Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397272.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_12.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3572271
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 44823 characters in sequence are not A, C, G, or T
File 4 of 9
Found at i:1184936 original size:34 final size:35
Alignment explanation
Indices: 1184832--1184946 Score: 110
Period size: 35 Copynumber: 3.3 Consensus size: 35
1184822 ACATTGTACA
* * *
1184832 CAGAACAACCAAAACGAGTGAAA-CACTACTTCACA
1 CAGAACAACTAAAACAAGT-AAAGCACTACTTCACG
* * * *
1184867 TAGAACACCTAAAACAAGTGAAGTACTA-TTACACG
1 CAGAACAACTAAAACAAGTAAAGCACTACTT-CACG
*
1184902 CA-AACAACTAAAACAAGTAAAGCGCTACTTCACG
1 CAGAACAACTAAAACAAGTAAAGCACTACTTCACG
*
1184936 CAGAATAACTA
1 CAGAACAACTA
1184947 GAATAAGTGG
Statistics
Matches: 63, Mismatches: 13, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
34 31 0.49
35 32 0.51
ACGTcount: A:0.48, C:0.24, G:0.12, T:0.16
Consensus pattern (35 bp):
CAGAACAACTAAAACAAGTAAAGCACTACTTCACG
Found at i:1190564 original size:35 final size:35
Alignment explanation
Indices: 1190476--1190574 Score: 101
Period size: 35 Copynumber: 2.8 Consensus size: 35
1190466 CATTGTACAG
* * * *
1190476 AGAACAACCAAAACGAGTGAAACATTACTTCACAC
1 AGAACAACTAAAACAAGTGAAGCACTACTTCACAC
* *
1190511 AGAACAACTAAAACAAGTGAAGTACTACTTCACGC
1 AGAACAACTAAAACAAGTGAAGCACTACTTCACAC
* * *
1190546 AGAAC-AGTAAGAATAAGTGGAGCACTACT
1 AGAACAACTAA-AACAAGTGAAGCACTACT
1190575 CCATATGAGA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
34 4 0.08
35 49 0.92
ACGTcount: A:0.46, C:0.21, G:0.16, T:0.16
Consensus pattern (35 bp):
AGAACAACTAAAACAAGTGAAGCACTACTTCACAC
Found at i:1199992 original size:20 final size:20
Alignment explanation
Indices: 1199955--1199992 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1199945 GAAGAAATAG
*
1199955 AGAGAAAAAGAACCAAAATT
1 AGAGAAAAAGAAACAAAATT
*
1199975 AGAGAAAAAGAAAGAAAA
1 AGAGAAAAAGAAACAAAA
1199993 AGAAAAATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.05, G:0.18, T:0.05
Consensus pattern (20 bp):
AGAGAAAAAGAAACAAAATT
Found at i:1205220 original size:22 final size:22
Alignment explanation
Indices: 1205195--1205237 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1205185 ATATATACAT
*
1205195 ATAACAAACTAAAATATTTTAA
1 ATAACAAAATAAAATATTTTAA
* *
1205217 ATAATAAAATAATATATTTTA
1 ATAACAAAATAAAATATTTTA
1205238 TGCATATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAACAAAATAAAATATTTTAA
Found at i:1206234 original size:22 final size:23
Alignment explanation
Indices: 1206209--1206261 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
1206199 TTATGAAGGA
*
1206209 TTAATAAAATTTTAA-AAAAAAT
1 TTAATAAAATTTAAATAAAAAAT
1206231 TTAAT-AAATTTAAATAAAAAAT
1 TTAATAAAATTTAAATAAAAAAT
1206253 TTAA-AAAAT
1 TTAATAAAAT
1206262 AGTAATACTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
TTAATAAAATTTAAATAAAAAAT
Found at i:1206268 original size:22 final size:22
Alignment explanation
Indices: 1206224--1206266 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1206214 AAAATTTTAA
* *
1206224 AAAAAATTTAATAAATTTAAAT
1 AAAAAATTTAAAAAATGTAAAT
1206246 AAAAAATTTAAAAAATAGTAA
1 AAAAAATTTAAAAAAT-GTAA
1206267 TACTGATGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAAAATTTAAAAAATGTAAAT
Found at i:1208301 original size:23 final size:24
Alignment explanation
Indices: 1208275--1208319 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1208265 AGGAAAGAGG
*
1208275 GGGA-GAAATTAGGTCGGGGGGGT
1 GGGAGGAAATTAGGCCGGGGGGGT
*
1208298 GGGAGGCAATTAGGCCGGGGGG
1 GGGAGGAAATTAGGCCGGGGGG
1208320 TGAAATTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.20, C:0.09, G:0.58, T:0.13
Consensus pattern (24 bp):
GGGAGGAAATTAGGCCGGGGGGGT
Found at i:1209022 original size:27 final size:28
Alignment explanation
Indices: 1208992--1209185 Score: 136
Period size: 27 Copynumber: 7.1 Consensus size: 28
1208982 ACACAACTTA
* *
1208992 TAACAACTAAATCTTCAACATCG-TGTG
1 TAACAACTAAATTTTCAACATGGATGTG
* *
1209019 TAACAACTACATTTTTCAACATGGCT-TG
1 TAACAACTA-AATTTTCAACATGGATGTG
* * *
1209047 TAACATCTAAATCTTT-AATAT-GATGTA
1 TAACAACTAAAT-TTTCAACATGGATGTG
* *
1209074 TAACAACTACATTTTTCAA-ATGG-CGTG
1 TAACAACTA-AATTTTCAACATGGATGTG
* *
1209101 TAACAACTAAATTTTCAACAT-AATATG
1 TAACAACTAAATTTTCAACATGGATGTG
* * * * *
1209128 TAATAATTATATTTTTCAATAT-GACGTG
1 TAACAACTA-AATTTTCAACATGGATGTG
*
1209156 TAATAACTAAATTTTCAACATGGAT-TG
1 TAACAACTAAATTTTCAACATGGATGTG
1209183 TAA
1 TAA
1209186 TACTTACATT
Statistics
Matches: 129, Mismatches: 27, Indels: 22
0.72 0.15 0.12
Matches are distributed among these distances:
26 10 0.08
27 66 0.51
28 52 0.40
29 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37
Consensus pattern (28 bp):
TAACAACTAAATTTTCAACATGGATGTG
Found at i:1209033 original size:55 final size:55
Alignment explanation
Indices: 1208961--1209198 Score: 160
Period size: 55 Copynumber: 4.3 Consensus size: 55
1208951 TCATCTTAAC
* *
1208961 GTGTAACAATTAAATTTTTCAACACAACTTATAACAACTAAATCTTCAACATCG-T
1 GTGTAACAACTACATTTTTCAACACAACTTATAACAACTAAATCTTCAACAT-GAT
*** * * * *
1209016 GTGTAACAACTACATTTTTCAACATGGCTTGTAACATCTAAATCTTTAATATGAT
1 GTGTAACAACTACATTTTTCAACACAACTTATAACAACTAAATCTTCAACATGAT
* *** * * * *
1209071 GTATAACAACTACATTTTTCAA-ATGGCGTGTAACAACTAAATTTTCAACATAAT
1 GTGTAACAACTACATTTTTCAACACAACTTATAACAACTAAATCTTCAACATGAT
* * * * * ** * * * *
1209125 ATGTAATAATTATATTTTTCAATATGACGTGTAATAACTAAATTTTCAACATGGAT
1 GTGTAACAACTACATTTTTCAACACAACTTATAACAACTAAATCTTCAACAT-GAT
*
1209181 -TGTAA-TACTTACATTTTT
1 GTGTAACAAC-TACATTTTT
1209199 AGTGCAATTT
Statistics
Matches: 152, Mismatches: 27, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
54 45 0.30
55 105 0.69
56 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (55 bp):
GTGTAACAACTACATTTTTCAACACAACTTATAACAACTAAATCTTCAACATGAT
Found at i:1209187 original size:27 final size:26
Alignment explanation
Indices: 1208962--1209185 Score: 121
Period size: 27 Copynumber: 8.2 Consensus size: 26
1208952 CATCTTAACG
* **
1208962 TGTAACAATTAAATTTTTCAACACAACT
1 TGTAACAACTAAA-TTTTCAACATGA-T
* *
1208990 TATAACAACTAAATCTTCAACATCG-T
1 TGTAACAACTAAATTTTCAACAT-GAT
* *
1209016 GTGTAACAACTACATTTTTCAACATGGCT
1 -TGTAACAACTA-AATTTTCAACAT-GAT
* *
1209045 TGTAACATCTAAATCTTT-AATATGAT
1 TGTAACAACTAAAT-TTTCAACATGAT
* * **
1209071 GTATAACAACTACATTTTTCAA-ATGGCG
1 -TGTAACAACTA-AATTTTCAACAT-GAT
*
1209099 TGTAACAACTAAATTTTCAACATAAT
1 TGTAACAACTAAATTTTCAACATGAT
* * * * *
1209125 ATGTAATAATTATATTTTTCAATATGACG
1 -TGTAACAACTA-AATTTTCAACATGA-T
*
1209154 TGTAATAACTAAATTTTCAACATGGAT
1 TGTAACAACTAAATTTTCAACAT-GAT
1209181 TGTAA
1 TGTAA
1209186 TACTTACATT
Statistics
Matches: 149, Mismatches: 33, Indels: 29
0.71 0.16 0.14
Matches are distributed among these distances:
26 11 0.07
27 74 0.50
28 63 0.42
29 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (26 bp):
TGTAACAACTAAATTTTCAACATGAT
Found at i:1209606 original size:26 final size:24
Alignment explanation
Indices: 1209577--1209652 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 24
1209567 TTATAAAAGA
1209577 TATTTAAAT-TTAAATTAAATTATTTT
1 TATTTAAATATTAAA--AAA-TATTTT
1209603 TATTTAAATATTAAAAAATATTTT
1 TATTTAAATATTAAAAAATATTTT
* * *
1209627 TA-TTAATATTTTTAAATATATTTT
1 TATTTAA-ATATTAAAAAATATTTT
1209651 TA
1 TA
1209653 AAATCAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
23 4 0.09
24 24 0.53
25 3 0.07
26 9 0.20
27 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TATTTAAATATTAAAAAATATTTT
Found at i:1211106 original size:19 final size:18
Alignment explanation
Indices: 1211082--1211130 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 18
1211072 TTTTTTTTTG
1211082 TTAAGAACGATGACTT-TCA
1 TTAAGAA-GATGACTTCT-A
1211101 TTAAGAAGGATGACTTCTA
1 TTAAGAA-GATGACTTCTA
1211120 TTAAGAAGATG
1 TTAAGAAGATG
1211131 GTAATAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 4 0.14
19 23 0.82
20 1 0.04
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (18 bp):
TTAAGAAGATGACTTCTA
Found at i:1211585 original size:18 final size:17
Alignment explanation
Indices: 1211554--1211601 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
1211544 AATTTGTTGT
*
1211554 ACTCTTCTTCTTTATTTA
1 ACTCTTC-TATTTATTTA
* *
1211572 ATTCTTCATATTTATTTC
1 ACTCTTC-TATTTATTTA
1211590 ACTCTTCTATTT
1 ACTCTTCTATTT
1211602 GAAATTACTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.19, C:0.21, G:0.00, T:0.60
Consensus pattern (17 bp):
ACTCTTCTATTTATTTA
Found at i:1213235 original size:26 final size:26
Alignment explanation
Indices: 1213186--1213238 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1213176 TGAATTTAAG
* *
1213186 AATAATTTTACCGCTAGAAGTGGATA
1 AATAATTTTACCGCTAAAAATGGATA
1213212 AATAATTTTACC-CTAAAAAATGGATA
1 AATAATTTTACCGCT-AAAAATGGATA
1213238 A
1 A
1213239 GTGCTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.30
Consensus pattern (26 bp):
AATAATTTTACCGCTAAAAATGGATA
Found at i:1217767 original size:19 final size:19
Alignment explanation
Indices: 1217739--1217783 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1217729 AATAAGATTT
1217739 TTTCTCTCCCCCTAAATAC
1 TTTCTCTCCCCCTAAATAC
* ** *
1217758 TTTCTTTCCCTTTAAATAT
1 TTTCTCTCCCCCTAAATAC
1217777 TTTCTCT
1 TTTCTCT
1217784 TATAGTTGTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.18, C:0.31, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTCTCTCCCCCTAAATAC
Found at i:1220073 original size:6 final size:6
Alignment explanation
Indices: 1220062--1220088 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1220052 TTAAGGTCAA
1220062 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1220089 TTATAGAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:1229190 original size:74 final size:73
Alignment explanation
Indices: 1229063--1229285 Score: 306
Period size: 74 Copynumber: 3.0 Consensus size: 73
1229053 AGTAAAACAA
* * *
1229063 ATTGCAAGACAAAGAATACTTAATCGACTAAGAAGTATAGTTAGCTAGCTAAAAGTGCACTATCA
1 ATTGCAAGACAGAGAGTACTTAATCGACTAAGAAGTATAGTTAGCCAGCTAAAAGT-CACTATCA
1229128 AAGAATTTG
65 AAGAATTTG
* *
1229137 ATTGCAAGATAGAGAGTACTTAATCGACTAAGAAGTATAGTTAGCCAGTTAAAAGCTCA-TCATC
1 ATTGCAAGACAGAGAGTACTTAATCGACTAAGAAGTATAGTTAGCCAGCTAAAAG-TCACT-ATC
*
1229201 AGAGAATTTG
64 AAAGAATTTG
* *
1229211 ATTGCGAGACAGAGAAG-ACTTAATCGACTAAGAAGTATAGTTAGCCAACTAAAAGTTCACTATC
1 ATTGCAAGACAGAG-AGTACTTAATCGACTAAGAAGTATAGTTAGCCAGCTAAAAG-TCACTATC
*
1229275 AAAAAATTTG
64 AAAGAATTTG
1229285 A
1 A
1229286 ATTTTAGCCC
Statistics
Matches: 132, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
73 1 0.01
74 127 0.96
75 4 0.03
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (73 bp):
ATTGCAAGACAGAGAGTACTTAATCGACTAAGAAGTATAGTTAGCCAGCTAAAAGTCACTATCAA
AGAATTTG
Found at i:1236240 original size:19 final size:19
Alignment explanation
Indices: 1236216--1236257 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1236206 AAGTTTTCTC
*
1236216 AATTAGTATCTAGCTTTAA
1 AATTAGTATCAAGCTTTAA
*
1236235 AATTAGTATCAAGCTTTAT
1 AATTAGTATCAAGCTTTAA
1236254 AATT
1 AATT
1236258 GTCTCTTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (19 bp):
AATTAGTATCAAGCTTTAA
Found at i:1238292 original size:74 final size:74
Alignment explanation
Indices: 1238070--1238277 Score: 240
Period size: 74 Copynumber: 2.8 Consensus size: 74
1238060 AGTAAAGCAA
* * * * * *
1238070 ATTGCCAGACAAAGAATACTTAATCAACTAAGAAGTATAGTTAGCTAGCTAAAAGCTCACCATCA
1 ATTGCAAGATAAAGAAAACTTAATCAACTAAGAAGTATAGTTAGCCAACTAAAAGCTCATCATCA
1238135 AAGAATTTG
66 AAGAATTTG
** * * * *
1238144 ATTGTGAGATAAATAAAACTTAATCAACTACGAAGTATAGTTAGCCAGA-TAAAAGCTTATCGTC
1 ATTGCAAGATAAAGAAAACTTAATCAACTAAGAAGTATAGTTAGCCA-ACTAAAAGCTCATCATC
1238208 AAAGAATTTG
65 AAAGAATTTG
* * **
1238218 ATTGCAAGATAGAGAAGACTTAATTGACTAAGAAGTAT-GATTAGCCAACTAAAAGCTCAT
1 ATTGCAAGATAAAGAAAACTTAATCAACTAAGAAGTATAG-TTAGCCAACTAAAAGCTCAT
1238278 TATTAGAAAA
Statistics
Matches: 111, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
73 2 0.02
74 109 0.98
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.26
Consensus pattern (74 bp):
ATTGCAAGATAAAGAAAACTTAATCAACTAAGAAGTATAGTTAGCCAACTAAAAGCTCATCATCA
AAGAATTTG
Found at i:1262479 original size:53 final size:54
Alignment explanation
Indices: 1262419--1262555 Score: 159
Period size: 53 Copynumber: 2.5 Consensus size: 54
1262409 ATGAAAAACC
* * *
1262419 ATAAATGTCCATTCCCTAAAGTGAATGTAACAAACGAGCTAGTAAT-AAAAATT
1 ATAAATGTCCATTCTCTAAAGTGAATGTAACAAACGAGATACTAATAAAAAATT
* * * * *
1262472 ATGAATGTTCATTCTTTGAAGTGAATGTGACAAACGAGATACTAATAAAAAAATT
1 ATAAATGTCCATTCTCTAAAGTGAATGTAACAAACGAGATACTAAT-AAAAAATT
*
1262527 ATAAATCTGTCTATTCTCTAAAGTGAATG
1 ATAAA--TGTCCATTCTCTAAAGTGAATG
1262556 CGATATCATA
Statistics
Matches: 67, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
53 38 0.57
55 11 0.16
57 18 0.27
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (54 bp):
ATAAATGTCCATTCTCTAAAGTGAATGTAACAAACGAGATACTAATAAAAAATT
Found at i:1272262 original size:24 final size:24
Alignment explanation
Indices: 1272230--1272276 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1272220 TTTAAAAGTT
*
1272230 ATATATATATGATATAAATTTAAA
1 ATATATATATAATATAAATTTAAA
* *
1272254 ATATGTATATAATATTAATTTAA
1 ATATATATATAATATAAATTTAA
1272277 TTTTTTGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (24 bp):
ATATATATATAATATAAATTTAAA
Found at i:1273431 original size:76 final size:75
Alignment explanation
Indices: 1273312--1273514 Score: 212
Period size: 76 Copynumber: 2.7 Consensus size: 75
1273302 GCGAGGAAGA
* * * *
1273312 AAAGAAGAAGAAAGGGAG-TGCTGTCGGCTTGGGGAAGAGAAGAAAGAAGAAGAAGCGGCTATGG
1 AAAGAA-AAGAAA-GGAGCGGCTGTCGACTTGGGGAAGAAAAGAAAGAAGAAGAAGCGGATATGG
*
1273376 CAGTGGCTAGGC
64 CAATGGCTAGGC
* * * * *
1273388 AAATAAATGAAAGGAGTGGCTG-CTGACTTTGGGGAAGAAAAGAAAGAAGAAGGAGCGGATTTGG
1 AAAGAAAAGAAAGGAGCGGCTGTC-GAC-TTGGGGAAGAAAAGAAAGAAGAAGAAGCGGATATGG
* *
1273452 CAATGGTTAGGT
64 CAATGGCTAGGC
* * * *
1273464 AAAGAAAAGAGAGGAGCGGCTGTCGGCTTGGGGAAGAAAACAAAGAGGAAG
1 AAAGAAAAGAAAGGAGCGGCTGTCGACTTGGGGAAGAAAAGAAAGAAGAAG
1273515 GAGGAGCGAC
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
74 5 0.05
75 33 0.31
76 66 0.63
77 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.38, T:0.14
Consensus pattern (75 bp):
AAAGAAAAGAAAGGAGCGGCTGTCGACTTGGGGAAGAAAAGAAAGAAGAAGAAGCGGATATGGCA
ATGGCTAGGC
Found at i:1279179 original size:2 final size:2
Alignment explanation
Indices: 1279172--1279206 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1279162 TTGCAGACCT
1279172 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1279207 TTGGGCAGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1281312 original size:2 final size:2
Alignment explanation
Indices: 1281305--1281353 Score: 54
Period size: 2 Copynumber: 27.0 Consensus size: 2
1281295 GGATATAGGT
*
1281305 AG AG AG AG A- AG AG AG A- AG AG AG A- AG AG AG AA AG AG AG A-
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1281343 AG AG AG A- AG AG
1 AG AG AG AG AG AG
1281354 TTGGATACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
1 5 0.12
2 35 0.88
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1281319 original size:7 final size:7
Alignment explanation
Indices: 1281307--1281353 Score: 85
Period size: 7 Copynumber: 6.6 Consensus size: 7
1281297 ATATAGGTAG
1281307 AGAGAGA
1 AGAGAGA
1281314 AGAGAGA
1 AGAGAGA
1281321 AGAGAGA
1 AGAGAGA
1281328 AGAGAGAA
1 AGAGAG-A
1281336 AGAGAGA
1 AGAGAGA
1281343 AGAGAGA
1 AGAGAGA
1281350 AGAG
1 AGAG
1281354 TTGGATACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 32 0.82
8 7 0.18
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (7 bp):
AGAGAGA
Found at i:1285034 original size:6 final size:6
Alignment explanation
Indices: 1285015--1285052 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
1285005 AAAAGGGCAA
1285015 AAAAAG -AAAA- AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1285053 GCCAAACTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 8 0.27
6 22 0.73
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1290448 original size:53 final size:54
Alignment explanation
Indices: 1290370--1290486 Score: 164
Period size: 53 Copynumber: 2.2 Consensus size: 54
1290360 ATTAATAATT
* * *
1290370 TTTTTTATTAGTATCTCGTTTGTCACACTCACTTCAGGAAATGAACATTCATAA
1 TTTTTTATTAGAAGCTCATTTGTCACACTCACTTCAGGAAATGAACATTCATAA
* * * *
1290424 TTTTTT-TTAGAAGCTCATTTGTCACATTTACTTCAGGAAATGAACATTTATAG
1 TTTTTTATTAGAAGCTCATTTGTCACACTCACTTCAGGAAATGAACATTCATAA
1290477 TTTTTTATTA
1 TTTTTTATTA
1290487 ATAGTTATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
53 46 0.84
54 9 0.16
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (54 bp):
TTTTTTATTAGAAGCTCATTTGTCACACTCACTTCAGGAAATGAACATTCATAA
Found at i:1291867 original size:2 final size:2
Alignment explanation
Indices: 1291855--1291893 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1291845 AAACAAAATT
*
1291855 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1291894 TGACAATCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1295546 original size:2 final size:2
Alignment explanation
Indices: 1295541--1295579 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1295531 TGTGTGTGGC
*
1295541 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1295580 GATTTAAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1296720 original size:2 final size:2
Alignment explanation
Indices: 1296715--1296752 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1296705 ATATACGTAC
1296715 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1296753 GGATGGTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1309386 original size:21 final size:22
Alignment explanation
Indices: 1309351--1309394 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1309341 CTCTTAAAGT
1309351 AATTTAAAATAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
*
1309373 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
1309394 A
1 A
1309395 TTAATCACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTTAAAATAAAATAACTTAA
Found at i:1315116 original size:21 final size:20
Alignment explanation
Indices: 1315078--1315116 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1315068 CAAACCTAAG
* *
1315078 ACAAAAGTATTGATACTTCC
1 ACAAAAGTATAGAGACTTCC
1315098 ACAAGAAGTATAGAGACTT
1 ACAA-AAGTATAGAGACTT
1315117 TGGTCGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (20 bp):
ACAAAAGTATAGAGACTTCC
Found at i:1327434 original size:15 final size:13
Alignment explanation
Indices: 1327394--1327465 Score: 58
Period size: 14 Copynumber: 5.4 Consensus size: 13
1327384 CGTTGATCAA
1327394 ATAAAATATAAAT
1 ATAAAATATAAAT
*
1327407 AAAAAATTATAAATT
1 ATAAAA-TATAAA-T
1327422 ATTAAAATATAAA-
1 A-TAAAATATAAAT
* *
1327435 ATAATAT-TAAAA
1 ATAAAATATAAAT
*
1327447 ATAAAATATCAATT
1 ATAAAATAT-AAAT
1327461 ATAAA
1 ATAAA
1327466 TCAATTAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
11 4 0.09
12 11 0.23
13 7 0.15
14 13 0.28
15 8 0.17
16 4 0.09
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAAAATATAAAT
Found at i:1327452 original size:17 final size:18
Alignment explanation
Indices: 1327421--1327454 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1327411 AATTATAAAT
1327421 TATTAAAATATAAAATAA
1 TATTAAAATATAAAATAA
1327439 TATTAAAA-ATAAAATA
1 TATTAAAATATAAAATA
1327455 TCAATTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TATTAAAATATAAAATAA
Found at i:1327454 original size:47 final size:48
Alignment explanation
Indices: 1327396--1327490 Score: 124
Period size: 47 Copynumber: 2.0 Consensus size: 48
1327386 TTGATCAAAT
*
1327396 AAAATATAAATAAAAAATTATAAAT-TATTAAAATATA-AAATAATATTA
1 AAAATATAAAT-AAAAATTATAAATCAATTAAAA-ATACAAATAATATTA
**
1327444 AAAATA-AAATATCAATTATAAATCAATTAAAAATACAAATAATATTA
1 AAAATATAAATAAAAATTATAAATCAATTAAAAATACAAATAATATTA
1327491 TTGTGTTTGC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
46 14 0.33
47 22 0.52
48 6 0.14
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (48 bp):
AAAATATAAATAAAAATTATAAATCAATTAAAAATACAAATAATATTA
Found at i:1327461 original size:18 final size:17
Alignment explanation
Indices: 1327392--1327466 Score: 57
Period size: 18 Copynumber: 4.2 Consensus size: 17
1327382 TTCGTTGATC
*
1327392 AAATAAAATATAAATAAA
1 AAATAAAATAT-AATTAA
1327410 AAATTATAAAT-T-ATTAA
1 AAA-TA-AAATATAATTAA
1327427 AATATAAAATA-ATATTAA
1 AA-ATAAAATATA-ATTAA
*
1327445 AAATAAAATATCAATTAT
1 AAATAAAATAT-AATTAA
1327463 AAAT
1 AAAT
1327467 CAATTAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
16 4 0.09
17 16 0.34
18 19 0.40
19 4 0.09
20 4 0.09
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATAAAATATAATTAA
Found at i:1328574 original size:72 final size:73
Alignment explanation
Indices: 1328438--1328628 Score: 174
Period size: 72 Copynumber: 2.6 Consensus size: 73
1328428 ACTATAATTT
* * * * *
1328438 CAAAAACCAAACATCAAAACAAATACAAAATGATAGTGACAGTAATGTTGTTACCATCCGTAAAC
1 CAAAAACCAAACATCAAAACAAATACAAAATGATAGTGACAATAATGTAGTCAACATCAGTAAAC
1328503 CACACTCA
66 CACACTCA
*
1328511 CAAAAACCAAACATC-AAACAAATACAAAATGATAGTGGA-AATAA-G-AGCATCAACATCATTA
1 CAAAAACCAAACATCAAAACAAATACAAAATGATAGT-GACAATAATGTAG--TCAACATCAGTA
* **
1328572 AACCACAATTG
63 AACCACACTCA
** *** * * *
1328583 CAATGATGGAACATCAAAACAAATACCAAATAATAGTGAAAATAAT
1 CAAAAACCAAACATCAAAACAAATACAAAATGATAGTGACAATAAT
1328629 AATGTTACTA
Statistics
Matches: 96, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
70 1 0.01
71 1 0.01
72 53 0.55
73 41 0.43
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.18
Consensus pattern (73 bp):
CAAAAACCAAACATCAAAACAAATACAAAATGATAGTGACAATAATGTAGTCAACATCAGTAAAC
CACACTCA
Found at i:1329055 original size:14 final size:14
Alignment explanation
Indices: 1329036--1329062 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1329026 GCGTTATGCA
1329036 CCATAAATGATAAG
1 CCATAAATGATAAG
1329050 CCATAAATGATAA
1 CCATAAATGATAA
1329063 ATGACATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (14 bp):
CCATAAATGATAAG
Found at i:1329272 original size:4 final size:4
Alignment explanation
Indices: 1329258--1329290 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
1329248 AGTCATTAAC
*
1329258 ACAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1329291 TGTGTGAGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.48, C:0.24, G:0.03, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:1338873 original size:3 final size:3
Alignment explanation
Indices: 1338865--1338955 Score: 83
Period size: 3 Copynumber: 30.3 Consensus size: 3
1338855 ATATACAAAT
* * * * * * * * *
1338865 TTA TTA TTA CTA TTA TTA TCA TCA TCA TCA TCA TCA TCA TTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1338913 TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1338956 GACATTTACG
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:1347299 original size:85 final size:85
Alignment explanation
Indices: 1347122--1347540 Score: 467
Period size: 85 Copynumber: 5.0 Consensus size: 85
1347112 TTATATTACT
* * * ** * * *
1347122 TATAAATTTTTTATATTAGTTGAATTTATAAACAAACAAATGTAAAATTAATTTATTTTAC-T--
1 TATAAAATTTTTATATAAGTTGAACTTGCAAACTAA-AAATATAAAATTAATTTATATTACTTGA
*
1347184 --TATGATGCAAATTTAAATA
65 ACTATGATGCAAACTTAAATA
* * *
1347203 TATAAATTTTTTATATAAGTTGAACTTGCAAACTAATAAAAATAAAATTTA-TTATATTACTTGA
1 TATAAAATTTTTATATAAGTTGAACTTGCAAACTAA-AAATATAAAATTAATTTATATTACTTGA
1347267 ACTATGATGCAAACTTAAATA
65 ACTATGATGCAAACTTAAATA
** * * *
1347288 TATAAAATTTTTATATTAA-TTGAACTTATAAACTAAGAATGTAAAATTAATTTATATTA-TCTA
1 TATAAAATTTTTATA-TAAGTTGAACTTGCAAACTAAAAATATAAAATTAATTTATATTACT-TG
*
1347351 AACTATGATGCAAACTTCAATA
64 AACTATGATGCAAACTTAAATA
* * ** * *
1347373 TTTAAAATTTTTATATTAGTTGAACTTTTAAACTAAAAATGTAAAATTAATTTATATTACATGAA
1 TATAAAATTTTTATATAAGTTGAACTTGCAAACTAAAAATATAAAATTAATTTATATTACTTGAA
**
1347438 CTATGACACAAACTTAAATA
66 CTATGATGCAAACTTAAATA
* * *
1347458 TACAAAATTTTTATATTAGTTGAACTTGCAAACTAACAAATATAAAATTAATTTATATTATTTGA
1 TATAAAATTTTTATATAAGTTGAACTTGCAAACTAA-AAATATAAAATTAATTTATATTACTTGA
*
1347523 ACTCTGATGCAAACTTAA
65 ACTATGATGCAAACTTAA
1347541 TAACATATCA
Statistics
Matches: 288, Mismatches: 39, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
80 8 0.03
81 43 0.15
84 13 0.05
85 181 0.63
86 43 0.15
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.40
Consensus pattern (85 bp):
TATAAAATTTTTATATAAGTTGAACTTGCAAACTAAAAATATAAAATTAATTTATATTACTTGAA
CTATGATGCAAACTTAAATA
Found at i:1347388 original size:44 final size:43
Alignment explanation
Indices: 1347184--1347542 Score: 190
Period size: 40 Copynumber: 8.4 Consensus size: 43
1347174 TTATTTTACT
* * *
1347184 TATGATGCAAATTTAAATATATAAATTTTTTATATAAGT-TGAAC
1 TATGATGCAAACTT-AATATATAAAATTTTTATATTA-TCTGAAC
*
1347228 --T--TGCAAAC-TAATAAAAATAAAATTTATTATATTA-CTTGAAC
1 TATGATGCAAACTTAAT--ATATAAAATTT-TTATATTATC-TGAAC
1347269 TATGATGCAAACTTAAATATATAAAATTTTTATATTAAT-TGAAC
1 TATGATGCAAACTT-AATATATAAAATTTTTATATT-ATCTGAAC
* * *
1347313 T-T-AT--AAAC-TAAGAATGTAAAATTAATTTATATTATCTAAAC
1 TATGATGCAAACTTAA-TATATAAAATT--TTTATATTATCTGAAC
*
1347354 TATGATGCAAACTTCAATATTTAAAATTTTTATATTAGT-TGAAC
1 TATGATGCAAACTT-AATATATAAAATTTTTATATTA-TCTGAAC
* * * *
1347398 T-T--T-TAAACTAAAAATGTAAAATTAATTTATATTA-CATGAAC
1 TATGATGCAAACTTAATATATAAAATT--TTTATATTATC-TGAAC
** *
1347439 TATGACACAAACTTAAATATACAAAATTTTTATATTAGT-TGAAC
1 TATGATGCAAACTT-AATATATAAAATTTTTATATTA-TCTGAAC
* * *
1347483 --T--TGCAAACTAACAAATATAAAATTAATTTATATTATTTGAAC
1 TATGATGCAAACTTA-ATATATAAAATT--TTTATATTATCTGAAC
*
1347525 TCTGATGCAAACTTAATA
1 TATGATGCAAACTTAATA
1347543 ACATATCATT
Statistics
Matches: 244, Mismatches: 28, Indels: 85
0.68 0.08 0.24
Matches are distributed among these distances:
38 5 0.02
39 23 0.09
40 42 0.17
41 42 0.17
42 20 0.08
43 5 0.02
44 42 0.17
45 30 0.12
46 30 0.12
47 5 0.02
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (43 bp):
TATGATGCAAACTTAATATATAAAATTTTTATATTATCTGAAC
Found at i:1347408 original size:170 final size:169
Alignment explanation
Indices: 1347122--1347542 Score: 539
Period size: 170 Copynumber: 2.5 Consensus size: 169
1347112 TTATATTACT
* * * *
1347122 TATAAATTTTTTATATTAGTTGAATTTATAAACAAACAAATGTAAAATTAATTTATTTTA-CT--
1 TATAAAATTTTTATATTAGTTGAACTTATAAACTAACAAATGTAAAATTAATTTATATTATCTAA
* *
1347184 -TATGATGCAAATTTAAATATATAAATTTTTTATATAAGTTGAACTTGCAAACTAATAAAAATAA
66 CTATGATGCAAACTT-AATATATAAAATTTTTATATAAGTTGAACTTGCAAACTAA-AAAAATAA
* * **
1347248 AATTTA-TTATATTACTTGAACTATGATGCAAACTTAAATA
129 AATTAATTTATATTACATGAACTATGACACAAACTTAAATA
* *
1347288 TATAAAATTTTTATATTAATTGAACTTATAAACTAA-GAATGTAAAATTAATTTATATTATCTAA
1 TATAAAATTTTTATATTAGTTGAACTTATAAACTAACAAATGTAAAATTAATTTATATTATCT-A
* * ** **
1347352 ACTATGATGCAAACTTCAATATTTAAAATTTTTATATTAGTTGAACTTTTAAACTAAAAATGTAA
65 ACTATGATGCAAACTT-AATATATAAAATTTTTATATAAGTTGAACTTGCAAACTAAAAAAATAA
1347417 AATTAATTTATATTACATGAACTATGACACAAACTTAAATA
129 AATTAATTTATATTACATGAACTATGACACAAACTTAAATA
* ** * *
1347458 TACAAAATTTTTATATTAGTTGAACTTGCAAACTAACAAATATAAAATTAATTTATATTATTTGA
1 TATAAAATTTTTATATTAGTTGAACTTATAAACTAACAAATGTAAAATTAATTTATATTATCT-A
*
1347523 ACTCTGATGCAAACTTAATA
65 ACTATGATGCAAACTTAATA
1347543 ACATATCATT
Statistics
Matches: 220, Mismatches: 28, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
165 21 0.10
166 34 0.15
169 11 0.05
170 115 0.52
171 39 0.18
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.40
Consensus pattern (169 bp):
TATAAAATTTTTATATTAGTTGAACTTATAAACTAACAAATGTAAAATTAATTTATATTATCTAA
CTATGATGCAAACTTAATATATAAAATTTTTATATAAGTTGAACTTGCAAACTAAAAAAATAAAA
TTAATTTATATTACATGAACTATGACACAAACTTAAATA
Found at i:1357892 original size:31 final size:30
Alignment explanation
Indices: 1357857--1357939 Score: 78
Period size: 31 Copynumber: 2.8 Consensus size: 30
1357847 AAACTCAAGC
* * *
1357857 ACCAAGGTCGAAACAATTGCCAAATCCAAA
1 ACCAAAGTCGAAACAATTACCAAAACCAAA
* * *
1357887 GACCAACGTCTAAACAAATACCAAAACCAAA
1 -ACCAAAGTCGAAACAATTACCAAAACCAAA
* *
1357918 CCCAAAGTTGAAACAA-TACCAA
1 ACCAAAGTCGAAACAATTACCAA
1357940 TTCCAAGTCC
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
29 6 0.14
30 12 0.28
31 25 0.58
ACGTcount: A:0.51, C:0.28, G:0.10, T:0.12
Consensus pattern (30 bp):
ACCAAAGTCGAAACAATTACCAAAACCAAA
Found at i:1357945 original size:29 final size:29
Alignment explanation
Indices: 1357898--1357962 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
1357888 ACCAACGTCT
*
1357898 AAACAAATACCAAAACCAAACCCAAAGTTG
1 AAAC-AATACCAAAACCAAACCCAAAATTG
** **
1357928 AAACAATACCAATTCCAAGTCCAAAATTG
1 AAACAATACCAAAACCAAACCCAAAATTG
1357957 AAACAA
1 AAACAA
1357963 ATATCGAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.55, C:0.25, G:0.06, T:0.14
Consensus pattern (29 bp):
AAACAATACCAAAACCAAACCCAAAATTG
Found at i:1369530 original size:115 final size:115
Alignment explanation
Indices: 1369382--1369592 Score: 332
Period size: 115 Copynumber: 1.8 Consensus size: 115
1369372 TGCTTGCTAT
* * *
1369382 GTCTAACTCGAAATTGATTCTAAATATTGATAAAATTATGAAAAATCGTAAAACTTGCATGTTCC
1 GTCTAACTCAAAATTGATTCTAAATATCGATAAAATTATAAAAAATCGTAAAACTTGCATGTTCC
*
1369447 TCACTATGATAATTAGAAATTCATTTTCTAAAGTTGAAATTGTTTACTAC
66 TCACTATCATAATTAGAAATTCATTTTCTAAAGTTGAAATTGTTTACTAC
* * *
1369497 GTCTAATTCAAAATTGATTCTAAATATCGATAAAATTATAAAAAATTGTAAAACTTGCATGTTGC
1 GTCTAACTCAAAATTGATTCTAAATATCGATAAAATTATAAAAAATCGTAAAACTTGCATGTTCC
* * *
1369562 TTATTGTCATAATTAGAAATTCATTTTCTAA
66 TCACTATCATAATTAGAAATTCATTTTCTAA
1369593 TGTCGGAATT
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
115 86 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.38
Consensus pattern (115 bp):
GTCTAACTCAAAATTGATTCTAAATATCGATAAAATTATAAAAAATCGTAAAACTTGCATGTTCC
TCACTATCATAATTAGAAATTCATTTTCTAAAGTTGAAATTGTTTACTAC
Found at i:1380747 original size:28 final size:28
Alignment explanation
Indices: 1380707--1380771 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
1380697 GGTAGATGTT
*
1380707 TATTGCAATAAAACTA-TTTAAAGAAGTA
1 TATTGCAATAAAACTACTTGAAA-AAGTA
1380735 TATTGCAATAAAACTACTTGAAAAAGTA
1 TATTGCAATAAAACTACTTGAAAAAGTA
1380763 TATTGCAAT
1 TATTGCAAT
1380772 TAGTATTACA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 30 0.86
29 5 0.14
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (28 bp):
TATTGCAATAAAACTACTTGAAAAAGTA
Found at i:1381530 original size:40 final size:39
Alignment explanation
Indices: 1381475--1381610 Score: 152
Period size: 40 Copynumber: 3.5 Consensus size: 39
1381465 AATTTAAAGT
*
1381475 GGTGCTCTTTATAATAACACGCAATTTGTTATCCTCGGAG
1 GGTGCTCTTTATAATAGCAC-CAATTTGTTATCCTCGGAG
** * *
1381515 GGTGCTCTTTATAATAGCACTTA-TTG--ATCCTTGGGG
1 GGTGCTCTTTATAATAGCACCAATTTGTTATCCTCGGAG
* * *
1381551 GGTGCTCTTTAAAATAGCACACAATTTATTATCCTCGGAA
1 GGTGCTCTTTATAATAGCAC-CAATTTGTTATCCTCGGAG
*
1381591 AGTGCTCTTTATAATAGCAC
1 GGTGCTCTTTATAATAGCAC
1381611 TTGTTGATCC
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
36 27 0.35
37 1 0.01
38 5 0.06
39 1 0.01
40 44 0.56
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (39 bp):
GGTGCTCTTTATAATAGCACCAATTTGTTATCCTCGGAG
Found at i:1381554 original size:36 final size:36
Alignment explanation
Indices: 1381505--1381646 Score: 135
Period size: 36 Copynumber: 3.8 Consensus size: 36
1381495 GCAATTTGTT
1381505 ATCCTCGGAGGGTGCTCTTTATAATAGCACTTATTG
1 ATCCTCGGAGGGTGCTCTTTATAATAGCACTTATTG
* * *
1381541 ATCCTTGGGGGGTGCTCTTTAAAATAGCACACAATTTATT-
1 ATCCTCGGAGGGTGCTCTTTATAATAG--CAC---TTATTG
** *
1381581 ATCCTCGGAAAGTGCTCTTTATAATAGCACTTGTTG
1 ATCCTCGGAGGGTGCTCTTTATAATAGCACTTATTG
* * *
1381617 ATCCTTAGG-GGGTGCCCTTTATACTAGCAC
1 ATCC-TCGGAGGGTGCTCTTTATAATAGCAC
1381647 ACAATTTAGA
Statistics
Matches: 85, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
35 4 0.05
36 45 0.53
37 3 0.04
38 6 0.07
40 22 0.26
41 5 0.06
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (36 bp):
ATCCTCGGAGGGTGCTCTTTATAATAGCACTTATTG
Found at i:1381601 original size:76 final size:76
Alignment explanation
Indices: 1381475--1381654 Score: 270
Period size: 76 Copynumber: 2.4 Consensus size: 76
1381465 AATTTAAAGT
* * * **
1381475 GGTGCTCTTTATAATAACACGCAATTTGTTATCCTCGGAGGGTGCTCTTTATAATAGCACTTATT
1 GGTGCTCTTTATAATAGCACACAATTTATTATCCTCGGAAAGTGCTCTTTATAATAGCACTTATT
*
1381540 GATCCTTGGGG
66 GATCCTTAGGG
* *
1381551 GGTGCTCTTTAAAATAGCACACAATTTATTATCCTCGGAAAGTGCTCTTTATAATAGCACTTGTT
1 GGTGCTCTTTATAATAGCACACAATTTATTATCCTCGGAAAGTGCTCTTTATAATAGCACTTATT
1381616 GATCCTTAGGG
66 GATCCTTAGGG
* *
1381627 GGTGCCCTTTATACTAGCACACAATTTA
1 GGTGCTCTTTATAATAGCACACAATTTA
1381655 GAATCACCAC
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
76 93 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (76 bp):
GGTGCTCTTTATAATAGCACACAATTTATTATCCTCGGAAAGTGCTCTTTATAATAGCACTTATT
GATCCTTAGGG
Found at i:1385369 original size:69 final size:63
Alignment explanation
Indices: 1385106--1385394 Score: 334
Period size: 63 Copynumber: 4.5 Consensus size: 63
1385096 TATATATATT
** * *
1385106 TTAAGGATTTTCAACTTAATAGGC---TTTTTGTTTGCCTTAACTTTTGCCTAAGTTGA-CCTA
1 TTAAGGATTTTCAACTTAGCAGGCTTTTTTTTTTTTGCCTTAACTTTTGCCTAAG-TCATCCTA
* * * * *
1385166 TTAAGGATTTTCAAGTTAGCAGGCTTTTTTTTTTTTACCTTAACATTTGCTTAAGTCATCCTG
1 TTAAGGATTTTCAACTTAGCAGGCTTTTTTTTTTTTGCCTTAACTTTTGCCTAAGTCATCCTA
* * * * * *
1385229 TTAAGGATTTTCTACTTAGCTGACTTTTTTTTTTTTGCCTTAACTTTTGCTTAAGTCGTCCTG
1 TTAAGGATTTTCAACTTAGCAGGCTTTTTTTTTTTTGCCTTAACTTTTGCCTAAGTCATCCTA
1385292 TTAAGGATTTTCAACTTAGCAGGCTTTTATTTTTATTTTTTTGCCTTAACTTTTGCCTAAGTCAT
1 TTAAGGATTTTCAACTTAGCAGGC-----TTTTT-TTTTTTTGCCTTAACTTTTGCCTAAGTCAT
1385357 CCTA
60 CCTA
* *
1385361 TTATGGATTTTCAACTTAGCACGCTTTTTTTTTT
1 TTAAGGATTTTCAACTTAGCAGGCTTTTTTTTTT
1385395 GTGCAGTTTA
Statistics
Matches: 195, Mismatches: 24, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
60 21 0.11
62 2 0.01
63 109 0.56
64 5 0.03
68 5 0.03
69 53 0.27
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.49
Consensus pattern (63 bp):
TTAAGGATTTTCAACTTAGCAGGCTTTTTTTTTTTTGCCTTAACTTTTGCCTAAGTCATCCTA
Found at i:1392224 original size:51 final size:51
Alignment explanation
Indices: 1392158--1392256 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
1392148 ACTTCACTTC
*
1392158 ATCTTCACTTCAAGGGTCTTAACAACTTAATCTTGATCACGAACACTTGAT
1 ATCTTCACTTCAAGGGTCTTAACAACTTAATCTTGATCACAAACACTTGAT
* * ** *
1392209 ATCTTCGCTTCAAGGGTCTTCAGGACTTGATCTTGATCACAAACACTT
1 ATCTTCACTTCAAGGGTCTTAACAACTTAATCTTGATCACAAACACTT
1392257 CAAGGGTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.33
Consensus pattern (51 bp):
ATCTTCACTTCAAGGGTCTTAACAACTTAATCTTGATCACAAACACTTGAT
Found at i:1392259 original size:38 final size:38
Alignment explanation
Indices: 1392216--1392294 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
1392206 GATATCTTCG
*
1392216 CTTCAAGGGTCTTCAGGACTTGATCTTGATCACAAACA
1 CTTCAAGGGTCTTCAGGACTTAATCTTGATCACAAACA
* * *
1392254 CTTCAAGGGTTTTCATGACTTAATCTTGATCACGAACA
1 CTTCAAGGGTCTTCAGGACTTAATCTTGATCACAAACA
1392292 CTT
1 CTT
1392295 GGTATCTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (38 bp):
CTTCAAGGGTCTTCAGGACTTAATCTTGATCACAAACA
Found at i:1392795 original size:82 final size:81
Alignment explanation
Indices: 1392657--1392909 Score: 327
Period size: 82 Copynumber: 3.2 Consensus size: 81
1392647 TTTGATTTTC
* * * ** *
1392657 ATCTCTAAATTAATAT-AATTA-TTAGAGATAAATTAAATGATCAATAAAC-AAATTTTGATTGG
1 ATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGATCAAT-AACTAATTTTTGATTGG
1392719 TCAAAAATATGAATATT
65 TCAAAAATATGAATATT
* *
1392736 ATCTCTAAATTATTTTGATTTATTTAGATGATAAATTGGATGATCAATAACTATTTTTTGTTTGG
1 ATCTCTAAATTATTTTGATTTATTTAGA-GATAAATTGGATGATCAATAACTAATTTTTGATTGG
1392801 TCAAAAATATGAATATT
65 TCAAAAATATGAATATT
* *
1392818 ATCTTTAAATTATTTTGATTTATTTAGAGATAAATTGGATGACCAATAACTAATTTTTGATTGGT
1 ATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGATCAATAACTAATTTTTGATTGGT
* * *
1392883 C--TAATTTAAATATT
66 CAAAAATATGAATATT
*
1392897 ATCTTTAAATTAT
1 ATCTCTAAATTAT
1392910 CTCAAGGGAT
Statistics
Matches: 155, Mismatches: 15, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
79 37 0.24
80 4 0.03
81 43 0.28
82 71 0.46
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (81 bp):
ATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGATCAATAACTAATTTTTGATTGGT
CAAAAATATGAATATT
Found at i:1399877 original size:18 final size:18
Alignment explanation
Indices: 1399854--1399892 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1399844 AAAGATAAAG
*
1399854 CATGAAGAATCGACTTTT
1 CATGAAGAATCGACTTCT
*
1399872 CATGAAGAATTGACTTCT
1 CATGAAGAATCGACTTCT
1399890 CAT
1 CAT
1399893 TAGACAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (18 bp):
CATGAAGAATCGACTTCT
Found at i:1410426 original size:69 final size:69
Alignment explanation
Indices: 1410313--1410450 Score: 258
Period size: 69 Copynumber: 2.0 Consensus size: 69
1410303 AATAGAGAGG
*
1410313 AAGAAGATTTTATCAGATGTCATCTAGATAGTTCTGTAGCTTGTTGTTTTTGGTTGGTAAAGTTT
1 AAGAAGATTTTATCAGATGTCATCTAGATAGTTCTGTAGCTTGTTGCTTTTGGTTGGTAAAGTTT
1410378 CCAA
66 CCAA
*
1410382 AAGAAGATTTTATCAGATGTCATCTAGATAGTTCTGTAGGTTGTTGCTTTTGGTTGGTAAAGTTT
1 AAGAAGATTTTATCAGATGTCATCTAGATAGTTCTGTAGCTTGTTGCTTTTGGTTGGTAAAGTTT
1410447 CCAA
66 CCAA
1410451 GAGTTTGTGC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.26, C:0.10, G:0.22, T:0.41
Consensus pattern (69 bp):
AAGAAGATTTTATCAGATGTCATCTAGATAGTTCTGTAGCTTGTTGCTTTTGGTTGGTAAAGTTT
CCAA
Found at i:1413204 original size:29 final size:30
Alignment explanation
Indices: 1413171--1413251 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 30
1413161 ATGCTATACG
* **
1413171 TGAACAGGTACAAGAGAGGAA-GCTGTACA
1 TGAACAGGTATAAGAGAAAAAGGCTGTACA
*
1413200 TGAACAGGTATAAGA-AAAAAGGCTGTACG
1 TGAACAGGTATAAGAGAAAAAGGCTGTACA
* *
1413229 TGAACAAGTATAAGAGAATAAGG
1 TGAACAGGTATAAGAGAAAAAGG
1413252 AAAAAACAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 3 0.07
29 35 0.80
30 6 0.14
ACGTcount: A:0.46, C:0.10, G:0.28, T:0.16
Consensus pattern (30 bp):
TGAACAGGTATAAGAGAAAAAGGCTGTACA
Found at i:1417094 original size:349 final size:344
Alignment explanation
Indices: 1416447--1417477 Score: 1111
Period size: 352 Copynumber: 2.9 Consensus size: 344
1416437 GTTTTATAAC
* * *
1416447 TTGATAGCAATAGGTTGGTTCAAGAATATGAGATAAAAAAGTTGTAAAAACTTTGTTTTTATAAG
1 TTGATGGCAATAGGTTAGTTCAAGAATATGAGATTAAAAAGTTGTAAAAA-TTTG-TTTTATAAG
** * ** * **
1416512 AAAACTGATCACTAGACAAAAATTGAGTGATGGGATGTTTGATGACAAGGTTGGTTTTCTAAAAG
64 AAAGTTGGTCACTAGACAAAAATTGAGT-AAAGGATGTTTGGTGACAAGGTTGGTTTT-TTGAAG
* * * * * *
1416577 AAAAGGTAGAATGATAGGCTTCAAGATATTTGTGTGGTTTTTTTGTCTGGTGCATTTTCTAAGCT
127 AAAAGGTACAATGATAGGCTTCAAGATATTTG-GTGGTTTTTCTATCTAGTGCTTTTTCTAGGCT
* * * * * *
1416642 GTACGGTATATGAAGAATCAATAGATGAGATAGAAGAATATGCAATTTCATTAGAATTCAAAAAT
191 ATA-GGTATATGAAGAATCAATAGATGGGATAGAAGAATGTGTAATTTCATGA-AATTCAAATAT
* * * * **
1416707 GGCAAGTTAGTATGTGCAGGAGTGTCATTGGAAGAAATAATAACATCTGTA-AAATTGCTAT-TT
254 GGCAAGTTAGTATATGCAGG-GTATTATTGGAAGAAATAATAACATCTGCAGAAA-TGCTATAAA
* * *
1416770 GAAGTTTTGAAATAAGGCTAGAAATAGA
317 CAAGTTCTGAAATAAAGCTAGAAATAGA
* * *
1416798 TTGATGGCAATAGGTTAATTCAAGAATATGAGATTAAAAAGTTGTAAAAATTACGTTTT-CAAGA
1 TTGATGGCAATAGGTTAGTTCAAGAATATGAGATTAAAAAGTTGTAAAAATT-TGTTTTATAAGA
* * *
1416862 AAGTTGGTCACTAGACAAAAATTTG-GTAACAGGATGTTTGGTGATAAGGTTTGTTTTTTGAAGG
65 AAGTTGGTCACTAGACAAAAA-TTGAGTAA-AGGATGTTTGGTGACAAGGTTGGTTTTTTGAAGA
* *
1416926 AAAGGTATAATGATAGGCTTCAAGATATTTAGGTGGTTTTTCTATCTAATGCTTTTTCTAGGCTA
128 AAAGGTACAATGATAGGCTTCAAGATATTT-GGTGGTTTTTCTATCTAGTGCTTTTTCTAGGCTA
* *
1416991 TGAGGTATATGAAGAATCAGTAAATGGGGATAGAAGAATGTGTAATTTCATGACAATTCAAATAT
192 T-AGGTATATGAAGAATCAATAGAT-GGGATAGAAGAATGTGTAATTTCATGA-AATTCAAATAT
* * * *
1417056 GGCAAGTTAATATATGTACGGGTATTATTAGAAGAAATAATAATATCTGCAGAAATGCTATAAAC
254 GGCAAGTTAGTATATGCA-GGGTATTATTGGAAGAAATAATAACATCTGCAGAAATGCTATAAAC
*
1417121 AAGTTCTGAAATAAAGCTAGAAATAGC
318 AAGTTCTGAAATAAAGCTAGAAATAGA
** * * * * * * *
1417148 TCAATGGTAGTAGGTTAGTTTAGGAATATGAGA-TAAAGAAGCTATAAATACTTTGTGTTTATAA
1 TTGATGGCAATAGGTTAGTTCAAGAATATGAGATTAAA-AAGTTGTAAA-AATTTGT-TTTATAA
* * * * * * *
1417212 GAAAGTTAGTCACTTGATAGAAATTGAGTAATGGTATGTTTAGTGACAAGGTTGGTTTTTTGAAA
63 GAAAGTTGGTCACTAGACAAAAATTGAGTAAAGG-ATGTTTGGTGACAAGGTTGGTTTTTTGAAG
* *
1417277 AAAAGGTACAATGATAGGCTTTAAGATATTTGGGTGGTTTGTTCTATTTAGTGCTTTTTCTAGGT
127 AAAAGGTACAATGATAGGCTTCAAGATATTT-GGTGGTTT-TTCTATCTAGTGCTTTTTCTAGG-
* * * *
1417342 CGTA-AGGCATATGAAGAATCAATAGATAGGACAGAAGAATGTGTAATTTTATGAATATTCAAAT
189 C-TATAGGTATATGAAGAATCAATAGATGGGATAGAAGAATGTGTAATTTCATGAA-ATTCAAAT
* * * * *
1417406 ATGGCAAGTTAGTATTTGCAAGGGTATTATTGGAAGAAATAATATCATCTACATAAATGCTATTA
252 ATGGCAAGTTAGTATATGC-AGGGTATTATTGGAAGAAATAATAACATCTGCAGAAATGCTATAA
1417471 ACAAGTT
316 ACAAGTT
1417478 TTGAGATAGG
Statistics
Matches: 571, Mismatches: 89, Indels: 39
0.82 0.13 0.06
Matches are distributed among these distances:
348 81 0.14
349 132 0.23
350 74 0.13
351 59 0.10
352 180 0.32
353 42 0.07
354 1 0.00
355 2 0.00
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.34
Consensus pattern (344 bp):
TTGATGGCAATAGGTTAGTTCAAGAATATGAGATTAAAAAGTTGTAAAAATTTGTTTTATAAGAA
AGTTGGTCACTAGACAAAAATTGAGTAAAGGATGTTTGGTGACAAGGTTGGTTTTTTGAAGAAAA
GGTACAATGATAGGCTTCAAGATATTTGGTGGTTTTTCTATCTAGTGCTTTTTCTAGGCTATAGG
TATATGAAGAATCAATAGATGGGATAGAAGAATGTGTAATTTCATGAAATTCAAATATGGCAAGT
TAGTATATGCAGGGTATTATTGGAAGAAATAATAACATCTGCAGAAATGCTATAAACAAGTTCTG
AAATAAAGCTAGAAATAGA
Found at i:1431695 original size:21 final size:21
Alignment explanation
Indices: 1431671--1431724 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1431661 TTACTTTGTA
* *
1431671 CATTGTGTGACTGACTTTCAG
1 CATTGCGTGACTGAATTTCAG
**
1431692 CATTGCGTGACTGAATTTTGG
1 CATTGCGTGACTGAATTTCAG
1431713 CATTGCGTGACT
1 CATTGCGTGACT
1431725 AGTTGGTAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (21 bp):
CATTGCGTGACTGAATTTCAG
Found at i:1431767 original size:23 final size:23
Alignment explanation
Indices: 1431711--1431815 Score: 140
Period size: 23 Copynumber: 4.6 Consensus size: 23
1431701 ACTGAATTTT
*
1431711 GGCATTGCGTGACTAGTTGGT-A
1 GGCATTGCGTGACTAGTTAGTAA
*
1431733 GGCATTGCGTGACTTGTTAGTAA
1 GGCATTGCGTGACTAGTTAGTAA
* *
1431756 GCCATTGTGTGACTAGTTAGTAA
1 GGCATTGCGTGACTAGTTAGTAA
*
1431779 GGCATTGCATGACTAGTTAGTAA
1 GGCATTGCGTGACTAGTTAGTAA
* *
1431802 AGCATTGTGTGACT
1 GGCATTGCGTGACT
1431816 TAGGCATTGC
Statistics
Matches: 71, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
22 19 0.27
23 52 0.73
ACGTcount: A:0.24, C:0.13, G:0.30, T:0.33
Consensus pattern (23 bp):
GGCATTGCGTGACTAGTTAGTAA
Found at i:1431879 original size:21 final size:22
Alignment explanation
Indices: 1431835--1431908 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
1431825 CTTAAAGATT
*
1431835 AATCATGCAATGCCTAAAAACC
1 AATCACGCAATGCCTAAAAACC
* *
1431857 AATCACGCAATG-CTTATAACC
1 AATCACGCAATGCCTAAAAACC
** * *
1431878 AATCACATAATGTCTAAAAATC
1 AATCACGCAATGCCTAAAAACC
1431900 AATCACGCA
1 AATCACGCA
1431909 GTAATTAAGT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 17 0.41
22 24 0.59
ACGTcount: A:0.45, C:0.26, G:0.08, T:0.22
Consensus pattern (22 bp):
AATCACGCAATGCCTAAAAACC
Found at i:1437913 original size:51 final size:51
Alignment explanation
Indices: 1437826--1437929 Score: 131
Period size: 51 Copynumber: 2.0 Consensus size: 51
1437816 GACTATCAAA
* *
1437826 GGCTAAAGATTGAAACTTGAGAAAGAATGCTGCCTATTGA-CATTGTAAGTG
1 GGCTAAAGATTGAAACCTGAGAAAGAATGCTACCTATT-ACCATTGTAAGTG
* * *
1437877 GGCTAAAGATTGAAGCCTGAGAAAGAGTG-TCACCTATTACCATTGTGAGTG
1 GGCTAAAGATTGAAACCTGAGAAAGAATGCT-ACCTATTACCATTGTAAGTG
1437928 GG
1 GG
1437930 TTTAATTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
50 2 0.04
51 44 0.96
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (51 bp):
GGCTAAAGATTGAAACCTGAGAAAGAATGCTACCTATTACCATTGTAAGTG
Found at i:1438214 original size:53 final size:53
Alignment explanation
Indices: 1438134--1438241 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 53
1438124 GAAGCTATGA
*
1438134 TGAACCGCTAAGAGTAAATTACCCTAGGTGAATGATAAATAAGATGATTTGAT
1 TGAACCCCTAAGAGTAAATTACCCTAGGTGAATGATAAATAAGATGATTTGAT
* *
1438187 TGAACCCCTAAGAGTAAATTACCCTAGGTGAATGATAACTGAGATGATTTGAT
1 TGAACCCCTAAGAGTAAATTACCCTAGGTGAATGATAAATAAGATGATTTGAT
1438240 TG
1 TG
1438242 GAGACTTAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (53 bp):
TGAACCCCTAAGAGTAAATTACCCTAGGTGAATGATAAATAAGATGATTTGAT
Found at i:1439712 original size:20 final size:20
Alignment explanation
Indices: 1439672--1439712 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1439662 CTCAGTGATG
* *
1439672 TATTGGTACATTTGGCAATA
1 TATTGATACATTTGCCAATA
*
1439692 TATTGATACATTTGCCTATA
1 TATTGATACATTTGCCAATA
1439712 T
1 T
1439713 TTCTACTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (20 bp):
TATTGATACATTTGCCAATA
Found at i:1443861 original size:20 final size:20
Alignment explanation
Indices: 1443833--1443873 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1443823 CTCCATTCAT
1443833 AGGCCTTTGAAAACAGAATA
1 AGGCCTTTGAAAACAGAATA
*
1443853 AGGCTTTTGAAAACAGAATA
1 AGGCCTTTGAAAACAGAATA
1443873 A
1 A
1443874 TAGTTTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22
Consensus pattern (20 bp):
AGGCCTTTGAAAACAGAATA
Found at i:1457249 original size:26 final size:26
Alignment explanation
Indices: 1457220--1457270 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1457210 GATTGTTCCT
* *
1457220 AGGTAAGTCTAGTCTAATTTGTCCCA
1 AGGTAAGTCCAGTCTAATTTATCCCA
*
1457246 AGGTCAGTCCAGTCTAATTTATCCC
1 AGGTAAGTCCAGTCTAATTTATCCC
1457271 CAAGAAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (26 bp):
AGGTAAGTCCAGTCTAATTTATCCCA
Found at i:1460193 original size:1 final size:1
Alignment explanation
Indices: 1460189--1460224 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
1460179 AAATCCCTCT
1460189 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1460225 TGGGCACCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1465968 original size:4 final size:4
Alignment explanation
Indices: 1465959--1465987 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1465949 TCTTAGAATA
1465959 TATC TATC TATC TATC TATC TATC TATC T
1 TATC TATC TATC TATC TATC TATC TATC T
1465988 TTGAAATAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:1469985 original size:3 final size:3
Alignment explanation
Indices: 1469977--1470009 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1469967 TGATAAAAGC
1469977 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1470010 TATGTATGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1470474 original size:59 final size:59
Alignment explanation
Indices: 1470392--1470519 Score: 168
Period size: 59 Copynumber: 2.1 Consensus size: 59
1470382 ATCTACAAGT
* * *
1470392 CCCTCTTTACCTACTCATGGGAACTCCCCACGCCACCAAATATGAATCGAGGCTTTAGGTC
1 CCCT-TTTACCTACTCA-GGGAACTCCCCACGCCACCAAATATAAATCAAAGCTTTAGGTC
* **
1470453 CCCTTTTACCTACTC-GAGGAACTCCCCACTCTGCCAAATATAAATCAAAGCTTTAGGTC
1 CCCTTTTACCTACTCAG-GGAACTCCCCACGCCACCAAATATAAATCAAAGCTTTAGGTC
1470512 CCCTTTTA
1 CCCTTTTA
1470520 TTATTCACCA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
58 1 0.02
59 44 0.73
60 11 0.18
61 4 0.07
ACGTcount: A:0.26, C:0.34, G:0.13, T:0.27
Consensus pattern (59 bp):
CCCTTTTACCTACTCAGGGAACTCCCCACGCCACCAAATATAAATCAAAGCTTTAGGTC
Found at i:1475188 original size:23 final size:23
Alignment explanation
Indices: 1475162--1475206 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1475152 AAAATAAGCT
1475162 AGATGAACATCTATCGATAGATA
1 AGATGAACATCTATCGATAGATA
* *
1475185 AGATGAACGTCTATTGATAGAT
1 AGATGAACATCTATCGATAGAT
1475207 TGCCTTATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (23 bp):
AGATGAACATCTATCGATAGATA
Found at i:1475844 original size:18 final size:19
Alignment explanation
Indices: 1475808--1475849 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
1475798 CTAAGAAATA
* *
1475808 AATGTTTTTGTGATGTTTT
1 AATGTGTTTGTGATATTTT
1475827 AATGTGTTT-TGATATTTT
1 AATGTGTTTGTGATATTTT
*
1475845 GATGT
1 AATGT
1475850 TTTATCAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.19, C:0.00, G:0.21, T:0.60
Consensus pattern (19 bp):
AATGTGTTTGTGATATTTT
Found at i:1478999 original size:20 final size:20
Alignment explanation
Indices: 1478971--1479059 Score: 60
Period size: 20 Copynumber: 4.6 Consensus size: 20
1478961 CTACTGCAAA
*
1478971 AACAAAAAATAAACATAAAT
1 AACATAAAATAAACATAAAT
* * *
1478991 AACATAAAATTAACATTATT
1 AACATAAAATAAACATAAAT
* * **
1479011 AGCTTAAAATAAACATTTA-
1 AACATAAAATAAACATAAAT
*
1479030 AACATAAATTAAAC-TAAACT
1 AACATAAAATAAACATAAA-T
1479050 -A-ATAAAATAA
1 AACATAAAATAA
1479060 CTAAAAACAC
Statistics
Matches: 52, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
18 10 0.19
19 12 0.23
20 30 0.58
ACGTcount: A:0.63, C:0.10, G:0.01, T:0.26
Consensus pattern (20 bp):
AACATAAAATAAACATAAAT
Found at i:1481021 original size:25 final size:25
Alignment explanation
Indices: 1480983--1481041 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
1480973 GTGGTTGCAA
* *
1480983 TCACGTATAACAACTTATGGCCTAG
1 TCACATATAACAACTCATGGCCTAG
* * *
1481008 TCACATATACCAACTCGTGGCCTTG
1 TCACATATAACAACTCATGGCCTAG
*
1481033 TCATATATA
1 TCACATATA
1481042 TATATATATC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (25 bp):
TCACATATAACAACTCATGGCCTAG
Found at i:1490978 original size:2 final size:2
Alignment explanation
Indices: 1490971--1490999 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1490961 ACAAGCTCTT
1490971 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1491000 GTTTTGAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1491243 original size:17 final size:16
Alignment explanation
Indices: 1491209--1491243 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1491199 TTTTCATTTC
*
1491209 AGAAAAGTTTTTGCAA
1 AGAAAAGTTTTTGAAA
1491225 AGAAAAGTTTTTCGAAA
1 AGAAAAGTTTTT-GAAA
1491242 AG
1 AG
1491244 TGATTCTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.29
Consensus pattern (16 bp):
AGAAAAGTTTTTGAAA
Found at i:1491526 original size:19 final size:19
Alignment explanation
Indices: 1491502--1491543 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
1491492 ATATCTTAAG
1491502 GATGCTTTTGCTTGGTAGA
1 GATGCTTTTGCTTGGTAGA
*
1491521 GATGCTTTTGCTTTGTAGA
1 GATGCTTTTGCTTGGTAGA
1491540 GATG
1 GATG
1491544 TCATGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.17, C:0.10, G:0.31, T:0.43
Consensus pattern (19 bp):
GATGCTTTTGCTTGGTAGA
Found at i:1502011 original size:18 final size:19
Alignment explanation
Indices: 1501988--1502027 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1501978 TAAGTGAAAA
1501988 ATTTTA-GAATAAAATAAT
1 ATTTTATGAATAAAATAAT
* *
1502006 ATTTTATTAATAAAATGAT
1 ATTTTATGAATAAAATAAT
1502025 ATT
1 ATT
1502028 AAAATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
ATTTTATGAATAAAATAAT
Found at i:1503059 original size:14 final size:14
Alignment explanation
Indices: 1503042--1503086 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
1503032 GGAATCACCC
*
1503042 AAGAGGAAGAAATA
1 AAGAGGAAGAAAAA
1503056 AAGA-GAAGAAAAA
1 AAGAGGAAGAAAAA
*
1503069 AAGAGAAAGAAAGAA
1 AAGAGGAAGAAA-AA
1503084 AAG
1 AAG
1503087 GCTTGGGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 12 0.44
14 10 0.37
15 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (14 bp):
AAGAGGAAGAAAAA
Found at i:1507920 original size:16 final size:16
Alignment explanation
Indices: 1507886--1507919 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1507876 TGAAACCAAA
1507886 TTTAGATTTTGATTCT
1 TTTAGATTTTGATTCT
1507902 TTTAGATTTTGATT-T
1 TTTAGATTTTGATTCT
1507917 TTT
1 TTT
1507920 TGATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.18, C:0.03, G:0.12, T:0.68
Consensus pattern (16 bp):
TTTAGATTTTGATTCT
Found at i:1509028 original size:16 final size:17
Alignment explanation
Indices: 1508997--1509029 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1508987 ATTATTTATG
1508997 AATATACTATGTATGTA
1 AATATACTATGTATGTA
*
1509014 AATATGCTA-GTATGTA
1 AATATACTATGTATGTA
1509030 TTAGTTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.39
Consensus pattern (17 bp):
AATATACTATGTATGTA
Found at i:1519355 original size:6 final size:6
Alignment explanation
Indices: 1519344--1519370 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1519334 TGTGTTAACC
1519344 GATTAT GATTAT GATTAT GATTAT GAT
1 GATTAT GATTAT GATTAT GATTAT GAT
1519371 CATAAGTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (6 bp):
GATTAT
Found at i:1524491 original size:22 final size:23
Alignment explanation
Indices: 1524459--1524505 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1524449 ATATAGAGTT
1524459 ATTTGGGCTTAATT-TTGATAATA
1 ATTTGGGCTTAATTCTT-ATAATA
*
1524482 ATTT-GGCTTAGTTCTTATAATA
1 ATTTGGGCTTAATTCTTATAATA
1524504 AT
1 AT
1524506 GCATAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49
Consensus pattern (23 bp):
ATTTGGGCTTAATTCTTATAATA
Found at i:1528660 original size:2 final size:2
Alignment explanation
Indices: 1528653--1528682 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1528643 TTGATCATTG
1528653 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1528683 GATGTATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1535780 original size:15 final size:16
Alignment explanation
Indices: 1535750--1535791 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1535740 AAAGCTGAAT
*
1535750 GAAAGAGAAGGAGA-G
1 GAAAGAGAAAGAGAGG
*
1535765 GAAAGAGAAAGTGAGG
1 GAAAGAGAAAGAGAGG
1535781 GAAAAGAGAAA
1 G-AAAGAGAAA
1535792 ACGTGCGGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 12 0.52
16 2 0.09
17 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.02
Consensus pattern (16 bp):
GAAAGAGAAAGAGAGG
Found at i:1536702 original size:22 final size:23
Alignment explanation
Indices: 1536652--1536703 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 23
1536642 TTAATTTTCT
*
1536652 TTTCCT-TTCTTTCTCTCTCATC
1 TTTCCTCTTCTTTCTCTCTCATA
1536674 TTT--TCTT-TTTCTCTCTCATA
1 TTTCCTCTTCTTTCTCTCTCATA
1536694 TTTCCTCTTC
1 TTTCCTCTTC
1536704 CTCTTTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 16 0.64
21 2 0.08
22 7 0.28
ACGTcount: A:0.06, C:0.33, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTCCTCTTCTTTCTCTCTCATA
Found at i:1542625 original size:18 final size:19
Alignment explanation
Indices: 1542599--1542646 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1542589 GTGACGGATG
*
1542599 AAAAAAATATTTTA-AAAT
1 AAAATAATATTTTATAAAT
1542617 AAAATAATATTTTATAAAT
1 AAAATAATATTTTATAAAT
1542636 AAAATAATATT
1 AAAATAATATT
1542647 AAAATATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATAATATTTTATAAAT
Found at i:1544691 original size:2 final size:2
Alignment explanation
Indices: 1544684--1544713 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1544674 ACGGCCTATG
*
1544684 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1544714 GCGTGTCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1550894 original size:10 final size:10
Alignment explanation
Indices: 1550881--1550905 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1550871 CATAACTATG
1550881 CATATATATA
1 CATATATATA
1550891 CATATATATA
1 CATATATATA
1550901 CATAT
1 CATAT
1550906 TGAATTACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (10 bp):
CATATATATA
Found at i:1553357 original size:26 final size:26
Alignment explanation
Indices: 1553294--1553359 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
1553284 AATAACACTG
* *
1553294 TTTTGTATCATGTCCATATTATTCTT
1 TTTTGTATCATTTACATATTATTCTT
* *
1553320 TGTTGTATCATTTACATATTTTTCTT
1 TTTTGTATCATTTACATATTATTCTT
1553346 TTTTGTATCATTTA
1 TTTTGTATCATTTA
1553360 ACAAAAAAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.61
Consensus pattern (26 bp):
TTTTGTATCATTTACATATTATTCTT
Found at i:1553732 original size:23 final size:23
Alignment explanation
Indices: 1553657--1553755 Score: 74
Period size: 23 Copynumber: 4.3 Consensus size: 23
1553647 CAAGTATTTG
* * * *
1553657 ATATGGAATCATGCGACGACTAA
1 ATATGGAATCACGTGACTAGTAA
* * * *
1553680 ATTTTGAATCACGTGACTAATCGA
1 ATATGGAATCACGTGACTAGT-AA
1553704 AT-TGGAATCACGTGACTAGTAA
1 ATATGGAATCACGTGACTAGTAA
** * *
1553726 ATATGGAATTGCATGAGTAGTAA
1 ATATGGAATCACGTGACTAGTAA
1553749 ATATGGA
1 ATATGGA
1553756 GTTACTAGAG
Statistics
Matches: 60, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
22 3 0.05
23 54 0.90
24 3 0.05
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.28
Consensus pattern (23 bp):
ATATGGAATCACGTGACTAGTAA
Found at i:1553766 original size:23 final size:23
Alignment explanation
Indices: 1553720--1553778 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
1553710 ATCACGTGAC
* *
1553720 TAGTAAATATGGAATTGCATGAG
1 TAGTAAATATGGAGTTACATGAG
1553743 TAGTAAATATGGAGTTAC-TAGAG
1 TAGTAAATATGGAGTTACAT-GAG
1553766 TAGT--ATATGGAGT
1 TAGTAAATATGGAGT
1553779 GGCATTACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.27
22 1 0.03
23 23 0.70
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.32
Consensus pattern (23 bp):
TAGTAAATATGGAGTTACATGAG
Found at i:1559734 original size:20 final size:21
Alignment explanation
Indices: 1559699--1559737 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1559689 ACAAGAAGGG
*
1559699 AAGAAAAGATAAAGAGAGAAA
1 AAGAAAAGAGAAAGAGAGAAA
1559720 AAGAAAA-AGAAAGAGAGA
1 AAGAAAAGAGAAAGAGAGA
1559738 CCGGCGAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.03
Consensus pattern (21 bp):
AAGAAAAGAGAAAGAGAGAAA
Found at i:1559770 original size:68 final size:66
Alignment explanation
Indices: 1559591--1559806 Score: 179
Period size: 66 Copynumber: 3.2 Consensus size: 66
1559581 GGGGCCTACG
* * * * **
1559591 AAAAGGAAGAAAGGCCGACGGCGAAAGAAGAAA-AGAGAAGGGAAGAAAAGAAAAAGAGAGAAAA
1 AAAAGAAAGAGAGACCGGCGGCGAAAGAAGAAACA-AGAAAAGAAGAAAAG-AAAAGAGAGAAAA
*
1559655 GGA
64 AGA
* * * **
1559658 GAAAA-AAGGAAAGA-CTGCGGCGAAAGAAGAAACAAGAAGGGAAGAAAAGATAAAGAGAGAAAA
1 -AAAAGAAAGAGAGACCGGCGGCGAAAGAAGAAACAAGAAAAGAAGAAAAGA-AAAGAGAGAAAA
1559721 AGA
64 AGA
* ** * *
1559724 AAAAGAAAGAGAGACCGGCGAGGGAAAGAAGAAGGAAGAAAAGAAGAAAAAGAAAGAAAGAAAAA
1 AAAAGAAAGAGAGACCGGCG-GCGAAAGAAGAAACAAGAAAAGAAG-AAAAGAAA-AGAGAGAAA
1559789 AAGA
63 AAGA
*
1559793 AAAAG-TAGAGAGAC
1 AAAAGAAAGAGAGAC
1559807 GAGAGGGAGT
Statistics
Matches: 124, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
65 5 0.04
66 52 0.42
67 11 0.09
68 34 0.27
69 22 0.18
ACGTcount: A:0.62, C:0.06, G:0.31, T:0.01
Consensus pattern (66 bp):
AAAAGAAAGAGAGACCGGCGGCGAAAGAAGAAACAAGAAAAGAAGAAAAGAAAAGAGAGAAAAAG
A
Found at i:1559796 original size:9 final size:8
Alignment explanation
Indices: 1559762--1559796 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
1559752 AAGAAGGAAG
1559762 AAAAGAAGA
1 AAAAGAA-A
1559771 AAAAGAAA
1 AAAAGAAA
*
1559779 GAAAGAAA
1 AAAAGAAA
1559787 AAAAGAAA
1 AAAAGAAA
1559795 AA
1 AA
1559797 GTAGAGAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:1563124 original size:203 final size:203
Alignment explanation
Indices: 1562755--1563572 Score: 1138
Period size: 203 Copynumber: 4.0 Consensus size: 203
1562745 ACACATTCAT
* * * **
1562755 GCAATGCCTAAAAACTAGTGAACAAAAGCCTTAAAACAAGAGATGAATTGCACAAGTCACGTACC
1 GCAATGCCTACAAACTAGTGAACAAAAGCCTCAAAACAAAAGATGAATTGCACAAGTCACACACC
* *
1562820 GT-CAGTCTCGCAATACCTAATAATAAGTCACTTAATGCGTAATATCCACTCACATTATGCCAAC
66 -TCCAGTCTCGCAATACCTAATAATAAGTCACTCAATGCCTAATATCCACTCACATTATGCCAAC
* * * * * **
1562884 ATACCCAGTCATGTAACAGCCCAATGTCATACAATACATAACAACAAGTCACGCAATACATAAAA
130 ATAACCAGTCACGTAACGGCCTAATCTCACGCAATACATAACAACAAGTCACGCAATACATAAAA
* * *
1562949 ATCGGTCAT
195 ACCAGTCAC
* * * * * * *
1562958 GCAGTGCCTACAAACTACTGAACAAAAACCTCAAAACAAGAGATGAATTGTACAAGTTACGCACC
1 GCAATGCCTACAAACTAGTGAACAAAAGCCTCAAAACAAAAGATGAATTGCACAAGTCACACACC
* * *
1563023 TCCAGTCTCGCAATATCTAATAATAAGTCACTCAATGCATAATATCCACTCACATTATGCTAACA
66 TCCAGTCTCGCAATACCTAATAATAAGTCACTCAATGCCTAATATCCACTCACATTATGCCAACA
* * *
1563088 TAACCAGTCACGTAACGGCCTAATCTCACGCAATACATAATAACAGGTCATGCAATACATAAAAA
131 TAACCAGTCACGTAACGGCCTAATCTCACGCAATACATAACAACAAGTCACGCAATACATAAAAA
1563153 CCAGTCAC
196 CCAGTCAC
* *
1563161 GCAATGCCTGCAAACTAGTGAACAAAAGCCTTAAAACAAAAGATGAATTGCACAAGTCACACACC
1 GCAATGCCTACAAACTAGTGAACAAAAGCCTCAAAACAAAAGATGAATTGCACAAGTCACACACC
* *
1563226 TCCAGTCTCGCAATACCTATTAATAAGTCACTCGATGCCTAATATCCACTCACATTATGCCAACA
66 TCCAGTCTCGCAATACCTAATAATAAGTCACTCAATGCCTAATATCCACTCACATTATGCCAACA
* * * * * *
1563291 TAACCAGTCACGTAACGGCCTAATCTCATGTAATACATAACAACAGGTCATGCAATAAATAGAAA
131 TAACCAGTCACGTAACGGCCTAATCTCACGCAATACATAACAACAAGTCACGCAATACATAAAAA
1563356 CCAGTCAC
196 CCAGTCAC
* *
1563364 ACAATGCCTGCAAACTAGTGAACAAAAGCCTCAAAACAAAAGATGAATTGCACAAGTCACACACC
1 GCAATGCCTACAAACTAGTGAACAAAAGCCTCAAAACAAAAGATGAATTGCACAAGTCACACACC
* *
1563429 TCCAGTCTCACAATACCTATTAATAAGTCACTCAATGCCTAATATCCACTCACATTATGCCAACA
66 TCCAGTCTCGCAATACCTAATAATAAGTCACTCAATGCCTAATATCCACTCACATTATGCCAACA
* * * * *
1563494 TAACCAGTCATGT-ACTGACCTAATGTCACGCAATACATAACCACAAGTCAC-CATATACATACA
131 TAACCAGTCACGTAAC-GGCCTAATCTCACGCAATACATAACAACAAGTCACGCA-ATACATAAA
*
1563557 AACCATTCAC
194 AACCAGTCAC
1563567 GCAATG
1 GCAATG
1563573 TCTCAATAGA
Statistics
Matches: 552, Mismatches: 60, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
202 5 0.01
203 547 0.99
ACGTcount: A:0.40, C:0.27, G:0.12, T:0.21
Consensus pattern (203 bp):
GCAATGCCTACAAACTAGTGAACAAAAGCCTCAAAACAAAAGATGAATTGCACAAGTCACACACC
TCCAGTCTCGCAATACCTAATAATAAGTCACTCAATGCCTAATATCCACTCACATTATGCCAACA
TAACCAGTCACGTAACGGCCTAATCTCACGCAATACATAACAACAAGTCACGCAATACATAAAAA
CCAGTCAC
Found at i:1563159 original size:22 final size:22
Alignment explanation
Indices: 1563113--1563165 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
1563103 CGGCCTAATC
*
1563113 TCACGCAATACATAATAACAGG
1 TCACGCAATACATAAAAACAGG
*
1563135 TCATGCAATACATAAAAACCA-G
1 TCACGCAATACATAAAAA-CAGG
1563157 TCACGCAAT
1 TCACGCAAT
1563166 GCCTGCAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.45, C:0.25, G:0.11, T:0.19
Consensus pattern (22 bp):
TCACGCAATACATAAAAACAGG
Found at i:1565081 original size:22 final size:22
Alignment explanation
Indices: 1565025--1565083 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
1565015 TAGGTAGATA
* *
1565025 AAGTCATGCAATGCCTACAAAC
1 AAGTCAAGCAATGCTTACAAAC
* **
1565047 AACTCAAATAATGCTTACAAAC
1 AAGTCAAGCAATGCTTACAAAC
*
1565069 AAGTCACGCAATGCT
1 AAGTCAAGCAATGCT
1565084 CAACAAATAT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.20
Consensus pattern (22 bp):
AAGTCAAGCAATGCTTACAAAC
Found at i:1565109 original size:15 final size:15
Alignment explanation
Indices: 1565089--1565136 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
1565079 ATGCTCAACA
1565089 AATATTCAGTCACAT
1 AATATTCAGTCACAT
*
1565104 AATATTCAATCACAT
1 AATATTCAGTCACAT
*
1565119 AATATTCAGTCACGT
1 AATATTCAGTCACAT
1565134 AAT
1 AAT
1565137 GCCAAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (15 bp):
AATATTCAGTCACAT
Found at i:1567105 original size:30 final size:29
Alignment explanation
Indices: 1567047--1567102 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1567037 GTTATACATT
1567047 TTTGGCAGTTCATTTTTCTCACTTTTTGA
1 TTTGGCAGTTCATTTTTCTCACTTTTTGA
* *
1567076 TTTGGTAGTTCATTTTTCTTACTTTTT
1 TTTGGCAGTTCATTTTTCTCACTTTTT
1567103 TGAGTAGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.12, C:0.14, G:0.12, T:0.61
Consensus pattern (29 bp):
TTTGGCAGTTCATTTTTCTCACTTTTTGA
Found at i:1568147 original size:18 final size:19
Alignment explanation
Indices: 1568121--1568157 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1568111 ATATAACTTA
1568121 TTCTACAAAAT-TGTTCAT
1 TTCTACAAAATGTGTTCAT
*
1568139 TTCTTCAAAATGTGTTCAT
1 TTCTACAAAATGTGTTCAT
1568158 CAAATGTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (19 bp):
TTCTACAAAATGTGTTCAT
Found at i:1581074 original size:19 final size:19
Alignment explanation
Indices: 1581050--1581091 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1581040 CAAATTAGAA
1581050 TAAACACTTCAATTTTCAT
1 TAAACACTTCAATTTTCAT
1581069 TAAACACTTCAATTTTCAT
1 TAAACACTTCAATTTTCAT
1581088 TAAA
1 TAAA
1581092 GATAAATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAACACTTCAATTTTCAT
Found at i:1587072 original size:60 final size:60
Alignment explanation
Indices: 1586996--1587503 Score: 445
Period size: 60 Copynumber: 8.4 Consensus size: 60
1586986 TCAGTTAGCA
* * * * *
1586996 TTGAGATAGGTCAAGCCCATATTAAGTATAGGAGTTTCAAATTTTTAAATCACATTTGTT
1 TTGAGATAGGTCAAGCCTAGATTAAGTATAGGAATTTCAAATTTTTAAATCAAACTTGTT
* * * * * * *
1587056 TTAAGATAAGTCAAGCCTAGATTAAATGTA-ACG-ACTTCAATTTTTTAAGTCGAACTTG-T
1 TTGAGATAGGTCAAGCCTAGATT-AA-GTATAGGAATTTCAAATTTTTAAATCAAACTTGTT
* * * * *
1587115 TTGTAGATAGGTCGAGCCTAGTTTAAGTCTAGGAAATTT-AAATTTTTAAATCTAACTTGAT
1 TTG-AGATAGGTCAAGCCTAGATTAAGTATAGG-AATTTCAAATTTTTAAATCAAACTTGTT
* * * *
1587176 TTGAGATAAGTCAAGCCTA-AGTTAAGTTTAGGAATTTCAATTTTTTAAATCAAACCTGTT
1 TTGAGATAGGTCAAGCCTAGA-TTAAGTATAGGAATTTCAAATTTTTAAATCAAACTTGTT
* * * * * *
1587236 TTCAGATAGGTCGAGCCTAGATTAAGTTTAAGAAATTCAATTTTTTAAATCAAACTTGTT
1 TTGAGATAGGTCAAGCCTAGATTAAGTATAGGAATTTCAAATTTTTAAATCAAACTTGTT
* ** *
1587296 TTGAGATAGGTCAAGCCTAGATTAAGTTTAAAAATTTCAAAATTTTAAATCAAACTTGTT
1 TTGAGATAGGTCAAGCCTAGATTAAGTATAGGAATTTCAAATTTTTAAATCAAACTTGTT
* * * * * ** * *
1587356 GTGAGATAGGTCTAGCCTAAATTAAGTCTAAGAGCTTCAAATTTCTAAGTCAAACTTG-T
1 TTGAGATAGGTCAAGCCTAGATTAAGTATAGGAATTTCAAATTTTTAAATCAAACTTGTT
* * * * * * *
1587415 ATGTAGATAAGTTAAGCCTATATTAAGTATAGAAACTTT-AAATTTTATAAATCGAACTTGCT
1 TTG-AGATAGGTCAAGCCTAGATTAAGTATAGGAA-TTTCAAATTTT-TAAATCAAACTTGTT
* * *
1587477 TTGAGATAGGTCGAGCTTACATTAAGT
1 TTGAGATAGGTCAAGCCTAGATTAAGT
1587504 TTGTGAACTT
Statistics
Matches: 363, Mismatches: 71, Indels: 27
0.79 0.15 0.06
Matches are distributed among these distances:
58 2 0.01
59 15 0.04
60 296 0.82
61 44 0.12
62 6 0.02
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (60 bp):
TTGAGATAGGTCAAGCCTAGATTAAGTATAGGAATTTCAAATTTTTAAATCAAACTTGTT
Found at i:1587215 original size:120 final size:121
Alignment explanation
Indices: 1586999--1587503 Score: 504
Period size: 120 Copynumber: 4.2 Consensus size: 121
1586989 GTTAGCATTG
* * * * * ** * * *
1586999 AGATAGGTCAAGCCCATATTAAGTATAGGAGTTTCAAATTTTTAAATCACATTTGTTTTAAGATA
1 AGATAGGTCGAGCCTAGATTAAGTCTAAGAAATTCAAATTTTTAAATCAAACTTGTTTTGAGATA
* * * * * *
1587064 AGTCAAGCCTAGATTAAATGTA-ACGACTTCAATTTTTTAAGTCGAACTTGTTTGT-
66 AGTCAAGCCTAGATTAAGTTTAGA-AATTTCAATTTTTTAAATCAAACTTGTTTGTC
* * * * *
1587119 AGATAGGTCGAGCCTAGTTTAAGTCTAGGAAATTTAAATTTTTAAATCTAACTTGATTTGAGATA
1 AGATAGGTCGAGCCTAGATTAAGTCTAAGAAATTCAAATTTTTAAATCAAACTTGTTTTGAGATA
* *
1587184 AGTCAAGCCTA-AGTTAAGTTTAGGAATTTCAATTTTTTAAATCAAACCTGTTT-TC
66 AGTCAAGCCTAGA-TTAAGTTTAGAAATTTCAATTTTTTAAATCAAACTTGTTTGTC
* *
1587239 AGATAGGTCGAGCCTAGATTAAGTTTAAGAAATTCAATTTTTTAAATCAAACTTGTTTTGAGATA
1 AGATAGGTCGAGCCTAGATTAAGTCTAAGAAATTCAAATTTTTAAATCAAACTTGTTTTGAGATA
* * ** *
1587304 GGTCAAGCCTAGATTAAGTTTAAAAATTTCAAAATTTTAAATCAAACTTG-TTGTG
66 AGTCAAGCCTAGATTAAGTTTAGAAATTTCAATTTTTTAAATCAAACTTGTTTGTC
* * ** * * *
1587359 AGATAGGTCTAGCCTAAATTAAGTCTAAGAGCTTCAAATTTCTAAGTCAAACTTG-TATGTAGAT
1 AGATAGGTCGAGCCTAGATTAAGTCTAAGAAATTCAAATTTTTAAATCAAACTTGTTTTG-AGAT
* * * * * *
1587423 AAGTTAAGCCTATATTAAGTATAGAAACTTTAAATTTTATAAATCGAACTTGCTTTG--
65 AAGTCAAGCCTAGATTAAGTTTAGAAA-TTTCAATTTTTTAAATCAAACTTG-TTTGTC
* *
1587480 AGATAGGTCGAGCTTACATTAAGT
1 AGATAGGTCGAGCCTAGATTAAGT
1587504 TTGTGAACTT
Statistics
Matches: 319, Mismatches: 57, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
119 7 0.02
120 268 0.84
121 41 0.13
123 3 0.01
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (121 bp):
AGATAGGTCGAGCCTAGATTAAGTCTAAGAAATTCAAATTTTTAAATCAAACTTGTTTTGAGATA
AGTCAAGCCTAGATTAAGTTTAGAAATTTCAATTTTTTAAATCAAACTTGTTTGTC
Found at i:1587305 original size:180 final size:176
Alignment explanation
Indices: 1586996--1587503 Score: 545
Period size: 180 Copynumber: 2.8 Consensus size: 176
1586986 TCAGTTAGCA
* * *
1586996 TTGAGATAGGTCAAGCCCATATTAAGTATAGGAGTTTCAAATTTTTAAATCACATTTGTTTTAAG
1 TTGAGATAGGTCAAGCCTA-ATTAAGTATAGGAGTTTCAAATTTTTAAATCAAACTTGTTTT-AG
* * * *
1587061 ATAAGTCAAGCCTAGATTAAATGTAACG-ACTTCAATTTTTTAAGTCGAACTTGTTTGTAGATAG
64 ATAAGTCAAGCCTAGATTAAGTATAA-GAAATTCAATTTTTTAAATCGAACTTGTTTG-AGATAG
* * * *
1587125 GTCGAGCCTAGTTTAAGTCTAGGAAATTT-AAATTTTTAAATCTAACTTGAT
127 GTCGAGCCTAGATTAAGTCTA-AAAATTTCAAAATTTTAAATCAAACTTG-T
* * * * *
1587176 TTGAGATAAGTCAAGCCTAAGTTAAGTTTAGGAATTTCAATTTTTTAAATCAAACCTGTTTTCAG
1 TTGAGATAGGTCAAGCCTAA-TTAAGTATAGGAGTTTCAAATTTTTAAATCAAACTTGTTTT-AG
* * * *
1587241 ATAGGTCGAGCCTAGATTAAGTTTAAGAAATTCAATTTTTTAAATCAAACTTGTTTTGAGATAGG
64 ATAAGTCAAGCCTAGATTAAGTATAAGAAATTCAATTTTTTAAATCGAACTTG-TTTGAGATAGG
* *
1587306 TCAAGCCTAGATTAAGTTTAAAAATTTCAAAATTTTAAATCAAACTTGT
128 TCGAGCCTAGATTAAGTCTAAAAATTTCAAAATTTTAAATCAAACTTGT
* * * * * * *
1587355 TGTGAGATAGGTCTAGCCTAAATTAAGTCTAAGAGCTTCAAATTTCTAAGTCAAACTTGTATGTA
1 T-TGAGATAGGTCAAGCCT-AATTAAGTATAGGAGTTTCAAATTTTTAAATCAAACTTGT-TTTA
* * * *
1587420 GATAAGTTAAGCCTATATTAAGTAT-AGAAACTTTAAATTTTATAAATCGAACTTGCTTTGAGAT
63 GATAAGTCAAGCCTAGATTAAGTATAAGAAA--TTCAATTTTTTAAATCGAACTTG-TTTGAGAT
* *
1587484 AGGTCGAGCTTACATTAAGT
125 AGGTCGAGCCTAGATTAAGT
1587504 TTGTGAACTT
Statistics
Matches: 274, Mismatches: 45, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
179 15 0.05
180 206 0.75
181 53 0.19
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (176 bp):
TTGAGATAGGTCAAGCCTAATTAAGTATAGGAGTTTCAAATTTTTAAATCAAACTTGTTTTAGAT
AAGTCAAGCCTAGATTAAGTATAAGAAATTCAATTTTTTAAATCGAACTTGTTTGAGATAGGTCG
AGCCTAGATTAAGTCTAAAAATTTCAAAATTTTAAATCAAACTTGT
Found at i:1587637 original size:6 final size:6
Alignment explanation
Indices: 1587630--1587664 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1587620 ATTTTGTTTC
* *
1587630 ATTTTC ATTTTT ATTTTT ATTCTT ATTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
1587665 ATTCTTGCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (6 bp):
ATTTTT
Found at i:1587658 original size:17 final size:17
Alignment explanation
Indices: 1587636--1587670 Score: 61
Period size: 17 Copynumber: 2.0 Consensus size: 17
1587626 TTTCATTTTC
1587636 ATTTTTATTTTTATTCTT
1 ATTTTTA-TTTTATTCTT
1587654 ATTTTTATTTTATTCTT
1 ATTTTTATTTTATTCTT
1587671 GCTTATGCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (17 bp):
ATTTTTATTTTATTCTT
Found at i:1587951 original size:22 final size:21
Alignment explanation
Indices: 1587923--1587964 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1587913 CATTTTGGAA
1587923 AATAAGGAACAAAAAAGAAAAC
1 AATAAGGAA-AAAAAAGAAAAC
*
1587945 AATAAGGAAAAAAAGGAAAA
1 AATAAGGAAAAAAAAGAAAA
1587965 GAGACAACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.74, C:0.05, G:0.17, T:0.05
Consensus pattern (21 bp):
AATAAGGAAAAAAAAGAAAAC
Found at i:1593789 original size:35 final size:35
Alignment explanation
Indices: 1593750--1593902 Score: 195
Period size: 35 Copynumber: 4.4 Consensus size: 35
1593740 NNNNNNNNNN
*
1593750 TTAATTAAACAATTTAATTAATTAGGCTCAATAAC
1 TTAATTAAACAATTTAATCAATTAGGCTCAATAAC
* * * * * *
1593785 TTAATTAAATAATTTGATCATTTAAGCCCATTAAC
1 TTAATTAAACAATTTAATCAATTAGGCTCAATAAC
*
1593820 TTGATTAAACAAATTTAATCAATTAGGCTCAATAAC
1 TTAATTAAAC-AATTTAATCAATTAGGCTCAATAAC
*
1593856 TTAATTAAACAATTTAATCAATTAGG--C-ACAAC
1 TTAATTAAACAATTTAATCAATTAGGCTCAATAAC
1593888 TTAATTAAACAATTT
1 TTAATTAAACAATTT
1593903 TAATTAAGTA
Statistics
Matches: 101, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
32 19 0.19
33 1 0.01
35 52 0.51
36 29 0.29
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (35 bp):
TTAATTAAACAATTTAATCAATTAGGCTCAATAAC
Found at i:1611564 original size:21 final size:21
Alignment explanation
Indices: 1611525--1611565 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1611515 AAAAGTTTAC
*
1611525 TTTAATAAAAACTATAATAAG
1 TTTAATAAAAAATATAATAAG
1611546 TTTAATAAAGAAATA-AATAA
1 TTTAATAAA-AAATATAATAA
1611566 AGATTAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (21 bp):
TTTAATAAAAAATATAATAAG
Found at i:1612456 original size:2 final size:2
Alignment explanation
Indices: 1612445--1612477 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1612435 TATGTGTGTG
*
1612445 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1612478 TTATTTCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1617202 original size:30 final size:31
Alignment explanation
Indices: 1617168--1617243 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 31
1617158 TTGTTATTAC
1617168 TGTTGGTGGATCTTTAG-GAGGGCCTAC-ACT
1 TGTTGGTGGATCTTTAGAGAGGGCCTACGA-T
* * *
1617198 TGTTGGTGCATCTTT-GAGAGGGCTTGCGAT
1 TGTTGGTGGATCTTTAGAGAGGGCCTACGAT
*
1617228 TATTGGTGGATCTTTA
1 TGTTGGTGGATCTTTA
1617244 AAGTAGTCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
29 1 0.03
30 36 0.95
31 1 0.03
ACGTcount: A:0.16, C:0.13, G:0.33, T:0.38
Consensus pattern (31 bp):
TGTTGGTGGATCTTTAGAGAGGGCCTACGAT
Found at i:1619826 original size:22 final size:22
Alignment explanation
Indices: 1619801--1619847 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1619791 ATTGATGAGT
1619801 TCATTCATCTTGCTATTGGTAA
1 TCATTCATCTTGCTATTGGTAA
* *
1619823 TCATTTATCTTGCTGTTGGTAA
1 TCATTCATCTTGCTATTGGTAA
1619845 TCA
1 TCA
1619848 AATTTATCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.21, C:0.17, G:0.15, T:0.47
Consensus pattern (22 bp):
TCATTCATCTTGCTATTGGTAA
Found at i:1620543 original size:2 final size:2
Alignment explanation
Indices: 1620536--1620563 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1620526 AAGATGCTTC
1620536 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1620564 GCACGCACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1621457 original size:6 final size:6
Alignment explanation
Indices: 1621448--1621475 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1621438 CTCTCATAAT
1621448 CATATA CATATA CATATA CATATA CATA
1 CATATA CATATA CATATA CATATA CATA
1621476 GTTTCCAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (6 bp):
CATATA
Found at i:1625103 original size:19 final size:20
Alignment explanation
Indices: 1625081--1625118 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1625071 TTCAAACAAA
1625081 ATGC-TCTTAGTCAATTAAC
1 ATGCTTCTTAGTCAATTAAC
*
1625100 ATGCTTCTTAGTCGATTAA
1 ATGCTTCTTAGTCAATTAA
1625119 GTCGTTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGCTTCTTAGTCAATTAAC
Found at i:1638229 original size:28 final size:28
Alignment explanation
Indices: 1638177--1638254 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
1638167 TAAATGGATC
* *
1638177 ACCCACAAAAAATGGATGGATACTTGTT-
1 ACCCACCAAAAATGGATGAATACTT-TTA
* * *
1638205 ACCTACCAGAAGTGGATGAATACTTTTA
1 ACCCACCAAAAATGGATGAATACTTTTA
1638233 ACCCACCAAAAATGGATGAATA
1 ACCCACCAAAAATGGATGAATA
1638255 ATGAAAAGAT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 2 0.05
28 39 0.95
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (28 bp):
ACCCACCAAAAATGGATGAATACTTTTA
Found at i:1643970 original size:24 final size:24
Alignment explanation
Indices: 1643926--1643972 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1643916 AGGGGAAAGA
**
1643926 GATGACTAAAAGCAATGATCAATG
1 GATGACTAAAAGCAAAAATCAATG
*
1643950 GATGACTAAAAGTAAAAATCAAT
1 GATGACTAAAAGCAAAAATCAAT
1643973 AGTCTCTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.11, G:0.17, T:0.21
Consensus pattern (24 bp):
GATGACTAAAAGCAAAAATCAATG
Found at i:1646955 original size:24 final size:25
Alignment explanation
Indices: 1646928--1646986 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
1646918 TTAAATTTTA
*
1646928 TAATAATAATAT-AATTAAT-TGTAT
1 TAATAATAATATAAATTAATAT-AAT
1646952 TAATAAT-ATATAAATTAATATAAT
1 TAATAATAATATAAATTAATATAAT
1646976 TAATAA-AATAT
1 TAATAATAATAT
1646987 CTATCTATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
23 4 0.13
24 26 0.84
25 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
TAATAATAATATAAATTAATATAAT
Found at i:1653320 original size:2 final size:2
Alignment explanation
Indices: 1653313--1653355 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1653303 TAGCTTGGGC
*
1653313 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1653355 T
1 T
1653356 TGTTCCAATC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Done.