Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007772.1 Hibiscus syriacus cultivar Beakdansim tig00110053_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: 1636317
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 9
Found at i:578861 original size:14 final size:15
Alignment explanation
Indices: 578825--578861 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
578815 TATATAATAA
578825 TAATAATAATAATTT
1 TAATAATAATAATTT
*
578840 TAGT-ATAATAA-TT
1 TAATAATAATAATTT
578853 TAATAATAA
1 TAATAATAA
578862 AATAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
13 5 0.26
14 11 0.58
15 3 0.16
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
TAATAATAATAATTT
Found at i:579154 original size:75 final size:76
Alignment explanation
Indices: 578989--579620 Score: 1090
Period size: 75 Copynumber: 8.5 Consensus size: 76
578979 GATGGAAATG
* * *
578989 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC-AAAGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
579052 CCCGAAGGCTT
66 CCCGAAGGCTT
579063 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
579127 CCTGAAGGCTT
66 CCCGAAGGCTT
*
579138 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAAGC
579203 TCCCGAAGGCTT
65 TCCCGAAGGCTT
579215 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
579280 CCCGAAGGC-T
66 CCCGAAGGCTT
*
579290 TTTGGAAACATCATGCACTGAAGGACTTACAGACGA-CCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
579354 CCCG-AGGCTT
66 CCCGAAGGCTT
*
579364 TTTGG-AACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACAT-TAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
579427 CCCGAA-GCTT
66 CCCGAAGGCTT
*
579437 TTT--AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
579500 CCCGAAGGCTT
66 CCCGAAGGCTT
*
579511 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTG-AAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
579575 CCCGAAGGCTT
66 CCCGAAGGCTT
579586 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
579621 TGGGAAATAG
Statistics
Matches: 534, Mismatches: 12, Indels: 23
0.94 0.02 0.04
Matches are distributed among these distances:
72 49 0.09
73 64 0.12
74 109 0.20
75 170 0.32
76 68 0.13
77 74 0.14
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:589198 original size:30 final size:32
Alignment explanation
Indices: 589145--589203 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 32
589135 TGCAAATAAA
*
589145 ATGAAATATTAATAAGAAAATATATAAATACT
1 ATGAAATATTAATAAGAAAATATAAAAATACT
* *
589177 ATGAAA-A-TAATAAGTATATATAAAAAT
1 ATGAAATATTAATAAGAAAATATAAAAAT
589204 TTTGAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.71
31 1 0.04
32 6 0.25
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.31
Consensus pattern (32 bp):
ATGAAATATTAATAAGAAAATATAAAAATACT
Found at i:589902 original size:148 final size:146
Alignment explanation
Indices: 589711--590008 Score: 429
Period size: 148 Copynumber: 2.0 Consensus size: 146
589701 TATAAATAAA
*
589711 ATATTTATTTATTTAGAAATATCAGAAAAGGGCTTCTAGGTGTTTTAAGACAGCTCTTTTCTTCA
1 ATATTTACTTATTTAGAAATATCAGAAAAGGGCTTCTAGGTGTTTTAAGACAGCTCTTTTCTTCA
*
589776 ATATTAAAAAATGAATAAATATAAAAACATTTTTCTAAAAAT-A-AAAAAAAAATAGATTGATAC
66 ATATTAAAAAA--AATAAATATAAAAACATTTTTATAAAAATGATAAAAAAAAATAGATT-A-AC
589839 ATATAATTTATAAAAGTAAG
127 ATATAATTTATAAAAGTAAG
* *
589859 ATATTTACTTATTTAGAAATATCAGAAAAGGGCTTCTAGGTGTTTTAAGACAGTTCTTTTCTTCG
1 ATATTTACTTATTTAGAAATATCAGAAAAGGGCTTCTAGGTGTTTTAAGACAGCTCTTTTCTTCA
* * * ** * *
589924 ATATTTAAAAAAATATATATAAAAATATTTTTATAAAAATGATAATGATAAATAGATTAATATAT
66 ATATTAAAAAAAATAAATATAAAAACATTTTTATAAAAATGATAAAAAAAAATAGATTAACATAT
* *
589989 AATTTATATATGTAAG
131 AATTTATAAAAGTAAG
590005 ATAT
1 ATAT
590009 AAAATAAATA
Statistics
Matches: 135, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
146 49 0.36
147 2 0.01
148 84 0.62
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.38
Consensus pattern (146 bp):
ATATTTACTTATTTAGAAATATCAGAAAAGGGCTTCTAGGTGTTTTAAGACAGCTCTTTTCTTCA
ATATTAAAAAAAATAAATATAAAAACATTTTTATAAAAATGATAAAAAAAAATAGATTAACATAT
AATTTATAAAAGTAAG
Found at i:591003 original size:13 final size:13
Alignment explanation
Indices: 590985--591013 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
590975 TGAGTTCGTG
590985 GCTCGTCTCTGTT
1 GCTCGTCTCTGTT
590998 GCTCGTCTCTGTT
1 GCTCGTCTCTGTT
591011 GCT
1 GCT
591014 TGTTTCCCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.24, T:0.45
Consensus pattern (13 bp):
GCTCGTCTCTGTT
Found at i:591543 original size:3 final size:3
Alignment explanation
Indices: 591535--591598 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
591525 ATATATATAT
* *
591535 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TATT TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
*
591581 -ATT TAA TAA TAA TAA TAA
1 TA-A TAA TAA TAA TAA TAA
591599 AATTTAAATG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
2 1 0.02
3 49 0.92
4 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:604090 original size:22 final size:22
Alignment explanation
Indices: 604045--604091 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
604035 GAAGGTAATA
*
604045 ATTTCTAGGGAAAGAATATTTT
1 ATTTCTAGGGAAAGAATATATT
*
604067 ATTTTTAGGGAAAGAA-AGTATT
1 ATTTCTAGGGAAAGAATA-TATT
604089 ATT
1 ATT
604092 AGTATTATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.40
Consensus pattern (22 bp):
ATTTCTAGGGAAAGAATATATT
Found at i:608102 original size:16 final size:16
Alignment explanation
Indices: 608083--608116 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
608073 TAAAGTTATT
608083 TATC-TTTAGGGTAAGA
1 TATCTTTTAGGG-AAGA
608099 TATCTTTTAGGGAAGA
1 TATCTTTTAGGGAAGA
608115 TA
1 TA
608117 AAGATGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (16 bp):
TATCTTTTAGGGAAGA
Found at i:608249 original size:15 final size:15
Alignment explanation
Indices: 608231--608269 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
608221 GTCAACCTCG
608231 TACTCCTCAAGCTTC
1 TACTCCTCAAGCTTC
608246 TACT-CTCAAGCTTC
1 TACTCCTCAAGCTTC
*
608260 TACTCTTCAA
1 TACTCCTCAA
608270 CCAAACATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.23, C:0.36, G:0.05, T:0.36
Consensus pattern (15 bp):
TACTCCTCAAGCTTC
Found at i:610301 original size:22 final size:23
Alignment explanation
Indices: 610264--610311 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
610254 AAGGCCTAGG
610264 CTTGTATAAATAATTGTAAGCTTC
1 CTTGTAT-AATAATTGTAAGCTTC
610288 CTTGTAT-ATAATTGTAAGCTTC
1 CTTGTATAATAATTGTAAGCTTC
610310 CT
1 CT
610312 ACACATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 17 0.71
24 7 0.29
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (23 bp):
CTTGTATAATAATTGTAAGCTTC
Found at i:611033 original size:29 final size:29
Alignment explanation
Indices: 610999--611061 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
610989 ATCCCAATGC
610999 AGTATATTGTAAATGAATATATCTCATGA
1 AGTATATTGTAAATGAATATATCTCATGA
611028 AGTATATTGTAAATGAATATATCTCATGA
1 AGTATATTGTAAATGAATATATCTCATGA
611057 AGTAT
1 AGTAT
611062 CGTTGAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.38
Consensus pattern (29 bp):
AGTATATTGTAAATGAATATATCTCATGA
Found at i:611043 original size:16 final size:15
Alignment explanation
Indices: 611001--611049 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
610991 CCCAATGCAG
611001 TATATTGTAAATGAA
1 TATATTGTAAATGAA
* *
611016 TATA-TCT-CATGAA
1 TATATTGTAAATGAA
611029 GTATATTGTAAATGAA
1 -TATATTGTAAATGAA
611045 TATAT
1 TATAT
611050 CTCATGAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 5 0.19
14 6 0.22
15 11 0.41
16 5 0.19
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (15 bp):
TATATTGTAAATGAA
Found at i:623473 original size:22 final size:22
Alignment explanation
Indices: 623445--623486 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
623435 AGTCGAGGGT
*
623445 TACATAGGTCCTTCGTGACATA
1 TACATAGGTCCTTCGGGACATA
623467 TACATAGGTCCTTCGGGACA
1 TACATAGGTCCTTCGGGACA
623487 AATTTCACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (22 bp):
TACATAGGTCCTTCGGGACATA
Found at i:631964 original size:3 final size:3
Alignment explanation
Indices: 631956--632009 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
631946 AAAAAATATG
* **
631956 TAA TAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
632002 TAA -AA TAA
1 TAA TAA TAA
632010 CGATAAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 5 0.12
3 37 0.88
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:632009 original size:26 final size:25
Alignment explanation
Indices: 631961--632015 Score: 92
Period size: 26 Copynumber: 2.2 Consensus size: 25
631951 ATATGTAATA
*
631961 ATAATAATAAAATAATAAGATAACG
1 ATAATAATAAAATAATAAAATAACG
631986 ATAATAATAATAATAATAAAATAACG
1 ATAATAATAA-AATAATAAAATAACG
632012 ATAA
1 ATAA
632016 AAAAACCCGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 10 0.36
26 18 0.64
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.25
Consensus pattern (25 bp):
ATAATAATAAAATAATAAAATAACG
Found at i:632230 original size:43 final size:44
Alignment explanation
Indices: 632161--632545 Score: 209
Period size: 46 Copynumber: 9.0 Consensus size: 44
632151 TCTGTTGGTG
* * ** * *
632161 GGGACGACACTGCTCATACGCAATGAAGAGGTCTGGTCATCTAA
1 GGGATGACACGGCTCATACGTGATGAGGAGATCTGGTCATCTAA
* *
632205 GGG-TGACACGGCTCATACGTGATGAAGAGATCTGG---TC--G
1 GGGATGACACGGCTCATACGTGATGAGGAGATCTGGTCATCTAA
* ** * *
632243 GGGAATGACACGACTCATACGCAATGAAGAGTTCTGG-CTATCTAAA
1 GGG-ATGACACGGCTCATACGTGATGAGGAGATCTGGTC-ATCT-AA
* * * * *
632289 GGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT-A
1 GG-GATGACACGGCTCATACGTGATGAGGA-GATCTGGTCATCTAA
* * * *
632333 GGG-TGACACGACTCATACGTGATGAAGAAATCTGG---TCT-G
1 GGGATGACACGGCTCATACGTGATGAGGAGATCTGGTCATCTAA
* * * * *
632372 GGGATGACACGGTTCCTACATGATGAGGACG-GCTGGCCATCTAAA
1 GGGATGACACGGCTCATACGTGATGAGGA-GATCTGGTCATCT-AA
* * * * *
632417 GGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT-A
1 GG-GATGACACGGCTCATACGTGATGAGGA-GATCTGGTCATCTAA
* * * *
632461 TGGTTGACACGGCTCCTACGTGATGAGGAGATCTGG---TCT-G
1 GGGATGACACGGCTCATACGTGATGAGGAGATCTGGTCATCTAA
632501 GGGAATGACACGGCTCATACGTGATGAGGAGATCTGGTCATCTAA
1 GGG-ATGACACGGCTCATACGTGATGAGGAGATCTGGTCATCTAA
632546 AGGAGTTATG
Statistics
Matches: 265, Mismatches: 50, Indels: 51
0.72 0.14 0.14
Matches are distributed among these distances:
38 3 0.01
39 6 0.02
40 59 0.22
41 31 0.12
42 25 0.09
43 61 0.23
44 11 0.04
45 2 0.01
46 65 0.25
47 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.23
Consensus pattern (44 bp):
GGGATGACACGGCTCATACGTGATGAGGAGATCTGGTCATCTAA
Found at i:632358 original size:88 final size:82
Alignment explanation
Indices: 632248--632407 Score: 203
Period size: 82 Copynumber: 1.9 Consensus size: 82
632238 GGTCGGGGAA
** * *
632248 TGACACGACTCATACGCAATGAAGAGTTCTGGCTATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGACTCATACGCAATGAAGAAATCTGG---TCT---GGGGATAACACGGTTCCTACATGA
632313 TGAGGACGGCTGGTTATCTAGGG
60 TGAGGACGGCTGGTTATCTAGGG
** *
632336 TGACACGACTCATACGTGATGAAGAAATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGA
1 TGACACGACTCATACGCAATGAAGAAATCTGGTCTGGGGATAACACGGTTCCTACATGATGAGGA
632401 CGGCTGG
66 CGGCTGG
632408 CCATCTAAAG
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
82 34 0.52
85 3 0.05
88 28 0.43
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (82 bp):
TGACACGACTCATACGCAATGAAGAAATCTGGTCTGGGGATAACACGGTTCCTACATGATGAGGA
CGGCTGGTTATCTAGGG
Found at i:632432 original size:128 final size:129
Alignment explanation
Indices: 632193--632548 Score: 511
Period size: 128 Copynumber: 2.8 Consensus size: 129
632183 ATGAAGAGGT
* *
632193 CTGGTCATCTAAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTC-GGGGAATGACACGAC
1 CTGGTTATCT-AGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGAATGACACGGC
** * * *
632257 TCATACGCAATGAAGAGTTCTGGCTATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
65 TCATACGTGATGAGGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
* * *
632322 CTGGTTATCTAGGGTGACACGACTCATACGTGATGAAGAAATCTGGTCTGGGG-ATGACACGGTT
1 CTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGAATGACACGGCT
* * *
632386 CCTACATGATGAGGACG-GCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
66 CATACGTGATGAGGA-GATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
* * *
632450 CTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGAATGACACGGC
1 CTGGTTATCTA-GGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGAATGACACGGC
*
632515 TCATACGTGATGAGGAGATCTGGTCATCTAAAGG
65 TCATACGTGATGAGGAGATCTGGCCATCTAAAGG
632549 AGTTATGGTT
Statistics
Matches: 200, Mismatches: 22, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
128 111 0.56
129 52 0.26
130 37 0.19
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (129 bp):
CTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGAATGACACGGCT
CATACGTGATGAGGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
Found at i:632694 original size:63 final size:62
Alignment explanation
Indices: 632626--632743 Score: 177
Period size: 63 Copynumber: 1.9 Consensus size: 62
632616 TTTCAAAAGC
632626 AACTGTCTCAAAAGAGACAAAATTTTGTTTCAAA-GGAAATGA-CTCAAAGATTGTTTAAAGGAA
1 AACTGTCTCAAAAGAGACAAAA-TTTGTTT-AAAGGGAAATGATCTCAAAGA-TGTTTAAAGGAA
* *
632689 AACTGTCTCGAATGAGACAAAATTTGTTTAAAGGGAAATGATCTCAAAGATGTTT
1 AACTGTCTCAAAAGAGACAAAATTTGTTTAAAGGGAAATGATCTCAAAGATGTTT
632744 GTTTTGTTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
61 3 0.06
62 20 0.39
63 28 0.55
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.29
Consensus pattern (62 bp):
AACTGTCTCAAAAGAGACAAAATTTGTTTAAAGGGAAATGATCTCAAAGATGTTTAAAGGAA
Found at i:632971 original size:28 final size:28
Alignment explanation
Indices: 632930--632997 Score: 102
Period size: 28 Copynumber: 2.4 Consensus size: 28
632920 TTAAGAGAGA
*
632930 CAAA-ATTTTGTTCCCAAAGAAACAAACT
1 CAAAGATTTT-TTCCAAAAGAAACAAACT
*
632958 CAAAGATTTTTTCCAAAAGAAACAATCT
1 CAAAGATTTTTTCCAAAAGAAACAAACT
632986 CAAAGATTTTTT
1 CAAAGATTTTTT
632998 TCACAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 32 0.86
29 5 0.14
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (28 bp):
CAAAGATTTTTTCCAAAAGAAACAAACT
Found at i:633042 original size:54 final size:55
Alignment explanation
Indices: 632984--633090 Score: 153
Period size: 55 Copynumber: 2.0 Consensus size: 55
632974 AAGAAACAAT
* ** *
632984 CTCAAAGATTTTTTTCA-CAAAATTGTCTAAAGAGAGACAAAACTTTGTTTCAGA
1 CTCAAAGATTGTTTAAAGCAAAACTGTCTAAAGAGAGACAAAACTTTGTTTCAGA
* *
633038 CTCAAAGATTGTTTAAAGGAAAACTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTGTTTAAAGCAAAACTGTCTAAAGAGAGACAAAACTTTGTTTCA
633091 AAATAAATAG
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
54 14 0.30
55 32 0.70
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (55 bp):
CTCAAAGATTGTTTAAAGCAAAACTGTCTAAAGAGAGACAAAACTTTGTTTCAGA
Found at i:633115 original size:26 final size:25
Alignment explanation
Indices: 633086--633207 Score: 100
Period size: 28 Copynumber: 4.5 Consensus size: 25
633076 CAAAACTTTG
* *
633086 TTTCAAAATAAATAGACTCAAAGATT
1 TTTCAAAAGAAACA-ACTCAAAGATT
633112 TTTCAAAAGAAACAACTCAAAGATATT
1 TTTCAAAAGAAACAACTCAAAG--ATT
* *
633139 TATTCAAAAGGAACAAACTCCAAGATTT
1 T-TTCAAAAGAAAC-AACTCAAAGA-TT
* *
633167 TATTTAAAAGGAACTAACTCAAAGATTT
1 T-TTCAAAAGAAAC-AACTCAAAGA-TT
*
633195 TTTCAAGAGAAAC
1 TTTCAAAAGAAAC
633208 TGTCTCAAGA
Statistics
Matches: 81, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
25 8 0.10
26 12 0.15
27 14 0.17
28 39 0.48
29 8 0.10
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (25 bp):
TTTCAAAAGAAACAACTCAAAGATT
Found at i:633153 original size:28 final size:27
Alignment explanation
Indices: 633101--633200 Score: 123
Period size: 28 Copynumber: 3.7 Consensus size: 27
633091 AAATAAATAG
*
633101 ACTCAAAGA-TTTTTCAAAAGAAAC-A
1 ACTCAAAGATTTTTTCAAAAGGAACAA
633126 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGAT-TTT-TTCAAAAGGAACAA
* * *
633155 ACTCCAAGATTTTATTTAAAAGGAACTA
1 ACTCAAAGATTTT-TTCAAAAGGAACAA
633183 ACTCAAAGATTTTTTCAA
1 ACTCAAAGATTTTTTCAA
633201 GAGAAACTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.14
27 7 0.11
28 39 0.60
29 10 0.15
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (27 bp):
ACTCAAAGATTTTTTCAAAAGGAACAA
Found at i:633495 original size:34 final size:36
Alignment explanation
Indices: 633448--633565 Score: 116
Period size: 35 Copynumber: 3.4 Consensus size: 36
633438 AGAAAATGAT
*
633448 GTCTCAAGCGAGACAAAATTTG-CTTTA-AGATATA
1 GTCTCAAGCGAGACAAAATTTGTCTTTAGAGAAATA
** * * *
633482 GTCTCAAATGAGACAACATTTGTTTTTAGAGAAATT
1 GTCTCAAGCGAGACAAAATTTGTCTTTAGAGAAATA
* * *
633518 GTCTCAAGCGAGACAAAGTTTGT-TTTTGAGAAACA
1 GTCTCAAGCGAGACAAAATTTGTCTTTAGAGAAATA
* *
633553 ATCTCAAGTGAGA
1 GTCTCAAGCGAGA
633566 TCAACTTTGT
Statistics
Matches: 67, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
34 19 0.28
35 24 0.36
36 24 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAAATTTGTCTTTAGAGAAATA
Found at i:633531 original size:36 final size:36
Alignment explanation
Indices: 633448--633577 Score: 126
Period size: 36 Copynumber: 3.7 Consensus size: 36
633438 AGAAAATGAT
* * *
633448 GTCTCAAGCGAGACAAAATTTG-CTTTA-AGATATA
1 GTCTCAAGCGAGACAACATTTGTTTTTAGAGAAATA
** *
633482 GTCTCAAATGAGACAACATTTGTTTTTAGAGAAATT
1 GTCTCAAGCGAGACAACATTTGTTTTTAGAGAAATA
*
633518 GTCTCAAGCGAGACAA-AGTTTGTTTTT-GAGAAACA
1 GTCTCAAGCGAGACAACA-TTTGTTTTTAGAGAAATA
* *
633553 ATCTCAAGTGAGATCAAC-TTTGTTT
1 GTCTCAAGCGAGA-CAACATTTGTTT
633578 AATGTGAAAC
Statistics
Matches: 79, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
34 19 0.24
35 29 0.37
36 31 0.39
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (36 bp):
GTCTCAAGCGAGACAACATTTGTTTTTAGAGAAATA
Found at i:633744 original size:105 final size:105
Alignment explanation
Indices: 633518--633737 Score: 265
Period size: 105 Copynumber: 2.1 Consensus size: 105
633508 TAGAGAAATT
* *
633518 GTCTCAAGCGAGACAAAGTTTGTTTTTG--AG--A-AACAATCTCAAGTGAGATCAACTTTGTTT
1 GTCTCAAGCGAGACAAAATTT-ATTTTGAAAGAAACAACAATCTCAAGTGAGATCAACTTTGTTT
* * *
633578 AATGTGAAACAAATTCGAAATTTGGATCTCCAAGGGAAAAG
65 AATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
633619 GTCTCAAGCGAGACAAAATTTATTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACAAAATTTATTTTGAAAGAAACAACAATCTCAA-GTGAGATCAACTTTG-TT
* ** *
633683 TAA-GTGAATCAAATTCAAAATTTTTATCTCAAAGGAAAAAT
64 TAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
633724 GTCTCAAGCGAGAC
1 GTCTCAAGCGAGAC
633738 GCAATTTGTT
Statistics
Matches: 101, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
100 5 0.05
101 20 0.20
102 2 0.02
104 3 0.03
105 66 0.65
106 5 0.05
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (105 bp):
GTCTCAAGCGAGACAAAATTTATTTTGAAAGAAACAACAATCTCAAGTGAGATCAACTTTGTTTA
ATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:634219 original size:4 final size:4
Alignment explanation
Indices: 634203--634248 Score: 58
Period size: 4 Copynumber: 11.2 Consensus size: 4
634193 ATACAAATTT
*
634203 TATG TAT- TATG TATG TATGCG TATT TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TAT--G TATG TATG TATG TATG TATG TATG T
634249 TTTCTCGATC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
3 3 0.08
4 30 0.81
6 4 0.11
ACGTcount: A:0.24, C:0.02, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:637878 original size:27 final size:28
Alignment explanation
Indices: 637826--637879 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 28
637816 AAAATGACAC
637826 AAACAAAAGAGAAGAAATAAGTTAGTAT
1 AAACAAAAGAGAAGAAATAAGTTAGTAT
637854 AAACAAAAGAGAA-AAATAAGTTAGTA
1 AAACAAAAGAGAAGAAATAAGTTAGTA
637880 CATGTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.63, C:0.04, G:0.17, T:0.17
Consensus pattern (28 bp):
AAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:641192 original size:3 final size:3
Alignment explanation
Indices: 641186--641246 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
641176 AAAAAATATG
* **
641186 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
641230 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
641247 CGATAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:664793 original size:2 final size:2
Alignment explanation
Indices: 664788--664812 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
664778 GTGAGAGACC
664788 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
664813 TACAAGTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:664893 original size:19 final size:19
Alignment explanation
Indices: 664869--664907 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
664859 AATCAAACAT
664869 TCCATCTTTTAATTTTAAG
1 TCCATCTTTTAATTTTAAG
664888 TCCATCTTTTAATTTTAAG
1 TCCATCTTTTAATTTTAAG
664907 T
1 T
664908 ATAACTCGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.05, T:0.54
Consensus pattern (19 bp):
TCCATCTTTTAATTTTAAG
Found at i:665077 original size:15 final size:18
Alignment explanation
Indices: 665043--665079 Score: 53
Period size: 15 Copynumber: 2.2 Consensus size: 18
665033 AATGTTTATA
665043 TATAATATTATATGTTTT
1 TATAATATTATATGTTTT
665061 TATAA-ATT-TAT-TTTT
1 TATAATATTATATGTTTT
665076 TATA
1 TATA
665080 TTATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.42
16 3 0.16
17 3 0.16
18 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TATAATATTATATGTTTT
Found at i:665087 original size:18 final size:18
Alignment explanation
Indices: 665034--665087 Score: 51
Period size: 20 Copynumber: 3.0 Consensus size: 18
665024 TAACTTTTTA
*
665034 ATGTTTATATATAATATTAT
1 ATGTTTTTATAT-ATATT-T
665054 ATGTTTTTATA-A-ATTT
1 ATGTTTTTATATATATTT
665070 AT-TTTTTATATTATATTT
1 ATGTTTTTATA-TATATTT
665088 TTATGTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
15 8 0.27
16 3 0.10
17 4 0.13
18 5 0.17
20 10 0.33
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (18 bp):
ATGTTTTTATATATATTT
Found at i:668226 original size:29 final size:28
Alignment explanation
Indices: 668194--668291 Score: 67
Period size: 29 Copynumber: 3.4 Consensus size: 28
668184 TAATTAATTA
668194 AATTAATTATAATGATTACAAGTTAAAAT
1 AATTAATTATAAT-ATTACAAGTTAAAAT
* * *
668223 AATTTATT-TACAT-TCGACATGCTTAATAA-
1 AATTAATTATA-ATAT-TACAAG-TTAA-AAT
*
668252 AATTAATTATAATCATTAAAAGTTAAAAT
1 AATTAATTATAAT-ATTACAAGTTAAAAT
*
668281 AAGTTATTTAT
1 AA-TTAATTAT
668292 TGAACACGAT
Statistics
Matches: 52, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
27 1 0.02
28 8 0.15
29 28 0.54
30 14 0.27
31 1 0.02
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (28 bp):
AATTAATTATAATATTACAAGTTAAAAT
Found at i:668312 original size:58 final size:56
Alignment explanation
Indices: 668170--668317 Score: 165
Period size: 58 Copynumber: 2.6 Consensus size: 56
668160 ATTAAGTAAT
* * * *
668170 TTATTTATTGAACATAATTAATT-AAATTAATTATAATGATTACAAGTTAAAATAAT
1 TTATTTATTGAACATGATT-ATTAAAATTAATTATAATCATTAAAAGTTAAAATAAG
* *
668226 TTATTTACATTCG-ACATGCTTAATAAAATTAATTATAATCATTAAAAGTTAAAATAAG
1 TTATTT--ATT-GAACATGATTATTAAAATTAATTATAATCATTAAAAGTTAAAATAAG
*
668284 TTATTTATTGAACACGATTATTTAAAAATTAATT
1 TTATTTATTGAACATGATTA-TT-AAAATTAATT
668318 TAAATGTATA
Statistics
Matches: 76, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
55 1 0.01
56 16 0.21
57 3 0.04
58 55 0.72
59 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (56 bp):
TTATTTATTGAACATGATTATTAAAATTAATTATAATCATTAAAAGTTAAAATAAG
Found at i:669287 original size:17 final size:18
Alignment explanation
Indices: 669239--669288 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
669229 CCTACAAAAT
669239 TAAAATTAAAATCATTAA
1 TAAAATTAAAATCATTAA
669257 TAATCAATTCAAAAT-ATTAA
1 TAA--AATT-AAAATCATTAA
*
669277 TGAAATTAAAAT
1 TAAAATTAAAAT
669289 TAAAAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 5 0.18
18 7 0.25
20 11 0.39
21 5 0.18
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (18 bp):
TAAAATTAAAATCATTAA
Found at i:671729 original size:55 final size:55
Alignment explanation
Indices: 671645--671783 Score: 134
Period size: 55 Copynumber: 2.5 Consensus size: 55
671635 TCTCGATTAG
* * * * * *
671645 AGAAGATGAACAGAGACATAAGCATATGAAGTGTCTCGATTAGATATAGGGTTAA
1 AGAAGATGAACAGAGACAGAAGCAGATGAAGAGCCTCGATTAGATACAAGGTTAA
* * * * * * *
671700 AGAAGATGAACATAGGCAGAAGTAGATGAAGAGCCTTGGTTAGATACAATGTTAG
1 AGAAGATGAACAGAGACAGAAGCAGATGAAGAGCCTCGATTAGATACAAGGTTAA
* * *
671755 AGAAGATGAACAAAGACAAAAGAAGATGA
1 AGAAGATGAACAGAGACAGAAGCAGATGA
671784 TGATAAACAG
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
55 67 1.00
ACGTcount: A:0.45, C:0.09, G:0.27, T:0.19
Consensus pattern (55 bp):
AGAAGATGAACAGAGACAGAAGCAGATGAAGAGCCTCGATTAGATACAAGGTTAA
Found at i:680517 original size:21 final size:21
Alignment explanation
Indices: 680491--680530 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
680481 CAGAACCCCA
*
680491 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
680512 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
680531 TCAAAGGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:680565 original size:21 final size:21
Alignment explanation
Indices: 680512--680574 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
680502 ATTCCCCTGT
680512 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
* * *
680535 AGGAGGAATCGGTTCCCTCAG
1 GGGGGGAATCGGTTCCCTCAA
*
680556 GGGGGGAATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
680575 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 19 0.56
22 3 0.09
23 12 0.35
ACGTcount: A:0.19, C:0.25, G:0.35, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:684422 original size:22 final size:21
Alignment explanation
Indices: 684380--684419 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
684370 GAGTTTGTTT
*
684380 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
684401 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
684420 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:687220 original size:2 final size:2
Alignment explanation
Indices: 687208--687634 Score: 166
Period size: 2 Copynumber: 215.5 Consensus size: 2
687198 AACACAATTG
* * *
687208 TA TA GTA TA TA TA TA CA TA TA TA TA CTA TA TA AA TA -A TT TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
*
687251 T- TA -A TA AA CTA TA TA -A CT- TA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
687290 TA TA TA TA TA T- TA TA TA GTT TA GA CA TA GTA TA TA GA TA TA AA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA
* * * *
687333 CTA TA TA GTT TA CA TA TA -A TT TA TA TA GTT TA TA TA TA TA GT-
1 -TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA
* * * *
687375 TCA TA TA TA CA -A TA TA CA -A TT TA TA TA TA -A TA TA TG TA TA
1 T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * ** * *
687415 TA T- TA TG TA TA AA CTA CG TA GTT TA TA CA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * *
687457 AA T- TA TA TA TA -A TA TA TA TA GT- TC CA -A TA TA GTT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA
* *
687497 T- TA TA TA GT- TGC TA TA TA GTT TA TA -A TA TA TA TA -A T- TCA
1 TA TA TA TA -TA T-A TA TA TA -TA TA TA TA TA TA TA TA TA TA T-A
* * * * * * *
687536 CA TA CTA TA TA GTT TA GA TA TA TA TA TA AA TA TA AA T- TG CA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
687579 -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
687620 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
687635 TATGATTGTT
Statistics
Matches: 314, Mismatches: 65, Indels: 92
0.67 0.14 0.20
Matches are distributed among these distances:
1 25 0.08
2 266 0.85
3 23 0.07
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:687348 original size:31 final size:32
Alignment explanation
Indices: 687286--687348 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
687276 TATATATATA
* * *
687286 TATATATATATATATTATATAGTTTAGACATAG
1 TATATAGATATAAACTATATAGTTTA-ACATAG
687319 TATATAGATATAAACTATATAGTTT-ACATA
1 TATATAGATATAAACTATATAGTTTAACATA
687349 TAATTTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 5 0.19
33 22 0.81
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (32 bp):
TATATAGATATAAACTATATAGTTTAACATAG
Found at i:687463 original size:9 final size:11
Alignment explanation
Indices: 687438--687476 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
687428 CTACGTAGTT
*
687438 TATACATAATA
1 TATATATAATA
687449 TATATATAA-A
1 TATATATAATA
687459 TTATATATAATA
1 -TATATATAATA
687471 TATATA
1 TATATA
687477 GTTCCAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 1 0.04
11 23 0.92
12 1 0.04
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (11 bp):
TATATATAATA
Found at i:687757 original size:16 final size:16
Alignment explanation
Indices: 687736--687769 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
687726 TTTTTTTTTC
*
687736 TTTAATTTATTTAATT
1 TTTAATTCATTTAATT
687752 TTTAATTCATTTAATT
1 TTTAATTCATTTAATT
687768 TT
1 TT
687770 ATATTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTAATTCATTTAATT
Found at i:691803 original size:2 final size:2
Alignment explanation
Indices: 691798--691884 Score: 174
Period size: 2 Copynumber: 43.5 Consensus size: 2
691788 ACCGAAGTAA
691798 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
691840 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
691882 AT A
1 AT A
691885 GGGTAGAGAC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:697743 original size:31 final size:31
Alignment explanation
Indices: 697708--697775 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
697698 TTGCCATACA
697708 GTCCCCCAATATTTAGTCTGTTTGCAATATG
1 GTCCCCCAATATTTAGTCTGTTTGCAATATG
*
697739 GTCCCCCAATATTTAGTTTGTTTGCAATATG
1 GTCCCCCAATATTTAGTCTGTTTGCAATATG
*
697770 CTCCCC
1 GTCCCC
697776 GACGTAACCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38
Consensus pattern (31 bp):
GTCCCCCAATATTTAGTCTGTTTGCAATATG
Found at i:700100 original size:19 final size:20
Alignment explanation
Indices: 700061--700104 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
700051 ACAATTGAAT
700061 TTGCCACGACATTTCATTCAA
1 TTGCCACGACA-TTCATTCAA
700082 CTTGCCACGACA-T-ATTCAA
1 -TTGCCACGACATTCATTCAA
700101 TTGC
1 TTGC
700105 AACCACACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 1 0.05
22 11 0.50
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (20 bp):
TTGCCACGACATTCATTCAA
Found at i:702245 original size:23 final size:23
Alignment explanation
Indices: 702192--702251 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
702182 ACAATCTTAT
*
702192 ATGGCACTACGGTGCAATTCTAC
1 ATGGCACTTCGGTGCAATTCTAC
** * *
702215 GCGACACTTCGTTGCAATTCTAC
1 ATGGCACTTCGGTGCAATTCTAC
702238 ATGGCACTTCGGTG
1 ATGGCACTTCGGTG
702252 TATTTATACG
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (23 bp):
ATGGCACTTCGGTGCAATTCTAC
Found at i:706084 original size:16 final size:16
Alignment explanation
Indices: 706053--706086 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
706043 ATATGTTTGA
*
706053 AAAGAATAAAGCAAGT
1 AAAGAATAAAGAAAGT
*
706069 AAAGAATAAGGAAAGT
1 AAAGAATAAAGAAAGT
706085 AA
1 AA
706087 GGATTTTGAG
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:0.65, C:0.03, G:0.21, T:0.12
Consensus pattern (16 bp):
AAAGAATAAAGAAAGT
Found at i:709080 original size:23 final size:22
Alignment explanation
Indices: 709046--709105 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 22
709036 AATCTTATAT
*
709046 GGCACTATGGTGTAATTCTACGC
1 GGCACT-TGGTGCAATTCTACGC
709069 GGCACTTCGGTGCAATTCTACGC
1 GGCACTT-GGTGCAATTCTACGC
709092 GGCACTTTGGTGCA
1 GGCAC-TTGGTGCA
709106 TTTATATGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
22 1 0.03
23 31 0.91
24 2 0.06
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.28
Consensus pattern (22 bp):
GGCACTTGGTGCAATTCTACGC
Found at i:710302 original size:3 final size:3
Alignment explanation
Indices: 710288--710318 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
710278 ACTCTTCTCC
*
710288 CTT CTT CAT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
710319 CTCCCTTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:713510 original size:59 final size:59
Alignment explanation
Indices: 713411--713532 Score: 154
Period size: 59 Copynumber: 2.1 Consensus size: 59
713401 CAGCAGGCTG
** * * *
713411 CATATTTGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACAACCTTGTGTGT
1 CATATTTGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGT
* ** * *
713470 CATATTTGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTTGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGT
713529 CATA
1 CATA
713533 CTCGAGATTG
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (59 bp):
CATATTTGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGT
Found at i:713637 original size:20 final size:20
Alignment explanation
Indices: 713597--713638 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
713587 TTGTATATTG
* *
713597 GGCTATTGTCTATTGTTTAT
1 GGCTATTGTCTATGGTATAT
713617 GGCTATTGTCTATGGTATAT
1 GGCTATTGTCTATGGTATAT
713637 GG
1 GG
713639 TTATGGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.10, G:0.26, T:0.48
Consensus pattern (20 bp):
GGCTATTGTCTATGGTATAT
Found at i:713688 original size:44 final size:44
Alignment explanation
Indices: 713639--713877 Score: 399
Period size: 44 Copynumber: 5.4 Consensus size: 44
713629 TGGTATATGG
* *
713639 TTATGGA-ATAATGGCAAGTTTATTGGTAAAATAAGCTTACGAGC
1 TTATGGATA-AATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
713683 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* *
713727 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGA
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
713771 TTATGGATAAATGGTAAGTATAATGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
713815 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
713859 TTATGGTATTAAATGGTAA
1 TTATGG-A-TAAATGGTAA
713878 ATATTGAACA
Statistics
Matches: 184, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
44 172 0.93
45 2 0.01
46 10 0.05
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.32
Consensus pattern (44 bp):
TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:713693 original size:25 final size:25
Alignment explanation
Indices: 713665--713737 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
713655 AGTTTATTGG
713665 TAAAATAAGCTTACGAGCTTATGGA
1 TAAAATAAGCTTACGAGCTTATGGA
* **
713690 T-AAAT--G-GTA--AGTATATTGG-
1 TAAAATAAGCTTACGAGCTTA-TGGA
713709 TAAAATAAGCTTACGAGCTTATGGA
1 TAAAATAAGCTTACGAGCTTATGGA
713734 TAAA
1 TAAA
713738 TGGTAAGTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 16
0.61 0.11 0.29
Matches are distributed among these distances:
19 5 0.15
20 7 0.21
21 2 0.06
22 2 0.06
23 2 0.06
24 7 0.21
25 9 0.26
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (25 bp):
TAAAATAAGCTTACGAGCTTATGGA
Found at i:713738 original size:24 final size:24
Alignment explanation
Indices: 713667--713738 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
713657 TTTATTGGTA
713667 AAATAAGCTTACGAGCTTATGGAT
1 AAATAAGCTTACGAGCTTATGGAT
*
713691 AAAT--G-GTA--AG-TATATTGG-T
1 AAATAAGCTTACGAGCT-TA-TGGAT
713710 AAAATAAGCTTACGAGCTTATGGAT
1 -AAATAAGCTTACGAGCTTATGGAT
713735 AAAT
1 AAAT
713739 GGTAAGTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 20
0.62 0.03 0.34
Matches are distributed among these distances:
18 1 0.03
19 5 0.14
20 7 0.19
21 2 0.06
22 2 0.06
23 2 0.06
24 11 0.31
25 5 0.14
26 1 0.03
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (24 bp):
AAATAAGCTTACGAGCTTATGGAT
Found at i:713820 original size:24 final size:24
Alignment explanation
Indices: 713793--713866 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
713783 GGTAAGTATA
713793 ATGGTAAAATAAGCTTACGAGCTT
1 ATGGTAAAATAAGCTTACGAGCTT
* **
713817 ATGG-ATAAAT--G-GTA--AGTAT
1 ATGGTA-AAATAAGCTTACGAGCTT
713836 ATTGGTAAAATAAGCTTACGAGCTT
1 A-TGGTAAAATAAGCTTACGAGCTT
713861 ATGGTA
1 ATGGTA
713867 TTAAATGGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 16
0.62 0.10 0.28
Matches are distributed among these distances:
19 4 0.11
20 7 0.19
21 3 0.08
22 2 0.06
23 3 0.08
24 13 0.36
25 4 0.11
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (24 bp):
ATGGTAAAATAAGCTTACGAGCTT
Found at i:716794 original size:40 final size:36
Alignment explanation
Indices: 716701--716801 Score: 139
Period size: 40 Copynumber: 2.7 Consensus size: 36
716691 TTTTTGAAAG
*
716701 TATATTATATAATTTTTGAAAACATTTTGAAATTATA
1 TATAATATATAA-TTTTGAAAACATTTTGAAATTATA
716738 TATAATATATAATTTTGAAAACATTTTGAAAACATATATA
1 TATAATATATAATTTTGAAAACATTTTG--AA-AT-TATA
*
716778 TATAATATATAGTTTTGAAAACAT
1 TATAATATATAATTTTGAAAACAT
716802 ATATATAATA
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
36 16 0.28
37 11 0.19
38 2 0.03
39 2 0.03
40 27 0.47
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.44
Consensus pattern (36 bp):
TATAATATATAATTTTGAAAACATTTTGAAATTATA
Found at i:716811 original size:27 final size:27
Alignment explanation
Indices: 716761--716961 Score: 186
Period size: 25 Copynumber: 8.0 Consensus size: 27
716751 TTTGAAAACA
716761 TTTTGAAAACATATATATATAATATATAG
1 TTTTGAAAAC--ATATATATAATATATAG
716790 TTTTGAAAACATATATATAATATATAG
1 TTTTGAAAACATATATATAATATATAG
716817 TTTTGAAAAC--ATATATAATATATAG
1 TTTTGAAAACATATATATAATATATAG
716842 TTTTGAAAAC--ATATATAATATATAG
1 TTTTGAAAACATATATATAATATATAG
* * * *
716867 TTTT-AAAA-ATAT-TTTGAAAACATTG
1 TTTTGAAAACATATATAT-AATATATAG
*
716892 TTTTGAAAAC------ATAA-A-ACA-
1 TTTTGAAAACATATATATAATATATAG
716910 TTTTGAAAACATATATATAATATATAG
1 TTTTGAAAACATATATATAATATATAG
*
716937 TTTTTGAAAACAT-T-TAAAATATATA
1 -TTTTGAAAACATATATATAATATATA
716962 TATATATATA
Statistics
Matches: 148, Mismatches: 9, Indels: 33
0.78 0.05 0.17
Matches are distributed among these distances:
18 10 0.07
19 1 0.01
20 1 0.01
21 2 0.01
22 1 0.01
24 10 0.07
25 57 0.39
26 16 0.11
27 28 0.19
28 12 0.08
29 10 0.07
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.40
Consensus pattern (27 bp):
TTTTGAAAACATATATATAATATATAG
Found at i:716949 original size:28 final size:26
Alignment explanation
Indices: 716910--716961 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
716900 ACATAAAACA
*
716910 TTTTGAAAACATATATATAATATATAGT
1 TTTTGAAAACAT-T-TAAAATATATAGT
716938 TTTTGAAAACATTTAAAATATATA
1 TTTTGAAAACATTTAAAATATATA
716962 TATATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 10 0.43
27 1 0.04
28 12 0.52
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (26 bp):
TTTTGAAAACATTTAAAATATATAGT
Found at i:716962 original size:2 final size:2
Alignment explanation
Indices: 716955--716984 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
716945 AACATTTAAA
716955 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
716985 GTTTTTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:716987 original size:49 final size:47
Alignment explanation
Indices: 716920--717023 Score: 138
Period size: 49 Copynumber: 2.1 Consensus size: 47
716910 TTTTGAAAAC
716920 ATATATATAATATATAGTTTTTGAAAACA-TTTAAAATATATATATAT
1 ATATATATAATATATAGTTTTTGAAAACATTTTAAAATATATATA-AT
* *
716967 ATATATATATATAATATAGTTTTTTAAAACATTTTTTTAAATATATATAAT
1 ATATATATA-AT-ATATAGTTTTTGAAAACA--TTTTAAAATATATATAAT
717018 ATATAT
1 ATATAT
717024 TTGTTTTAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
47 9 0.18
48 2 0.04
49 17 0.34
51 8 0.16
52 14 0.28
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (47 bp):
ATATATATAATATATAGTTTTTGAAAACATTTTAAAATATATATAAT
Found at i:718195 original size:10 final size:9
Alignment explanation
Indices: 718183--718234 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
718173 TTTTAGCATT
718183 TTTTTATTA
1 TTTTTATTA
718192 TTTTTTATTA
1 -TTTTTATTA
718202 TTTTT-TTA
1 TTTTTATTA
*
718210 CTTCTTATTA
1 -TTTTTATTA
718220 TTTTTATTA
1 TTTTTATTA
*
718229 CTTTTA
1 TTTTTA
718235 AAATTTAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
8 3 0.08
9 22 0.59
10 12 0.32
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTATTA
Found at i:718205 original size:18 final size:19
Alignment explanation
Indices: 718183--718233 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
718173 TTTTAGCATT
718183 TTTTTATTATTTTTTATTA
1 TTTTTATTATTTTTTATTA
* *
718202 TTTTT-TTACTTCTTATTA
1 TTTTTATTATTTTTTATTA
718220 TTTTTATTACTTTT
1 TTTTTATTA-TTTT
718234 AAAATTTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 16 0.62
19 8 0.31
20 2 0.08
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTATTATTTTTTATTA
Found at i:718294 original size:23 final size:21
Alignment explanation
Indices: 718255--718306 Score: 86
Period size: 23 Copynumber: 2.4 Consensus size: 21
718245 TTTTTTATTT
718255 TTTATTTTATTTTCCCTTTGA
1 TTTATTTTATTTTCCCTTTGA
718276 TTTATTTTATTTTTTCCCTTTGA
1 TTTATTTTA--TTTTCCCTTTGA
718299 TTTATTTT
1 TTTATTTT
718307 TTTATTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 9 0.31
23 20 0.69
ACGTcount: A:0.13, C:0.12, G:0.04, T:0.71
Consensus pattern (21 bp):
TTTATTTTATTTTCCCTTTGA
Found at i:719782 original size:22 final size:22
Alignment explanation
Indices: 719757--719805 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
719747 GATGTATTTA
*
719757 ATTTT-CTATACATATATAAATT
1 ATTTTACTATAAATATA-AAATT
*
719779 ATTTTAATTATAAATATAAAATT
1 ATTTT-ACTATAAATATAAAATT
719802 ATTT
1 ATTT
719806 AAATATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 9 0.39
24 9 0.39
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTTACTATAAATATAAAATT
Found at i:719808 original size:16 final size:15
Alignment explanation
Indices: 719789--719845 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
719779 ATTTTAATTA
719789 TAAATATAAAATTATT
1 TAAATATAAAA-TATT
*
719805 TAAATATTAAAA-AAT
1 TAAATA-TAAAATATT
719820 TAAATATAAAAATATT
1 TAAATAT-AAAATATT
719836 TAAA-ATAAAA
1 TAAATATAAAA
719846 ATTAAATTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 5 0.14
15 14 0.39
16 12 0.33
17 5 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAATATAAAATATT
Found at i:719815 original size:23 final size:24
Alignment explanation
Indices: 719763--719809 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
719753 TTTAATTTTC
* *
719763 TATACATATATAAATTATTTTAAT
1 TATAAATATATAAATTATTTAAAT
719787 TATAAATATA-AAATTATTTAAAT
1 TATAAATATATAAATTATTTAAAT
719810 ATTAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TATAAATATATAAATTATTTAAAT
Found at i:719824 original size:15 final size:14
Alignment explanation
Indices: 719789--719863 Score: 64
Period size: 16 Copynumber: 5.0 Consensus size: 14
719779 ATTTTAATTA
*
719789 TAAATATAAAATTATT
1 TAAATATAAAA--AAT
719805 TAAATATTAAAAAAT
1 TAAATA-TAAAAAAT
719820 TAAATATAAAAATATT
1 TAAATATAAAAA-A-T
719836 TAAA-AT-AAAAAT
1 TAAATATAAAAAAT
719848 TAAATTACTAAAAAAT
1 TAAA-TA-TAAAAAAT
719864 GAATATACAT
Statistics
Matches: 51, Mismatches: 1, Indels: 14
0.77 0.02 0.21
Matches are distributed among these distances:
12 5 0.10
13 1 0.02
14 11 0.22
15 12 0.24
16 17 0.33
17 5 0.10
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAATATAAAAAAT
Found at i:719863 original size:31 final size:31
Alignment explanation
Indices: 719789--719861 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
719779 ATTTTAATTA
*
719789 TAAATATAAAATTATTTAAATATTAAAAAAT
1 TAAATATAAAAATATTTAAATATTAAAAAAT
719820 TAAATATAAAAATATTTAAA-A-T-AAAAAT
1 TAAATATAAAAATATTTAAATATTAAAAAAT
719848 TAAATTACTAAAAA
1 TAAA-TA-TAAAAA
719862 ATGAATATAC
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
28 10 0.26
29 3 0.08
30 7 0.18
31 19 0.49
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (31 bp):
TAAATATAAAAATATTTAAATATTAAAAAAT
Found at i:720273 original size:25 final size:25
Alignment explanation
Indices: 720245--720305 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
720235 TCAATTAGTC
720245 TAAAATTTTTAACTCTCGACTAATT
1 TAAAATTTTTAACTCTCGACTAATT
** * *
720270 TAAAATTTACAAGTCTTGACTAATT
1 TAAAATTTTTAACTCTCGACTAATT
*
720295 T-AATTTTTTAA
1 TAAAATTTTTAA
720306 AATATCAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 7 0.24
25 22 0.76
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (25 bp):
TAAAATTTTTAACTCTCGACTAATT
Found at i:720709 original size:25 final size:25
Alignment explanation
Indices: 720681--720746 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
720671 AGAAAACATA
*
720681 ATAAATTTCGACTAATTCAAAATTT
1 ATAAATCTCGACTAATTCAAAATTT
* * *
720706 ATAAGTCTCGACTAATTTAAATTTT
1 ATAAATCTCGACTAATTCAAAATTT
*
720731 ATAAATCTCGATTAAT
1 ATAAATCTCGACTAAT
720747 CTAATAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (25 bp):
ATAAATCTCGACTAATTCAAAATTT
Found at i:722171 original size:12 final size:12
Alignment explanation
Indices: 722156--722191 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
722146 CCCTTGTACT
722156 ATTATATGTATA
1 ATTATATGTATA
722168 ATTATATGTATA
1 ATTATATGTATA
722180 ATTATATGTATA
1 ATTATATGTATA
722192 GTATAACACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATTATATGTATA
Found at i:726414 original size:18 final size:20
Alignment explanation
Indices: 726400--726441 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
726390 AATTTATTTA
726400 AAAAATATTATTTATAATAT
1 AAAAATATTATTTATAATAT
*
726420 AAATATATTATTTATAGATAT
1 AAAAATATTATTTATA-ATAT
726441 A
1 A
726442 TTATTTGGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AAAAATATTATTTATAATAT
Found at i:726440 original size:15 final size:15
Alignment explanation
Indices: 726417--726447 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
726407 TTATTTATAA
726417 TATAAATATATTATT
1 TATAAATATATTATT
*
726432 TATAGATATATTATT
1 TATAAATATATTATT
726447 T
1 T
726448 GGGGTGGGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TATAAATATATTATT
Found at i:733986 original size:75 final size:75
Alignment explanation
Indices: 733855--734036 Score: 188
Period size: 75 Copynumber: 2.4 Consensus size: 75
733845 TGATTTGGGT
* * * *
733855 TTAATATTATGGTTTGAGT-TTTAAGATTTAACACTTTAATATTATGATTTTATTATGGATTTCA
1 TTAATATTATGGTTTGAATCTTGAA-ATTTGACACTTTAATATTATGATTGTATTATGGATTTCA
* *
733919 TTATTCCAGAG
65 TTATTCCAAAC
* * * *
733930 TTAATATTATGGTTTGAATCTTGAAATTTGACATTTTAATATTGTGGCTTGT-TTATGGATTTTA
1 TTAATATTATGGTTTGAATCTTGAAATTTGACACTTTAATATTAT-GATTGTATTATGGATTTCA
* *
733994 TTGTTCTAAAC
65 TTATTCCAAAC
* * * *
734005 TTAATATTGTTGTTTGACTCTTGATATTTGAC
1 TTAATATTATGGTTTGAATCTTGAAATTTGAC
734037 TTTATTTATA
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
75 81 0.91
76 8 0.09
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (75 bp):
TTAATATTATGGTTTGAATCTTGAAATTTGACACTTTAATATTATGATTGTATTATGGATTTCAT
TATTCCAAAC
Found at i:734377 original size:22 final size:19
Alignment explanation
Indices: 734308--734397 Score: 81
Period size: 19 Copynumber: 4.4 Consensus size: 19
734298 AATGCGATTT
*
734308 TGAAAAATGTGTTGTGATAG
1 TGAAAAA-GTGTTGCGATAG
* * *
734328 TTAAAATGTGTTGCGAGAG
1 TGAAAAAGTGTTGCGATAG
734347 TTTGAAAAACGTGTTATTGCGATAG
1 --TGAAAAA-GTG---TTGCGATAG
734372 TGAAAAAGTGTTGCGATAG
1 TGAAAAAGTGTTGCGATAG
734391 TGAAAAA
1 TGAAAAA
734398 TCCAAAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
19 26 0.46
20 5 0.09
21 5 0.09
22 6 0.11
23 7 0.12
25 8 0.14
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.31
Consensus pattern (19 bp):
TGAAAAAGTGTTGCGATAG
Found at i:734834 original size:21 final size:20
Alignment explanation
Indices: 734810--734881 Score: 67
Period size: 21 Copynumber: 3.6 Consensus size: 20
734800 ATTTTGGAAA
734810 ATCGCAATGCGAACTTCGACT
1 ATCGCAA-GCGAACTTCGACT
* * **
734831 ATCGCAA-CGAATTTGGAAA
1 ATCGCAAGCGAACTTCGACT
*
734850 ATCTCAACGCGAACTTCGACT
1 ATCGCAA-GCGAACTTCGACT
734871 ATCGCAA-CGAA
1 ATCGCAAGCGAA
734882 TTTGGACTAA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
19 18 0.46
21 21 0.54
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAAGCGAACTTCGACT
Found at i:734846 original size:40 final size:40
Alignment explanation
Indices: 734802--734887 Score: 154
Period size: 40 Copynumber: 2.1 Consensus size: 40
734792 TCGTTGCGAT
*
734802 TTTGGAAAATCGCAATGCGAACTTCGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAA
*
734842 TTTGGAAAATCTCAACGCGAACTTCGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAA
734882 TTTGGA
1 TTTGGA
734888 CTAACGTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (40 bp):
TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAA
Found at i:734889 original size:19 final size:19
Alignment explanation
Indices: 734827--734890 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
734817 TGCGAACTTC
734827 GACTATCGCAACGAATTTG
1 GACTATCGCAACGAATTTG
** * * *
734846 GAAAATCTCAACGCGAACTTC
1 GACTATCGCAA--CGAATTTG
734867 GACTATCGCAACGAATTTG
1 GACTATCGCAACGAATTTG
734886 GACTA
1 GACTA
734891 ACGTAAATTT
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
19 19 0.58
21 14 0.42
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (19 bp):
GACTATCGCAACGAATTTG
Found at i:735403 original size:33 final size:33
Alignment explanation
Indices: 735361--735428 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
735351 TTCTTTTTTC
735361 GATTTCTATGACTTATATCAAGTTATTGATGCA
1 GATTTCTATGACTTATATCAAGTTATTGATGCA
735394 GATTTCTATGACTTATATCAAGTTATTGATGCA
1 GATTTCTATGACTTATATCAAGTTATTGATGCA
735427 GA
1 GA
735429 AACTAGACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (33 bp):
GATTTCTATGACTTATATCAAGTTATTGATGCA
Found at i:746554 original size:2 final size:2
Alignment explanation
Indices: 746547--746628 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
746537 TACGGTAAAC
746547 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
746589 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
746629 CAATATCGGA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:749412 original size:16 final size:16
Alignment explanation
Indices: 749391--749423 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
749381 TAAATTTCAC
749391 CATATTTTGTATTTAA
1 CATATTTTGTATTTAA
749407 CATATTTTGTATTTAA
1 CATATTTTGTATTTAA
749423 C
1 C
749424 TTATATAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (16 bp):
CATATTTTGTATTTAA
Found at i:749740 original size:30 final size:29
Alignment explanation
Indices: 749695--749800 Score: 74
Period size: 29 Copynumber: 3.6 Consensus size: 29
749685 AAAAATTATC
*
749695 TTTATAATATTATTAAAATATTTATTTAAT
1 TTTA-AATAATATTAAAATATTTATTTAAT
* * *
749725 TTTAACATCATATT-AATTAATTATTTAA-
1 TTTAA-ATAATATTAAAATATTTATTTAAT
* * * * *
749753 ATTAATATTATTTTTAAATGATCTATTTAAT
1 TTTAA-ATAATATTAAAAT-ATTTATTTAAT
749784 TTTAAATAAT-TTAAAAT
1 TTTAAATAATATTAAAAT
749801 TTAAGTAAAT
Statistics
Matches: 58, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
28 10 0.17
29 22 0.38
30 22 0.38
31 4 0.07
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (29 bp):
TTTAAATAATATTAAAATATTTATTTAAT
Found at i:749895 original size:16 final size:15
Alignment explanation
Indices: 749865--749906 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
749855 TTTTGAAACT
749865 AAATAGATAATTTAA
1 AAATAGATAATTTAA
*
749880 AAATAGTATTATTT-A
1 AAATAG-ATAATTTAA
*
749895 AAATAAATAATT
1 AAATAGATAATT
749907 AACATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 5 0.22
15 12 0.52
16 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (15 bp):
AAATAGATAATTTAA
Found at i:749918 original size:17 final size:18
Alignment explanation
Indices: 749898--749943 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
749888 TTATTTAAAA
749898 TAAATAATTAACAT-TTT
1 TAAATAATTAACATATTT
* *
749915 TAAATAAATAATATGATTT
1 TAAATAATTAACAT-ATTT
749934 TAAA-AATTAA
1 TAAATAATTAA
749944 ATAAATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 12 0.50
18 5 0.21
19 7 0.29
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (18 bp):
TAAATAATTAACATATTT
Found at i:749940 original size:21 final size:20
Alignment explanation
Indices: 749894--749958 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 20
749884 AGTATTATTT
*
749894 AAAATAAATAATTAACATTTT-
1 AAAATAAATAA-T-ATATTTTA
*
749915 TAAATAAATAATATGATTTTA
1 AAAATAAATAATAT-ATTTTA
749936 AAAATTAAATAA-ATATTTTA
1 AAAA-TAAATAATATATTTTA
749956 AAA
1 AAA
749959 TATTTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.03
20 15 0.39
21 15 0.39
22 7 0.18
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
AAAATAAATAATATATTTTA
Found at i:749953 original size:20 final size:22
Alignment explanation
Indices: 749919--749958 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
749909 CATTTTTAAA
749919 TAAATAATATGATTTTAAAAAT
1 TAAATAATATGATTTTAAAAAT
749941 TAAATAA-AT-ATTTTAAAA
1 TAAATAATATGATTTTAAAA
749959 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (22 bp):
TAAATAATATGATTTTAAAAAT
Found at i:749958 original size:19 final size:21
Alignment explanation
Indices: 749891--749959 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
749881 AATAGTATTA
**
749891 TTTAAAA-TAAATAATTAACAT
1 TTTAAAATTAAATAA-TATGAT
*
749912 TTTTAAA-TAAATAATATGAT
1 TTTAAAATTAAATAATATGAT
749932 TTTAAAAATTAAATAA-AT-AT
1 TTT-AAAATTAAATAATATGAT
749952 TTTAAAAT
1 TTTAAAAT
749960 ATTTTTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
19 5 0.12
20 12 0.29
21 18 0.43
22 7 0.17
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (21 bp):
TTTAAAATTAAATAATATGAT
Found at i:751503 original size:56 final size:55
Alignment explanation
Indices: 751443--751560 Score: 134
Period size: 57 Copynumber: 2.1 Consensus size: 55
751433 AATGCATTTC
* *
751443 ATGCATCGATGCA-CATACTATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCGA
1 ATGCATCGATGCACCA-ACCATGCATCGATACACTCAG-GCTATTT-TG-AAACATCGA
* *
751499 ATGCATTTGATGCACCAGCCATGCATCGATACACTCAGGCTATTTTGAAACATCGA
1 ATGCA-TCGATGCACCAACCATGCATCGATACACTCAGGCTATTTTGAAACATCGA
751555 ATGCAT
1 ATGCAT
751561 TTTATACATC
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
55 1 0.02
56 20 0.37
57 28 0.52
58 5 0.09
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (55 bp):
ATGCATCGATGCACCAACCATGCATCGATACACTCAGGCTATTTTGAAACATCGA
Found at i:752381 original size:14 final size:14
Alignment explanation
Indices: 752359--752394 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
752349 AGTTTAATAA
752359 ATTCAAGTCGAGAT
1 ATTCAAGTCGAGAT
* *
752373 ATTCGAGTCGAGTT
1 ATTCAAGTCGAGAT
752387 ATTCAAGT
1 ATTCAAGT
752395 TTCTATGCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (14 bp):
ATTCAAGTCGAGAT
Found at i:753871 original size:13 final size:13
Alignment explanation
Indices: 753853--753881 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
753843 ATTCGAAGAC
753853 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
753866 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
753879 AAA
1 AAA
753882 TTTTATTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:753871 original size:15 final size:15
Alignment explanation
Indices: 753848--753877 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
753838 GCATAATTCG
*
753848 AAGACAAAAAAAAAA
1 AAGAAAAAAAAAAAA
753863 AAGAAAAAAAAAAAA
1 AAGAAAAAAAAAAAA
753878 GAAATTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAAAAA
Found at i:754711 original size:14 final size:14
Alignment explanation
Indices: 754692--754720 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
754682 CATTCAGATC
754692 TGAATCTAACTAAT
1 TGAATCTAACTAAT
754706 TGAATCTAACTAAT
1 TGAATCTAACTAAT
754720 T
1 T
754721 AAGTAATTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (14 bp):
TGAATCTAACTAAT
Found at i:759390 original size:2 final size:2
Alignment explanation
Indices: 759385--759438 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
759375 TTAAACTTTG
759385 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
*
759427 AT AT AT TT AT AT
1 AT AT AT AT AT AT
759439 GAAAATTTCT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:760137 original size:15 final size:15
Alignment explanation
Indices: 760117--760145 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
760107 CTCAGTTAGT
760117 TTCGTTAAAAAATAC
1 TTCGTTAAAAAATAC
760132 TTCGTTAAAAAATA
1 TTCGTTAAAAAATA
760146 AAATGATAAA
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:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (15 bp):
TTCGTTAAAAAATAC
Found at i:761711 original size:13 final size:13
Alignment explanation
Indices: 761688--761750 Score: 63
Period size: 13 Copynumber: 4.5 Consensus size: 13
761678 GTCACAACCC
761688 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
761701 TACCTGACCCGTT
1 GACCCGACCCGTT
761714 GACCCGACCCAACCTGTT
1 GACCCGA--C--CC-GTT
761732 GACCCGACCCGTT
1 GACCCGACCCGTT
761745 GACCCG
1 GACCCG
761751 TTGACCGTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 25 0.61
14 2 0.05
15 1 0.02
16 1 0.02
17 2 0.05
18 10 0.24
ACGTcount: A:0.17, C:0.44, G:0.21, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:761722 original size:31 final size:31
Alignment explanation
Indices: 761684--761750 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
761674 ATCGGTCACA
* * *
761684 ACCCGACCCGACCCGTTTACCTGACCCGTTG
1 ACCCGACCCAACCCGTTGACCCGACCCGTTG
*
761715 ACCCGACCCAACCTGTTGACCCGACCCGTTG
1 ACCCGACCCAACCCGTTGACCCGACCCGTTG
761746 ACCCG
1 ACCCG
761751 TTGACCGTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.18, C:0.46, G:0.19, T:0.16
Consensus pattern (31 bp):
ACCCGACCCAACCCGTTGACCCGACCCGTTG
Found at i:761760 original size:15 final size:17
Alignment explanation
Indices: 761740--761773 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
761730 TTGACCCGAC
761740 CCGTTGACC-C-GTTGA
1 CCGTTGACCACTGTTGA
761755 CCGTTGACCACTGTTGA
1 CCGTTGACCACTGTTGA
761772 CC
1 CC
761774 AAAACTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 1 0.06
17 7 0.41
ACGTcount: A:0.15, C:0.35, G:0.24, T:0.26
Consensus pattern (17 bp):
CCGTTGACCACTGTTGA
Found at i:763088 original size:18 final size:18
Alignment explanation
Indices: 763062--763096 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
763052 TCAAAATGAC
*
763062 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
763080 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
763097 CCGGATGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:764099 original size:12 final size:12
Alignment explanation
Indices: 764084--764152 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
764074 GATAGGTTAC
764084 CTGAATTCTGTT
1 CTGAATTCTGTT
*
764096 CTG-ATTCTGAT
1 CTGAATTCTGTT
*
764107 CTGGATTCTGTT
1 CTGAATTCTGTT
*
764119 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
*
764131 ATGAATTCTGTT
1 CTGAATTCTGTT
* *
764143 TTGATTTCTG
1 CTGAATTCTG
764153 ATATCTCCGT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
11 12 0.26
12 33 0.70
13 2 0.04
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.49
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:764138 original size:24 final size:23
Alignment explanation
Indices: 764085--764156 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 23
764075 ATAGGTTACC
*
764085 TGAATTCTGTTCTGATTCTGATC
1 TGAATTCTGTTCTGATTCTGATA
*
764108 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGAT-TCTGATA
*
764132 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGA-TTCTGATA
764156 T
1 T
764157 CTCCGTTTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
23 15 0.35
24 27 0.63
25 1 0.02
ACGTcount: A:0.19, C:0.12, G:0.18, T:0.50
Consensus pattern (23 bp):
TGAATTCTGTTCTGATTCTGATA
Found at i:768164 original size:27 final size:27
Alignment explanation
Indices: 768126--768186 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
768116 TTAACCTAAA
768126 GAACCTTACCATCAAACCCAAATGACT
1 GAACCTTACCATCAAACCCAAATGACT
768153 GAACCTTACCATCAAACCCAAATGACT
1 GAACCTTACCATCAAACCCAAATGACT
*
768180 AAACCTT
1 GAACCTT
768187 GGAACAACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.41, C:0.33, G:0.07, T:0.20
Consensus pattern (27 bp):
GAACCTTACCATCAAACCCAAATGACT
Found at i:771834 original size:2 final size:2
Alignment explanation
Indices: 771829--771914 Score: 77
Period size: 2 Copynumber: 42.5 Consensus size: 2
771819 CTCTCAACTC
771829 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
* * * * * *
771871 CA TA TG TA AA AA TA TCA CA -A TA TA TA TA TA TG TA TA TCA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA T-A TA TA
771914 T
1 T
771915 GGTTATAAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
1 2 0.03
2 64 0.91
3 4 0.06
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (2 bp):
TA
Found at i:773855 original size:21 final size:19
Alignment explanation
Indices: 773822--773861 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
773812 TTTCTATAAG
*
773822 ATTTTTTTCTTAAAATAAAT
1 ATTTTTTTATT-AAATAAAT
773842 ATTTATTTTATTAAATAAAT
1 ATTT-TTTTATTAAATAAAT
773862 CTAACTACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTTTTTATTAAATAAAT
Found at i:774428 original size:19 final size:18
Alignment explanation
Indices: 774394--774440 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
774384 TATTAAATGT
774394 ATCCCAAAAC-TCGGTAAAG
1 ATCCCAAAACATCGGT--AG
*
774413 ATCCCAAAACAT-GGTAT
1 ATCCCAAAACATCGGTAG
774430 ATCCCAAAACA
1 ATCCCAAAACA
774441 CTCTTCCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 12 0.46
19 13 0.50
20 1 0.04
ACGTcount: A:0.45, C:0.28, G:0.11, T:0.17
Consensus pattern (18 bp):
ATCCCAAAACATCGGTAG
Found at i:776023 original size:18 final size:18
Alignment explanation
Indices: 776002--776046 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
775992 AAATTTTAGG
776002 AATTTAATAATAATA-AAA
1 AATTTAA-AATAATATAAA
*
776020 AATTT-AAATTATATAAA
1 AATTTAAAATAATATAAA
776037 AATTTAAAAT
1 AATTTAAAAT
776047 TCAAAATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 6 0.25
17 9 0.38
18 9 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTTAAAATAATATAAA
Found at i:776047 original size:18 final size:17
Alignment explanation
Indices: 776002--776047 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
775992 AAATTTTAGG
*
776002 AATTTAATAATAATAAAA
1 AATTTAA-AATTATAAAA
776020 AATTT-AAATTATATAAA
1 AATTTAAAATTATA-AAA
776037 AATTTAAAATT
1 AATTTAAAATT
776048 CAAAATACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 6 0.24
17 9 0.36
18 10 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTTAAAATTATAAAA
Found at i:776929 original size:25 final size:26
Alignment explanation
Indices: 776882--776932 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
776872 TTCGATTTGA
* *
776882 TTCGATTCGATTCTAACTTTAAACTT
1 TTCGAATCGAATCTAACTTTAAACTT
776908 TTCGAATCGAATC-AACTTTAAACTT
1 TTCGAATCGAATCTAACTTTAAACTT
776933 AATTCCCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (26 bp):
TTCGAATCGAATCTAACTTTAAACTT
Found at i:780706 original size:29 final size:28
Alignment explanation
Indices: 780673--780827 Score: 121
Period size: 29 Copynumber: 5.4 Consensus size: 28
780663 ATACTGATGT
*
780673 GTCCTGATTCTGTATGAGATTATACCACC
1 GTCCTGATTCTGCATGAGATTATACC-CC
* * *
780702 GTCCTGATTCTACATGGGATTGTATCCCC
1 GTCCTGATTCTGCATGAGATTATA-CCCC
* * * *
780731 ATCCTGATTTTGCAGGAGATTATATCTCC
1 GTCCTGATTCTGCATGAGATTATA-CCCC
** * * *
780760 GTTTTGATTCTGTATGGGATTATATCCCT
1 GTCCTGATTCTGCATGAGATTATA-CCCC
* * *
780789 GTCCTGTTTCTGCATAAGATTATATCCC
1 GTCCTGATTCTGCATGAGATTATACCCC
*
780817 GTCCTGTTTCT
1 GTCCTGATTCT
780828 ATTTGGGATA
Statistics
Matches: 97, Mismatches: 28, Indels: 3
0.76 0.22 0.02
Matches are distributed among these distances:
28 13 0.13
29 82 0.85
30 2 0.02
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (28 bp):
GTCCTGATTCTGCATGAGATTATACCCC
Found at i:780754 original size:58 final size:57
Alignment explanation
Indices: 780674--780828 Score: 159
Period size: 58 Copynumber: 2.7 Consensus size: 57
780664 TACTGATGTG
* * * *
780674 TCCTGATTCTGTATGAGATTATACCACCGTCCTGATTCTACATGGGATTGTATCCCCA
1 TCCTGATTTTGCATGAGATTATATC-CCGTCCTGATTCTACATGGGATTATATCCCCA
* ** ** **
780732 TCCTGATTTTGCAGGAGATTATATCTCCGTTTTGATTCTGTATGGGATTATATCCCTG
1 TCCTGATTTTGCATGAGATTATATC-CCGTCCTGATTCTACATGGGATTATATCCCCA
* *
780790 TCCTG-TTTCTGCATAAGATTATATCCCGTCCTGTTTCTA
1 TCCTGATTT-TGCATGAGATTATATCCCGTCCTGATTCTA
780829 TTTGGGATAC
Statistics
Matches: 78, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
57 13 0.17
58 65 0.83
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (57 bp):
TCCTGATTTTGCATGAGATTATATCCCGTCCTGATTCTACATGGGATTATATCCCCA
Found at i:784099 original size:22 final size:22
Alignment explanation
Indices: 784047--784115 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
784037 CAAAGAAACT
*
784047 AAAAATAT-AATGAAAATA-AA
1 AAAAATATAAATAAAAATATAA
*
784067 TAAATAGTATAAAT-AAAATATTAA
1 -AAA-AATATAAATAAAAATA-TAA
*
784091 AAAAATATATATAAAAATATAA
1 AAAAATATAAATAAAAATATAA
784113 AAA
1 AAA
784116 TGTATGTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
21 3 0.08
22 23 0.57
23 12 0.30
24 2 0.05
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (22 bp):
AAAAATATAAATAAAAATATAA
Found at i:784100 original size:13 final size:12
Alignment explanation
Indices: 784062--784115 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 12
784052 TATAATGAAA
*
784062 ATAAATAAATAGT
1 ATAAAAAAATA-T
784075 ATAAATAAAATAT
1 ATAAA-AAAATAT
784088 -TAAAAAAATAT
1 ATAAAAAAATAT
*
784099 ATATAAAAATAT
1 ATAAAAAAATAT
784111 A-AAAA
1 ATAAAA
784116 TGTATGTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.28
12 15 0.42
13 6 0.17
14 5 0.14
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (12 bp):
ATAAAAAAATAT
Found at i:784126 original size:22 final size:23
Alignment explanation
Indices: 784063--784115 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 23
784053 ATAATGAAAA
* *
784063 TAAATAAATAGTATAAATAAAATAT
1 TAAAAAAATA-TATATA-AAAATAT
784088 TAAAAAAATATATATAAAAATA-
1 TAAAAAAATATATATAAAAATAT
784110 TAAAAA
1 TAAAAA
784116 TGTATGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 6 0.23
23 6 0.23
24 5 0.19
25 9 0.35
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
TAAAAAAATATATATAAAAATAT
Found at i:784136 original size:44 final size:44
Alignment explanation
Indices: 784047--784136 Score: 103
Period size: 44 Copynumber: 2.0 Consensus size: 44
784037 CAAAGAAACT
* *
784047 AAAAATATAATGAAAATAAATAAATAGTATAAATAAAATATTAA
1 AAAAATATAATAAAAATAAATAAATAGTATAAATAAAATAATAA
** *
784091 AAAAATATATATAAAAATATAA-AAAT-GTATGTATAATATAATAA
1 AAAAATATA-ATAAAAATA-AATAAATAGTATAAATAAAATAATAA
784135 AA
1 AA
784137 TACTAAATAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
44 25 0.64
45 12 0.31
46 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (44 bp):
AAAAATATAATAAAAATAAATAAATAGTATAAATAAAATAATAA
Found at i:784166 original size:23 final size:23
Alignment explanation
Indices: 784050--784179 Score: 74
Period size: 23 Copynumber: 5.4 Consensus size: 23
784040 AGAAACTAAA
784050 AATATAATGAAAATAAATAAATAGT
1 AATATAAT-AAAAT-AATAAATAGT
* *
784075 -ATA-AATAAAATATTAAA-A-A
1 AATATAATAAAATAATAAATAGT
*
784094 AATATATATAAAAATATAAAAATGTATGTAT
1 AATATA-AT-AAAATA-ATAAA--TA-G--T
*
784125 AATATAATAAAATACTAAATAGT
1 AATATAATAAAATAATAAATAGT
784148 AATAATAATAAAA-AATAAATA-T
1 AAT-ATAATAAAATAATAAATAGT
784170 ACATATAATA
1 A-ATATAATA
784180 TTAACTAAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 31
0.68 0.07 0.25
Matches are distributed among these distances:
20 4 0.05
21 6 0.07
22 15 0.18
23 22 0.27
24 15 0.18
25 1 0.01
26 2 0.02
27 1 0.01
28 3 0.04
29 6 0.07
30 2 0.02
31 6 0.07
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (23 bp):
AATATAATAAAATAATAAATAGT
Found at i:784237 original size:2 final size:2
Alignment explanation
Indices: 784230--784290 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
784220 TAAAGTAAGA
784230 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
784272 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
784291 ACATTAGGAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:784380 original size:20 final size:21
Alignment explanation
Indices: 784323--784387 Score: 58
Period size: 23 Copynumber: 3.0 Consensus size: 21
784313 AAACATAGTA
* * *
784323 AATAAGTAAACATAGATAAAAT
1 AATAAGAAAATATA-ATATAAT
*
784345 AATAATAATAATATATATATAAT
1 AATAAGAA-AATATA-ATATAAT
*
784368 AATAGGAAAATATAATATAA
1 AATAAGAAAATATAATATAA
784388 CACAAAGAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
21 6 0.17
22 12 0.34
23 17 0.49
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (21 bp):
AATAAGAAAATATAATATAAT
Found at i:784428 original size:23 final size:24
Alignment explanation
Indices: 784397--784444 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
784387 ACACAAAGAA
*
784397 AAATGAAAAACAATTATAA-TAAAT
1 AAATGAAAAA-AAATATAATTAAAT
784421 AAAT-AAAAAAAATATAATTAAAT
1 AAATGAAAAAAAATATAATTAAAT
784444 A
1 A
784445 TATACATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 11 0.50
24 4 0.18
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (24 bp):
AAATGAAAAAAAATATAATTAAAT
Found at i:784910 original size:37 final size:37
Alignment explanation
Indices: 784869--784953 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
784859 GGATCATATC
* *
784869 TTTAGGAGTTTAAATAATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
* ** *
784906 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCCTATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
784943 TTTAGGAGTTT
1 TTTAGGAGTTT
784954 GAATCCTAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (37 bp):
TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
Done.