATTATATACTTTTAAAAACAATTTTTTG--AA-AT
* * *
270845 ATATTACATAGTTTGTATAGTTTTGAAAACAATTTTTTGAAAAT
1 ATA-T--ATA--TTATATACTTTTAAAAACAATTTTTTG-AAAT
** ** *
270889 ATATAATATTATATGGTTTCGAAAATAA-TTTTTGAAAAT
1 ATAT-ATATTATATACTTTTAAAAACAATTTTTTG-AAAT
* ** *
270928 ATATATATTATATAGTTTTAAAATGATTTTTTTGAAA
1 ATATATATTATATACTTTTAAAAACAATTTTTTGAAA
270965 ACATATTATA
Statistics
Matches: 199, Mismatches: 23, Indels: 31
0.79 0.09 0.12
Matches are distributed among these distances:
36 5 0.03
37 17 0.09
38 35 0.18
39 61 0.31
40 28 0.14
41 20 0.10
42 3 0.02
43 11 0.06
44 9 0.05
45 4 0.02
46 6 0.03
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (38 bp):
ATATATATTATATACTTTTAAAAACAATTTTTTGAAAT
Found at i:270769 original size:39 final size:38
Alignment explanation
Indices: 270718--270983 Score: 276
Period size: 39 Copynumber: 6.8 Consensus size: 38
270708 AAAAAAATCA
270718 ATTTTTTG--AATATATATATTATATAGTTTTGAAAAC
1 ATTTTTTGAAAATATATATATTATATAGTTTTGAAAAC
270754 ATTTTTTTGAAAATATATATATTATATAAGTTTTGAAAAC
1 A-TTTTTTGAAAATATATATATTATAT-AGTTTTGAAAAC
* *
270794 ATTTTTCGAAAATATATATAATATATAGTTTTG-AAAC
1 ATTTTTTGAAAATATATATATTATATAGTTTTGAAAAC
*
270831 A-TTTTTGAAAATATATATTACATAGTTTGTATAGTTTTGAAAAC
1 ATTTTTTG-AAA-ATATA-T--ATA--TTATATAGTTTTGAAAAC
* * *
270875 AATTTTTTGAAAATATATAATATTATATGGTTTCGAAAAT
1 -ATTTTTTGAAAATATAT-ATATTATATAGTTTTGAAAAC
* *
270915 AATTTTTGAAAATATATATATTATATAGTTTT-AAAATG
1 ATTTTTTGAAAATATATATATTATATAGTTTTGAAAA-C
* *
270953 ATTTTTTTGAAAACATAT-TA-TATTTAGTTTT
1 A-TTTTTTGAAAATATATATATTATATAGTTTT
270984 TATTATATAT
Statistics
Matches: 197, Mismatches: 17, Indels: 31
0.80 0.07 0.13
Matches are distributed among these distances:
36 6 0.03
37 29 0.15
38 28 0.14
39 70 0.36
40 27 0.14
41 3 0.02
42 3 0.02
43 12 0.06
44 9 0.05
45 4 0.02
46 6 0.03
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.48
Consensus pattern (38 bp):
ATTTTTTGAAAATATATATATTATATAGTTTTGAAAAC
Found at i:270993 original size:23 final size:24
Alignment explanation
Indices: 270967--271027 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 24
270957 TTTTGAAAAC
*
270967 ATATTATATTTAGTTTTTATTA-T
1 ATATTATATTTAATTTTTATTACT
*
270990 ATATTATA-TTATTTTTTATTACT
1 ATATTATATTTAATTTTTATTACT
271013 -TATT-TATTTAATTTT
1 ATATTATATTTAATTTT
271028 ATTTTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 2 0.06
22 23 0.68
23 9 0.26
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (24 bp):
ATATTATATTTAATTTTTATTACT
Found at i:276539 original size:16 final size:16
Alignment explanation
Indices: 276506--276539 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
276496 TTACTTCTTG
**
276506 TTATATTTTATTTTTT
1 TTATATTTTATTACTT
276522 TTATATTTTATTACTT
1 TTATATTTTATTACTT
276538 TT
1 TT
276540 GAATTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATATTTTATTACTT
Found at i:276539 original size:25 final size:24
Alignment explanation
Indices: 276484--276583 Score: 85
Period size: 26 Copynumber: 3.9 Consensus size: 24
276474 TTTAAACATT
* *
276484 ATTTTA-TATTTTTTACTTCTTGTTA
1 ATTTTATTTTTTTTTA-TT-TTATTA
276509 TATTTTATTTTTTTTATATTTTATTA
1 -ATTTTATTTTTTTT-TATTTTATTA
* *
276535 CTTTTGAATTTTTTTTTATTTTCTTA
1 ATTTT--ATTTTTTTTTATTTTATTA
*
276561 ATTTAATATTTTTTTTATTTTAT
1 ATTTTAT-TTTTTTTTATTTTAT
276584 CTTTGATTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
24 2 0.03
25 18 0.29
26 23 0.37
27 17 0.27
28 2 0.03
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (24 bp):
ATTTTATTTTTTTTTATTTTATTA
Found at i:285716 original size:20 final size:20
Alignment explanation
Indices: 285693--285741 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
285683 TCAAAATTAT
* *
285693 TTTTCAAAAATTTCATTTTG
1 TTTTCAAAAATCTAATTTTG
**
285713 TTTTTTAAAATCTAATTTTG
1 TTTTCAAAAATCTAATTTTG
*
285733 CTTTCAAAA
1 TTTTCAAAA
285742 CCAAATCATT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.53
Consensus pattern (20 bp):
TTTTCAAAAATCTAATTTTG
Found at i:290151 original size:42 final size:42
Alignment explanation
Indices: 290092--290207 Score: 169
Period size: 42 Copynumber: 2.8 Consensus size: 42
290082 TTTCCCCGAA
*
290092 TTCCCGTGTTTGTTTCACGTAATTTGTTTTCCGGAAAATATT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATT
* *
290134 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCTGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATT
** * *
290176 TTCAAGTGTTTGTTTCACATAATTGGTTTTCC
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCC
290208 TGAACGTAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.18, C:0.16, G:0.17, T:0.48
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATT
Found at i:290517 original size:54 final size:55
Alignment explanation
Indices: 290404--290550 Score: 153
Period size: 54 Copynumber: 2.7 Consensus size: 55
290394 TATTAATTTA
*
290404 TTAAT-ATATATAATAATATATTATATTTTTAATATTATATAAAAAATCAATTAT
1 TTAATAATATATAATAATATATTATATTTTTAATAATATATAAAAAATCAATTAT
* * * **
290458 ATAATAATATA-AGATATTATATT-TTTTTTTAATAATATAATAAAAAATTTA-TAT
1 TTAATAATATATA-ATAATATATTATATTTTTAATAATAT-ATAAAAAATCAATTAT
*
290512 TTAATAATGA-ATAATATTAT-TTATATATTTTAATAATAT
1 TTAATAAT-ATATAATAATATATTATAT-TTTTAATAATAT
290551 TTTAATAAAG
Statistics
Matches: 78, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
53 2 0.03
54 38 0.49
55 38 0.49
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (55 bp):
TTAATAATATATAATAATATATTATATTTTTAATAATATATAAAAAATCAATTAT
Found at i:290566 original size:14 final size:11
Alignment explanation
Indices: 290521--290558 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
290511 TTTAATAATG
290521 AATAATATTATT
1 AATAATATT-TT
*
290533 TAT-ATATTTT
1 AATAATATTTT
290543 AATAATATTTT
1 AATAATATTTT
290554 AATAA
1 AATAA
290559 AGATATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 4 0.17
11 17 0.74
12 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATAATATTTT
Found at i:290579 original size:23 final size:23
Alignment explanation
Indices: 290553--290597 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
290543 AATAATATTT
290553 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
290576 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
290598 ATATAATACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:290704 original size:29 final size:30
Alignment explanation
Indices: 290639--290696 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
290629 TAATATTTAT
*
290639 AATATTTTTATTTCACTAAAATATAAAAAA
1 AATATTTTTATTTCAATAAAATATAAAAAA
290669 AATATTTTTA-TT-AATAAAATTATAAAAA
1 AATATTTTTATTTCAATAAAA-TATAAAAA
290697 TACTATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 6 0.23
29 10 0.38
30 10 0.38
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (30 bp):
AATATTTTTATTTCAATAAAATATAAAAAA
Found at i:290763 original size:19 final size:19
Alignment explanation
Indices: 290690--290763 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 19
290680 TAATAAAATT
*
290690 ATAAA-AATACTATTTAATA
1 ATAAATAATATTATTT-ATA
*
290709 ATAAATAA-ATTATTTTTA
1 ATAAATAATATTATTTATA
* * *
290727 AT-AATAAAAATTTTTTATG
1 ATAAAT-AATATTATTTATA
290746 ATAAATAATATTATTTAT
1 ATAAATAATATTATTTAT
290764 TGTATTTAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
17 3 0.07
18 6 0.14
19 30 0.68
20 5 0.11
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (19 bp):
ATAAATAATATTATTTATA
Found at i:290954 original size:20 final size:20
Alignment explanation
Indices: 290917--290955 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
290907 CCGAAAAACG
**
290917 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
290937 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
290956 CAATAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:290972 original size:29 final size:30
Alignment explanation
Indices: 290930--291001 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
290920 TCCAGAAATG
290930 TAATTCATTTTCCAG-AATTCAAATTCCAA
1 TAATTCATTTTCCAGTAATTCAAATTCCAA
*
290959 TAATTCATTTTCCAGTAATTCAAATTCCAG
1 TAATTCATTTTCCAGTAATTCAAATTCCAA
290989 TAATTCATTTTCC
1 TAATTCATTTTCC
291002 GGAAAACCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 15 0.37
30 26 0.63
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (30 bp):
TAATTCATTTTCCAGTAATTCAAATTCCAA
Found at i:291001 original size:15 final size:15
Alignment explanation
Indices: 290929--291001 Score: 94
Period size: 15 Copynumber: 4.9 Consensus size: 15
290919 TTCCAGAAAT
290929 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
290944 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
*
290958 ATAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
290973 GTAATTCAAATTCCA
1 GTAATTCATTTTCCA
290988 GTAATTCATTTTCC
1 GTAATTCATTTTCC
291002 GGAAAACCAA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
14 11 0.23
15 36 0.77
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:293841 original size:21 final size:20
Alignment explanation
Indices: 293817--293878 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
293807 ATTATAACAA
293817 TTATTATTTCTATTATTATTT
1 TTATTATTT-TATTATTATTT
293838 TTATT-TTTTA-TATGT-TTT
1 TTATTATTTTATTAT-TATTT
*
293856 TTTTTAATTTT-TTATTATTT
1 TTATT-ATTTTATTATTATTT
293876 TTA
1 TTA
293879 CAGGCTTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
18 10 0.29
19 4 0.12
20 15 0.44
21 5 0.15
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.76
Consensus pattern (20 bp):
TTATTATTTTATTATTATTT
Found at i:293866 original size:11 final size:10
Alignment explanation
Indices: 293817--293877 Score: 54
Period size: 11 Copynumber: 6.1 Consensus size: 10
293807 ATTATAACAA
293817 TTATTA-TTT
1 TTATTATTTT
* *
293826 CTATTATTAT
1 TTATTATTTT
293836 TT-TTATTTT
1 TTATTATTTT
*
293845 TTATATGTTTT
1 TTAT-TATTTT
*
293856 TTTTTAATTTT
1 TTATT-ATTTT
293867 TTATTATTTT
1 TTATTATTTT
293877 T
1 T
293878 ACAGGCTTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
9 13 0.32
10 11 0.28
11 16 0.40
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (10 bp):
TTATTATTTT
Found at i:295363 original size:2 final size:2
Alignment explanation
Indices: 295356--295381 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
295346 TGGATATTTA
295356 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
295382 TTAATAATTT
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:299263 original size:14 final size:14
Alignment explanation
Indices: 299244--299282 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
299234 CATATACATC
299244 ATACATTGCATAAT
1 ATACATTGCATAAT
*
299258 ATACATTACATAAT
1 ATACATTGCATAAT
299272 ATACATTGCAT
1 ATACATTGCAT
299283 CTTAACATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (14 bp):
ATACATTGCATAAT
Found at i:300764 original size:19 final size:18
Alignment explanation
Indices: 300740--300808 Score: 59
Period size: 18 Copynumber: 3.8 Consensus size: 18
300730 AAAATATAGA
*
300740 GAGAGAGAGAGATAAAAAG
1 GAGAGAGA-AGAAAAAAAG
300759 GAGAGAGAAGAAAAAAA-
1 GAGAGAGAAGAAAAAAAG
* *
300776 GAGAAAAAAGGAAAAAAAG
1 GAGAGAGAA-GAAAAAAAG
* * *
300795 AAAAGAAAAGAAAA
1 GAGAGAGAAGAAAA
300809 GAAAAAAGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
17 7 0.17
18 21 0.50
19 14 0.33
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (18 bp):
GAGAGAGAAGAAAAAAAG
Found at i:300800 original size:5 final size:5
Alignment explanation
Indices: 300772--300905 Score: 145
Period size: 5 Copynumber: 26.8 Consensus size: 5
300762 AGAGAAGAAA
* *
300772 AAAAG AGAA- AAAAG GAAA- AAAAG AAAAG AAAAG AAAAG AAAAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG --AAAAG AAAAG
*
300822 AAAAG AAAAG AAAAG GAAAG -AAA- AAAAG AAAAG AAAAG AAAAG AAAAAGG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG -AAAA-G
300872 AAAAG -AAAG AAAAG AAAA- AAGATAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AA-A-AG AAAAG AAAA
300906 AGGGGAAAAG
Statistics
Matches: 112, Mismatches: 5, Indels: 24
0.79 0.04 0.17
Matches are distributed among these distances:
4 18 0.16
5 76 0.68
6 10 0.09
7 8 0.07
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:300816 original size:22 final size:22
Alignment explanation
Indices: 300788--300906 Score: 122
Period size: 22 Copynumber: 5.2 Consensus size: 22
300778 GAAAAAAGGA
300788 AAAAAAGAAAAGAAAAGAAAAG
1 AAAAAAGAAAAGAAAAGAAAAG
300810 AAAAAAGAAAAGAAAAGAAAAG
1 AAAAAAGAAAAGAAAAGAAAAG
300832 AAAAGGAA-AGAAA-AAAAGAAAAG
1 AAAA--AAGA-AAAGAAAAGAAAAG
300855 --AAAAGAAAAGAAAAAGGAAAAG
1 AAAAAAGAAAAG-AAAA-GAAAAG
300877 AAAGAAAAGAAAA-AAGATAGAAAAG
1 -AA-AAAAGAAAAGAA-A-AGAAAAG
300902 AAAAA
1 AAAAA
300907 GGGGAAAAGA
Statistics
Matches: 84, Mismatches: 0, Indels: 25
0.77 0.00 0.23
Matches are distributed among these distances:
19 5 0.06
20 1 0.01
21 6 0.07
22 32 0.38
23 14 0.17
24 9 0.11
25 7 0.08
26 10 0.12
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (22 bp):
AAAAAAGAAAAGAAAAGAAAAG
Found at i:300852 original size:55 final size:53
Alignment explanation
Indices: 300766--300905 Score: 196
Period size: 55 Copynumber: 2.6 Consensus size: 53
300756 AAGGAGAGAG
*
300766 AAGAAAA-AAAGAGAAAAAAGGAAAAAAAGAAAAGAAAAGAAAAGAAAAAAGAA
1 AAGAAAAGAAA-AGAAAAAAAGAAAAAAAGAAAAGAAAAGAAAAGAAAAAAGAA
*
300819 AAGAAAAGAAAAGAAAAGGAAAGAAAAAAAGAAAAGAAAAGAAAAGAAAAAGGAA
1 AAGAAAAGAAAAGAAAA--AAAGAAAAAAAGAAAAGAAAAGAAAAGAAAAAAGAA
*
300874 AAG-AAAGAAAAG-AAAAAAGATAGAAAAGAAAA
1 AAGAAAAGAAAAGAAAAAAAGA-AAAAAAGAAAA
300906 AGGGGAAAAG
Statistics
Matches: 80, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
51 5 0.06
52 10 0.12
53 16 0.20
54 12 0.15
55 37 0.46
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (53 bp):
AAGAAAAGAAAAGAAAAAAAGAAAAAAAGAAAAGAAAAGAAAAGAAAAAAGAA
Found at i:300913 original size:9 final size:9
Alignment explanation
Indices: 300901--300934 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
300891 AGATAGAAAA
300901 GAAAAAG-G
1 GAAAAAGAG
*
300909 GGAAAAGAG
1 GAAAAAGAG
300918 GAAAAAGAG
1 GAAAAAGAG
300927 GAAAAAGA
1 GAAAAAGA
300935 AACAAATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 6 0.26
9 17 0.74
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (9 bp):
GAAAAAGAG
Found at i:302711 original size:42 final size:40
Alignment explanation
Indices: 302664--303190 Score: 434
Period size: 42 Copynumber: 13.0 Consensus size: 40
302654 TTCATGAATT
*
302664 TGTTATTCTTGACTCCCTCATGAAGAGGAGTCAATATTTCAA
1 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAAT-TTTC-A
* ** *
302706 TGTTATTCTTGACTTCCTCGTGAAGAAAAGTCAATCTT--
1 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATTTTCA
302744 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCAA
1 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAAT-TTTC-A
* * * * *
302786 TGTTATTATTGACTTCCTCATGAAGAGAAGTCAATCTT--
1 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATTTTCA
*
302824 TGTTATTCTTAACTCCCTCGTGAAGAGGAGTCAATCTTTCAA
1 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAAT-TTTC-A
* * * *
302866 TGTCATTCTTGACTTCTTCGTGAAGA-GATGTCAATCTT--
1 TGTTATTCTTGACTCCCTCGTGAAGAGGA-GTCAATTTTCA
** * *
302904 TGTTATTCTT-AGCT-CCTCGTGAAGAAAAGTTAATCTT--
1 TGTTATTCTTGA-CTCCCTCGTGAAGAGGAGTCAATTTTCA
* *
302941 TGTTATTCTTGACTCCCTCGTGAAAAAGAGTCAATCTTTCAA
1 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAAT-TTTC-A
* ** * **
302983 TGTCATTCTTGACTTTCTCATGAAGATAAGTCAATATTTCGGTA
1 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAAT-TTTC---A
303027 TTGTCT-TTCTTGACTCCCTCGTGAAGAGGAGTCAATATTTCAA
1 -TGT-TATTCTTGACTCCCTCGTGAAGAGGAGTCAAT-TTTC-A
* * * *
303070 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTTAATCTT--
1 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATTTTCA
*
303108 TGTTATTCTTGACTCCCTCGTGAAGATGAGTCAATCTTTCA
1 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAAT-TTTCA
* ** * *
303149 TTGTCATTCTTGACTTTCTCGTGAAGAGAATTCAATCTTTCA
1 -TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAAT-TTTCA
303191 GTATTGTAAT
Statistics
Matches: 395, Mismatches: 64, Indels: 52
0.77 0.13 0.10
Matches are distributed among these distances:
37 31 0.08
38 123 0.31
39 8 0.02
41 11 0.03
42 187 0.47
43 1 0.00
44 1 0.00
45 33 0.08
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (40 bp):
TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATTTTCA
Found at i:302798 original size:80 final size:80
Alignment explanation
Indices: 302662--303190 Score: 499
Period size: 80 Copynumber: 6.5 Consensus size: 80
302652 TGTTCATGAA
* * * *
302662 TTTGTTATTCTTGACTCCCTCATGAAGAGGAGTCAATATTTCAATGTTATTCTTGACTTCCTCGT
1 TTTGTTATTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTCAATGTTATTCTTGACTCCCTCGT
*
302727 GAAGAAAAGTCAATC
66 GAAGAGAAGTCAATC
* * * *
302742 TTTGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTATTGACTTCCTCAT
1 TTTGTTATTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTCAATGTTATTCTTGACTCCCTCGT
302807 GAAGAGAAGTCAATC
66 GAAGAGAAGTCAATC
* * * * *
302822 TTTGTTATTCTTAACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTCATTCTTGACTTCTTCGT
1 TTTGTTATTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTCAATGTTATTCTTGACTCCCTCGT
*
302887 GAAGAGATGTCAATC
66 GAAGAGAAGTCAATC
* *
302902 TTTGTTATTCTT-AGCT-CCTCGTGAAGAAAAGTTAATC-TT---TGTTATTCTTGACTCCCTCG
1 TTTGTTATTCTTGA-CTCCCTCGTGAAGAGAAGTCAATCTTTCAATGTTATTCTTGACTCCCTCG
*
302961 TGAA-AAAGAGTCAATC
65 TGAAGAGA-AGTCAATC
* ** * * * *
302977 TTTCAATGTCATTCTTGACTTTCTCATGAAGATAAGTCAATATTTCGGTATTGTCT-TTCTTGAC
1 -TT---TGTTATTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTC---AATGT-TATTCTTGAC
* *
303041 TCCCTCGTGAAGAGGAGTCAATAT
58 TCCCTCGTGAAGAGAAGTCAAT-C
* *
303065 TTCAATGTTATTCTTGACTTCCTCGTGAAGAGAAGTTAATC-TT---TGTTATTCTTGACTCCCT
1 TT---TGTTATTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTCAATGTTATTCTTGACTCCCT
303126 CGTGAAGATG-AGTCAATC
63 CGTGAAGA-GAAGTCAATC
* ** *
303144 TTTCATTGTCATTCTTGACTTTCTCGTGAAGAGAATTCAATCTTTCA
1 --T--TTGTTATTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTCA
303191 GTATTGTAAT
Statistics
Matches: 383, Mismatches: 39, Indels: 51
0.81 0.08 0.11
Matches are distributed among these distances:
74 2 0.01
75 28 0.07
76 2 0.01
78 2 0.01
79 31 0.08
80 243 0.63
81 6 0.02
83 1 0.00
86 2 0.01
87 64 0.17
88 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (80 bp):
TTTGTTATTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTCAATGTTATTCTTGACTCCCTCGT
GAAGAGAAGTCAATC
Found at i:304024 original size:134 final size:134
Alignment explanation
Indices: 303836--304443 Score: 768
Period size: 134 Copynumber: 4.5 Consensus size: 134
303826 AATGTTTGAT
* * ** * * * * * * *
303836 TTTCAGATTTAGTCTTCCTGAAGAGAAGCAAAGCAAACCACATTC-AATTTAATCTTTCTTAAAG
1 TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATC-GATTCTGATTCAATCTTCCCTGAAG
* * * * * *
303900 AGCATTAAAGTAGATCAAAGATTTCTTGAGTCTGATATCCCCTAAAGAGTAGTGGAGCACATTCT
65 AACAGTAAAGTGGATCAAAGTTTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGCATATTCT
303965 TCTTC
130 TCTTC
*
303970 TTTCAGATTTGGTCTTCTTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
1 TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
* * * * * **
304035 ATAGTAAAGTGGATCAAAGTTTTCTCGAGTCTGGTCTCTCCTAAAGAGTGGTGGAATATATTCTT
66 ACAGTAAAGTGGATCAAAGTTTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGCATATTCTT
304100 CTTC
131 CTTC
* * *
304104 TTTCAAATTTGGTCTTCCTGAAGAGTAGTGAAGCAAATCGATTTTGATTCAATCTTCCCTGAAGA
1 TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
** * * *
304169 GTACTGAAGTGGATCAAAGTTTTCTCGAGTTTGATATCCCCTAAAGAGTAGTGGAGCATATTCTT
66 ACAGTAAAGTGGATCAAAGTTTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGCATATTCTT
304234 CTTC
131 CTTC
* * *
304238 TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAACAAATTGATTTTGATTCAATCTTCTTCCTGAA
1 TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTC--CCTGAA
* * * * *
304303 GAACAGTGAAGCGGATCAAATTTTTCTCGAGTCTGATCTCCCTTAAAGAGTAGTGGAGCATATTC
64 GAACAGTAAAGTGGATCAAAGTTTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGCATATTC
304368 TTCTTC
129 TTCTTC
* * * * *
304374 TTTCAGATTTAGTCTTCCTAAAGAGCAGTGAAGCAAATCGATTATGATTCAATCTTCCATGAAAA
1 TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
304439 ACAGT
66 ACAGT
304444 GGAATGAATC
Statistics
Matches: 413, Mismatches: 58, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
133 4 0.01
134 288 0.70
136 121 0.29
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (134 bp):
TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
ACAGTAAAGTGGATCAAAGTTTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGCATATTCTT
CTTC
Found at i:304376 original size:136 final size:134
Alignment explanation
Indices: 303907--304471 Score: 785
Period size: 134 Copynumber: 4.2 Consensus size: 134
303897 AAGAGCATTA
* * * *
303907 AAGTAGATCAAAGATTTCTTGAGTCTGATATCCCCTAAAGAGTAGTGGAGCACATTCTTCTTCTT
1 AAGTGGATCAAAGTTTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGCATATTCTTCTTCTT
* *
303972 TCAGATTTGGTCTTCTTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAAT
66 TCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTTTGATTCAATCTTCCCTGAAGAAT
*
304037 AGTA
131 AGTG
* * * * **
304041 AAGTGGATCAAAGTTTTCTCGAGTCTGGTCTCTCCTAAAGAGTGGTGGAATATATTCTTCTTCTT
1 AAGTGGATCAAAGTTTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGCATATTCTTCTTCTT
* * *
304106 TCAAATTTGGTCTTCCTGAAGAGTAGTGAAGCAAATCGATTTTGATTCAATCTTCCCTGAAGAGT
66 TCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTTTGATTCAATCTTCCCTGAAGAAT
*
304171 ACTG
131 AGTG
*
304175 AAGTGGATCAAAGTTTTCTCGAGTTTGATATCCCCTAAAGAGTAGTGGAGCATATTCTTCTTCTT
1 AAGTGGATCAAAGTTTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGCATATTCTTCTTCTT
* *
304240 TCAGATTTGGTCTTCCTGAAGAGCAGTGAAACAAATTGATTTTGATTCAATCTTCTTCCTGAAGA
66 TCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTTTGATTCAATCTTC--CCTGAAGA
*
304305 ACAGTG
129 ATAGTG
* * * *
304311 AAGCGGATCAAATTTTTCTCGAGTCTGATCTCCCTTAAAGAGTAGTGGAGCATATTCTTCTTCTT
1 AAGTGGATCAAAGTTTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGCATATTCTTCTTCTT
* * * * * *
304376 TCAGATTTAGTCTTCCTAAAGAGCAGTGAAGCAAATCGATTATGATTCAATCTTCCATGAAAAAC
66 TCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTTTGATTCAATCTTCCCTGAAGAAT
304441 AGTGG
131 AGT-G
* *
304446 AA-TGAATCAACG-TTTCTCGA-TCTGAT
1 AAGTGGATCAAAGTTTTCTCGAGTCTGAT
304472 CTACCCTACA
Statistics
Matches: 381, Mismatches: 47, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
132 6 0.02
133 8 0.02
134 243 0.64
135 3 0.01
136 121 0.32
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (134 bp):
AAGTGGATCAAAGTTTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGCATATTCTTCTTCTT
TCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTTTGATTCAATCTTCCCTGAAGAAT
AGTG
Found at i:304425 original size:270 final size:268
Alignment explanation
Indices: 303907--304436 Score: 819
Period size: 270 Copynumber: 2.0 Consensus size: 268
303897 AAGAGCATTA
*
303907 AAGTAGATCAAAGATTTCTTGAGTCTGATATCCCCTAAAGAGTAGTGGAGCACATTCTTCTTCTT
1 AAGTAGATCAAAGATTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGCACATTCTTCTTCTT
* * *
303972 TCAGATTTGGTCTTCTTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAAT
66 TCAGATTTGGTCTTCCTGAAGAGCAGTGAAACAAATCGATTCTGATTCAATCTTCCCTGAAGAAC
* * * *
304037 AGTAAAGTGGATCAAAGTTTTCTCGAGTCTGGTCTCTCCTAAAGAGTGGTGGAATATATTCTTCT
131 AGTAAAGCGGATCAAAGTTTTCTCGAGTCTGATCTCTCCTAAAGAGTAGTGGAACATATTCTTCT
* * * * *
304102 TCTTTCAAATTTGGTCTTCCTGAAGAGTAGTGAAGCAAATCGATTTTGATTCAATCTTCCCTGAA
196 TCTTTCAAATTTAGTCTTCCTAAAGAGCAGTGAAGCAAATCGATTATGATTCAATCTTCCATGAA
304167 GAGTACTG
261 GAGTACTG
* * * *
304175 AAGTGGATCAAAGTTTTCTCGAGTTTGATATCCCCTAAAGAGTAGTGGAGCATATTCTTCTTCTT
1 AAGTAGATCAAAGATTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGCACATTCTTCTTCTT
* *
304240 TCAGATTTGGTCTTCCTGAAGAGCAGTGAAACAAATTGATTTTGATTCAATCTTCTTCCTGAAGA
66 TCAGATTTGGTCTTCCTGAAGAGCAGTGAAACAAATCGATTCTGATTCAATCTTC--CCTGAAGA
* * *
304305 ACAGTGAAGCGGATCAAATTTTTCTCGAGTCTGATCTC-CCTTAAAGAGTAGTGGAGCATATTCT
129 ACAGTAAAGCGGATCAAAGTTTTCTCGAGTCTGATCTCTCC-TAAAGAGTAGTGGAACATATTCT
*
304369 TCTTCTTTCAGATTTAGTCTTCCTAAAGAGCAGTGAAGCAAATCGATTATGATTCAATCTTCCAT
193 TCTTCTTTCAAATTTAGTCTTCCTAAAGAGCAGTGAAGCAAATCGATTATGATTCAATCTTCCAT
304434 GAA
258 GAA
304437 AAACAGTGGA
Statistics
Matches: 236, Mismatches: 23, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
268 111 0.47
269 2 0.01
270 123 0.52
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (268 bp):
AAGTAGATCAAAGATTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGCACATTCTTCTTCTT
TCAGATTTGGTCTTCCTGAAGAGCAGTGAAACAAATCGATTCTGATTCAATCTTCCCTGAAGAAC
AGTAAAGCGGATCAAAGTTTTCTCGAGTCTGATCTCTCCTAAAGAGTAGTGGAACATATTCTTCT
TCTTTCAAATTTAGTCTTCCTAAAGAGCAGTGAAGCAAATCGATTATGATTCAATCTTCCATGAA
GAGTACTG
Found at i:305478 original size:2 final size:2
Alignment explanation
Indices: 305471--305498 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
305461 TGGATATTTA
305471 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
305499 TATGTCACGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:309954 original size:2 final size:2
Alignment explanation
Indices: 309949--310001 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
309939 TTTTACAAAG
309949 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
309991 AT AT AT AT AT A
1 AT AT AT AT AT A
310002 GGTTAAGGTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:310701 original size:37 final size:37
Alignment explanation
Indices: 310646--310753 Score: 198
Period size: 37 Copynumber: 2.9 Consensus size: 37
310636 AACATAACGT
*
310646 TAGAGTTTTACTAAGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
*
310683 TAGAGTTTTACTATGATTCAAACTCTTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
310720 TAGAGTTTTACTATGATTCAAACTCCTAAAAATA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATA
310754 AGATCCATAA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
Found at i:311147 original size:21 final size:21
Alignment explanation
Indices: 311117--311170 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
311107 TACTTCATTA
311117 TTATTATTATATTTTATA-TGTT
1 TTATT-TTAT-TTTTATATTGTT
* *
311139 TTATTTTATTTTTTTATTTTT
1 TTATTTTATTTTTATATTGTT
311160 TTATTTT-TTTT
1 TTATTTTATTTT
311171 AAAACATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 10 0.34
21 14 0.48
22 5 0.17
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.80
Consensus pattern (21 bp):
TTATTTTATTTTTATATTGTT
Found at i:311155 original size:8 final size:8
Alignment explanation
Indices: 311142--311169 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
311132 ATATGTTTTA
311142 TTTTATTT
1 TTTTATTT
311150 TTTTATTT
1 TTTTATTT
311158 TTTTATTT
1 TTTTATTT
311166 TTTT
1 TTTT
311170 TAAAACATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTATTT
Found at i:311567 original size:11 final size:11
Alignment explanation
Indices: 311553--311577 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
311543 ATTTGTTTTA
311553 TTTATTTGTAT
1 TTTATTTGTAT
311564 TTTATTTGTAT
1 TTTATTTGTAT
311575 TTT
1 TTT
311578 TTTATTTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTATTTGTAT
Found at i:314774 original size:13 final size:12
Alignment explanation
Indices: 314753--314822 Score: 52
Period size: 12 Copynumber: 5.3 Consensus size: 12
314743 CAATCAGAAC
314753 AAAAA-AAAGTGA
1 AAAAACAAAG-GA
314765 AAAAACAAAGGA
1 AAAAACAAAGGA
*
314777 AAAAGCAAAGAGA
1 AAAAACAAAG-GA
*
314790 AAATAAAAAAGAGAAA
1 AAA-AACAAAG-G--A
314806 CAAAAACAAAGGA
1 -AAAAACAAAGGA
314819 AAAA
1 AAAA
314823 GTAAAGAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
12 20 0.42
13 10 0.21
14 7 0.15
15 1 0.02
16 7 0.15
17 3 0.06
ACGTcount: A:0.76, C:0.06, G:0.16, T:0.03
Consensus pattern (12 bp):
AAAAACAAAGGA
Found at i:314822 original size:12 final size:13
Alignment explanation
Indices: 314753--314805 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 13
314743 CAATCAGAAC
*
314753 AAAAA-AAAGTGA
1 AAAAACAAAGAGA
314765 AAAAACAAAG-GA
1 AAAAACAAAGAGA
*
314777 AAAAGCAAAGAGA
1 AAAAACAAAGAGA
*
314790 AAATAAAAAAGAGA
1 AAA-AACAAAGAGA
314804 AA
1 AA
314806 CAAAAACAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 16 0.46
13 9 0.26
14 10 0.29
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (13 bp):
AAAAACAAAGAGA
Found at i:315968 original size:32 final size:32
Alignment explanation
Indices: 315898--315969 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
315888 TCACCTTTGA
* *
315898 AGATTCAACATCAAATGTTGGGGCATTTTTAG
1 AGATTCAACATCAAATATTGGGGCATCTTTAG
* * *
315930 AAATTCAACATCGAATATTGGGGCATCTTTGG
1 AGATTCAACATCAAATATTGGGGCATCTTTAG
*
315962 GGATTCAA
1 AGATTCAA
315970 AATCCTGGTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (32 bp):
AGATTCAACATCAAATATTGGGGCATCTTTAG
Found at i:316900 original size:221 final size:221
Alignment explanation
Indices: 316493--317008 Score: 811
Period size: 221 Copynumber: 2.3 Consensus size: 221
316483 TCGAGACAAG
* * **
316493 CTGACTGTCAACAAATAACTTTTT-AGTTTCATTCAGAGTCAATTTCATTTTCACAGCGAAGGAT
1 CTGACTATCAACAAACAACTTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
* * * *
316557 ATTGGACTTGAGATAACACAAGCTCGAGATCACAGCGAAGGGGCGACTGACTATCAACAAACAAC
66 ATTGGACTCGAGACAACACAAGCTCAACATCACAGCGAAGGGGCGACTGACTATCAACAAACAAC
* *
316622 TTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAATGATATTGGACTCGAGACAACACA
131 CTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
*
316687 AGCTCAACTTCACAGCGAATGGGCGA
196 AGCTCAACTTCACAGCGAAGGGGCGA
* *
316713 CTGACTATTAACATACAACTTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
1 CTGACTATCAACAAACAACTTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
* * *
316778 ATTGGACTCGAGACAACACAAGCTCAACTTCACGGCGAAGGGGCGACTGACTGTCAACAAACAAC
66 ATTGGACTCGAGACAACACAAGCTCAACATCACAGCGAAGGGGCGACTGACTATCAACAAACAAC
* *
316843 CTTTCAGTTTCATTCAGAGTCAATTTTAACTTCACAGTGAAGGATATTGGACTCGAGACAACACA
131 CTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
316908 AGCTCAACTTCACAGCGAAGGGGCGA
196 AGCTCAACTTCACAGCGAAGGGGCGA
* * * *
316934 CTGATTGTCAACAAACAAC-TTCTCAGTTTCATTCAGAGTTAATTTCAACTTCACAGCGAAGGAT
1 CTGACTATCAACAAACAACTTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
*
316998 ATTGAACTCGA
66 ATTGGACTCGA
317009 AGTGACACAA
Statistics
Matches: 270, Mismatches: 25, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
220 73 0.27
221 197 0.73
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.26
Consensus pattern (221 bp):
CTGACTATCAACAAACAACTTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
ATTGGACTCGAGACAACACAAGCTCAACATCACAGCGAAGGGGCGACTGACTATCAACAAACAAC
CTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
AGCTCAACTTCACAGCGAAGGGGCGA
Found at i:317018 original size:110 final size:110
Alignment explanation
Indices: 316493--317008 Score: 816
Period size: 110 Copynumber: 4.7 Consensus size: 110
316483 TCGAGACAAG
* * **
316493 CTGACTGTCAACAAATAACTTTTTAGTTTCATTCAGAGTCAATTTCATTTTCACAGCGAAGGATA
1 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATA
* * * **
316558 TTGGACTTGAGATAACACAAGCTCGAGATCACAGCGAAGGGGCGA
66 TTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGA
* *
316603 CTGACTATCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAATGATA
1 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATA
*
316668 TTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAATGGGCGA
66 TTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGA
* * *
316713 CTGACTATTAACATACAACTTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
1 CTGACTGTCAACAAACAAC-TTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
*
316778 ATTGGACTCGAGACAACACAAGCTCAACTTCACGGCGAAGGGGCGA
65 ATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGA
* * *
316824 CTGACTGTCAACAAACAACCTTTCAGTTTCATTCAGAGTCAATTTTAACTTCACAGTGAAGGATA
1 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATA
316889 TTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGA
66 TTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGA
* * *
316934 CTGATTGTCAACAAACAACTTCTCAGTTTCATTCAGAGTTAATTTCAACTTCACAGCGAAGGATA
1 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATA
*
316999 TTGAACTCGA
66 TTGGACTCGA
317009 AGTGACACAA
Statistics
Matches: 374, Mismatches: 31, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
110 270 0.72
111 104 0.28
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.26
Consensus pattern (110 bp):
CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATA
TTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGA
Found at i:318092 original size:37 final size:37
Alignment explanation
Indices: 318051--318199 Score: 271
Period size: 37 Copynumber: 4.0 Consensus size: 37
318041 AACATAACGT
*
318051 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
*
318088 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGTA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
*
318125 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
318162 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
318199 T
1 T
318200 CCATAAGCAT
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 107 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
Found at i:318466 original size:22 final size:22
Alignment explanation
Indices: 318438--318484 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
318428 TTTTTTTCAA
318438 AACTAACTTTTTAGATCTACGG
1 AACTAACTTTTTAGATCTACGG
318460 AACTAACTTTTTAGATCTACGG
1 AACTAACTTTTTAGATCTACGG
318482 AAC
1 AAC
318485 CCCGAGGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (22 bp):
AACTAACTTTTTAGATCTACGG
Found at i:318908 original size:3 final size:3
Alignment explanation
Indices: 318900--318937 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
318890 CTTATTGTTT
*
318900 TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
318938 CTATTTTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:321104 original size:3 final size:3
Alignment explanation
Indices: 321096--321121 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
321086 ATTAAAAAAT
321096 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
321122 TCAAATAAAT
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:322000 original size:102 final size:107
Alignment explanation
Indices: 321869--322362 Score: 304
Period size: 102 Copynumber: 4.5 Consensus size: 107
321859 GTAATATTTA
* * *
321869 TTTTTATTTTTAAATA-ATAATTATTAGACTATTTATTTTGATTTTACATATTAAGTTGTATTTG
1 TTTTTA-TTGTAAATATA-AATTATTAGACTATTTATTTTGATTTTACATATTAAATCGTATTTG
* * *
321933 AGTAGTTTGTTAAGTTTAGT-TTAAA-TTA-TATTT-TTT-A-T
64 AGTAGTTTGGTAAGTTTAGTGTAAAATTTATTATTTGTTTAAGG
* * ***
321971 TTTTTATTG-AGTAATATAAATTATGAGACTAATTAATTTT-ATTTTATGGATTAAATCGTATTT
1 TTTTTATTGTA--AATATAAATTATTAGACT-ATTTATTTTGATTTTACATATTAAATCGTATTT
* *
322034 GAGTGGTTTGGTAAGTTTAGTGTAAAATTTATTGTTTAGGGTTTAAGG
63 GAGTAGTTTGGTAAGTTTAGTGTAAAATTTATTATTT---GTTTAAGG
*
322082 TTTTTATTGTAAATATAAATTAATTAGACTATTTAGTTTGATTTTACATATTAAA-C-TATATTC
1 TTTTTATTGTAAATATAAATT-ATTAGACTATTTATTTTGATTTTACATATTAAATCGTAT-TT-
* * ** ** *
322145 GAGTGGATTGGTAAGTTTAATTTATATTTTCGTGTAATTTTTAGTATAATTTTGATTTTTGA
63 GAGTAGTTTGGTAAG------TT-TA-----GTGTAAAATTTA-T-T-A-TTTG-TTTAAGG
* * * *
322207 TTTTTAATTTAAAT-TATAATTATTAGACTATTTATTTTTGATTTTACATATTAAGTTGTATTTG
1 TTTTTATTGTAAATATA-AATTATTAGACTATTTA-TTTTGATTTTACATATTAAATCGTATTTG
* *
322271 AGTAGTTTGGTAAGTTTAGT-TTAAA-TTA-TATTT-TTTAA-T
64 AGTAGTTTGGTAAGTTTAGTGTAAAATTTATTATTTGTTTAAGG
* *
322310 TTTTTAATG-AGTAATATAAATTAATTAGACTATTTATTTTGATTTAACATATT
1 TTTTTATTGTA--AATATAAATT-ATTAGACTATTTATTTTGATTTTACATATT
322363 TTTTGTTTAA
Statistics
Matches: 308, Mismatches: 41, Indels: 84
0.71 0.09 0.19
Matches are distributed among these distances:
100 1 0.00
101 2 0.01
102 59 0.19
103 21 0.07
104 29 0.09
105 19 0.06
106 3 0.01
107 1 0.00
108 1 0.00
109 6 0.02
110 21 0.07
111 45 0.15
112 3 0.01
113 2 0.01
117 2 0.01
118 4 0.01
119 2 0.01
123 10 0.03
124 17 0.06
125 52 0.17
126 2 0.01
127 6 0.02
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.53
Consensus pattern (107 bp):
TTTTTATTGTAAATATAAATTATTAGACTATTTATTTTGATTTTACATATTAAATCGTATTTGAG
TAGTTTGGTAAGTTTAGTGTAAAATTTATTATTTGTTTAAGG
Found at i:324899 original size:2 final size:2
Alignment explanation
Indices: 324892--324949 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
324882 AAACATCAAG
324892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
324934 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
324950 TATTTTCTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:327507 original size:21 final size:21
Alignment explanation
Indices: 327478--327524 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
327468 AATATGTAAA
*
327478 TCGCATTGCGATTTTACGAAT
1 TCGCATTGCGATTTTACAAAT
* *
327499 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
327520 TCGCA
1 TCGCA
327525 ACGCGAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:327545 original size:20 final size:20
Alignment explanation
Indices: 327520--327566 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
327510 TTTTCCAAAT
327520 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
*
327540 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATATGTAAA
327560 TCGCAAC
1 TCGCAAC
327567 ACATAAGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:327682 original size:20 final size:20
Alignment explanation
Indices: 327657--327706 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
327647 CTGAATTTCA
327657 AATTTGCAACTCGATTTCTG
1 AATTTGCAACTCGATTTCTG
*
327677 AATTTGCAACTCGATTTTTG
1 AATTTGCAACTCGATTTCTG
*
327697 AATTCGCAAC
1 AATTTGCAAC
327707 ACAAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (20 bp):
AATTTGCAACTCGATTTCTG
Found at i:328690 original size:24 final size:24
Alignment explanation
Indices: 328663--328716 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
328653 GTATTCGAAA
328663 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
328687 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
328711 TTTGAT
1 TTTGAT
328717 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:331037 original size:18 final size:18
Alignment explanation
Indices: 331014--331049 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
331004 AAGCAAAAGG
331014 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
331032 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
331050 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:331284 original size:29 final size:29
Alignment explanation
Indices: 331223--331284 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
331213 ATTTTTTGTT
* ****
331223 GCGATTGTTGCGAAAGTCAAATTTGCGTT
1 GCGATTGTTGCGAAAGTCAAATTCGAAAC
331252 GCGATTGTTGCGAAAGTCAAATTCGAAAC
1 GCGATTGTTGCGAAAGTCAAATTCGAAAC
331281 GCGA
1 GCGA
331285 AATCGCAACG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.27
Consensus pattern (29 bp):
GCGATTGTTGCGAAAGTCAAATTCGAAAC
Found at i:332843 original size:21 final size:22
Alignment explanation
Indices: 332814--332927 Score: 62
Period size: 21 Copynumber: 5.5 Consensus size: 22
332804 GTGAATCGGG
*
332814 CTCTCGAACGGTGGGAGA-GAC
1 CTCTTGAACGGTGGGAGAGGAC
* * * *
332835 CTCTTGAACGAT-GAAAAGGGC
1 CTCTTGAACGGTGGGAGAGGAC
*
332856 CTCTTGAACGGTGGGAG-GG-G
1 CTCTTGAACGGTGGGAGAGGAC
* ** *
332876 CTCTT-AAAGGATGATA-AGGGC
1 CTCTTGAACGG-TGGGAGAGGAC
* *
332897 CTCTTGAACGATAGGAGAGG-C
1 CTCTTGAACGGTGGGAGAGGAC
332918 CTCTTGAACG
1 CTCTTGAACG
332928 ATGACAGGTG
Statistics
Matches: 68, Mismatches: 18, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
19 4 0.06
20 13 0.19
21 43 0.63
22 8 0.12
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.20
Consensus pattern (22 bp):
CTCTTGAACGGTGGGAGAGGAC
Found at i:332895 original size:41 final size:42
Alignment explanation
Indices: 332814--332931 Score: 139
Period size: 41 Copynumber: 2.8 Consensus size: 42
332804 GTGAATCGGG
* *
332814 CTCTCGAACGGTGGGAGAGACCTCTTGAACGATGAAAAGGGC
1 CTCTTGAACGGTGGGAGAGACCTCTTAAACGATGAAAAGGGC
** * *
332856 CTCTTGAACGGTGGGAG-GGGCTCTTAAAGGATGATAAGGGC
1 CTCTTGAACGGTGGGAGAGACCTCTTAAACGATGAAAAGGGC
* * * *
332897 CTCTTGAACGATAGGAGAGGCCTCTTGAACGATGA
1 CTCTTGAACGGTGGGAGAGACCTCTTAAACGATGA
332932 CAGGTGAATC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 34 0.53
42 30 0.47
ACGTcount: A:0.27, C:0.19, G:0.34, T:0.20
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGAGACCTCTTAAACGATGAAAAGGGC
Found at i:332928 original size:21 final size:21
Alignment explanation
Indices: 332827--332929 Score: 77
Period size: 21 Copynumber: 5.0 Consensus size: 21
332817 TCGAACGGTG
*
332827 GGAGAGACCTCTTGAACGAT-
1 GGAGAGGCCTCTTGAACGATA
* * * *
332847 GAAAAGGGCCTCTTGAACGGTG
1 GGAGA-GGCCTCTTGAACGATA
* * *
332869 GGAG-GGGCTCTTAAAGGATGA
1 GGAGAGGCCTCTTGAACGAT-A
**
332890 TAAG-GGCCTCTTGAACGATA
1 GGAGAGGCCTCTTGAACGATA
332910 GGAGAGGCCTCTTGAACGAT
1 GGAGAGGCCTCTTGAACGAT
332930 GACAGGTGAA
Statistics
Matches: 61, Mismatches: 18, Indels: 7
0.71 0.21 0.08
Matches are distributed among these distances:
20 17 0.28
21 42 0.69
22 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.34, T:0.20
Consensus pattern (21 bp):
GGAGAGGCCTCTTGAACGATA
Found at i:335436 original size:22 final size:22
Alignment explanation
Indices: 335410--335466 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
335400 GATGGAGATA
335410 GACGGATTTCGCCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
* * *
335432 GACGGATTTCGTCGGAGTTGGG
1 GACGGATTTCGCCAGAGATGGG
*
335454 GACGGATGTCGCC
1 GACGGATTTCGCC
335467 TTAGAGAGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.18, C:0.19, G:0.42, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:335666 original size:21 final size:21
Alignment explanation
Indices: 335640--335685 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
335630 CTTCTCTGTT
*
335640 GCGAATTTGGAAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
* *
335661 GCGAATTCGTAAAATCGCAAT
1 GCGAATTCGGAAAATCGCAAC
335682 GCGA
1 GCGA
335686 TTTACATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAAC
Found at i:335918 original size:24 final size:25
Alignment explanation
Indices: 335891--335938 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
335881 TAATGGTGCC
*
335891 ATTA-TTTTTGTCATTATAATAAAT
1 ATTATTTTTTATCATTATAATAAAT
335915 ATTATTTTTTATCATTATAATAAA
1 ATTATTTTTTATCATTATAATAAA
335939 AAAATTCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (25 bp):
ATTATTTTTTATCATTATAATAAAT
Found at i:336249 original size:25 final size:25
Alignment explanation
Indices: 336221--336280 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
336211 TAATGTTGTC
*
336221 ATTATTTTTCGTCATTATAATAAAT
1 ATTATTTTTCATCATTATAATAAAT
336246 ATTATTTTTCATCATTATAATAAAT
1 ATTATTTTTCATCATTATAATAAAT
336271 ATTATTTTTC
1 ATTATTTTTC
336281 TACTACAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (25 bp):
ATTATTTTTCATCATTATAATAAAT
Found at i:342021 original size:117 final size:117
Alignment explanation
Indices: 341815--342048 Score: 468
Period size: 117 Copynumber: 2.0 Consensus size: 117
341805 AATATAGATG
341815 TCACATCACTTTAAAAGCATTTCCTTATTTAAATATCTGTAAAATTTTGTTTCTTTTTATAAAAC
1 TCACATCACTTTAAAAGCATTTCCTTATTTAAATATCTGTAAAATTTTGTTTCTTTTTATAAAAC
341880 ATTTTAATTTAGTGATAAATAAACATTCATTAAACTTACGTAGGTAAACAAA
66 ATTTTAATTTAGTGATAAATAAACATTCATTAAACTTACGTAGGTAAACAAA
341932 TCACATCACTTTAAAAGCATTTCCTTATTTAAATATCTGTAAAATTTTGTTTCTTTTTATAAAAC
1 TCACATCACTTTAAAAGCATTTCCTTATTTAAATATCTGTAAAATTTTGTTTCTTTTTATAAAAC
341997 ATTTTAATTTAGTGATAAATAAACATTCATTAAACTTACGTAGGTAAACAAA
66 ATTTTAATTTAGTGATAAATAAACATTCATTAAACTTACGTAGGTAAACAAA
342049 AAATAATGTT
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 117 1.00
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (117 bp):
TCACATCACTTTAAAAGCATTTCCTTATTTAAATATCTGTAAAATTTTGTTTCTTTTTATAAAAC
ATTTTAATTTAGTGATAAATAAACATTCATTAAACTTACGTAGGTAAACAAA
Found at i:342563 original size:55 final size:55
Alignment explanation
Indices: 342474--342643 Score: 279
Period size: 55 Copynumber: 3.1 Consensus size: 55
342464 ATGAATTTCT
* * *
342474 TAGTGCCCATACAAAAATTCATAAACCTACTATGAATTTCTTAGTTTTGCACACA
1 TAGTGCCCATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACA
* * *
342529 AAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAATTTTGCACACA
1 TAGTGCCCATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACA
342584 TAGTGCCCATACAGAAATTCATAAACTTATTATGAATTTCTTAG-TTTGCACACA
1 TAGTGCCCATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACA
342638 TAGTGC
1 TAGTGC
342644 AATTCGGTAA
Statistics
Matches: 106, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
54 16 0.15
55 90 0.85
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.34
Consensus pattern (55 bp):
TAGTGCCCATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACA
Found at i:349418 original size:55 final size:55
Alignment explanation
Indices: 349351--349616 Score: 417
Period size: 55 Copynumber: 4.9 Consensus size: 55
349341 CCCACTATCA
* * * *
349351 ATACGAAAATTCATAAACTTATTATGAATTGCTTAGTTTTGCACATACAGTTCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
* * * * *
349406 ATACGGTAATTCATAAACTTACTATGAATTTCTTAGTTTTGCAAACAAAGTGCCT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
*
349461 ATAAGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
349516 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
* *
349571 ATATGGAAATTTATAAACTTATTATGAATTTCTTAG-TTTGCACACA
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACA
349617 TAGTCTCATT
Statistics
Matches: 193, Mismatches: 18, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
54 10 0.05
55 183 0.95
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (55 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
Found at i:355886 original size:2 final size:2
Alignment explanation
Indices: 355873--355913 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
355863 AAGTATTCCT
355873 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
355914 ATAGGAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:364931 original size:32 final size:31
Alignment explanation
Indices: 364888--364971 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 31
364878 CTAATCCAGG
*
364888 TGCATTTAGATAATGCACATCATG-GCAAGGTT
1 TGCATTCAGATAATGCACAT-ATGTGCAA-GTT
* * *
364920 TGCATTCAGATAATGCATAGTATGTTCGAGTT
1 TGCATTCAGATAATGCACA-TATGTGCAAGTT
*
364952 TGCATTCAGAAAATGCACAT
1 TGCATTCAGATAATGCACAT
364972 GAGTATCATG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
31 1 0.02
32 40 0.91
33 3 0.07
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (31 bp):
TGCATTCAGATAATGCACATATGTGCAAGTT
Found at i:366167 original size:22 final size:22
Alignment explanation
Indices: 366142--366183 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
366132 TGTTATTATT
*
366142 AAATAAATATGATGTGTATGTG
1 AAATAAATATGATGAGTATGTG
* *
366164 AAATATATATTATGAGTATG
1 AAATAAATATGATGAGTATG
366184 AAAATAGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (22 bp):
AAATAAATATGATGAGTATGTG
Found at i:366213 original size:2 final size:2
Alignment explanation
Indices: 366206--366247 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
366196 TTATACATGC
* *
366206 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
366248 GTTATATGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:366277 original size:3 final size:3
Alignment explanation
Indices: 366269--366310 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
366259 ATATAAAATA
366269 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT GTAT ATAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT TAT TA
366311 ATGATAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.78
4 6 0.17
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:367177 original size:2 final size:2
Alignment explanation
Indices: 367172--367205 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
367162 CCTTTTTTAC
367172 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
367206 GTTTGCAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:367270 original size:27 final size:29
Alignment explanation
Indices: 367240--367299 Score: 88
Period size: 27 Copynumber: 2.1 Consensus size: 29
367230 CGTATATGAT
*
367240 TATAGTTTTTAAAATA-TTTTGAAAA-TA
1 TATAGTTTTTAAAACATTTTTGAAAACTA
*
367267 TATATTTTTTAAAACATTTTTGAAAACTA
1 TATAGTTTTTAAAACATTTTTGAAAACTA
367296 TATA
1 TATA
367300 ATATATAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 14 0.48
28 9 0.31
29 6 0.21
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (29 bp):
TATAGTTTTTAAAACATTTTTGAAAACTA
Done.