Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007790.1 Hibiscus syriacus cultivar Beakdansim tig00110076_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: 2956777
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1427472 original size:28 final size:26
Alignment explanation
Indices: 1427425--1427479 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
1427415 GAAATTGGGG
* * *
1427425 TTTTTTAAAACATAATATTATTTAAA
1 TTTTTTAAAAAATAAAATTATATAAA
1427451 TTTTTTAAAAAAATCAAAATTATATAAA
1 TTTTTT-AAAAAAT-AAAATTATATAAA
1427479 T
1 T
1427480 GAGACATGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.25
27 6 0.25
28 12 0.50
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (26 bp):
TTTTTTAAAAAATAAAATTATATAAA
Found at i:1427683 original size:32 final size:32
Alignment explanation
Indices: 1427642--1427707 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
1427632 ACATTAAGCC
* *
1427642 TAAAAATAAATTATATTATCATTAGTTTAGTT
1 TAAAAATAAATTAAATTAACATTAGTTTAGTT
*
1427674 TAAAAATAAATTAAATTAACTTTAGTTTAGTT
1 TAAAAATAAATTAAATTAACATTAGTTTAGTT
1427706 TA
1 TA
1427708 GAAGTGATAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (32 bp):
TAAAAATAAATTAAATTAACATTAGTTTAGTT
Found at i:1439443 original size:34 final size:34
Alignment explanation
Indices: 1439404--1439472 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
1439394 TGGCAATTGG
* *
1439404 AAGTTTAATAGTTTTTCCATAGCATTTTTACTTT
1 AAGTTTAATAGTTTTGCCATAGAATTTTTACTTT
* *
1439438 AAGTTTAATAGTTTTGCCATATAATTTTTATTTT
1 AAGTTTAATAGTTTTGCCATAGAATTTTTACTTT
1439472 A
1 A
1439473 CTTCTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.54
Consensus pattern (34 bp):
AAGTTTAATAGTTTTGCCATAGAATTTTTACTTT
Found at i:1446635 original size:2 final size:2
Alignment explanation
Indices: 1446628--1446666 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1446618 AAAGTGCATA
1446628 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1446667 CATAAGTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1447760 original size:3 final size:3
Alignment explanation
Indices: 1447744--1447791 Score: 69
Period size: 3 Copynumber: 15.3 Consensus size: 3
1447734 AAATGTAAAC
*
1447744 ATA ATA ATTG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATTA ATA
1 ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
1447791 A
1 A
1447792 GAATTTTTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 36 0.88
4 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1448256 original size:129 final size:129
Alignment explanation
Indices: 1448087--1448447 Score: 399
Period size: 129 Copynumber: 2.8 Consensus size: 129
1448077 TGATAACTTG
* * * * * *
1448087 GTTCCTATGCGATGAGGACGGA-TGGTTAT-TAAAGGTTGACACAGCTCCTACATAATGAGGAAA
1 GTTCCTACGTGATGAGGAC-GACTGGTTATCT-AGGGTTGACACGGCTCCTACGTGATGAGGAAA
* * * * * * *
1448150 TCT-TGTCGGGTGATGATACGGTTCCTACGCGATGAGGATGGCAGGCCATCTAAGGGTGATAACA
64 T-TAGGTCAGATGATGACACAGTTCCTACGCGATAAGGACGGCAGGCCATCTAAGGGTGATAACA
*
1448214 -T
128 CA
* * * *
1448215 GATTCCTACGTGATGAGGATGACTGGTTATCTGGGGTTGACACGGCTCCTACGTGATAAGGAGAT
1 G-TTCCTACGTGATGAGGACGACTGGTTATCTAGGGTTGACACGGCTCCTACGTGATGAGGAAAT
*
1448280 TAGGTCAGATGATGACACAGTTCCTGCGCGATAAGGACGGCAGGCCATCTAAGGGTGATAACACA
65 TAGGTCAGATGATGACACAGTTCCTACGCGATAAGGACGGCAGGCCATCTAAGGGTGATAACACA
* * * *
1448345 GTTCCTACGTGATGAGGACGGCTGGTTATCTAGGGTTGACATGGCTCCTACGTGATGAGGAGATC
1 GTTCCTACGTGATGAGGACGACTGGTTATCTAGGGTTGACACGGCTCCTACGTGATGAGGAAATT
* * * *
1448410 AGGTCAAATGATGACA-TGATTCCTACGCAATGAGGACG
66 AGGTCAGATGATGACACAG-TTCCTACGCGATAAGGACG
1448448 ATAGGTTGGG
Statistics
Matches: 197, Mismatches: 30, Indels: 11
0.83 0.13 0.05
Matches are distributed among these distances:
128 5 0.03
129 190 0.96
130 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (129 bp):
GTTCCTACGTGATGAGGACGACTGGTTATCTAGGGTTGACACGGCTCCTACGTGATGAGGAAATT
AGGTCAGATGATGACACAGTTCCTACGCGATAAGGACGGCAGGCCATCTAAGGGTGATAACACA
Found at i:1448376 original size:46 final size:45
Alignment explanation
Indices: 1448157--1448405 Score: 135
Period size: 46 Copynumber: 5.7 Consensus size: 45
1448147 AAATCTTGTC
* * * *
1448157 GGGTGATGATACGGTTCCTACGCGATGAGGATGGCAGGCCATCTAA
1 GGGTGATGACACAGTTCCTACGTGATGAGGACGGCAGGCCATCT-A
* * * **
1448203 GGGTGAT-A-ACATGATTCCTACGTGATGAGGATGACTGGTTATCT-
1 GGGTGATGACACA-G-TTCCTACGTGATGAGGACGGCAGGCCATCTA
* * * * **
1448247 GGG-GTTGACACGGCTCCTACGTGATAAGGA-GATTAGG---TC-A
1 GGGTGATGACACAGTTCCTACGTGATGAGGACG-GCAGGCCATCTA
* * * *
1448287 -GATGATGACACAGTTCCTGCGCGATAAGGACGGCAGGCCATCTAA
1 GGGTGATGACACAGTTCCTACGTGATGAGGACGGCAGGCCATCT-A
* * **
1448332 GGGTGATAACACAGTTCCTACGTGATGAGGACGGCTGGTTATCTA
1 GGGTGATGACACAGTTCCTACGTGATGAGGACGGCAGGCCATCTA
** *
1448377 GGGT--TGACATGGCTCCTACGTGATGAGGA
1 GGGTGATGACACAGTTCCTACGTGATGAGGA
1448406 GATCAGGTCA
Statistics
Matches: 156, Mismatches: 33, Indels: 31
0.71 0.15 0.14
Matches are distributed among these distances:
39 1 0.01
40 27 0.17
41 1 0.01
42 1 0.01
43 42 0.27
44 7 0.04
45 10 0.06
46 67 0.43
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (45 bp):
GGGTGATGACACAGTTCCTACGTGATGAGGACGGCAGGCCATCTA
Found at i:1448944 original size:35 final size:35
Alignment explanation
Indices: 1448855--1448948 Score: 93
Period size: 35 Copynumber: 2.7 Consensus size: 35
1448845 AATTGTCTCA
* *
1448855 GTTTCAAGAGAAACAAACTCAAAG--ATTTAATTC
1 GTTTCAAGGGAAACAGACTCAAAGATATTTAATTC
* ** * ** *
1448888 ATTTCAAGGGAAATGGTCTCAAAGATATTTGTTTT
1 GTTTCAAGGGAAACAGACTCAAAGATATTTAATTC
1448923 GTTTCAAGGGAAACAGACTCAAAGAT
1 GTTTCAAGGGAAACAGACTCAAAGAT
1448949 GGGTATTTCA
Statistics
Matches: 46, Mismatches: 13, Indels: 2
0.75 0.21 0.03
Matches are distributed among these distances:
33 18 0.39
35 28 0.61
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (35 bp):
GTTTCAAGGGAAACAGACTCAAAGATATTTAATTC
Found at i:1448945 original size:118 final size:119
Alignment explanation
Indices: 1448737--1448973 Score: 440
Period size: 118 Copynumber: 2.0 Consensus size: 119
1448727 AGAAGGTTTT
1448737 GTTTCAAGAGAAACAAACTCAAAGAATTAATTCATTTCAAGGGAAATGGTCTCAAAGATATTTGT
1 GTTTCAAGAGAAACAAACTCAAAGAATTAATTCATTTCAAGGGAAATGGTCTCAAAGATATTTGT
* *
1448802 TTTGTTTCAAGGGCAATAGACTCAAAGAT-GGTATTTCACAAGAAATTGTCTCA
66 TTTGTTTCAAGGGAAACAGACTCAAAGATGGGTATTTCACAAGAAATTGTCTCA
*
1448855 GTTTCAAGAGAAACAAACTCAAAGATTTAATTCATTTCAAGGGAAATGGTCTCAAAGATATTTGT
1 GTTTCAAGAGAAACAAACTCAAAGAATTAATTCATTTCAAGGGAAATGGTCTCAAAGATATTTGT
1448920 TTTGTTTCAAGGGAAACAGACTCAAAGATGGGTATTTCACAAGAAATTGTCTCA
66 TTTGTTTCAAGGGAAACAGACTCAAAGATGGGTATTTCACAAGAAATTGTCTCA
1448974 AAAGAGACAA
Statistics
Matches: 115, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
118 91 0.79
119 24 0.21
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (119 bp):
GTTTCAAGAGAAACAAACTCAAAGAATTAATTCATTTCAAGGGAAATGGTCTCAAAGATATTTGT
TTTGTTTCAAGGGAAACAGACTCAAAGATGGGTATTTCACAAGAAATTGTCTCA
Found at i:1449132 original size:33 final size:32
Alignment explanation
Indices: 1449053--1449134 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
1449043 GAAAATAAGA
* * *
1449053 TTTATTTCAAGAGAAACGCTCTCTAAGATGTT
1 TTTATTTCAAGTGAAACGCACTCAAAGATGTT
* * * * *
1449085 GTTGTTTCCAGTGAAACGGACTCAAAGTTGATT
1 TTTATTTCAAGTGAAACGCACTCAAAGATG-TT
1449118 TTTATTTCAAGTGAAAC
1 TTTATTTCAAGTGAAAC
1449135 AATTTTAGAA
Statistics
Matches: 38, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
32 22 0.58
33 16 0.42
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (32 bp):
TTTATTTCAAGTGAAACGCACTCAAAGATGTT
Found at i:1459734 original size:17 final size:18
Alignment explanation
Indices: 1459712--1459747 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1459702 TCAGACTTTA
*
1459712 ATTTT-GGGATTTATTTT
1 ATTTTGGGGATTTAATTT
1459729 ATTTTGGGGATTTAATTT
1 ATTTTGGGGATTTAATTT
1459747 A
1 A
1459748 AACAATTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.58
Consensus pattern (18 bp):
ATTTTGGGGATTTAATTT
Found at i:1467793 original size:23 final size:23
Alignment explanation
Indices: 1467763--1467838 Score: 152
Period size: 23 Copynumber: 3.3 Consensus size: 23
1467753 TGAGGCCACT
1467763 GTCGTTGTTTCGACGCTCCTCCG
1 GTCGTTGTTTCGACGCTCCTCCG
1467786 GTCGTTGTTTCGACGCTCCTCCG
1 GTCGTTGTTTCGACGCTCCTCCG
1467809 GTCGTTGTTTCGACGCTCCTCCG
1 GTCGTTGTTTCGACGCTCCTCCG
1467832 GTCGTTG
1 GTCGTTG
1467839 AAGTTCTGAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.04, C:0.33, G:0.28, T:0.36
Consensus pattern (23 bp):
GTCGTTGTTTCGACGCTCCTCCG
Found at i:1475511 original size:292 final size:295
Alignment explanation
Indices: 1474964--1475551 Score: 1146
Period size: 292 Copynumber: 2.0 Consensus size: 295
1474954 CCGACACTGA
1474964 TAAGGGTAGTGTTTCCATTCCCTCTCTTTTGCACTAAATTACATTTTAGGATAAAATGACTTAAG
1 TAAGGGTAGTGTTTCCATTCCCTCTCTTTTGCACTAAATTACATTTTAGGATAAAATGACTTAAG
1475029 TGAGGGGGTGGAAGTTGCATCAAATTTACCTTACTTATTCAATTAGTTGGACTTGAATTTTTCTT
66 TGAGGGGGTGGAAGTTGCATCAAATTTACCTTACTTATTCAATTAGTTGGACTTGAATTTTTCTT
*
1475094 GAATTGATGTGTTGAAATAAATTGTTGCGCATCTTAGTTTTGCCATGTTTCTTTGATTTTTCTTG
131 GAATTGATGTGTTGAAATAAATTGTTGCACATCTTAGTTTTGCCATGTTTCTTTGATTTTTCTTG
1475159 TGAATTTTAATCTTTCTTTTGTTGGAACTTATGAAGCATGAAAGAAATAGGCATGATTAATTGGT
196 TGAATTTTAATCTTTCTTTTGTTGGAACTTATGAAGCATGAAAGAAATAGGCATGATTAATTGGT
1475224 TTTTCTTTAAAAAAAAATTGAAATTTCATGCATTT
261 TTTTCTTTAAAAAAAAATTGAAATTTCATGCATTT
1475259 TAAGGGTAGTG-TTCCATT-CC-CTCTTTTGCACTAAATTACATTTTAGGATAAAATGACTTAAG
1 TAAGGGTAGTGTTTCCATTCCCTCTCTTTTGCACTAAATTACATTTTAGGATAAAATGACTTAAG
1475321 TGAGGGGGTGGAAGTTGCATCAAATTTACCTTACTTATTCAATTAGTTGGACTTGAATTTTTCTT
66 TGAGGGGGTGGAAGTTGCATCAAATTTACCTTACTTATTCAATTAGTTGGACTTGAATTTTTCTT
1475386 GAATTGATGTGTTGAAATAAATTGTTGCACATCTTAGTTTTGCCATGTTTCTTTGATTTTTCTTG
131 GAATTGATGTGTTGAAATAAATTGTTGCACATCTTAGTTTTGCCATGTTTCTTTGATTTTTCTTG
1475451 TGAATTTTAATCTTTCTTTTGTTGGAACTTATGAAGCATGAAAGAAATAGGCATGATTAATTGGT
196 TGAATTTTAATCTTTCTTTTGTTGGAACTTATGAAGCATGAAAGAAATAGGCATGATTAATTGGT
1475516 TTTTCTTTAAAAAAAAATTGAAATTTCATGCATTT
261 TTTTCTTTAAAAAAAAATTGAAATTTCATGCATTT
1475551 T
1 T
1475552 TTGGTTGAAA
Statistics
Matches: 292, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
292 272 0.93
293 2 0.01
294 7 0.02
295 11 0.04
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (295 bp):
TAAGGGTAGTGTTTCCATTCCCTCTCTTTTGCACTAAATTACATTTTAGGATAAAATGACTTAAG
TGAGGGGGTGGAAGTTGCATCAAATTTACCTTACTTATTCAATTAGTTGGACTTGAATTTTTCTT
GAATTGATGTGTTGAAATAAATTGTTGCACATCTTAGTTTTGCCATGTTTCTTTGATTTTTCTTG
TGAATTTTAATCTTTCTTTTGTTGGAACTTATGAAGCATGAAAGAAATAGGCATGATTAATTGGT
TTTTCTTTAAAAAAAAATTGAAATTTCATGCATTT
Found at i:1478872 original size:15 final size:16
Alignment explanation
Indices: 1478852--1478881 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1478842 AAATGATGTT
1478852 TTAAAT-GTTTTATTA
1 TTAAATAGTTTTATTA
1478867 TTAAATAGTTTTATT
1 TTAAATAGTTTTATT
1478882 TAAAGAGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (16 bp):
TTAAATAGTTTTATTA
Found at i:1481712 original size:173 final size:171
Alignment explanation
Indices: 1481423--1481766 Score: 609
Period size: 173 Copynumber: 2.0 Consensus size: 171
1481413 GGCATAATAG
* *
1481423 TAGACCCTAAGAAAATTTAGGCTATAATAGAATGGAAACCCCCAAATAATTTCTCATAGGTTCGT
1 TAGACCCCAAGAAAATTTAGGCTACAATAGAATGGAAACCCCCAAATAATTTCTCATAGGTTCGT
1481488 AGTTTCTTGGGAATTGCTCGTTATTATCAAAGGTTCGTGAAGAACTTTTCGATTATAGCTTCACC
66 AGTTTCTTGGGAATTGCTCGTTATTATCAAAGGTTCGTGAAGAACTTTTCGATTATAG--TCACC
* *
1481553 ACTAACCAAT-ATTTTAAGAAAAGATGTGGTTTTTGTTTGGACA
129 ACTAACC-ATGATTTTAAGAAAAGACGTGGCTTTTGTTTGGACA
1481596 TAGACCCCAAGAAAATTTAGGCTACAATAGAATGGAAACCCCCAAATAATTTCTCATAGGTTCGT
1 TAGACCCCAAGAAAATTTAGGCTACAATAGAATGGAAACCCCCAAATAATTTCTCATAGGTTCGT
1481661 AGTTTCTTGGGAATTGCTCGTTATTATCAAAGGTTCGTGAAGAACTTTTCGATTATAGTCACCAC
66 AGTTTCTTGGGAATTGCTCGTTATTATCAAAGGTTCGTGAAGAACTTTTCGATTATAGTCACCAC
*
1481726 TAACCATGATTTTAAGAAAATACGTGGCTTTTGTTTGGACA
131 TAACCATGATTTTAAGAAAAGACGTGGCTTTTGTTTGGACA
1481767 GAGAAGTGCA
Statistics
Matches: 165, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
170 2 0.01
171 42 0.25
173 121 0.73
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (171 bp):
TAGACCCCAAGAAAATTTAGGCTACAATAGAATGGAAACCCCCAAATAATTTCTCATAGGTTCGT
AGTTTCTTGGGAATTGCTCGTTATTATCAAAGGTTCGTGAAGAACTTTTCGATTATAGTCACCAC
TAACCATGATTTTAAGAAAAGACGTGGCTTTTGTTTGGACA
Found at i:1486003 original size:61 final size:62
Alignment explanation
Indices: 1485926--1486061 Score: 168
Period size: 63 Copynumber: 2.2 Consensus size: 62
1485916 TGCAACCTCA
* * *
1485926 TGCAATAAGTGTACACTCTAGTGCTGAT-CTGGATAT-GACACATAAGGTCGTGCCCACCACC
1 TGCACTAAGTGTACACTCTAGTGCTAATAC-GCATATAGACACATAAGGTCGTGCCCACCACC
* * * *
1485987 TGCACTAAGTTTACACTCTAGTGCTAATACGCATATCATATACATAAGGTCGTGCCCACCACG
1 TGCACTAAGTGTACACTCTAGTGCTAATACGCATAT-AGACACATAAGGTCGTGCCCACCACC
*
1486050 TGCACTTAGTGT
1 TGCACTAAGTGT
1486062 CCTTACACAC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
61 30 0.48
62 1 0.02
63 32 0.51
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (62 bp):
TGCACTAAGTGTACACTCTAGTGCTAATACGCATATAGACACATAAGGTCGTGCCCACCACC
Found at i:1486703 original size:16 final size:17
Alignment explanation
Indices: 1486682--1486715 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1486672 GTTTTCTTTT
1486682 TTACTTTCTTTG-ATAA
1 TTACTTTCTTTGAATAA
1486698 TTACTTTCTTTGAATAA
1 TTACTTTCTTTGAATAA
1486715 T
1 T
1486716 ACCTTGGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (17 bp):
TTACTTTCTTTGAATAA
Found at i:1493630 original size:57 final size:59
Alignment explanation
Indices: 1493569--1493732 Score: 248
Period size: 58 Copynumber: 2.8 Consensus size: 59
1493559 TTAAAAATAT
* *
1493569 ATTTTTCTATAA-ATTAATCTT-TTTTTAATTTAGTATTATGACTAAAATTATTTATTA
1 ATTTTTCTATAATATTAATTTTGTTTTTTATTTAGTATTATGACTAAAATTATTTATTA
1493626 ATTTTTC-ATAATATTAATTTTGTTTTTTATTTAGTATTATGACTAAAATTATTTATTA
1 ATTTTTCTATAATATTAATTTTGTTTTTTATTTAGTATTATGACTAAAATTATTTATTA
* *
1493684 TTTTTTCT-TAATATTAATTTTGTTTTTTATTTAGTTTTATGTAC-AAAAT
1 ATTTTTCTATAATATTAATTTTGTTTTTTATTTAGTATTATG-ACTAAAAT
1493733 AATTAATACT
Statistics
Matches: 99, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
56 4 0.04
57 15 0.15
58 78 0.79
59 2 0.02
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.59
Consensus pattern (59 bp):
ATTTTTCTATAATATTAATTTTGTTTTTTATTTAGTATTATGACTAAAATTATTTATTA
Found at i:1493686 original size:29 final size:29
Alignment explanation
Indices: 1493596--1493686 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
1493586 TCTTTTTTTA
1493596 ATTTAGTATTATGACTAAAATTATTTATT
1 ATTTAGTATTATGACTAAAATTATTTATT
* * * ** * *
1493625 AATTT-TTCATAAT-ATTAATTTTGTTTTTT
1 -ATTTAGT-ATTATGACTAAAATTATTTATT
1493654 ATTTAGTATTATGACTAAAATTATTTATT
1 ATTTAGTATTATGACTAAAATTATTTATT
1493683 ATTT
1 ATTT
1493687 TTTCTTAATA
Statistics
Matches: 44, Mismatches: 14, Indels: 7
0.68 0.22 0.11
Matches are distributed among these distances:
28 8 0.18
29 28 0.64
30 8 0.18
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.57
Consensus pattern (29 bp):
ATTTAGTATTATGACTAAAATTATTTATT
Found at i:1493713 original size:29 final size:29
Alignment explanation
Indices: 1493627--1493715 Score: 81
Period size: 29 Copynumber: 3.1 Consensus size: 29
1493617 TATTTATTAA
*
1493627 TTTTTCATAATATTAATTTTGTTTTTTAT
1 TTTTTCTTAATATTAATTTTGTTTTTTAT
** * * ** * *
1493656 TTAGTATT-ATGACTAAAATTATTTATTAT
1 TTTTTCTTAAT-ATTAATTTTGTTTTTTAT
1493685 TTTTTCTTAATATTAATTTTGTTTTTTAT
1 TTTTTCTTAATATTAATTTTGTTTTTTAT
1493714 TT
1 TT
1493716 AGTTTTATGT
Statistics
Matches: 41, Mismatches: 17, Indels: 4
0.66 0.27 0.06
Matches are distributed among these distances:
28 2 0.05
29 37 0.90
30 2 0.05
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.65
Consensus pattern (29 bp):
TTTTTCTTAATATTAATTTTGTTTTTTAT
Found at i:1493791 original size:31 final size:32
Alignment explanation
Indices: 1493743--1493806 Score: 112
Period size: 31 Copynumber: 2.0 Consensus size: 32
1493733 AATTAATACT
*
1493743 AAAAAAACTTAATAAATAATTTTAGTCATAAG
1 AAAAAAACTTAACAAATAATTTTAGTCATAAG
1493775 AAAAAAA-TTAACAAATAATTTTAGTCATAAG
1 AAAAAAACTTAACAAATAATTTTAGTCATAAG
1493806 A
1 A
1493807 CTAAATTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 24 0.77
32 7 0.23
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.30
Consensus pattern (32 bp):
AAAAAAACTTAACAAATAATTTTAGTCATAAG
Found at i:1494963 original size:25 final size:25
Alignment explanation
Indices: 1494904--1494963 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
1494894 ATAAATATAT
* * *
1494904 TTATAAATGATATTATATTATTATA
1 TTATAAATAATATTATAATATTAAA
* *
1494929 TCATATATAATATT-TCAATATTAAA
1 TTATAAATAATATTAT-AATATTAAA
1494954 TTATAAATAA
1 TTATAAATAA
1494964 AAATTAGTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (25 bp):
TTATAAATAATATTATAATATTAAA
Found at i:1495003 original size:23 final size:24
Alignment explanation
Indices: 1494977--1495030 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
1494967 TTAGTATGTC
* *
1494977 TATATTGTAAAAATAAATTA-TTT
1 TATATTATAAAAATAAATAATTTT
* *
1495000 TATAGTATAAAAATAAGTAATTTT
1 TATATTATAAAAATAAATAATTTT
1495024 TATATTA
1 TATATTA
1495031 AATTTTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (24 bp):
TATATTATAAAAATAAATAATTTT
Found at i:1495832 original size:16 final size:15
Alignment explanation
Indices: 1495804--1495842 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1495794 TTCAAGTTTT
1495804 TTTCGATTCAGTTAC
1 TTTCGATTCAGTTAC
* *
1495819 TTTCTATTCGAGTTGC
1 TTTCGATTC-AGTTAC
1495835 TTTCGATT
1 TTTCGATT
1495843 TAGGCGACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.15, C:0.18, G:0.15, T:0.51
Consensus pattern (15 bp):
TTTCGATTCAGTTAC
Found at i:1496297 original size:23 final size:23
Alignment explanation
Indices: 1496256--1496299 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1496246 AAAAATATTA
*
1496256 TTTATCTAATAATATTTAATTTC
1 TTTATCTAATAATAATTAATTTC
1496279 TTTAT-TAATAATAAATTAATT
1 TTTATCTAATAAT-AATTAATT
1496300 ATTATTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTATCTAATAATAATTAATTTC
Found at i:1496331 original size:50 final size:48
Alignment explanation
Indices: 1496266--1496375 Score: 159
Period size: 50 Copynumber: 2.2 Consensus size: 48
1496256 TTTATCTAAT
* *
1496266 AATATTTAATTTCTTTA-TTAATAATAAATTAATTATTATTCAATTTCAAA
1 AATATTTATTTTCTTTACTT-ATAATAAATTAATTATCATTCAA-TT-AAA
*
1496316 AATATTTCTTTTCTTTACTTATAATAAATTAATTATCATTCAATTAAA
1 AATATTTATTTTCTTTACTTATAATAAATTAATTATCATTCAATTAAA
1496364 AATATTTATTTT
1 AATATTTATTTT
1496376 TTTTTTACAA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
48 14 0.25
49 2 0.04
50 37 0.67
51 2 0.04
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (48 bp):
AATATTTATTTTCTTTACTTATAATAAATTAATTATCATTCAATTAAA
Found at i:1502701 original size:28 final size:28
Alignment explanation
Indices: 1502661--1502729 Score: 138
Period size: 28 Copynumber: 2.5 Consensus size: 28
1502651 GGACTCCTTT
1502661 TATTTTCTTCTTTTGTTAGATCTATACA
1 TATTTTCTTCTTTTGTTAGATCTATACA
1502689 TATTTTCTTCTTTTGTTAGATCTATACA
1 TATTTTCTTCTTTTGTTAGATCTATACA
1502717 TATTTTCTTCTTT
1 TATTTTCTTCTTT
1502730 AATAATATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.19, C:0.14, G:0.06, T:0.61
Consensus pattern (28 bp):
TATTTTCTTCTTTTGTTAGATCTATACA
Found at i:1504496 original size:21 final size:20
Alignment explanation
Indices: 1504458--1504496 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1504448 CATTCTTGAT
* *
1504458 TTTTGCCTCCATATATCCTC
1 TTTTGCCTCAATAAATCCTC
1504478 TTTTGCTCTCAATAAATCC
1 TTTTGC-CTCAATAAATCC
1504497 CATAACTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.21, C:0.31, G:0.05, T:0.44
Consensus pattern (20 bp):
TTTTGCCTCAATAAATCCTC
Found at i:1508087 original size:20 final size:20
Alignment explanation
Indices: 1508062--1508114 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1508052 GACCAACAAA
1508062 TTCGCAACGCGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
* **
1508082 TTCGCAACTC-AGTTTCCAAT
1 TTCGCAACGCGA-ACTCCAAT
1508102 TTCGCAACGCGAA
1 TTCGCAACGCGAA
1508115 TATGTAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 24 0.92
21 1 0.04
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Found at i:1508126 original size:20 final size:20
Alignment explanation
Indices: 1508103--1508251 Score: 136
Period size: 20 Copynumber: 7.3 Consensus size: 20
1508093 GTTTCCAATT
*
1508103 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATTTGTAAA
** * ** *
1508123 TCGCATTGCGATTTTCCAATT
1 TCGCAACGCGAATTTGTAA-A
*
1508144 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATTTGTAAA
** * ** *
1508164 TCGCATTGCGATTTTCCAATT
1 TCGCAACGCGAATTTGTAA-A
*
1508185 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATTTGTAAA
*
1508205 TCGCAACGTGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
1508225 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
1508245 TCGCAAC
1 TCGCAAC
1508252 ACAGAAGTCA
Statistics
Matches: 96, Mismatches: 31, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
20 70 0.73
21 26 0.27
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:1508147 original size:21 final size:21
Alignment explanation
Indices: 1508123--1508189 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1508113 AATATGTAAA
1508123 TCGCATTGCGATTTTCCAATT
1 TCGCATTGCGATTTTCCAATT
** * * ** *
1508144 TCGCAACGCGAATATGTAA-A
1 TCGCATTGCGATTTTCCAATT
1508164 TCGCATTGCGATTTTCCAATT
1 TCGCATTGCGATTTTCCAATT
1508185 TCGCA
1 TCGCA
1508190 ACGCGAATCT
Statistics
Matches: 31, Mismatches: 14, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAATT
Found at i:1508151 original size:41 final size:41
Alignment explanation
Indices: 1508094--1508249 Score: 224
Period size: 41 Copynumber: 3.8 Consensus size: 41
1508084 CGCAACTCAG
1508094 TTTCCAATTTCGCAACGCGAATATGTAAATCGCATTGCGAT
1 TTTCCAATTTCGCAACGCGAATATGTAAATCGCATTGCGAT
1508135 TTTCCAATTTCGCAACGCGAATATGTAAATCGCATTGCGAT
1 TTTCCAATTTCGCAACGCGAATATGTAAATCGCATTGCGAT
* ** * *
1508176 TTTCCAATTTCGCAACGCGAATCTGTAAATCGCAACGTGAA
1 TTTCCAATTTCGCAACGCGAATATGTAAATCGCATTGCGAT
** * *
1508217 TTTGTAA-ATCGCAACGCGAATTTGTAAATCGCA
1 TTTCCAATTTCGCAACGCGAATATGTAAATCGCA
1508250 ACACAGAAGT
Statistics
Matches: 106, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 24 0.23
41 82 0.77
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (41 bp):
TTTCCAATTTCGCAACGCGAATATGTAAATCGCATTGCGAT
Found at i:1508269 original size:40 final size:41
Alignment explanation
Indices: 1508225--1508371 Score: 144
Period size: 40 Copynumber: 3.7 Consensus size: 41
1508215 AATTTGTAAA
*
1508225 TCGCAACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAAT
1 TCGCAACGCGAA-TAGTCAAATTCGCAACACAGAAGTCAAAT
* **
1508265 TCGCAATGCG-ATAGTCAAATTCGCAATGC-GATAGTCAAAT
1 TCGCAACGCGAATAGTCAAATTCGCAACACAGA-AGTCAAAT
* * * * *
1508305 TCACAACAC-AAAAGTCAAATTTGCAACACAAAAGTCAAAT
1 TCGCAACGCGAATAGTCAAATTCGCAACACAGAAGTCAAAT
*
1508345 TCGCAACGCGAA-AGTCAAATTTGCAAC
1 TCGCAACGCGAATAGTCAAATTCGCAAC
1508372 GCGAAACACA
Statistics
Matches: 87, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
38 3 0.03
39 6 0.07
40 75 0.86
41 3 0.03
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.20
Consensus pattern (41 bp):
TCGCAACGCGAATAGTCAAATTCGCAACACAGAAGTCAAAT
Found at i:1508289 original size:60 final size:61
Alignment explanation
Indices: 1508225--1508365 Score: 164
Period size: 60 Copynumber: 2.4 Consensus size: 61
1508215 AATTTGTAAA
* * * ** * *
1508225 TCGCAACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAATTCGCAATGCGATAGTCAAAT
1 TCGCAACGCGAA-TAGTCAAATTCACAACACAAAAGTCAAATTCGCAACACAAAAGTCAAAT
* *
1508285 TCGCAATGCG-ATAGTCAAATTCACAACACAAAAGTCAAATTTGCAACACAAAAGTCAAAT
1 TCGCAACGCGAATAGTCAAATTCACAACACAAAAGTCAAATTCGCAACACAAAAGTCAAAT
1508345 TCGCAACGCGAA-AGTCAAATT
1 TCGCAACGCGAATAGTCAAATT
1508366 TGCAACGCGA
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
58 3 0.04
59 4 0.06
60 60 0.88
61 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.21
Consensus pattern (61 bp):
TCGCAACGCGAATAGTCAAATTCACAACACAAAAGTCAAATTCGCAACACAAAAGTCAAAT
Found at i:1508377 original size:20 final size:20
Alignment explanation
Indices: 1508256--1508377 Score: 145
Period size: 20 Copynumber: 6.1 Consensus size: 20
1508246 CGCAACACAG
*
1508256 AAGTCAAATTCGCAATGCGA
1 AAGTCAAATTCGCAACGCGA
* *
1508276 TAGTCAAATTCGCAATGCGA
1 AAGTCAAATTCGCAACGCGA
* * * *
1508296 TAGTCAAATTCACAACACAA
1 AAGTCAAATTCGCAACGCGA
* * *
1508316 AAGTCAAATTTGCAACACAA
1 AAGTCAAATTCGCAACGCGA
1508336 AAGTCAAATTCGCAACGCGA
1 AAGTCAAATTCGCAACGCGA
*
1508356 AAGTCAAATTTGCAACGCGA
1 AAGTCAAATTCGCAACGCGA
1508376 AA
1 AA
1508378 CACAATATTA
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 90 1.00
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (20 bp):
AAGTCAAATTCGCAACGCGA
Found at i:1508505 original size:22 final size:22
Alignment explanation
Indices: 1508480--1508537 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
1508470 TCACTCTCTA
* *
1508480 CGACGACATCCTTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
1508502 CGACGAAATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
*
1508524 CGGCGAAATCCGTC
1 CGACGAAATCCGTC
1508538 TATCTCCATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.21, C:0.45, G:0.16, T:0.19
Consensus pattern (22 bp):
CGACGAAATCCGTCCCCATCTC
Found at i:1508909 original size:20 final size:20
Alignment explanation
Indices: 1508886--1508944 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
1508876 ACTTAAATTT
1508886 GCAACACGAAAATGAAAATC
1 GCAACACGAAAATGAAAATC
1508906 GC-A-ACG----TGAAAATC
1 GCAACACGAAAATGAAAATC
* *
1508920 GCATCGCGAAAATGAAAATC
1 GCAACACGAAAATGAAAATC
1508940 GCAAC
1 GCAAC
1508945 GTGATTTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 12
0.67 0.07 0.27
Matches are distributed among these distances:
14 10 0.33
16 2 0.07
18 3 0.10
19 1 0.03
20 14 0.47
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (20 bp):
GCAACACGAAAATGAAAATC
Found at i:1508917 original size:14 final size:14
Alignment explanation
Indices: 1508898--1508932 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1508888 AACACGAAAA
1508898 TGAAAATCGCAACG
1 TGAAAATCGCAACG
*
1508912 TGAAAATCGCATCG
1 TGAAAATCGCAACG
*
1508926 CGAAAAT
1 TGAAAAT
1508933 GAAAATCGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (14 bp):
TGAAAATCGCAACG
Found at i:1509001 original size:40 final size:39
Alignment explanation
Indices: 1508947--1509038 Score: 148
Period size: 40 Copynumber: 2.3 Consensus size: 39
1508937 ATCGCAACGT
1508947 GATTTTAGTTTCGCGTTGCGATTTTCATTTTCGCGTTGC
1 GATTTTAGTTTCGCGTTGCGATTTTCATTTTCGCGTTGC
*
1508986 GATTTTCATTTTCGCGTTGCGATTTTCATTTTCGCGTTGC
1 GATTTT-AGTTTCGCGTTGCGATTTTCATTTTCGCGTTGC
*
1509026 GAATTTAAGTTTC
1 G-ATTTTAGTTTC
1509039 AGAAACTACT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 6 0.12
40 38 0.79
41 4 0.08
ACGTcount: A:0.13, C:0.17, G:0.21, T:0.49
Consensus pattern (39 bp):
GATTTTAGTTTCGCGTTGCGATTTTCATTTTCGCGTTGC
Found at i:1509038 original size:20 final size:20
Alignment explanation
Indices: 1508955--1509027 Score: 146
Period size: 20 Copynumber: 3.6 Consensus size: 20
1508945 GTGATTTTAG
1508955 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
1508975 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
1508995 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
1509015 TTTCGCGTTGCGA
1 TTTCGCGTTGCGA
1509028 ATTTAAGTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.10, C:0.21, G:0.22, T:0.48
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:1511211 original size:21 final size:21
Alignment explanation
Indices: 1511164--1511267 Score: 79
Period size: 21 Copynumber: 4.9 Consensus size: 21
1511154 GATACACCTA
**
1511164 TCATCATTCAAGAGGTGCCT-
1 TCATCATTCAAGAGGCCCCTC
1511184 TCTATCATTCAAGAGGCCCCTC
1 TC-ATCATTCAAGAGGCCCCTC
*
1511206 TCATCA-TCGAAGAAGCCCCTC
1 TCATCATTC-AAGAGGCCCCTC
* * *
1511227 -CTACCGTTCAAGAGGCCCCTG
1 TC-ATCATTCAAGAGGCCCCTC
* *
1511248 TCATCGTTCAATAGGTCCCC
1 TCATCATTCAAGAGG-CCCC
1511268 CCCGCCGTTC
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
20 5 0.07
21 54 0.79
22 9 0.13
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.25
Consensus pattern (21 bp):
TCATCATTCAAGAGGCCCCTC
Found at i:1511211 original size:42 final size:42
Alignment explanation
Indices: 1511164--1511266 Score: 109
Period size: 42 Copynumber: 2.5 Consensus size: 42
1511154 GATACACCTA
* * *
1511164 TCATCATTCAAGAGGTGCCTTCTATCATTCAAGAGGCCCCTC
1 TCATCATTCAAGAGGTCCCTCCTACCATTCAAGAGGCCCCTC
* * * *
1511206 TCATCA-TCGAAGAAGCCCCTCCTACCGTTCAAGAGGCCCCTG
1 TCATCATTC-AAGAGGTCCCTCCTACCATTCAAGAGGCCCCTC
* *
1511248 TCATCGTTCAATAGGTCCC
1 TCATCATTCAAGAGGTCCC
1511267 CCCCGCCGTT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
41 2 0.04
42 44 0.92
43 2 0.04
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.25
Consensus pattern (42 bp):
TCATCATTCAAGAGGTCCCTCCTACCATTCAAGAGGCCCCTC
Found at i:1513139 original size:25 final size:25
Alignment explanation
Indices: 1513111--1513160 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1513101 CATTATTTTC
*
1513111 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
1513136 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
1513161 TTAATTGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:1513257 original size:20 final size:20
Alignment explanation
Indices: 1513232--1513310 Score: 71
Period size: 20 Copynumber: 4.2 Consensus size: 20
1513222 AAGGTAAACT
*
1513232 TTCGCAATGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
1513252 TTCGCAACGCGAAA-T--AA
1 TTCGCAACGCGAAAGTCAAA
*** *
1513269 ---GCGTTGCGATAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
1513286 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
1513306 TTCGC
1 TTCGC
1513311 GTTGCGATTT
Statistics
Matches: 44, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
14 7 0.16
15 1 0.02
17 4 0.09
19 1 0.02
20 31 0.70
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:1513317 original size:20 final size:20
Alignment explanation
Indices: 1513269--1513317 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1513259 CGCGAAATAA
*
1513269 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGAAAGTCAAATTC
***
1513289 GCAACGCGAAAGTCAAATTC
1 GCGTTGCGAAAGTCAAATTC
1513309 GCGTTGCGA
1 GCGTTGCGA
1513318 TTTTCAGTTT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (20 bp):
GCGTTGCGAAAGTCAAATTC
Found at i:1513357 original size:20 final size:20
Alignment explanation
Indices: 1513332--1513381 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1513322 CAGTTTGCGA
1513332 TTTCGCGTTGCAAATTTGAC
1 TTTCGCGTTGCAAATTTGAC
*
1513352 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCAAATTTGAC
*
1513372 TTTCACGTTG
1 TTTCGCGTTG
1513382 ATTGCAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (20 bp):
TTTCGCGTTGCAAATTTGAC
Found at i:1513688 original size:18 final size:18
Alignment explanation
Indices: 1513665--1513700 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1513655 AAGCCGGTTG
*
1513665 TGATTGGGATTTTCATTT
1 TGATTGCGATTTTCATTT
*
1513683 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTCATTT
1513701 CCTTTTTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTCATTT
Found at i:1516018 original size:24 final size:24
Alignment explanation
Indices: 1515967--1516018 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1515957 ATCTGAGTAT
** *
1515967 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
1515991 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
1516015 TGAC
1 TGAC
1516019 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:1516997 original size:19 final size:19
Alignment explanation
Indices: 1516972--1517058 Score: 129
Period size: 19 Copynumber: 4.5 Consensus size: 19
1516962 ATTCGTGTTA
*
1516972 CGAATTTGAAATTTAGTTG
1 CGAATTTGAAATTCAGTTG
*
1516991 GGAATTTGAAATTCAGTTG
1 CGAATTTGAAATTCAGTTG
1517010 CGAATTTGAAATTCAGTTG
1 CGAATTTGAAATTCAGTTG
*
1517029 CGAATTTGAAATTCCGCGTTG
1 CGAATTTGAAATT-C-AGTTG
1517050 CGAATTTGA
1 CGAATTTGA
1517059 TTTTTGTGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
19 48 0.77
20 1 0.02
21 13 0.21
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (19 bp):
CGAATTTGAAATTCAGTTG
Found at i:1517089 original size:20 final size:20
Alignment explanation
Indices: 1517025--1517140 Score: 78
Period size: 20 Copynumber: 5.8 Consensus size: 20
1517015 TTGAAATTCA
*
1517025 GTTGCGAATTTGA-AATTCCGC
1 GTTGCGAATTTGACTA-T-CGC
* * * *
1517046 GTTGCGAATTTGATTTTTGT
1 GTTGCGAATTTGACTATCGC
*
1517066 GTTGCAAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
* *
1517086 GTTGTGAATTTGACT-TCTGT
1 GTTGCGAATTTGACTATC-GC
*
1517106 GTTGCG-ATTT-ACAAATTCGC
1 GTTGCGAATTTGAC-TA-TCGC
1517126 GTTGCGAATTTGACT
1 GTTGCGAATTTGACT
1517141 TCTATGTGCG
Statistics
Matches: 72, Mismatches: 16, Indels: 14
0.71 0.16 0.14
Matches are distributed among these distances:
18 2 0.03
19 6 0.08
20 42 0.58
21 20 0.28
22 2 0.03
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:1517163 original size:39 final size:40
Alignment explanation
Indices: 1517043--1517172 Score: 167
Period size: 40 Copynumber: 3.3 Consensus size: 40
1517033 TTTGAAATTC
* * *
1517043 CGCGTTGCGAATTTGATTTTTGTGTTGCAAATTTGAC-TA-T
1 CGCGTTGCGAATTTGACTTCTGTGTTGC-GATTT-ACATATT
* *
1517083 CGCGTTGTGAATTTGACTTCTGTGTTGCGATTTACAAATT
1 CGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACATATT
*
1517123 CGCGTTGCGAATTTGACTTCTATG-TGCGATTTACATATT
1 CGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACATATT
1517162 CGCGTTGCGAA
1 CGCGTTGCGAA
1517173 ATTGGAAACT
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
38 2 0.03
39 30 0.38
40 48 0.60
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (40 bp):
CGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACATATT
Found at i:1517208 original size:20 final size:20
Alignment explanation
Indices: 1517162--1517212 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1517152 TTTACATATT
1517162 CGCGTTGCGAAATTGGAAAC
1 CGCGTTGCGAAATTGGAAAC
* * **
1517182 TGGGTTGCGAAATTGGAGTC
1 CGCGTTGCGAAATTGGAAAC
1517202 CGCGTTGCGAA
1 CGCGTTGCGAA
1517213 TTTGAGATCG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.24
Consensus pattern (20 bp):
CGCGTTGCGAAATTGGAAAC
Found at i:1517764 original size:16 final size:16
Alignment explanation
Indices: 1517743--1517775 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1517733 TAATAAATAG
1517743 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1517759 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1517775 A
1 A
1517776 AAATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1517856 original size:10 final size:10
Alignment explanation
Indices: 1517841--1517899 Score: 62
Period size: 10 Copynumber: 6.7 Consensus size: 10
1517831 CATTTAATAA
1517841 ATAAACGAAC
1 ATAAACGAAC
1517851 ATAAACGAAC
1 ATAAACGAAC
1517861 ----ACGAAC
1 ATAAACGAAC
1517867 ATAAACGAAC
1 ATAAACGAAC
1517877 ----ACGAAC
1 ATAAACGAAC
1517883 ATAAACGAAC
1 ATAAACGAAC
1517893 ATAAACG
1 ATAAACG
1517900 TTGGAGACCC
Statistics
Matches: 41, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
6 12 0.29
10 29 0.71
ACGTcount: A:0.58, C:0.22, G:0.12, T:0.08
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1517866 original size:16 final size:16
Alignment explanation
Indices: 1517845--1517893 Score: 98
Period size: 16 Copynumber: 3.1 Consensus size: 16
1517835 TAATAAATAA
1517845 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1517861 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1517877 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1517893 A
1 A
1517894 TAAACGTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.57, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1517877 original size:26 final size:26
Alignment explanation
Indices: 1517841--1517899 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
1517831 CATTTAATAA
* *
1517841 ATAAACGAACATAAACGA-ACACGAAC
1 ATAAACGAACACAAAC-ATAAACGAAC
*
1517867 ATAAACGAACACGAACATAAACGAAC
1 ATAAACGAACACAAACATAAACGAAC
1517893 ATAAACG
1 ATAAACG
1517900 TTGGAGACCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 1 0.03
26 28 0.97
ACGTcount: A:0.58, C:0.22, G:0.12, T:0.08
Consensus pattern (26 bp):
ATAAACGAACACAAACATAAACGAAC
Found at i:1518664 original size:14 final size:14
Alignment explanation
Indices: 1518647--1518702 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
1518637 AATGAACATA
*
1518647 AACGAACATAATCG
1 AACGAACATAACCG
1518661 AACGAACAT-A---
1 AACGAACATAACCG
1518671 AACGAACATAACCG
1 AACGAACATAACCG
1518685 AACGAACATAACCG
1 AACGAACATAACCG
1518699 AACG
1 AACG
1518703 TTCACGAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.52, C:0.25, G:0.14, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1518667 original size:24 final size:24
Alignment explanation
Indices: 1518627--1518701 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
1518617 GATTGGGTTA
*
1518627 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
1518651 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* *
1518675 AACATAACCGAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
1518699 AAC
1 AAC
1518702 GTTCACGAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 3 0.06
24 44 0.94
ACGTcount: A:0.55, C:0.21, G:0.12, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:1518701 original size:10 final size:10
Alignment explanation
Indices: 1518640--1518687 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
1518630 ATAAATGAAT
1518640 GAACATAAAC
1 GAACATAAAC
1518650 GAACATAATCGAAC
1 GAACAT-A---AAC
1518664 GAACATAAAC
1 GAACATAAAC
*
1518674 GAACATAACC
1 GAACATAAAC
1518684 GAAC
1 GAAC
1518688 GAACATAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:1528295 original size:35 final size:35
Alignment explanation
Indices: 1528214--1528420 Score: 238
Period size: 35 Copynumber: 5.9 Consensus size: 35
1528204 AGCAAAGTTA
* *
1528214 ATCTTAAGCCTTCACCAAAGAGGAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGC-AACC
* * *
1528250 ATCTTAAGCCTTCACCGGAGAGTAGTGAAACAATC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAACC
* * * **
1528285 ATCTTAAGCCTTCACAGAAAAATAGTGAAGCAGTC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAACC
*
1528320 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGC-ACC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAACC
** * *
1528354 ATCTTAAGCCTTCATAGAGGAGTATTGAAGC-ACC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAACC
* *
1528388 ATCTTAAGCATTCATCGAAGAGTAGTGAAGCAA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAA
1528421 ATCCATCCAT
Statistics
Matches: 148, Mismatches: 22, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
34 59 0.40
35 62 0.42
36 27 0.18
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (35 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAACC
Found at i:1528512 original size:21 final size:21
Alignment explanation
Indices: 1528488--1528528 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1528478 GATGTTTTAA
1528488 GAAG-ATGAAATTTTTGAAAAC
1 GAAGAATGAAATTTTT-AAAAC
*
1528509 GAAGAATGCAATTTTTAAAA
1 GAAGAATGAAATTTTTAAAA
1528529 TTTCACGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.49, C:0.05, G:0.17, T:0.29
Consensus pattern (21 bp):
GAAGAATGAAATTTTTAAAAC
Found at i:1528799 original size:216 final size:215
Alignment explanation
Indices: 1528423--1529630 Score: 1942
Period size: 216 Copynumber: 5.6 Consensus size: 215
1528413 TGAAGCAAAT
*
1528423 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATG-AAAAATGATGTTTTA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTTTA
* * * *
1528487 AGAAGATGAAATTTTTGAAAACGAAGAATGCAATTTTTAAAATTTCACGATTTATAAGTCCTACG
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTTCG
* * * *
1528552 GGCCATCAGTATGTCTTTCGAGCAGGATGCTTAAATCCTTCGAGTCATCTGTAAGCCTTCAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
* *
1528617 AAAATGATAAGTCCTTCGGA
196 AAGATGATAAGTCCTTCGGG
*
1528637 CCATCCATAAAACCTTCGAGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAAATGATGTTTT
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATG-AAAAAATGATGTTTT
*
1528702 AAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTATTAGTCCTTC
65 AAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTTC
* **
1528767 AGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAAGTCATCTGTAAGCCTTTAGAG
130 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
*
1528832 CAAGATGTTAAGTCCTTCGGG
195 CAAGATGATAAGTCCTTCGGG
1528853 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTTTA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTTTA
*
1528918 AGAAGATGGAATTTTTGAAAATGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTTCG
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTTCG
* * *
1528983 AGCCATCAGTAAGTCTTTCAACCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
1529048 AAGATGATAAGTCCTTCGGG
196 AAGATGATAAGTCCTTCGGG
* * *
1529068 CCATCCATAAAACCTTTGGGTAGGATGTTTTCACATGAATTTGTGAATGAAAAAACGATGTTTT-
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTTTA
1529132 --AAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTTCG
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTTCG
*
1529195 GGCCATCAGTAAGTCTTTCGAGCATGATGCCTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
*
1529260 AAGATGATAAGTCTTTCGGG
196 AAGATGATAAGTCCTTCGGG
* * *
1529280 CCATCCATAAAACCTTCGGGTAGGATGTTTTCATATGAATTTGAAAATTAAAAAAATGATGTTTT
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAA-TGAAAAAATGATGTTTT
* * * * * *
1529345 AAAAAAATGAAATTATTGAAAACGAAGAATGCGATTTTCAAAATGTCACAATTTATAAGTCCTTC
65 AAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTTC
*
1529410 AGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
130 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
* *
1529475 CAAGATGATAAGTACTTCGAG
195 CAAGATGATAAGTCCTTCGGG
* * * *
1529496 CCATCTATAAAACCTTCGGGTAGAATGTTTTCAAATAAATTTGAGAATG-AAAAATGATGTTTTA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTTTA
* * * *
1529560 A-AAAATGTAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGCCCTTCG
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTTCG
1529624 GGCCATC
131 GGCCATC
1529631 CATAAGACCT
Statistics
Matches: 927, Mismatches: 61, Indels: 13
0.93 0.06 0.01
Matches are distributed among these distances:
212 185 0.20
213 80 0.09
214 63 0.07
215 219 0.24
216 380 0.41
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Consensus pattern (215 bp):
CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTTTA
AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTTCG
GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
AAGATGATAAGTCCTTCGGG
Found at i:1528822 original size:42 final size:41
Alignment explanation
Indices: 1528761--1528849 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 41
1528751 GATTTATTAG
* * * *
1528761 TCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCAAGCCATCAGTAAGCCTTTAGAGCAAGATG-TTAAA
* * *
1528803 TCCTTCAAGTCATCTGTAAGCCTTTAGAGCAAGATGTTAAG
1 TCCTTCAAGCCATCAGTAAGCCTTTAGAGCAAGATGTTAAA
1528844 TCCTTC
1 TCCTTC
1528850 GGGCCATCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 10 0.25
42 30 0.75
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (41 bp):
TCCTTCAAGCCATCAGTAAGCCTTTAGAGCAAGATGTTAAA
Found at i:1529715 original size:130 final size:129
Alignment explanation
Indices: 1529489--1529760 Score: 420
Period size: 130 Copynumber: 2.1 Consensus size: 129
1529479 ATGATAAGTA
* *
1529489 CTTCGAGCCATCTATAAAACCTTCGGGTAGAATGTTTTCAAATAAATTTGAGAATGAAAAATGAT
1 CTTCGGGCCATCCATAAAACCTTCGGGTAGAATGTTTTCAAATAAATTTGAGAATGAAAAATGAT
*
1529554 GTTTTAAAAAATGTAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGCC
66 GTTTT-AAAAATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGCC
* * *
1529619 CTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAGAATGAAAAAAATG
1 CTTCGGGCCATCCATAAAACCTTCGGGTAGAATGTTTTCAAATAAATTTGAGAATG--AAAAATG
** * *
1529684 ATGTTTT-AGGATGGAATTTTTGAAAACGAAGAATGTGATTTTCAAAATTTCACAATTTATAAGT
64 ATGTTTTAAAAATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGC
1529748 C
129 C
1529749 CTTCGGGCCATC
1 CTTCGGGCCATC
1529761 AGTAAGTCTT
Statistics
Matches: 130, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
130 116 0.89
132 14 0.11
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (129 bp):
CTTCGGGCCATCCATAAAACCTTCGGGTAGAATGTTTTCAAATAAATTTGAGAATGAAAAATGAT
GTTTTAAAAATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGCC
Found at i:1536996 original size:31 final size:29
Alignment explanation
Indices: 1536925--1537003 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 29
1536915 CAAATTTTAG
* ** *
1536925 TTAGCGACCAAAACATAAATTTTGAAAGT
1 TTAGGGACCAAAGTATAAAGTTTGAAAGT
1536954 TTAGTGG-CCAAAGTATAAAGTTTGAAAATGT
1 TTAG-GGACCAAAGTATAAAGTTTG-AAA-GT
1536985 TTAGGGACCAAAGTGATAA
1 TTAGGGACCAAAGT-ATAA
1537004 TTTTCTCGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
29 18 0.44
30 6 0.15
31 13 0.32
32 4 0.10
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (29 bp):
TTAGGGACCAAAGTATAAAGTTTGAAAGT
Found at i:1540164 original size:12 final size:12
Alignment explanation
Indices: 1540142--1540194 Score: 54
Period size: 13 Copynumber: 4.3 Consensus size: 12
1540132 GTATCAGGAA
1540142 GAAAA-GAATAT
1 GAAAATGAATAT
1540153 GAAAATGAATAT
1 GAAAATGAATAT
* *
1540165 GAAAGTGATAGAT
1 GAAAATGA-ATAT
*
1540178 GAAAATAAAATAT
1 GAAAAT-GAATAT
1540191 GAAA
1 GAAA
1540195 TGTTCTGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
11 5 0.15
12 13 0.38
13 15 0.44
14 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.19, T:0.21
Consensus pattern (12 bp):
GAAAATGAATAT
Found at i:1541419 original size:39 final size:39
Alignment explanation
Indices: 1541365--1541454 Score: 135
Period size: 39 Copynumber: 2.3 Consensus size: 39
1541355 AGGACCTGCT
* * *
1541365 GTAAGGACTTACCTTGAGCTCAAAGCTGAGGAGCATGTG
1 GTAAGGACTTACCTTGAGCACAAAGCCGAGGAGCATGAG
*
1541404 GTAAGGACTTACCTTGAGCACAAAGCCGAGGTGCATGAG
1 GTAAGGACTTACCTTGAGCACAAAGCCGAGGAGCATGAG
*
1541443 GTAAGCACTTAC
1 GTAAGGACTTAC
1541455 AAGTAATAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.21
Consensus pattern (39 bp):
GTAAGGACTTACCTTGAGCACAAAGCCGAGGAGCATGAG
Found at i:1542175 original size:18 final size:18
Alignment explanation
Indices: 1542149--1542200 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
1542139 AAATGTCAAT
* *
1542149 GTCGGTCAACGGTCAACG
1 GTCGGTCAACGATCAACA
* *
1542167 GTCGATCAACGATGAACA
1 GTCGGTCAACGATCAACA
1542185 GTCGGTCAACGATCAA
1 GTCGGTCAACGATCAA
1542201 TAGTTAACGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.17
Consensus pattern (18 bp):
GTCGGTCAACGATCAACA
Found at i:1549026 original size:23 final size:25
Alignment explanation
Indices: 1548984--1549032 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
1548974 ATTAGTTCGG
1548984 GTCGGATCAGGTCAGATCGGGTCGA
1 GTCGGATCAGGTCAGATCGGGTCGA
*
1549009 GTCGG-TCA-GTCAGGTCGGGTCGA
1 GTCGGATCAGGTCAGATCGGGTCGA
1549032 G
1 G
1549033 GCGGCCCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 15 0.65
24 3 0.13
25 5 0.22
ACGTcount: A:0.16, C:0.20, G:0.43, T:0.20
Consensus pattern (25 bp):
GTCGGATCAGGTCAGATCGGGTCGA
Found at i:1549574 original size:29 final size:29
Alignment explanation
Indices: 1549520--1549575 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1549510 GATTTGGGAT
* *
1549520 CCGAATTTAATCAAAATTTTACTTTAGCC
1 CCGAATTTAATCAAAATTTCAATTTAGCC
* *
1549549 CCGAATTTAGTTAAAATTTCAATTTAG
1 CCGAATTTAATCAAAATTTCAATTTAG
1549576 TTCTCGAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (29 bp):
CCGAATTTAATCAAAATTTCAATTTAGCC
Found at i:1557889 original size:15 final size:16
Alignment explanation
Indices: 1557857--1557889 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1557847 AAAATCTTTC
1557857 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
1557873 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
1557888 TT
1 TT
1557890 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:1568991 original size:20 final size:20
Alignment explanation
Indices: 1568966--1569004 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1568956 GCCCAATATC
*
1568966 ACATTCTAACATCAATTTCA
1 ACATTCTAAAATCAATTTCA
*
1568986 ACATTCTAAAATTAATTTC
1 ACATTCTAAAATCAATTTC
1569005 TAGCATAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (20 bp):
ACATTCTAAAATCAATTTCA
Found at i:1570222 original size:29 final size:30
Alignment explanation
Indices: 1570176--1570241 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
1570166 AAATTACCTT
1570176 TTTGGTC-CTAAACTTTTCCAA-CTTTATAC
1 TTTGGTCACTAAACTTTT-CAAGCTTTATAC
**
1570205 TTTGGTCACTAAAC-TTTCAAGCTTTATGT
1 TTTGGTCACTAAACTTTTCAAGCTTTATAC
1570234 TTTGGTCA
1 TTTGGTCA
1570242 TTAACCAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 3 0.09
29 24 0.73
30 6 0.18
ACGTcount: A:0.23, C:0.20, G:0.12, T:0.45
Consensus pattern (30 bp):
TTTGGTCACTAAACTTTTCAAGCTTTATAC
Found at i:1577760 original size:39 final size:39
Alignment explanation
Indices: 1577702--1577825 Score: 153
Period size: 39 Copynumber: 3.2 Consensus size: 39
1577692 CTAATCAAAT
* *
1577702 ATATGCACCGTAGTAATTACACATAAGGTTGTGCCCACC
1 ATATGCACCGTAGTGATTACACATAAGGTCGTGCCCACC
*
1577741 ATATGCACCGTAGTGATTACATATAAGGTCGTGCCCA-C
1 ATATGCACCGTAGTGATTACACATAAGGTCGTGCCCACC
* * * *
1577779 ATATGC-CTTGAATTGCTTACACATAAGGTCGTGCCCACC
1 ATATGCAC-CGTAGTGATTACACATAAGGTCGTGCCCACC
*
1577818 GTATGCAC
1 ATATGCAC
1577826 AAAAGTGCTT
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
37 1 0.01
38 31 0.42
39 40 0.55
40 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (39 bp):
ATATGCACCGTAGTGATTACACATAAGGTCGTGCCCACC
Found at i:1582207 original size:20 final size:20
Alignment explanation
Indices: 1582182--1582220 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1582172 GCCCAATATC
1582182 ACATTCTAACATCAATTTCA
1 ACATTCTAACATCAATTTCA
*
1582202 ACATTCTAACATTAATTTC
1 ACATTCTAACATCAATTTC
1582221 CAGCATAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (20 bp):
ACATTCTAACATCAATTTCA
Found at i:1583431 original size:30 final size:29
Alignment explanation
Indices: 1583388--1583457 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
1583378 AAATTACATT
* *
1583388 TTTGGTC-CTAAACTTTTCCAGCTTTATAC
1 TTTGGTCACTAAAC-TTTCAAGATTTATAC
1583417 TTTGGTCACTAAACTTTCAAGATTTATAC
1 TTTGGTCACTAAACTTTCAAGATTTATAC
1583446 TTTGGTCACTAA
1 TTTGGTCACTAA
1583458 CCAAAATCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 32 0.84
30 6 0.16
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (29 bp):
TTTGGTCACTAAACTTTCAAGATTTATAC
Found at i:1596122 original size:39 final size:39
Alignment explanation
Indices: 1596068--1596187 Score: 161
Period size: 39 Copynumber: 3.1 Consensus size: 39
1596058 TTAGTGAAAT
* **
1596068 ATATGCACCGTAGTGCTTACACATAAGGTTATGCCCACC
1 ATATGCACTGTAGTGCTTACACATAAGGTCGTGCCCACC
*
1596107 ATATGCACTGTAGTGCTTACACATAAGGTCGTGCCCACT
1 ATATGCACTGTAGTGCTTACACATAAGGTCGTGCCCACC
* * *
1596146 ATATGC-CTAGAATTGCTTACATATAAGGTCGTGCCCACC
1 ATATGCACT-GTAGTGCTTACACATAAGGTCGTGCCCACC
1596185 ATA
1 ATA
1596188 AGCCCCGAAG
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 2 0.03
39 70 0.97
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (39 bp):
ATATGCACTGTAGTGCTTACACATAAGGTCGTGCCCACC
Found at i:1607682 original size:19 final size:19
Alignment explanation
Indices: 1607660--1607697 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1607650 AAATTAATTC
1607660 ATATGATGGCTATGTCTTA
1 ATATGATGGCTATGTCTTA
1607679 ATATGATGGCTATGTCTTA
1 ATATGATGGCTATGTCTTA
1607698 TATTTTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (19 bp):
ATATGATGGCTATGTCTTA
Found at i:1610748 original size:18 final size:18
Alignment explanation
Indices: 1610696--1610753 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
1610686 AGTCTTGGTC
* **
1610696 TTTTACAGTACAAGGGCC
1 TTTTGCAGTACAAGGGTA
1610714 TTTTGCAGTACAAGGGTA
1 TTTTGCAGTACAAGGGTA
*
1610732 TTTTGCAGTATAAGGGTA
1 TTTTGCAGTACAAGGGTA
1610750 TTTT
1 TTTT
1610754 TGTAATTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (18 bp):
TTTTGCAGTACAAGGGTA
Found at i:1620666 original size:20 final size:20
Alignment explanation
Indices: 1620627--1620667 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1620617 CATTGCAGGA
*
1620627 ATTTATGGCTTCGACGAAAG
1 ATTTATGGCTTCCACGAAAG
1620647 ATTTCATGGCTTCCAC-AAAG
1 ATTT-ATGGCTTCCACGAAAG
1620667 A
1 A
1620668 CCTTGATGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (20 bp):
ATTTATGGCTTCCACGAAAG
Found at i:1631690 original size:17 final size:18
Alignment explanation
Indices: 1631668--1631705 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
1631658 CGATACCCCT
1631668 TCAAGG-AGTATCGATAC
1 TCAAGGTAGTATCGATAC
1631685 TCAAGGTATAGTATCGATAC
1 TCAAGG--TAGTATCGATAC
1631705 T
1 T
1631706 GAGGCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
20 12 0.67
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (18 bp):
TCAAGGTAGTATCGATAC
Found at i:1637996 original size:59 final size:59
Alignment explanation
Indices: 1637868--1637982 Score: 169
Period size: 59 Copynumber: 1.9 Consensus size: 59
1637858 CCAAAGAGCA
* *
1637868 AACCCGAATATGACACACAAGATCGTGCTCACCAACTGCACTAAGTATCCTTTAGTCCT
1 AACCCGAATATGACACACAAGATCGTGCCCACCAACTGCACTAAGTATACTTTAGTCCT
* * *
1637927 AACCCGAATATGACACATAAGGTCGTGCCCACCATA-TGCATTAAGTATACTTTAGT
1 AACCCGAATATGACACACAAGATCGTGCCCACCA-ACTGCACTAAGTATACTTTAGT
1637983 GCTATGTCGA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
59 49 0.98
60 1 0.02
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (59 bp):
AACCCGAATATGACACACAAGATCGTGCCCACCAACTGCACTAAGTATACTTTAGTCCT
Found at i:1639927 original size:31 final size:31
Alignment explanation
Indices: 1639777--1639920 Score: 234
Period size: 31 Copynumber: 4.6 Consensus size: 31
1639767 GTGAAGTGTT
* * **
1639777 CATTTTGTTACAAATCAATAACATTAGTCAC
1 CATTTTGTTACAAATCGATAACGTTAGTTGC
*
1639808 CATTTTGTTACAAATCAATAACGTTAGTTGC
1 CATTTTGTTACAAATCGATAACGTTAGTTGC
1639839 CATTTTGTTACAAATCGATAACGTTAGTTGC
1 CATTTTGTTACAAATCGATAACGTTAGTTGC
1639870 CATTTTGTTACAAATCGATAACGTTAGTTGC
1 CATTTTGTTACAAATCGATAACGTTAGTTGC
*
1639901 CATTTTGTTACAAATTGATA
1 CATTTTGTTACAAATCGATA
1639921 GTGTTAGCAA
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 108 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (31 bp):
CATTTTGTTACAAATCGATAACGTTAGTTGC
Found at i:1640679 original size:24 final size:22
Alignment explanation
Indices: 1640646--1640704 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 22
1640636 TTTCAAATTG
1640646 TTAATT-TTAAAAAAT-TTATA
1 TTAATTATTAAAAAATATTATA
1640666 GCTTATATTATTAAACAAAATATTATA
1 --TTA-ATTATT-AA-AAAATATTATA
1640693 TTAATTATTAAA
1 TTAATTATTAAA
1640705 CATACGGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
22 4 0.12
23 5 0.16
24 8 0.25
25 5 0.16
26 5 0.16
27 5 0.16
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (22 bp):
TTAATTATTAAAAAATATTATA
Found at i:1640691 original size:27 final size:23
Alignment explanation
Indices: 1640656--1640706 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 23
1640646 TTAATTTTAA
1640656 AAAATTTATAGCTTATATTATTAAAC
1 AAAATTTATA--TTA-ATTATTAAAC
1640682 AAAATATTATATTAATTATTAAAC
1 AAAAT-TTATATTAATTATTAAAC
1640706 A
1 A
1640707 TACGGTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 11 0.46
25 3 0.12
26 5 0.21
27 5 0.21
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (23 bp):
AAAATTTATATTAATTATTAAAC
Found at i:1643032 original size:21 final size:21
Alignment explanation
Indices: 1643006--1643073 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
1642996 GCCTTTGAGG
1643006 ATACATAATTAATGAATGAAA
1 ATACATAATTAATGAATGAAA
* *** ** *
1643027 ATACAT-GTGCCTTTATGAAG
1 ATACATAATTAATGAATGAAA
1643047 ATACATAATTAATGAATGAAA
1 ATACATAATTAATGAATGAAA
1643068 ATACAT
1 ATACAT
1643074 GCCCCTTTGC
Statistics
Matches: 32, Mismatches: 14, Indels: 2
0.67 0.29 0.04
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.31
Consensus pattern (21 bp):
ATACATAATTAATGAATGAAA
Found at i:1643058 original size:41 final size:39
Alignment explanation
Indices: 1642989--1643074 Score: 145
Period size: 41 Copynumber: 2.2 Consensus size: 39
1642979 GATTCGGGGT
*
1642989 TACATGTGCCTTTGAGGATACATAATTAATGAATGAAAA
1 TACATGTGCCTTTGAAGATACATAATTAATGAATGAAAA
1643028 TACATGTGCCTTTATGAAGATACATAATTAATGAATGAAAA
1 TACATGTGCC-TT-TGAAGATACATAATTAATGAATGAAAA
1643069 TACATG
1 TACATG
1643075 CCCCTTTGCA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
39 10 0.23
40 2 0.05
41 32 0.73
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.31
Consensus pattern (39 bp):
TACATGTGCCTTTGAAGATACATAATTAATGAATGAAAA
Found at i:1643475 original size:4 final size:4
Alignment explanation
Indices: 1643461--1643507 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
1643451 GTGAAATAGA
* * *
1643461 TAGC TAAC TAGC TAGG TAGC TTAGG TAGC TAGC TAG- TAGC TAGC TAG
1 TAGC TAGC TAGC TAGC TAGC -TAGC TAGC TAGC TAGC TAGC TAGC TAG
1643508 GTACCTAGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (4 bp):
TAGC
Found at i:1643480 original size:8 final size:8
Alignment explanation
Indices: 1643469--1643515 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
1643459 GATAGCTAAC
1643469 TAGCTAGG
1 TAGCTAGG
1643477 TAGCTTAGG
1 TAGC-TAGG
*
1643486 TAGCTAGC
1 TAGCTAGG
*
1643494 TAG-TAGC
1 TAGCTAGG
1643501 TAGCTAGG
1 TAGCTAGG
*
1643509 TACCTAG
1 TAGCTAG
1643516 TGTCACTCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 7 0.21
8 19 0.56
9 8 0.24
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (8 bp):
TAGCTAGG
Found at i:1648100 original size:52 final size:51
Alignment explanation
Indices: 1647994--1648106 Score: 140
Period size: 51 Copynumber: 2.2 Consensus size: 51
1647984 TGGTGTACAC
* * * *
1647994 ATGTGTTAAGTGTTACACTTTTTTATTTTATTCACTTATACTGATGTAAGT
1 ATGTGTTATGTGCTACACTTTTTTACTTTATTCACTTACACTGATGTAAGT
*
1648045 ATGTGTTATGTGCTACACTTTTTTACTTTATTTA-TGCTACACT-AGTGTAAGT
1 ATGTGTTATGTGCTACACTTTTTTACTTTATTCACT--TACACTGA-TGTAAGT
1648097 ATGTGTTATG
1 ATGTGTTATG
1648107 CTTTATCACT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
50 1 0.02
51 31 0.57
52 22 0.41
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.50
Consensus pattern (51 bp):
ATGTGTTATGTGCTACACTTTTTTACTTTATTCACTTACACTGATGTAAGT
Found at i:1659246 original size:45 final size:46
Alignment explanation
Indices: 1659161--1659248 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 46
1659151 AAATAGCCTG
* * * * *
1659161 AGTGCATCGATTCATGGTCTTGTGCATCGATGAATCAAATGCACTA
1 AGTGCATCGATGCAGGGTCATGCGCATCGATGAATAAAATGCACTA
*
1659207 AGTGCATCGATGCAGGGT-ATGCGCATCGATGCATAAAATGCA
1 AGTGCATCGATGCAGGGTCATGCGCATCGATGAATAAAATGCA
1659249 TTCGATGTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 20 0.56
46 16 0.44
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (46 bp):
AGTGCATCGATGCAGGGTCATGCGCATCGATGAATAAAATGCACTA
Found at i:1660393 original size:21 final size:21
Alignment explanation
Indices: 1660369--1660412 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1660359 CTGGAGTTGG
*
1660369 AGGAGGAGCACGAGAGGAGCT
1 AGGAGGAGCACGAGAGGAACT
* * *
1660390 AGGAGTAGCTCGTGAGGAACT
1 AGGAGGAGCACGAGAGGAACT
1660411 AG
1 AG
1660413 CTCCCGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.43, T:0.11
Consensus pattern (21 bp):
AGGAGGAGCACGAGAGGAACT
Found at i:1662030 original size:44 final size:44
Alignment explanation
Indices: 1661974--1662067 Score: 122
Period size: 44 Copynumber: 2.1 Consensus size: 44
1661964 TCTGTGCATT
*
1661974 GATGCACATTC-AAGGCATGCATCGGTGCA-TCA-GCAAGATGAATC
1 GATGCACATTCAAAGGCATGCATCGATGCACT-ATG-AAG-TGAATC
*
1662018 GATGCACATTCAAAGGGATGCATCGATGCACTATGAAGTGAATC
1 GATGCACATTCAAAGGCATGCATCGATGCACTATGAAGTGAATC
1662062 GATGCA
1 GATGCA
1662068 TTAAGCATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
44 23 0.51
45 20 0.44
46 2 0.04
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (44 bp):
GATGCACATTCAAAGGCATGCATCGATGCACTATGAAGTGAATC
Found at i:1662042 original size:24 final size:23
Alignment explanation
Indices: 1661968--1662048 Score: 78
Period size: 24 Copynumber: 3.6 Consensus size: 23
1661958 CATGACTCTG
* *
1661968 TGCATTGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* *
1661991 TGCATCGGTGCATCA-GCAA--GA
1 TGCATCGATGCA-CATTCAAGGGA
*
1662012 TGAATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
1662036 TGCATCGATGCAC
1 TGCATCGATGCAC
1662049 TATGAAGTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
20 2 0.04
21 12 0.27
22 2 0.04
23 13 0.29
24 16 0.36
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:1670412 original size:14 final size:14
Alignment explanation
Indices: 1670393--1670422 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1670383 GTAATTGGTT
*
1670393 TTCTGGAAATTGAA
1 TTCTGGAAAATGAA
1670407 TTCTGGAAAATGAA
1 TTCTGGAAAATGAA
1670421 TT
1 TT
1670423 ACATTTATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (14 bp):
TTCTGGAAAATGAA
Found at i:1670466 original size:15 final size:14
Alignment explanation
Indices: 1670431--1670467 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1670421 TTACATTTAT
1670431 GGAAAATGTTTTCC
1 GGAAAATGTTTTCC
*
1670445 GGGAAATGTTTTCC
1 GGAAAATGTTTTCC
1670459 AGGAAAATG
1 -GGAAAATG
1670468 AATTACATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (14 bp):
GGAAAATGTTTTCC
Found at i:1670803 original size:23 final size:23
Alignment explanation
Indices: 1670777--1670823 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1670767 TTATATTATA
*
1670777 TTTAAAAATATTAATTAGAATAT
1 TTTAAAAATATTAATTAAAATAT
* * *
1670800 TTTAAATATCTTTATTAAAATAT
1 TTTAAAAATATTAATTAAAATAT
1670823 T
1 T
1670824 ATTAGATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTAAAAATATTAATTAAAATAT
Found at i:1670885 original size:26 final size:25
Alignment explanation
Indices: 1670856--1670951 Score: 78
Period size: 26 Copynumber: 3.8 Consensus size: 25
1670846 AATTATAAAA
1670856 AATAATATTATTCATTATTATAATTT
1 AATAATATTATT-ATTATTATAATTT
*
1670882 AATAATATCT-TATATTATTATAATAT
1 AATAATAT-TAT-TATTATTATAATTT
1670908 AAT--TGATTATT-TTATTATAATATT
1 AATAAT-ATTATTATTATTATAAT-TT
1670932 AA-AATATAATATTA-TATTAT
1 AATAATAT--TATTATTATTAT
1670952 TAGAAATATT
Statistics
Matches: 58, Mismatches: 2, Indels: 20
0.73 0.03 0.25
Matches are distributed among these distances:
23 10 0.17
24 8 0.14
25 4 0.07
26 34 0.59
27 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (25 bp):
AATAATATTATTATTATTATAATTT
Found at i:1670926 original size:31 final size:29
Alignment explanation
Indices: 1670891--1670963 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 29
1670881 TAATAATATC
* * *
1670891 TTATATTATTATAATATAATTGATTATTTTA
1 TTATAATATTAAAATATAA-T-ATTATATTA
1670922 TTATAATATTAAAATATAATATTATATTA
1 TTATAATATTAAAATATAATATTATATTA
*
1670951 TTAGAAATATTAA
1 TTA-TAATATTAA
1670964 TAAATATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 11 0.30
30 9 0.24
31 17 0.46
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (29 bp):
TTATAATATTAAAATATAATATTATATTA
Found at i:1670946 original size:21 final size:23
Alignment explanation
Indices: 1670920--1670965 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
1670910 TTGATTATTT
1670920 TATTATAATATTA-AAATA-TAA
1 TATTATAATATTAGAAATATTAA
*
1670941 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAGAAATATTAA
1670964 TA
1 TA
1670966 AATATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.55
22 5 0.23
23 5 0.23
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TATTATAATATTAGAAATATTAA
Found at i:1670972 original size:29 final size:29
Alignment explanation
Indices: 1670913--1670973 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
1670903 AATATAATTG
* * *
1670913 ATTATTTTATTATAATATTAAAATATAAT
1 ATTATATTATTAAAATATTAAAAAATAAT
*
1670942 ATTATATTATTAGAAATATTAATAAAT-AT
1 ATTATATTATTA-AAATATTAAAAAATAAT
1670971 ATT
1 ATT
1670974 TTAAACATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
ATTATATTATTAAAATATTAAAAAATAAT
Found at i:1681622 original size:81 final size:81
Alignment explanation
Indices: 1681363--1681625 Score: 384
Period size: 81 Copynumber: 3.2 Consensus size: 81
1681353 AATTTTCTAA
* * * **
1681363 AGTAAAAGATTAATAGCCTAGTTGTGCATTTGACATAAATGTGTAAATTATGAAAGTTAGATGAA
1 AGTAAAAGATTAATAGTCTAGCTGTGCATTTGACATAAATGTGTCAATTATGCCAGTTAGATGAA
* *
1681428 ATGTTAAATACCATTG
66 AGGTTAAATACCTTTG
* * *
1681444 AGTAAAAGATTAATAG-CTTAGCTGTGTATATGACATAAATGTGTCAATTATGCCAGTTATATGA
1 AGTAAAAGATTAATAGTC-TAGCTGTGCATTTGACATAAATGTGTCAATTATGCCAGTTAGATGA
1681508 AAGGTTAAATACCTTTG
65 AAGGTTAAATACCTTTG
* * *
1681525 AGTAAAAGATTAATAGTCTAGCTGTGCATTTTACAGAAATATGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATAGTCTAGCTGTGCATTTGACATAAATGTGTCAATTATGCCAGTTAGATGAA
1681590 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
*
1681606 ATTAAAAGATTAATAGTCTA
1 AGTAAAAGATTAATAGTCTA
1681626 TGCCAGTTAG
Statistics
Matches: 164, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
80 1 0.01
81 162 0.99
82 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (81 bp):
AGTAAAAGATTAATAGTCTAGCTGTGCATTTGACATAAATGTGTCAATTATGCCAGTTAGATGAA
AGGTTAAATACCTTTG
Found at i:1681649 original size:51 final size:51
Alignment explanation
Indices: 1681573--1681671 Score: 189
Period size: 51 Copynumber: 1.9 Consensus size: 51
1681563 ATATGTCAAT
*
1681573 TATGCCAGTTAGATGAAAGGTTAAATACCTTTGATTAAAAGATTAATAGTC
1 TATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGTC
1681624 TATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATA
1 TATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATA
1681672 TGCTAGCTGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.32
Consensus pattern (51 bp):
TATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGTC
Found at i:1681736 original size:132 final size:132
Alignment explanation
Indices: 1681492--1681737 Score: 368
Period size: 132 Copynumber: 1.9 Consensus size: 132
1681482 ATGTGTCAAT
* *
1681492 TATGCCAGTTATATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGTCTAGCTGTGCATTTT
1 TATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGTCTAGCTGTGCATTTG
* * * * *
1681557 ACAGAAATATGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGATTAAAAGATTAATAG
66 ACAGAAAGATGTCAATCATGCAAGATAGATGAAAGGCTAAATACCTTTGATTAAAAGATTAATAG
1681622 TC
131 TC
1681624 TATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATA-TGCTAGCTGTGCATTT
1 TATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGT-CTAGCTGTGCATTT
* * * * *
1681688 GGCAGAAAGGTGTCAATCATGCAAGATATATGAAAGGCTAATTGCCTTTG
65 GACAGAAAGATGTCAATCATGCAAGATAGATGAAAGGCTAAATACCTTTG
1681738 GGTAAAATAC
Statistics
Matches: 101, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
131 1 0.01
132 100 0.99
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (132 bp):
TATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGTCTAGCTGTGCATTTG
ACAGAAAGATGTCAATCATGCAAGATAGATGAAAGGCTAAATACCTTTGATTAAAAGATTAATAG
TC
Found at i:1692815 original size:10 final size:10
Alignment explanation
Indices: 1692800--1692824 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1692790 ATACTTTAAT
1692800 ATTATCTTTA
1 ATTATCTTTA
1692810 ATTATCTTTA
1 ATTATCTTTA
1692820 ATTAT
1 ATTAT
1692825 TATCTTTATT
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:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTATCTTTA
Found at i:1692828 original size:13 final size:12
Alignment explanation
Indices: 1692793--1692832 Score: 57
Period size: 13 Copynumber: 3.4 Consensus size: 12
1692783 TTATTACATA
1692793 CTTTAATATTAT
1 CTTTAATATTAT
1692805 CTTT-A-ATTAT
1 CTTTAATATTAT
1692815 CTTTAATTATTAT
1 CTTTAA-TATTAT
1692828 CTTTA
1 CTTTA
1692833 TTCTTATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.36
11 2 0.08
12 4 0.16
13 10 0.40
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (12 bp):
CTTTAATATTAT
Found at i:1693630 original size:17 final size:17
Alignment explanation
Indices: 1693610--1693657 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
1693600 AGCACATTAA
*
1693610 TCATTAAAGCATGTAGT
1 TCATTAAAGCATGTACT
*
1693627 TCATTCAAGCATGTACT
1 TCATTAAAGCATGTACT
*
1693644 TCATTTAAGCATGT
1 TCATTAAAGCATGT
1693658 TAGCTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (17 bp):
TCATTAAAGCATGTACT
Found at i:1695106 original size:7 final size:7
Alignment explanation
Indices: 1695094--1695257 Score: 314
Period size: 7 Copynumber: 23.7 Consensus size: 7
1695084 AGAGTAGTTA
1695094 AAAAAGG
1 AAAAAGG
1695101 AAAAAGG
1 AAAAAGG
1695108 AAAAAGG
1 AAAAAGG
1695115 AAAAAGG
1 AAAAAGG
1695122 AAAAAGG
1 AAAAAGG
1695129 AAAAAGG
1 AAAAAGG
1695136 AAAAAGG
1 AAAAAGG
1695143 AAAAAGG
1 AAAAAGG
1695150 AAAAAGG
1 AAAAAGG
1695157 AAAAAGG
1 AAAAAGG
1695164 AAAAAGG
1 AAAAAGG
1695171 AAAAAGG
1 AAAAAGG
1695178 AAAAAGG
1 AAAAAGG
1695185 AAAAA--
1 AAAAAGG
1695190 AAAAAGG
1 AAAAAGG
1695197 AAAAAGG
1 AAAAAGG
1695204 AAAAAGG
1 AAAAAGG
1695211 AAAAAGG
1 AAAAAGG
1695218 AAAAAGG
1 AAAAAGG
1695225 AAAAAGG
1 AAAAAGG
1695232 AAAAAGG
1 AAAAAGG
1695239 AAAAAGG
1 AAAAAGG
1695246 AAAAAGG
1 AAAAAGG
1695253 AAAAA
1 AAAAA
1695258 AAGAATTTGA
Statistics
Matches: 155, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.03
7 150 0.97
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:1696743 original size:13 final size:13
Alignment explanation
Indices: 1696725--1696784 Score: 66
Period size: 13 Copynumber: 4.2 Consensus size: 13
1696715 CCGACCTGAA
1696725 CCGTTTACCCGAC
1 CCGTTTACCCGAC
1696738 CCGTTTACCCGAC
1 CCGTTTACCCGAC
1696751 CCGACCTGTTAACCCGAC
1 CCG---T-TT-ACCCGAC
*
1696769 CCGTTGACCCGAC
1 CCGTTTACCCGAC
1696782 CCG
1 CCG
1696785 CTGACCGTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
13 26 0.63
14 1 0.02
15 1 0.02
16 1 0.02
17 2 0.05
18 10 0.24
ACGTcount: A:0.17, C:0.47, G:0.18, T:0.18
Consensus pattern (13 bp):
CCGTTTACCCGAC
Found at i:1696751 original size:31 final size:31
Alignment explanation
Indices: 1696713--1696784 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
1696703 ACCGGTCATA
* * *
1696713 ACCCGACCTGAACC-GTTTACCCGACCCGTTT
1 ACCCGACCCG-ACCTGTTAACCCGACCCGTTG
1696744 ACCCGACCCGACCTGTTAACCCGACCCGTTG
1 ACCCGACCCGACCTGTTAACCCGACCCGTTG
1696775 ACCCGACCCG
1 ACCCGACCCG
1696785 CTGACCGTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 3 0.08
31 34 0.92
ACGTcount: A:0.19, C:0.46, G:0.18, T:0.17
Consensus pattern (31 bp):
ACCCGACCCGACCTGTTAACCCGACCCGTTG
Found at i:1696784 original size:18 final size:18
Alignment explanation
Indices: 1696731--1696771 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1696721 TGAACCGTTT
*
1696731 ACCCGACCCGTTTACCCG
1 ACCCGACCCGTTAACCCG
*
1696749 ACCCGACCTGTTAACCCG
1 ACCCGACCCGTTAACCCG
1696767 ACCCG
1 ACCCG
1696772 TTGACCCGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.49, G:0.17, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGTTAACCCG
Found at i:1696789 original size:13 final size:13
Alignment explanation
Indices: 1696748--1696790 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
1696738 CCGTTTACCC
*
1696748 GACCCGACCTGTT
1 GACCCGACCCGTT
*
1696761 AACCCGACCCGTT
1 GACCCGACCCGTT
*
1696774 GACCCGACCCGCT
1 GACCCGACCCGTT
1696787 GACC
1 GACC
1696791 GTTGACCGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.19, C:0.47, G:0.21, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1699488 original size:54 final size:54
Alignment explanation
Indices: 1699425--1700151 Score: 916
Period size: 54 Copynumber: 13.4 Consensus size: 54
1699415 ATAAGTTCTT
* * * * *
1699425 TGGGGTGCACACATAGTGCCGATACGGTCATTCATAAGCTCATTATGAATTCCG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
* **
1699479 TGGGTTGCACACTTAGTGCCGATACGATCGTTCATAAACTTATTATGAATTTTG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
* * *
1699533 TGGGTTGCACACTTAGTGTCGATACGATCGTTCATAAACTTATTATGAATTCTG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
* * * * **
1699587 TGGGTTGCACATTTAGTACCGATACGGTCATTCATAAACTAATTATGAATTATG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
* * *
1699641 TGGGTTGCACACTTAGTGCCGATATGGTCGTTCATAAACTTCTTATGAATTTCG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
** ** **
1699695 TGGGTTGTTCACTTAGTATCGATACGGTCGTTCATAAACTTATTATGAATTTTG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
* ** * * * * *
1699749 TGGATTGCACGGTTAGTTCCAATACAGTCGCTCATAAACTTATTATGAATACCG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
* * * *
1699803 TGGGTTGTACACTTAGTGTCGATACGGTCATTCATAAA-TTCATTATGAATTCCA
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT-ATTATGAATTCCG
* *
1699857 TGGGTTGCACACTTAGTGCCGATACGGTTGTTCATAAACTTATTATGAATTCTG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
* *
1699911 TGGGTTGCACACTTAGTGCCGATACGGTCGTTTCATAAACTCATTATGAATTCCA
1 TGGGTTGCACACTTAGTGCCGATACGGTCG-TTCATAAACTTATTATGAATTCCG
* * *
1699966 TGGGTTGCACACTTAGTTCCGATACAGTTGTTCATAAACTTATTATGAATTCCG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
* * * * * * *
1700020 TGGGTTGCACACTTAGTACTGATACAGTCATTCATAAACTTATTTTGAGTTCCA
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
* * * *
1700074 TGGGTTGTACACTTAGTGTCGATACGGTCATTCATAAACTTATTATGAATTCCA
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
*
1700128 TGGGTTGCACACTTAGTTCCGATA
1 TGGGTTGCACACTTAGTGCCGATA
1700152 GTACACATAG
Statistics
Matches: 581, Mismatches: 89, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
53 2 0.00
54 529 0.91
55 50 0.09
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (54 bp):
TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
Found at i:1707377 original size:22 final size:21
Alignment explanation
Indices: 1707351--1707428 Score: 72
Period size: 22 Copynumber: 3.7 Consensus size: 21
1707341 CCGAAAGGGG
*
1707351 AGTATCGGTACCATAGAGTAAT
1 AGTATCGATACCATAGAG-AAT
1707373 AGTATCGATA-C-TGAGAGAA-
1 AGTATCGATACCAT-AGAGAAT
* *
1707392 AGGTATCGGTACCATAGTGAAGT
1 A-GTATCGATACCATAGAGAA-T
1707415 AGTATCGATACCAT
1 AGTATCGATACCAT
1707429 GGTAGGGGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
19 1 0.02
20 11 0.24
21 11 0.24
22 22 0.48
23 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (21 bp):
AGTATCGATACCATAGAGAAT
Found at i:1707883 original size:55 final size:55
Alignment explanation
Indices: 1707769--1707887 Score: 150
Period size: 55 Copynumber: 2.2 Consensus size: 55
1707759 AATGGCACTA
* * * *
1707769 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGTGCACTT
1 TGTGTGCAAAAATAAGAAATTCATAATAAGTTTATGAATTTACGTATGTGCAATG
* * * *
1707824 TGTGTGCAAAAATAATAAATTCCTAATAAGTTTATGAATTTAGGTAT-TGGTAATG
1 TGTGTGCAAAAATAAGAAATTCATAATAAGTTTATGAATTTACGTATGT-GCAATG
1707879 TGTGTGCAA
1 TGTGTGCAA
1707888 CCCACATAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 1 0.02
55 54 0.98
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (55 bp):
TGTGTGCAAAAATAAGAAATTCATAATAAGTTTATGAATTTACGTATGTGCAATG
Found at i:1708135 original size:81 final size:81
Alignment explanation
Indices: 1708018--1708509 Score: 687
Period size: 81 Copynumber: 6.1 Consensus size: 81
1708008 TATTCCAAAA
* * * * * * *
1708018 TAAAGGATTAATGGCCCAGTTGTGCATTTGACAGAAAGATGCCATTTATGCCGGTTAGACGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1708083 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * **
1708099 TAAAAGATTAATGCCCTAGTTGTGCATTTGAAAGAAATATGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1708164 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
1708180 TAAAAGATTAATGGCCTAGATGTGTATTTGACAGAAAGGTGTGAATTACGCCAGTTAGAAGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1708245 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
*
1708261 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATAAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
1708326 TTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
** * *
1708342 TAAAAGATTAATGGCCTAGTTGTTTATTTGACAGAAAGGTGTCAATCATGTCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1708407 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * * **
1708423 TAAAAGAATAATGGCCTAGCTGTGCATTTGACAGGAAGGTCTCAATCATGTAAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* * * *
1708488 GCTATATGCCTTTGGG
66 GTTAAATACCTTTGAG
1708504 TAAAAG
1 TAAAAG
1708510 TCTAAATGCT
Statistics
Matches: 369, Mismatches: 42, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 369 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:1711693 original size:45 final size:45
Alignment explanation
Indices: 1711625--1711839 Score: 235
Period size: 45 Copynumber: 4.9 Consensus size: 45
1711615 AACAAGTGAA
* * *
1711625 CAAAATAATAATGCA-AT---T-CATTATTGCCATAAAAGGATAC
1 CAAAATAATAATGCATATGGGTGCATTATCGGCATAAAAGGATGC
* *
1711665 CAAAATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGGCATAAAAGGATGC
* * * * *
1711710 CAAAATAATAATACATATGTGTGCATTATCGGCATGAAACGATTC
1 CAAAATAATAATGCATATGGGTGCATTATCGGCATAAAAGGATGC
*
1711755 CAAAATAATAATGCATATGGATGCATTATCGGCATAAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGGCATAAAAGGATGC
** * * *
1711800 CATAGTTGA-AATGTATATGGGTGCATTATCAGCATAAAAG
1 CA-AAATAATAATGCATATGGGTGCATTATCGGCATAAAAG
1711840 TATGTTATAT
Statistics
Matches: 149, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
40 15 0.10
41 2 0.01
44 1 0.01
45 128 0.86
46 3 0.02
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (45 bp):
CAAAATAATAATGCATATGGGTGCATTATCGGCATAAAAGGATGC
Found at i:1718611 original size:45 final size:45
Alignment explanation
Indices: 1718461--1718602 Score: 248
Period size: 45 Copynumber: 3.2 Consensus size: 45
1718451 AACAAATGAA
1718461 CAAAATAATAATGCATATGGGTGCATTATCGGCATAAAAGTATTG
1 CAAAATAATAATGCATATGGGTGCATTATCGGCATAAAAGTATTG
*
1718506 CAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGTATTG
1 CAAAATAATAATGCATATGGGTGCATTATCGGCATAAAAGTATTG
* * *
1718551 CAAAATAATAATGCATATGGGTGCATTATTGGCATAAAAGGATTC
1 CAAAATAATAATGCATATGGGTGCATTATCGGCATAAAAGTATTG
1718596 CAAAATA
1 CAAAATA
1718603 TGGGTGCATT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 92 1.00
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (45 bp):
CAAAATAATAATGCATATGGGTGCATTATCGGCATAAAAGTATTG
Found at i:1718646 original size:35 final size:35
Alignment explanation
Indices: 1718572--1718682 Score: 111
Period size: 35 Copynumber: 3.1 Consensus size: 35
1718562 TGCATATGGG
* **
1718572 TGCATTATTGGCATAAAAGGAT-TCCAAAAT-ATGGG
1 TGCATTATTGGCATGAAAGGATGT-CAAAATAAT-AA
*
1718607 TGCATTATTGGCATGAAAGGATGTTAAAATAATAA
1 TGCATTATTGGCATGAAAGGATGTCAAAATAATAA
* *
1718642 TGCA-TATGGGTGCATGAAAGGATGCCAAAATAATAA
1 TGCATTAT-TG-GCATGAAAGGATGTCAAAATAATAA
1718678 TGCAT
1 TGCAT
1718683 ATGGGTGCAT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
34 3 0.05
35 31 0.48
36 30 0.47
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.28
Consensus pattern (35 bp):
TGCATTATTGGCATGAAAGGATGTCAAAATAATAA
Found at i:1718649 original size:45 final size:45
Alignment explanation
Indices: 1718600--1718740 Score: 131
Period size: 45 Copynumber: 3.3 Consensus size: 45
1718590 GGATTCCAAA
**
1718600 ATATGGGTGCATTATTGGCATGAAAGGATGTTAAAATAATAATGC
1 ATATGGGTGCATTATTGGCATGAAAGGATGCCAAAATAATAATGC
1718645 ATAT-GG-G------T-GCATGAAAGGATGCCAAAATAATAATGC
1 ATATGGGTGCATTATTGGCATGAAAGGATGCCAAAATAATAATGC
* * * ** *
1718681 ATATGGGTGCATTATCGGCATGAAATGATGGCATAGCTGA-AATGC
1 ATATGGGTGCATTATTGGCATGAAAGGATGCCA-AAATAATAATGC
1718726 ATATGGGTGCATTAT
1 ATATGGGTGCATTAT
1718741 CAACATAAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 20
0.74 0.08 0.19
Matches are distributed among these distances:
36 30 0.38
37 3 0.04
38 1 0.01
43 1 0.01
44 2 0.03
45 38 0.49
46 3 0.04
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.28
Consensus pattern (45 bp):
ATATGGGTGCATTATTGGCATGAAAGGATGCCAAAATAATAATGC
Done.