Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397282.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_25.0, 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: 1368273
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 33278 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:1119897 original size:42 final size:43
Alignment explanation
Indices: 1119837--1119930 Score: 131
Period size: 42 Copynumber: 2.2 Consensus size: 43
1119827 ACTTCAAAAC
1119837 ATCATGTGCATGACGTGTAA-TATCATGTGCATAGTGTGTAA-T
1 ATCATGTGCATGACGTGTAACT-TCATGTGCATAGTGTGTAACT
** *
1119879 ATCATGTGCATGGTGTGTAACTTCATGTGCATGGTGTGTAACT
1 ATCATGTGCATGACGTGTAACTTCATGTGCATAGTGTGTAACT
1119922 -TCATGTGCA
1 ATCATGTGCA
1119931 CTTGATATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
42 45 0.96
43 2 0.04
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (43 bp):
ATCATGTGCATGACGTGTAACTTCATGTGCATAGTGTGTAACT
Found at i:1125384 original size:23 final size:23
Alignment explanation
Indices: 1125358--1125403 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1125348 TATGCTCTTG
* *
1125358 ATTTCTTTCTTTTGTGCTTTCAA
1 ATTTCTTTCTCTTGCGCTTTCAA
1125381 ATTTCTTTCTCTTGCGCTTTCAA
1 ATTTCTTTCTCTTGCGCTTTCAA
1125404 GACACCAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.13, C:0.22, G:0.09, T:0.57
Consensus pattern (23 bp):
ATTTCTTTCTCTTGCGCTTTCAA
Found at i:1125858 original size:29 final size:29
Alignment explanation
Indices: 1125825--1125901 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
1125815 TGAACATGGT
1125825 GTGTAACAATAATATTTTTTCAATATAAC
1 GTGTAACAATAATATTTTTTCAATATAAC
* * **
1125854 GTGTAACAACAACATTTTTTTCAATATGGC
1 GTGTAACAATAATA-TTTTTTCAATATAAC
* *
1125884 ATATAACAATAATATTTT
1 GTGTAACAATAATATTTT
1125902 CTTTTTCACC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 16 0.41
30 23 0.59
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (29 bp):
GTGTAACAATAATATTTTTTCAATATAAC
Found at i:1126012 original size:26 final size:24
Alignment explanation
Indices: 1125975--1126028 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1125965 ACGTGTAAAA
*
1125975 ATAATAATATTTTTTAACCATGGCAT
1 ATAATAATATTTTAT-A-CATGGCAT
1126001 ATAAT-ATGATTTTATACATGGCAT
1 ATAATAAT-ATTTTATACATGGCAT
1126025 ATAA
1 ATAA
1126029 CAACAGTACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 12 0.46
25 3 0.12
26 11 0.42
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (24 bp):
ATAATAATATTTTATACATGGCAT
Found at i:1127902 original size:23 final size:23
Alignment explanation
Indices: 1127876--1127940 Score: 130
Period size: 23 Copynumber: 2.8 Consensus size: 23
1127866 ATGGGATTTT
1127876 ATTTTATTTTTTATAAATTTAAA
1 ATTTTATTTTTTATAAATTTAAA
1127899 ATTTTATTTTTTATAAATTTAAA
1 ATTTTATTTTTTATAAATTTAAA
1127922 ATTTTATTTTTTATAAATT
1 ATTTTATTTTTTATAAATT
1127941 AGATCATCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
ATTTTATTTTTTATAAATTTAAA
Found at i:1133184 original size:30 final size:30
Alignment explanation
Indices: 1133148--1133208 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
1133138 ATAATGATAC
*
1133148 AAGAAAGTTTTCAAGTGTAAAAGTGCCAAA
1 AAGAAAGTTTCCAAGTGTAAAAGTGCCAAA
1133178 AAGAAAGTTTCCAAGTGTAAAAGTGCCAAA
1 AAGAAAGTTTCCAAGTGTAAAAGTGCCAAA
1133208 A
1 A
1133209 CGATTTGGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.21
Consensus pattern (30 bp):
AAGAAAGTTTCCAAGTGTAAAAGTGCCAAA
Found at i:1134596 original size:20 final size:17
Alignment explanation
Indices: 1134561--1134607 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
1134551 TTTATGTGAA
1134561 TTTGAATTTCTAAATTATG
1 TTTGAA-TTCTAAATT-TG
1134580 TCTTGAATTCTAGAATTTG
1 T-TTGAATTCTA-AATTTG
1134599 TTTG-ATTCT
1 TTTGAATTCT
1134608 CTCTTAAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.19
18 3 0.12
19 9 0.35
20 9 0.35
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.53
Consensus pattern (17 bp):
TTTGAATTCTAAATTTG
Found at i:1134960 original size:3 final size:3
Alignment explanation
Indices: 1134952--1134987 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1134942 AATTGTGATG
*
1134952 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1134988 TGTTTGAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1153810 original size:39 final size:39
Alignment explanation
Indices: 1153726--1153809 Score: 161
Period size: 39 Copynumber: 2.2 Consensus size: 39
1153716 TATATTGTGT
1153726 ACAAAAATGACAGCTTTAACATGTTTGTTTTAATTTAGA
1 ACAAAAATGACAGCTTTAACATGTTTGTTTTAATTTAGA
1153765 ACAAAAATGACAGCTTTAACATGTTTGTTTTAATTTAG-
1 ACAAAAATGACAGCTTTAACATGTTTGTTTTAATTTAGA
1153803 ACAAAAA
1 ACAAAAA
1153810 AACATGTTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 7 0.16
39 38 0.84
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.36
Consensus pattern (39 bp):
ACAAAAATGACAGCTTTAACATGTTTGTTTTAATTTAGA
Found at i:1153830 original size:29 final size:28
Alignment explanation
Indices: 1153782--1153870 Score: 106
Period size: 29 Copynumber: 3.1 Consensus size: 28
1153772 TGACAGCTTT
*
1153782 AACATGTTTGTTTTAATTTAGACAAAAA
1 AACATGTTTGTATTAATTTAGACAAAAA
* *
1153810 AACATGTTTGGTATTCATTTAGACAAGAA
1 AACATGTTT-GTATTAATTTAGACAAAAA
* *
1153839 AATATGTTTGTCTTAATTTAAGACAAGAAA
1 AACATGTTTGTATTAATTT-AGACAA-AAA
1153869 AA
1 AA
1153871 TATTTTTTAN
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
28 17 0.33
29 30 0.59
30 4 0.08
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (28 bp):
AACATGTTTGTATTAATTTAGACAAAAA
Found at i:1155424 original size:6 final size:6
Alignment explanation
Indices: 1155413--1155438 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1155403 AGGGAGGGGA
1155413 CAAAGC CAAAGC CAAAGC CAAAGC CA
1 CAAAGC CAAAGC CAAAGC CAAAGC CA
1155439 GTGAATTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.35, G:0.15, T:0.00
Consensus pattern (6 bp):
CAAAGC
Found at i:1161134 original size:29 final size:28
Alignment explanation
Indices: 1161085--1161235 Score: 151
Period size: 29 Copynumber: 5.3 Consensus size: 28
1161075 TAGAAGCTTT
*
1161085 AACATGTTTGTCTTAATTTAGACAAGAA
1 AACATATTTGTCTTAATTTAGACAAGAA
* * *
1161113 AATATATTTGATCTCAATTTAGGCAAGAA
1 AACATATTTG-TCTTAATTTAGACAAGAA
* * *
1161142 AACATGTTATGTCTTAATTTAGATAAGGA
1 AACATATT-TGTCTTAATTTAGACAAGAA
*
1161171 AACATATTTTGTCTTAATCTAGACAAG-A
1 AACATA-TTTGTCTTAATTTAGACAAGAA
* * * * *
1161199 AACATGTTTGCCTCAATTTAGATAAGAT
1 AACATATTTGTCTTAATTTAGACAAGAA
1161227 AACATATTT
1 AACATATTT
1161236 TTATTTTAAT
Statistics
Matches: 99, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
27 16 0.16
28 22 0.22
29 57 0.58
30 4 0.04
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (28 bp):
AACATATTTGTCTTAATTTAGACAAGAA
Found at i:1161178 original size:58 final size:55
Alignment explanation
Indices: 1161085--1161235 Score: 178
Period size: 58 Copynumber: 2.7 Consensus size: 55
1161075 TAGAAGCTTT
* * * * *
1161085 AACATGTTTGTCTTAATTTAGACAAGAAAATATATTTGATCTCAATTTAGGCAAGAA
1 AACATGTTTGTCTTAATTTAGATAAGGAAACATATTTG-TCTCAATCTAGACAAG-A
*
1161142 AACATGTTATGTCTTAATTTAGATAAGGAAACATATTTTGTCTTAATCTAGACAAGA
1 AACATGTT-TGTCTTAATTTAGATAAGGAAACATA-TTTGTCTCAATCTAGACAAGA
* *
1161199 AACATGTTTGCCTCAATTTAGATAA-GATAACATATTT
1 AACATGTTTGTCTTAATTTAGATAAGGA-AACATATTT
1161236 TTATTTTAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
55 5 0.06
56 21 0.25
57 17 0.20
58 36 0.43
59 4 0.05
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (55 bp):
AACATGTTTGTCTTAATTTAGATAAGGAAACATATTTGTCTCAATCTAGACAAGA
Found at i:1161253 original size:87 final size:87
Alignment explanation
Indices: 1161091--1161255 Score: 190
Period size: 87 Copynumber: 1.9 Consensus size: 87
1161081 CTTTAACATG
* * * * *
1161091 TTTGTCTTAATTTAGACAAGAAAATATATTTGATCTCAATTTAGGCAAGAAAACATGTTATGTCT
1 TTTGTCTTAATCTAGACAAGAAAACATATTTGACCTCAATTTAGACAAGAAAACATGTTATATCT
*
1161156 TAATTTAGATAAGGAAACATAT
66 TAATTAAGATAAGGAAACATAT
* * * * * *
1161178 TTTGTCTTAATCTAGACAAG-AAACATGTTTG-CCTCAATTTAGATAAGATAACATATTTTTATT
1 TTTGTCTTAATCTAGACAAGAAAACATATTTGACCTCAATTTAGACAAGAAAACAT-GTTATATC
1161241 TTAATTAAAGATAAG
65 TTAATT-AAGATAAG
1161256 AGTTGTCGTA
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
85 19 0.30
86 19 0.30
87 26 0.41
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (87 bp):
TTTGTCTTAATCTAGACAAGAAAACATATTTGACCTCAATTTAGACAAGAAAACATGTTATATCT
TAATTAAGATAAGGAAACATAT
Found at i:1175158 original size:17 final size:17
Alignment explanation
Indices: 1175136--1175180 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
1175126 TTATTGCTAA
1175136 AATAAAATTCAGTTAAG
1 AATAAAATTCAGTTAAG
1175153 AATAAAATTCAGTTAAG
1 AATAAAATTCAGTTAAG
1175170 AATAAAATTCA
1 AATAAAATTCA
1175181 TTATTACCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.56, C:0.07, G:0.09, T:0.29
Consensus pattern (17 bp):
AATAAAATTCAGTTAAG
Found at i:1183169 original size:90 final size:90
Alignment explanation
Indices: 1182999--1183175 Score: 232
Period size: 90 Copynumber: 2.0 Consensus size: 90
1182989 CTCTCAAGTT
* * *
1182999 TTGGTATTATTTTATTTTTATCATCTTCAAACTTCAAAAGGATTTCAATTGTTAGGTTTTAATTT
1 TTGGTATTATTTTATTTTCATCATCTCCAAACTTCAAAAGGATTTCAATGGTTAGGTTTTAATTT
* *
1183064 CAAGTTTTAGCAAATCAAGTAAATG
66 CAAGTTGTAACAAATCAAGTAAATG
* * * *
1183089 TTGGTATTATTTTGTTTTCATCATCTCCAAGCTTTAAAGGGATTTCAATGGTTA-GTCTTTAATT
1 TTGGTATTATTTTATTTTCATCATCTCCAAACTTCAAAAGGATTTCAATGGTTAGGT-TTTAATT
*
1183153 TCTAA-TTGTAATAAATCAAGTAA
65 TC-AAGTTGTAACAAATCAAGTAA
1183176 GTGACTCAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
89 2 0.03
90 71 0.95
91 2 0.03
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (90 bp):
TTGGTATTATTTTATTTTCATCATCTCCAAACTTCAAAAGGATTTCAATGGTTAGGTTTTAATTT
CAAGTTGTAACAAATCAAGTAAATG
Found at i:1183688 original size:28 final size:28
Alignment explanation
Indices: 1183656--1183717 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1183646 TCACTAGAAA
1183656 TAGATGAATACTTGTAACCCACCAAAAG
1 TAGATGAATACTTGTAACCCACCAAAAG
* * * * *
1183684 TAGATGAGTACTTTTAACTCACTAGAAG
1 TAGATGAATACTTGTAACCCACCAAAAG
1183712 TAGATG
1 TAGATG
1183718 GATAATGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (28 bp):
TAGATGAATACTTGTAACCCACCAAAAG
Found at i:1184069 original size:13 final size:13
Alignment explanation
Indices: 1184033--1184078 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1184023 ATGTTCTCAT
* *
1184033 TATATTTAAATGA
1 TATATTTTAATTA
* *
1184046 TATGTTCTAATTA
1 TATATTTTAATTA
1184059 TATATTTTAATTA
1 TATATTTTAATTA
1184072 TATATTT
1 TATATTT
1184079 AATGTTCTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (13 bp):
TATATTTTAATTA
Found at i:1186118 original size:27 final size:28
Alignment explanation
Indices: 1186088--1186157 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
1186078 ATTCGTAATC
*
1186088 AACAT-ATCAAAATGTCAAAAATAA-CTA
1 AACATCATCAAAAT-TCAAAAACAACCTA
* *
1186115 AACATCATCAGAATTCATAAACAACCTA
1 AACATCATCAAAATTCAAAAACAACCTA
*
1186143 AACATCATCAGAATT
1 AACATCATCAAAATT
1186158 AGACTCCTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 13 0.34
28 25 0.66
ACGTcount: A:0.53, C:0.20, G:0.04, T:0.23
Consensus pattern (28 bp):
AACATCATCAAAATTCAAAAACAACCTA
Found at i:1193712 original size:35 final size:35
Alignment explanation
Indices: 1193625--1193712 Score: 104
Period size: 35 Copynumber: 2.5 Consensus size: 35
1193615 TTTCACCAAG
* * *
1193625 CTTTTACAATAGTTTTTCACAAGTTCAGTCACAAA
1 CTTTAACAATGGTTTTTCACAAGTTCAATCACAAA
* ** *
1193660 CTTTACCAATGACTTTTCACAGGTTCAATCACAAA
1 CTTTAACAATGGTTTTTCACAAGTTCAATCACAAA
*
1193695 CTTTAATAATGGTTTTTC
1 CTTTAACAATGGTTTTTC
1193713 CTAAGATTAA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (35 bp):
CTTTAACAATGGTTTTTCACAAGTTCAATCACAAA
Found at i:1201046 original size:52 final size:52
Alignment explanation
Indices: 1200989--1201087 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
1200979 TGAAAAGACC
* *
1200989 AAATAATAAATCAAGTTAAAATATTTTCCTAA-ATCAAATGCAAGCAAAGCAT
1 AAATAATAAATCAAGGTAAAATATTTTCCTAACCT-AAATGCAAGCAAAGCAT
* *
1201041 AAATAATGAATTAAGGTAAAATATTTTCCTAACCTAAATGCAAGCAA
1 AAATAATAAATCAAGGTAAAATATTTTCCTAACCTAAATGCAAGCAA
1201088 TAAATCATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 41 0.98
53 1 0.02
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.27
Consensus pattern (52 bp):
AAATAATAAATCAAGGTAAAATATTTTCCTAACCTAAATGCAAGCAAAGCAT
Found at i:1201269 original size:35 final size:34
Alignment explanation
Indices: 1201230--1201300 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
1201220 AGATCTAGTG
*
1201230 AAACCCTCACAATAGCTTTTTCACAAGATCAAGCA
1 AAACCCTCACAA-AGCTTTTTCACAAGATCAAACA
** *
1201265 AAACCCTTGCAAAGCTTTTTCACAAGGTCAAACA
1 AAACCCTCACAAAGCTTTTTCACAAGATCAAACA
1201299 AA
1 AA
1201301 TCCTTTCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 22 0.69
35 10 0.31
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.23
Consensus pattern (34 bp):
AAACCCTCACAAAGCTTTTTCACAAGATCAAACA
Found at i:1203622 original size:24 final size:24
Alignment explanation
Indices: 1203586--1203643 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
1203576 TTGAGATTTC
* * *
1203586 ACAAGAAACACATATCAGCAATAA
1 ACAACAAATACATATCACCAATAA
1203610 ACAACAAATACATATCACCAATAA
1 ACAACAAATACATATCACCAATAA
1203634 ACAACAAATA
1 ACAACAAATA
1203644 ACAACAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.60, C:0.22, G:0.03, T:0.14
Consensus pattern (24 bp):
ACAACAAATACATATCACCAATAA
Found at i:1208009 original size:2 final size:2
Alignment explanation
Indices: 1208004--1208031 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1207994 TATTTCCTCC
1208004 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
1208032 TTGTCTATGT
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:1210619 original size:16 final size:16
Alignment explanation
Indices: 1210598--1210630 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1210588 AAGATTGAAG
1210598 AATTGATCACTCCACT
1 AATTGATCACTCCACT
1210614 AATTGATCACTCCACT
1 AATTGATCACTCCACT
1210630 A
1 A
1210631 GTTAACACAT
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:0.33, C:0.30, G:0.06, T:0.30
Consensus pattern (16 bp):
AATTGATCACTCCACT
Found at i:1212968 original size:56 final size:56
Alignment explanation
Indices: 1212897--1213009 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
1212887 TTGGGTGGAT
*
1212897 ACAGACTGGTCTTCTGTTGATGTCATCTCTCTTCCTTGAACCTTGGCTCTAATACC
1 ACAGACTGGTCTTCTGTTAATGTCATCTCTCTTCCTTGAACCTTGGCTCTAATACC
1212953 ACAGACTGGTCTTCTGTTAATGTCATCTCTCTTCCTTGAACCTTGGCTCTAATACC
1 ACAGACTGGTCTTCTGTTAATGTCATCTCTCTTCCTTGAACCTTGGCTCTAATACC
1213009 A
1 A
1213010 ACTATCACGT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.37
Consensus pattern (56 bp):
ACAGACTGGTCTTCTGTTAATGTCATCTCTCTTCCTTGAACCTTGGCTCTAATACC
Found at i:1213587 original size:13 final size:13
Alignment explanation
Indices: 1213569--1213595 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1213559 AAATAATTTT
1213569 TTTTTAATTAATG
1 TTTTTAATTAATG
1213582 TTTTTAATTAATG
1 TTTTTAATTAATG
1213595 T
1 T
1213596 AAATGAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:1213910 original size:18 final size:18
Alignment explanation
Indices: 1213884--1213947 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
1213874 TCATTTTTAA
* *
1213884 ATATATTATTAATATCAT
1 ATATTTTATTAATATTAT
**
1213902 ATATTTTATTTTTATTAT
1 ATATTTTATTAATATTAT
*
1213920 A-ATTTTA-TATATTTTAT
1 ATATTTTATTA-ATATTAT
1213937 ATATTTTATTA
1 ATATTTTATTA
1213948 TAATTTTTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
16 1 0.03
17 12 0.33
18 21 0.58
19 2 0.06
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTTTATTAATATTAT
Found at i:1213916 original size:24 final size:26
Alignment explanation
Indices: 1213887--1213951 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 26
1213877 TTTTTAAATA
1213887 TATTATTAATATCATATATTTTATTTT
1 TATTA-TAATATCATATATTTTATTTT
* *
1213914 TATTATAATTTTATATATTTTATATATTT
1 TATTATAATATCATATA-TTT-TAT-TTT
1213943 TATTATAAT
1 TATTATAAT
1213952 TTTTTATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 10 0.30
27 8 0.24
28 3 0.09
29 12 0.36
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (26 bp):
TATTATAATATCATATATTTTATTTT
Found at i:1213933 original size:9 final size:9
Alignment explanation
Indices: 1213900--1213972 Score: 73
Period size: 9 Copynumber: 8.2 Consensus size: 9
1213890 TATTAATATC
1213900 ATATATTTT
1 ATATATTTT
*
1213909 AT-TTTTATT
1 ATATATT-TT
1213918 ATA-ATTTT
1 ATATATTTT
1213926 ATATATTTT
1 ATATATTTT
1213935 ATATATTTT
1 ATATATTTT
1213944 ATTATAATTTT
1 A-TAT-ATTTT
*
1213955 -T-TATATT
1 ATATATTTT
1213962 ATATATTTT
1 ATATATTTT
1213971 AT
1 AT
1213973 TTTATTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
7 4 0.08
8 10 0.19
9 31 0.58
10 3 0.06
11 5 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
ATATATTTT
Found at i:1213971 original size:27 final size:27
Alignment explanation
Indices: 1213901--1213983 Score: 105
Period size: 27 Copynumber: 3.0 Consensus size: 27
1213891 ATTAATATCA
*
1213901 TATATTTTAT-TTTTATTATAATTTTAT
1 TATATTATATATTTTATTATAATTTT-T
*
1213928 ATATTTTATATATTTTATTATAATTTTT
1 -TATATTATATATTTTATTATAATTTTT
* *
1213956 TATATTATATATTTTATTTTATTTTTT
1 TATATTATATATTTTATTATAATTTTT
1213983 T
1 T
1213984 CTTTTAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
27 25 0.51
28 9 0.18
29 15 0.31
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (27 bp):
TATATTATATATTTTATTATAATTTTT
Found at i:1220196 original size:29 final size:30
Alignment explanation
Indices: 1220158--1220220 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
1220148 CACCTATTTA
* *
1220158 TAATAGCTAAGATAAATCCTTATTAAATAG
1 TAATAGCTAAGATAAATCCTAATCAAATAG
1220188 TAAT-GCTAAGATAAATCCTAATCAAATAG
1 TAATAGCTAAGATAAATCCTAATCAAATAG
1220217 TAAT
1 TAAT
1220221 CCTANNNNNN
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.32
Consensus pattern (30 bp):
TAATAGCTAAGATAAATCCTAATCAAATAG
Found at i:1225501 original size:29 final size:29
Alignment explanation
Indices: 1225467--1225529 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
1225457 ATTTATAGTA
*
1225467 GCTAAGATAAATCCTAATCAAATAGTAAT
1 GCTAAGATAAATCCTAATAAAATAGTAAT
*
1225496 GCTAAGATAAATCTTAATAAAATAGTAAT
1 GCTAAGATAAATCCTAATAAAATAGTAAT
*
1225525 CCTAA
1 GCTAA
1225530 TCCTAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.29
Consensus pattern (29 bp):
GCTAAGATAAATCCTAATAAAATAGTAAT
Found at i:1225618 original size:26 final size:25
Alignment explanation
Indices: 1225560--1225621 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
1225550 TACTAAAATT
1225560 CTAATAAAGATAAAAAAAATCTCAAA
1 CTAATAAA-ATAAAAAAAATCTCAAA
*
1225586 CTAAATAAAATAAAATAAAATC-CTAAG
1 CT-AATAAAATAAAA-AAAATCTC-AAA
1225613 CTAATAAAA
1 CTAATAAAA
1225622 ATACTGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 16 0.50
27 16 0.50
ACGTcount: A:0.65, C:0.11, G:0.03, T:0.21
Consensus pattern (25 bp):
CTAATAAAATAAAAAAAATCTCAAA
Found at i:1225622 original size:27 final size:26
Alignment explanation
Indices: 1225560--1225624 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
1225550 TACTAAAATT
*
1225560 CTAATAAAGATAAAAAAAATCTCAAA
1 CTAATAAAAATAAAAAAAATCTCAAA
*
1225586 CTAA-ATAAAATAAAATAAAATC-CTAAG
1 CTAATA-AAAATAAAA-AAAATCTC-AAA
1225613 CTAATAAAAATA
1 CTAATAAAAATA
1225625 CTGAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
25 1 0.03
26 13 0.39
27 18 0.55
28 1 0.03
ACGTcount: A:0.65, C:0.11, G:0.03, T:0.22
Consensus pattern (26 bp):
CTAATAAAAATAAAAAAAATCTCAAA
Found at i:1232682 original size:38 final size:38
Alignment explanation
Indices: 1232627--1232699 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
1232617 AATCCTTTTC
* *
1232627 TTTTCTTCCTTAGAATCTGTAAGGGAAATTCGATGCTA
1 TTTTCTTCCTTAAAATCTATAAGGGAAATTCGATGCTA
* *
1232665 TTTTTTTCCTTAAAATCTATAAGGGAAATTTGATG
1 TTTTCTTCCTTAAAATCTATAAGGGAAATTCGATG
1232700 GTGTTGAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.42
Consensus pattern (38 bp):
TTTTCTTCCTTAAAATCTATAAGGGAAATTCGATGCTA
Found at i:1234127 original size:117 final size:116
Alignment explanation
Indices: 1233892--1234119 Score: 268
Period size: 117 Copynumber: 1.9 Consensus size: 116
1233882 TACATTTTCG
* *
1233892 TTATCTTTCTTAAGTTATTCATTGACTAATAGTTTATATAATATAATATCTCTTCATTCTATATT
1 TTATCTTTCTTAAGTTACTCATAGACTAATAGTTTATATAATATAATATCTC-TCATTCTATATT
* * *
1233957 AGATGTTTACATTTGACTTGAATGAAAATTTAAAAAATTTTTTTTATATTTTTA
65 AGATGTTTACATTTGACTTGAATGAAAATTTAAAAAA--TTATCTAGATTTTTA
* *
1234011 TTATC-TTCTTTAGTTACTCATAGACTAATAGTTTATATTAATA-ACATATCTC-CATTCTATTT
1 TTATCTTTCTTAAGTTACTCATAGACTAATAGTTTATA-TAATATA-ATATCTCTCATTCTATAT
** *
1234073 TAGATGTTTATGTTTGACTTGTATGAAAA-TTAAGTAAAA-TATCTAGA
64 TAGATGTTTACATTTGACTTGAATGAAAATTTAA--AAAATTATCTAGA
1234120 CTGTTTTAAG
Statistics
Matches: 95, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
115 5 0.05
116 4 0.04
117 35 0.37
118 34 0.36
119 17 0.18
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.48
Consensus pattern (116 bp):
TTATCTTTCTTAAGTTACTCATAGACTAATAGTTTATATAATATAATATCTCTCATTCTATATTA
GATGTTTACATTTGACTTGAATGAAAATTTAAAAAATTATCTAGATTTTTA
Found at i:1237929 original size:8 final size:8
Alignment explanation
Indices: 1237916--1237941 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1237906 ATCACAGCAA
1237916 ACTATCCT
1 ACTATCCT
1237924 ACTATCCT
1 ACTATCCT
1237932 ACTATCCT
1 ACTATCCT
1237940 AC
1 AC
1237942 AAGGATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.38, G:0.00, T:0.35
Consensus pattern (8 bp):
ACTATCCT
Found at i:1238834 original size:33 final size:32
Alignment explanation
Indices: 1238777--1238839 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
1238767 TTTGCAATGT
1238777 TATAATTAAAATAAAAAACTTTAAAATAAAATA
1 TATAATTAAAATAAAAAAC-TTAAAATAAAATA
*
1238810 TATAATATAAGAATAAAAAA-TTAAAGTAAA
1 TATAAT-TAA-AATAAAAAACTTAAAATAAA
1238840 TTAAAATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 15 0.56
34 3 0.11
35 9 0.33
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.29
Consensus pattern (32 bp):
TATAATTAAAATAAAAAACTTAAAATAAAATA
Found at i:1239282 original size:23 final size:23
Alignment explanation
Indices: 1239252--1239298 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1239242 TGAAAGATGT
1239252 AGAGTTTTCTTTTCCTAAATAAC
1 AGAGTTTTCTTTTCCTAAATAAC
1239275 AGAGTTTTCTTTTCCTAAATAAC
1 AGAGTTTTCTTTTCCTAAATAAC
1239298 A
1 A
1239299 TGGTATCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.43
Consensus pattern (23 bp):
AGAGTTTTCTTTTCCTAAATAAC
Found at i:1249459 original size:21 final size:20
Alignment explanation
Indices: 1249417--1249467 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1249407 AATACTTATG
1249417 TATAAATTAATATTTGTATA
1 TATAAATTAATATTTGTATA
*
1249437 TATAAATATATTATTT-TATTA
1 TATAAAT-TAATATTTGTA-TA
*
1249458 TATATATTAA
1 TATAAATTAA
1249468 ATTAATGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TATAAATTAATATTTGTATA
Found at i:1249840 original size:214 final size:213
Alignment explanation
Indices: 1249274--1249898 Score: 789
Period size: 220 Copynumber: 2.9 Consensus size: 213
1249264 TAAAACTATA
** * * *
1249274 ATGTTATAATGCTTTATATCAAAGTCTATATAAATAATAACTAATTATAAACAATATGTTATAAA
1 ATGTTATAATATTTTATATCAAAGTTTGTATAAATAATAACTAATTACAAACAATATGTTATAAA
* *
1249339 AACTAAGATGATAAATAATTAAGTTATTAAGTGTAATTATATAAATAAAGTTTATTATAAATTAT
66 AACTAAGATGATAACTAATAAAGTTATTAAGTGTAATTATATAAATAAAGTTTATTATAAATTAT
* * *
1249404 AATAATACTTATGTATAAATT-AATATTTGTATATATAAATATATTATTTTATTATATATATTAA
131 AGTAATACTTATGTATAAATTAAATATATGTATATATATATATATTATTTTATTATATATATTAA
*
1249468 ATTAATGATACAACTTAT
196 ATTAATGACACAACTTAT
* *
1249486 ATGTTATAATGTTTTAGTTGTTATAACAAAGCTTGTATAAATAATAACTAATT-CTAAACAATAT
1 ATGTTATAA-----TA-TT-TTATATCAAAGTTTGTATAAATAATAACTAATTAC-AAAC-A-AT
* * *
1249550 ATGTT-TAAAAACTAAGATAATAACTAATAAAGTTATTAAGTGTAATCATATAAATAAAATTTAT
56 ATGTTATAAAAACTAAGATGATAACTAATAAAGTTATTAAGTGTAATTATATAAATAAAGTTTAT
* * * *
1249614 TATAAGTTATAGTAATGCTTATGCATAAATTAAATATATGTGTATATATA-ATATTATTTTATTA
121 TATAAATTATAGTAATACTTATGTATAAATTAAATATATGTATATATATATATATTATTTTATTA
*
1249678 TATATATATGAAATTAATGACACAATTTAT
186 TATATAT-T-AAATTAATGACACAACTTAT
** *
1249708 ATGTTATAATATTTTATATCAAAGTTTGTATTGATAATAACTAATTACAAGCAATATGTTATAAA
1 ATGTTATAATATTTTATATCAAAGTTTGTATAAATAATAACTAATTACAAACAATATGTTATAAA
* * * *
1249773 AACTAATG-TGATAACTAATAAAGCTATTAAGTATAATTATATAAAGAAAGTTTAATATAAATTA
66 AACTAA-GATGATAACTAATAAAGTTATTAAGTGTAATTATATAAATAAAGTTTATTATAAATTA
***
1249837 TAGTAATACTTATGTA-AATATTAAATATATGTATATA-ATATAT-TTATACAATTATATATATT
130 TAGTAATACTTATGTATAA-ATTAAATATATGTATATATATATATATTATTTTATTATATATATT
1249899 CATAACATTT
Statistics
Matches: 355, Mismatches: 40, Indels: 36
0.82 0.09 0.08
Matches are distributed among these distances:
212 10 0.03
213 27 0.08
214 92 0.26
215 33 0.09
216 3 0.01
217 3 0.01
218 1 0.00
219 33 0.09
220 103 0.29
221 23 0.06
222 27 0.08
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (213 bp):
ATGTTATAATATTTTATATCAAAGTTTGTATAAATAATAACTAATTACAAACAATATGTTATAAA
AACTAAGATGATAACTAATAAAGTTATTAAGTGTAATTATATAAATAAAGTTTATTATAAATTAT
AGTAATACTTATGTATAAATTAAATATATGTATATATATATATATTATTTTATTATATATATTAA
ATTAATGACACAACTTAT
Found at i:1256345 original size:2 final size:2
Alignment explanation
Indices: 1256338--1256372 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1256328 CTTTGGCAAC
*
1256338 AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1256373 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1263173 original size:16 final size:16
Alignment explanation
Indices: 1263147--1263184 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1263137 ATGGGTTGAA
1263147 ATTTT-TCACCATTTT
1 ATTTTCTCACCATTTT
1263162 ATTTTCTCACCATTTT
1 ATTTTCTCACCATTTT
1263178 AGTTTTC
1 A-TTTTC
1263185 CCATCATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.24
16 11 0.52
17 5 0.24
ACGTcount: A:0.18, C:0.21, G:0.03, T:0.58
Consensus pattern (16 bp):
ATTTTCTCACCATTTT
Found at i:1263192 original size:17 final size:16
Alignment explanation
Indices: 1263153--1263192 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1263143 TGAAATTTTT
*
1263153 CACCATTTTATTTTCT
1 CACCATTTTATTTTCC
1263169 CACCATTTTAGTTTTCC
1 CACCATTTTA-TTTTCC
*
1263186 CATCATT
1 CACCATT
1263193 GACCCAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.20, C:0.28, G:0.03, T:0.50
Consensus pattern (16 bp):
CACCATTTTATTTTCC
Found at i:1265578 original size:28 final size:28
Alignment explanation
Indices: 1265537--1265591 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1265527 TGATAAACTG
* *
1265537 TGATTATACATGGCAAGGCCACGGGTTA
1 TGATTATACATGGCAAAGCCACAGGTTA
*
1265565 TGATTATACGTGGCAAAGCCACAGGTT
1 TGATTATACATGGCAAAGCCACAGGTT
1265592 GTTGCATAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.25
Consensus pattern (28 bp):
TGATTATACATGGCAAAGCCACAGGTTA
Found at i:1275314 original size:2 final size:2
Alignment explanation
Indices: 1275307--1275331 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1275297 ACTCCTGACT
1275307 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
1275332 TGTCCATTTT
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:1277211 original size:25 final size:25
Alignment explanation
Indices: 1277182--1277254 Score: 146
Period size: 25 Copynumber: 2.9 Consensus size: 25
1277172 CCAATATTGG
1277182 GAACCTTTACATCCAAACCCTAATT
1 GAACCTTTACATCCAAACCCTAATT
1277207 GAACCTTTACATCCAAACCCTAATT
1 GAACCTTTACATCCAAACCCTAATT
1277232 GAACCTTTACATCCAAACCCTAA
1 GAACCTTTACATCCAAACCCTAA
1277255 CCATTAGCGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.37, C:0.33, G:0.04, T:0.26
Consensus pattern (25 bp):
GAACCTTTACATCCAAACCCTAATT
Found at i:1288876 original size:27 final size:28
Alignment explanation
Indices: 1288830--1288923 Score: 100
Period size: 27 Copynumber: 3.4 Consensus size: 28
1288820 TGCGTGCAAT
* * *
1288830 AACTTTTTTTCTTAACATGACATGTAAT
1 AACTTTTTTTCTCAATATGACATGTAAC
*
1288858 AA-TTTTTTTCTCAATATGACGTGTAAC
1 AACTTTTTTTCTCAATATGACATGTAAC
* * **
1288885 AATTATTTTTTTTCAATATGGTATGTAAC
1 AACT-TTTTTTCTCAATATGACATGTAAC
1288914 AACTTTTTTT
1 AACTTTTTTT
1288924 TCACGTACGC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
27 23 0.42
28 9 0.16
29 23 0.42
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.50
Consensus pattern (28 bp):
AACTTTTTTTCTCAATATGACATGTAAC
Found at i:1288924 original size:29 final size:28
Alignment explanation
Indices: 1288833--1288925 Score: 98
Period size: 29 Copynumber: 3.3 Consensus size: 28
1288823 GTGCAATAAC
* * *
1288833 TTTTTTTCTTAACATGACATGTAATAA-
1 TTTTTTTCTCAATATGACATGTAACAAT
*
1288860 TTTTTTTCTCAATATGACGTGTAACAAT
1 TTTTTTTCTCAATATGACATGTAACAAT
* **
1288888 TATTTTTTTTCAATATGGTATGTAACAACT
1 T-TTTTTTCTCAATATGACATGTAACAA-T
1288918 TTTTTTTC
1 TTTTTTTC
1288926 ACGTACGCTT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
27 23 0.43
28 1 0.02
29 28 0.52
30 2 0.04
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.52
Consensus pattern (28 bp):
TTTTTTTCTCAATATGACATGTAACAAT
Found at i:1289288 original size:123 final size:123
Alignment explanation
Indices: 1289065--1289292 Score: 339
Period size: 123 Copynumber: 1.9 Consensus size: 123
1289055 AGAGTATCCC
* * *
1289065 TTTTTATTTAACTTTGGAGTATATCCTTCTTAATTATGATAATAAATAGAACACCGACTATTAAT
1 TTTTTATTTAACTGTGGAGTATATCCTTCTTAATTATGATAATAAATACAACACCAACTATTAAT
* * *** *
1289130 CTAATACTATTTAATAACTTTAAATTGTCTGTTAAAGTCTGTTTTCTTTACTGTTATA
66 CTAATAATATTTAATAACATTAAATCACCTATTAAAGTCTGTTTTCTTTACTGTTATA
* * * *
1289188 TTTTTATTTAACTGTGGAGTTTATCCTTCTTAATTATGATAATAAATACAATAGCAACTATTAGT
1 TTTTTATTTAACTGTGGAGTATATCCTTCTTAATTATGATAATAAATACAACACCAACTATTAAT
1289253 CTAATAATATTTAATAACATTAAATCACCTATTAAAGTCT
66 CTAATAATATTTAATAACATTAAATCACCTATTAAAGTCT
1289293 CTATAATAAT
Statistics
Matches: 92, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
123 92 1.00
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.44
Consensus pattern (123 bp):
TTTTTATTTAACTGTGGAGTATATCCTTCTTAATTATGATAATAAATACAACACCAACTATTAAT
CTAATAATATTTAATAACATTAAATCACCTATTAAAGTCTGTTTTCTTTACTGTTATA
Found at i:1290886 original size:14 final size:14
Alignment explanation
Indices: 1290867--1290894 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1290857 AGCATGAAAG
1290867 TGTCACGGGCCACA
1 TGTCACGGGCCACA
1290881 TGTCACGGGCCACA
1 TGTCACGGGCCACA
1290895 GCCCAGACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.36, G:0.29, T:0.14
Consensus pattern (14 bp):
TGTCACGGGCCACA
Found at i:1290952 original size:27 final size:27
Alignment explanation
Indices: 1290920--1290977 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
1290910 GAGGCCCAAG
1290920 AGGGTGCCAGCCCACCAAGACCCATGT
1 AGGGTGCCAGCCCACCAAGACCCATGT
1290947 AGGGTGCCAGCCCACCAAGACCCATGT
1 AGGGTGCCAGCCCACCAAGACCCATGT
1290974 AGGG
1 AGGG
1290978 ATTTCCCTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.26, C:0.34, G:0.29, T:0.10
Consensus pattern (27 bp):
AGGGTGCCAGCCCACCAAGACCCATGT
Found at i:1291015 original size:15 final size:15
Alignment explanation
Indices: 1290995--1291052 Score: 91
Period size: 15 Copynumber: 3.9 Consensus size: 15
1290985 TCCCAAATAG
1290995 TTTTGGAGGGAAATC
1 TTTTGGAGGGAAATC
1291010 TTTTGGAGGGAAATC
1 TTTTGGAGGGAAATC
* *
1291025 CTTTGGAGGGAAA-A
1 TTTTGGAGGGAAATC
1291039 TTTTGGAGGGAAAT
1 TTTTGGAGGGAAAT
1291053 GGGTGGGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
14 12 0.31
15 27 0.69
ACGTcount: A:0.29, C:0.05, G:0.34, T:0.31
Consensus pattern (15 bp):
TTTTGGAGGGAAATC
Found at i:1291050 original size:29 final size:30
Alignment explanation
Indices: 1290996--1291052 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
1290986 CCCAAATAGT
*
1290996 TTTGGAGGGAAATCTTTTGGAGGGAAATCC
1 TTTGGAGGGAAATATTTTGGAGGGAAATCC
1291026 TTTGGAGGGAAA-ATTTTGGAGGGAAAT
1 TTTGGAGGGAAATATTTTGGAGGGAAAT
1291053 GGGTGGGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (30 bp):
TTTGGAGGGAAATATTTTGGAGGGAAATCC
Found at i:1298376 original size:18 final size:19
Alignment explanation
Indices: 1298353--1298392 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1298343 CAAATAGAGA
*
1298353 ATTTTA-GAGTAAAATAAT
1 ATTTTATGAATAAAATAAT
*
1298371 ATTTTATTAATAAAATAAT
1 ATTTTATGAATAAAATAAT
1298390 ATT
1 ATT
1298393 AAAATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
ATTTTATGAATAAAATAAT
Found at i:1322697 original size:41 final size:41
Alignment explanation
Indices: 1322642--1322736 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
1322632 TGTCTCAATA
*
1322642 AATGTGTGCATAAAATGAATATCTATGAGAATGATTTGAAT
1 AATGTGTGCATAAAATGAATATCAATGAGAATGATTTGAAT
*
1322683 AATGTGTGCTTAAAATGAATATCAATGAGAATGATTTGAAT
1 AATGTGTGCATAAAATGAATATCAATGAGAATGATTTGAAT
1322724 AATGTGTGCATAA
1 AATGTGTGCATAA
1322737 TTTCTTTGTA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (41 bp):
AATGTGTGCATAAAATGAATATCAATGAGAATGATTTGAAT
Found at i:1327161 original size:30 final size:30
Alignment explanation
Indices: 1327033--1327192 Score: 133
Period size: 30 Copynumber: 5.4 Consensus size: 30
1327023 ACTAAATTAT
* * * * *
1327033 TACATGCCATGCCTAAAATTCTTGAGCTGC
1 TACATGCCATGCATAAAAATCATAAGTTGC
* * * *
1327063 TACACGCTAAGCCTAAAAATCATAAGTTGC
1 TACATGCCATGCATAAAAATCATAAGTTGC
** * *
1327093 TACACACCATGCTTAAAAATCGTAAGTTGC
1 TACATGCCATGCATAAAAATCATAAGTTGC
*
1327123 TACATGCCATGCATCAAAATCATAAGTTGC
1 TACATGCCATGCATAAAAATCATAAGTTGC
* * * * * *
1327153 TTCGTGCCATGCCTAACAGTC-TACGTTGC
1 TACATGCCATGCATAAAAATCATAAGTTGC
1327182 TACATGCCATG
1 TACATGCCATG
1327193 TTGAAATTCA
Statistics
Matches: 104, Mismatches: 26, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
29 16 0.15
30 88 0.85
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (30 bp):
TACATGCCATGCATAAAAATCATAAGTTGC
Found at i:1327163 original size:60 final size:59
Alignment explanation
Indices: 1327078--1327192 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 59
1327068 GCTAAGCCTA
*
1327078 AAAATCATAAGTTGCTACACACCATGCTTAAAAATCGTAAGTTGCTACATGCCATGCATC
1 AAAATCATAAGTTGCTACACACCATGCCTAAAAATC-TAAGTTGCTACATGCCATGCATC
* *** * * *
1327138 AAAATCATAAGTTGCTTCGTGCCATGCCTAACAGTCTACGTTGCTACATGCCATG
1 AAAATCATAAGTTGCTACACACCATGCCTAAAAATCTAAGTTGCTACATGCCATG
1327193 TTGAAATTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
59 18 0.38
60 29 0.62
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (59 bp):
AAAATCATAAGTTGCTACACACCATGCCTAAAAATCTAAGTTGCTACATGCCATGCATC
Found at i:1327826 original size:28 final size:28
Alignment explanation
Indices: 1327795--1327882 Score: 142
Period size: 28 Copynumber: 3.2 Consensus size: 28
1327785 ATCAGTAAAA
*
1327795 TTTTTTGAACATGACGTATAACAATATT
1 TTTTTTGAACATGACGTGTAACAATATT
1327823 TTTTTTGAACATGACGTGTAACAATATT
1 TTTTTTGAACATGACGTGTAACAATATT
* *
1327851 TTTTTT-AACATGACGTGTAACATTAGT
1 TTTTTTGAACATGACGTGTAACAATATT
1327878 TTTTT
1 TTTTT
1327883 CGATATGGCG
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 24 0.42
28 33 0.58
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (28 bp):
TTTTTTGAACATGACGTGTAACAATATT
Found at i:1327852 original size:27 final size:27
Alignment explanation
Indices: 1327795--1327882 Score: 131
Period size: 27 Copynumber: 3.2 Consensus size: 27
1327785 ATCAGTAAAA
*
1327795 TTTTTTGAACATGACGTATAACAATATT
1 TTTTTTGAACATGACGTGTAACAATA-T
1327823 TTTTTTGAACATGACGTGTAACAATAT
1 TTTTTTGAACATGACGTGTAACAATAT
* * *
1327850 TTTTTTTAACATGACGTGTAACATTAG
1 TTTTTTGAACATGACGTGTAACAATAT
1327877 TTTTTT
1 TTTTTT
1327883 CGATATGGCG
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
27 31 0.55
28 25 0.45
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (27 bp):
TTTTTTGAACATGACGTGTAACAATAT
Found at i:1334371 original size:2 final size:2
Alignment explanation
Indices: 1334366--1334411 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1334356 GAGTGTGTAC
* *
1334366 AT AT AT GT AT AT AT AT AT AT AT GT 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
1334408 AT AT
1 AT AT
1334412 CCCATATTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1335347 original size:2 final size:2
Alignment explanation
Indices: 1335340--1335375 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1335330 CCACATGATG
1335340 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
1335376 GTAGAACACT
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:1336197 original size:11 final size:11
Alignment explanation
Indices: 1336149--1336198 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
1336139 TCTTTAAATT
1336149 TTTTATTTAAAA
1 TTTTA-TTAAAA
*
1336161 -TATATTAAGAA
1 TTTTATTAA-AA
1336172 TTTT-TTAAAA
1 TTTTATTAAAA
*
1336182 TTTTATTAATA
1 TTTTATTAAAA
1336193 TTTTAT
1 TTTTAT
1336199 AAGAAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
10 10 0.31
11 20 0.62
12 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (11 bp):
TTTTATTAAAA
Found at i:1336210 original size:22 final size:21
Alignment explanation
Indices: 1336157--1336214 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
1336147 TTTTTTATTT
* *
1336157 AAAATATATTAAGAATTTTTTA
1 AAAATATATTAA-TATTTTATA
* *
1336179 AAATTTTATTAATATTTTATA
1 AAAATATATTAATATTTTATA
1336200 AGAAATATATTAATA
1 A-AAATATATTAATA
1336215 AAATCAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 8 0.28
22 21 0.72
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
AAAATATATTAATATTTTATA
Found at i:1336435 original size:17 final size:17
Alignment explanation
Indices: 1336413--1336447 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1336403 AATTATTATC
*
1336413 TTATTTTTTATAACATA
1 TTATTTTTCATAACATA
1336430 TTATTTTTCATAACATA
1 TTATTTTTCATAACATA
1336447 T
1 T
1336448 ATATATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATTTTTCATAACATA
Found at i:1359785 original size:18 final size:18
Alignment explanation
Indices: 1359764--1359800 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1359754 CTCAGTTGTT
1359764 TTAGCTCCCTCAACTCTC
1 TTAGCTCCCTCAACTCTC
*
1359782 TTAGCTCTCTCAACTCTC
1 TTAGCTCCCTCAACTCTC
1359800 T
1 T
1359801 CAATTGAGTT
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:0.16, C:0.41, G:0.05, T:0.38
Consensus pattern (18 bp):
TTAGCTCCCTCAACTCTC
Done.