Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397258.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4.1, 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: 11097736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 71999 characters in sequence are not A, C, G, or T
File 3 of 22
Found at i:1077468 original size:72 final size:72
Alignment explanation
Indices: 1077383--1077559 Score: 248
Period size: 72 Copynumber: 2.5 Consensus size: 72
1077373 ATAAGTTATT
* * * *
1077383 TGGTTCAATTCCTTCTACTCTAGGTAAGTTAACCAATTTAGAGACCCTGTATTTGTTTTGTAACT
1 TGGTTCAATTCCTTCCACTCTAGGTAAGTTAACCAATTTAGAGACCCTATATTTGTCTTATAACT
1077448 -CACTTAA
66 AC-CTTAA
* * * *
1077455 TGGTTCCATTCCTTCCACTCTAGGTGACTTAACCAATTTAGAGATCCTATATTTGTCTTATAACT
1 TGGTTCAATTCCTTCCACTCTAGGTAAGTTAACCAATTTAGAGACCCTATATTTGTCTTATAACT
*
1077520 ACCTTGA
66 ACCTTAA
*
1077527 TGGTTCGATTCCTTCCACTCTAGGTAAGTTAAC
1 TGGTTCAATTCCTTCCACTCTAGGTAAGTTAAC
1077560 AAAACTGCAA
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
72 91 0.99
73 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (72 bp):
TGGTTCAATTCCTTCCACTCTAGGTAAGTTAACCAATTTAGAGACCCTATATTTGTCTTATAACT
ACCTTAA
Found at i:1078939 original size:3 final size:3
Alignment explanation
Indices: 1078931--1078962 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1078921 AGGATCATTA
*
1078931 ATT ATT ATT ATT ATT ATT AGT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1078963 GTTTTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1080603 original size:15 final size:16
Alignment explanation
Indices: 1080583--1080621 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
1080573 AATAAGAAAT
1080583 TTTTTAAAATA-ATTC
1 TTTTTAAAATATATTC
*
1080598 TTTTTAAAATATATTT
1 TTTTTAAAATATATTC
1080614 TTTTTAAA
1 TTTTTAAA
1080622 CCGCAAGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTTAAAATATATTC
Found at i:1085108 original size:40 final size:38
Alignment explanation
Indices: 1085064--1085185 Score: 126
Period size: 40 Copynumber: 3.2 Consensus size: 38
1085054 TTTATTAAAA
* *
1085064 AATATTTTTAATTTTAATAATATTAAATCAATTAAATATT
1 AATATTTTTAATTTTAATAATATT--TTAAATTAAATATT
* *
1085104 AATA-TTTTAA-ATTAA-AATTTTTTAAATTAAATATT
1 AATATTTTTAATTTTAATAATATTTTAAATTAAATATT
*
1085139 AATATGTTATTAATTTT-TTAACTATTTTAAATTAAATATT
1 AATAT-TT-TTAATTTTAATAA-TATTTTAAATTAAATATT
1085179 AATATTT
1 AATATTT
1085186 ATCAAATCTA
Statistics
Matches: 69, Mismatches: 7, Indels: 13
0.78 0.08 0.15
Matches are distributed among these distances:
35 16 0.23
37 7 0.10
38 8 0.12
39 12 0.17
40 26 0.38
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (38 bp):
AATATTTTTAATTTTAATAATATTTTAAATTAAATATT
Found at i:1091620 original size:60 final size:60
Alignment explanation
Indices: 1091535--1091654 Score: 170
Period size: 60 Copynumber: 2.0 Consensus size: 60
1091525 CAGCTTCCTG
* * *
1091535 AACTTAGCAAAGGTGACTCTTGGTAGCTCTAACCATACTAG-CATAAACATATGCTTCAGC
1 AACTCAGCAAAGGTAACTCTAGGTAGCTCTAACCATACT-GCCATAAACATATGCTTCAGC
* * *
1091595 AACTCAGCAAAGGTAACTCTAGGTAGCTCTAACTATACTGCCATAAGCGTATGCTTCAGC
1 AACTCAGCAAAGGTAACTCTAGGTAGCTCTAACCATACTGCCATAAACATATGCTTCAGC
1091655 TCGATGGCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 1 0.02
60 52 0.98
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (60 bp):
AACTCAGCAAAGGTAACTCTAGGTAGCTCTAACCATACTGCCATAAACATATGCTTCAGC
Found at i:1093754 original size:22 final size:22
Alignment explanation
Indices: 1093728--1093776 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1093718 CTGACTTTGG
**
1093728 GTATTGCGTGACTAGTTTTTAA
1 GTATTGCGTGACTAAATTTTAA
*
1093750 GTATTGTGTGACTAAATTTTAA
1 GTATTGCGTGACTAAATTTTAA
1093772 GTATT
1 GTATT
1093777 ATATGACTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.27, C:0.06, G:0.20, T:0.47
Consensus pattern (22 bp):
GTATTGCGTGACTAAATTTTAA
Found at i:1093783 original size:22 final size:22
Alignment explanation
Indices: 1093744--1093786 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1093734 CGTGACTAGT
* *
1093744 TTTTAAGTATTGTGTGACTAAA
1 TTTTAAGTATTATATGACTAAA
1093766 TTTTAAGTATTATATGACTAA
1 TTTTAAGTATTATATGACTAA
1093787 CTTTGGGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (22 bp):
TTTTAAGTATTATATGACTAAA
Found at i:1093893 original size:23 final size:23
Alignment explanation
Indices: 1093867--1093920 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1093857 TGCATGATTT
* *
1093867 GTTAGTAAGGCATTGCTTAACTA
1 GTTAGTAAGGCATTACGTAACTA
* *
1093890 GTTAATAAGGCATTACGTGACTA
1 GTTAGTAAGGCATTACGTAACTA
1093913 GTTAGTAA
1 GTTAGTAA
1093921 AACATTATGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (23 bp):
GTTAGTAAGGCATTACGTAACTA
Found at i:1093926 original size:23 final size:23
Alignment explanation
Indices: 1093886--1093934 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1093876 GCATTGCTTA
**
1093886 ACTAGTTAATAAGGCATTACGTG
1 ACTAGTTAATAAAACATTACGTG
* *
1093909 ACTAGTTAGTAAAACATTATGTG
1 ACTAGTTAATAAAACATTACGTG
1093932 ACT
1 ACT
1093935 TAGACATTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (23 bp):
ACTAGTTAATAAAACATTACGTG
Found at i:1094066 original size:22 final size:22
Alignment explanation
Indices: 1094035--1094079 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1094025 GTAGTAATTA
1094035 AGTTTGGCAATACTTAAAAACT
1 AGTTTGGCAATACTTAAAAACT
*
1094057 AGTTTTGCAATACTTAAAAACT
1 AGTTTGGCAATACTTAAAAACT
1094079 A
1 A
1094080 ATCTAATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.33
Consensus pattern (22 bp):
AGTTTGGCAATACTTAAAAACT
Found at i:1096880 original size:26 final size:27
Alignment explanation
Indices: 1096842--1096893 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1096832 TATATAAATA
*
1096842 AATTTTGAAAA-TTATTTAAAAGAATC
1 AATTTTGAAAATTTAGTTAAAAGAATC
1096868 AATTTT-AATAATTTAGTTAAAAGAAT
1 AATTTTGAA-AATTTAGTTAAAAGAAT
1096894 TAACTAGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 2 0.09
26 8 0.35
27 13 0.57
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (27 bp):
AATTTTGAAAATTTAGTTAAAAGAATC
Found at i:1103489 original size:148 final size:148
Alignment explanation
Indices: 1103280--1103576 Score: 594
Period size: 148 Copynumber: 2.0 Consensus size: 148
1103270 AGATCTTGGC
1103280 ACCCTTTTGATAAATAAGCATGAATATATTATATTCATGCTAAATGGGATTACGTATAATGTACC
1 ACCCTTTTGATAAATAAGCATGAATATATTATATTCATGCTAAATGGGATTACGTATAATGTACC
1103345 ATCACCTCATTTCTATGTTAGACTATTTTCTTTATTAAACCAAGCATTATATTAAAAATCATAAA
66 ATCACCTCATTTCTATGTTAGACTATTTTCTTTATTAAACCAAGCATTATATTAAAAATCATAAA
1103410 CGATATATAAATTCGACT
131 CGATATATAAATTCGACT
1103428 ACCCTTTTGATAAATAAGCATGAATATATTATATTCATGCTAAATGGGATTACGTATAATGTACC
1 ACCCTTTTGATAAATAAGCATGAATATATTATATTCATGCTAAATGGGATTACGTATAATGTACC
1103493 ATCACCTCATTTCTATGTTAGACTATTTTCTTTATTAAACCAAGCATTATATTAAAAATCATAAA
66 ATCACCTCATTTCTATGTTAGACTATTTTCTTTATTAAACCAAGCATTATATTAAAAATCATAAA
1103558 CGATATATAAATTCGACT
131 CGATATATAAATTCGACT
1103576 A
1 A
1103577 ATTATATTAC
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
148 149 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.37
Consensus pattern (148 bp):
ACCCTTTTGATAAATAAGCATGAATATATTATATTCATGCTAAATGGGATTACGTATAATGTACC
ATCACCTCATTTCTATGTTAGACTATTTTCTTTATTAAACCAAGCATTATATTAAAAATCATAAA
CGATATATAAATTCGACT
Found at i:1122891 original size:1 final size:1
Alignment explanation
Indices: 1122885--1122931 Score: 94
Period size: 1 Copynumber: 47.0 Consensus size: 1
1122875 GCCAACCACA
1122885 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1122932 TTCCCCACTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1127406 original size:2 final size:2
Alignment explanation
Indices: 1127399--1127452 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1127389 CCAATGGATG
1127399 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1127441 TC TC TC TC TC TC
1 TC TC TC TC TC TC
1127453 NNNNNNNNNN
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1143335 original size:45 final size:45
Alignment explanation
Indices: 1143275--1143420 Score: 193
Period size: 45 Copynumber: 3.2 Consensus size: 45
1143265 CACTTTTGGA
*
1143275 GCATCTTCATCCGCAGCAAGTTCAACAGGTTCATCTTTATTCGGG
1 GCATCTTCATCCGCAGCAAGTACAACAGGTTCATCTTTATTCGGG
* * *
1143320 GCAACTTCATTCGCAGCGAGTACAACAGGTTCATCTTTATTCGGG
1 GCATCTTCATCCGCAGCAAGTACAACAGGTTCATCTTTATTCGGG
* * * ** * *
1143365 CCATCTTCACCCACAGCTGGTACAACAGGTTCGTCTTTATTCGTG
1 GCATCTTCATCCGCAGCAAGTACAACAGGTTCATCTTTATTCGGG
1143410 GCATCTTCATC
1 GCATCTTCATC
1143421 GGCTTCTACT
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 86 1.00
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (45 bp):
GCATCTTCATCCGCAGCAAGTACAACAGGTTCATCTTTATTCGGG
Found at i:1153090 original size:16 final size:16
Alignment explanation
Indices: 1153071--1153109 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1153061 ATTAAATGTT
1153071 TAAAAAATTTTCAAAA
1 TAAAAAATTTTCAAAA
*
1153087 T-AAATATTTTCAAAA
1 TAAAAAATTTTCAAAA
*
1153102 TAACAAAT
1 TAAAAAAT
1153110 AAATTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAAAATTTTCAAAA
Found at i:1161658 original size:31 final size:31
Alignment explanation
Indices: 1161616--1161692 Score: 147
Period size: 31 Copynumber: 2.5 Consensus size: 31
1161606 GATTACTTGG
1161616 TAAA-AAATACATGGCCAAATTTTCAAAAAA
1 TAAACAAATACATGGCCAAATTTTCAAAAAA
1161646 TAAACAAATACATGGCCAAATTTTCAAAAAA
1 TAAACAAATACATGGCCAAATTTTCAAAAAA
1161677 TAAACAAATACATGGC
1 TAAACAAATACATGGC
1161693 TTGCACAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 4 0.09
31 42 0.91
ACGTcount: A:0.55, C:0.16, G:0.08, T:0.22
Consensus pattern (31 bp):
TAAACAAATACATGGCCAAATTTTCAAAAAA
Found at i:1164094 original size:16 final size:16
Alignment explanation
Indices: 1164068--1164101 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1164058 TTATATATAT
1164068 TTAGATTTAGATGTAAA
1 TTAGATTTAGAT-TAAA
1164085 TTAG-TTTAGATTAAA
1 TTAGATTTAGATTAAA
1164100 TT
1 TT
1164102 TAAGATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 7 0.41
17 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (16 bp):
TTAGATTTAGATTAAA
Found at i:1170530 original size:14 final size:15
Alignment explanation
Indices: 1170504--1170536 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1170494 TACAATCTAA
1170504 AATT-ATCACATTAT
1 AATTAATCACATTAT
1170518 AATTAATCA-ATTAT
1 AATTAATCACATTAT
1170532 AATTA
1 AATTA
1170537 TTTTTACTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTAATCACATTAT
Found at i:1172158 original size:17 final size:18
Alignment explanation
Indices: 1172131--1172167 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1172121 GACAGGTTCT
*
1172131 TTTTAATCAGTCAGGTTG
1 TTTTAATCAGTCAGCTTG
1172149 TTTT-ATCAGTCAGCTTG
1 TTTTAATCAGTCAGCTTG
1172166 TT
1 TT
1172168 CCTTGCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (18 bp):
TTTTAATCAGTCAGCTTG
Found at i:1176605 original size:2 final size:2
Alignment explanation
Indices: 1176598--1176640 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1176588 CCTTTTTCTT
* *
1176598 TA TA TA TA TA TA TG TA TG 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
1176640 T
1 T
1176641 TCGAAGCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1177854 original size:2 final size:2
Alignment explanation
Indices: 1177847--1177875 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1177837 TCCTCCACCT
1177847 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1177876 CAGAAAGAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1192727 original size:15 final size:15
Alignment explanation
Indices: 1192709--1192738 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1192699 ATTTTGTTAG
*
1192709 GTATTTGATTGTCGA
1 GTATGTGATTGTCGA
1192724 GTATGTGATTGTCGA
1 GTATGTGATTGTCGA
1192739 AAAGATAAGT
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:0.20, C:0.07, G:0.30, T:0.43
Consensus pattern (15 bp):
GTATGTGATTGTCGA
Found at i:1192886 original size:20 final size:21
Alignment explanation
Indices: 1192844--1192886 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
1192834 AATACTTCAT
*
1192844 TAAAAATATAATATAAATTTA
1 TAAAAATATAATATAAATATA
* *
1192865 TAAAATTAT-ATATATATATA
1 TAAAAATATAATATAAATATA
1192885 TA
1 TA
1192887 CATGAAAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAAAATATAATATAAATATA
Found at i:1194405 original size:29 final size:28
Alignment explanation
Indices: 1194336--1194407 Score: 74
Period size: 30 Copynumber: 2.5 Consensus size: 28
1194326 TTCAACTATT
* *
1194336 TAAATAAAATTTATTTTTTTATTACAAT
1 TAAATAAATTTTATTTTTTTATTACAAA
* *
1194364 TAATTAAATTTTTATATTTTTATTTTA-AAA
1 TAAATAAA-TTTTAT-TTTTT-TATTACAAA
1194394 TAAATAAATTTTAT
1 TAAATAAATTTTAT
1194408 GAGTAATAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 7 0.19
29 11 0.31
30 14 0.39
31 4 0.11
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (28 bp):
TAAATAAATTTTATTTTTTTATTACAAA
Found at i:1227568 original size:25 final size:25
Alignment explanation
Indices: 1227535--1227591 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 25
1227525 TTAAATAAAT
*
1227535 TTTTATAAT-TAATGATTATTTAATTA
1 TTTTATAATATAAT-ATTATAT-ATTA
1227561 TTTT-TAATCATAATATTATATATTA
1 TTTTATAAT-ATAATATTATATATTA
1227586 TTTTAT
1 TTTTAT
1227592 GTCAGATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
25 12 0.44
26 11 0.41
27 4 0.15
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTTATAATATAATATTATATATTA
Found at i:1228843 original size:102 final size:102
Alignment explanation
Indices: 1228665--1228911 Score: 300
Period size: 102 Copynumber: 2.4 Consensus size: 102
1228655 GATGGTGATG
* * * * *
1228665 AGAATCGGCGGAGAGAACGCTT-TGGAGCTTTTGATGAAGAAGACAAGCGTGCCAATAGAGATAG
1 AGAATAGGCGGAGAGAAC-ATTCGGGATCTTCTGATGAAGAAGACAAGCGTGCCAATAGAGATAG
* * * **
1228729 GAAGCGAGAAAGAGAAAGAATTCGTGATGATGATGTTA
65 GAAGCGAGAAAGAGAAAAAATTCATGATGATGAGGAGA
* * * *
1228767 AGGATAGGCGGAGAGAACATTCGGGATCTTCTGATGAAGAAGACGAGCTTGGCAATAGAGAT-GG
1 AGAATAGGCGGAGAGAACATTCGGGATCTTCTGATGAAGAAGACAAGCGTGCCAATAGAGATAGG
*
1228831 AAGGCGAGAAAGAGAAAAAATTCATGATGATGAGGAGG
66 AA-GCGAGAAAGAGAAAAAATTCATGATGATGAGGAGA
* * *
1228869 AGAATAGGCGGAGAGAGCATTCTGGATCTTCTGATGAGGAAGA
1 AGAATAGGCGGAGAGAACATTCGGGATCTTCTGATGAAGAAGA
1228912 AGGCAAACAT
Statistics
Matches: 124, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
101 6 0.05
102 118 0.95
ACGTcount: A:0.37, C:0.11, G:0.34, T:0.19
Consensus pattern (102 bp):
AGAATAGGCGGAGAGAACATTCGGGATCTTCTGATGAAGAAGACAAGCGTGCCAATAGAGATAGG
AAGCGAGAAAGAGAAAAAATTCATGATGATGAGGAGA
Found at i:1229112 original size:330 final size:330
Alignment explanation
Indices: 1228505--1229277 Score: 1022
Period size: 330 Copynumber: 2.3 Consensus size: 330
1228495 AAGGCGTGGA
*
1228505 AGAGAAAGAGACAGGAATT-ATGATGAGGAGGAGGAGAATAGGCGGAGAGAGCATTCTGGATCTT
1 AGAGAAAGAGA-AGGAATTCATGATGATGAGGAGGAGAATAGGCGGAGAGAGCATTCTGGATCTT
* *
1228569 CTGATGAGGAAGAAGGCAAGCGTGGTAATAGAGATAGAAGGCGCGGAAA-CGAAAGGGAAAGAGG
65 CTGATGAGGAAGAAGGCAAGCATGCTAATAGAGATAGAAGGCGC-GAAAGCGAAAGGGAAAGAGG
* * * * * *
1228633 ACAAGAGAGGAATCAAGATGGCGATGGTGATGAGAATCGGCGGAGAGAACGCTTTGGAGCTTTTG
129 AAAAGAAAGAAATCAAGATGGCGATGGTGATGAGAATAGGCAGAGAGAACGCTCTGGAGCTTTTG
* * * *
1228698 ATGAAGAAGACAAGCGTGCCAATAGAGATAGGAAGCGAGAAAGAGAAAGAATTCGTGATGATGAT
194 ATGAAGAAGACAAGCGTGCCAATAGAGATAGAAAACGAGAAAGACAAAGAATTCATGATGATGAT
* * * * * *
1228763 GTTAAGGATAGGCGGAGAGAACATTC-GGGATCTTCTGATGAAGAAGACGAGCTTGGCAATAGAG
259 GCTAAGAATAGGCGGAGAGAACACTCTGGG-TCTTCGGATGAAGAAGACAAGCTTGACAATAGAG
*
1228827 ATGGAAGG
323 ATAGAAGG
* **
1228835 CGAGAAAGAGAAAAAATTCATGATGATGAGGAGGAGAATAGGCGGAGAGAGCATTCTGGATCTTC
1 AGAGAAAGAGAAGGAATTCATGATGATGAGGAGGAGAATAGGCGGAGAGAGCATTCTGGATCTTC
* * * *
1228900 TGATGAGGAAGAAGGCAAACATGCTAATAGAGGTAGGAGGCGCGAAAGTGAAAGAGG-AAGAGGA
66 TGATGAGGAAGAAGGCAAGCATGCTAATAGAGATAGAAGGCGCGAAAGCGAAAG-GGAAAGAGGA
* * * *
1228964 AAAGAAAGAAATCAAGATGGTGATGTTGGTGAGAATAGGCAGAGAGAACG-TCCTGGATCTTTTG
130 AAAGAAAGAAATCAAGATGGCGATGGTGATGAGAATAGGCAGAGAGAACGCT-CTGGAGCTTTTG
*
1229028 ATGAAGAAGACAAGTC-TGCCAATAGAGATAGAAAACGAGAAAGACAAAGAATTCATGATGGTGA
194 ATGAAGAAGACAAG-CGTGCCAATAGAGATAGAAAACGAGAAAGACAAAGAATTCATGATGATGA
* *
1229092 TGCTAAGAATAGGTGGAGAGAACACTCTGGGTCTTCGGATGAAGAAGATAAGCTTGACAATAGAG
258 TGCTAAGAATAGGCGGAGAGAACACTCTGGGTCTTCGGATGAAGAAGACAAGCTTGACAATAGAG
1229157 ATAGAAGG
323 ATAGAAGG
* * * * *
1229165 AGAGAAAGACAAGGAATTCGTGATGATGATGGTA--AGAGTAGGCGGAGAGAACATTCTAGATCT
1 AGAGAAAGAGAAGGAATTCATGATGATGA-GG-AGGAGAATAGGCGGAGAGAGCATTCTGGATCT
* * ** *
1229228 TCTGATGAAGAAGAAGACAAGCATGCTGCTAGAGATAGAAGGCGAGAAAG
64 TCTGATGAGGAAGAAGGCAAGCATGCTAATAGAGATAGAAGGCGCGAAAG
1229278 AGAGAGACTT
Statistics
Matches: 385, Mismatches: 50, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
329 10 0.03
330 366 0.95
331 8 0.02
332 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.34, T:0.17
Consensus pattern (330 bp):
AGAGAAAGAGAAGGAATTCATGATGATGAGGAGGAGAATAGGCGGAGAGAGCATTCTGGATCTTC
TGATGAGGAAGAAGGCAAGCATGCTAATAGAGATAGAAGGCGCGAAAGCGAAAGGGAAAGAGGAA
AAGAAAGAAATCAAGATGGCGATGGTGATGAGAATAGGCAGAGAGAACGCTCTGGAGCTTTTGAT
GAAGAAGACAAGCGTGCCAATAGAGATAGAAAACGAGAAAGACAAAGAATTCATGATGATGATGC
TAAGAATAGGCGGAGAGAACACTCTGGGTCTTCGGATGAAGAAGACAAGCTTGACAATAGAGATA
GAAGG
Found at i:1229291 original size:105 final size:101
Alignment explanation
Indices: 1228995--1229316 Score: 287
Period size: 102 Copynumber: 3.2 Consensus size: 101
1228985 GATGTTGGTG
* * * ** * *
1228995 AGAATAGGCAGAGAGAAC-GTCCTGGATCTTTTGATGAAGAAGACAAGTC-TGCCAATAGAGATA
1 AGAATAGGCGGAGAGAACACT-CTAGATCTTCGGAAGAAGAAGACAAG-CATGACAATAGAGATA
** * *
1229058 GAAAACGAGAAAGACAAAGAATTCATGATGGTGATGCTA
64 GAAGGCGAGAAAGAC-AAGAATTCGTGATGATGATGCTA
* * * * * *
1229097 AGAATAGGTGGAGAGAACACTCTGGGTCTTCGGATGAAGAAGATAAGCTTGACAATAGAGATAGA
1 AGAATAGGCGGAGAGAACACTCTAGATCTTCGGAAGAAGAAGACAAGCATGACAATAGAGATAGA
* *
1229162 AGGAGAGAAAGACAAGGAATTCGTGATGATGATGGTA
66 AGGCGAGAAAGACAA-GAATTCGTGATGATGATGCTA
* * **
1229199 AGAGTAGGCGGAGAGAACATTCTAGATCTTCTGATGAAGAAGAAGACAAGCATG-CTGCTAGAGA
1 AGAATAGGCGGAGAGAACACTCTAGATCTTC-G--GAAGAAGAAGACAAGCATGAC-AATAGAGA
* *
1229263 TAGAAGGCGAGAAAGAGAGAGACTTCGTGATGATGA---TA
62 TAGAAGGCGAGAAAGACA-AGAATTCGTGATGATGATGCTA
*
1229301 GGAATAGGCGGAGAGA
1 AGAATAGGCGGAGAGA
1229317 TGCAGTGGAG
Statistics
Matches: 183, Mismatches: 29, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
101 3 0.02
102 123 0.67
103 2 0.01
104 1 0.01
105 53 0.29
106 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.31, T:0.19
Consensus pattern (101 bp):
AGAATAGGCGGAGAGAACACTCTAGATCTTCGGAAGAAGAAGACAAGCATGACAATAGAGATAGA
AGGCGAGAAAGACAAGAATTCGTGATGATGATGCTA
Found at i:1236020 original size:17 final size:17
Alignment explanation
Indices: 1235998--1236032 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1235988 CTTAAGAGTT
1235998 AAAATTAACAAAACAAA
1 AAAATTAACAAAACAAA
* *
1236015 AAAATTAATAAAAGAAA
1 AAAATTAACAAAACAAA
1236032 A
1 A
1236033 TTAAAAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.14
Consensus pattern (17 bp):
AAAATTAACAAAACAAA
Found at i:1239407 original size:76 final size:76
Alignment explanation
Indices: 1239257--1239408 Score: 207
Period size: 76 Copynumber: 2.0 Consensus size: 76
1239247 TATACTCAAT
* * *
1239257 GCAAATTTATAATAGCCGTTTGTTTATAATTTTGCTATGAGAAGTTTGCAACAATCATGAGTACC
1 GCAAATTTATAATAGCCATTTGTTTATAATTTTCCTATGAGAAGTTTGCAACAACCATGAGTACC
* *
1239322 TAACGGATTCC
66 GAAAGGATTCC
* * * *
1239333 GCAAATTTATAATAGTCATTTGTTTATACTTTTCCTATGAGAGGTTTGCAACAACCATGAGTA-G
1 GCAAATTTATAATAGCCATTTGTTTATAATTTTCCTATGAGAAGTTTGCAACAACCATGAGTACC
1239397 GAAAGAGATTCC
66 GAAAG-GATTCC
1239409 AACTCTCAGC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
75 3 0.05
76 63 0.95
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (76 bp):
GCAAATTTATAATAGCCATTTGTTTATAATTTTCCTATGAGAAGTTTGCAACAACCATGAGTACC
GAAAGGATTCC
Found at i:1241657 original size:30 final size:30
Alignment explanation
Indices: 1241579--1241677 Score: 112
Period size: 30 Copynumber: 3.3 Consensus size: 30
1241569 AAATTTTAAC
* *
1241579 AAATTTTTATATTTTTATTGTG--TTCAAT
1 AAATTTTTATATTTTTATTTTGAATTAAAT
* * ** *
1241607 CAAATATTTGTGCTTATATTTTGAATTAAAT
1 -AAATTTTTATATTTTTATTTTGAATTAAAT
1241638 AAATTTTTATATTTTTATTTTGAATTAAAT
1 AAATTTTTATATTTTTATTTTGAATTAAAT
1241668 AAATTTTTAT
1 AAATTTTTAT
1241678 GATTAATTTA
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
29 16 0.29
30 35 0.62
31 5 0.09
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (30 bp):
AAATTTTTATATTTTTATTTTGAATTAAAT
Found at i:1246987 original size:15 final size:15
Alignment explanation
Indices: 1246967--1246998 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1246957 TATGTCATGT
1246967 TCCTCCTTCTCCTCC
1 TCCTCCTTCTCCTCC
1246982 TCCTCCTTCTCCTCC
1 TCCTCCTTCTCCTCC
1246997 TC
1 TC
1246999 TGTGTGTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (15 bp):
TCCTCCTTCTCCTCC
Found at i:1253234 original size:10 final size:10
Alignment explanation
Indices: 1253219--1253250 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
1253209 TCTTTCCTTC
1253219 TTTATTATTG
1 TTTATTATTG
1253229 TTTATTATTG
1 TTTATTATTG
1253239 TTTATTATTG
1 TTTATTATTG
1253249 TT
1 TT
1253251 GTGTTTCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (10 bp):
TTTATTATTG
Found at i:1263588 original size:24 final size:24
Alignment explanation
Indices: 1263561--1263631 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
1263551 GAAGCGACTG
** *
1263561 TGTGGGCTAACTAGGCCCAATTTC
1 TGTGGGCTGTCTAGGCCCAATTTA
1263585 TGTGGGCTGTCTAGGCCCAATTTA
1 TGTGGGCTGTCTAGGCCCAATTTA
1263609 TGTGGGCTGTCTAGGCCCAATTT
1 TGTGGGCTGTCTAGGCCCAATTT
1263632 GAGAAAGCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.32
Consensus pattern (24 bp):
TGTGGGCTGTCTAGGCCCAATTTA
Found at i:1273209 original size:12 final size:12
Alignment explanation
Indices: 1273192--1273231 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
1273182 GATGGCCCCG
1273192 ATGGGGATGGGA
1 ATGGGGATGGGA
*
1273204 ATGGGGATGGGC
1 ATGGGGATGGGA
*
1273216 ATGGGCATGGGA
1 ATGGGGATGGGA
1273228 ATGG
1 ATGG
1273232 TGGTCATGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.23, C:0.05, G:0.55, T:0.17
Consensus pattern (12 bp):
ATGGGGATGGGA
Found at i:1273212 original size:18 final size:18
Alignment explanation
Indices: 1273191--1273231 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1273181 TGATGGCCCC
*
1273191 GATGGGGATGGGAATGGG
1 GATGGGCATGGGAATGGG
*
1273209 GATGGGCATGGGCATGGG
1 GATGGGCATGGGAATGGG
*
1273227 AATGG
1 GATGG
1273232 TGGTCATGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.22, C:0.05, G:0.56, T:0.17
Consensus pattern (18 bp):
GATGGGCATGGGAATGGG
Found at i:1276832 original size:21 final size:21
Alignment explanation
Indices: 1276808--1276850 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1276798 TTATATTCTC
* *
1276808 TCATTCTTTATTTTTTTAAAA
1 TCATTCTTTAATATTTTAAAA
*
1276829 TCATTTTTTAATATTTTAAAA
1 TCATTCTTTAATATTTTAAAA
1276850 T
1 T
1276851 AATTTTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (21 bp):
TCATTCTTTAATATTTTAAAA
Found at i:1277722 original size:16 final size:16
Alignment explanation
Indices: 1277701--1277763 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
1277691 TAAACTCATT
*
1277701 TATTAATATATATAAA
1 TATTAATATTTATAAA
*
1277717 TATTAATATTTTTATAA
1 TATTAATATTTATA-AA
**
1277734 TAATTAATATTTATGTA
1 T-ATTAATATTTATAAA
*
1277751 TATTAATTTTTAT
1 TATTAATATTTAT
1277764 TATATTTAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
16 23 0.59
17 5 0.13
18 11 0.28
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
TATTAATATTTATAAA
Found at i:1277754 original size:34 final size:35
Alignment explanation
Indices: 1277702--1277767 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 35
1277692 AAACTCATTT
1277702 ATTAATATATATAAATATTAATATTT-TTATAATA
1 ATTAATATATATAAATATTAATATTTATTATAATA
* ** *
1277736 ATTAATATTTATGTATATTAATTTTTATTATA
1 ATTAATATATATAAATATTAATATTTATTATA
1277768 TTTAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 22 0.81
35 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (35 bp):
ATTAATATATATAAATATTAATATTTATTATAATA
Found at i:1277801 original size:19 final size:19
Alignment explanation
Indices: 1277754--1277805 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1277744 TTATGTATAT
1277754 TAATTTTTATTATATTTAG
1 TAATTTTTATTATATTTAG
* *
1277773 TAAATATTATTATATTTA-
1 TAATTTTTATTATATTTAG
1277791 TAATTTTTTATTATA
1 TAA-TTTTTATTATA
1277806 AATTTGAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 3 0.11
19 25 0.89
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TAATTTTTATTATATTTAG
Found at i:1277941 original size:25 final size:26
Alignment explanation
Indices: 1277911--1277980 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 26
1277901 TTTAATTATG
1277911 TTAATTATGTCATATTATAT-AA-ATT
1 TTAATT-TGTCATATTATATAAATATT
1277936 TTAATTTGAT-ATATT-TAATAAATATT
1 TTAATTTG-TCATATTAT-ATAAATATT
*
1277962 TTAATCGTGTCATATTATA
1 TTAAT-TTGTCATATTATA
1277981 AATTTATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
23 1 0.03
24 9 0.24
25 9 0.24
26 9 0.24
27 8 0.22
28 1 0.03
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (26 bp):
TTAATTTGTCATATTATATAAATATT
Found at i:1286969 original size:23 final size:23
Alignment explanation
Indices: 1286903--1286964 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
1286893 TCAAATATAA
1286903 AAATTTTATTATACAAAATTTTT
1 AAATTTTATTATACAAAATTTTT
*
1286926 AAATTTTATTTTACAAAATTTTT
1 AAATTTTATTATACAAAATTTTT
1286949 AAATTTTATCTATACA
1 AAATTTTAT-TATACA
1286965 TATTTATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 31 0.86
24 5 0.14
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (23 bp):
AAATTTTATTATACAAAATTTTT
Found at i:1299722 original size:2 final size:2
Alignment explanation
Indices: 1299715--1299759 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1299705 ACTCAATTCA
*
1299715 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1299757 CT C
1 CT C
1299760 ACACATGCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:1312373 original size:2 final size:2
Alignment explanation
Indices: 1312366--1312395 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1312356 CCATATTCCC
1312366 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
1312396 GGTCCCATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1314770 original size:27 final size:26
Alignment explanation
Indices: 1314732--1314810 Score: 90
Period size: 26 Copynumber: 3.0 Consensus size: 26
1314722 TGGCATAATG
* * *
1314732 TTTTTAATTTTTT-TAATTATTTAAAA
1 TTTTTTATTTTTTATTATTAATT-AAA
1314758 TTTTTTATTTTTTATTATTAATTAAA
1 TTTTTTATTTTTTATTATTAATTAAA
*
1314784 -TTTTTATATTTTTATTTTTAATTAAA
1 TTTTTTAT-TTTTTATTATTAATTAAA
1314810 T
1 T
1314811 AAAATCTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
25 7 0.15
26 32 0.70
27 7 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTTTATTTTTTATTATTAATTAAA
Found at i:1314821 original size:30 final size:32
Alignment explanation
Indices: 1314759--1314821 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 32
1314749 TATTTAAAAT
* * *
1314759 TTTTTATTTTTTATTATTAATTAAATTTTTATA
1 TTTTTATTTTTTA-TATTAAATAAAATCTTATA
1314792 TTTTTA-TTTTTA-ATTAAATAAAATCTTATA
1 TTTTTATTTTTTATATTAAATAAAATCTTATA
1314822 ATTAAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 15 0.56
32 6 0.22
33 6 0.22
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (32 bp):
TTTTTATTTTTTATATTAAATAAAATCTTATA
Found at i:1321948 original size:45 final size:45
Alignment explanation
Indices: 1321913--1322117 Score: 272
Period size: 45 Copynumber: 4.6 Consensus size: 45
1321903 TAGCTGTGCA
* * * *
1321913 ATCACTAATGTCTTCAGCATCAATGGCATCAACAATGGCCATGCC
1 ATCACTAATGCCTTCTGCATCAGTGGAATCAACAATGGCCATGCC
* *
1321958 ATCACTAATGCCTTCTGCATCAGTGGAATCAATAATGGCCATTCC
1 ATCACTAATGCCTTCTGCATCAGTGGAATCAACAATGGCCATGCC
*
1322003 ATCACTAATGCCTTCTGCATCAGTGGAATCAACAATGACCATGCC
1 ATCACTAATGCCTTCTGCATCAGTGGAATCAACAATGGCCATGCC
* * **
1322048 ATCACTAATGTCTTCTGCATCAGTGGAGTCAACAATGGTGATG--
1 ATCACTAATGCCTTCTGCATCAGTGGAATCAACAATGGCCATGCC
* *
1322091 -TCACTATTGCCTTCTGCATCAATGGAA
1 ATCACTAATGCCTTCTGCATCAGTGGAA
1322118 CCTATTAGTG
Statistics
Matches: 142, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
42 23 0.16
45 119 0.84
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (45 bp):
ATCACTAATGCCTTCTGCATCAGTGGAATCAACAATGGCCATGCC
Found at i:1343736 original size:2 final size:2
Alignment explanation
Indices: 1343729--1343756 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1343719 CTAAAACCTC
1343729 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
1343757 TGACCCAAAT
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:1345935 original size:18 final size:19
Alignment explanation
Indices: 1345893--1345938 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
1345883 AATATTCTTT
*
1345893 ATAATATTTACTATAGTTAA
1 ATAATA-TTAATATAGTTAA
1345913 ATAATATTAATATA-TTAA
1 ATAATATTAATATAGTTAA
*
1345931 GTAATATT
1 ATAATATT
1345939 TAAATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 11 0.46
19 7 0.29
20 6 0.25
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (19 bp):
ATAATATTAATATAGTTAA
Found at i:1345945 original size:18 final size:18
Alignment explanation
Indices: 1345893--1345946 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
1345883 AATATTCTTT
*
1345893 ATAATATTTACTATAGTTAA
1 ATAATATTTA-AATA-TTAA
1345913 ATAATA-TTAATATATTAA
1 ATAATATTTAA-ATATTAA
*
1345931 GTAATATTTAAATATT
1 ATAATATTTAAATATT
1345947 TTCATTTCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 14 0.47
19 10 0.33
20 6 0.20
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (18 bp):
ATAATATTTAAATATTAA
Found at i:1349001 original size:21 final size:21
Alignment explanation
Indices: 1348975--1349016 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1348965 TTTCATTTGC
1348975 TTTGGGAAATGGCGGCGATAA
1 TTTGGGAAATGGCGGCGATAA
1348996 TTTGGGAAATGGCGGCGATAA
1 TTTGGGAAATGGCGGCGATAA
1349017 GGAATGCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.38, T:0.24
Consensus pattern (21 bp):
TTTGGGAAATGGCGGCGATAA
Found at i:1349317 original size:51 final size:51
Alignment explanation
Indices: 1349257--1349360 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 51
1349247 TAGAAGCATG
* * *
1349257 AGTAATTTATTAGAAGTCTTAATAGTTTAGACATTGTGTTTTACAAGAATT
1 AGTAATTTATTACAAGTCTTAATAGTTTAGACATTGTATTGTACAAGAATT
* * *
1349308 AGTAATTTATTTCAAGTCTTAATAGTTTAGATATTGTATTGTACAAGGATT
1 AGTAATTTATTACAAGTCTTAATAGTTTAGACATTGTATTGTACAAGAATT
1349359 AG
1 AG
1349361 GAAAGTTAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (51 bp):
AGTAATTTATTACAAGTCTTAATAGTTTAGACATTGTATTGTACAAGAATT
Found at i:1354240 original size:23 final size:23
Alignment explanation
Indices: 1354210--1354255 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1354200 CAAACAATCC
*
1354210 AAGGCCAACTTGGAAGTTGAGAA
1 AAGGCCAACTTAGAAGTTGAGAA
1354233 AAGGCCAACTTAGAAGTTGAGAA
1 AAGGCCAACTTAGAAGTTGAGAA
1354256 TAGCAAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.13, G:0.28, T:0.17
Consensus pattern (23 bp):
AAGGCCAACTTAGAAGTTGAGAA
Found at i:1355063 original size:2 final size:2
Alignment explanation
Indices: 1355056--1355086 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1355046 TTTGCAAGGA
1355056 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 A
1355087 AATTACATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1358606 original size:31 final size:31
Alignment explanation
Indices: 1358571--1358630 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1358561 AACTTTAGAT
* *
1358571 AAGTAATATAACAAGTAAATATTTTTTAAAA
1 AAGTAATATAACAAGCAAATATTTCTTAAAA
* *
1358602 AAGTAATGTAACAAGCACATATTTCTTAA
1 AAGTAATATAACAAGCAAATATTTCTTAA
1358631 CTTTCAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (31 bp):
AAGTAATATAACAAGCAAATATTTCTTAAAA
Found at i:1360836 original size:14 final size:14
Alignment explanation
Indices: 1360817--1360849 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1360807 TGGGAGAGAA
1360817 AAAAACAAAGAAAG
1 AAAAACAAAGAAAG
*
1360831 AAAAACAAATAAAG
1 AAAAACAAAGAAAG
1360845 AAAAA
1 AAAAA
1360850 TGAGGAGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.82, C:0.06, G:0.09, T:0.03
Consensus pattern (14 bp):
AAAAACAAAGAAAG
Found at i:1361718 original size:35 final size:35
Alignment explanation
Indices: 1361638--1361736 Score: 101
Period size: 35 Copynumber: 2.8 Consensus size: 35
1361628 AGAAAGAATG
* *
1361638 AAGTACTA-TTCTATGCAAAATAACTAAAACAAATA
1 AAGTACTACTTC-ATGCAAAACAATTAAAACAAATA
** * *
1361673 AAACATTACTTCATGCAAAACAATTAAAACAAGTA
1 AAGTACTACTTCATGCAAAACAATTAAAACAAATA
* *
1361708 AAGTACTACTTTATACAAAACAACTTAAA
1 AAGTACTACTTCATGCAAAACAA-TTAAA
1361737 CAACTACTCC
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
35 43 0.84
36 8 0.16
ACGTcount: A:0.54, C:0.16, G:0.05, T:0.25
Consensus pattern (35 bp):
AAGTACTACTTCATGCAAAACAATTAAAACAAATA
Found at i:1362374 original size:9 final size:9
Alignment explanation
Indices: 1362357--1362407 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
1362347 TTAGAACCCC
*
1362357 ATTACTATT
1 ATTAATATT
1362366 ATTAATATT
1 ATTAATATT
* *
1362375 ACTAATA-A
1 ATTAATATT
*
1362383 ATTACTATT
1 ATTAATATT
1362392 ATTAATATT
1 ATTAATATT
*
1362401 ACTAATA
1 ATTAATA
1362408 AATTAACTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
8 5 0.15
9 28 0.85
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (9 bp):
ATTAATATT
Found at i:1362386 original size:26 final size:26
Alignment explanation
Indices: 1362357--1362412 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
1362347 TTAGAACCCC
1362357 ATTACTATTATTAATATTACTAATAA
1 ATTACTATTATTAATATTACTAATAA
1362383 ATTACTATTATTAATATTACTAATAA
1 ATTACTATTATTAATATTACTAATAA
1362409 ATTA
1 ATTA
1362413 ACTTTACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTACTATTATTAATATTACTAATAA
Found at i:1362391 original size:17 final size:17
Alignment explanation
Indices: 1362392--1362426 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1362382 AATTACTATT
1362392 ATTAATATTACTAATAA
1 ATTAATATTACTAATAA
1362409 ATTAACT-TTACTAATAA
1 ATTAA-TATTACTAATAA
1362426 A
1 A
1362427 GATAGATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.94
18 1 0.06
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTAATATTACTAATAA
Found at i:1362423 original size:26 final size:26
Alignment explanation
Indices: 1362357--1362424 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
1362347 TTAGAACCCC
*
1362357 ATTACTATTATTAATATTACTAATAA
1 ATTACTATTACTAATATTACTAATAA
*
1362383 ATTACTATTATTAATATTACTAATAA
1 ATTACTATTACTAATATTACTAATAA
1362409 ATTAACT-TTACTAATA
1 ATT-ACTATTACTAATA
1362425 AAGATAGATA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 37 0.93
27 3 0.08
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTACTATTACTAATATTACTAATAA
Found at i:1362771 original size:46 final size:47
Alignment explanation
Indices: 1362713--1362803 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 47
1362703 AATATTGAAG
1362713 AGAGAGTAAGAAGGAT-AAGAATAACCAAGAAAACTAAAAATACTAC
1 AGAGAGTAAGAAGGATCAAGAATAACCAAGAAAACTAAAAATACTAC
* * *
1362759 AGAGAGTCAGAAGGATCAAGAATAATCAAGAAAGCTAAAAATACT
1 AGAGAGTAAGAAGGATCAAGAATAACCAAGAAAACTAAAAATACT
1362804 TGAAGAGATG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 15 0.37
47 26 0.63
ACGTcount: A:0.56, C:0.11, G:0.19, T:0.14
Consensus pattern (47 bp):
AGAGAGTAAGAAGGATCAAGAATAACCAAGAAAACTAAAAATACTAC
Found at i:1376436 original size:2 final size:2
Alignment explanation
Indices: 1376429--1376455 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1376419 GATGTAAACA
1376429 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1376456 ATTGGTACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1387283 original size:2 final size:2
Alignment explanation
Indices: 1387245--1387272 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1387235 GTGTGTGTGT
1387245 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1387273 TAAGCGAGAG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1396611 original size:15 final size:15
Alignment explanation
Indices: 1396582--1396623 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
1396572 TTGGGTTGGG
1396582 TTTT-TCTTCTCTTTT
1 TTTTCTCTTCT-TTTT
1396597 TTTTCTCTTCTTTTT
1 TTTTCTCTTCTTTTT
1396612 TTTTCTCTTCTT
1 TTTTCTCTTCTT
1396624 CTTGAGCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 20 0.77
16 6 0.23
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCTCTTCTTTTT
Found at i:1396800 original size:16 final size:17
Alignment explanation
Indices: 1396774--1396814 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
1396764 CTTCTCTCTC
*
1396774 TCTATTTTTTTTATT-T
1 TCTAATTTTTTTATTAT
*
1396790 TCTTATTTTTTTATTAT
1 TCTAATTTTTTTATTAT
1396807 TCTAATTT
1 TCTAATTT
1396815 ACTTGTGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (17 bp):
TCTAATTTTTTTATTAT
Found at i:1400225 original size:2 final size:2
Alignment explanation
Indices: 1400218--1400248 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1400208 ATTTTTGTTC
1400218 TA TA TA 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 TA TA TA T
1400249 TCATTAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1400610 original size:29 final size:29
Alignment explanation
Indices: 1400542--1400604 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 29
1400532 GGGCTCCCAA
*
1400542 TATTTCAAATATTTATAAATTTTTTTGTTT
1 TATTTTAAA-ATTTATAAATTTTTTTGTTT
*
1400572 TATTTTAAAATTTA-AAATTTTTAT-TTT
1 TATTTTAAAATTTATAAATTTTTTTGTTT
1400599 TATTTT
1 TATTTT
1400605 TTAAAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 9 0.29
28 9 0.29
29 5 0.16
30 8 0.26
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (29 bp):
TATTTTAAAATTTATAAATTTTTTTGTTT
Found at i:1401736 original size:20 final size:20
Alignment explanation
Indices: 1401696--1401742 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1401686 TATGATTTAA
* *
1401696 TGATAAGATCATGTAACAAT
1 TGATATGATCATATAACAAT
*
1401716 TGATATGATCATATAATAAT
1 TGATATGATCATATAACAAT
*
1401736 TAATATG
1 TGATATG
1401743 GTTACATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (20 bp):
TGATATGATCATATAACAAT
Found at i:1402750 original size:159 final size:159
Alignment explanation
Indices: 1402461--1402778 Score: 519
Period size: 159 Copynumber: 2.0 Consensus size: 159
1402451 AAAATGGTAG
1402461 TGCAAGCTGTTACTTCTCCTTTCACTCACCCTTGCATTAATCTAGATTTAATACAAGCAATTAAA
1 TGCAAGCTGTTACTTCTCCTTTCACTCACCCTTGCATTAATCTAGATTTAATACAAGCAATTAAA
** * * *
1402526 GAAATGTTACATTGACAGTGAGAGGAAAGTCTCAGTAAATCATATTTACCGAGAAGGTAATTGAG
66 GAAATGTTACATCAACAGTGAGAGGAAAGTCTCAATAAATCATACTTACCAAGAAGGTAATTGAG
*
1402591 TAGTTGATCTTATGACTAATAAGGGTTTT
131 TAGTTGATCTTATAACTAATAAGGGTTTT
*
1402620 TGCAAGCTGTTACTTCTCCTTTCACTCACTCTTGCATTAATCTAGATTTAATACAAGCAATTAAA
1 TGCAAGCTGTTACTTCTCCTTTCACTCACCCTTGCATTAATCTAGATTTAATACAAGCAATTAAA
* * * * *
1402685 GAAATGTTACATCAACAGTGGGAGGAAAGTTTCAATAAATTATACTTATCAAGAAGGTATTTGAG
66 GAAATGTTACATCAACAGTGAGAGGAAAGTCTCAATAAATCATACTTACCAAGAAGGTAATTGAG
*
1402750 TGGTTGATCTTATAACTAATAAGGGTTTT
131 TAGTTGATCTTATAACTAATAAGGGTTTT
1402779 GAACTAGAGA
Statistics
Matches: 146, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
159 146 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (159 bp):
TGCAAGCTGTTACTTCTCCTTTCACTCACCCTTGCATTAATCTAGATTTAATACAAGCAATTAAA
GAAATGTTACATCAACAGTGAGAGGAAAGTCTCAATAAATCATACTTACCAAGAAGGTAATTGAG
TAGTTGATCTTATAACTAATAAGGGTTTT
Found at i:1417055 original size:20 final size:20
Alignment explanation
Indices: 1417030--1417209 Score: 94
Period size: 19 Copynumber: 9.3 Consensus size: 20
1417020 TAAAAATTTT
1417030 AAAATAAAATATATAATATA
1 AAAATAAAATATATAATATA
*
1417050 AAAATAAAAAATATAATAT-
1 AAAATAAAATATATAATATA
* * * *
1417069 AATATAAAAAAT-TAAAATT
1 AAAATAAAATATATAATATA
* * * * *
1417088 TATATAATATAGATAAAAT-
1 AAAATAAAATATATAATATA
*
1417107 AAATTAAAATA-A-AATATA
1 AAAATAAAATATATAATATA
* *
1417125 TAATATAAAAAATAT-AT-TA
1 -AAAATAAAATATATAATATA
1417144 AAAATAAAA-ATAATATATATA
1 AAAATAAAATAT-ATA-ATATA
* * *
1417165 ATATTATAATA-ATAA-ATA
1 AAAATAAAATATATAATATA
1417183 AAAATAAAATATATGACAT-TA
1 AAAATAAAATATAT-A-ATATA
1417204 AAAATA
1 AAAATA
1417210 TATTTAAAAA
Statistics
Matches: 123, Mismatches: 22, Indels: 29
0.71 0.13 0.17
Matches are distributed among these distances:
17 6 0.05
18 27 0.22
19 39 0.32
20 33 0.27
21 17 0.14
22 1 0.01
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (20 bp):
AAAATAAAATATATAATATA
Found at i:1417154 original size:33 final size:33
Alignment explanation
Indices: 1417016--1417195 Score: 118
Period size: 33 Copynumber: 5.6 Consensus size: 33
1417006 TATTATAATT
* * *
1417016 AAAATAAAAAT-TTTAAAATAAAATATATAATATA
1 AAAATAAAAATATATAATATAAAAAATAT-AT-TA
1417050 AAAATAAAAA-ATATAATAT----AATATA--A
1 AAAATAAAAATATATAATATAAAAAATATATTA
* *
1417076 AAAATTAAAATTTATATAATATAGATAAAATAAATT-
1 AAAA-TAAAA-ATATATAATATA-A-AAAATATATTA
1417112 AAAAT-AAAATATATAATATAAAAAATATATTA
1 AAAATAAAAATATATAATATAAAAAATATATTA
* * *
1417144 AAAATAAAAATA-AT-ATATATAATATTATAATA
1 AAAATAAAAATATATAATATA-AAAAATATATTA
1417176 ATAAATAAAAATA-A-AATATA
1 A-AAATAAAAATATATAATATA
1417196 TGACATTAAA
Statistics
Matches: 119, Mismatches: 10, Indels: 35
0.73 0.06 0.21
Matches are distributed among these distances:
26 5 0.04
27 5 0.04
29 10 0.08
30 4 0.03
31 14 0.12
32 18 0.15
33 34 0.29
34 19 0.16
35 6 0.05
36 4 0.03
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.32
Consensus pattern (33 bp):
AAAATAAAAATATATAATATAAAAAATATATTA
Found at i:1417196 original size:33 final size:34
Alignment explanation
Indices: 1417051--1417196 Score: 126
Period size: 33 Copynumber: 4.4 Consensus size: 34
1417041 TATAATATAA
* * *
1417051 AAATAAAAAATATAATAT-AAT-ATAAAAAATTA
1 AAATAAAATATATAATATAAATAATAATAAATAA
* * *
1417083 AAAT---TTATATAATATAGATAA-AATAAATTA
1 AAATAAAATATATAATATAAATAATAATAAATAA
*
1417113 AAATAAAATATATAATATAAAAAATATATTAAAAATAA
1 AAATAAAATATATAATATAAATAATA-A-T--AAATAA
* *
1417151 AAATAATATATATAATAT-TATAATAATAAATAA
1 AAATAAAATATATAATATAAATAATAATAAATAA
1417184 AAATAAAATATAT
1 AAATAAAATATAT
1417197 GACATTAAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
29 9 0.10
30 14 0.15
31 1 0.01
32 4 0.04
33 32 0.35
34 1 0.01
35 2 0.02
36 2 0.02
37 5 0.05
38 22 0.24
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (34 bp):
AAATAAAATATATAATATAAATAATAATAAATAA
Found at i:1417237 original size:71 final size:72
Alignment explanation
Indices: 1417070--1417258 Score: 194
Period size: 71 Copynumber: 2.7 Consensus size: 72
1417060 ATATAATATA
* * * * *
1417070 ATATAAAAAATTAAAAT-TTATATAAT-ATA-GATAA-AATAAATTAAAATAAAATATATAATAT
1 ATATTAAAAATAAAAATATTATATAATAATATAATAATAATAAATAAAAATAAAATATATAACAT
1417131 AAAAAAT
66 AAAAAAT
* * *
1417138 ATATTAAAAATAAAAATAATATAT-ATAATATTATAATAATAAATAAAAATAAAATATATGACAT
1 ATATTAAAAATAAAAATATTATATAATAATATAATAATAATAAATAAAAATAAAATATATAACAT
*
1417202 TAAAAAT
66 AAAAAAT
* *** * *
1417209 ATATTTAAAA-AATTGTATTATATAATAAT-TAATAATAAAAAATATAAATA
1 ATATTAAAAATAAAAATATTATATAATAATATAATAATAATAAATAAAAATA
1417259 TATTAAACTT
Statistics
Matches: 100, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
68 17 0.17
69 8 0.08
70 31 0.31
71 44 0.44
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.34
Consensus pattern (72 bp):
ATATTAAAAATAAAAATATTATATAATAATATAATAATAATAAATAAAAATAAAATATATAACAT
AAAAAAT
Found at i:1417434 original size:15 final size:16
Alignment explanation
Indices: 1417414--1417455 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
1417404 ATTTTTCTTA
1417414 CAATCACATTACT-TG
1 CAATCACATTACTCTG
1417429 CAATCACATTA-TCTG
1 CAATCACATTACTCTG
*
1417444 TAATCACATTAC
1 CAATCACATTAC
1417456 ATTGTAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 1 0.04
15 23 0.96
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (16 bp):
CAATCACATTACTCTG
Found at i:1424742 original size:2 final size:2
Alignment explanation
Indices: 1424735--1424767 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1424725 ACCAAAATCC
*
1424735 CT CT CT CT CT CT CT CT CC CT CT CT CT CT C- CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1424768 TAACGTCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (2 bp):
CT
Found at i:1430067 original size:23 final size:23
Alignment explanation
Indices: 1430016--1430068 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
1430006 TATATAACGT
* *
1430016 ATATGTTAATATTATAATATATG
1 ATATGTAAATATTATAATATATA
*
1430039 AT-TGTAAATATTTTACATAT-TA
1 ATATGTAAATATTATA-ATATATA
1430061 ATATGTAA
1 ATATGTAA
1430069 GAATTACTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (23 bp):
ATATGTAAATATTATAATATATA
Found at i:1430157 original size:17 final size:17
Alignment explanation
Indices: 1430132--1430166 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1430122 AATTGTGTAA
1430132 ATATATAATATATACAT
1 ATATATAATATATACAT
* *
1430149 ATATTTAATTTATACAT
1 ATATATAATATATACAT
1430166 A
1 A
1430167 AACATTGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATATAATATATACAT
Found at i:1430371 original size:208 final size:211
Alignment explanation
Indices: 1430136--1430563 Score: 612
Period size: 208 Copynumber: 2.0 Consensus size: 211
1430126 GTGTAAATAT
**
1430136 ATAATATATACATATATTTAATTTATACATAAACATTGTTACAACTTATAATAAACTTTATTTGT
1 ATAATATATACATATATTTAATTTATACATAAACATTACTACAACTTATAATAAACTTTATTTGT
* * * *
1430201 ATAATTACATTTAATAGTTTTATTAGTTAGCACCTTACTTTTTATAACATATTGTTTATAATTAG
66 ATAATTACATTCAATAATTTTATTAGTTAGCACCTGAATTTTTATAACATATTGTTTATAATTAG
* * * * *
1430266 TTATTATTTATACAAATTTTGATAT-AGAA-T-ATA-ATAATATATAAATTGTGTCATTAATTTC
131 TTATTATTTATACAAACTTTAATATAAAAATTAATATATAACATATAAATTGTCTCATTAATTTC
1430327 ATATATATATAATAAA
196 ATATATATATAATAAA
* ** *
1430343 ATAATATATTATATATATTTAATTTATACATAAGTATTACTATAACTTATAATAAACTTTATTTG
1 ATAATATA-TACATATATTTAATTTATACATAAACATTACTACAACTTATAATAAACTTTATTTG
* * *
1430408 TATAATTATATTCAATAATTTTATTAGTTATCACCTGAATTTTTTTAACATATTGTTTATAATTA
65 TATAATTACATTCAATAATTTTATTAGTTAGCACCTGAATTTTTATAACATATTGTTTATAATTA
*
1430473 GTTATTATTTATACAAACTTTAATATAAAAATTAAAATATTATAACATATAAGTTGTCTCATTAA
130 GTTATTATTTATACAAACTTTAATATAAAAATT--AATA-TATAACATATAAATTGTCTCATTAA
1430538 TTTCATATATATATAATAAA
192 TTTCATATATATATAATAAA
*
1430558 GTAATA
1 ATAATA
1430564 CATATAAATA
Statistics
Matches: 193, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
207 8 0.04
208 132 0.68
209 3 0.02
210 1 0.01
213 3 0.02
215 46 0.24
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (211 bp):
ATAATATATACATATATTTAATTTATACATAAACATTACTACAACTTATAATAAACTTTATTTGT
ATAATTACATTCAATAATTTTATTAGTTAGCACCTGAATTTTTATAACATATTGTTTATAATTAG
TTATTATTTATACAAACTTTAATATAAAAATTAATATATAACATATAAATTGTCTCATTAATTTC
ATATATATATAATAAA
Found at i:1442269 original size:123 final size:123
Alignment explanation
Indices: 1442110--1442350 Score: 383
Period size: 123 Copynumber: 2.0 Consensus size: 123
1442100 TCCTCGCAAC
* *
1442110 GACTTTCTTTTCTGCATGGGACAGTGCCCGTGACATCTCCGCGAAGTTGTAAAGTGCCTTGTTCT
1 GACTTTCTTTTCTGCATGGGACAGTGCCCGTGACATCTCCGCGAAGTCGTAAAGAGCCTTGTTCT
* * *
1442175 CACCAGGCGGGACGATAACGGGATGGGATTCTGCTTCCATGATTACCTCTTTCTCAAG
66 CACCAGGCGGAACGACAACGGGATGGGATTCTGCTTCCATAATTACCTCTTTCTCAAG
* *
1442233 GACTTTCTTTTCTGCATGGTACAGTGTCCGTGACATCTCCGCGAAGTCGTAAAGAGCCTTGTTCT
1 GACTTTCTTTTCTGCATGGGACAGTGCCCGTGACATCTCCGCGAAGTCGTAAAGAGCCTTGTTCT
** * *
1442298 GGCCCGGCGGAACGACAACTGGATGGGATTCTGCTTCCATAATTACCTCTTTC
66 CACCAGGCGGAACGACAACGGGATGGGATTCTGCTTCCATAATTACCTCTTTC
1442351 ACGGTGTGGT
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
123 107 1.00
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (123 bp):
GACTTTCTTTTCTGCATGGGACAGTGCCCGTGACATCTCCGCGAAGTCGTAAAGAGCCTTGTTCT
CACCAGGCGGAACGACAACGGGATGGGATTCTGCTTCCATAATTACCTCTTTCTCAAG
Found at i:1451295 original size:22 final size:24
Alignment explanation
Indices: 1451249--1451296 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
1451239 AAGAAATGGA
1451249 AATAAAAAATTGTATTAATAATTT
1 AATAAAAAATTGTATTAATAATTT
* *
1451273 AATAATAAATT-T-TTAATATTTT
1 AATAAAAAATTGTATTAATAATTT
1451295 AA
1 AA
1451297 ATTTTAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.50
23 1 0.05
24 10 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
AATAAAAAATTGTATTAATAATTT
Found at i:1454836 original size:4 final size:4
Alignment explanation
Indices: 1454827--1454858 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
1454817 ATCTCTATAG
*
1454827 ATCT ATCT ATCT ATCT ATCT ATCT ATTT ATCT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
1454859 TTTGCATGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (4 bp):
ATCT
Found at i:1456349 original size:2 final size:2
Alignment explanation
Indices: 1456292--1456336 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
1456282 GATAGAGAAA
* * *
1456292 AG AG AG AT AG AG AA AG CG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1456334 AG A
1 AG A
1456337 AAACAAGGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.44, T:0.02
Consensus pattern (2 bp):
AG
Found at i:1464704 original size:21 final size:21
Alignment explanation
Indices: 1464672--1464724 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
1464662 TTATATTATT
* *
1464672 TTTGATTAAATAAGATTATAAA
1 TTTGA-TAAATAAAATTACAAA
*
1464694 TTTGATAAATAAAATTACGAA
1 TTTGATAAATAAAATTACAAA
1464715 TTTGAATAAA
1 TTTG-ATAAA
1464725 AATTAGATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (21 bp):
TTTGATAAATAAAATTACAAA
Found at i:1466278 original size:10 final size:10
Alignment explanation
Indices: 1466263--1466287 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1466253 TATTCAAATA
1466263 TTTATATTAT
1 TTTATATTAT
1466273 TTTATATTAT
1 TTTATATTAT
1466283 TTTAT
1 TTTAT
1466288 TTGTTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTATATTAT
Found at i:1468268 original size:39 final size:39
Alignment explanation
Indices: 1468214--1468292 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
1468204 TATAAATATC
1468214 TTAAAGTGTTTAGAAGCATCCAAAAATTAGAAATTTATA
1 TTAAAGTGTTTAGAAGCATCCAAAAATTAGAAATTTATA
1468253 TTAAAGTGTTTAGAAGCATCCAAAAATTAGAAATTTATA
1 TTAAAGTGTTTAGAAGCATCCAAAAATTAGAAATTTATA
1468292 T
1 T
1468293 AATGTCTAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.34
Consensus pattern (39 bp):
TTAAAGTGTTTAGAAGCATCCAAAAATTAGAAATTTATA
Found at i:1469373 original size:22 final size:21
Alignment explanation
Indices: 1469297--1469373 Score: 59
Period size: 22 Copynumber: 3.6 Consensus size: 21
1469287 ATTAATCATG
1469297 TAATACTTAAAAATAGTCTCG--
1 TAATACTTAAAAATAGT-T-GTA
* *
1469318 TAATATTTAAAAAGTAGTTATA
1 TAATACTTAAAAA-TAGTTGTA
* **
1469340 CAATACCCAAAAATCAGTTGTA
1 TAATACTTAAAAAT-AGTTGTA
1469362 TAATACTTAAAA
1 TAATACTTAAAA
1469374 CTACCAAAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
21 14 0.33
22 28 0.67
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (21 bp):
TAATACTTAAAAATAGTTGTA
Found at i:1472404 original size:2 final size:2
Alignment explanation
Indices: 1472397--1472422 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1472387 ACATACATAC
1472397 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
1472423 CTTCTGTACA
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:1477568 original size:17 final size:19
Alignment explanation
Indices: 1477536--1477572 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
1477526 AAGAAGTTAT
1477536 ACTTATATTAATTTAAAAA
1 ACTTATATTAATTTAAAAA
1477555 ACTTAT-TTAA-TTAAAAA
1 ACTTATATTAATTTAAAAA
1477572 A
1 A
1477573 ATTTTAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 4 0.22
19 6 0.33
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
ACTTATATTAATTTAAAAA
Found at i:1477573 original size:19 final size:19
Alignment explanation
Indices: 1477536--1477573 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1477526 AAGAAGTTAT
*
1477536 ACTTATATTAATTTAAAAA
1 ACTTATATTAATTAAAAAA
1477555 ACTTAT-TTAATTAAAAAA
1 ACTTATATTAATTAAAAAA
1477573 A
1 A
1477574 TTTTAAAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
ACTTATATTAATTAAAAAA
Found at i:1489735 original size:2 final size:2
Alignment explanation
Indices: 1489728--1489770 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
1489718 TTAATTAAAG
* * * *
1489728 TA TA TA TA TA TA TA TA TA TG TA TG TA TG TA TA AA 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
1489770 T
1 T
1489771 TTGTACTTGA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1503296 original size:40 final size:39
Alignment explanation
Indices: 1503236--1503315 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 39
1503226 TTTAATATTC
*
1503236 TGGGGGGGATTGAAACATTTGTAAATGTCTTGTAAGTGT
1 TGGGGGGGATTGAAACATTTGTAAATATCTTGTAAGTGT
*
1503275 TGGGAGGGGATTAGAAA-ATTTGTAACTATCTTGTAAGTGT
1 TGGG-GGGGATT-GAAACATTTGTAAATATCTTGTAAGTGT
1503315 T
1 T
1503316 TAGAATGACT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 4 0.11
40 29 0.78
41 4 0.11
ACGTcount: A:0.28, C:0.05, G:0.31, T:0.36
Consensus pattern (39 bp):
TGGGGGGGATTGAAACATTTGTAAATATCTTGTAAGTGT
Found at i:1503512 original size:21 final size:21
Alignment explanation
Indices: 1503472--1503514 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1503462 AATACTATTT
*
1503472 ATTAAAATATTTAACTTTTAA
1 ATTAAAATATTTAACATTTAA
1503493 ATTAAAATATTTATA-ATTTAA
1 ATTAAAATATTTA-ACATTTAA
1503514 A
1 A
1503515 CATTAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTAAAATATTTAACATTTAA
Found at i:1509035 original size:118 final size:120
Alignment explanation
Indices: 1508825--1509057 Score: 398
Period size: 118 Copynumber: 2.0 Consensus size: 120
1508815 ATTCATGAAT
* *
1508825 AAGTTGTATATTCCTAAAAGAAATTAAATACAATTCATGAATATATAATGACTGAAAGTTTCATT
1 AAGTTGTATATTCCTAAAAGAAATTAAATACAATTCATAAATATATAATGACTAAAAGTTTCATT
*
1508890 TGAAGAAAGAAACACCTAAAAGTATTAGCAATAACAACCAAGAGGAAAAAATAAC
66 TGAAGAAAGAAACACCTAAAAGTATTAGCAATAACAACCAAAAGGAAAAAATAAC
* *
1508945 AAGTTGTATATTCCTAAAAGAAATT-AATACAATTCATAAATATCT-ATTACTAAAAGTTTCATT
1 AAGTTGTATATTCCTAAAAGAAATTAAATACAATTCATAAATATATAATGACTAAAAGTTTCATT
*
1509008 TGAAGAAAGAAACACCTAAATGTATTAGCAATAACAACCAAAAGGAAAAA
66 TGAAGAAAGAAACACCTAAAAGTATTAGCAATAACAACCAAAAGGAAAAA
1509058 GTAATGATAA
Statistics
Matches: 107, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
118 64 0.60
119 18 0.17
120 25 0.23
ACGTcount: A:0.51, C:0.12, G:0.11, T:0.26
Consensus pattern (120 bp):
AAGTTGTATATTCCTAAAAGAAATTAAATACAATTCATAAATATATAATGACTAAAAGTTTCATT
TGAAGAAAGAAACACCTAAAAGTATTAGCAATAACAACCAAAAGGAAAAAATAAC
Found at i:1513956 original size:14 final size:15
Alignment explanation
Indices: 1513937--1513975 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1513927 AATAATCATA
1513937 ATTTTAAAATATTT-
1 ATTTTAAAATATTTG
*
1513951 ATTTTAAAAAATTTG
1 ATTTTAAAATATTTG
*
1513966 ACTTTAAAAT
1 ATTTTAAAAT
1513976 TTAAATGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (15 bp):
ATTTTAAAATATTTG
Found at i:1514007 original size:18 final size:18
Alignment explanation
Indices: 1513986--1514022 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1513976 TTAAATGTTT
*
1513986 ATTAAATAATACTGTATA
1 ATTAAATAATAATGTATA
1514004 ATTAAATAATAATGTATA
1 ATTAAATAATAATGTATA
1514022 A
1 A
1514023 ATAACATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (18 bp):
ATTAAATAATAATGTATA
Found at i:1533771 original size:13 final size:15
Alignment explanation
Indices: 1533738--1533772 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1533728 GACCACCGTG
*
1533738 TCTCTCTCTCCACCC
1 TCTCTCTCCCCACCC
*
1533753 TCTCTCTCCCCACCT
1 TCTCTCTCCCCACCC
1533768 TCTCT
1 TCTCT
1533773 GGCCTCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.57, G:0.00, T:0.37
Consensus pattern (15 bp):
TCTCTCTCCCCACCC
Found at i:1535154 original size:29 final size:29
Alignment explanation
Indices: 1535110--1535213 Score: 172
Period size: 29 Copynumber: 3.6 Consensus size: 29
1535100 TGCCTTAATT
* *
1535110 GAAAATTGAAAAATCTTTTACCACATAAA
1 GAAAATTGAAAAATCTTGTACCAAATAAA
* *
1535139 GAAAATTGAAATATCTTGTACCAAATGAA
1 GAAAATTGAAAAATCTTGTACCAAATAAA
1535168 GAAAATTGAAAAATCTTGTACCAAATAAA
1 GAAAATTGAAAAATCTTGTACCAAATAAA
1535197 GAAAATTGAAAAATCTT
1 GAAAATTGAAAAATCTT
1535214 TTCTCTCTCT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 69 1.00
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.27
Consensus pattern (29 bp):
GAAAATTGAAAAATCTTGTACCAAATAAA
Found at i:1560497 original size:21 final size:21
Alignment explanation
Indices: 1560425--1560497 Score: 51
Period size: 21 Copynumber: 3.5 Consensus size: 21
1560415 TGTATATTAT
* *
1560425 TTTTAATTATAAAATATTATTA
1 TTTTAATT-TAAAAAATTAATA
* * * *
1560447 -TTAAACTTAAAAAAATAAAA
1 TTTTAATTTAAAAAATTAATA
*
1560467 TTATT-TTTTAAAAAATTAATA
1 TT-TTAATTTAAAAAATTAATA
1560488 TTTTAATTTA
1 TTTTAATTTA
1560498 TTTATTAACA
Statistics
Matches: 36, Mismatches: 12, Indels: 7
0.65 0.22 0.13
Matches are distributed among these distances:
20 11 0.31
21 24 0.67
22 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTTAATTTAAAAAATTAATA
Found at i:1563374 original size:22 final size:22
Alignment explanation
Indices: 1563333--1563374 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1563323 ATTGAGCATT
* * *
1563333 TTTATTATAAAATTTTTTAAAA
1 TTTAATATAAAATATATTAAAA
1563355 TTTAATATAAAATATATTAA
1 TTTAATATAAAATATATTAA
1563375 GTAAAAAATT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTAATATAAAATATATTAAAA
Found at i:1575485 original size:19 final size:19
Alignment explanation
Indices: 1575452--1575490 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1575442 TCTTTGTTTG
1575452 AAATAAAGTGAGAAAAGAAA
1 AAATAAAGTGAGAAAA-AAA
1575472 AAATAAAG-GAGAAAAAAA
1 AAATAAAGTGAGAAAAAAA
1575490 A
1 A
1575491 GTTGTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 7 0.37
20 8 0.42
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (19 bp):
AAATAAAGTGAGAAAAAAA
Found at i:1588359 original size:26 final size:27
Alignment explanation
Indices: 1588329--1588390 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
1588319 TATTCAAAAA
1588329 AATTCAAATAAATATTTCTTTTAAAG-
1 AATTCAAATAAATATTTCTTTTAAAGC
* * *
1588355 AATTCAAATAAGTCTTTTTTTTAAAGC
1 AATTCAAATAAATATTTCTTTTAAAGC
*
1588382 AAGTCAAAT
1 AATTCAAAT
1588391 TTAAATCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 23 0.74
27 8 0.26
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (27 bp):
AATTCAAATAAATATTTCTTTTAAAGC
Found at i:1602679 original size:20 final size:19
Alignment explanation
Indices: 1602650--1602697 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1602640 TACCCTAATC
*
1602650 TAATAATAAATTATAATTTT
1 TAATATTAAATT-TAATTTT
*
1602670 TAATATTAAAATTTTATTTT
1 TAATATT-AAATTTAATTTT
*
1602690 TTATATTA
1 TAATATTA
1602698 TTTAACGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 18 0.75
21 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TAATATTAAATTTAATTTT
Found at i:1602690 original size:21 final size:20
Alignment explanation
Indices: 1602657--1602697 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1602647 ATCTAATAAT
1602657 AAATTATAATTTTTAATATTA
1 AAATTATAATTTTT-ATATTA
* *
1602678 AAATTTTATTTTTTATATTA
1 AAATTATAATTTTTATATTA
1602698 TTTAACGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
AAATTATAATTTTTATATTA
Found at i:1613796 original size:19 final size:21
Alignment explanation
Indices: 1613757--1613801 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
1613747 TAAGGTATAA
1613757 TATTTAAAGAAATTCTTAAAT
1 TATTTAAAGAAATTCTTAAAT
1613778 TATTTAAA-AAATT-TTAAAT
1 TATTTAAAGAAATTCTTAAAT
*
1613797 AATTT
1 TATTT
1613802 TTTTATTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.43
20 5 0.22
21 8 0.35
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
TATTTAAAGAAATTCTTAAAT
Found at i:1638883 original size:4 final size:4
Alignment explanation
Indices: 1638876--1638901 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1638866 TATATATATA
1638876 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
1638902 TAACTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:1638916 original size:2 final size:2
Alignment explanation
Indices: 1638909--1638974 Score: 57
Period size: 2 Copynumber: 34.5 Consensus size: 2
1638899 TTTTAACTTT
* * * *
1638909 TA TA TA TA GA TG TA TA TA TA TA TA TA TA -A TA TA -A T- TG TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1638948 TG TG 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 TA T
1638975 GGTGTTTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
1 3 0.05
2 53 0.95
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1644606 original size:20 final size:20
Alignment explanation
Indices: 1644568--1644606 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1644558 ATCTAGTTCA
**
1644568 TTTCTTATTTGTTCTTTTTT
1 TTTCTTATTTGTTAATTTTT
*
1644588 TTTCTTTTTTGTTAATTTT
1 TTTCTTATTTGTTAATTTT
1644607 AACTGCAAAA
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:0.08, C:0.08, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTCTTATTTGTTAATTTTT
Found at i:1651011 original size:2 final size:2
Alignment explanation
Indices: 1651004--1651047 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1650994 AAGGTTTGCA
* *
1651004 AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG AG GG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1651046 AG
1 AG
1651048 GGGAAGAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1660505 original size:14 final size:15
Alignment explanation
Indices: 1660486--1660527 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
1660476 AGAACACAGG
*
1660486 GAAAAATAAAAA-GT
1 GAAAAATAAAAATAT
1660500 GAAAAATACAAAATAT
1 GAAAAATA-AAAATAT
1660516 GAATAAATAAAA
1 GAA-AAATAAAA
1660528 TATTATAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 8 0.33
15 4 0.17
16 7 0.29
17 5 0.21
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (15 bp):
GAAAAATAAAAATAT
Found at i:1681102 original size:5 final size:5
Alignment explanation
Indices: 1681092--1681118 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1681082 TTCCATTAAA
1681092 AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA
1681119 GAGCATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1689270 original size:17 final size:17
Alignment explanation
Indices: 1689256--1689328 Score: 68
Period size: 16 Copynumber: 4.6 Consensus size: 17
1689246 GTTTATTTTT
1689256 TTATTTATATTATTTAA
1 TTATTTATATTATTTAA
1689273 TTATTTATA-TATTTAA
1 TTATTTATATTATTTAA
* *
1689289 GTATTT-TA-TA--AAA
1 TTATTTATATTATTTAA
*
1689302 TTATATATATT-TTTAA
1 TTATTTATATTATTTAA
*
1689318 CTATTTATATT
1 TTATTTATATT
1689329 TTATGTATTA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
13 6 0.13
14 2 0.04
15 5 0.11
16 23 0.51
17 9 0.20
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (17 bp):
TTATTTATATTATTTAA
Found at i:1689297 original size:29 final size:28
Alignment explanation
Indices: 1689265--1689345 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
1689255 TTTATTTATA
*
1689265 TTATTTAATTATTTATATATTTAAGTATT
1 TTATTTAATTATTTATAT-TTTAACTATT
** *
1689294 TTATAAAATTATATATATTTTTAACTATT
1 TTATTTAATTATTTATA-TTTTAACTATT
*
1689323 TATATTTTATGTA-TTATATTTTA
1 T-TATTTAAT-TATTTATATTTTA
1689346 TAAATTTAAG
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
29 29 0.71
30 10 0.24
31 2 0.05
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.60
Consensus pattern (28 bp):
TTATTTAATTATTTATATTTTAACTATT
Found at i:1693565 original size:2 final size:2
Alignment explanation
Indices: 1693553--1693586 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1693543 GATAATAGTT
* *
1693553 TA TA CA TA TA TA TA TA TA TC 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
1693587 AAATGAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1716268 original size:2 final size:2
Alignment explanation
Indices: 1716261--1716285 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1716251 ACATACATAC
1716261 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 A
1716286 AGGATGAAAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1720939 original size:2 final size:2
Alignment explanation
Indices: 1720932--1720967 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1720922 ACATGGAGTT
1720932 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
1720968 GATAATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1730562 original size:3 final size:3
Alignment explanation
Indices: 1730554--1730579 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1730544 TATAAGCTTA
1730554 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
1730580 AATTTTCTTA
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:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1732033 original size:29 final size:30
Alignment explanation
Indices: 1731977--1732038 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
1731967 AGGATTAATC
* *
1731977 ATAAAGATTTAATTGATTGAAAA-TAAAAT
1 ATAAAGATTTAATTGAATGAAAAGAAAAAT
*
1732006 ATAAAGATTTTATT-AATGAAATAGAAAAAT
1 ATAAAGATTTAATTGAATGAAA-AGAAAAAT
1732036 ATA
1 ATA
1732039 GAATTTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 14 0.50
30 8 0.29
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (30 bp):
ATAAAGATTTAATTGAATGAAAAGAAAAAT
Found at i:1752055 original size:15 final size:17
Alignment explanation
Indices: 1752035--1752069 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1752025 TTGTTAACAA
1752035 ATAAAT-TTAAAAAT-T
1 ATAAATCTTAAAAATAT
1752050 ATAAATCTTAAAAATAT
1 ATAAATCTTAAAAATAT
1752067 ATA
1 ATA
1752070 TTCATAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 8 0.44
17 4 0.22
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAAATCTTAAAAATAT
Done.