Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008495.1 Hibiscus syriacus cultivar Beakdansim tig00111338_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5120959
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 21
Found at i:1188024 original size:257 final size:257
Alignment explanation
Indices: 1187507--1188131 Score: 878
Period size: 257 Copynumber: 2.4 Consensus size: 257
1187497 ATAATCTAAT
*
1187507 TTTGGAAATAGTTTACTGGGTAAAAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATT
1 TTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATT
* * * ** *
1187572 TTCTAAAAACATTAAATGAAAAACTTTAAAAATCACTTTCTCATTTCTCAAAAATCATGTGAGAA
66 TTCTGAAAATACTAAATGAAAAACTTTGGAAATCACTTTCTCATTTCTCAAAAATCATGTGAAAA
* * * *
1187637 CATCCTAATCGAAGGTCTTATAGAGGGCCCAAAGGACTTAATATCTTACTCGAAAGAGTGACAAA
131 CATCCTAATCGAAGGTCTTACAGAGGGACCAAAGGACTTAATATCTCACTCGAAAGACTGACAAA
* * *
1187702 AGACCAGAAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCCCGAATGACTTATCAA
196 AGACCAGAAGGATTTAATCATCATGCTTGAAAGACTTACTAATGGCCCGAAGGACTTACCAA
* *
1187764 TTTGGTAAATAGTTTACTGGGTAAGAAACTTTGGAAATCACTTTCATACTTTTCAAAAAATTCAT
1 TTTGG-AAATAGTTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCAT
* * * *
1187829 TTTCTGAAAATACTAAATGAAAAAATTTGGAAATCGCTTTCTCATTTTTC-AAATTCATGTGAAA
65 TTTCTGAAAATACTAAATGAAAAACTTTGGAAATCACTTTCTCATTTCTCAAAAATCATGTGAAA
* * * * * *
1187893 ACATCCT-ACCTGAAGGTCTTACAGATGGATCAAATGACTT-ATCATCTCGCTCGAAAGACTTAC
130 ACATCCTAATC-GAAGGTCTTACAGAGGGACCAAAGGACTTAAT-ATCTCACTCGAAAGACTGAC
* * * *
1187956 AGATGACCTGAATGATTTAATCATCATGCTTGAAAGACTTACTAATGGCCCGAAGGACTTACCAA
193 AAAAGACCAGAAGGATTTAATCATCATGCTTGAAAGACTTACTAATGGCCCGAAGGACTTACCAA
* * *
1188021 TTTGGGAAATAGTTTACTGGGTAAGAAATTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTAAT
1 TTT-GGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCAT
* *
1188086 TTTCTGAAAGTACTAAATGAGAAACTTTGGAAATCACTTTCTCATT
65 TTTCTGAAAATACTAAATGAAAAACTTTGGAAATCACTTTCTCATT
1188132 ACGGGAAACT
Statistics
Matches: 325, Mismatches: 39, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
256 4 0.01
257 221 0.68
258 100 0.31
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (257 bp):
TTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATT
TTCTGAAAATACTAAATGAAAAACTTTGGAAATCACTTTCTCATTTCTCAAAAATCATGTGAAAA
CATCCTAATCGAAGGTCTTACAGAGGGACCAAAGGACTTAATATCTCACTCGAAAGACTGACAAA
AGACCAGAAGGATTTAATCATCATGCTTGAAAGACTTACTAATGGCCCGAAGGACTTACCAA
Found at i:1188537 original size:543 final size:543
Alignment explanation
Indices: 1187592--1188727 Score: 1728
Period size: 543 Copynumber: 2.1 Consensus size: 543
1187582 ATTAAATGAA
* * * * * *
1187592 AAACTTTAAAAATCACTTTCTCATTTCTCAAAAATCATGTGAGAACATCCTAATCGAAGGTCTTA
1 AAACTTTGAAAATCGCTTTCCCATTTTTC-AAAATTATGTGAAAACATCCTAATCGAAGGTCTTA
* *
1187657 TAGAGGGCCCAAAGGACTTAATATCTTACTCGAAAGAGTGACAAAAGACCAGAAGGATTTAATCA
65 TAGAGGGCCCAAAGGACATAATATCTTACTCGAAAGACTGACAAAAGACCAGAAGGATTTAATCA
* * *
1187722 TCATGCTTGAAAGACTTACTGATGGCCCGAATGACTTATCAATTTGGTAAATAGTTTACTGGGTA
130 TCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTACCAATTTGGTAAATAGTTTACTAGGTA
1187787 AGAAACTTTGGAAATCACTTTCATACTTTTCAAAAAATTCATTTTCTGAAAATACTAAATGAAAA
195 AGAAACTTTGGAAATCACTTTCATACTTTTCAAAAAATTCATTTTCTGAAAATACTAAATGAAAA
1187852 AATTTGGAAATCGCTTTCTCATTTTTCAAATTCATGTGAAAACATCCTACCTGAAGGTCTTACAG
260 AATTTGGAAATCGCTTTCTCATTTTTCAAATTCATGTGAAAACATCCTACCTGAAGGTCTTACAG
* *
1187917 ATGGATCAAATGACTTATCATCTCGCTCGAAAGACTTACAGATGACCTGAATGATTTAATCATCA
325 ATGGACCAAATGACTTATCATCTCGCTCGAAAGACTTACAGATGACCCGAATGATTTAATCATCA
** *
1187982 TGCTTGAAAGACTTACTAATGGCCCGAAGGACTTACCAATTTGGGAAATAGTTTACTGGGTAAGA
390 TGCTCAAAAGACTTACTAATGGCCCGAAGGACTTACCAATTTGGAAAATAGTTTACT-GGTAAGA
** * *
1188047 AATTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTAATTTTCTGAAAGTACTAAATGAGAAACT
454 AACATTGGAAATCACTTTCTTACTTTTCAAAAATTTAATTTTCTGAAAATACTAAATGAGAAACT
1188112 TTGGAAATCACTTTCTCATTACGGG
519 TTGGAAATCACTTTCTCATTACGGG
* ** *
1188137 AAACTTTGAAAATCGCTTTCCCATTTTTCAAAGTTATGTGAAAACATCCTGCTTGAAGGTCTTA-
1 AAACTTTGAAAATCGCTTTCCCATTTTTCAAAATTATGTGAAAACATCCTAATCGAAGGTCTTAT
* * * * *
1188201 CGGGTGGCCCAAAGGACAT-ATCATCTTACTCGAAAGACTGGCAGATGACCCA-AAGGATTTAAT
66 AGAG-GGCCCAAAGGACATAAT-ATCTTACTCGAAAGACTGACAAAAGA-CCAGAAGGATTTAAT
1188264 CATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTACCAATTTAGG-AAATAGTTTACTAG
128 CATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTACCAATTT-GGTAAATAGTTTACTAG
* * *
1188328 GTAA-AAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTTTGAAAATACTAAATGA
192 GTAAGAAACTTTGGAAATCACTTTCATACTTTTCAAAAAATTCATTTTCTGAAAATACTAAATGA
* * *
1188392 GAAACTTTGGAAATCGCTTTCTCATTTTTCAAATT-ATTGTGAAAACATTCTACCTGAAGGTCTT
257 AAAAATTTGGAAATCGCTTTCTCATTTTTCAAATTCA-TGTGAAAACATCCTACCTGAAGGTCTT
* * * * *
1188456 ACGGAT-GACCCAAATGGCTTATCATCTCGCTTGAAAGACTTATATATGACCCGAATGATTTAAT
321 ACAGATGGA-CCAAATGACTTATCATCTCGCTCGAAAGACTTACAGATGACCCGAATGATTTAAT
*
1188520 CATCATGCTCAAAAGACTTACTAATGGCCTGAAGGACTTACCAATTTGGAAAATAGTTTACTGGT
385 CATCATGCTCAAAAGACTTACTAATGGCCCGAAGGACTTACCAATTTGGAAAATAGTTTACTGGT
1188585 AAGAAACATTGGAAATCACTTTCTTACTTTTCAAAAATTTAATTTTCTGAAAATACTAAATGAGA
450 AAGAAACATTGGAAATCACTTTCTTACTTTTCAAAAATTTAATTTTCTGAAAATACTAAATGAGA
** *
1188650 AACTTTGGAAATTTCTTTCTCATTATGGG
515 AACTTTGGAAATCACTTTCTCATTACGGG
* * *
1188679 AAACTTTGAAACTCGCTTTCCCATTTTTCAAATTTATGTGAAAATATCC
1 AAACTTTGAAAATCGCTTTCCCATTTTTCAAAATTATGTGAAAACATCC
1188728 CACCCGAAGT
Statistics
Matches: 538, Mismatches: 47, Indels: 15
0.90 0.08 0.03
Matches are distributed among these distances:
542 139 0.26
543 232 0.43
544 137 0.25
545 30 0.06
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (543 bp):
AAACTTTGAAAATCGCTTTCCCATTTTTCAAAATTATGTGAAAACATCCTAATCGAAGGTCTTAT
AGAGGGCCCAAAGGACATAATATCTTACTCGAAAGACTGACAAAAGACCAGAAGGATTTAATCAT
CATGCTCGAAAGACTTACTGATGGCCCGAATGACTTACCAATTTGGTAAATAGTTTACTAGGTAA
GAAACTTTGGAAATCACTTTCATACTTTTCAAAAAATTCATTTTCTGAAAATACTAAATGAAAAA
ATTTGGAAATCGCTTTCTCATTTTTCAAATTCATGTGAAAACATCCTACCTGAAGGTCTTACAGA
TGGACCAAATGACTTATCATCTCGCTCGAAAGACTTACAGATGACCCGAATGATTTAATCATCAT
GCTCAAAAGACTTACTAATGGCCCGAAGGACTTACCAATTTGGAAAATAGTTTACTGGTAAGAAA
CATTGGAAATCACTTTCTTACTTTTCAAAAATTTAATTTTCTGAAAATACTAAATGAGAAACTTT
GGAAATCACTTTCTCATTACGGG
Found at i:1188599 original size:256 final size:256
Alignment explanation
Indices: 1188136--1188673 Score: 778
Period size: 256 Copynumber: 2.1 Consensus size: 256
1188126 CTCATTACGG
* * * *
1188136 GAAACTTTGAAAATCGCTTTCCCATTTTTCAAAGTTATGTGAAAACATCCTGCTTGAAGGTCTTA
1 GAAACTTTGGAAATCGCTTTCTCATTTTTCAAAGTTATGTGAAAACATCCTACCTGAAGGTCTTA
* * * *
1188201 CGGGTGGCCCAAAGGACATATCATCTTACTCGAAAGACTGGCAGATGACCCAAAGGATTTAATCA
66 CGGATGACCCAAAGGACATATCATCTCACTCGAAAGACTGACAGATGACCCAAAGGATTTAATCA
* * *
1188266 TCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTACCAATTTAGGAAATAGTTTACTAGGTA
131 TCATGCTCAAAAGACTTACTAATGGCCCGAAGGACTTACCAATTTAGGAAATAGTTTACTAGGTA
* * *
1188331 AAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTTTGAAAATACTAAATGA
196 AAAACATTGGAAATCACTTTCTTACTTTTCAAAAATTTAATTTTCTGAAAATACTAAATGA
*
1188392 GAAACTTTGGAAATCGCTTTCTCATTTTTCAAA-TTATTGTGAAAACATTCTACCTGAAGGTCTT
1 GAAACTTTGGAAATCGCTTTCTCATTTTTCAAAGTTA-TGTGAAAACATCCTACCTGAAGGTCTT
* * * * * * * *
1188456 ACGGATGACCCAAATGG-CTTATCATCTCGCTTGAAAGACTTATATATGACCCGAATGATTTAAT
65 ACGGATGACCCAAA-GGACATATCATCTCACTCGAAAGACTGACAGATGACCCAAAGGATTTAAT
*
1188520 CATCATGCTCAAAAGACTTACTAATGGCCTGAAGGACTTACCAATTT-GGAAAATAGTTTACT-G
129 CATCATGCTCAAAAGACTTACTAATGGCCCGAAGGACTTACCAATTTAGG-AAATAGTTTACTAG
1188583 GTAAGAAACATTGGAAATCACTTTCTTACTTTTCAAAAATTTAATTTTCTGAAAATACTAAATGA
193 GTAA-AAACATTGGAAATCACTTTCTTACTTTTCAAAAATTTAATTTTCTGAAAATACTAAATGA
**
1188648 GAAACTTTGGAAATTTCTTTCTCATT
1 GAAACTTTGGAAATCGCTTTCTCATT
1188674 ATGGGAAACT
Statistics
Matches: 252, Mismatches: 26, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
255 10 0.04
256 240 0.95
257 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (256 bp):
GAAACTTTGGAAATCGCTTTCTCATTTTTCAAAGTTATGTGAAAACATCCTACCTGAAGGTCTTA
CGGATGACCCAAAGGACATATCATCTCACTCGAAAGACTGACAGATGACCCAAAGGATTTAATCA
TCATGCTCAAAAGACTTACTAATGGCCCGAAGGACTTACCAATTTAGGAAATAGTTTACTAGGTA
AAAACATTGGAAATCACTTTCTTACTTTTCAAAAATTTAATTTTCTGAAAATACTAAATGA
Found at i:1201700 original size:94 final size:95
Alignment explanation
Indices: 1201523--1201700 Score: 252
Period size: 94 Copynumber: 1.9 Consensus size: 95
1201513 ACCAAAAGGG
* * *
1201523 AAAGTATATATACCATGGATTCCAGAATGTCGAAATGGTATCGATACTGAAATGGAGTATTGGTA
1 AAAGTATATATACCATGGATTCCAGAATGTAGAAATGGTATCAATACTGAAATGGAGTATCGGTA
* * *
1201588 CTATAGTATAGAACTATCGGTACTAGGAGT
66 CCACAATATAGAACTATCGGTACTAGGAGT
*
1201618 AAAGTAT-TGATACCATGGA-TCCATAATGTAGAAATGGTATCAATACTGAAATGGAGTATCGGT
1 AAAGTATAT-ATACCATGGATTCCAGAATGTAGAAATGGTATCAATACTGAAATGGAGTATCGGT
* *
1201681 ACCACAATATATAAGTATCG
65 ACCACAATATAGAACTATCG
1201701 ATACCATGGT
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
94 56 0.77
95 17 0.23
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (95 bp):
AAAGTATATATACCATGGATTCCAGAATGTAGAAATGGTATCAATACTGAAATGGAGTATCGGTA
CCACAATATAGAACTATCGGTACTAGGAGT
Found at i:1202295 original size:81 final size:80
Alignment explanation
Indices: 1202130--1202295 Score: 224
Period size: 81 Copynumber: 2.1 Consensus size: 80
1202120 CCTAGCTGTG
* * *
1202130 CATTTGACATAAAGGTGTCAATCATGCAGTTAGATGAAAGTTTAAATACATTTGAATAAAAGATT
1 CATTTGACAGAAAGGTGTCAATCATGCAGTTAGATGAAAGGTTAAATACATTTGAATAAAAGACT
* * * ** *
1202195 AATTGCCTAGCTGTG
66 AAATGCATAACAATA
* *
1202210 CATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGAC
1 CATTTGACAGAAAGGTGTCAATCATG-CAGTTAGATGAAAGGTTAAATACATTTGAATAAAAGAC
1202275 TAAATGCATAACAATA
65 TAAATGCATAACAATA
1202291 CATTT
1 CATTT
1202296 TTAGATAAAT
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
80 25 0.34
81 49 0.66
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (80 bp):
CATTTGACAGAAAGGTGTCAATCATGCAGTTAGATGAAAGGTTAAATACATTTGAATAAAAGACT
AAATGCATAACAATA
Found at i:1202836 original size:11 final size:11
Alignment explanation
Indices: 1202820--1202847 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1202810 AGCTAAAGGT
1202820 TTAGCTGATTC
1 TTAGCTGATTC
1202831 TTAGCTGATTC
1 TTAGCTGATTC
1202842 TTAGCT
1 TTAGCT
1202848 AAAACCGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.46
Consensus pattern (11 bp):
TTAGCTGATTC
Found at i:1208482 original size:93 final size:95
Alignment explanation
Indices: 1208313--1208483 Score: 240
Period size: 93 Copynumber: 1.8 Consensus size: 95
1208303 AAAAGGAGAG
* * ** *
1208313 TATCGATACCATGGATTCCAAAATGTCAAAATGGTATCGATACTGAAAGGGAGTATTGGTACCAT
1 TATCGATACCATGGATTCCAAAATGTCAAAATGGTATAGATACTGAAAGGGAGTATCGACACCAC
* *
1208378 AGTATAGAAGTATAGGTACTAGGAGGAAAC
66 AATATAAAAGTATAGGTACTAGGAGGAAAC
*
1208408 TATCGATACCATGGA-TCCAGAATGT-ATAAAT-GTATAGATACTGAAAGGGAGTATCGACACCA
1 TATCGATACCATGGATTCCAAAATGTCA-AAATGGTATAGATACTGAAAGGGAGTATCGACACCA
1208470 CAATATAAAAGTAT
65 CAATATAAAAGTAT
1208484 TGATACCATG
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
93 39 0.58
94 13 0.19
95 15 0.22
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (95 bp):
TATCGATACCATGGATTCCAAAATGTCAAAATGGTATAGATACTGAAAGGGAGTATCGACACCAC
AATATAAAAGTATAGGTACTAGGAGGAAAC
Found at i:1209404 original size:81 final size:81
Alignment explanation
Indices: 1208893--1209382 Score: 696
Period size: 81 Copynumber: 6.1 Consensus size: 81
1208883 ATTTTAAAAT
* * * * *
1208893 AAAGATTAATTGCCTAGCTATGCATTTGATAGAAAAGTGTCAATCATGCTAGTTAGGTGAAAGGT
1 AAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGT
1208958 TAAATACCTTTGAGTA
66 TAAATACCTTTGAGTA
* * * * * *
1208974 AAA-ATTAATTGCCTAGTTGTGCATTTTACAGAAAGGTTTTAATCATGCTAGTTAGATAAAAGGT
1 AAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGT
*
1209038 TAAATACCTTTAAGTA
66 TAAATACCTTTGAGTA
* * *
1209054 AAAGATTAATTGCCTAGCTATGCATTTGACAAAAAGGTGTCAATCATGCCAGGTAGATGAAAGGT
1 AAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGT
1209119 TAAATACCTTTGAGTA
66 TAAATACCTTTGAGTA
* * * * * * *
1209135 AAAGATTAATTGCATTGTTGTGAATTTGACAGAAAGGTTTTAATCATGCCAGTTAGATGAAGGGT
1 AAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGT
*
1209200 TAAATATCTTTGAGTA
66 TAAATACCTTTGAGTA
* * *
1209216 AAAGATTAATTGTCTAGCAGTGCATTTGACAGAAAGGTGTCAATCATGCTAGTTATG-TGAAAGG
1 AAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTA-GATGAAAGG
1209280 TTAAATACCTTTGAGTA
65 TTAAATACCTTTGAGTA
* * *
1209297 AAAGATAAATTGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATCATACCAGTTAGATGAAAGGT
1 AAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGT
1209362 TAAATACCTTTGAGTA
66 TAAATACCTTTGAGTA
1209378 AAAGA
1 AAAGA
1209383 CTAAATGCTT
Statistics
Matches: 358, Mismatches: 48, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
80 71 0.20
81 286 0.80
82 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (81 bp):
AAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGT
TAAATACCTTTGAGTA
Found at i:1214110 original size:25 final size:25
Alignment explanation
Indices: 1214081--1214135 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1214071 CTTAGAATAA
* *
1214081 GAAAAAGAAGAAGGAAAGGAAAAA-T
1 GAAAAAAAAGAA-GAAAAGAAAAATT
1214106 GAAAAAAAAAGAAGAAAAGAAAAATT
1 G-AAAAAAAAGAAGAAAAGAAAAATT
1214132 GAAA
1 GAAA
1214136 GATGGTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (25 bp):
GAAAAAAAAGAAGAAAAGAAAAATT
Found at i:1214117 original size:26 final size:26
Alignment explanation
Indices: 1214082--1214135 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
1214072 TTAGAATAAG
* *
1214082 AAAAAGAAGAAGGAAAGGAAAAA-TGA
1 AAAAAAAAGAA-GAAAAGAAAAATTGA
1214108 AAAAAAAAGAAGAAAAGAAAAATTGA
1 AAAAAAAAGAAGAAAAGAAAAATTGA
1214134 AA
1 AA
1214136 GATGGTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (26 bp):
AAAAAAAAGAAGAAAAGAAAAATTGA
Found at i:1215474 original size:114 final size:113
Alignment explanation
Indices: 1215284--1215614 Score: 346
Period size: 114 Copynumber: 2.9 Consensus size: 113
1215274 CAATGAAGAG
* * * * * *
1215284 TTCATAATGAGAATAGCTCATC-CAAGGAGGGAGAGAGTTCATAATAAGAAGAACTTGTTCAACC
1 TTCATAATGAGAAGAACTCATCTTAACGAGGAAGA-AGTTCATAATGAGAAGAACTTGTTCAACC
* *
1215348 TTTACTCAAATCTATCACATAAGGAGGTTGATCAACATTTCCAATTGAGAA
65 TTTACTCAAATCTATCACAGAAGGAGGTTGATCAACATTTCCAA--CAGAA
* * *
1215399 TTCATAATGAGAAGAACGCATCTTAA-GAGGAAGAAGTTCATAATGAGAAGAACTTGTTTAACAT
1 TTCATAATGAGAAGAACTCATCTTAACGAGGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
** * ** **
1215463 TTACTCAAATCTATCACAGAAAAAGATAT-ATCAACATTTTTAACAGGG
66 TTACTCAAATCTATCACAGAAGGAGGT-TGATCAACATTTCCAACAGAA
* * * *
1215511 TTCATAATGAGAAGAACTCAT-TTGAACAATGAGAAGAAGTTCATAATGAGAAGAACCTATTCGA
1 TTCATAATGAGAAGAACTCATCTT-AACGA-G-GAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* *
1215575 CCTTTCACTCAAATCTATCATAGAAGGAGGTGGATCAACA
63 CCTTT-ACTCAAATCTATCACAGAAGGAGGTTGATCAACA
1215615 CTTTTAACAT
Statistics
Matches: 179, Mismatches: 29, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
111 2 0.01
112 24 0.13
113 1 0.01
114 63 0.35
115 59 0.33
116 30 0.17
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (113 bp):
TTCATAATGAGAAGAACTCATCTTAACGAGGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
TTACTCAAATCTATCACAGAAGGAGGTTGATCAACATTTCCAACAGAA
Found at i:1218851 original size:31 final size:31
Alignment explanation
Indices: 1218816--1218877 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1218806 GTTTTTTTAG
* * * *
1218816 TATTTATTGTAGTTATTCTAGTCAAATAAAT
1 TATTTATTCTACTGATTCTAGTAAAATAAAT
1218847 TATTTATTCTACTGATTCTAGTAAAATAAAT
1 TATTTATTCTACTGATTCTAGTAAAATAAAT
1218878 GGAAATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (31 bp):
TATTTATTCTACTGATTCTAGTAAAATAAAT
Found at i:1219259 original size:21 final size:21
Alignment explanation
Indices: 1219233--1219273 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1219223 AATTACTGAT
*
1219233 AAAAGTTCTATATATCTATAG
1 AAAAGTTCGATATATCTATAG
*
1219254 AAAAGTTGGATATATCTATA
1 AAAAGTTCGATATATCTATA
1219274 TTCTATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (21 bp):
AAAAGTTCGATATATCTATAG
Found at i:1219299 original size:19 final size:20
Alignment explanation
Indices: 1219267--1219305 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
1219257 AGTTGGATAT
1219267 ATCTATATTCTATATAATAA
1 ATCTATATTCTATATAATAA
1219287 ATCTATA-TCTATATAATAA
1 ATCTATATTCTATATAATAA
1219306 TAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (20 bp):
ATCTATATTCTATATAATAA
Found at i:1219314 original size:26 final size:26
Alignment explanation
Indices: 1219264--1219312 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1219254 AAAAGTTGGA
**
1219264 TATATCTATATTCTATATAATAAATC
1 TATATCTATATAATATATAATAAATC
1219290 TATATCTATATAATA-ATAATAAA
1 TATATCTATATAATATATAATAAA
1219313 ATTAAGAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (26 bp):
TATATCTATATAATATATAATAAATC
Found at i:1221093 original size:138 final size:138
Alignment explanation
Indices: 1220841--1221574 Score: 879
Period size: 138 Copynumber: 5.3 Consensus size: 138
1220831 TATTTTAGAT
* * * * * *
1220841 TTAGTCCTTTAATTTAG-GGAAATTTTTAATTTCGTCCTTGCTTATGGTCGAGGTTGCATTTTAA
1 TTAGTCCTTTAATTTTGAGG-AATTTTTAATTTGGTCCTCGCTTATGCTCGAGGTTCCATTGTAA
* * * * *
1220905 TTATTCGAATCAATAATTGGATAAAATTGACAAGGTCAATAATTAGAGCCTCTACCTTAGGCTTA
65 TTATTCGAATCAATAATTGGTTAAAATTGACTAGGTTAATAATTAGAGCCTCCACCTTAGACTTA
1220970 ATTTCAAAC
130 ATTTCAAAC
* * * * *
1220979 TTAGTCCTTTAATTTTGAGGAATTTTTAGTTTGGTCTTTGCTTATGCTTGAGGTTCCATTTTAAT
1 TTAGTCCTTTAATTTTGAGGAATTTTTAATTTGGTCCTCGCTTATGCTCGAGGTTCCATTGTAAT
* *
1221044 TATTCGAATCAATAATTGGTTAAAATTGACTAGGTTAATAATTAAAGCCTCCA-CTTCAGGCTTA
66 TATTCGAATCAATAATTGGTTAAAATTGACTAGGTTAATAATTAGAGCCTCCACCTT-AGACTTA
1221108 ATTTCAAAC
130 ATTTCAAAC
* * * * * * *
1221117 TTATTCATTT-CTTTTAGAGGAATTTTTTATTTGGTCCTCTCTTATGCTCAAGGTTCTATTGTAA
1 TTAGTCCTTTAATTTT-GAGGAATTTTTAATTTGGTCCTCGCTTATGCTCGAGGTTCCATTGTAA
* * * * *
1221181 TTATTCGAATCAATAATTGATTAAAATTAACTAGGTTAATAATTAGATCCTTCACTTTAGACTTA
65 TTATTCGAATCAATAATTGGTTAAAATTGACTAGGTTAATAATTAGAGCCTCCACCTTAGACTTA
* *
1221246 ATTTTAAAT
130 ATTTCAAAC
* * * *
1221255 TTAGTCCTTTAATTTAGGGGGAA-TTTTAACTTT-GTCCTCACTTATGCTCGAGGTTTCATTGTA
1 TTAGTCCTTTAATTT-TGAGGAATTTTTAA-TTTGGTCCTCGCTTATGCTCGAGGTTCCATTGTA
* * * *
1221318 ATTTTTCGAATCAATAATTGGTTAAAATGGACTAGGTTAATAAGTAGAGCCTCCACCTTATACTT
64 ATTATTCGAATCAATAATTGGTTAAAATTGACTAGGTTAATAATTAGAGCCTCCACCTTAGACTT
1221383 AATTTCAAAC
129 AATTTCAAAC
* * * * *
1221393 ATAGTCCTTTAA-TTTAAGGGAATTTTTAATTTGGACCTCGCTTATGCTCGAAGTTCCAATGTAA
1 TTAGTCCTTTAATTTTGA-GGAATTTTTAATTTGGTCCTCGCTTATGCTCGAGGTTCCATTGTAA
* * * ** * *
1221457 TTATTTGAATCAATAATTGGTTAAAATTCACTAGGTTAAAAATTAGATTCTCCACATTAGCCTTA
65 TTATTCGAATCAATAATTGGTTAAAATTGACTAGGTTAATAATTAGAGCCTCCACCTTAGACTTA
1221522 ATTTCAAAC
130 ATTTCAAAC
* *
1221531 TTAGTCCCTTAATTTT-AGGGATTTTTAATTTGGTCCTCGCTTAT
1 TTAGTCCTTTAATTTTGAGGAATTTTTAATTTGGTCCTCGCTTAT
1221575 TGATAACTGT
Statistics
Matches: 507, Mismatches: 78, Indels: 23
0.83 0.13 0.04
Matches are distributed among these distances:
137 41 0.08
138 448 0.88
139 18 0.04
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (138 bp):
TTAGTCCTTTAATTTTGAGGAATTTTTAATTTGGTCCTCGCTTATGCTCGAGGTTCCATTGTAAT
TATTCGAATCAATAATTGGTTAAAATTGACTAGGTTAATAATTAGAGCCTCCACCTTAGACTTAA
TTTCAAAC
Found at i:1222459 original size:19 final size:19
Alignment explanation
Indices: 1222435--1222472 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1222425 TTAAAATAAT
*
1222435 ATTCTAAATCCTAATTAAA
1 ATTCTAAAACCTAATTAAA
*
1222454 ATTCTAAAACCTATTTAAA
1 ATTCTAAAACCTAATTAAA
1222473 CTAAAATACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTCTAAAACCTAATTAAA
Found at i:1222518 original size:32 final size:32
Alignment explanation
Indices: 1222477--1222537 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1222467 TTTAAACTAA
1222477 AATACCTAAAA-TAAATATAAAATA-TAAAAAT
1 AATACCTAAAACTAAAT-TAAAATACTAAAAAT
*
1222508 AATATCCTAAAACTTAATTAAAATACTAAA
1 AATA-CCTAAAACTAAATTAAAATACTAAA
1222538 GCCTATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 4 0.15
32 14 0.54
33 8 0.31
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (32 bp):
AATACCTAAAACTAAATTAAAATACTAAAAAT
Found at i:1222572 original size:76 final size:76
Alignment explanation
Indices: 1222375--1222557 Score: 238
Period size: 76 Copynumber: 2.5 Consensus size: 76
1222365 ATCTTAAATA
*
1222375 CTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAA-ATAATAT----T-T-AAAAT
1 CTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAATA-AATATAAAATATAAAAAT
* *
1222432 AATATTCTAAATC
64 AATATCCTAAAAC
*
1222445 CTAATTAAAATTCTAAAACCTATTTAAACTAAAATACCTAAAATAAATATAAAATATAAAAATAA
1 CTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAATAAATATAAAATATAAAAATAA
1222510 TATCCTAAAAC
66 TATCCTAAAAC
* *
1222521 TTAATTAAAATACTAAAGCCTATTTAAACTAAAATAC
1 CTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
1222558 AAAGATAAAA
Statistics
Matches: 98, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
69 5 0.05
70 40 0.41
71 1 0.01
74 1 0.01
75 1 0.01
76 50 0.51
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (76 bp):
CTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAATAAATATAAAATATAAAAATAA
TATCCTAAAAC
Found at i:1222581 original size:76 final size:74
Alignment explanation
Indices: 1222375--1222581 Score: 228
Period size: 76 Copynumber: 2.8 Consensus size: 74
1222365 ATCTTAAATA
* * *
1222375 CTAATTAAAACACTTAAAACTATTTAAACTAAAATAC---CTAAAA-ATAATATTT-AAAATAAT
1 CTAATTAAAATAC-TAAACCTATTTAAACTAAAATACAAAATAAAATATAATATTTAAAAATAAT
* *
1222435 ATTCTAAATC
65 ATCCTAAAAC
* * *
1222445 CTAATTAAAATTCTAAAACCTATTTAAACTAAAATACCTAAAAT-AAATATAAAATATAAAAATA
1 CTAATTAAAATACT-AAACCTATTTAAACTAAAATA-C-AAAATAAAATATAATATTTAAAAATA
1222509 ATATCCTAAAAC
63 ATATCCTAAAAC
* *
1222521 TTAATTAAAATACTAAAGCCTATTTAAACTAAAATACAAAGATAAAATATAATGTTTAAAA
1 CTAATTAAAATACTAAA-CCTATTTAAACTAAAATACAAA-ATAAAATATAATATTTAAAA
1222582 TATTATTATA
Statistics
Matches: 113, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
69 1 0.01
70 31 0.27
71 1 0.01
74 6 0.05
75 14 0.12
76 60 0.53
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.31
Consensus pattern (74 bp):
CTAATTAAAATACTAAACCTATTTAAACTAAAATACAAAATAAAATATAATATTTAAAAATAATA
TCCTAAAAC
Found at i:1224262 original size:5 final size:5
Alignment explanation
Indices: 1224249--1224290 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
1224239 AAACAAAACA
*
1224249 AAAT- AAATG GAATG AAATG AAATG AAATG AAATG AAAT- AAAT
1 AAATG AAATG AAATG AAATG AAATG AAATG AAATG AAATG AAAT
1224291 TTGGCTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 8 0.23
5 27 0.77
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.21
Consensus pattern (5 bp):
AAATG
Found at i:1227983 original size:70 final size:74
Alignment explanation
Indices: 1227902--1228092 Score: 245
Period size: 70 Copynumber: 2.6 Consensus size: 74
1227892 AACCTAAAAC
* *
1227902 ATCTTAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCT-A-AAA-ATAATAT-
1 ATCTTAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAACAAAGATAAAATA
*
1227962 TTAAAATAAT
65 TAAAAATAAT
1227972 AT-TCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAA
1 ATCT-TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT--AACAAAGATAAAA
1228036 TATAAAAATAAT
63 TATAAAAATAAT
* *
1228048 ATCTTAAAT-TTAATT-AAATACTAAAATCTATTTAAACTAAAATAC
1 ATCTTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
1228093 AAAGATAAAA
Statistics
Matches: 107, Mismatches: 5, Indels: 14
0.85 0.04 0.11
Matches are distributed among these distances:
69 6 0.06
70 40 0.37
73 1 0.01
74 32 0.30
75 11 0.10
76 16 0.15
77 1 0.01
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.32
Consensus pattern (74 bp):
ATCTTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAACAAAGATAAAATAT
AAAAATAAT
Found at i:1228116 original size:74 final size:73
Alignment explanation
Indices: 1227902--1228116 Score: 230
Period size: 74 Copynumber: 2.9 Consensus size: 73
1227892 AACCTAAAAC
* **
1227902 ATCTTAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATAC-CTA-AAAATA-ATATTT
1 ATCTTAAATCCTAATTAAAATAC-TAAAACTATTTAAACTAAAATACAAAATAAAATATATATTT
1227964 -AAAATAAT
65 AAAAATAAT
* *
1227972 AT-TCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATA-AA
1 ATCT-TAAATCCTAATTAAAATACTAAAA-CTATTTAAACTAAAATA-C-AAAATAAA-ATATAT
*
1228035 ATATAAAAATAAT
61 ATTTAAAAATAAT
*
1228048 ATCTTAAAT-TTAATT-AAATACTAAAATCTATTTAAACTAAAATACAAAGATAAAATATATTAT
1 ATCTTAAATCCTAATTAAAATACTAAAA-CTATTTAAACTAAAATACAAA-ATAAAATATA-TAT
1228111 TTAAAA
63 TTAAAA
1228117 TATTATTATA
Statistics
Matches: 123, Mismatches: 10, Indels: 20
0.80 0.07 0.13
Matches are distributed among these distances:
69 6 0.05
70 37 0.30
71 1 0.01
72 6 0.05
73 7 0.06
74 38 0.31
75 12 0.10
76 15 0.12
77 1 0.01
ACGTcount: A:0.56, C:0.11, G:0.01, T:0.32
Consensus pattern (73 bp):
ATCTTAAATCCTAATTAAAATACTAAAACTATTTAAACTAAAATACAAAATAAAATATATATTTA
AAAATAAT
Found at i:1228580 original size:138 final size:138
Alignment explanation
Indices: 1228328--1229246 Score: 1071
Period size: 138 Copynumber: 6.7 Consensus size: 138
1228318 GCACTTATCA
** * * *
1228328 CTTATGCTCGAGGTTCCATCATAATTATTCGAATCAATAATTAGTTAAAATTGACTAGATTAATA
1 CTTATGCTCGAGGTTCCATTGTAATTATTCGAATCAATAATTGGTTAAAATTAACTAGGTTAATA
* * * ** *
1228393 ATTAGAGCCTCTACTTTAGGCATAATTTCAAACTTAGTCCTTTCTTTTAGGGGATTTGTTTAA-T
66 ATTAGAGCCTCCATTTTAGGCTTAATTTCAAACTTAGTCCTTTAATTTAGGGGAATT-TTTAACT
1228457 TGGTCCTCG
130 TGGTCCTCG
* *
1228466 CTCATGCTCGAGGTTCGATTGTAATTATTCGAATCAATAATTGGTTAAAATTAACTAGGTTAATA
1 CTTATGCTCGAGGTTCCATTGTAATTATTCGAATCAATAATTGGTTAAAATTAACTAGGTTAATA
** * * *
1228531 ATTAGAGCCTCCATTTTAGGCTTAATTTTGAATTTAGTCCTTTAATTTAGGGGGATTTTGAACTT
66 ATTAGAGCCTCCATTTTAGGCTTAATTTCAAACTTAGTCCTTTAATTTAGGGGAATTTTTAACTT
*
1228596 GGTCCTCA
131 GGTCCTCG
* * * *
1228604 TTTATGCTCGAGGTTCCATTGTAAATT-TT-GAATCAATAATT-GCTAAAAATAGACTAGGCTAA
1 CTTATGCTCGAGGTTCCATTGT-AATTATTCGAATCAATAATTGGTTAAAATTA-ACTAGGTTAA
* * * *
1228666 TAAGTAGAGCCTCCATCTTAGGCTTAATTTCAAACATAATCCTTTAATTTAGGGGAATTTTTAA-
64 TAATTAGAGCCTCCATTTTAGGCTTAATTTCAAACTTAGTCCTTTAATTTAGGGGAATTTTTAAC
* *
1228730 TTCAGTTCTCG
129 TT-GGTCCTCG
* * *
1228741 CTTATGCTCGAGGTTCCATTATAATTATTTGAATAAATAATTGGTTAAAATTAACTAGGTTAATA
1 CTTATGCTCGAGGTTCCATTGTAATTATTCGAATCAATAATTGGTTAAAATTAACTAGGTTAATA
* * * * *
1228806 ATTATAGCCTACACTTTAGGCTTAATTTCAAATTTAGTCCTTTAATTTAGGGGGATTTTTAACTT
66 ATTAGAGCCTCCATTTTAGGCTTAATTTCAAACTTAGTCCTTTAATTTAGGGGAATTTTTAACTT
*
1228871 GGTCCTTAG
131 GGTCC-TCG
* * **
1228880 -TTATGCTCGAGGTTCCATTGTAATTTTTTGAATCAATAATTGGTTAAAATGGACTAGGTTAATA
1 CTTATGCTCGAGGTTCCATTGTAATTATTCGAATCAATAATTGGTTAAAATTAACTAGGTTAATA
* * * ** * * * * *
1228944 AGTACAACCTCCACCTTATGCTTAATTTTAAACATAGTCCTTTAATTTTGGGGAATTTTTAATTT
66 ATTAGAGCCTCCATTTTAGGCTTAATTTCAAACTTAGTCCTTTAATTTAGGGGAATTTTTAACTT
1229009 GGTCCTCG
131 GGTCCTCG
* *
1229017 CTTATGCTCGAGGTTCCAATGTAATT-TTCGAATCAATAATTGGTTAAAATTAACTAGCTTAATA
1 CTTATGCTCGAGGTTCCATTGTAATTATTCGAATCAATAATTGGTTAAAATTAACTAGGTTAATA
* * * ** **
1229081 ATTAGAGACTCTATTTTAGGTTTAATTTCAAACTTAGTCCTTTAATTTAGAAGAATTCCTAA-TT
66 ATTAGAGCCTCCATTTTAGGCTTAATTTCAAACTTAGTCCTTTAATTTAGGGGAATTTTTAACTT
*
1229145 CGGTCCTCA
131 -GGTCCTCG
* * * ** * * * * *
1229154 CTTATGCTCAAGGTTTCATTCTAATTATTTAAATCAATAATTCGTTAAAGTGAACTAGGATAAAA
1 CTTATGCTCGAGGTTCCATTGTAATTATTCGAATCAATAATTGGTTAAAATTAACTAGGTTAATA
*
1229219 ATGAGAGCCTCCATTTTAGGCTTAATTT
66 ATTAGAGCCTCCATTTTAGGCTTAATTT
1229247 TATATTTAAT
Statistics
Matches: 658, Mismatches: 111, Indels: 24
0.83 0.14 0.03
Matches are distributed among these distances:
136 16 0.02
137 218 0.33
138 408 0.62
139 16 0.02
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (138 bp):
CTTATGCTCGAGGTTCCATTGTAATTATTCGAATCAATAATTGGTTAAAATTAACTAGGTTAATA
ATTAGAGCCTCCATTTTAGGCTTAATTTCAAACTTAGTCCTTTAATTTAGGGGAATTTTTAACTT
GGTCCTCG
Found at i:1229108 original size:413 final size:412
Alignment explanation
Indices: 1228325--1229246 Score: 1172
Period size: 413 Copynumber: 2.2 Consensus size: 412
1228315 TAAGCACTTA
* * * *
1228325 TCACTTATGCTCGAGGTTCCATCATAATTATTCGAATCAATAATTAGTTAAAATTGACTAGATTA
1 TCACTTATGCTCGAGGTTCCATTATAATTATTTGAATCAATAATTAGTTAAAATTAACTAGGTTA
* **
1228390 ATAATTAGAGCCTCTACTTTAGGCATAATTTCAAACTTAGTCCTTTCTTTTAGGGGATTTGTTTA
66 ATAATTAGAGCCTC-ACTTTAGGCTTAATTTCAAACTTAGTCCTTTAATTTAGGGGATTTGTTTA
* * *
1228455 ATTGGTCCTCGCTCATGCTCGAGGTTCGATTGTAATTATTCGAATCAATAATTGGTTAAAATTAA
130 ATTGGTCCTAGCTCATGCTCGAGGTTCCATTGTAATTATTCGAATCAATAATTGGTTAAAATGAA
* * * ** * ** *
1228520 CTAGGTTAATAATTAGAGCCTCCATTTTAGGCTTAATTTTGAATTTAGTCCTTTAATTTAGGGGG
195 CTAGGTTAATAAGTACAACCTCCACCTTAGGCTTAATTTTAAACATAGTCCTTTAATTTAGGGGA
* *
1228585 ATTTTGAACTTGGTCCTCATTTATGCTCGAGGTTCCATTGTAAATTTTGAATCAATAATTGCTAA
260 ATTTTGAACTTGGTCCTCACTTATGCTCGAGGTTCCAATGTAAATTTTGAATCAATAATTGCTAA
*
1228650 AAATAGACTAGGCTAATAAGTAGAGCCTCCATCTTAGGCTTAATTTCAAACATAATCCTTTAATT
325 AAATAGACTAGGCTAATAAGTAGAGACTCCATCTTAGGCTTAATTTCAAACATAATCCTTTAATT
** ** *
1228715 TAGGGGAATTTTTAATTCAGTTC
390 TAGAAGAATTCCTAATTCAGTCC
* * *
1228738 TCGCTTATGCTCGAGGTTCCATTATAATTATTTGAATAAATAATTGGTTAAAATTAACTAGGTTA
1 TCACTTATGCTCGAGGTTCCATTATAATTATTTGAATCAATAATTAGTTAAAATTAACTAGGTTA
* *
1228803 ATAATTATAGCCTACACTTTAGGCTTAATTTCAAATTTAGTCCTTTAATTTAGGGGGA-TT-TTT
66 ATAATTAGAGCCT-CACTTTAGGCTTAATTTCAAACTTAGTCCTTTAATTTA-GGGGATTTGTTT
* * *
1228866 AACTTGGTCCTTAG-TTATGCTCGAGGTTCCATTGTAATTTTTTGAATCAATAATTGGTTAAAAT
129 AA-TTGGTCC-TAGCTCATGCTCGAGGTTCCATTGTAATTATTCGAATCAATAATTGGTTAAAAT
* * *
1228930 GGACTAGGTTAATAAGTACAACCTCCACCTTATGCTTAATTTTAAACATAGTCCTTTAATTTTGG
192 GAACTAGGTTAATAAGTACAACCTCCACCTTAGGCTTAATTTTAAACATAGTCCTTTAATTTAGG
* * *
1228995 GGAATTTTTAATTTGGTCCTCGCTTATGCTCGAGGTTCCAATGT-AATTTTCGAATCAATAATTG
257 GGAATTTTGAACTTGGTCCTCACTTATGCTCGAGGTTCCAATGTAAATTTT-GAATCAATAATT-
* * * * * * * *
1229059 GTTAAAATTA-ACTA-GCTTAATAATTAGAGACTCTATTTTAGGTTTAATTTCAAACTTAGTCCT
320 GCTAAAAATAGACTAGGC-TAATAAGTAGAGACTCCATCTTAGGCTTAATTTCAAACATAATCCT
*
1229122 TTAATTTAGAAGAATTCCTAATTCGGTCC
384 TTAATTTAGAAGAATTCCTAATTCAGTCC
* * * * * * * *
1229151 TCACTTATGCTCAAGGTTTCATTCTAATTATTTAAATCAATAATTCGTTAAAGTGAACTAGGATA
1 TCACTTATGCTCGAGGTTCCATTATAATTATTTGAATCAATAATTAGTTAAAATTAACTAGGTTA
* * *
1229216 AAAATGAGAGCCTCCATTTTAGGCTTAATTT
66 ATAATTAGAGCCT-CACTTTAGGCTTAATTT
1229247 TATATTTAAT
Statistics
Matches: 437, Mismatches: 65, Indels: 14
0.85 0.13 0.03
Matches are distributed among these distances:
412 13 0.03
413 408 0.93
414 16 0.04
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (412 bp):
TCACTTATGCTCGAGGTTCCATTATAATTATTTGAATCAATAATTAGTTAAAATTAACTAGGTTA
ATAATTAGAGCCTCACTTTAGGCTTAATTTCAAACTTAGTCCTTTAATTTAGGGGATTTGTTTAA
TTGGTCCTAGCTCATGCTCGAGGTTCCATTGTAATTATTCGAATCAATAATTGGTTAAAATGAAC
TAGGTTAATAAGTACAACCTCCACCTTAGGCTTAATTTTAAACATAGTCCTTTAATTTAGGGGAA
TTTTGAACTTGGTCCTCACTTATGCTCGAGGTTCCAATGTAAATTTTGAATCAATAATTGCTAAA
AATAGACTAGGCTAATAAGTAGAGACTCCATCTTAGGCTTAATTTCAAACATAATCCTTTAATTT
AGAAGAATTCCTAATTCAGTCC
Found at i:1229248 original size:275 final size:273
Alignment explanation
Indices: 1228325--1229246 Score: 1126
Period size: 275 Copynumber: 3.3 Consensus size: 273
1228315 TAAGCACTTA
*
1228325 TCACTTATGCTCGAGGTTCCA-TCATAATTATTCGAATCAATAATTAGTTAAAATTG-ACTA-GA
1 TCACTTATGCTCGAGGTTCCATTC-TAATTATTTGAATCAATAATT-GTTAAAA-TGAACTAGGA
* * * * * * *
1228387 TTAATAATTAGAGCCTCTACTTTAGGCATAATTTCAAACTTAGTCCTTT-CTTTTAGGGGATTTG
63 -TAATAAGTAGAGCCTCCACCTTAGGCTTAATTTCAAACATAGTCCTTTAATTTT-GGGGAATT-
* *
1228451 TTTAA-TTGGTCCTCGCTCATGCTCGAGGTTCGATTGTAATTATTCGAATCAATAATTGGTTAAA
125 TTTAATTTGGTCCTCGCTTATGCTCGAGGTTCCATTGTAATTATTCGAATCAATAATTGGTTAAA
**
1228515 ATTAACTAGGTTAATAATTAGAGCCTCCATTTTAGGCTTAATTTTGAATTTAGTCCTTTAATTTA
190 ATTAACTAGGTTAATAATTAGAGCCT-CATTTTAGGCTTAATTTCAAATTTAGTCCTTTAATTTA
1228580 GGGGGATTTTGAACTTGGTCC
254 GGGGGATTTT-AACTTGGTCC
* * * * *
1228601 TCATTTATGCTCGAGGTTCCATTGTAAAT-TTTGAATCAATAATTGCTAAAAAT-AGACTAGGCT
1 TCACTTATGCTCGAGGTTCCATTCTAATTATTTGAATCAATAATTG-TTAAAATGA-ACTAGGAT
* * *
1228664 AATAAGTAGAGCCTCCATCTTAGGCTTAATTTCAAACATAATCCTTTAATTTAGGGGAATTTTTA
64 AATAAGTAGAGCCTCCACCTTAGGCTTAATTTCAAACATAGTCCTTTAATTTTGGGGAATTTTTA
** * * * *
1228729 ATTCAGTTCTCGCTTATGCTCGAGGTTCCATTATAATTATTTGAATAAATAATTGGTTAAAATTA
129 ATTTGGTCCTCGCTTATGCTCGAGGTTCCATTGTAATTATTCGAATCAATAATTGGTTAAAATTA
* *
1228794 ACTAGGTTAATAATTATAGCCTACACTTTAGGCTTAATTTCAAATTTAGTCCTTTAATTTAGGGG
194 ACTAGGTTAATAATTAGAGCCT-CATTTTAGGCTTAATTTCAAATTTAGTCCTTTAATTTAGGGG
1228859 GATTTTTAACTTGGTCC
258 GA-TTTTAACTTGGTCC
* * * * * *
1228876 TTAGTTATGCTCGAGGTTCCATTGTAATTTTTTGAATCAATAATTGGTTAAAATGGACTAGGTTA
1 TCACTTATGCTCGAGGTTCCATTCTAATTATTTGAATCAATAATT-GTTAAAATGAACTAGGATA
* * * *
1228941 ATAAGTACAACCTCCACCTTATGCTTAATTTTAAACATAGTCCTTTAATTTTGGGGAATTTTTAA
65 ATAAGTAGAGCCTCCACCTTAGGCTTAATTTCAAACATAGTCCTTTAATTTTGGGGAATTTTTAA
*
1229006 TTTGGTCCTCGCTTATGCTCGAGGTTCCAATGTAATT-TTCGAATCAATAATTGGTTAAAATTAA
130 TTTGGTCCTCGCTTATGCTCGAGGTTCCATTGTAATTATTCGAATCAATAATTGGTTAAAATTAA
* * * * ** *
1229070 CTAGCTTAATAATTAGAGACTCTATTTTAGGTTTAATTTCAAACTTAGTCCTTTAATTTAGAAGA
195 CTAGGTTAATAATTAGAGCCTC-ATTTTAGGCTTAATTTCAAATTTAGTCCTTTAATTTAGGGGG
*
1229135 ATTCCTAA-TTCGGTCC
259 ATT-TTAACTT-GGTCC
* * * *
1229151 TCACTTATGCTCAAGGTTTCATTCTAATTATTTAAATCAATAATTCGTTAAAGTGAACTAGGATA
1 TCACTTATGCTCGAGGTTCCATTCTAATTATTTGAATCAATAATT-GTTAAAATGAACTAGGATA
* **
1229216 A-AAATGAGAGCCTCCATTTTAGGCTTAATTT
65 ATAAGT-AGAGCCTCCACCTTAGGCTTAATTT
1229247 TATATTTAAT
Statistics
Matches: 555, Mismatches: 76, Indels: 31
0.84 0.11 0.05
Matches are distributed among these distances:
274 15 0.03
275 387 0.70
276 151 0.27
277 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (273 bp):
TCACTTATGCTCGAGGTTCCATTCTAATTATTTGAATCAATAATTGTTAAAATGAACTAGGATAA
TAAGTAGAGCCTCCACCTTAGGCTTAATTTCAAACATAGTCCTTTAATTTTGGGGAATTTTTAAT
TTGGTCCTCGCTTATGCTCGAGGTTCCATTGTAATTATTCGAATCAATAATTGGTTAAAATTAAC
TAGGTTAATAATTAGAGCCTCATTTTAGGCTTAATTTCAAATTTAGTCCTTTAATTTAGGGGGAT
TTTAACTTGGTCC
Found at i:1229639 original size:13 final size:13
Alignment explanation
Indices: 1229621--1229646 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1229611 CTTACAACTC
1229621 CCTCAATAATTAT
1 CCTCAATAATTAT
1229634 CCTCAATAATTAT
1 CCTCAATAATTAT
1229647 ACCCCAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (13 bp):
CCTCAATAATTAT
Found at i:1236583 original size:23 final size:23
Alignment explanation
Indices: 1236553--1236601 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
1236543 TCCAACCTCA
1236553 GTCATTCTACAGTTGGTTGATCG
1 GTCATTCTACAGTTGGTTGATCG
1236576 GTCATTCTACAGTTGGTTGATCG
1 GTCATTCTACAGTTGGTTGATCG
1236599 GTC
1 GTC
1236602 TTATGTGCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.39
Consensus pattern (23 bp):
GTCATTCTACAGTTGGTTGATCG
Found at i:1240123 original size:27 final size:27
Alignment explanation
Indices: 1240085--1240139 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1240075 CCCAAGAGTT
*
1240085 TGCTTTTCTTAATTGAGCAAATATTAG
1 TGCTTTTCTTAATTAAGCAAATATTAG
1240112 TGCTTTTCTTAATTAAGCAAATATTAG
1 TGCTTTTCTTAATTAAGCAAATATTAG
1240139 T
1 T
1240140 TGCCTAGGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (27 bp):
TGCTTTTCTTAATTAAGCAAATATTAG
Found at i:1252345 original size:30 final size:31
Alignment explanation
Indices: 1252306--1252384 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 31
1252296 AATGGATTTA
* *
1252306 TTTA-GTGACCAAATTATAAAT-TTGTTAAAG
1 TTTAGGTGACCAAAATATAAATATTG-AAAAG
*
1252336 TTT-GGTGACCAAAGTATAAATATTGAAAAG
1 TTTAGGTGACCAAAATATAAATATTGAAAAG
1252366 TTTAGG-GACCAAAATATAA
1 TTTAGGTGACCAAAATATAA
1252385 TTTTAAAAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
30 38 0.88
31 5 0.12
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (31 bp):
TTTAGGTGACCAAAATATAAATATTGAAAAG
Found at i:1253336 original size:30 final size:30
Alignment explanation
Indices: 1253282--1253352 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
1253272 TCTAAAGGCC
* * *
1253282 TTAGAAAA-TTTAGGGACCATTTTGTAATT
1 TTAGAAAAGTTGAGAGACCAATTTGTAATT
1253311 TTAGAAAAGTTGAGAGACCAATTTGTAATT
1 TTAGAAAAGTTGAGAGACCAATTTGTAATT
1253341 TT-GAAAAAGTTG
1 TTAG-AAAAGTTG
1253353 GGAATGGTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.24
30 28 0.76
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.37
Consensus pattern (30 bp):
TTAGAAAAGTTGAGAGACCAATTTGTAATT
Found at i:1254273 original size:40 final size:40
Alignment explanation
Indices: 1254190--1254310 Score: 217
Period size: 40 Copynumber: 3.0 Consensus size: 40
1254180 TGCAGGTTTA
*
1254190 TAATACACTTTGGTGTATATGGT-GGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
1254229 TAATACACTTCGGTGTATATGGTGGGCATGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1254269 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1254309 TA
1 TA
1254311 GCACGACGGT
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 22 0.28
40 56 0.72
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:1254490 original size:45 final size:45
Alignment explanation
Indices: 1254421--1254726 Score: 463
Period size: 45 Copynumber: 6.8 Consensus size: 45
1254411 GCTAACCATG
* * *
1254421 AAAATAAGCTTACAAACTTTTGGAATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
1254466 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
1254511 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* * * * *
1254556 AAAATAAGTTTATGATCTTATTGAAAAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* *
1254601 AAAATATGCTTACGAGCTTATGGAAT-AATGGTAAGTATTTTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* *
1254645 AAAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATAGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
*
1254690 AAAAATAAGCTTACGAGCTTATAGG-ATAAATGATAAG
1 -AAAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAG
1254727 AAATTTTATA
Statistics
Matches: 237, Mismatches: 21, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
44 41 0.17
45 163 0.69
46 31 0.13
47 2 0.01
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
Found at i:1257459 original size:25 final size:25
Alignment explanation
Indices: 1257421--1257481 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
1257411 ATATATATAA
* *
1257421 AAAACAACAGGAAAA-AAGAAAGAAG
1 AAAACAAAAAGAAAAGAAG-AAGAAG
1257446 AAAACAAAAAGAAAAGAAGAAGAAG
1 AAAACAAAAAGAAAAGAAGAAGAAG
*
1257471 AAGAAGAAAAA
1 AA-AACAAAAA
1257482 TATAGAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 21 0.68
26 10 0.32
ACGTcount: A:0.75, C:0.05, G:0.20, T:0.00
Consensus pattern (25 bp):
AAAACAAAAAGAAAAGAAGAAGAAG
Found at i:1257461 original size:19 final size:20
Alignment explanation
Indices: 1257433--1257480 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1257423 AACAACAGGA
1257433 AAAAAG-AAAGAAGAA-AAC
1 AAAAAGAAAAGAAGAAGAAC
*
1257451 AAAAAGAAAAGAAGAAGAAG
1 AAAAAGAAAAGAAGAAGAAC
*
1257471 AAGAAGAAAA
1 AAAAAGAAAA
1257481 ATATAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 6 0.23
19 9 0.35
20 11 0.42
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAGAAGAAGAAC
Found at i:1257513 original size:27 final size:28
Alignment explanation
Indices: 1257433--1257514 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 28
1257423 AACAACAGGA
* *
1257433 AAAAAGAAAGAAGAA-AACAAAAAGA-A-
1 AAAAAG-AAGAAGAAGAAGAAAAATATAG
*
1257459 AAGAAGAAGAAGAAGAAGAAAAATATAG
1 AAAAAGAAGAAGAAGAAGAAAAATATAG
*
1257487 AAAAAGAA-AAGAAGGA-AAAAATGATAG
1 AAAAAGAAGAAGAAGAAGAAAAAT-ATAG
1257514 A
1 A
1257515 TGCTTAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
25 8 0.17
26 19 0.40
27 13 0.28
28 7 0.15
ACGTcount: A:0.73, C:0.01, G:0.21, T:0.05
Consensus pattern (28 bp):
AAAAAGAAGAAGAAGAAGAAAAATATAG
Found at i:1259360 original size:30 final size:30
Alignment explanation
Indices: 1259325--1259383 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1259315 GATTTATTTA
* *
1259325 GTGACCAAATTATAAA-TTTGTTAAAGTTTG
1 GTGACCAAAGTATAAACTTTG-AAAAGTTTG
1259355 GTGACCAAAGTATAAACTTTGAAAAGTTT
1 GTGACCAAAGTATAAACTTTGAAAAGTTT
1259384 AGGGAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (30 bp):
GTGACCAAAGTATAAACTTTGAAAAGTTTG
Found at i:1260392 original size:30 final size:29
Alignment explanation
Indices: 1260350--1260406 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
1260340 AAGACCATAG
* *
1260350 AAAATTTGGGGACCATTTTATAATTTTCA
1 AAAAGTTGGGGACCAATTTATAATTTTCA
*
1260379 AAAAGTTGAGGGACCAATTTGTAATTTT
1 AAAAGTTG-GGGACCAATTTATAATTTT
1260407 GGAAAAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.39
Consensus pattern (29 bp):
AAAAGTTGGGGACCAATTTATAATTTTCA
Found at i:1261525 original size:45 final size:45
Alignment explanation
Indices: 1261417--1261674 Score: 389
Period size: 45 Copynumber: 5.8 Consensus size: 45
1261407 GGAACCGTCC
* *
1261417 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATATT-GTG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
1261461 AAATAAGCTTACGAGCTTATGGACTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
1261506 AAATAAGCTTATGAGCTTATTGAATAAATGGTAAGTATATTTGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
1261551 AAATAAGCTTACGAGCTTATGGAAT-AATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1261595 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
1261640 AAATAAG-TGTACGAGCATATAGG-ATAAATGATAAG
1 AAATAAGCT-TACGAGCTTAT-GGAATAAATGGTAAG
1261675 AAATTGTATA
Statistics
Matches: 196, Mismatches: 14, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
44 82 0.42
45 112 0.57
46 2 0.01
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:1261525 original size:89 final size:88
Alignment explanation
Indices: 1261417--1261674 Score: 394
Period size: 89 Copynumber: 2.9 Consensus size: 88
1261407 GGAACCGTCC
*
1261417 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATATTGTGAAATAAGCTTACGAGCTTATG
1 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATG
1261482 GACTAAATGGTAAGTATATTGGTA
66 GA-TAAATGGTAAGTATATTGGTA
*
1261506 AAATAAGCTTATGAGCTTATTGAATAAATGGTAAGTATATTTGTAAAATAAGCTTACGAGCTTAT
1 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATA-TTGTAAAATAAGCTTACGAGCTTAT
*
1261571 GGA-ATAATGGTAAGTATTTTGGTA
65 GGATA-AATGGTAAGTATATTGGTA
* *
1261595 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAG-TGTACGAGCATA
1 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATATT-GTAAAATAAGCT-TACGAGCTTA
*
1261659 TAGGATAAATGATAAG
64 T-GGATAAATGGTAAG
1261675 AAATTGTATA
Statistics
Matches: 156, Mismatches: 7, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
88 4 0.03
89 113 0.72
90 38 0.24
91 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (88 bp):
AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATG
GATAAATGGTAAGTATATTGGTA
Found at i:1261667 original size:134 final size:134
Alignment explanation
Indices: 1261417--1261674 Score: 403
Period size: 134 Copynumber: 1.9 Consensus size: 134
1261407 GGAACCGTCC
* *
1261417 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATATTGTGAAATAAGCTTACGAGCTTATG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATG
* * * * *
1261482 GACTAAATGGTAAGTATATTGGTAAAATAAGCTTATGAGCTTATTGAATAAATGGTAAGTATATT
66 GAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCATATAGAATAAATGATAAGTATATT
1261547 TGTA
131 TGTA
*
1261551 AAATAAGCTTACGAGCTTATGGAAT-AATGGTAAGTATTTTGGTAAAATAAGCTTACGAGCTTAT
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATT-GTAAAATAAGCTTACGAGCTTAT
*
1261615 GGAATAAATGGTAAGTATATTGGTAAAATAAG-TGTACGAGCATATAGGATAAATGATAAG
65 GGAATAAATGGTAAGTATATTGGTAAAATAAGCT-TACGAGCATATAGAATAAATGATAAG
1261675 AAATTGTATA
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
133 15 0.13
134 98 0.87
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (134 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGTAAAATAAGCTTACGAGCTTATG
GAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCATATAGAATAAATGATAAGTATATT
TGTA
Found at i:1265728 original size:18 final size:18
Alignment explanation
Indices: 1265702--1265739 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1265692 GTTATATTCG
*
1265702 AATAATTAAATTGAATAT
1 AATAATTAAATCGAATAT
*
1265720 AATATTTAAATCGAATAT
1 AATAATTAAATCGAATAT
1265738 AA
1 AA
1265740 AATCTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (18 bp):
AATAATTAAATCGAATAT
Found at i:1266660 original size:26 final size:26
Alignment explanation
Indices: 1266605--1266661 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1266595 AAGGTATGCG
* * *
1266605 AGTCAGTAAGATGCACTTTTTGTACC
1 AGTCAGTAAGATGAACTTTTAGTACA
* *
1266631 AGTCAGTGAGATGAACTTTTAGTGCA
1 AGTCAGTAAGATGAACTTTTAGTACA
1266657 AGTCA
1 AGTCA
1266662 ATGTACAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (26 bp):
AGTCAGTAAGATGAACTTTTAGTACA
Found at i:1273726 original size:41 final size:41
Alignment explanation
Indices: 1273621--1273772 Score: 150
Period size: 41 Copynumber: 3.7 Consensus size: 41
1273611 GCATAATCAA
* * * *
1273621 AAAATAAAAATC-CAAGAGATTGAATAATATTGGGCAATCAG
1 AAAATAAAAATCTC-AGAGATTGAGTAATCTAGGGCAATTAG
* * *
1273662 AAAATAGAAATCCCA-ACGATTGAGTGATCTAGGGCAATTAG
1 AAAATAAAAATCTCAGA-GATTGAGTAATCTAGGGCAATTAG
* **
1273703 AAAATAGAAATCTCAGAGATTGAGTTGTCTTA-GGCAATTAG
1 AAAATAAAAATCTCAGAGATTGAGTAATC-TAGGGCAATTAG
*
1273744 AAAATAAAAATCTTAGAGA-TGAGTAATCT
1 AAAATAAAAATCTCAGAGATTGAGTAATCT
1273773 TGGGTGGCAC
Statistics
Matches: 94, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
39 1 0.01
40 8 0.09
41 81 0.86
42 4 0.04
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.25
Consensus pattern (41 bp):
AAAATAAAAATCTCAGAGATTGAGTAATCTAGGGCAATTAG
Found at i:1274964 original size:20 final size:19
Alignment explanation
Indices: 1274927--1274966 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1274917 GTTTATGATA
1274927 GAATTATGAAATTAAAGGT
1 GAATTATGAAATTAAAGGT
* *
1274946 GAATTCATGTAATTCAAGGT
1 GAATT-ATGAAATTAAAGGT
1274966 G
1 G
1274967 GAAATGAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.33
Consensus pattern (19 bp):
GAATTATGAAATTAAAGGT
Found at i:1275333 original size:39 final size:39
Alignment explanation
Indices: 1275290--1275378 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 39
1275280 TGACTCTAAT
1275290 ATTCTAAATTAAAAATTCCTTAAATTATTTCACAATAAC
1 ATTCTAAATTAAAAATTCCTTAAATTATTTCACAATAAC
*** * * **
1275329 ATTCTAAATTCTTAGTTTCTTAAATTATTTCACCTTAAC
1 ATTCTAAATTAAAAATTCCTTAAATTATTTCACAATAAC
1275368 ATTCTAAATTA
1 ATTCTAAATTA
1275379 TTTTCAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.39, C:0.16, G:0.01, T:0.44
Consensus pattern (39 bp):
ATTCTAAATTAAAAATTCCTTAAATTATTTCACAATAAC
Found at i:1275492 original size:35 final size:37
Alignment explanation
Indices: 1275453--1275533 Score: 89
Period size: 35 Copynumber: 2.3 Consensus size: 37
1275443 TTTCAATAAG
* *
1275453 TTTTATATTTGA-ATTGTGTAATT-T-GAATTTTTAAA
1 TTTTATATTTGAGATTATATAATTATAG-ATTTTTAAA
*
1275488 TTTTAT-TTTTAGATTATATAATTATAGATTTTTAAA
1 TTTTATATTTGAGATTATATAATTATAGATTTTTAAA
*
1275524 ATTTATATTT
1 TTTTATATTT
1275534 TATATTTTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
34 4 0.11
35 15 0.39
36 15 0.39
37 4 0.11
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (37 bp):
TTTTATATTTGAGATTATATAATTATAGATTTTTAAA
Found at i:1277723 original size:20 final size:19
Alignment explanation
Indices: 1277700--1277744 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1277690 GGAAGTTTGG
1277700 AAACTTTTAAGAAAGTTTCA
1 AAACTTTTAA-AAAGTTTCA
* * *
1277720 AAACTATTGAAAAGTTTCT
1 AAACTTTTAAAAAGTTTCA
1277739 AAACTT
1 AAACTT
1277745 CAAAGTATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (19 bp):
AAACTTTTAAAAAGTTTCA
Found at i:1280404 original size:36 final size:36
Alignment explanation
Indices: 1280357--1280429 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
1280347 CTGACTTTTT
1280357 AGGGAATTATTATTTGAGCCAAAAAAAATTAAAAAA
1 AGGGAATTATTATTTGAGCCAAAAAAAATTAAAAAA
* *
1280393 AGGGAATTATTATTTGAGCCAAAAAAATTTTAAAAA
1 AGGGAATTATTATTTGAGCCAAAAAAAATTAAAAAA
1280429 A
1 A
1280430 TATAGGTGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.27
Consensus pattern (36 bp):
AGGGAATTATTATTTGAGCCAAAAAAAATTAAAAAA
Found at i:1282806 original size:46 final size:46
Alignment explanation
Indices: 1282726--1282815 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 46
1282716 AATAAATGCT
*
1282726 TGAGAACTAGAAAGCATGCGGTTTGGTTTATTTTTCTAAATAAGTA
1 TGAGAACTAGAAAGCATGCGGTTAGGTTTATTTTTCTAAATAAGTA
* * * * *
1282772 TGAGAATTAGAAATCATGTGGTTAGGATTT-TTTTTTTGAATAAG
1 TGAGAACTAGAAAGCATGCGGTTAGG-TTTATTTTTCTAAATAAG
1282816 CGTGTGAACT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
46 34 0.92
47 3 0.08
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.40
Consensus pattern (46 bp):
TGAGAACTAGAAAGCATGCGGTTAGGTTTATTTTTCTAAATAAGTA
Found at i:1283581 original size:20 final size:19
Alignment explanation
Indices: 1283543--1283585 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
1283533 GGAATTAGCA
*
1283543 CATTTTGCATCTGCATTTG
1 CATTTTGCATCTACATTTG
1283562 CATTTTGCATTCTACATTTG
1 CATTTTGCA-TCTACATTTG
1283582 CATT
1 CATT
1283586 ACATTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.49
Consensus pattern (19 bp):
CATTTTGCATCTACATTTG
Found at i:1288427 original size:21 final size:22
Alignment explanation
Indices: 1288401--1288449 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 22
1288391 GTAATATAGT
1288401 AGTAAGTGAGTATAAACAAGTG
1 AGTAAGTGAGTATAAACAAGTG
1288423 A-TAAGTGAGTATAAACAAGTG
1 AGTAAGTGAGTATAAACAAGTG
1288444 AGTAAG
1 AGTAAG
1288450 GATGTTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.47, C:0.04, G:0.27, T:0.22
Consensus pattern (22 bp):
AGTAAGTGAGTATAAACAAGTG
Found at i:1289487 original size:39 final size:39
Alignment explanation
Indices: 1289414--1289526 Score: 149
Period size: 39 Copynumber: 2.9 Consensus size: 39
1289404 TATACTTAAA
* *
1289414 AAAACACTCTCCAACTTCCAAGA-CCTCTTAAATTCACAAT
1 AAAACACTCT--AACTCCCAAGAGACTCTTAAATTCACAAT
* *
1289454 AAAACACT-TGAACTCCCAAGATACTTTTAAATTCACAAT
1 AAAACACTCT-AACTCCCAAGAGACTCTTAAATTCACAAT
1289493 AAAACACTCTAACTCCCAAGAGACTCTTAAATTC
1 AAAACACTCTAACTCCCAAGAGACTCTTAAATTC
1289527 TCCCCTTAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
38 10 0.15
39 46 0.71
40 9 0.14
ACGTcount: A:0.42, C:0.28, G:0.04, T:0.26
Consensus pattern (39 bp):
AAAACACTCTAACTCCCAAGAGACTCTTAAATTCACAAT
Found at i:1290426 original size:20 final size:21
Alignment explanation
Indices: 1290401--1290452 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1290391 TTTTCCCAAT
*
1290401 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1290421 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1290442 TCGCAATGCGA
1 TCGCAATGCGA
1290453 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1290466 original size:20 final size:20
Alignment explanation
Indices: 1290441--1290494 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1290431 AATTGGGAAA
1290441 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1290461 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
1290481 ATCGCAATGCGATA
1 ATCGCAATGCGATA
1290495 ATATAAAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1291070 original size:19 final size:19
Alignment explanation
Indices: 1291025--1291072 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1291015 TTCGAGAATG
*
1291025 AAAATCGCAACGCGGAAAT
1 AAAATCGCAACGCGGAAAC
*
1291044 AACTATCGCAACGC-GAAACC
1 AA-AATCGCAACGCGGAAA-C
1291064 AAAATCGCA
1 AAAATCGCA
1291073 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.46, C:0.27, G:0.17, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGGAAAC
Found at i:1291090 original size:19 final size:19
Alignment explanation
Indices: 1291068--1291146 Score: 122
Period size: 19 Copynumber: 4.1 Consensus size: 19
1291058 GAAACCAAAA
*
1291068 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1291087 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1291106 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
1291125 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1291145 TC
1 TC
1291147 AACCAAAAGA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
19 38 0.69
20 17 0.31
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1291141 original size:39 final size:38
Alignment explanation
Indices: 1291068--1291146 Score: 122
Period size: 39 Copynumber: 2.1 Consensus size: 38
1291058 GAAACCAAAA
*
1291068 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCATTTCGCGTTGCGATTTTCATT
* *
1291106 TCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCATT-TCGCGTTGCGATTTTCATT
1291145 TC
1 TC
1291147 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 17 0.46
39 20 0.54
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.47
Consensus pattern (38 bp):
TCGCATTGCGATTCTCATTTCGCGTTGCGATTTTCATT
Found at i:1293305 original size:21 final size:21
Alignment explanation
Indices: 1293281--1293431 Score: 58
Period size: 21 Copynumber: 7.2 Consensus size: 21
1293271 TCATTTCTCG
1293281 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** *
1293302 AGAGGCCACTGTCATCC-CTCA
1 AGAGTCCCCTCCCA-CCGTTCA
* * * *
1293323 AGAGTCCACTCCTATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
* ** *
1293344 AGAGGCCCCTATCATTCC--TCG
1 AGAGTCCCCTCCCA--CCGTTCA
1293365 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1293386 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1293407 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1293428 AGAG
1 AGAG
1293432 GTCGATTCAC
Statistics
Matches: 86, Mismatches: 37, Indels: 15
0.62 0.27 0.11
Matches are distributed among these distances:
19 2 0.02
20 2 0.02
21 78 0.91
22 3 0.03
23 1 0.01
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1293305 original size:42 final size:42
Alignment explanation
Indices: 1293229--1293432 Score: 196
Period size: 42 Copynumber: 4.9 Consensus size: 42
1293219 GACTCGCCTG
* * * * *
1293229 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * *
1293271 TCATTTCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
1293313 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * *
1293355 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * *
1293397 TCA-TCGTTGAAGAGGTCC-CTCCCACCATTCAAGAGG
1 TCATTCCTCG-AGA-GTCCACTCCCACCGTTCAAGAGG
1293433 TCGATTCACA
Statistics
Matches: 131, Mismatches: 29, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
41 4 0.03
42 123 0.94
43 4 0.03
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:1293410 original size:84 final size:84
Alignment explanation
Indices: 1293226--1293401 Score: 343
Period size: 84 Copynumber: 2.1 Consensus size: 84
1293216 CCCGACTCGC
*
1293226 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTTCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1293291 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
1293310 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1293375 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
1293394 CTGTCATC
1 CTGTCATC
1293402 GTTGAAGAGG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 91 1.00
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:1293431 original size:84 final size:84
Alignment explanation
Indices: 1293226--1293432 Score: 290
Period size: 84 Copynumber: 2.5 Consensus size: 84
1293216 CCCGACTCGC
* * * * *
1293226 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTTCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1293291 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * *
1293310 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1293375 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** *
1293394 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAGG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAGG
1293433 TCGATTCACA
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
84 110 0.96
85 4 0.04
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:1293432 original size:21 final size:21
Alignment explanation
Indices: 1293371--1293434 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
1293361 CTCGAGAGTC
1293371 CCCTCCCACCGTTCAAGAGG-
1 CCCTCCCACCGTTCAAGAGGT
** * *
1293391 CCACTGTCATCGTTGAAGAGGT
1 CC-CTCCCACCGTTCAAGAGGT
*
1293413 CCCTCCCACCATTCAAGAGGT
1 CCCTCCCACCGTTCAAGAGGT
1293434 C
1 C
1293435 GATTCACATG
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.20
Consensus pattern (21 bp):
CCCTCCCACCGTTCAAGAGGT
Found at i:1294807 original size:14 final size:14
Alignment explanation
Indices: 1294788--1294823 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1294778 ATTGTTTAAT
1294788 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1294802 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1294816 TGATTTGT
1 TGATTTGT
1294824 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1294954 original size:19 final size:19
Alignment explanation
Indices: 1294930--1295009 Score: 89
Period size: 19 Copynumber: 4.5 Consensus size: 19
1294920 AAAAAGTACT
*
1294930 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1294949 ATCGCAACGAGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1294968 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
1294982 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1295001 ATTGCAACG
1 ATCGCAACG
1295010 AGAGAATCGC
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 1 0.02
18 1 0.02
19 35 0.70
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1294986 original size:14 final size:14
Alignment explanation
Indices: 1294967--1295023 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1294957 GAGAAATGAA
1294967 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1294981 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1295000 AATTGCAACGAGAG
1 AATCGCAACGAGAG
1295014 AATCGCAACG
1 AATCGCAACG
1295024 TGAAATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1294990 original size:33 final size:33
Alignment explanation
Indices: 1294948--1295038 Score: 137
Period size: 33 Copynumber: 2.8 Consensus size: 33
1294938 GCGAAATGAA
1294948 AATCGCAACGAGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGAGAAATGAAAATCGCAACGAGAG
* *
1294981 AATCGCAACGCGAAATGAAAATTGCAACGAGAG
1 AATCGCAACGAGAAATGAAAATCGCAACGAGAG
* * *
1295014 AATCGCAACGTGAAATTAAATTCGC
1 AATCGCAACGAGAAATGAAAATCGC
1295039 GTTGCGATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAACGAGAAATGAAAATCGCAACGAGAG
Found at i:1295056 original size:19 final size:19
Alignment explanation
Indices: 1295034--1295184 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
1295024 TGAAATTAAA
1295034 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1295053 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1295068 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1295086 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
1295100 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1295119 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1295134 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * ** *
1295152 TTCGCATTGTGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1295171 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1295185 AGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 28 0.30
16 6 0.06
17 6 0.06
19 44 0.47
20 9 0.10
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1295080 original size:33 final size:32
Alignment explanation
Indices: 1295038--1295160 Score: 185
Period size: 33 Copynumber: 3.8 Consensus size: 32
1295028 ATTAAATTCG
1295038 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1295071 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1295104 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1295137 CGTTGCGATTTTCATTTCGCATTG
1 CGTTGCGATTTTCATTTCGCATTG
1295161 TGATAGTAAT
Statistics
Matches: 82, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
31 3 0.04
33 76 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1295114 original size:66 final size:66
Alignment explanation
Indices: 1295031--1295160 Score: 242
Period size: 66 Copynumber: 2.0 Consensus size: 66
1295021 ACGTGAAATT
*
1295031 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1295096 G
66 G
*
1295097 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTG
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTG
1295161 TGATAGTAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1297473 original size:12 final size:12
Alignment explanation
Indices: 1297456--1297492 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
1297446 TCTTCGGGGA
1297456 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1297468 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1297480 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1297492 C
1 C
1297493 AGGATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1297701 original size:24 final size:24
Alignment explanation
Indices: 1297667--1297720 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1297657 CTGAAACATC
*
1297667 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
1297691 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1297715 ATCAAA
1 ATCAAA
1297721 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1298630 original size:20 final size:20
Alignment explanation
Indices: 1298541--1298632 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
1298531 TGCGAATTTG
* *
1298541 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
1298561 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
1298581 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
1298602 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
1298622 GAAAATCGCAA
1 GAAAATCGCAA
1298633 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:1298921 original size:20 final size:20
Alignment explanation
Indices: 1298846--1298913 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
1298836 CAACGGGGAA
1298846 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
1298866 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
1298886 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1298906 ATCGCAAC
1 ATCGCAAC
1298914 TAGAAAATCG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:1298962 original size:14 final size:14
Alignment explanation
Indices: 1298945--1298998 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1298935 GAAAATTGCA
1298945 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
1298959 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
1298976 CATTGCGATTTTCTAG
1 --TTGCGATTTTCTCG
1298992 TTGCGAT
1 TTGCGAT
1298999 AGCCATTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
16 2 0.06
17 3 0.09
19 11 0.32
ACGTcount: A:0.13, C:0.19, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:1299006 original size:33 final size:33
Alignment explanation
Indices: 1298942--1299006 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
1298932 AATGAAAATT
* ***
1298942 GCATTGCGATTTTCTCGTTGCGATTTTCATTTC
1 GCATTGCGATTTTCTAGTTGCGATAGCCATTTC
1298975 GCATTGCGATTTTCTAGTTGCGATAGCCATTT
1 GCATTGCGATTTTCTAGTTGCGATAGCCATTT
1299007 TCGCGTTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.45
Consensus pattern (33 bp):
GCATTGCGATTTTCTAGTTGCGATAGCCATTTC
Found at i:1299144 original size:14 final size:14
Alignment explanation
Indices: 1299125--1299161 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1299115 CATCAATTAA
1299125 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1299139 ACAAATCATCTTTT
1 ACAAATCAACATTT
1299153 ACAAATCAA
1 ACAAATCAA
1299162 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1301053 original size:20 final size:20
Alignment explanation
Indices: 1301000--1301078 Score: 77
Period size: 20 Copynumber: 4.0 Consensus size: 20
1300990 GAAGAATAGT
* * *
1301000 TTACTTTCGCAACACGAAAC
1 TTACTATCGCAACGCGAAAA
**
1301020 TTAAAATCGCAACGCGAAAA
1 TTACTATCGCAACGCGAAAA
*
1301040 TTACTATCGCAACGCGGAAA
1 TTACTATCGCAACGCGAAAA
** *
1301060 TGGCTATCGCAATGCGAAA
1 TTACTATCGCAACGCGAAA
1301079 TGAAAATCGC
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
TTACTATCGCAACGCGAAAA
Found at i:1301100 original size:14 final size:14
Alignment explanation
Indices: 1301081--1301171 Score: 83
Period size: 14 Copynumber: 5.9 Consensus size: 14
1301071 ATGCGAAATG
1301081 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1301095 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
1301114 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1301128 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1301144 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1301160 AAAATCGCAACG
1 AAAATCGCAACG
1301172 CGAAACACAA
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 31 0.48
15 1 0.02
16 10 0.16
17 2 0.03
18 10 0.16
19 10 0.16
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1301156 original size:32 final size:33
Alignment explanation
Indices: 1301065--1301176 Score: 208
Period size: 33 Copynumber: 3.4 Consensus size: 33
1301055 GGAAATGGCT
1301065 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1301098 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1301131 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1301163 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1301177 CACAAATCGC
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 29 0.37
33 49 0.63
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1301736 original size:18 final size:18
Alignment explanation
Indices: 1301710--1301754 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1301700 GTCGATCAGA
*
1301710 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1301728 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1301746 TGATGGCTC
1 TGATGGCTC
1301755 CCAAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1303122 original size:20 final size:20
Alignment explanation
Indices: 1303074--1303132 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1303064 AATAGTTTCT
** *
1303074 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
1303094 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
1303114 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
1303133 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:1303649 original size:20 final size:20
Alignment explanation
Indices: 1303624--1303675 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1303614 ATTATGTATT
1303624 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
1303644 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
1303664 ATCTCGTTGCGA
1 ATCGCGTTGCGA
1303676 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:1303710 original size:21 final size:20
Alignment explanation
Indices: 1303686--1303737 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1303676 TTTTGTATTA
*
1303686 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
1303707 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
1303727 TCGCATTGCGA
1 TCGCATTGCGA
1303738 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:1305755 original size:182 final size:182
Alignment explanation
Indices: 1305448--1305900 Score: 762
Period size: 182 Copynumber: 2.5 Consensus size: 182
1305438 ACTTTTTTAC
* *
1305448 TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTATTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
* * * * *
1305513 TACATTTTTATAAATTATTGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACACCTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
* * *
1305578 TGTCGATACTTATAATAAAGTATCGACACTTTCAACATATTCGGTAGCTCTT
131 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
1305630 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
*
1305695 TACATTTTTATAAAGTATCGACACCTTATTAGTGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACACCTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
1305760 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
131 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
* ** * *
1305812 TACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTTTATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
1305877 TACATTTTTATAAAGTATCGACAC
66 TACATTTTTATAAAGTATCGACAC
1305901 TTTCAATATA
Statistics
Matches: 255, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
182 255 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
TACATTTTTATAAAGTATCGACACCTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
Found at i:1305860 original size:20 final size:20
Alignment explanation
Indices: 1305810--1305861 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1305800 CCGGTAGCGC
1305810 TTTACCTGTTTTGTCATTTA
1 TTTACCTGTTTTGTCATTTA
** * *
1305830 TAGACCGGTTTTGTCATTTT
1 TTTACCTGTTTTGTCATTTA
1305850 TTTACCTGTTTT
1 TTTACCTGTTTT
1305862 ATTGTTATGG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.15, G:0.13, T:0.58
Consensus pattern (20 bp):
TTTACCTGTTTTGTCATTTA
Found at i:1306141 original size:112 final size:112
Alignment explanation
Indices: 1305774--1306234 Score: 773
Period size: 112 Copynumber: 4.1 Consensus size: 112
1305764 GATACTTATA
* *
1305774 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
1305839 TTTGTCATTTTTTTACCTGTTTTATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
1305886 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATTGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
1305951 TTTGTCA-TTTTTTACCTGTTATATTGTTATAGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * * *
1305997 ATAAAGGATCGACATTTTCAATATATCTGGTAGCGCTTTACCTATTTTTTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
1306062 TTTGTCATTTTTCTACCAGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
1306109 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1306174 TTTGTCATTTTTTTA-CTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
1306220 ATAAACTATCAACAC
1 ATAAAGTATCGACAC
1306235 AAACCGACAA
Statistics
Matches: 325, Mismatches: 23, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
111 147 0.45
112 178 0.55
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:1306173 original size:223 final size:223
Alignment explanation
Indices: 1305774--1306224 Score: 769
Period size: 223 Copynumber: 2.0 Consensus size: 223
1305764 GATACTTATA
* *
1305774 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGGATCGACACTATCAACATATCCGGTAGCGCTTTACCTATTTTGTCATTTATAGACCGGT
* * *
1305839 TTTGTCATTTTTTTACCTGTTTTATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
66 TTTGTCATTTTTCTACCAGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
* *
1305904 CAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATTGACCGGTTTTGTCA-TTTTTTACCT
131 CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTA-CT
1305968 GTTATATTGTTATAGATCGATACATTTTT
195 GTTATATTGTTATAGATCGATACATTTTT
* * * * *
1305997 ATAAAGGATCGACATTTTCAATATATCTGGTAGCGCTTTACCTATTTTTTCATTTATAGACCGGT
1 ATAAAGGATCGACACTATCAACATATCCGGTAGCGCTTTACCTATTTTGTCATTTATAGACCGGT
1306062 TTTGTCATTTTTCTACCAGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
66 TTTGTCATTTTTCTACCAGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
1306127 CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACTG
131 CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACTG
*
1306192 TTATATTGTTATGGATCGATACATTTTT
196 TTATATTGTTATAGATCGATACATTTTT
1306220 ATAAA
1 ATAAA
1306225 CTATCAACAC
Statistics
Matches: 214, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
223 207 0.97
224 7 0.03
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45
Consensus pattern (223 bp):
ATAAAGGATCGACACTATCAACATATCCGGTAGCGCTTTACCTATTTTGTCATTTATAGACCGGT
TTTGTCATTTTTCTACCAGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACTG
TTATATTGTTATAGATCGATACATTTTT
Found at i:1307499 original size:30 final size:30
Alignment explanation
Indices: 1307465--1307521 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
1307455 AAGTTGTATG
1307465 TGGTGAATCTAAAGACATTGAAATAAAATA
1 TGGTGAATCTAAAGACATTGAAATAAAATA
*
1307495 TGGTGAATCTAAAGACTTTGAAATAAA
1 TGGTGAATCTAAAGACATTGAAATAAA
1307522 GTAAGATGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.28
Consensus pattern (30 bp):
TGGTGAATCTAAAGACATTGAAATAAAATA
Found at i:1308541 original size:43 final size:43
Alignment explanation
Indices: 1308460--1308541 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
1308450 ATTTTCTAAC
* * *
1308460 AAAAAATGCCGCAATAGGTTTTGTTATTTAGTGACGTTTGTAA
1 AAAAAATGCCGCAATAGGTATTGATATTTAGCGACGTTTGTAA
* *
1308503 AAAAAATGCCGCAATAGGTATTGATGTTTAGCGGCGTTT
1 AAAAAATGCCGCAATAGGTATTGATATTTAGCGACGTTT
1308542 TCCCTACAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (43 bp):
AAAAAATGCCGCAATAGGTATTGATATTTAGCGACGTTTGTAA
Found at i:1308557 original size:43 final size:43
Alignment explanation
Indices: 1308510--1308813 Score: 126
Period size: 43 Copynumber: 7.1 Consensus size: 43
1308500 TAAAAAAAAT
*
1308510 GCCGCAATAGGTATTGATG-TTTAGCGGCGTTTTCCCTACAAAC
1 GCCGCAATAGGTATTGA-GATTTAGCGGCGTTTTACCTACAAAC
* * *
1308553 GCCGCAGTAGGTGTTGAGATTTAGCGGCGTTTTACTTACAAAC
1 GCCGCAATAGGTATTGAGATTTAGCGGCGTTTTACCTACAAAC
* * * * * * * *
1308596 GCCACAGA-AGGTTTTGATATTTTGCGGCATTTTTCC-ATAAAT
1 GCCGCA-ATAGGTATTGAGATTTAGCGGCGTTTTACCTACAAAC
* * * * * *
1308638 GTCACAGA-ATGTGA-TGATG-TTTAGCGGTGTTTTTCCCACAAAC
1 GCCGCA-ATAGGT-ATTGA-GATTTAGCGGCGTTTTACCTACAAAC
* * * * * * * *
1308681 GTCACAGTAGGTTTTCAGATTTAGCAGCGTTTGTATCGA-AAAC
1 GCCGCAATAGGTATTGAGATTTAGCGGCGTTT-TACCTACAAAC
* * * * *
1308724 GACGCAATAAGGT-GTGAGAATTAGCGGCGTTTTTA-TTGA-AAAT
1 GCCGCAAT-AGGTATTGAGATTTAGCGGCG-TTTTACCT-ACAAAC
* * * * *
1308767 GTCGTAATAGGTGTTGAGATTTAGCGGCGTTTT-CATACAAAT
1 GCCGCAATAGGTATTGAGATTTAGCGGCGTTTTACCTACAAAC
1308809 GCCGC
1 GCCGC
1308814 TAAAGTTCGG
Statistics
Matches: 197, Mismatches: 49, Indels: 31
0.71 0.18 0.11
Matches are distributed among these distances:
41 1 0.01
42 49 0.25
43 137 0.70
44 10 0.05
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (43 bp):
GCCGCAATAGGTATTGAGATTTAGCGGCGTTTTACCTACAAAC
Found at i:1308751 original size:128 final size:128
Alignment explanation
Indices: 1308524--1308757 Score: 271
Period size: 128 Copynumber: 1.8 Consensus size: 128
1308514 CAATAGGTAT
* * *
1308524 TGATGTTTAGCGGCGTTTTCCCTACAAACGCCGCAGTAGGTGTTGAGATTTAGCGGCGTTTTACT
1 TGATGTTTAGCGGCGTTTTCCCTACAAACGCCACAGTAGGTGTTCAGATTTAGCAGCGTTTTACT
* * * * *
1308589 TACAAACGCCACAGAAGGTTTTGATATTTTGCGGCATTTTTCCATAAATGTCACAGAATGTGA
66 GACAAACGCCACAGAAGGTTGTGAGAATTAGCGGCATTTTTCCATAAATGTCACAGAATGTGA
* * *
1308652 TGATGTTTAGCGGTGTTTTTCCC-ACAAACGTCACAGTAGGTTTTCAGATTTAGCAGCGTTTGTA
1 TGATGTTTAGCGGCG-TTTTCCCTACAAACGCCACAGTAGGTGTTCAGATTTAGCAGCGTTT-TA
* *
1308716 -TCGA-AAACGACGCA-ATAAGG-TGTGAGAATTAGCGGCGTTTTT
64 CT-GACAAACG-C-CACAGAAGGTTGTGAGAATTAGCGGCATTTTT
1308758 ATTGAAAATG
Statistics
Matches: 88, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
128 70 0.80
129 16 0.18
130 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (128 bp):
TGATGTTTAGCGGCGTTTTCCCTACAAACGCCACAGTAGGTGTTCAGATTTAGCAGCGTTTTACT
GACAAACGCCACAGAAGGTTGTGAGAATTAGCGGCATTTTTCCATAAATGTCACAGAATGTGA
Found at i:1308882 original size:44 final size:42
Alignment explanation
Indices: 1308788--1308903 Score: 139
Period size: 42 Copynumber: 2.8 Consensus size: 42
1308778 TGTTGAGATT
* *
1308788 TAGCGGCGTTTT-CATACAAATGCCGCTAAA-GTTCGGTATA
1 TAGCGGCGTTTTGTATACAAACGCCGCTAAATGTTCGGTATA
1308828 TAGCGGCGTTTCTAGTATACAAACGCCGCTAAATGTAT-GGTATA
1 TAGCGGCGTTT-T-GTATACAAACGCCGCTAAATGT-TCGGTATA
* * *
1308872 TTGCGGCGTTTTTTTTACAAACGCCGCTAAAT
1 TAGCGGCGTTTTGTATACAAACGCCGCTAAAT
1308904 AGCACAAAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
40 11 0.17
41 1 0.02
42 18 0.27
43 17 0.26
44 18 0.27
45 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (42 bp):
TAGCGGCGTTTTGTATACAAACGCCGCTAAATGTTCGGTATA
Found at i:1310018 original size:13 final size:13
Alignment explanation
Indices: 1310017--1310079 Score: 63
Period size: 13 Copynumber: 4.5 Consensus size: 13
1310007 CCGTTTACCC
1310017 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
1310030 TACCCGACCTGTT
1 GACCCGACCCGTT
1310043 GACCCGACCCGACCCGTT
1 G-----ACCCGACCCGTT
1310061 GACCCGACCCGTT
1 GACCCGACCCGTT
1310074 GACCCG
1 GACCCG
1310080 TTGACCGTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 29 0.71
18 12 0.29
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1310018 original size:18 final size:18
Alignment explanation
Indices: 1309995--1310085 Score: 93
Period size: 18 Copynumber: 5.2 Consensus size: 18
1309985 ACCGGTCACA
*
1309995 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
1310013 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
* *
1310030 ----TACCCGACCTGTTG
1 ACCCGACCCGACCCGTTG
1310044 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1310062 ACCCGACCCGTTGACCCGTTG
1 ACCCGACCC---GACCCGTTG
1310083 ACC
1 ACC
1310086 GTTGACCCGT
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
13 11 0.18
18 38 0.62
21 12 0.20
ACGTcount: A:0.16, C:0.47, G:0.20, T:0.16
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1310036 original size:31 final size:31
Alignment explanation
Indices: 1309999--1310079 Score: 135
Period size: 31 Copynumber: 2.6 Consensus size: 31
1309989 GTCACAACCC
*
1309999 GACCCGACCCGTTTACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* *
1310030 TACCCGACCTGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
1310061 GACCCGACCCGTTGACCCG
1 GACCCGACCCGTTGACCCG
1310080 TTGACCGTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.16, C:0.47, G:0.21, T:0.16
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:1310064 original size:8 final size:8
Alignment explanation
Indices: 1310053--1310107 Score: 75
Period size: 8 Copynumber: 7.5 Consensus size: 8
1310043 GACCCGACCC
1310053 GACCCGTT
1 GACCCGTT
1310061 GACCC---
1 GACCCGTT
1310066 GACCCGTT
1 GACCCGTT
1310074 GACCCGTT
1 GACCCGTT
1310082 GA-CCGTT
1 GACCCGTT
1310089 GACCCGTT
1 GACCCGTT
1310097 GA-CCGTT
1 GACCCGTT
1310104 GACC
1 GACC
1310108 GGAGTTGACC
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
5 5 0.12
7 14 0.33
8 23 0.55
ACGTcount: A:0.15, C:0.38, G:0.25, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:1310089 original size:7 final size:7
Alignment explanation
Indices: 1310069--1310108 Score: 62
Period size: 7 Copynumber: 5.4 Consensus size: 7
1310059 TTGACCCGAC
1310069 CCGTTGA
1 CCGTTGA
1310076 CCCGTTGA
1 -CCGTTGA
1310084 CCGTTGA
1 CCGTTGA
1310091 CCCGTTGA
1 -CCGTTGA
1310099 CCGTTGA
1 CCGTTGA
1310106 CCG
1 CCG
1310109 GAGTTGACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 17 0.55
8 14 0.45
ACGTcount: A:0.12, C:0.35, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:1310089 original size:15 final size:15
Alignment explanation
Indices: 1310069--1310107 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
1310059 TTGACCCGAC
1310069 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
1310084 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
1310099 CCGTTGACC
1 CCGTTGACC
1310108 GGAGTTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.13, C:0.36, G:0.26, T:0.26
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:1312690 original size:24 final size:24
Alignment explanation
Indices: 1312596--1312695 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
1312586 ATATTTTATC
* *
1312596 TGATTTCTGATTTGAATTCTGTTT
1 TGATATCTGATCTGAATTCTGTTT
* * * *
1312620 TAACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTCTGTTT
* * * *
1312644 TGAT-TCCTAAACTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTCTGTTT
*
1312668 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTCTGTTT
1312692 TGAT
1 TGAT
1312696 TTTTGATATC
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 1 0.02
24 54 0.96
25 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTT
Found at i:1314861 original size:13 final size:13
Alignment explanation
Indices: 1314860--1314920 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 13
1314850 CCGTTTACCC
1314860 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
1314873 TACCCGACCTGTT
1 GACCCGACCCGTT
1314886 GACCCGACCCGACCCGTT
1 G-----ACCCGACCCGTT
1314904 GACCCGACCCGTT
1 GACCCGACCCGTT
1314917 GACC
1 GACC
1314921 GTTGACCGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
13 27 0.69
18 12 0.31
ACGTcount: A:0.16, C:0.46, G:0.21, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1314861 original size:18 final size:18
Alignment explanation
Indices: 1314838--1314914 Score: 92
Period size: 18 Copynumber: 4.6 Consensus size: 18
1314828 ACCGGTCACA
*
1314838 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
1314856 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
* *
1314873 ----TACCCGACCTGTTG
1 ACCCGACCCGACCCGTTG
1314887 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1314905 ACCCGACCCG
1 ACCCGACCCG
1314915 TTGACCGTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
13 11 0.22
18 39 0.78
ACGTcount: A:0.17, C:0.49, G:0.19, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1314879 original size:31 final size:31
Alignment explanation
Indices: 1314842--1314920 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
1314832 GTCACAACCC
*
1314842 GACCCGACCCGTTTACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* *
1314873 TACCCGACCTGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
1314904 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
1314921 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.16, C:0.47, G:0.20, T:0.16
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:1314924 original size:7 final size:7
Alignment explanation
Indices: 1314912--1314950 Score: 69
Period size: 7 Copynumber: 5.4 Consensus size: 7
1314902 TTGACCCGAC
1314912 CCGTTGA
1 CCGTTGA
1314919 CCGTTGA
1 CCGTTGA
1314926 CCGTTGA
1 CCGTTGA
1314933 CCCGTTGA
1 -CCGTTGA
1314941 CCGTTGA
1 CCGTTGA
1314948 CCG
1 CCG
1314951 GAGTTGACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 24 0.77
8 7 0.23
ACGTcount: A:0.13, C:0.33, G:0.28, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:1314937 original size:15 final size:15
Alignment explanation
Indices: 1314912--1314949 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1314902 TTGACCCGAC
1314912 CCGTTGA-CCGTTGA
1 CCGTTGACCCGTTGA
1314926 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
1314941 CCGTTGACC
1 CCGTTGACC
1314950 GGAGTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.26
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:1314937 original size:22 final size:22
Alignment explanation
Indices: 1314909--1314950 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1314899 CCGTTGACCC
1314909 GACCCGTTGACCGTTGACCGTT
1 GACCCGTTGACCGTTGACCGTT
1314931 GACCCGTTGACCGTTGACCG
1 GACCCGTTGACCGTTGACCG
1314951 GAGTTGACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.33, G:0.29, T:0.24
Consensus pattern (22 bp):
GACCCGTTGACCGTTGACCGTT
Found at i:1317532 original size:24 final size:24
Alignment explanation
Indices: 1317438--1317537 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
1317428 ATATTTTATC
* *
1317438 TGATTTCTGATTTGAATTCTGTTT
1 TGATATCTGATCTGAATTCTGTTT
* * * *
1317462 TAACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTCTGTTT
* * * *
1317486 TGAT-TCCTAAACTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTCTGTTT
*
1317510 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTCTGTTT
1317534 TGAT
1 TGAT
1317538 TTTGATATCT
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 1 0.02
24 54 0.96
25 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTT
Found at i:1319712 original size:17 final size:18
Alignment explanation
Indices: 1319678--1319720 Score: 79
Period size: 17 Copynumber: 2.4 Consensus size: 18
1319668 ACCGGTCACA
1319678 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
1319696 ACCCGACCCGA-CCGTTT
1 ACCCGACCCGACCCGTTT
1319713 ACCCGACC
1 ACCCGACC
1319721 TGTTGACCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.19, C:0.51, G:0.16, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:1319719 original size:30 final size:30
Alignment explanation
Indices: 1319682--1319760 Score: 115
Period size: 30 Copynumber: 2.6 Consensus size: 30
1319672 GTCACAACCC
*
1319682 GACCCGACCCGTTTACCCGACCCGA-CCGTT
1 GACCCGACCCGTTGACCCGA-CCGACCCGTT
* *
1319712 TACCCGACCTGTTGACCCGACCGACCCGTT
1 GACCCGACCCGTTGACCCGACCGACCCGTT
1319742 GACCCGACCCGTTGACCCG
1 GACCCGACCCGTTGACCCG
1319761 TTGACCGTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 4 0.09
30 39 0.91
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (30 bp):
GACCCGACCCGTTGACCCGACCGACCCGTT
Found at i:1319735 original size:17 final size:17
Alignment explanation
Indices: 1319678--1319750 Score: 66
Period size: 17 Copynumber: 4.5 Consensus size: 17
1319668 ACCGGTCACA
*
1319678 ACCCGACCCGACCCGTTT
1 ACCCGA-CCGACCCGTTG
*
1319696 ACCCGACCCGA-CCGTTT
1 ACCCGA-CCGACCCGTTG
*
1319713 A--C--CCGACCTGTTG
1 ACCCGACCGACCCGTTG
1319726 ACCCGACCGACCCGTTG
1 ACCCGACCGACCCGTTG
1319743 ACCCGACC
1 ACCCGACC
1319751 CGTTGACCCG
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
12 4 0.09
13 5 0.11
15 2 0.04
17 25 0.53
18 11 0.23
ACGTcount: A:0.18, C:0.48, G:0.19, T:0.15
Consensus pattern (17 bp):
ACCCGACCGACCCGTTG
Found at i:1319748 original size:13 final size:13
Alignment explanation
Indices: 1319700--1319760 Score: 61
Period size: 13 Copynumber: 4.5 Consensus size: 13
1319690 CCGTTTACCC
1319700 GACCCGA-CCGTT
1 GACCCGACCCGTT
* *
1319712 TACCCGACCTGTT
1 GACCCGACCCGTT
1319725 GACCCGACCGACCCGTT
1 GA--C--CCGACCCGTT
1319742 GACCCGACCCGTT
1 GACCCGACCCGTT
1319755 GACCCG
1 GACCCG
1319761 TTGACCGTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
12 6 0.15
13 21 0.52
15 2 0.05
17 11 0.28
ACGTcount: A:0.16, C:0.44, G:0.23, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1319770 original size:7 final size:7
Alignment explanation
Indices: 1319750--1319786 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
1319740 TTGACCCGAC
1319750 CCGTTGA
1 CCGTTGA
1319757 CCCGTTGA
1 -CCGTTGA
1319765 CCGTTGA
1 CCGTTGA
1319772 CCGTTGA
1 CCGTTGA
1319779 CCGTTGA
1 CCGTTGA
1319786 C
1 C
1319787 GGAGTTGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.14, C:0.32, G:0.27, T:0.27
Consensus pattern (7 bp):
CCGTTGA
Found at i:1322359 original size:24 final size:24
Alignment explanation
Indices: 1322266--1322364 Score: 76
Period size: 24 Copynumber: 4.2 Consensus size: 24
1322256 ATATTTTATC
* *
1322266 TGATTTCTGATTTGAATTCTGTTT
1 TGATATCTGATCTGAATTCTGTTT
* * * *
1322290 TAACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTCTGTTT
* * * *
1322314 TGAT-TCCTAAACTGGATT-TGTTA
1 TGATAT-CTGATCTGAATTCTGTTT
*
1322337 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTCTGTTT
1322361 TGAT
1 TGAT
1322365 TTTTGATATC
Statistics
Matches: 55, Mismatches: 17, Indels: 6
0.71 0.22 0.08
Matches are distributed among these distances:
23 18 0.33
24 37 0.67
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.47
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTT
Found at i:1323194 original size:21 final size:22
Alignment explanation
Indices: 1323137--1323196 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
1323127 TGTGCTGTTG
* * *
1323137 CTGCTTCTTTCTCTTCTTCCGA
1 CTGCTGCTCTCTCTGCTTCCGA
**
1323159 -TGCTGCTCTGGCTGCTTCC-A
1 CTGCTGCTCTCTCTGCTTCCGA
1323179 CTGCTGCTCTCTCTGCTT
1 CTGCTGCTCTCTCTGCTT
1323197 TCCTTCCTTC
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.03, C:0.37, G:0.17, T:0.43
Consensus pattern (22 bp):
CTGCTGCTCTCTCTGCTTCCGA
Found at i:1331823 original size:40 final size:39
Alignment explanation
Indices: 1331779--1331860 Score: 94
Period size: 40 Copynumber: 2.1 Consensus size: 39
1331769 ATTTGTGCTT
*
1331779 AAAACACCACT-AAGTACGACCTTTAGCGGTGTTTTATATA
1 AAAACACCACTAAAGTAC-AACTTTAGCGG-GTTTTATATA
* * * *
1331819 AAAACGCCATTAAAGTACAATTTTATCGGGTTTTATATA
1 AAAACACCACTAAAGTACAACTTTAGCGGGTTTTATATA
1331858 AAA
1 AAA
1331861 CGTCACTATA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 13 0.36
40 17 0.47
41 6 0.17
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (39 bp):
AAAACACCACTAAAGTACAACTTTAGCGGGTTTTATATA
Found at i:1331893 original size:160 final size:159
Alignment explanation
Indices: 1331468--1332000 Score: 494
Period size: 160 Copynumber: 3.3 Consensus size: 159
1331458 TGAAATCAAG
* * * * * * *
1331468 ACGACCTTTAGCAGTGTTTTTTTAAAAACGCCACTAATGCACTAGTATTTAGCGGCTTTTATGTT
1 ACGACCTTTAGCAGCG-TTTTAT-AAAACGCCACTAAAGTAC-AGTATTTATCGGGTTTTAT-AT
* * *
1331533 AAAAACGCCACTAAAGTACGTGTAATTAGCAGCGTTTGTGCATAAAATGCCAC-AAAAAATATGT
62 -AAAACGTCACTAAAGTATGTGTAATTAGCAGCGTTTGTGCATAAAATGCCACTAAAGAA-A-GT
*
1331597 GTAATTAGCGGCGTTTGTGCTTGCAATGCCACTAAAGT
124 GTAATTAGCGGC-TTTGTGCTT-AAATGCCACTAAAGT
* * * * * *
1331635 ACTACCGTTAGC-GACG-TTTGTAAAACACCAC-AAAGTACAGTATTTCTCGACG-TTTATATAA
1 ACGACCTTTAGCAG-CGTTTTATAAAACGCCACTAAAGTACAGTATTTATCG-GGTTTTATATAA
* * * * *
1331696 AA-ATGCAACTAGAGTATGTGTAATTAGCGGCGTTTGTGCATAAAACGCCACTAAAGAAAGTATA
64 AACGT-C-ACTAAAGTATGTGTAATTAGCAGCGTTTGTGCATAAAATGCCACTAAAGAAAGTGTA
**
1331760 ATTAGCGGCATTTGTGCTTAAAACACCACT-AAGT
127 ATTAGCGGC-TTTGTGCTT-AAATGCCACTAAAGT
* * * *
1331794 ACGACCTTTAGCGGTGTTTTATATAAAAACGCCATTAAAGTACAAT-TTTATCGGGTTTTATATA
1 ACGACCTTTAGCAGCG-TTT-TAT-AAAACGCCACTAAAGTACAGTATTTATCGGGTTTTATATA
* * * * *
1331858 AAACGTCACTATAGTGTGTGTAATTAGC-G-GTTTGTGCGTAAAATGCCACTAAAGTACGTGTAA
63 AAACGTCACTAAAGTATGTGTAATTAGCAGCGTTTGTGCATAAAATGCCACTAAAGAAAGTGTAA
*
1331921 TTTAGCGGCGTTGTGCTTAAATGCCACTAAAGT
128 -TTAGCGGCTTTGTGCTTAAATGCCACTAAAGT
*
1331954 ACGACCTTTAGCAGCGTTTCTATAAAACGCCACT-AAGTACATTATTT
1 ACGACCTTTAGCAGCGTTT-TATAAAACGCCACTAAAGTACAGTATTT
1332001 TCTAGCATTT
Statistics
Matches: 300, Mismatches: 50, Indels: 41
0.77 0.13 0.10
Matches are distributed among these distances:
157 8 0.03
158 13 0.04
159 29 0.10
160 90 0.30
161 53 0.18
162 41 0.14
163 31 0.10
164 19 0.06
165 4 0.01
166 1 0.00
167 11 0.04
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (159 bp):
ACGACCTTTAGCAGCGTTTTATAAAACGCCACTAAAGTACAGTATTTATCGGGTTTTATATAAAA
CGTCACTAAAGTATGTGTAATTAGCAGCGTTTGTGCATAAAATGCCACTAAAGAAAGTGTAATTA
GCGGCTTTGTGCTTAAATGCCACTAAAGT
Found at i:1331908 original size:40 final size:41
Alignment explanation
Indices: 1331875--1331956 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
1331865 ACTATAGTGT
*
1331875 GTGTAA-TTAGCGG-TTTGTGCGTAAAATGCCACTAAAGTAC
1 GTGTAATTTAGCGGCGTTGTGC-TAAAATGCCACTAAAGTAC
*
1331915 GTGTAATTTAGCGGCGTTGTGCTTAAATGCCACTAAAGTAC
1 GTGTAATTTAGCGGCGTTGTGCTAAAATGCCACTAAAGTAC
1331956 G
1 G
1331957 ACCTTTAGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 6 0.16
41 26 0.68
42 6 0.16
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (41 bp):
GTGTAATTTAGCGGCGTTGTGCTAAAATGCCACTAAAGTAC
Found at i:1337687 original size:2 final size:2
Alignment explanation
Indices: 1337680--1337769 Score: 152
Period size: 2 Copynumber: 47.0 Consensus size: 2
1337670 CCCTTTATGC
1337680 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- 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
1337720 AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1337760 AT AT AT AT AT
1 AT AT AT AT AT
1337770 TATTTTTTAA
Statistics
Matches: 84, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
1 4 0.05
2 80 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1337996 original size:24 final size:23
Alignment explanation
Indices: 1337945--1337999 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
1337935 CTTTATCATG
*
1337945 TTTATTTATTATTATTTTACTTTG
1 TTTATTTATTATTATTTTA-TTTA
1337969 TTTATTTCAATTATTATTTT-TTTA
1 TTTATTT--ATTATTATTTTATTTA
1337993 TTTATTT
1 TTTATTT
1338000 TATTTGTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 17 0.61
26 11 0.39
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTATTTATTATTATTTTATTTA
Found at i:1352895 original size:135 final size:135
Alignment explanation
Indices: 1352650--1353287 Score: 800
Period size: 135 Copynumber: 4.7 Consensus size: 135
1352640 TAAACCAATC
* ** * * *
1352650 AACATTTCCAATGGAAAGTTTGTAATGAGAAGAACTCATCCAATAGAGGGAGAAGAAGTTTATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAAGGAGAAGAAGTTCATAA
* * * *
1352715 TGAGAATAACTTGTTCAACCTTTGCTCGATTCACAATATTTTGAATCAGCGACGCCTCACTTGAG
66 TGAGAAGAACTTGTTCAACCTTTGCTCGATTCACAACATTTCGAATCAGCAACGCCTCACTTGAG
1352780 GGATT
131 GGATT
* *
1352785 AATATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAAGGAGAATAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAAGGAGAAGAAGTTCATAA
* * * * * * * ** * * *
1352850 TGTGAAGAACTTGTTCAACATTTGCTTGATTTAGAGCATTTTGAATCAGTGACACTTTACTTGAG
66 TGAGAAGAACTTGTTCAACCTTTGCTCGATTCACAACATTTCGAATCAGCAACGCCTCACTTGAG
1352915 GGATT
131 GGATT
* *
1352920 AACATTTCCAACGGAGAGTTCATAATGAGAAGAACTCATCCGATA-AAGGGAGAAAAAGTTCATA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAA-GGAGAAGAAGTTCATA
* * * * *
1352984 ATAAGAAGAACTTGTTCAGCCTTTGCTCGATTCACAATATTTCGAATCAACAACGTCTCACTTGA
65 ATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACAACATTTCGAATCAGCAACGCCTCACTTGA
1353049 GGGATT
130 GGGATT
* * *
1353055 AACATTTCCAATGGAGAGTTTC-TAATGAGAAGAACTCATTCGATA-AAGGGATAAGAATTTCAT
1 AACATTTCCAATGGAGAG-TTCATAATGAGAAGAACTCATCCGATAGAA-GGAGAAGAAGTTCAT
* * * * * *
1353118 AATAAGAAGAACTTGTTCAACCTTTGGTTGATGCA-AAGCATTTCGAATCAGCAACGTCTTACTT
64 AATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACAA-CATTTCGAATCAGCAACGCCTCACTT
1353182 GAGGGATT
128 GAGGGATT
**
1353190 AACATTTCCAATGGAGAGTTTGTAATGAGAAGAACTCATCCGATAG-AGAGAGAAGAAGTTCATA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAAG-GAGAAGAAGTTCATA
* *
1353254 ATGAGAAGAACTTTTTCAACCTTTACTCGATTCA
65 ATGAGAAGAACTTGTTCAACCTTTGCTCGATTCA
1353288 TCGCACATGG
Statistics
Matches: 435, Mismatches: 62, Indels: 12
0.85 0.12 0.02
Matches are distributed among these distances:
134 7 0.02
135 425 0.98
136 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (135 bp):
AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAAGGAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTGCTCGATTCACAACATTTCGAATCAGCAACGCCTCACTTGAG
GGATT
Done.