Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008656.1 Hibiscus syriacus cultivar Beakdansim tig00111650_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: 2456495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 12
Found at i:1247898 original size:14 final size:14
Alignment explanation
Indices: 1247879--1247906 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1247869 ATAAGCTTAG
1247879 AAAATGACGTAAGT
1 AAAATGACGTAAGT
1247893 AAAATGACGTAAGT
1 AAAATGACGTAAGT
1247907 TCAATTAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (14 bp):
AAAATGACGTAAGT
Found at i:1256484 original size:11 final size:11
Alignment explanation
Indices: 1256468--1256492 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1256458 ATAAAAAATA
1256468 CCCCTTAGCAG
1 CCCCTTAGCAG
1256479 CCCCTTAGCAG
1 CCCCTTAGCAG
1256490 CCC
1 CCC
1256493 ATGTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.52, G:0.16, T:0.16
Consensus pattern (11 bp):
CCCCTTAGCAG
Found at i:1259813 original size:15 final size:16
Alignment explanation
Indices: 1259785--1259816 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1259775 TAAATCTTTC
1259785 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
1259801 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
1259816 T
1 T
1259817 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:1260588 original size:16 final size:16
Alignment explanation
Indices: 1260564--1260595 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1260554 TATCGCCGAC
*
1260564 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
1260580 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
1260596 TGTGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:1260968 original size:11 final size:11
Alignment explanation
Indices: 1260952--1260976 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1260942 TATAAAAATA
1260952 CCCCTTAGCAG
1 CCCCTTAGCAG
1260963 CCCCTTAGCAG
1 CCCCTTAGCAG
1260974 CCC
1 CCC
1260977 ATGTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.52, G:0.16, T:0.16
Consensus pattern (11 bp):
CCCCTTAGCAG
Found at i:1263717 original size:160 final size:158
Alignment explanation
Indices: 1263436--1263764 Score: 624
Period size: 160 Copynumber: 2.1 Consensus size: 158
1263426 CTGATTGATT
*
1263436 TTTTAATT-AAAAATAATATGATTTTAGAAAACCTCTCGTTTCGAAAATTTTGGGATTCCTTTTT
1 TTTTAATTAAAAAAAAATATGATTTTAGAAAACCTCTCGTTTCGAAAATTTTGGGATTCCTTTTT
1263500 AAAATAAAATGTATAGTTCGAGGAGTCGTCACCAATCTTTGATTAGGGTGTGATTGGACACCCAA
66 AAAATAAAATGTATAGTTCGAGGAGTCGTCACCAATCTTTGATTAGGGTGTGATTGGACACCCAA
1263565 AAACGTTGTCATTTTAAATAAAAATTAA
131 AAACGTTGTCATTTTAAATAAAAATTAA
1263593 TTTTAATTAAAATAAAAATAATGATTTTAGAAAACCTCTCGTTTCGAAAATTTTGGGATTCCTTT
1 TTTTAATTAAAA-AAAAAT-ATGATTTTAGAAAACCTCTCGTTTCGAAAATTTTGGGATTCCTTT
1263658 TTAAAATAAAATGTATAGTTCGAGGAGTCGTCACCAATCTTTGATTAGGGTGTGATTGGACACCC
64 TTAAAATAAAATGTATAGTTCGAGGAGTCGTCACCAATCTTTGATTAGGGTGTGATTGGACACCC
1263723 AAAAACGTTGTCATTTTAAATAAAAATTAA
129 AAAAACGTTGTCATTTTAAATAAAAATTAA
1263753 TTTTAATTAAAA
1 TTTTAATTAAAA
1263765 CAACAAATTA
Statistics
Matches: 168, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
157 8 0.05
158 3 0.02
159 5 0.03
160 152 0.90
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (158 bp):
TTTTAATTAAAAAAAAATATGATTTTAGAAAACCTCTCGTTTCGAAAATTTTGGGATTCCTTTTT
AAAATAAAATGTATAGTTCGAGGAGTCGTCACCAATCTTTGATTAGGGTGTGATTGGACACCCAA
AAACGTTGTCATTTTAAATAAAAATTAA
Found at i:1266710 original size:80 final size:80
Alignment explanation
Indices: 1266520--1266713 Score: 343
Period size: 80 Copynumber: 2.4 Consensus size: 80
1266510 TGCACAAAAT
* *
1266520 GCTTAAAAATTACCCGAAGGATTTAATCATAATGCTCGAAAGACTTATTGATGGATTTGCTTCAC
1 GCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGATTTGCTTCAC
* *
1266585 TACTCTTAGGTGAAG
66 CACTCTCAGGTGAAG
1266600 GCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGATTTGCTTCAC
1 GCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGATTTGCTTCAC
*
1266665 CACTCTCATGTGAAG
66 CACTCTCAGGTGAAG
1266680 GCTTACAAATTACCCGAAGGATTTAATCATCATG
1 GCTTACAAATTACCCGAAGGATTTAATCATCATG
1266714 GTGTGAAAAC
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 109 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (80 bp):
GCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGATTTGCTTCAC
CACTCTCAGGTGAAG
Found at i:1266992 original size:217 final size:217
Alignment explanation
Indices: 1266745--1267784 Score: 1681
Period size: 217 Copynumber: 4.8 Consensus size: 217
1266735 AAGTCTTATG
* * *
1266745 GATGACCCAAAGGA-TTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCGAAAGACTTATAAA
1 GATGACCCGAAGGATTTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA
* *
1266809 TTGTGAAATTTTGAAAACCGTATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTT
66 TTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTT
*
1266874 CTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGATGGACTTA
131 -TTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTA
1266939 TCATCTTGCTCTAAAGGCTTACA
195 TCATCTTGCTCTAAAGGCTTACA
* *
1266962 TATGACCCGAAGGA-TTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCGAAGGACTTATAAA
1 GATGACCCGAAGGATTTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA
*
1267026 TTGTGAAATTTTGAAAATCGCCTTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTT
66 TTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTT
* *
1267091 TTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAAGTTTTATTGATGGCCCGAAGGACTTAT
131 TTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTAT
* *
1267156 CATCTTGATCTAAAGGCTTTC-
196 CATCTTGCTCTAAAGGCTTACA
* *
1267177 GAATGACCCGAAGGATTTTAAGCATCATGCTCAAAAGACTTATTGATGGCCCGAAGGACTTATAA
1 G-ATGACCCGAAGGATTTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
1267242 ATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTT
65 ATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTT
*
1267307 TTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCTGAAGGACTTA
130 TTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTA
1267372 TCATCTTGCTCTAAAGGCTTACA
195 TCATCTTGCTCTAAAGGCTTACA
*
1267395 GATAACCCGAAGGATTTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA
1 GATGACCCGAAGGATTTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA
* * * *
1267460 TTGTGAAATTTTAAAAATCACATTCTTTGTTTTAAAAAATTCCATCTTCTTAAAACATCATTTTT
66 TTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTT
* * * * *
1267525 TTCATTCTCAAATTCATTTGAAATCACCCTACCCGAAGGTATTATGGATGGCCCGAAGGACTTAT
131 TTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTAT
*
1267590 CATCTTGCTCAAAAGGCTTACA
196 CATCTTGCTCTAAAGGCTTACA
* * *
1267612 GATGACCCAAAGGATTTTAAGCATCATGCTCGAAAGACTTACTGATGGCCAGAAGGACTTATACA
1 GATGACCCGAAGGATTTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA
*
1267677 TTGTGAAA-TTT-----T-GCATTCTTCATTTTCAAAAATTCCATCTTCTTAAAACA-CTATTTT
66 TTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATC-ATTTT
*
1267734 TTT-ATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGG
130 TTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGG
1267785 ATTTGCTTCA
Statistics
Matches: 771, Mismatches: 48, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
209 44 0.06
210 42 0.05
211 1 0.00
216 97 0.13
217 586 0.76
218 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (217 bp):
GATGACCCGAAGGATTTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA
TTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTT
TTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTAT
CATCTTGCTCTAAAGGCTTACA
Found at i:1267232 original size:43 final size:41
Alignment explanation
Indices: 1267132--1267238 Score: 108
Period size: 43 Copynumber: 2.6 Consensus size: 41
1267122 CCCGAAAGTT
* * * *
1267132 TTATTGATGGCCCGAAGGACTTATCATCTTGATCTAAAGGC
1 TTATTGATGGCCCGAAGGACTTAGCATCATGATCAAAAGAC
* * * *
1267173 TT-TCGAATGACCCGAAGGATTTTAAGCATCATGCTCAAAAGAC
1 TTATTG-ATGGCCCGAAGGA-CTT-AGCATCATGATCAAAAGAC
1267216 TTATTGATGGCCCGAAGGACTTA
1 TTATTGATGGCCCGAAGGACTTA
1267239 TAAATTGTGA
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
40 2 0.04
41 15 0.29
42 4 0.08
43 28 0.55
44 2 0.04
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (41 bp):
TTATTGATGGCCCGAAGGACTTAGCATCATGATCAAAAGAC
Found at i:1267826 original size:34 final size:33
Alignment explanation
Indices: 1267788--1267923 Score: 173
Period size: 34 Copynumber: 3.9 Consensus size: 33
1267778 TGGATGGATT
1267788 TGCTTCACTACTCTTCGATGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTCG-TGAAGGCTTAAGATGG
*
1267822 TGCTTCACTACTCCTCTGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTC-GTGAAGGCTTAAGATGG
*
1267856 TGCTTCACTACTCTCCGGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTC-GTGAAGGCTTAAGATGG
* * *
1267890 TTTGCTTCACTCCTCTTTGTTGAATGCTTAAGAT
1 --TGCTTCACTACTCTTCG-TGAAGGCTTAAGAT
1267924 TGACTTACCC
Statistics
Matches: 90, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
34 62 0.69
35 2 0.02
36 26 0.29
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (33 bp):
TGCTTCACTACTCTTCGTGAAGGCTTAAGATGG
Found at i:1267863 original size:68 final size:69
Alignment explanation
Indices: 1267788--1267923 Score: 195
Period size: 68 Copynumber: 2.0 Consensus size: 69
1267778 TGGATGGATT
*
1267788 TGCTTCACTACTCTTCGATGAAGGCTTAAGATGG-TGCTTCACTACTCCTCTG-TGAAGGCTTAA
1 TGCTTCACTACTCTCCGATGAAGGCTTAAGATGGTTGCTTCACTACT-CTCTGTTGAAGGCTTAA
1267851 GATGG
65 GATGG
* * * *
1267856 TGCTTCACTACTCTCCGGTGAAGGCTTAAGATGGTTTGCTTCACTCCTCTTTGTTGAATGCTTAA
1 TGCTTCACTACTCTCCGATGAAGGCTTAAGATGG-TTGCTTCACTACTCTCTGTTGAAGGCTTAA
1267921 GAT
65 GAT
1267924 TGACTTACCC
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
68 32 0.53
69 4 0.07
70 24 0.40
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (69 bp):
TGCTTCACTACTCTCCGATGAAGGCTTAAGATGGTTGCTTCACTACTCTCTGTTGAAGGCTTAAG
ATGG
Found at i:1274395 original size:6 final size:6
Alignment explanation
Indices: 1274386--1274421 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1274376 CAAAAATAAG
* *
1274386 AATGCA AATGCA TATGCA TATGCA AATGCA AATGCA
1 AATGCA AATGCA AATGCA AATGCA AATGCA AATGCA
1274422 CGAGGTGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (6 bp):
AATGCA
Found at i:1274410 original size:18 final size:18
Alignment explanation
Indices: 1274387--1274421 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1274377 AAAAATAAGA
*
1274387 ATGCAAATGCATATGCAT
1 ATGCAAATGCAAATGCAT
1274405 ATGCAAATGCAAATGCA
1 ATGCAAATGCAAATGCA
1274422 CGAGGTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (18 bp):
ATGCAAATGCAAATGCAT
Found at i:1274693 original size:21 final size:21
Alignment explanation
Indices: 1274668--1274743 Score: 134
Period size: 21 Copynumber: 3.6 Consensus size: 21
1274658 AAATGCAAAG
1274668 TGGTCTTCATGTCTTTATGAA
1 TGGTCTTCATGTCTTTATGAA
*
1274689 GGGTCTTCATGTCTTTATGAA
1 TGGTCTTCATGTCTTTATGAA
*
1274710 TGGTATTCATGTCTTTATGAA
1 TGGTCTTCATGTCTTTATGAA
1274731 TGGTCTTCATGTC
1 TGGTCTTCATGTC
1274744 CTCGGTGAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.18, C:0.14, G:0.21, T:0.46
Consensus pattern (21 bp):
TGGTCTTCATGTCTTTATGAA
Found at i:1286914 original size:23 final size:22
Alignment explanation
Indices: 1286871--1286914 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1286861 CGAAATTATA
*
1286871 TATTTATAAAAAATAGTATTTT
1 TATTTATAAAAAATAGGATTTT
1286893 TATTTA-ATAAAAATAGGGATTT
1 TATTTATA-AAAAATA-GGATTT
1286915 AAGGGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 1 0.05
22 13 0.68
23 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (22 bp):
TATTTATAAAAAATAGGATTTT
Found at i:1288890 original size:13 final size:15
Alignment explanation
Indices: 1288859--1288892 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
1288849 ACTTTTTATT
1288859 ATTCAAACTTTACAA
1 ATTCAAACTTTACAA
1288874 ATTCAAAC-TTA-AA
1 ATTCAAACTTTACAA
1288887 ATTCAA
1 ATTCAA
1288893 TTTGATACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 3 0.16
15 8 0.42
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (15 bp):
ATTCAAACTTTACAA
Found at i:1290699 original size:16 final size:16
Alignment explanation
Indices: 1290657--1290702 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1290647 TTCGATATTG
1290657 AAAAATAAA-TATTAA
1 AAAAATAAATTATTAA
* **
1290672 AATAATTTATTATTAA
1 AAAAATAAATTATTAA
1290688 AAAAATAAATTATTA
1 AAAAATAAATTATTA
1290703 TTTATTATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAAATAAATTATTAA
Found at i:1291656 original size:14 final size:15
Alignment explanation
Indices: 1291633--1291669 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1291623 TTGTGGGTTA
1291633 TTTG-TTCTTTGTT-
1 TTTGTTTCTTTGTTC
1291646 TTTGTTTCTTTGTTC
1 TTTGTTTCTTTGTTC
*
1291661 TCTGTTTCT
1 TTTGTTTCT
1291670 GGTTCTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.19
14 9 0.43
15 8 0.38
ACGTcount: A:0.00, C:0.14, G:0.14, T:0.73
Consensus pattern (15 bp):
TTTGTTTCTTTGTTC
Found at i:1291675 original size:21 final size:21
Alignment explanation
Indices: 1291628--1291675 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1291618 GCTGGTTGTG
* * *
1291628 GGTTATTTGTTCTTTGTTTTT
1 GGTTCTTTGTTCTCTGTTTCT
*
1291649 GTTTCTTTGTTCTCTGTTTCT
1 GGTTCTTTGTTCTCTGTTTCT
1291670 GGTTCT
1 GGTTCT
1291676 CTCTCCGTCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.12, G:0.19, T:0.67
Consensus pattern (21 bp):
GGTTCTTTGTTCTCTGTTTCT
Found at i:1292100 original size:3 final size:3
Alignment explanation
Indices: 1292069--1292145 Score: 86
Period size: 3 Copynumber: 25.0 Consensus size: 3
1292059 CCGGGTTTTG
* *
1292069 TAA TAT TAA TAAA TAAA TAA T-A TATA TAA TAA TAA TAA TAT TATA TAA
1 TAA TAA TAA T-AA T-AA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA
1292117 TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1292146 ATAAAATTAA
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
2 4 0.06
3 49 0.75
4 12 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1293044 original size:113 final size:113
Alignment explanation
Indices: 1292372--1293041 Score: 877
Period size: 113 Copynumber: 6.0 Consensus size: 113
1292362 TAGAGTCATT
* ** * *
1292372 CAAAAGGTTGAATAAGCTCTTCTCATTATGAA---CTTC-TCCTTCTCCTGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* * *
1292433 TTATGAAC-TTCTCTGGAAAAACTGACCCATCAAGTGATGGATTTGAG
66 TTATGAACTTTATCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
* * * * *
1292480 CAAAA-ATCTGAATAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTTTTCTC
1 CAAAAGGT-TGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
* * * *
1292544 ATTAAGAACTTTTTCTAGAAAAGTTGATCCATCAAGTGATGGATTTGAG
65 ATTATGAACTTTATCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
*
1292593 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
** * * * *
1292658 TTATGAACTCGAACTGGAAAAGCTAATCTATCAAGTGATAGATTTGAG
66 TTATGAACTTTATCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
1292706 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
** * * * *
1292771 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
66 TTATGAACTTTATCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
*
1292819 CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
** * *
1292884 TTATGAACTTCCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAA
66 TTATGAACTTTATCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
* * * * * *
1292932 CATAAGGTTGAATAAATTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* * *
1292997 TTATGAACTTTTTCTGGAAAAGCCGATCCATTGAA-TGATGGATTT
66 TTATGAACTTTATCTGGAAAAGCTGATCCA-TCAAGTGATGGATTT
1293042 AAATCTTTGC
Statistics
Matches: 502, Mismatches: 52, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
107 1 0.00
108 27 0.05
111 4 0.01
112 28 0.06
113 438 0.87
114 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTATCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
Found at i:1294068 original size:83 final size:83
Alignment explanation
Indices: 1293875--1294109 Score: 371
Period size: 83 Copynumber: 2.8 Consensus size: 83
1293865 TGGTTTTGGG
* * *
1293875 GTTCATACCAAACCAGATCAGATATCTCAAATAACACTTCCAGAAGATGCTATTGGGCACATTCA
1 GTTC-TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCA
1293940 TCTTTCCAAATTCAATAACTA
64 T-TTTCCAAATTCAATAACTA
* *
1293961 GTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTACATTCATT
1 GTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATT
* *
1294026 TTTCAAATTCAATAACTG
66 TTCCAAATTCAATAACTA
*
1294044 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATT
1 GTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATT
1294109 T
66 T
1294110 GTTCCAGTTA
Statistics
Matches: 139, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
83 80 0.58
84 11 0.08
85 45 0.32
86 3 0.02
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.27
Consensus pattern (83 bp):
GTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATT
TTCCAAATTCAATAACTA
Found at i:1295254 original size:1 final size:1
Alignment explanation
Indices: 1295250--1295373 Score: 104
Period size: 1 Copynumber: 124.0 Consensus size: 1
1295240 TGACCCCCCA
* * * * * * * * * *
1295250 TTTTTCTTTTTTTTCTCTTTTTTCTCTTTTTTTTCTCTTTTTTTTTCTCTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * *
1295315 TCTTTTTTTCTTTTTTTTCTTTTTTTTTCTTTTTTTTTTTTTTTTTCTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1295374 CTTCAAGCAT
Statistics
Matches: 91, Mismatches: 32, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 91 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:1295264 original size:9 final size:9
Alignment explanation
Indices: 1295250--1295366 Score: 150
Period size: 9 Copynumber: 13.2 Consensus size: 9
1295240 TGACCCCCCA
1295250 TTTTTCTTT
1 TTTTTCTTT
*
1295259 TTTTTCTCT
1 TTTTTCTTT
*
1295268 TTTTTCTCT
1 TTTTTCTTT
*
1295277 TTTTT-TTC
1 TTTTTCTTT
*
1295285 TCTTT-TTT
1 TTTTTCTTT
*
1295293 TTTCTCTTT
1 TTTTTCTTT
1295302 TTTTTCTTT
1 TTTTTCTTT
1295311 TTTTTC-TT
1 TTTTTCTTT
1295319 TTTTTCTTT
1 TTTTTCTTT
1295328 TTTTTCTTTT
1 TTTTTC-TTT
1295338 TTTTTCTTT
1 TTTTTCTTT
*
1295347 TTTTTTTTT
1 TTTTTCTTT
1295356 TTTTTCTTT
1 TTTTTCTTT
1295365 TT
1 TT
1295367 CTTTTTTCTT
Statistics
Matches: 95, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
8 18 0.19
9 68 0.72
10 9 0.09
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:1295270 original size:11 final size:11
Alignment explanation
Indices: 1295250--1295376 Score: 124
Period size: 11 Copynumber: 11.8 Consensus size: 11
1295240 TGACCCCCCA
1295250 TTTT-TCTTTT
1 TTTTCTCTTTT
1295260 TTTTCTC--TT
1 TTTTCTCTTTT
1295269 TTTTCTCTTTT
1 TTTTCTCTTTT
1295280 TTTTCTCTTTTT
1 TTTTCTC-TTTT
1295292 TTTTCTCTTTT
1 TTTTCTCTTTT
*
1295303 TTTTCTTTTTT
1 TTTTCTCTTTT
* *
1295314 TTCTTTTTTTCTT
1 TT-TTCTCTT-TT
*
1295327 TTTTTTCTTTT
1 TTTTCTCTTTT
1295338 TTTT-TCTTTT
1 TTTTCTCTTTT
1295348 TTTT-T-TTTT
1 TTTTCTCTTTT
1295357 TTTTCT-TTTT
1 TTTTCTCTTTT
*
1295367 CTTTTTTCTT
1 -TTTTCTCTT
1295377 CAAGCATAAT
Statistics
Matches: 104, Mismatches: 4, Indels: 16
0.84 0.03 0.13
Matches are distributed among these distances:
9 17 0.16
10 20 0.19
11 38 0.37
12 25 0.24
13 4 0.04
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTCTCTTTT
Found at i:1295297 original size:32 final size:31
Alignment explanation
Indices: 1295250--1295376 Score: 160
Period size: 32 Copynumber: 4.3 Consensus size: 31
1295240 TGACCCCCCA
1295250 TTTTTC-TTTTTTTTCTCTTTTTTCTCTTTT
1 TTTTTCTTTTTTTTTCTCTTTTTTCTCTTTT
*
1295280 TTTTCTCTTTTTTTTTCTCTTTTTTTTC-TTT
1 TTTT-TCTTTTTTTTTCTCTTTTTTCTCTTTT
1295311 TTTTTC--TTTTTTTCT-TTTTTT-TCTTTT
1 TTTTTCTTTTTTTTTCTCTTTTTTCTCTTTT
* *
1295338 TTTTTCTTTTTTTTT-TTTTTTTTCTTTTTCT
1 TTTTTCTTTTTTTTTCTCTTTTTTCTCTTT-T
1295369 TTTTTCTT
1 TTTTTCTT
1295377 CAAGCATAAT
Statistics
Matches: 87, Mismatches: 2, Indels: 15
0.84 0.02 0.14
Matches are distributed among these distances:
26 2 0.02
27 15 0.17
28 10 0.11
29 13 0.15
30 10 0.11
31 18 0.21
32 19 0.22
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (31 bp):
TTTTTCTTTTTTTTTCTCTTTTTTCTCTTTT
Found at i:1306736 original size:16 final size:16
Alignment explanation
Indices: 1306694--1306737 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1306684 TTCGATATTG
1306694 AAAAATAAA-TATTAA
1 AAAAATAAATTATTAA
* **
1306709 AATAATTTATTATTAA
1 AAAAATAAATTATTAA
1306725 AAAAATAAATTAT
1 AAAAATAAATTAT
1306738 ATTTATTATA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAAATAAATTATTAA
Found at i:1307697 original size:14 final size:15
Alignment explanation
Indices: 1307674--1307710 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1307664 TTGTGGGTTA
1307674 TTTG-TTCTTTGTT-
1 TTTGTTTCTTTGTTC
1307687 TTTGTTTCTTTGTTC
1 TTTGTTTCTTTGTTC
*
1307702 TCTGTTTCT
1 TTTGTTTCT
1307711 GGTTCTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.19
14 9 0.43
15 8 0.38
ACGTcount: A:0.00, C:0.14, G:0.14, T:0.73
Consensus pattern (15 bp):
TTTGTTTCTTTGTTC
Found at i:1307716 original size:21 final size:21
Alignment explanation
Indices: 1307669--1307716 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1307659 GCTGGTTGTG
* * *
1307669 GGTTATTTGTTCTTTGTTTTT
1 GGTTCTTTGTTCTCTGTTTCT
*
1307690 GTTTCTTTGTTCTCTGTTTCT
1 GGTTCTTTGTTCTCTGTTTCT
1307711 GGTTCT
1 GGTTCT
1307717 CTCTCCGTCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.12, G:0.19, T:0.67
Consensus pattern (21 bp):
GGTTCTTTGTTCTCTGTTTCT
Found at i:1308159 original size:6 final size:5
Alignment explanation
Indices: 1308131--1308188 Score: 52
Period size: 5 Copynumber: 11.8 Consensus size: 5
1308121 TGTAATATTA
*
1308131 ATAA- ATAAT ATATAT ATAAT ATAATT ATAAA ATAAT AATAAT A-AA-
1 ATAAT ATAAT ATA-AT ATAAT ATAA-T ATAAT ATAAT -ATAAT ATAAT
1308176 ATAAT ATAA- ATAA
1 ATAAT ATAAT ATAA
1308189 AATTAAAATG
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
3 1 0.02
4 12 0.26
5 18 0.39
6 15 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (5 bp):
ATAAT
Found at i:1308168 original size:14 final size:14
Alignment explanation
Indices: 1308133--1308181 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
1308123 TAATATTAAT
1308133 AAATAAT-ATATATA
1 AAATAATAAT-TATA
*
1308147 TAAT-ATAATTATA
1 AAATAATAATTATA
*
1308160 AAATAATAATAATA
1 AAATAATAATTATA
1308174 AAATAATA
1 AAATAATA
1308182 TAAATAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 9 0.30
14 21 0.70
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATAATAATTATA
Found at i:1308169 original size:3 final size:3
Alignment explanation
Indices: 1308123--1308181 Score: 52
Period size: 3 Copynumber: 19.7 Consensus size: 3
1308113 TCGGGTTTTG
* *
1308123 TAA TAT TAA TAAA TAA TATA TATA TAA T-A TAA TTA TAA -AA TAA TAA
1 TAA TAA TAA T-AA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA
1308169 TAA TAA -AA TAA TA
1 TAA TAA TAA TAA TA
1308182 TAAATAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
2 6 0.13
3 31 0.66
4 10 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1308170 original size:30 final size:28
Alignment explanation
Indices: 1308123--1308191 Score: 74
Period size: 30 Copynumber: 2.5 Consensus size: 28
1308113 TCGGGTTTTG
* *
1308123 TAATATTAAT-AAATAAT-AT-AT-ATA
1 TAATATAAATAAAATAATAATAATAAAA
1308147 TAATATAATTATAAAATAATAATAATAAAA
1 TAATATAA--ATAAAATAATAATAATAAAA
1308177 TAATATAAATAAAAT
1 TAATATAAATAAAAT
1308192 TAAAATGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
24 7 0.19
26 2 0.05
27 7 0.19
28 9 0.24
29 2 0.05
30 10 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
TAATATAAATAAAATAATAATAATAAAA
Found at i:1308187 original size:14 final size:14
Alignment explanation
Indices: 1308146--1308191 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 14
1308136 TAATATATAT
1308146 ATAATATAATTATAAA
1 ATAATATAA--ATAAA
1308162 ATAATA-ATAATAAA
1 ATAATATA-AATAAA
1308176 ATAATATAAATAAA
1 ATAATATAAATAAA
1308190 AT
1 AT
1308192 TAAAATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 19 0.68
15 2 0.07
16 7 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATATAAATAAA
Found at i:1324770 original size:26 final size:26
Alignment explanation
Indices: 1324719--1324770 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1324709 ATATATATAT
* * **
1324719 TATAATTTATGATTTTTTTTTTAAAA
1 TATAATATATAATTTTTTTTAGAAAA
1324745 TATAATATATAATTTTTTTTAGAAAA
1 TATAATATATAATTTTTTTTAGAAAA
1324771 CGGTTTTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (26 bp):
TATAATATATAATTTTTTTTAGAAAA
Found at i:1324863 original size:2 final size:2
Alignment explanation
Indices: 1324856--1324889 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1324846 TGATTTTTGA
1324856 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1324890 GTTTGCAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1324906 original size:54 final size:52
Alignment explanation
Indices: 1324820--1324928 Score: 157
Period size: 53 Copynumber: 2.1 Consensus size: 52
1324810 ATTTTTAAGA
* *
1324820 ATATATATATTATATAGCTTTGAAAATGATTTTTGAATATATATATATATATAT
1 ATATATATATTATATAGCTTTGAAAATGA-TTTTGAAAAAATATATATA-ATAT
*
1324874 ATATATATATTATATAG-TTTGCAAATGAATTTTGAAAAAATATATATAATAT
1 ATATATATATTATATAGCTTTGAAAATG-ATTTTGAAAAAATATATATAATAT
1324926 ATA
1 ATA
1324929 GGTTTTGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
52 7 0.14
53 26 0.51
54 18 0.35
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (52 bp):
ATATATATATTATATAGCTTTGAAAATGATTTTGAAAAAATATATATAATAT
Found at i:1324928 original size:39 final size:37
Alignment explanation
Indices: 1324874--1325177 Score: 369
Period size: 36 Copynumber: 8.2 Consensus size: 37
1324864 ATATATATAT
*
1324874 ATATATATATTATATAG-TTTGCAAATGA-ATTTTGAAAAA
1 ATATATATAATATATAGTTTTG-AAA--ACATTTTG-AAAA
1324913 ATATATATAATATATAGGTTTTGAAAACATTTTG-AAA
1 ATATATATAATATATA-GTTTTGAAAACATTTTGAAAA
1324950 ATATATATAATATATAGTTTTTGAAAACATTTTGAAAAA
1 ATATATATAATATATAG-TTTTGAAAACATTTTG-AAAA
*
1324989 ATATATATAATATATAGTTTTTGAAAACATTTTAAAAA
1 ATATATATAATATATAG-TTTTGAAAACATTTTGAAAA
*
1325027 AT-TATATAATATATAGTTTTGAAATCATTTTGAAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTGAAAA
*
1325063 CT-TATATAATATATAGTTTT-AAAACATTTTTG-AAA
1 ATATATATAATATATAGTTTTGAAAACA-TTTTGAAAA
*
1325098 ACATATATAATATATAGTTTT-AAAACATTTTTG-AAA
1 ATATATATAATATATAGTTTTGAAAACA-TTTTGAAAA
* * *
1325134 A-CTATATAATGTATAGTTTTGAAAACATTTTTAAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTGAAAA
1325170 A-ATATATA
1 ATATATATA
1325178 GTATTAAAAT
Statistics
Matches: 243, Mismatches: 12, Indels: 23
0.87 0.04 0.08
Matches are distributed among these distances:
35 29 0.12
36 93 0.38
37 49 0.20
38 7 0.03
39 57 0.23
40 4 0.02
41 4 0.02
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.42
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTGAAAACATTTTGAAAA
Found at i:1325218 original size:26 final size:25
Alignment explanation
Indices: 1325168--1325242 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 25
1325158 ACATTTTTAA
*
1325168 AAAATATATAGTATTAAAATATTTTTG
1 AAAATATATA-TATT-ATATATTTTTG
1325195 AAAATATATATATTATATAGTTTTTG
1 AAAATATATATATTATATA-TTTTTG
*
1325221 GAAATATTATATATATATATAT
1 AAAATA-TATATAT-TATATAT
1325243 ATATATTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.09
26 15 0.35
27 18 0.42
28 6 0.14
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (25 bp):
AAAATATATATATTATATATTTTTG
Found at i:1325239 original size:64 final size:63
Alignment explanation
Indices: 1325090--1325243 Score: 163
Period size: 64 Copynumber: 2.4 Consensus size: 63
1325080 TTTAAAACAT
* *
1325090 TTTTGAAAACA--TATATA-ATATATAGTTTTAAAACATTTTTGAAAACTATATAATGTATAG
1 TTTTGAAAACATTTATATATATATATAGTATTAAAACATTTTTGAAAACTATATAATATATAG
* * * *
1325150 TTTTGAAAACATTTTTAAAAAATATATAGTATTAAAATATTTTTGAAAA-TATATATATTATATA
1 TTTTGAAAACATTTAT-ATATATATATAGTATTAAAACATTTTTGAAAACTATATA-A-TATATA
1325214 G
63 G
* *
1325215 TTTTTGGAAATATTATATATATATATATA
1 -TTTTGAAAACATT-TATATATATATATA
1325244 TATATTATTA
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
60 11 0.14
62 2 0.03
63 8 0.11
64 27 0.36
65 6 0.08
66 20 0.26
67 2 0.03
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (63 bp):
TTTTGAAAACATTTATATATATATATAGTATTAAAACATTTTTGAAAACTATATAATATATAG
Found at i:1325254 original size:3 final size:3
Alignment explanation
Indices: 1325246--1325295 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
1325236 TATATATATA
* *
1325246 TAT TAT TAT TAT TAT TAT TAT TAT TATT TGT TTT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
1325291 TAT TA
1 TAT TA
1325296 ACATTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:1325715 original size:23 final size:25
Alignment explanation
Indices: 1325684--1325730 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
1325674 AACAACGATC
1325684 CAACAACAACA-TCAA-ACCAAAAA
1 CAACAACAACAGTCAACACCAAAAA
* *
1325707 CAACCACAATAGTCAACACCAAAA
1 CAACAACAACAGTCAACACCAAAA
1325731 CACTGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 4 0.20
25 7 0.35
ACGTcount: A:0.60, C:0.32, G:0.02, T:0.06
Consensus pattern (25 bp):
CAACAACAACAGTCAACACCAAAAA
Found at i:1326489 original size:9 final size:9
Alignment explanation
Indices: 1326477--1326501 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1326467 ATTTTTTCAA
1326477 TATTTTTGT
1 TATTTTTGT
1326486 TATTTTTGT
1 TATTTTTGT
1326495 TATTTTT
1 TATTTTT
1326502 ATTTTCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (9 bp):
TATTTTTGT
Found at i:1326511 original size:23 final size:23
Alignment explanation
Indices: 1326480--1326524 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1326470 TTTTCAATAT
*
1326480 TTTTGTTATTTTTGTTATTTTTA
1 TTTTCTTATTTTTGTTATTTTTA
* *
1326503 TTTTCTTATTTTTTTTCTTTTT
1 TTTTCTTATTTTTGTTATTTTT
1326525 CCTTTCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.09, C:0.04, G:0.04, T:0.82
Consensus pattern (23 bp):
TTTTCTTATTTTTGTTATTTTTA
Found at i:1326530 original size:23 final size:23
Alignment explanation
Indices: 1326485--1326530 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1326475 AATATTTTTG
*
1326485 TTATTTTTGTTATTTTTATTTTC
1 TTATTTTTGTTATTTTTACTTTC
* * *
1326508 TTATTTTTTTTCTTTTTCCTTTC
1 TTATTTTTGTTATTTTTACTTTC
1326531 ATTTATTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.78
Consensus pattern (23 bp):
TTATTTTTGTTATTTTTACTTTC
Found at i:1327633 original size:21 final size:21
Alignment explanation
Indices: 1327608--1327647 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1327598 ACCTCACTAA
*
1327608 CTCTTTCCTTTCATTTTTGCT
1 CTCTTTCATTTCATTTTTGCT
*
1327629 CTCTTTCATTTTATTTTTG
1 CTCTTTCATTTCATTTTTG
1327648 TCATTTACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.23, G:0.05, T:0.65
Consensus pattern (21 bp):
CTCTTTCATTTCATTTTTGCT
Found at i:1330667 original size:99 final size:99
Alignment explanation
Indices: 1330558--1330754 Score: 297
Period size: 99 Copynumber: 2.0 Consensus size: 99
1330548 TAATATTATA
* * * * *
1330558 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGTAATTGGTTAAATG-CCTTGACTTTATGGATAA
1 TATACAATAAAGCTTGAGTTATCCCTCTAAAGCAATTGGTTAAACGCCCTAG-CTTTATGGATAA
** *
1330622 GATTCAGTTAGCTTGATAAAGGCGATTATAATATC
65 GATTCAACTAGCATGATAAAGGCGATTATAATATC
1330657 TATACAATAAAGCTTGAGTTATCCCTCTAAAGCAATTGGTTAAACGCCCTAGCTTTATGGATAAG
1 TATACAATAAAGCTTGAGTTATCCCTCTAAAGCAATTGGTTAAACGCCCTAGCTTTATGGATAAG
*
1330722 ATTCAACTAGCATGATAAAGGTGATTATAATAT
66 ATTCAACTAGCATGATAAAGGCGATTATAATAT
1330755 TAAGCTATCC
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
99 84 0.95
100 4 0.05
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Consensus pattern (99 bp):
TATACAATAAAGCTTGAGTTATCCCTCTAAAGCAATTGGTTAAACGCCCTAGCTTTATGGATAAG
ATTCAACTAGCATGATAAAGGCGATTATAATATC
Found at i:1332515 original size:85 final size:85
Alignment explanation
Indices: 1332357--1332582 Score: 231
Period size: 85 Copynumber: 2.7 Consensus size: 85
1332347 CTTATTATAG
* * * * * *
1332357 TATAACTCAAGGAGAGAAGAGCTATTTGTCAACCAAAACCTTCGAGTTCGATTATATTTAGCTCA
1 TATAACTCAAGGAGAGAAGAGCTATCTGACAACAAAAACCTTCGAGTTCGATTACATTCAACTCA
1332422 AGGACATATCAAATTTACAA
66 AGGACATATCAAATTTACAA
* * * * *
1332442 TATAACTCAAGGAGATAAGGGTTATCTGACAACAAAAACCTTCGAGTTCGATTCCATTCAACTTA
1 TATAACTCAAGGAGAGAAGAGCTATCTGACAACAAAAACCTTCGAGTTCGATTACATTCAACTCA
* *
1332507 TAGG-CATATCAAATTTATAG
66 -AGGACATATCAAATTTACAA
* * * * ** * * *
1332527 CATAGCTCAAGGCGAGAAG-GCTATCCGTTAACAAAAATCTTCAAGTTCGATGACAT
1 TATAACTCAAGGAGAGAAGAGCTATCTGACAACAAAAACCTTCGAGTTCGATTACAT
1332583 ACCAACCACA
Statistics
Matches: 115, Mismatches: 25, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
84 29 0.25
85 83 0.72
86 3 0.03
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (85 bp):
TATAACTCAAGGAGAGAAGAGCTATCTGACAACAAAAACCTTCGAGTTCGATTACATTCAACTCA
AGGACATATCAAATTTACAA
Found at i:1333453 original size:20 final size:20
Alignment explanation
Indices: 1333430--1333477 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
1333420 AACGCGATCT
1333430 CCAGAATCCCAAATCAGTTA
1 CCAGAATCCCAAATCAGTTA
1333450 CCAGAATCCCAAATCAGTTA
1 CCAGAATCCCAAATCAGTTA
1333470 CCAGAATC
1 CCAGAATC
1333478 GCAACGCGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.31, G:0.10, T:0.19
Consensus pattern (20 bp):
CCAGAATCCCAAATCAGTTA
Found at i:1333562 original size:20 final size:20
Alignment explanation
Indices: 1333537--1333831 Score: 226
Period size: 20 Copynumber: 14.7 Consensus size: 20
1333527 GATTTTCCAT
* *
1333537 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
1333557 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
* **
1333577 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
*
1333597 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * *
1333616 CTATCGCAACGAGTATCCGTA
1 -AATCGCAACGCGAATACGTA
*
1333637 AATCGCAACGAC-AATGCGTA
1 AATCGCAACG-CGAATACGTA
1333657 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
1333678 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
1333698 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
1333718 AACCGCAACACGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
*
1333738 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * * *
1333758 AATCGTAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
1333778 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
*
1333799 AATCGCAACGC-ATATCCGTA
1 AATCGCAACGCGA-ATACGTA
1333819 AATCGCAACGCGA
1 AATCGCAACGCGA
1333832 TTTTTAAAGC
Statistics
Matches: 225, Mismatches: 37, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
18 1 0.00
19 3 0.01
20 181 0.80
21 39 0.17
22 1 0.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:1333662 original size:40 final size:40
Alignment explanation
Indices: 1333537--1333828 Score: 286
Period size: 40 Copynumber: 7.2 Consensus size: 40
1333527 GATTTTCCAT
* * * * **
1333537 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACATATA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGTATC-CGTA
* * ** *
1333577 AATCGCAACGCGAACATATAAATCGCAACGCG-ATTC-TGA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGT-A
* * * * *
1333616 CTATCGCAACGAGTATCCGTAAATCGCAACGAC-AATGCGTA
1 -AATCGCAACGAGAATACGTAAATCGCAACG-CGTATCCGTA
*
1333657 AATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTA
* * *
1333698 AATCGCAACGAGAATACGTAAACCGCAACACGTATCTGTA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTA
* *
1333738 AATCGCAACGAGAATACGTAAATCGTAATGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTA
* *
1333778 AATCGCAACGACAATACGTAAAATCGCAACGCATATCCGTA
1 AATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTA
1333819 AATCGCAACG
1 AATCGCAACG
1333829 CGATTTTTAA
Statistics
Matches: 211, Mismatches: 33, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
38 1 0.00
39 1 0.00
40 140 0.66
41 68 0.32
42 1 0.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (40 bp):
AATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTA
Found at i:1333685 original size:121 final size:121
Alignment explanation
Indices: 1333537--1333828 Score: 317
Period size: 121 Copynumber: 2.4 Consensus size: 121
1333527 GATTTTCCAT
* * * *
1333537 AATCGCAACG-CGAATATG-AAAATCGCAACGCG-AACATATAAATCGCAACGCGAACATATAAA
1 AATCGCAACGAC-AATACGTAAAATCGCAACGCGTAAC-CATAAATCGCAACGAGAACACATAAA
* * * * * *
1333599 TCGCAACGCG-ATTCTG-ACTATCGCAACGAGTATCCGTAAATCGCAACGAC-AATGCGTA
64 CCGCAACACGTA-TCTGTA-AATCGCAACGAGAATACGTAAATCGCAACG-CGAATCCGTA
* * * *
1333657 AATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAACC
1 AATCGCAACGACAATACGTAAAATCGCAACGCGTAACCATAAATCGCAACGAGAACACATAAACC
* * *
1333722 GCAACACGTATCTGTAAATCGCAACGAGAATACGTAAATCGTAATGCGTATCCGTA
66 GCAACACGTATCTGTAAATCGCAACGAGAATACGTAAATCGCAACGCGAATCCGTA
* * *
1333778 AATCGCAACGACAATACGTAAAATCGCAACGCATATCCGTAAATCGCAACG
1 AATCGCAACGACAATACGTAAAATCGCAACGCGTAACCATAAATCGCAACG
1333829 CGATTTTTAA
Statistics
Matches: 148, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
120 16 0.11
121 128 0.86
122 4 0.03
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (121 bp):
AATCGCAACGACAATACGTAAAATCGCAACGCGTAACCATAAATCGCAACGAGAACACATAAACC
GCAACACGTATCTGTAAATCGCAACGAGAATACGTAAATCGCAACGCGAATCCGTA
Found at i:1334386 original size:20 final size:20
Alignment explanation
Indices: 1334361--1334452 Score: 89
Period size: 20 Copynumber: 4.6 Consensus size: 20
1334351 TTCTAAACTT
*
1334361 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
*
1334381 AAAATCGCAACACAAAAATG
1 AAAATCGCAACACGAAAATG
** *
1334401 ACTATCGCAACGA-GAGAAATT
1 AAAATCGCAAC-ACGA-AAATG
*
1334422 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
*
1334441 AAAATTGCAACA
1 AAAATCGCAACA
1334453 AGATAATCGC
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
19 14 0.25
20 28 0.49
21 15 0.26
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:1334561 original size:52 final size:52
Alignment explanation
Indices: 1334478--1334615 Score: 186
Period size: 52 Copynumber: 2.6 Consensus size: 52
1334468 GAAACCAAAA
* **
1334478 TCGCATTGCGATTTTCATTTCGCGTTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCTCGTTGCGATAGTCATT
* *
1334530 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCTCGTTGTGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCTCGTTGCGATAGTCATT
** *
1334582 TCCGCGTTGCGATAGTCATTCTCTCGTTGCGATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATT
1334616 TTCATTTCAA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
52 48 0.63
53 16 0.21
54 12 0.16
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (52 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCTCGTTGCGATAGTCATT
Found at i:1334620 original size:20 final size:19
Alignment explanation
Indices: 1334478--1334623 Score: 132
Period size: 19 Copynumber: 8.1 Consensus size: 19
1334468 GAAACCAAAA
*
1334478 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1334497 TCGCGTTGCGA--TT-A--
1 TCGCGTTGCGATTTTCATT
*
1334511 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1334530 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1334549 TCGCGTTGCGATTTTC---
1 TCGCGTTGCGATTTTCATT
* **
1334565 T--CGTTGTGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
1334582 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
1334602 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1334622 TC
1 TC
1334624 AACCAAAAGA
Statistics
Matches: 105, Mismatches: 10, Indels: 24
0.76 0.07 0.17
Matches are distributed among these distances:
14 20 0.19
16 4 0.04
17 4 0.04
19 46 0.44
20 30 0.29
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1335954 original size:21 final size:20
Alignment explanation
Indices: 1335883--1335955 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
1335873 CTCCACTTCG
1335883 AGAGCCATCACCTCAC--CC
1 AGAGCCATCACCTCACAACC
*
1335901 AGAGCCATCACCTGATCAACC
1 AGAGCCATCACCTCA-CAACC
* * *
1335922 CGA-CTATACACCTCTACAACG
1 AGAGCCAT-CACCTC-ACAACC
1335943 AGAGCCATCACCT
1 AGAGCCATCACCT
1335956 ATCCCCGTCA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
18 14 0.33
19 1 0.02
20 3 0.07
21 20 0.48
22 4 0.10
ACGTcount: A:0.32, C:0.41, G:0.12, T:0.15
Consensus pattern (20 bp):
AGAGCCATCACCTCACAACC
Found at i:1337946 original size:14 final size:14
Alignment explanation
Indices: 1337927--1337962 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1337917 ATTGTTTAAT
1337927 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1337941 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1337955 TGATTTGT
1 TGATTTGT
1337963 TTAATTAATG
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1338125 original size:19 final size:19
Alignment explanation
Indices: 1338073--1338153 Score: 68
Period size: 19 Copynumber: 4.5 Consensus size: 19
1338063 ATGACTATCA
*
1338073 CAATACGAAATGAAAATCG
1 CAATGCGAAATGAAAATCG
*
1338092 CAA--CG--A-GAGAATCG
1 CAATGCGAAATGAAAATCG
1338106 CAATGCGAAATGAAAATCG
1 CAATGCGAAATGAAAATCG
1338125 C-ATCGCGAAACT-AAAATCG
1 CAAT-GCGAAA-TGAAAATCG
*
1338144 CAACGCGAAA
1 CAATGCGAAA
1338154 CTAAATTCGC
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 3 0.06
19 31 0.61
20 2 0.04
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (19 bp):
CAATGCGAAATGAAAATCG
Found at i:1338170 original size:19 final size:19
Alignment explanation
Indices: 1338101--1338163 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
1338091 GCAACGAGAG
*
1338101 AATCGCAATGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
*
1338120 AATCGCATCGCGAAACTAA
1 AATCGCAACGCGAAACTAA
1338139 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
1338158 ATTCGC
1 AATCGC
1338164 GTTGCGATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 38 0.97
20 1 0.03
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.16
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:1338205 original size:33 final size:33
Alignment explanation
Indices: 1338163--1338362 Score: 231
Period size: 33 Copynumber: 5.8 Consensus size: 33
1338153 ACTAAATTCG
* *
1338163 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1338196 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
1338229 CGTTGCGATTTTCATTTTGCATTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CT
* * * *
1338268 CGTTGCGATTTT-AGTTTCACGTTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
*
1338301 CGTTGTGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1338334 CGTTGCGATTTTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
1338363 AGACATTAAG
Statistics
Matches: 141, Mismatches: 17, Indels: 17
0.81 0.10 0.10
Matches are distributed among these distances:
33 100 0.71
34 12 0.09
35 2 0.01
37 1 0.01
38 2 0.01
39 24 0.17
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1338304 original size:105 final size:106
Alignment explanation
Indices: 1338161--1338369 Score: 314
Period size: 105 Copynumber: 2.0 Consensus size: 106
1338151 AAACTAAATT
* *
1338161 CGCGTTGCGATTTTCATTTCGCTTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTC
1 CGCGTTGCGATTTTCATTTCACGTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTC
* *
1338226 TCTCGTTGCGATTTTCATTT-TGCATTGCGATAGTCATTTC
66 TCTCGTTGCGATTTTCATTTCCGCATTGCGATAGACATTTC
*** *
1338266 CGCGTTGCGATTTT-AGTTTCACGTTGCGATTTTGTCGTTGTGATTTTCATTTCGCATTGCGATT
1 CGCGTTGCGATTTTCA-TTTCACGTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATT
*
1338330 CTCTCGTTGCGATTTTCATTTCCGCGTTGCGATAGACATT
65 CTCTCGTTGCGATTTTCATTTCCGCATTGCGATAGACATT
1338370 AAGATGATTG
Statistics
Matches: 93, Mismatches: 9, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
104 1 0.01
105 77 0.83
106 15 0.16
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (106 bp):
CGCGTTGCGATTTTCATTTCACGTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTC
TCTCGTTGCGATTTTCATTTCCGCATTGCGATAGACATTTC
Found at i:1340913 original size:24 final size:24
Alignment explanation
Indices: 1340879--1340932 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1340869 CTGAAAAATC
1340879 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1340903 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1340927 ATCAAA
1 ATCAAA
1340933 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1340946 original size:24 final size:24
Alignment explanation
Indices: 1340879--1340946 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1340869 CTGAAAAATC
* * *
1340879 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1340903 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1340927 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1340947 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1341802 original size:19 final size:19
Alignment explanation
Indices: 1341778--1341831 Score: 108
Period size: 19 Copynumber: 2.8 Consensus size: 19
1341768 ATTCAGTATT
1341778 GCGATTACGTATTCGCAAC
1 GCGATTACGTATTCGCAAC
1341797 GCGATTACGTATTCGCAAC
1 GCGATTACGTATTCGCAAC
1341816 GCGATTACGTATTCGC
1 GCGATTACGTATTCGC
1341832 GTTGCGATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (19 bp):
GCGATTACGTATTCGCAAC
Found at i:1341838 original size:19 final size:19
Alignment explanation
Indices: 1341775--1341840 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 19
1341765 GAAATTCAGT
1341775 ATTGCGATTACGTATTCGC
1 ATTGCGATTACGTATTCGC
**
1341794 AACGCGATTACGTATTCGC
1 ATTGCGATTACGTATTCGC
**
1341813 AACGCGATTACGTATTCGC
1 ATTGCGATTACGTATTCGC
*
1341832 GTTGCGATT
1 ATTGCGATT
1341841 TACCAAATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (19 bp):
ATTGCGATTACGTATTCGC
Found at i:1342153 original size:2 final size:2
Alignment explanation
Indices: 1342146--1342177 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1342136 TGATTTTTGA
1342146 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1342178 GTTTTTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1342177 original size:51 final size:51
Alignment explanation
Indices: 1342066--1342214 Score: 225
Period size: 51 Copynumber: 3.0 Consensus size: 51
1342056 TTATTTTCTC
1342066 TATATTATATAGTTTTGAAAATGATTTTTGAATATATATA-AATATATATA
1 TATATTATATAGTTTTGAAAATGATTTTTGAATATATATATAATATATATA
*
1342116 TATATTATATAG-TTTGCAAATGATTTTTGAATATATATATATATATATATA
1 TATATTATATAGTTTTGAAAATGATTTTTGAATATATATATA-ATATATATA
* *
1342167 TATATAATATAGTTTTTGAAAAT-A-TTTTGAAAATATATATAATATATA
1 TATATTATATAG-TTTTGAAAATGATTTTTGAATATATATATAATATATA
1342215 GTTTTTGAAA
Statistics
Matches: 91, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
49 26 0.29
50 20 0.22
51 36 0.40
52 1 0.01
53 8 0.09
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (51 bp):
TATATTATATAGTTTTGAAAATGATTTTTGAATATATATATAATATATATA
Found at i:1342310 original size:34 final size:35
Alignment explanation
Indices: 1342165--1342466 Score: 279
Period size: 35 Copynumber: 8.5 Consensus size: 35
1342155 TATATATATA
*
1342165 TATATATAATATAGTTTTTGAAAATATTTTGAAAA-T
1 TATATAT-ATATAG-TTTTGAAAACATTTTGAAAACT
*
1342201 ATATATAATATATAGTTTTTGAAAACATTTT-AAATATAT
1 -TATAT-ATATATAG-TTTTGAAAACATTTTGAAA-A-CT
*
1342240 ATATATAATATATAGTTTTCGAAAACATTTTAAAAACT
1 -TATAT-ATATATAGTTTT-GAAAACATTTTGAAAACT
*
1342278 TATATA-ATATAGTTTTGAAATCATTTTGAAAACT
1 TATATATATATAGTTTTGAAAACATTTTGAAAACT
*
1342312 TATATAATATATAGTTTT--AAACATTTTTGAAAACA
1 TATAT-ATATATAGTTTTGAAAACA-TTTTGAAAACT
1342347 TATATAATATATAG-TTT-AAAACATTTTTGAAAAC-
1 TATAT-ATATATAGTTTTGAAAACA-TTTTGAAAACT
**
1342381 TATATA-ATATA-TTTTGAAAACATTTT-AAAAAA
1 TATATATATATAGTTTTGAAAACATTTTGAAAACT
*
1342413 TATATAATATATAGTTTT-AAAATATTTTTGAAAA-T
1 TATAT-ATATATAGTTTTGAAAACA-TTTTGAAAACT
1342448 ATATATATTATATAGTTTT
1 -TATATA-TATATAGTTTT
1342467 TGTAAATATT
Statistics
Matches: 236, Mismatches: 9, Indels: 41
0.83 0.03 0.14
Matches are distributed among these distances:
31 4 0.02
32 17 0.07
33 8 0.03
34 43 0.18
35 60 0.25
36 34 0.14
37 32 0.14
38 7 0.03
39 28 0.12
40 3 0.01
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (35 bp):
TATATATATATAGTTTTGAAAACATTTTGAAAACT
Found at i:1342461 original size:9 final size:10
Alignment explanation
Indices: 1342446--1342534 Score: 64
Period size: 9 Copynumber: 9.2 Consensus size: 10
1342436 ATTTTTGAAA
1342446 ATATATATATT
1 ATATAT-TATT
*
1342457 ATATAGTTTTT
1 ATATA-TTATT
* *
1342468 GTA-AATATT
1 ATATATTATT
* *
1342477 TTATATTTATA
1 ATATA-TTATT
1342488 ATATATTATT
1 ATATATTATT
1342498 AT-TATTATT
1 ATATATTATT
1342507 AT-TATTATT
1 ATATATTATT
1342516 AT-TATTATT
1 ATATATTATT
1342525 AT-TATT-TT
1 ATATATTATT
1342533 AT
1 AT
1342535 TAACACTTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
8 4 0.06
9 36 0.55
10 8 0.12
11 17 0.26
12 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
ATATATTATT
Found at i:1342481 original size:27 final size:25
Alignment explanation
Indices: 1342437--1342487 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
1342427 TTTTAAAATA
1342437 TTTTTGAAAATATATATATTATATAG
1 TTTTTGAAAATATATATATT-TATAG
* *
1342463 TTTTTGTAAATATTTTATATTTATA
1 TTTTTGAAAATA-TATATATTTATA
1342488 ATATATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (25 bp):
TTTTTGAAAATATATATATTTATAG
Found at i:1342499 original size:3 final size:3
Alignment explanation
Indices: 1342491--1342536 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
1342481 ATTTATAATA
1342491 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1342537 ACACTTTTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1343074 original size:19 final size:19
Alignment explanation
Indices: 1343029--1343067 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1343019 AAACGAATGA
1343029 GCACAGAGGAGCTTTGTCG
1 GCACAGAGGAGCTTTGTCG
1343048 GCACAGAGGAGCTTTGTCG
1 GCACAGAGGAGCTTTGTCG
1343067 G
1 G
1343068 GGCAGAGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.21
Consensus pattern (19 bp):
GCACAGAGGAGCTTTGTCG
Found at i:1345173 original size:5 final size:5
Alignment explanation
Indices: 1345163--1345193 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
1345153 ACTTTCTTCT
1345163 ATTTA ATTTA ATTTA ATTTA ATTTA TATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA -ATTTA
1345194 GAAAATAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATTTA
Found at i:1355102 original size:25 final size:25
Alignment explanation
Indices: 1355073--1355127 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
1355063 ACTGGGTAAC
* * *
1355073 TTGGGGCTTGTTGTGGGCTTTGGGT
1 TTGGGGCTTGTTATGGCCTTCGGGT
1355098 TTGGGGCTTGTTATGGCCTTCGGGT
1 TTGGGGCTTGTTATGGCCTTCGGGT
1355123 TTGGG
1 TTGGG
1355128 TTGGTCGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.02, C:0.11, G:0.45, T:0.42
Consensus pattern (25 bp):
TTGGGGCTTGTTATGGCCTTCGGGT
Found at i:1355193 original size:3 final size:3
Alignment explanation
Indices: 1355185--1355249 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
1355175 TGAAAAAATA
* * * *
1355185 AAT AAT AAT ATT AA- AAT AAT AAT GAT ATT AAT AAT ATT AAT ACAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
*
1355230 AAT AAT AAT AGT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
1355250 AAAAAAGTCT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1355758 original size:133 final size:134
Alignment explanation
Indices: 1355429--1355998 Score: 718
Period size: 133 Copynumber: 4.3 Consensus size: 134
1355419 TCAAGAAATG
* * * * * * * * *
1355429 TTGACTCATTCCACAGTTCTTTAGGGAATACTGAATCGAGGTAGACTTGTTCCACTGTCACTCAA
1 TTGATTCATTCAACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAG
* *
1355494 GGAATATCAAATCTTGAAAGAGATGGACTTGTTCCGCTTCTTCTTGAGGGAAAATTAGATCTGGG
66 GGAATATCAAATCTTGAAAGAGATGGACCTGTTCCGCTTCTTCTTGAGGGAAAATTAGATATGGG
*
1355559 GATA
131 GATT
* * *
1355563 TTGATTAATTCAACCGTTCCTT-AGGGAAGATTGAATCGAGGCAGACTTGTTCCACTATTACTCA
1 TTGATTCATTCAACTGTT-CTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCA
* ** * * *
1355627 GGGAATATCAAATCTTGAAAGAGATTGATTTGTTCCGCTTCTTCTTTAGAGAAAATAAGAT-TGG
65 GGGAATATCAAATCTTGAAAGAGATGGACCTGTTCCGCTTCTTCTTGAGGGAAAATTAGATATGG
1355691 GGATT
130 GGATT
* * *
1355696 TTGATTCATTCAACTATTTTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGCTACTCAG
1 TTGATTCATTCAACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAG
* *
1355761 GGAGTATCAAATCTTGATAGAGATGGACCTGTTCCGCTTCTTCTTGAGGGAAAATTAGATAT-GG
66 GGAATATCAAATCTTGAAAGAGATGGACCTGTTCCGCTTCTTCTTGAGGGAAAATTAGATATGGG
1355825 GATGT
131 GAT-T
** * * *
1355830 TT-ATTCATTCCTCTGTTCTTCAGGGAAGACTGAATCGAAGCAGACTTGTTCCACTGTTACTTAG
1 TTGATTCATTCAACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAG
* * * * *
1355894 GGAATATCAAATCTTCAAAGAGATGGATCTGTTCCACTTCTTCTTGAGGGAATATCAGATATGGG
66 GGAATATCAAATCTTGAAAGAGATGGACCTGTTCCGCTTCTTCTTGAGGGAAAATTAGATATGGG
**
1355959 GACG
131 GATT
* *
1355963 TTGATTCATTTC-ACTGTTCATCAAGGAAGATTGAAT
1 TTGATTCA-TTCAACTGTTCTTCAGGGAAGATTGAAT
1355999 TGAGTTCGAT
Statistics
Matches: 378, Mismatches: 51, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
132 2 0.01
133 231 0.61
134 139 0.37
135 6 0.02
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (134 bp):
TTGATTCATTCAACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAG
GGAATATCAAATCTTGAAAGAGATGGACCTGTTCCGCTTCTTCTTGAGGGAAAATTAGATATGGG
GATT
Found at i:1355969 original size:267 final size:267
Alignment explanation
Indices: 1355451--1355998 Score: 744
Period size: 267 Copynumber: 2.1 Consensus size: 267
1355441 ACAGTTCTTT
* * *
1355451 AGGGAATACTGAATCGAGGTAGACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGAAAGAG
1 AGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGAAAGAG
* *
1355516 ATGGACTTGTTCCGCTTCTTCTTGAGGGAAAATTAGATCTGGGGATATTGATTAATTCAACCGTT
66 ATGGACCTGTTCCGCTTCTTCTTGAGGGAAAATTAGATATGGGGATATTGATTAATTCAACCGTT
* * *
1355581 CCTTAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTATTACTCAGGGAATATCAAATCTTGAA
131 CCTTAGGGAAGACTGAATCGAAGCAGACTTGTTCCACTATTACTCAGGGAATATCAAATCTTCAA
* * * * **
1355646 AGAGATTGATTTGTTCCGCTTCTTCTTTAGAGAAAATAAGATTGGGGATTTTGATTCA-TTCAAC
196 AGAGATGGATCTGTTCCACTTCTTCTTGAGAGAAAATAAGATTGGGGACGTTGATTCATTTC-AC
**
1355710 TATTTTTC
260 TATTCATC
* * *
1355718 AGGGAAGATTGAATCGAGGCAGACTTGTTCCACTG-CTACTCAGGGAGTATCAAATCTTGATAGA
1 AGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTC-ACTCAAGGAATATCAAATCTTGAAAGA
* * * ** *
1355782 GATGGACCTGTTCCGCTTCTTCTTGAGGGAAAATTAGATAT-GGGATGTTTATTCATTCCTCTGT
65 GATGGACCTGTTCCGCTTCTTCTTGAGGGAAAATTAGATATGGGGATATTGATTAATTCAACCGT
* *
1355846 T-CTTCAGGGAAGACTGAATCGAAGCAGACTTGTTCCACTGTTACTTAGGGAATATCAAATCTTC
130 TCCTT-AGGGAAGACTGAATCGAAGCAGACTTGTTCCACTATTACTCAGGGAATATCAAATCTTC
* * *
1355910 AAAGAGATGGATCTGTTCCACTTCTTCTTGAGGGAATATCAGATATGGGGACGTTGATTCATTTC
194 AAAGAGATGGATCTGTTCCACTTCTTCTTGAGAGAAAATAAGAT-TGGGGACGTTGATTCATTTC
*
1355975 ACTGTTCATC
258 ACTATTCATC
*
1355985 AAGGAAGATTGAAT
1 AGGGAAGATTGAAT
1355999 TGAGTTCGAT
Statistics
Matches: 245, Mismatches: 32, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
265 3 0.01
266 110 0.45
267 129 0.53
268 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32
Consensus pattern (267 bp):
AGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGAAAGAG
ATGGACCTGTTCCGCTTCTTCTTGAGGGAAAATTAGATATGGGGATATTGATTAATTCAACCGTT
CCTTAGGGAAGACTGAATCGAAGCAGACTTGTTCCACTATTACTCAGGGAATATCAAATCTTCAA
AGAGATGGATCTGTTCCACTTCTTCTTGAGAGAAAATAAGATTGGGGACGTTGATTCATTTCACT
ATTCATC
Found at i:1357172 original size:27 final size:25
Alignment explanation
Indices: 1357142--1357205 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
1357132 TTGAACCCCT
* *
1357142 TTTTTATTTTTTATTCTTTTTTTTCTC
1 TTTTTATTTTCT-TTC-TTTCTTTCTC
*
1357169 TTTTTCATTTTCTTTCTTTCTTTCTT
1 TTTTT-ATTTTCTTTCTTTCTTTCTC
1357195 TATTTTATTTT
1 T-TTTTATTTT
1357206 ATTTTTTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
26 14 0.44
27 12 0.38
28 6 0.19
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (25 bp):
TTTTTATTTTCTTTCTTTCTTTCTC
Found at i:1357179 original size:26 final size:25
Alignment explanation
Indices: 1357150--1357214 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
1357140 CTTTTTTATT
1357150 TTTTATTCTTTTTTTTCTCTT-TTTCA
1 TTTTATT-TTTTTTTTCT-TTATTTCA
* * *
1357176 TTTTCTTTCTTTCTTTCTTTATTTTA
1 TTTTATTT-TTTTTTTCTTTATTTCA
1357202 TTTTATTTTTTTT
1 TTTTATTTTTTTT
1357215 CATTTTTCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
25 7 0.22
26 25 0.78
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (25 bp):
TTTTATTTTTTTTTTCTTTATTTCA
Found at i:1372358 original size:3 final size:3
Alignment explanation
Indices: 1372350--1372402 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
1372340 TACTTTACCC
1372350 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1372397 TAA TAA
1 TAA TAA
1372403 AAAAGGTCTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1373217 original size:22 final size:22
Alignment explanation
Indices: 1373189--1373233 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1373179 GTTTTGGCAA
1373189 ACCATATTTTAAGTGAAAAAAG
1 ACCATATTTTAAGTGAAAAAAG
1373211 ACCATATTTTAAGTGAAAAAAG
1 ACCATATTTTAAGTGAAAAAAG
1373233 A
1 A
1373234 AGATTATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.27
Consensus pattern (22 bp):
ACCATATTTTAAGTGAAAAAAG
Found at i:1375932 original size:35 final size:34
Alignment explanation
Indices: 1375880--1376009 Score: 102
Period size: 35 Copynumber: 3.7 Consensus size: 34
1375870 TGAAAGTATT
1375880 AAAATGGTTTTTC-AAGTTTGGTAA-CCAACTTTG
1 AAAATGG-TTTTCAAAGTTTGGTAATCCAACTTTG
****
1375913 AAAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 --AAAATGGTTTTCAAAGTTTGGT-AATCCAACTTTG
****
1375950 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGT-AATCCAACTTTG
*
1375985 AAAAATAGTTTTTCAAAGTTTGGTA
1 -AAAAT-GGTTTTCAAAGTTTGGTA
1376010 GATGTTTGTT
Statistics
Matches: 85, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
34 5 0.06
35 51 0.60
36 8 0.09
37 21 0.25
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.42
Consensus pattern (34 bp):
AAAATGGTTTTCAAAGTTTGGTAATCCAACTTTG
Found at i:1375940 original size:21 final size:21
Alignment explanation
Indices: 1375916--1375976 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1375906 AACTTTGAAA
1375916 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1375937 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
1375951 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
1375972 AAATG
1 AAATG
1375977 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:1376007 original size:37 final size:37
Alignment explanation
Indices: 1375908--1376026 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
1375898 TGGTAACCAA
1375908 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
1375945 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
1375980 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
1376017 -GTTGAAAAAT
1 CTTTGAAAAAT
1376027 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1380539 original size:21 final size:21
Alignment explanation
Indices: 1380515--1380575 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1380505 AACTTTGAAA
1380515 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1380536 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
1380550 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
1380571 AAATG
1 AAATG
1380576 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:1380606 original size:37 final size:37
Alignment explanation
Indices: 1380507--1380625 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
1380497 TGGTAACCAA
1380507 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
1380544 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
1380579 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
1380616 -GTTGAAAAAT
1 CTTTGAAAAAT
1380626 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1388213 original size:3 final size:3
Alignment explanation
Indices: 1388207--1388262 Score: 89
Period size: 3 Copynumber: 19.3 Consensus size: 3
1388197 AAAATATTAA
*
1388207 ATT ATT A-T ATT A-G ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1388253 ATT ATT ATT A
1 ATT ATT ATT A
1388263 ATTTACATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 3 0.06
3 46 0.94
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1393761 original size:12 final size:12
Alignment explanation
Indices: 1393746--1393797 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
1393736 ATCAAAGAAG
1393746 AGAAAAAAACAA
1 AGAAAAAAACAA
1393758 AG---AAAACAA
1 AGAAAAAAACAA
*
1393767 AGAAAAAATCAA
1 AGAAAAAAACAA
*
1393779 AGAAAAAATCAA
1 AGAAAAAAACAA
1393791 AGAAAAA
1 AGAAAAA
1393798 GAATAAAAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
9 9 0.25
12 27 0.75
ACGTcount: A:0.79, C:0.08, G:0.10, T:0.04
Consensus pattern (12 bp):
AGAAAAAAACAA
Found at i:1394883 original size:32 final size:32
Alignment explanation
Indices: 1394841--1394904 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1394831 AAGAAACGAT
*
1394841 GAATGATGGGGCATCTTT-GGAGATTCAACATC
1 GAATGATGGGGCATCTTTAAG-GATTCAACATC
*
1394873 GAATGTTGGGGCATCTTTAAGGATTCAACATC
1 GAATGATGGGGCATCTTTAAGGATTCAACATC
1394905 CTGATATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (32 bp):
GAATGATGGGGCATCTTTAAGGATTCAACATC
Found at i:1395066 original size:61 final size:61
Alignment explanation
Indices: 1394994--1395122 Score: 161
Period size: 61 Copynumber: 2.1 Consensus size: 61
1394984 GTTTTCTTAA
* * * ** *
1394994 AAAC-AAATTTTGTCTCTCGAGATAGTTTCTTTTGAAAAATCTTTGAGTATGTTTCTCTGG
1 AAACAAAATTTTGTATCTCGAGACAATTTCTTTAAAAAAATCTTTGAGTATGTTTCCCTGG
* * * *
1395054 AAACAAAATTTTGTATCTTGAGACAATTTGTTTAAAAAAATCTTTGAGTCTGTTTCCCTTG
1 AAACAAAATTTTGTATCTCGAGACAATTTCTTTAAAAAAATCTTTGAGTATGTTTCCCTGG
1395115 AAACAAAA
1 AAACAAAA
1395123 CAAACATCTT
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
60 4 0.07
61 54 0.93
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (61 bp):
AAACAAAATTTTGTATCTCGAGACAATTTCTTTAAAAAAATCTTTGAGTATGTTTCCCTGG
Found at i:1395347 original size:39 final size:40
Alignment explanation
Indices: 1395244--1395353 Score: 132
Period size: 39 Copynumber: 2.8 Consensus size: 40
1395234 TGGTCTGCCA
* * *
1395244 TCCTCATCAAGTAGGAACCTTGTCATCCCCTGACCAGACC
1 TCCTCATCAAGTAAGAACCATGTCATCCCCTCACCAGACC
* ** *
1395284 TCCTCATCACGTAAGAGTCGTGTCATCCCC-CACCAGACC
1 TCCTCATCAAGTAAGAACCATGTCATCCCCTCACCAGACC
* *
1395323 TCCTCATCATGTAAGAACCATGTCAACCCCT
1 TCCTCATCAAGTAAGAACCATGTCATCCCCT
1395354 AGATAACCAG
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 33 0.57
40 25 0.43
ACGTcount: A:0.25, C:0.38, G:0.14, T:0.23
Consensus pattern (40 bp):
TCCTCATCAAGTAAGAACCATGTCATCCCCTCACCAGACC
Found at i:1395473 original size:48 final size:48
Alignment explanation
Indices: 1395364--1395482 Score: 123
Period size: 51 Copynumber: 2.4 Consensus size: 48
1395354 AGATAACCAG
* * *
1395364 CCATCCTCATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGACCTA
1 CCATCCTCATCATGTAGGAACCGTGTTATCA--C-TCATAAAGATGACATA
* *
1395415 CCGTCCTCATCATGTAGGAACCGTGTTATCA-TCAATAAAGATGACATG
1 CCATCCTCATCATGTAGGAACCGTGTTATCACTC-ATAAAGATGACATA
* * *
1395463 TCATCCTCATCGTATAGGAA
1 CCATCCTCATCATGTAGGAA
1395483 TTGTGTCATC
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
47 2 0.03
48 27 0.47
51 29 0.50
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (48 bp):
CCATCCTCATCATGTAGGAACCGTGTTATCACTCATAAAGATGACATA
Found at i:1395653 original size:40 final size:40
Alignment explanation
Indices: 1395598--1395707 Score: 114
Period size: 43 Copynumber: 2.7 Consensus size: 40
1395588 AGATGGCCAG
* *
1395598 ATCTCTTCATTACGTATGAGCCGTGTCATCC-ACTGACCAA
1 ATCTCTTCATCACGTATGAGCCGTGTCACCCTAC-GACCAA
* * * *
1395638 ATCTCCTCATCACGTAGGAGCCATGTCACCCTTAGACGACCAG
1 ATCTCTTCATCACGTATGAGCCGTGTCACCC-T--ACGACCAA
*
1395681 ACCTCTTCATCACGTATGAGCCGTGTC
1 ATCTCTTCATCACGTATGAGCCGTGTC
1395708 GTCCCACAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
40 26 0.46
43 28 0.50
44 2 0.04
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (40 bp):
ATCTCTTCATCACGTATGAGCCGTGTCACCCTACGACCAA
Found at i:1400114 original size:16 final size:16
Alignment explanation
Indices: 1400093--1400124 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1400083 ACTTTAATAA
1400093 TTTCTAACGACTAACT
1 TTTCTAACGACTAACT
1400109 TTTCTAACGACTAACT
1 TTTCTAACGACTAACT
1400125 ACTAACTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (16 bp):
TTTCTAACGACTAACT
Found at i:1400330 original size:29 final size:31
Alignment explanation
Indices: 1400269--1400326 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
1400259 CGATTGTTTA
1400269 TTTTCTATTATTTACATTTCAACACTTTAAT
1 TTTTCTATTATTTACATTTCAACACTTTAAT
* *
1400300 TTTTGTATT-TTTA-ATTTCTAC-CTTTAA
1 TTTTCTATTATTTACATTTCAACACTTTAA
1400327 ATTTCAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.24
29 7 0.28
30 4 0.16
31 8 0.32
ACGTcount: A:0.26, C:0.14, G:0.02, T:0.59
Consensus pattern (31 bp):
TTTTCTATTATTTACATTTCAACACTTTAAT
Found at i:1400359 original size:15 final size:15
Alignment explanation
Indices: 1400336--1400398 Score: 67
Period size: 15 Copynumber: 4.3 Consensus size: 15
1400326 AATTTCAACA
*
1400336 TTTACATTTGAGTCT
1 TTTAAATTTGAGTCT
* *
1400351 TTTAAATTTGA-ACA
1 TTTAAATTTGAGTCT
*
1400365 TTTACATTTGAGTCT
1 TTTAAATTTGAGTCT
*
1400380 TTTAAATTTCAG-CT
1 TTTAAATTTGAGTCT
1400394 TTTAA
1 TTTAA
1400399 TTTTTTGCAC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 18 0.46
15 21 0.54
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.51
Consensus pattern (15 bp):
TTTAAATTTGAGTCT
Found at i:1400397 original size:14 final size:14
Alignment explanation
Indices: 1400322--1400398 Score: 64
Period size: 14 Copynumber: 5.4 Consensus size: 14
1400312 AATTTCTACC
* * *
1400322 TTTAAATTTCAACA
1 TTTAAATTTGAGCT
*
1400336 TTTACATTTGAGTCT
1 TTTAAATTTGAG-CT
* *
1400351 TTTAAATTTGAACA
1 TTTAAATTTGAGCT
*
1400365 TTTACATTTGAGTCT
1 TTTAAATTTGAG-CT
*
1400380 TTTAAATTTCAGCT
1 TTTAAATTTGAGCT
1400394 TTTAA
1 TTTAA
1400399 TTTTTTGCAC
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
14 27 0.55
15 22 0.45
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (14 bp):
TTTAAATTTGAGCT
Found at i:1400397 original size:29 final size:29
Alignment explanation
Indices: 1400322--1400390 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
1400312 AATTTCTACC
1400322 TTTAAATTTCAACATTTACATTTGAGTCT
1 TTTAAATTTCAACATTTACATTTGAGTCT
*
1400351 TTTAAATTTGAACATTTACATTTGAGTCT
1 TTTAAATTTCAACATTTACATTTGAGTCT
1400380 TTTAAATTTCA
1 TTTAAATTTCA
1400391 GCTTTTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (29 bp):
TTTAAATTTCAACATTTACATTTGAGTCT
Found at i:1405625 original size:20 final size:21
Alignment explanation
Indices: 1405589--1405627 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1405579 AATTTTTTAA
*
1405589 AAAAGAGAAAAATAAAAAAAT
1 AAAAGAGAAAAAGAAAAAAAT
1405610 AAAA-AGAAAAAGAAAAAA
1 AAAAGAGAAAAAGAAAAAA
1405628 TGTTGTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (21 bp):
AAAAGAGAAAAAGAAAAAAAT
Found at i:1408786 original size:21 final size:21
Alignment explanation
Indices: 1408761--1408800 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1408751 AACTTGCATA
1408761 GGGGTATCGGTACCCTATGAG
1 GGGGTATCGGTACCCTATGAG
*
1408782 GGGGTATCGGTACTCTATG
1 GGGGTATCGGTACCCTATG
1408801 GGCAATCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.38, T:0.28
Consensus pattern (21 bp):
GGGGTATCGGTACCCTATGAG
Found at i:1411398 original size:20 final size:20
Alignment explanation
Indices: 1411373--1411450 Score: 102
Period size: 20 Copynumber: 3.8 Consensus size: 20
1411363 CATAACTGAA
* *
1411373 GGGGGTATCGGTACTCTCAT
1 GGGGGTATCGATACCCTCAT
1411393 GGGGGTATCGATACCCTCAT
1 GGGGGTATCGATACCCTCAT
*
1411413 GGGGGTATCGATACCCATTCAAA
1 GGGGGTATCGATACCC--TC-AT
1411436 GGGGGTATCGATACC
1 GGGGGTATCGATACC
1411451 TAGCACACAG
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
20 34 0.65
22 2 0.04
23 16 0.31
ACGTcount: A:0.22, C:0.22, G:0.32, T:0.24
Consensus pattern (20 bp):
GGGGGTATCGATACCCTCAT
Found at i:1417316 original size:21 final size:21
Alignment explanation
Indices: 1417291--1417330 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1417281 AACTTACATA
1417291 GGGGTATCGGTACCCTATGAG
1 GGGGTATCGGTACCCTATGAG
1417312 GGGGTATCGGTACCCTATG
1 GGGGTATCGGTACCCTATG
1417331 GGCAATCTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.38, T:0.25
Consensus pattern (21 bp):
GGGGTATCGGTACCCTATGAG
Found at i:1422905 original size:31 final size:29
Alignment explanation
Indices: 1422854--1422993 Score: 128
Period size: 27 Copynumber: 4.6 Consensus size: 29
1422844 GCTACACTTG
1422854 AAGAAATAAGAAAAAAAGAGAAAAGAAAAAGA
1 AAGAAA-AAG-AAAAAAGAGAAAAGAAAAA-A
1422886 AAGAAAAATAAGAAAAGAGAGAGAAAATAGAAAAAA
1 AAG--AAA-AAGAAAA-A-AGAG-AAA-AGAAAAAA
*
1422922 AAGGAAAAAGGAAAAAG-G-AAA-AAAAAA
1 AA-GAAAAAGAAAAAAGAGAAAAGAAAAAA
*
1422949 AA-AAAAA-AAAAAAGAAAAAAGAAAAAA
1 AAGAAAAAGAAAAAAGAGAAAAGAAAAAA
1422976 AAGAAAAAGAAAAAAGAG
1 AAGAAAAAGAAAAAAGAG
1422994 GGTTCAAGAT
Statistics
Matches: 92, Mismatches: 4, Indels: 27
0.75 0.03 0.22
Matches are distributed among these distances:
24 6 0.07
25 5 0.05
26 3 0.03
27 16 0.17
28 6 0.07
29 10 0.11
31 1 0.01
32 5 0.05
33 5 0.05
34 14 0.15
35 7 0.08
36 6 0.07
37 8 0.09
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (29 bp):
AAGAAAAAGAAAAAAGAGAAAAGAAAAAA
Found at i:1422912 original size:20 final size:19
Alignment explanation
Indices: 1422857--1422983 Score: 87
Period size: 17 Copynumber: 7.2 Consensus size: 19
1422847 ACACTTGAAG
1422857 AAATAAG-AAAA-AAAG-A
1 AAATAAGAAAAAGAAAGAA
*
1422873 GAA-AAGAAAAAGAAAGAA
1 AAATAAGAAAAAGAAAGAA
*
1422891 AAATAAG-AAAAGAGAGAGA
1 AAATAAGAAAAAGAAAGA-A
*
1422910 AAAT-AGAAAAA-AAAGGA
1 AAATAAGAAAAAGAAAGAA
* *
1422927 AAA-AGGAAAAAGGAAAAAA
1 AAATAAGAAAAA-GAAAGAA
* * *
1422946 AAAAAAAAAAAAAAAAG-A
1 AAATAAGAAAAAGAAAGAA
1422964 AAA-AAGAAAAA-AAAGAA
1 AAATAAGAAAAAGAAAGAA
1422981 AAA
1 AAA
1422984 GAAAAAAGAG
Statistics
Matches: 87, Mismatches: 13, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
15 3 0.03
16 10 0.11
17 25 0.29
18 21 0.24
19 22 0.25
20 6 0.07
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (19 bp):
AAATAAGAAAAAGAAAGAA
Found at i:1422929 original size:7 final size:7
Alignment explanation
Indices: 1422854--1422992 Score: 92
Period size: 7 Copynumber: 19.6 Consensus size: 7
1422844 GCTACACTTG
*
1422854 AAGAAAT
1 AAGAAAA
1422861 AAGAAAAA
1 AAG-AAAA
*
1422869 AAGAGAA
1 AAGAAAA
1422876 AAG-AAA
1 AAGAAAA
*
1422882 AAGAAAG
1 AAGAAAA
*
1422889 AA-AAAT
1 AAGAAAA
1422895 AAGAAAA
1 AAGAAAA
1422902 GAGAGAGAAA
1 -A-AGA-AAA
1422912 ATAGAAAAAA
1 A-AG--AAAA
*
1422922 AAGGAAA
1 AAGAAAA
*
1422929 AAGGAAA
1 AAGAAAA
*
1422936 AAG-GAA
1 AAGAAAA
1422942 AA-AAAA
1 AAGAAAA
1422948 AA-AAAA
1 AAGAAAA
1422954 AA-AAAA
1 AAGAAAA
1422960 AAGAAAA
1 AAGAAAA
1422967 AAGAAAA
1 AAGAAAA
*
1422974 AAAAGAAA
1 AAGA-AAA
1422982 AAGAAAA
1 AAGAAAA
1422989 AAGA
1 AAGA
1422993 GGGTTCAAGA
Statistics
Matches: 109, Mismatches: 12, Indels: 22
0.76 0.08 0.15
Matches are distributed among these distances:
6 30 0.28
7 50 0.46
8 13 0.12
9 8 0.07
10 7 0.06
11 1 0.01
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (7 bp):
AAGAAAA
Found at i:1422944 original size:1 final size:1
Alignment explanation
Indices: 1422940--1422990 Score: 66
Period size: 1 Copynumber: 51.0 Consensus size: 1
1422930 AGGAAAAAGG
* * * *
1422940 AAAAAAAAAAAAAAAAAAAAAAGAAAAAAGAAAAAAAAGAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1422991 GAGGGTTCAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:1422947 original size:54 final size:54
Alignment explanation
Indices: 1422854--1422991 Score: 158
Period size: 54 Copynumber: 2.6 Consensus size: 54
1422844 GCTACACTTG
* * * * *
1422854 AAGAAATAAG-AAAAAAAGAGAAAA-GAAAAA-GAAAGAAAAATAAGAAAAGAGA
1 AAGAAAAAAGAAAAAAAAGA-AAAAGGAAAAAGGAAAGAAAAAAAAAAAAAAAAA
* *
1422906 GAGAAAATAGAAAAAAAAGGAAAAAGGAAAAAGGAAA-AAAAAAAAAAAAAAAAA
1 AAGAAAAAAGAAAAAAAA-GAAAAAGGAAAAAGGAAAGAAAAAAAAAAAAAAAAA
*
1422960 AAGAAAAAAGAAAAAAAAGAAAAAGAAAAAAG
1 AAGAAAAAAGAAAAAAAAGAAAAAGGAAAAAG
1422992 AGGGTTCAAG
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
52 7 0.10
53 24 0.33
54 37 0.51
55 4 0.06
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (54 bp):
AAGAAAAAAGAAAAAAAAGAAAAAGGAAAAAGGAAAGAAAAAAAAAAAAAAAAA
Found at i:1422982 original size:9 final size:9
Alignment explanation
Indices: 1422874--1422983 Score: 91
Period size: 9 Copynumber: 12.1 Consensus size: 9
1422864 AAAAAAAGAG
1422874 AAAAGAAAA
1 AAAAGAAAA
1422883 AGAAAGAAAA
1 A-AAAGAAAA
*
1422893 ATAAGAAAA
1 AAAAGAAAA
* * *
1422902 GAGAGAGAA
1 AAAAGAAAA
*
1422911 AATAGAAAA
1 AAAAGAAAA
*
1422920 AAAAG-GAA
1 AAAAGAAAA
*
1422928 AAAGGAAAA
1 AAAAGAAAA
1422937 AGGAAA-AAAA
1 A--AAAGAAAA
1422947 AAAA-AAAA
1 AAAAGAAAA
*
1422955 AAAAAAAGAA
1 AAAAGAA-AA
1422965 AAAAGAAAA
1 AAAAGAAAA
1422974 AAAAGAAAA
1 AAAAGAAAA
1422983 A
1 A
1422984 GAAAAAAGAG
Statistics
Matches: 81, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
8 17 0.21
9 40 0.49
10 22 0.27
11 2 0.02
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:1430622 original size:23 final size:23
Alignment explanation
Indices: 1430571--1430622 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
1430561 ATCGATACCG
* *
1430571 CCTTGCATGGGTACCGATTCCCA
1 CCTTGAATGGGTACCAATTCCCA
* *
1430594 CTTTGAATGGGTACCAATTCCCC
1 CCTTGAATGGGTACCAATTCCCA
1430617 CCTTGA
1 CCTTGA
1430623 GGGACGGATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.19, C:0.33, G:0.19, T:0.29
Consensus pattern (23 bp):
CCTTGAATGGGTACCAATTCCCA
Found at i:1435201 original size:36 final size:32
Alignment explanation
Indices: 1435137--1435197 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
1435127 ATTTAGATAC
1435137 ATTTGATTGCATGCATATCTTCATAAATAGAT
1 ATTTGATTGCATGCATATCTTCATAAATAGAT
1435169 ATTTGATTGCATGCATATCTTCATAAATA
1 ATTTGATTGCATGCATATCTTCATAAATA
1435198 AATACTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.41
Consensus pattern (32 bp):
ATTTGATTGCATGCATATCTTCATAAATAGAT
Found at i:1435888 original size:36 final size:36
Alignment explanation
Indices: 1435821--1435890 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
1435811 ATTGGATCCC
* *
1435821 ATCACATAAGGAGGTGGATCAATATTCCCTTTTTAT
1 ATCACATAAAGAGGTGGATCAACATTCCCTTTTTAT
*
1435857 ATCACATAAAGAGTTGGATCAACA-TCACCTTTTT
1 ATCACATAAAGAGGTGGATCAACATTC-CCTTTTT
1435891 GCTCTATTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 2 0.07
36 28 0.93
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (36 bp):
ATCACATAAAGAGGTGGATCAACATTCCCTTTTTAT
Found at i:1436044 original size:44 final size:44
Alignment explanation
Indices: 1435857--1436101 Score: 181
Period size: 44 Copynumber: 5.6 Consensus size: 44
1435847 CCCTTTTTAT
* * * * *
1435857 ATCACATAAAGAGTTGGATCAACATCACCTTTTTGCTCT-ATTCT
1 ATCACAGAAGGAGGTGGATCAACATCAACTTTTTGCT-TGATTCC
* * * * *
1435901 ATCATAGAAGGAGGTAGATCAGCATCGACATTTTG-TTCGATTCC
1 ATCACAGAAGGAGGTGGATCAACATCAACTTTTTGCTT-GATTCC
* * * * ** *
1435945 ATCACAGAAGGAGGTGGATCGACATTATAATTTCT-CTCAAATCC
1 ATCACAGAAGGAGGTGGATCAACATCA-ACTTTTTGCTTGATTCC
* * * * *
1435989 ATCGCATAAGGAGTTGGATCAACATCACCTTTTTGCTTGATTCT
1 ATCACAGAAGGAGGTGGATCAACATCAACTTTTTGCTTGATTCC
* * * * * *
1436033 ATCACAGAAGGAGGTAGATCATCATTAACATTATGTTTGATTCC
1 ATCACAGAAGGAGGTGGATCAACATCAACTTTTTGCTTGATTCC
*
1436077 ATCACAGAAGGAGGTGGATTAACAT
1 ATCACAGAAGGAGGTGGATCAACAT
1436102 TGCCATTTTT
Statistics
Matches: 148, Mismatches: 48, Indels: 10
0.72 0.23 0.05
Matches are distributed among these distances:
42 1 0.01
43 5 0.03
44 137 0.93
45 5 0.03
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (44 bp):
ATCACAGAAGGAGGTGGATCAACATCAACTTTTTGCTTGATTCC
Found at i:1436102 original size:132 final size:132
Alignment explanation
Indices: 1435861--1436102 Score: 387
Period size: 132 Copynumber: 1.8 Consensus size: 132
1435851 TTTTATATCA
*
1435861 CATAAAGAGTTGGATCAACATCACCTTTTTGCTCTATTCTATCATAGAAGGAGGTAGATCAGCAT
1 CATAAAGAGTTGGATCAACATCACCTTTTTGCTCTATTCTATCACAGAAGGAGGTAGATCAGCAT
* * *
1435926 CGACATTTTGTTCGATTCCATCACAGAAGGAGGTGGATCGACATTATAATTTCTCTCAAATCCAT
66 CAACATTATGTTCGATTCCATCACAGAAGGAGGTGGATCAACATTATAATTTCTCTCAAATCCAT
1435991 CG
131 CG
* *
1435993 CATAAGGAGTTGGATCAACATCACCTTTTTGCT-TGATTCTATCACAGAAGGAGGTAGATCATCA
1 CATAAAGAGTTGGATCAACATCACCTTTTTGCTCT-ATTCTATCACAGAAGGAGGTAGATCAGCA
* * *
1436057 TTAACATTATGTTTGATTCCATCACAGAAGGAGGTGGATTAACATT
65 TCAACATTATGTTCGATTCCATCACAGAAGGAGGTGGATCAACATT
1436103 GCCATTTTTG
Statistics
Matches: 100, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
131 1 0.01
132 99 0.99
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (132 bp):
CATAAAGAGTTGGATCAACATCACCTTTTTGCTCTATTCTATCACAGAAGGAGGTAGATCAGCAT
CAACATTATGTTCGATTCCATCACAGAAGGAGGTGGATCAACATTATAATTTCTCTCAAATCCAT
CG
Found at i:1436360 original size:22 final size:22
Alignment explanation
Indices: 1436335--1436410 Score: 57
Period size: 28 Copynumber: 3.3 Consensus size: 22
1436325 AAGAAAAATT
1436335 GAAAATTGAAAAAATAGAAAGA
1 GAAAATTGAAAAAATAGAAAGA
**
1436357 GAAAAAGGAAAAGAAAATGGGAGAAAGA
1 GAAAATTG--AA-AAAAT---AGAAAGA
*
1436385 GAAAATTGAAAAAACAG-AAGA
1 GAAAATTGAAAAAATAGAAAGA
1436406 -AAAAT
1 GAAAAT
1436411 AAAGTAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
20 5 0.12
21 4 0.09
22 8 0.19
24 2 0.05
25 9 0.21
26 2 0.05
28 13 0.30
ACGTcount: A:0.67, C:0.01, G:0.22, T:0.09
Consensus pattern (22 bp):
GAAAATTGAAAAAATAGAAAGA
Found at i:1437064 original size:9 final size:9
Alignment explanation
Indices: 1437050--1437089 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
1437040 AATTATTATT
1437050 ATATATTAA
1 ATATATTAA
1437059 ATATA-TAA
1 ATATATTAA
1437067 ATA-ATTAA
1 ATATATTAA
1437075 AT-TGATTAA
1 ATAT-ATTAA
1437084 ATATAT
1 ATATAT
1437090 ATATATATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
7 1 0.04
8 11 0.41
9 14 0.52
10 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (9 bp):
ATATATTAA
Found at i:1437158 original size:2 final size:2
Alignment explanation
Indices: 1437151--1437199 Score: 57
Period size: 2 Copynumber: 24.5 Consensus size: 2
1437141 TATACATGTA
*
1437151 AT AT AT AT AT AT AT AT AT AT AT AT AT GA- AT AT AGT CT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A-T AT AT AT AT
1437193 AT AT AT A
1 AT AT AT A
1437200 CATGTAAGCT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 2 0.05
2 37 0.90
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1437981 original size:2 final size:2
Alignment explanation
Indices: 1437974--1438008 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1437964 AGCCTTTTAT
1437974 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1438009 CAACTGAATA
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:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1442701 original size:18 final size:17
Alignment explanation
Indices: 1442672--1442719 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
1442662 GATAGAAGAA
*
1442672 AAAAAAAAAAAAATAAAT
1 AAAAAAAGAAAAAT-AAT
*
1442690 AAAAATAGAAAAATAAT
1 AAAAAAAGAAAAATAAT
1442707 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
1442720 ATGAATGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.85, C:0.00, G:0.04, T:0.10
Consensus pattern (17 bp):
AAAAAAAGAAAAATAAT
Found at i:1442713 original size:11 final size:10
Alignment explanation
Indices: 1442670--1442713 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
1442660 AAGATAGAAG
1442670 AAAAAA-AAA
1 AAAAAATAAA
1442679 AAAAAATAAA
1 AAAAAATAAA
*
1442689 TAAAAATAGAA
1 AAAAAATA-AA
*
1442700 AAATAATAAA
1 AAAAAATAAA
1442710 AAAA
1 AAAA
1442714 GAAAAAATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 6 0.21
10 15 0.52
11 8 0.28
ACGTcount: A:0.86, C:0.00, G:0.02, T:0.11
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:1442720 original size:18 final size:19
Alignment explanation
Indices: 1442671--1442721 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 19
1442661 AGATAGAAGA
*
1442671 AAAAAAAAAAAAAATAAAT
1 AAAAAAAGAAAAAATAAAT
*
1442690 AAAAATAG-AAAAAT-AAT
1 AAAAAAAGAAAAAATAAAT
1442707 AAAAAAAGAAAAAAT
1 AAAAAAAGAAAAAAT
1442722 GAATGAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 10 0.36
18 12 0.43
19 6 0.21
ACGTcount: A:0.84, C:0.00, G:0.04, T:0.12
Consensus pattern (19 bp):
AAAAAAAGAAAAAATAAAT
Done.