Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 89
Found at i:3583482 original size:91 final size:90
Alignment explanation
Indices: 3583378--3583547 Score: 234
Period size: 91 Copynumber: 1.9 Consensus size: 90
3583368 ATGGTAGGCC
* * *
3583378 ATCTTTAGGGATGATAACATGCTTCCTA-TATGATAAGGACGGTTGGTTATCTAGGGGTAACACG
1 ATCTTTAGAGATGATAACATGCTTCCTACGA-GATAAGGACGGCTGGTTATCTA-GGGTAACACG
3583442 ACTCCTACATGATGAGAACGAGAGGTA
64 ACTCCTACATGATGAGAACGAGAGGTA
* * * * *
3583469 ATCTTTAGAGATGATAACATGGTTCCTACGAGATGATGATGGCTGGTTATCTAGGGTGACACGAC
1 ATCTTTAGAGATGATAACATGCTTCCTACGAGATAAGGACGGCTGGTTATCTAGGGTAACACGAC
*
3583534 TCCTACGTGATGAG
66 TCCTACATGATGAG
3583548 GAGGTCTAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
90 24 0.35
91 44 0.64
92 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (90 bp):
ATCTTTAGAGATGATAACATGCTTCCTACGAGATAAGGACGGCTGGTTATCTAGGGTAACACGAC
TCCTACATGATGAGAACGAGAGGTA
Found at i:3583731 original size:65 final size:64
Alignment explanation
Indices: 3583642--3583770 Score: 179
Period size: 65 Copynumber: 2.0 Consensus size: 64
3583632 CGAATATAGG
*
3583642 TGTTTCAAGAGAAACAGTCACAAGAGAGTCAAAATTTTGTTTTAAGAGAAAAAGA-CTCAAAGTT
1 TGTTTCAAGAGAAACAGTCACAAGAGAGACAAAA-TTTGTTTTAAGAGAAAAA-ATCTCAAAGTT
3583706 T
64 T
* ** * *
3583707 TGTTTTAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTTAGGAGAAAAAATCTCAAAGTTT
1 TGTTTCAAGAGAAACAGTCACAAGAGAGACAAAATTTGTTTTAAGAGAAAAAATCTCAAAGTTT
3583771 GTCAATTTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
63 1 0.02
64 27 0.47
65 29 0.51
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (64 bp):
TGTTTCAAGAGAAACAGTCACAAGAGAGACAAAATTTGTTTTAAGAGAAAAAATCTCAAAGTTT
Found at i:3589997 original size:5 final size:5
Alignment explanation
Indices: 3589982--3590011 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
3589972 ATATTTTTCA
3589982 AAAAT -AAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
3590012 GGTAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:3591033 original size:23 final size:24
Alignment explanation
Indices: 3590991--3591052 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
3590981 TTTTCCCTTT
3590991 TCTTTTTT-T-TTATTTCGTTTGA
1 TCTTTTTTCTCTTATTTCGTTTGA
*
3591013 TCTTTTTTCTCTT-TTTTGTTTGA
1 TCTTTTTTCTCTTATTTCGTTTGA
*
3591036 T-TTTGTTTCTCTAATTT
1 TCTTT-TTTCTCTTATTT
3591053 TTTTCCTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 11 0.32
23 18 0.53
24 5 0.15
ACGTcount: A:0.08, C:0.11, G:0.08, T:0.73
Consensus pattern (24 bp):
TCTTTTTTCTCTTATTTCGTTTGA
Found at i:3595240 original size:6 final size:6
Alignment explanation
Indices: 3595231--3595269 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
3595221 CCAATATTCT
* *
3595231 TTTTTC TTTTTC TTTTTC -TTTTA TTCTTC TTTTTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT
3595270 GGAGTTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:3601052 original size:72 final size:72
Alignment explanation
Indices: 3600961--3601103 Score: 250
Period size: 72 Copynumber: 2.0 Consensus size: 72
3600951 TATTTAGAAC
* *
3600961 ATATATTAATTTCTAATCATCTTAGCTTAATAAAAAATTATAATAATGTCATACTTCATTTAAAA
1 ATATACTAATTTCTAATCATCTTAGCTTAATAAAAAATTATAATAATGTCACACTTCATTTAAAA
3601026 ATATAAT
66 ATATAAT
* *
3601033 ATATACTACTTTCTAATCATCTTAGCTTAATAAACAATTATAATAATGTCACACTTCATTTAAAA
1 ATATACTAATTTCTAATCATCTTAGCTTAATAAAAAATTATAATAATGTCACACTTCATTTAAAA
3601098 ATATAA
66 ATATAA
3601104 AGTAAATACA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.40
Consensus pattern (72 bp):
ATATACTAATTTCTAATCATCTTAGCTTAATAAAAAATTATAATAATGTCACACTTCATTTAAAA
ATATAAT
Found at i:3602815 original size:6 final size:6
Alignment explanation
Indices: 3602804--3602844 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
3602794 AGGGAGGGAC
3602804 GGAGGG GGAGGG GGAGGG GGAGGG GGA-GG GGAGGG GGAGGG
1 GGAGGG GGAGGG GGAGGG GGAGGG GGAGGG GGAGGG GGAGGG
3602845 AGAGAGAGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.17, C:0.00, G:0.83, T:0.00
Consensus pattern (6 bp):
GGAGGG
Found at i:3602828 original size:11 final size:11
Alignment explanation
Indices: 3602808--3602844 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
3602798 AGGGACGGAG
3602808 GGGGAGGGGGA
1 GGGGAGGGGGA
3602819 GGGGGAGGGGGA
1 -GGGGAGGGGGA
3602831 GGGGAGGGGGA
1 GGGGAGGGGGA
3602842 GGG
1 GGG
3602845 AGAGAGAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.16, C:0.00, G:0.84, T:0.00
Consensus pattern (11 bp):
GGGGAGGGGGA
Found at i:3605520 original size:21 final size:21
Alignment explanation
Indices: 3605496--3605539 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3605486 CCCCTTCACT
* * *
3605496 CCCTTCCCCTTCCCTTTCTTC
1 CCCTTACCCTTCACTCTCTTC
*
3605517 CCCTTATCCTTCACTCTCTTC
1 CCCTTACCCTTCACTCTCTTC
3605538 CC
1 CC
3605540 TGTTACTCTG
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:0.05, C:0.55, G:0.00, T:0.41
Consensus pattern (21 bp):
CCCTTACCCTTCACTCTCTTC
Found at i:3606811 original size:65 final size:64
Alignment explanation
Indices: 3606631--3606822 Score: 178
Period size: 65 Copynumber: 3.0 Consensus size: 64
3606621 GCACTAAGAG
* * * * *
3606631 TGCATTCGATGTTTCA-AAATAGCCA-GAGTGTATCGATGCATGGCTGGTGCATCGATGCATCAA
1 TGCATTCGATGTTTCATAAA-A-TCATCAGTGCATCGATGCATGGTTGGTGCATCAATGCATCAA
3606694 A
64 A
* * *
3606695 TGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT-GTGCATCAATGCATGAA
1 TGCATTCGATG-TTTCATAAAATCATCAGTGCATCGATGCATGGT-TGGTGCATCAATGCATCAA
3606759 A
64 A
** * *
3606760 TGCATTCGATG-TTCAATTTAATACAT-GGTGCATCGATGCATGGATTGGTGCATCAGTGCATCA
1 TGCATTCGATGTTTC-ATAAAAT-CATCAGTGCATCGATGCATGG-TTGGTGCATCAATGCATCA
3606823 CTCTGAAACA
Statistics
Matches: 105, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
63 3 0.03
64 33 0.31
65 65 0.62
66 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (64 bp):
TGCATTCGATGTTTCATAAAATCATCAGTGCATCGATGCATGGTTGGTGCATCAATGCATCAAA
Found at i:3613327 original size:22 final size:21
Alignment explanation
Indices: 3613285--3613324 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3613275 AATACTATTT
3613285 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
3613306 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
3613325 ATAGAGTCTT
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:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:3615359 original size:64 final size:63
Alignment explanation
Indices: 3615272--3615481 Score: 174
Period size: 65 Copynumber: 3.3 Consensus size: 63
3615262 TGCACTAAGA
* ** *
3615272 GTGCATCGATACATCAAGGGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGTTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTT-AAAATATCCAGAGTGCATCGATGCATGGTTG
* * ** * *
3615336 GTGCATCGATGCATCAAATGCATTTGATCTTTTTATAAA-ATCCTCAGTGCATCGGTGAATGGTA
1 GTGCATCGATGCATCAAATGCATTCGA--TGTTTA-AAATATCCAGAGTGCATCGATGCATGGT-
3615400 T-
62 TG
* * * ** *
3615401 GTGCATCGATGCATTAAATGTATTCTATGTTTAATTTAATTCATG-GTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTAAAAT-ATCCA-GAGTGCATCGATGCATGG-TT
3615465 G
63 G
*
3615466 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
3615482 CTTTGAAAGA
Statistics
Matches: 113, Mismatches: 24, Indels: 17
0.73 0.16 0.11
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 41 0.36
65 58 0.51
66 8 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTAAAATATCCAGAGTGCATCGATGCATGGTTG
Found at i:3616638 original size:30 final size:28
Alignment explanation
Indices: 3616602--3616658 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 28
3616592 TTGCAGAATG
3616602 AAATGTTAGACACCAAACTGAAATAAAAAA
1 AAATGTTAGACACCAAACT-AAA-AAAAAA
*
3616632 AAATGTTAGGCACCAAACTAAAAAAAA
1 AAATGTTAGACACCAAACTAAAAAAAA
3616659 GTATACGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 5 0.19
29 3 0.12
30 18 0.69
ACGTcount: A:0.60, C:0.14, G:0.11, T:0.16
Consensus pattern (28 bp):
AAATGTTAGACACCAAACTAAAAAAAAA
Found at i:3617249 original size:21 final size:20
Alignment explanation
Indices: 3617225--3617275 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
3617215 TTTCATTTAG
3617225 TTAAAATATTTTTAAAAATGT
1 TTAAAATATTTTT-AAAATGT
* * *
3617246 TTAAAAACAATTTTAAAATTT
1 TT-AAAATATTTTTAAAATGT
3617267 TTAAAATAT
1 TTAAAATAT
3617276 GAAAACATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 5 0.21
21 10 0.42
22 9 0.38
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
TTAAAATATTTTTAAAATGT
Found at i:3628308 original size:20 final size:21
Alignment explanation
Indices: 3628278--3628317 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
3628268 TAGACGTTGG
3628278 GCTTGATGGTATCGATACTAA
1 GCTTGATGGTATCGATACTAA
3628299 GCTT-ATGGTATCGATACTA
1 GCTTGATGGTATCGATACTA
3628318 CTATATAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (21 bp):
GCTTGATGGTATCGATACTAA
Found at i:3629842 original size:19 final size:20
Alignment explanation
Indices: 3629797--3629839 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3629787 TCAAAATCAT
* * *
3629797 TTTTCAAAATTTCATTTTTC
1 TTTTCAAAATATAATTTTGC
3629817 TTTTCAAAATATAATTTTGC
1 TTTTCAAAATATAATTTTGC
3629837 TTT
1 TTT
3629840 CAAGAGAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.28, C:0.12, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTTCAAAATATAATTTTGC
Found at i:3631739 original size:24 final size:24
Alignment explanation
Indices: 3631707--3631760 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3631697 ACTAAGCCTA
*
3631707 TGGTATTGATACTATTATGTAAAG
1 TGGTATTGATACTACTATGTAAAG
3631731 TGGTATTGATACTACTATGTAAAG
1 TGGTATTGATACTACTATGTAAAG
*
3631755 TTGTAT
1 TGGTAT
3631761 CGGTACTTCT
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:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (24 bp):
TGGTATTGATACTACTATGTAAAG
Found at i:3631767 original size:24 final size:24
Alignment explanation
Indices: 3631707--3631767 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
3631697 ACTAAGCCTA
* *
3631707 TGGTATTGATACTATTATGTAAAG
1 TGGTATCGATACTACTATGTAAAG
*
3631731 TGGTATTGATACTACTATGTAAAG
1 TGGTATCGATACTACTATGTAAAG
* *
3631755 TTGTATCGGTACT
1 TGGTATCGATACT
3631768 TCTTTGGGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (24 bp):
TGGTATCGATACTACTATGTAAAG
Found at i:3646067 original size:35 final size:34
Alignment explanation
Indices: 3645982--3646068 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
3645972 ATTTGATATT
*
3645982 TAAATACAACAAACTTACAATAAGAATTAAATGC
1 TAAATACAACAAAATTACAATAAGAATTAAATGC
* * *
3646016 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGC
3646054 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
3646069 ACTGAAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 5 0.11
38 9 0.20
ACGTcount: A:0.55, C:0.11, G:0.07, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGC
Found at i:3651249 original size:31 final size:32
Alignment explanation
Indices: 3651206--3651267 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
3651196 TAGCCATGTA
3651206 TGATCAAAATGAAAACAAAAGTTAA-TTTGAG
1 TGATCAAAATGAAAACAAAAGTTAACTTTGAG
* **
3651237 TGATGAAAATGAAAATGAAAGTTAACTTTGA
1 TGATCAAAATGAAAACAAAAGTTAACTTTGA
3651268 TGACTTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.27
Consensus pattern (32 bp):
TGATCAAAATGAAAACAAAAGTTAACTTTGAG
Found at i:3668780 original size:161 final size:162
Alignment explanation
Indices: 3668511--3669000 Score: 714
Period size: 161 Copynumber: 3.0 Consensus size: 162
3668501 CTGTTTTAAA
* * * * * *
3668511 TAAAAGATTAATTGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGATAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATCATGACAGTTAGATGAAAG
* * * * * * *
3668576 GTTAGATGAC-TTGAGTAAAAGATTAATTTCCTAGATGTGCATTTGACAGAAATGTGTCAATTAT
66 GCTAAATGCCTTTGAGTTAAAGATTAATTGCCTAGATGTGCATTTGACATAAAGGTGTCAATTAT
3668640 GCCAGTTAGATGAAAGGTTAAATGCCTTTGAG
131 GCCAGTTAGATGAAAGGTTAAATGCCTTTGAG
* *
3668672 TAAAAGATTAATTGCCTAGCTGTTCATTTGGCAGAAATGTGTCAATCAT-ACAGTTAGATGAAAT
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATCATGACAGTTAGATGAAAG
* *
3668736 GCTAAATGCCTTTGAGTTAAAGATTAATTGCCTAGCTTTGCATTTGACATAAAGGTGTCAATTAT
66 GCTAAATGCCTTTGAGTTAAAGATTAATTGCCTAGATGTGCATTTGACATAAAGGTGTCAATTAT
*
3668801 GCCAGTTAGATGAAAGATTAAATGCCTTTGAG
131 GCCAGTTAGATGAAAGGTTAAATGCCTTTGAG
* *
3668833 TAAAAGATTAATTGCCTAGCTATGCATTTGGCAGAAATGTGTCAATCATGATAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATCATGACAGTTAGATGAAAG
* * * * *
3668898 GCTAAATGCCTTTAAGTTAAAGATTAAATGCCTAGATGTGCATTTGTCATAAAGGTTTCAATCAT
66 GCTAAATGCCTTTGAGTTAAAGATTAATTGCCTAGATGTGCATTTGACATAAAGGTGTCAATTAT
* * *
3668963 GCAAGTTAGATGAAAGGCTAAATGCCTTTGGG
131 GCCAGTTAGATGAAAGGTTAAATGCCTTTGAG
3668995 TAAAAG
1 TAAAAG
3669001 CCTAAATGTT
Statistics
Matches: 294, Mismatches: 33, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
160 19 0.06
161 170 0.58
162 105 0.36
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.32
Consensus pattern (162 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATCATGACAGTTAGATGAAAG
GCTAAATGCCTTTGAGTTAAAGATTAATTGCCTAGATGTGCATTTGACATAAAGGTGTCAATTAT
GCCAGTTAGATGAAAGGTTAAATGCCTTTGAG
Found at i:3669008 original size:81 final size:81
Alignment explanation
Indices: 3668511--3669000 Score: 642
Period size: 81 Copynumber: 6.1 Consensus size: 81
3668501 CTGTTTTAAA
* * *
3668511 TAAAAGATTAATTGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGATAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
* * *
3668576 GTTAGATGAC-TTGAG
66 GCTAAATGCCTTTGAG
* * * *
3668591 TAAAAGATTAATTTCCTAGATGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
*
3668656 GTTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* * * * *
3668672 TAAAAGATTAATTGCCTAGCTGTTCATTTGGCAGAAATGTGTCAATCAT-ACAGTTAGATGAAAT
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
3668736 GCTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* * * *
3668752 TTAAAGATTAATTGCCTAGCTTTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
**
3668817 ATTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* * * **
3668833 TAAAAGATTAATTGCCTAGCTATGCATTTGGCAGAAATGTGTCAATCATGATAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
*
3668898 GCTAAATGCCTTTAAG
66 GCTAAATGCCTTTGAG
* * * * * * *
3668914 TTAAAGATTAAATGCCTAGATGTGCATTTGTCATAAAGGTTTCAATCATGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
*
3668979 GCTAAATGCCTTTGGG
66 GCTAAATGCCTTTGAG
3668995 TAAAAG
1 TAAAAG
3669001 CCTAAATGTT
Statistics
Matches: 359, Mismatches: 49, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
80 139 0.39
81 220 0.61
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
GCTAAATGCCTTTGAG
Found at i:3671556 original size:42 final size:42
Alignment explanation
Indices: 3671497--3671593 Score: 160
Period size: 42 Copynumber: 2.3 Consensus size: 42
3671487 TAGTTATATT
3671497 GGTGGTTGAGCATGAAAAATAAGATATATGAGTTCCTATCTA
1 GGTGGTTGAGCATGAAAAATAAGATATATGAGTTCCTATCTA
* *
3671539 GGTGGTTGAGCATGAAAAATAAGATATCTGAGTTCCTTTCTA
1 GGTGGTTGAGCATGAAAAATAAGATATATGAGTTCCTATCTA
*
3671581 GGTGATT-AGCATG
1 GGTGGTTGAGCATG
3671594 CCAATAAGTA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 6 0.12
42 46 0.88
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (42 bp):
GGTGGTTGAGCATGAAAAATAAGATATATGAGTTCCTATCTA
Found at i:3672051 original size:31 final size:29
Alignment explanation
Indices: 3671996--3672081 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 29
3671986 TGGTTAATGT
*
3671996 CTAAAATATAATTTTTGAAAGTTTAGTGG
1 CTAAAATATAATTTTTAAAAGTTTAGTGG
*
3672025 CTAAAGTATAAATTTTGTAAAAGTTTAG-GG
1 CTAAAATAT-AATTTT-TAAAAGTTTAGTGG
* * *
3672055 ACCAAAAATATAAATTTTAAAAATTTA
1 --CTAAAATATAATTTTTAAAAGTTTA
3672082 TATATTTTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
29 8 0.17
30 17 0.36
31 15 0.32
32 7 0.15
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (29 bp):
CTAAAATATAATTTTTAAAAGTTTAGTGG
Found at i:3687003 original size:3 final size:3
Alignment explanation
Indices: 3686995--3687022 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3686985 CTGCATCATG
3686995 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3687023 AACAAGTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3693497 original size:19 final size:19
Alignment explanation
Indices: 3693473--3693520 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
3693463 AAAGGTCCTA
3693473 AATAACTAAAGAATAAAAT
1 AATAACTAAAGAATAAAAT
3693492 AATAACTAAAGAATAAAAT
1 AATAACTAAAGAATAAAAT
3693511 AATAACTAAA
1 AATAACTAAA
3693521 CATGTCTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.21
Consensus pattern (19 bp):
AATAACTAAAGAATAAAAT
Found at i:3701580 original size:44 final size:43
Alignment explanation
Indices: 3701526--3701695 Score: 196
Period size: 44 Copynumber: 3.9 Consensus size: 43
3701516 TAGTAATTAT
* * *
3701526 TTATCATTTCATTTATAGCATCCTTTCATGCCTTAATTCACAA
1 TTATCATTTCAGTTATGGCATCCTTTCATGCCTTAATGCACAA
* * * * *
3701569 TTATGCATTTCAATTATGGCATCATTTCTTGCCTAAATGCACCA
1 TTAT-CATTTCAGTTATGGCATCCTTTCATGCCTTAATGCACAA
* * * *
3701613 TTATACATTTCAGTTACGACATCCTTTCATGCCTTAATGAACTA
1 TTAT-CATTTCAGTTATGGCATCCTTTCATGCCTTAATGCACAA
*
3701657 TTATTCATTTTAGTTATGGCATCCTTTCATGCCTTAATG
1 TTA-TCATTTCAGTTATGGCATCCTTTCATGCCTTAATG
3701696 ATAACATATT
Statistics
Matches: 106, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
43 4 0.04
44 101 0.95
45 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.42
Consensus pattern (43 bp):
TTATCATTTCAGTTATGGCATCCTTTCATGCCTTAATGCACAA
Found at i:3702084 original size:22 final size:22
Alignment explanation
Indices: 3702052--3702151 Score: 100
Period size: 22 Copynumber: 4.6 Consensus size: 22
3702042 TACCACTACC
*
3702052 ATGGTATCGATACTTCTATACT
1 ATGGTACCGATACTTCTATACT
3702074 ATGGTACCGATACTTCTATACT
1 ATGGTACCGATACTTCTATACT
* *
3702096 ATGGTACCAATACCTT-TCT-CT
1 ATGGTACCGATA-CTTCTATACT
* * *
3702117 CA--GTATCGATACTACTACACT
1 -ATGGTACCGATACTTCTATACT
3702138 ATGGTACCGATACT
1 ATGGTACCGATACT
3702152 CCCTTACGGT
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
19 2 0.03
20 9 0.14
21 4 0.06
22 45 0.71
23 3 0.05
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (22 bp):
ATGGTACCGATACTTCTATACT
Found at i:3707998 original size:64 final size:63
Alignment explanation
Indices: 3707862--3707999 Score: 152
Period size: 64 Copynumber: 2.2 Consensus size: 63
3707852 GCACTAAGTA
* * ****
3707862 TGCA-TCGATGCATAAAATGCATTCGATGTTTTGAATAAGCCTAAGTGCATCGATGCATGGTG
1 TGCATTCGATGCATAAAATGCATTCGATGTTTTCAATAAACCTAAGTGCATCGATGCATAAAC
** * * *
3707924 TGTGTATCGATGCATAAAATGCATTCGATGTTTTCATTAAAACCTGAGTGCATCGATGTATAAAC
1 TGCAT-TCGATGCATAAAATGCATTCGATGTTTTCAAT-AAACCTAAGTGCATCGATGCATAAAC
3707989 TGCATTCGATG
1 TGCATTCGATG
3708000 TTCAATTTAT
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
62 2 0.03
64 36 0.60
65 22 0.37
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33
Consensus pattern (63 bp):
TGCATTCGATGCATAAAATGCATTCGATGTTTTCAATAAACCTAAGTGCATCGATGCATAAAC
Found at i:3708040 original size:20 final size:20
Alignment explanation
Indices: 3708012--3708049 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3708002 CAATTTATTC
*
3708012 ATTGGTGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
*
3708032 ATTGATGCATCGGTGCAT
1 ATTGATGCATCGATGCAT
3708050 CCCTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:3710681 original size:23 final size:22
Alignment explanation
Indices: 3710650--3710709 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 22
3710640 GGCCTTATGC
3710650 ATCGATGCACATTCAAGGAGTGT
1 ATCGATGCACATTCAAGG-GTGT
* * *
3710673 ATCGGTGCACCTTC-ATGGTGT
1 ATCGATGCACATTCAAGGGTGT
3710694 ATCGATGCACATTCAA
1 ATCGATGCACATTCAA
3710710 ATGGATGCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 16 0.52
22 3 0.10
23 12 0.39
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (22 bp):
ATCGATGCACATTCAAGGGTGT
Found at i:3715363 original size:64 final size:65
Alignment explanation
Indices: 3715293--3715452 Score: 223
Period size: 65 Copynumber: 2.5 Consensus size: 65
3715283 CGGTGCACAA
* * *
3715293 AGTGTGCATTGATGCATAAAATGCATTCGATGTTTTAAAT-AAGCCTAAGTGCATTGATGCATGG
1 AGTGTGCATCGATGCATAAAATGCATTCGATGTTTTAAATAAAACCTAAGTGCATCGATGCATGG
* * * * *
3715357 TGTGTGCATCGATGCATAAAATGCATTCAATGTTTTCATTAAAACCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATAAAATGCATTCGATGTTTTAAATAAAACCTAAGTGCATCGATGCATGG
* *
3715422 AGAGTGCATCGATGCATAAATTGCATTCGAT
1 AGTGTGCATCGATGCATAAAATGCATTCGAT
3715453 ATTCAATTTA
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
64 35 0.42
65 48 0.58
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.32
Consensus pattern (65 bp):
AGTGTGCATCGATGCATAAAATGCATTCGATGTTTTAAATAAAACCTAAGTGCATCGATGCATGG
Found at i:3715491 original size:20 final size:20
Alignment explanation
Indices: 3715466--3715503 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3715456 CAATTTATTC
3715466 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
3715486 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
3715504 CCCTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:3717078 original size:44 final size:44
Alignment explanation
Indices: 3717012--3717269 Score: 356
Period size: 44 Copynumber: 5.9 Consensus size: 44
3717002 TAGTAATTAT
* *
3717012 TTAT-CATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCA
1 TTATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGCACCA
* *
3717055 TTATGCATTTCAATTATGTCATCCTTTCATGCCTTAATGCACCA
1 TTATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGCACCA
* * * *
3717099 ATATGCATTTCACTTATGGCATCCTTTCATGCCTTAATGAACTA
1 TTATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGCACCA
* * **
3717143 TTATGCATTTTAGTTATGGCATCCTTTCATGTCTTAATGCAGTA
1 TTATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGCACCA
* *
3717187 TTATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATACACCA
1 TTATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGCACCA
** *
3717231 TTATGCATTTTTGTTATGGCATCATTTCATGCCTTAATG
1 TTATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATG
3717270 GTAACATATT
Statistics
Matches: 193, Mismatches: 21, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
43 4 0.02
44 189 0.98
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (44 bp):
TTATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGCACCA
Found at i:3717788 original size:18 final size:21
Alignment explanation
Indices: 3717767--3717815 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
3717757 TCCCCTTGTT
3717767 AGTATCGATACC-C-T-CATC
1 AGTATCGATACCACTTACATC
3717785 AGTATCGATACCACTTACATC
1 AGTATCGATACCACTTACATC
*
3717806 AGTACCGATA
1 AGTATCGATA
3717816 TTGTTCGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 12 0.44
19 1 0.04
20 1 0.04
21 13 0.48
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.27
Consensus pattern (21 bp):
AGTATCGATACCACTTACATC
Found at i:3722027 original size:23 final size:23
Alignment explanation
Indices: 3721977--3722041 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
3721967 TTATGAAGCT
* *
3721977 TTATTCATATTTCTTATTTTAGAT
1 TTATTCATATTT-TTATTTGAGAG
*
3722001 TTATTCATATTTTTATTTGGGAG
1 TTATTCATATTTTTATTTGAGAG
*
3722024 TTATT-ATGATTATTATTT
1 TTATTCAT-ATTTTTATTT
3722042 ATGTAATTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 2 0.06
23 22 0.61
24 12 0.33
ACGTcount: A:0.25, C:0.05, G:0.09, T:0.62
Consensus pattern (23 bp):
TTATTCATATTTTTATTTGAGAG
Found at i:3728245 original size:18 final size:19
Alignment explanation
Indices: 3728217--3728256 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
3728207 TTCGGTGGAA
3728217 TTTCTTTTGCACCGAAAGT
1 TTTCTTTTGCACCGAAAGT
3728236 TTTC-TTTGCACCGAAAGT
1 TTTCTTTTGCACCGAAAGT
3728254 TTT
1 TTT
3728257 AAGCCAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (19 bp):
TTTCTTTTGCACCGAAAGT
Found at i:3730436 original size:14 final size:14
Alignment explanation
Indices: 3730417--3730444 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3730407 AGATCTTCGT
3730417 CAGCTTCGGGTGGA
1 CAGCTTCGGGTGGA
3730431 CAGCTTCGGGTGGA
1 CAGCTTCGGGTGGA
3730445 GCTTGTGAAG
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:0.14, C:0.21, G:0.43, T:0.21
Consensus pattern (14 bp):
CAGCTTCGGGTGGA
Found at i:3731956 original size:23 final size:21
Alignment explanation
Indices: 3731907--3731988 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
3731897 ACAGAACCCC
* **
3731907 AGGGGGGTATCGATTCCCCTGT
1 AGGGGGG-ATCGGTTCCCCTCA
*
3731929 GGGGGGGATCGGTTCCCCTTCAA
1 AGGGGGGATCGGTTCCCC-TC-A
*
3731952 AGGGGGAATCGGTT-CCCTCA
1 AGGGGGGATCGGTTCCCCTCA
* *
3731972 TGGGGGGATCGATTCCC
1 AGGGGGGATCGGTTCCC
3731989 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
20 12 0.25
21 14 0.29
22 10 0.21
23 12 0.25
ACGTcount: A:0.15, C:0.24, G:0.38, T:0.23
Consensus pattern (21 bp):
AGGGGGGATCGGTTCCCCTCA
Found at i:3731982 original size:20 final size:21
Alignment explanation
Indices: 3731930--3731990 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
3731920 TTCCCCTGTG
3731930 GGGGGGATCGGTTCCCCTTCAAA
1 GGGGGGATCGGTT-CCC-TCAAA
* *
3731953 GGGGGAATCGGTTCCCTC-AT
1 GGGGGGATCGGTTCCCTCAAA
*
3731973 GGGGGGATCGATTCCCTC
1 GGGGGGATCGGTTCCCTC
3731991 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 12 0.35
ACGTcount: A:0.15, C:0.26, G:0.36, T:0.23
Consensus pattern (21 bp):
GGGGGGATCGGTTCCCTCAAA
Found at i:3742671 original size:21 final size:21
Alignment explanation
Indices: 3742645--3742698 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
3742635 TTAAAAGGGT
*
3742645 AGTATCGATACTCA-TTCATAG
1 AGTATCGATACTCAGGTCA-AG
*
3742666 AGTATCGATAC-CAGGTCAGG
1 AGTATCGATACTCAGGTCAAG
3742686 AGTATCGATACTC
1 AGTATCGATACTC
3742699 CCCATAGGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (21 bp):
AGTATCGATACTCAGGTCAAG
Found at i:3750599 original size:23 final size:23
Alignment explanation
Indices: 3750524--3750624 Score: 82
Period size: 23 Copynumber: 4.4 Consensus size: 23
3750514 CACCGAAGTG
*
3750524 CCACGTAGAAATGTCCCAAAGGA
1 CCACGTAGAAATATCCCAAAGGA
* * * *
3750547 CTACATAGATATATTCCAAAGGA
1 CCACGTAGAAATATCCCAAAGGA
** *
3750570 CTGCGTAGAAATGTCCCGAAA-GA
1 CCACGTAGAAATATCCC-AAAGGA
*
3750593 CCACGTAG-AATATCCCGAAGGA
1 CCACGTAGAAATATCCCAAAGGA
3750615 -CAGCGTAGAA
1 CCA-CGTAGAA
3750625 CCTTCGACTT
Statistics
Matches: 60, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
21 4 0.07
22 14 0.23
23 39 0.65
24 3 0.05
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.17
Consensus pattern (23 bp):
CCACGTAGAAATATCCCAAAGGA
Found at i:3750611 original size:22 final size:22
Alignment explanation
Indices: 3750572--3750624 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
3750562 CCAAAGGACT
*
3750572 GCGTAGAAATGTCCCGAAAGACCA
1 GCGTAG-AATATCCCGAAAGA-CA
*
3750596 -CGTAGAATATCCCGAAGGACA
1 GCGTAGAATATCCCGAAAGACA
3750617 GCGTAGAA
1 GCGTAGAA
3750625 CCTTCGACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 2 0.08
22 19 0.73
23 5 0.19
ACGTcount: A:0.38, C:0.23, G:0.26, T:0.13
Consensus pattern (22 bp):
GCGTAGAATATCCCGAAAGACA
Found at i:3750795 original size:45 final size:45
Alignment explanation
Indices: 3750701--3750888 Score: 223
Period size: 45 Copynumber: 4.2 Consensus size: 45
3750691 TATAACATTT
* *** * ** * **
3750701 CACATAGCCTATATCACATAGACATATAATCAAATATATCATTGT
1 CACATAGCTTATATCACATTTTCATATAATCACATAGGTCAATAC
* * *
3750746 CACATAACTTATATCACATTTTCATAAAATTACATAGGTCAATAC
1 CACATAGCTTATATCACATTTTCATATAATCACATAGGTCAATAC
*
3750791 CACATAGCTTATATCACATTTTCATATAATCACATAGGTCAATGC
1 CACATAGCTTATATCACATTTTCATATAATCACATAGGTCAATAC
* *
3750836 CACATAGCTTATATCACATTTTCATGTAATCACATAGGTCAATAT
1 CACATAGCTTATATCACATTTTCATATAATCACATAGGTCAATAC
*
3750881 CATATAGC
1 CACATAGC
3750889 ATGGAATATA
Statistics
Matches: 122, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 122 1.00
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (45 bp):
CACATAGCTTATATCACATTTTCATATAATCACATAGGTCAATAC
Found at i:3752394 original size:54 final size:54
Alignment explanation
Indices: 3752364--3752764 Score: 604
Period size: 54 Copynumber: 7.4 Consensus size: 54
3752354 GAATTATGTG
* * * *
3752364 GGTTGAACACATAGTGTCAATACGGAAATTCATAAACTTATTAAGGATTTCTTA
1 GGTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTA
* * *
3752418 GGTTGCACACATAGTACCAATAAGGAAATTCATAAATTTATTATGAATTTCTTA
1 GGTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTA
* * *
3752472 GGTTGCAGACATAATGCCAATATGGAAATTCATAAACTTATTATGAATTTCTTA
1 GGTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTA
*
3752526 GGTTGCACACATAGTGCCAATATGGAAATTCATAAACTTATTATGAATTTCTTA
1 GGTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTA
* * *
3752580 GGTTGTACACATAGTGCCAATACGAAAATTCACAAACTTATTATGAATTTCTTA
1 GGTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTA
* ** * * *
3752634 TGTTGCACACATAGTGCCAATACAAAAATTCATAAACTTGTTAGGAATTTATTA
1 GGTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTA
* *
3752688 GGTTACACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTA
1 GGTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTA
3752742 GGTTGCACACATAGTGCCAATAC
1 GGTTGCACACATAGTGCCAATAC
3752765 ATACATTAAG
Statistics
Matches: 315, Mismatches: 32, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 315 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (54 bp):
GGTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTA
Found at i:3759362 original size:54 final size:52
Alignment explanation
Indices: 3759280--3759516 Score: 276
Period size: 54 Copynumber: 4.4 Consensus size: 52
3759270 TTCTGTGGTT
* * * *
3759280 TTGCACACATAGTGCCGATACGATAATTCAAAAACTCATTATGAATTACGTGGG
1 TTGCACACATAGTGCCAATACGA-AATTCATAAACTTATTATGAATT-CGTAGG
* * * *
3759334 TTGCGCACATAGTGTCAATACTGAAATTCATAAACTTATTATGGATTTGTTAGG
1 TTGCACACATAGTGCCAATAC-GAAATTCATAAACTTATTATGAATTCG-TAGG
* * *
3759388 TTGCACTCATAGTGCCAATACGAATATTTATAAACTTATTATGAATTTCTTAGG
1 TTGCACACATAGTGCCAATACGAA-ATTCATAAACTTATTATGAA-TTCGTAGG
* *
3759442 TTGCACACATAGTGCCAATATGAAAATTCATAAACTTATTATGAATTTCTTAGG
1 TTGCACACATAGTGCCAATACG-AAATTCATAAACTTATTATGAA-TTCGTAGG
*
3759496 TTGTACACATAGTGCCAATAC
1 TTGCACACATAGTGCCAATAC
3759517 ATACATTAGG
Statistics
Matches: 158, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
53 4 0.03
54 148 0.94
55 6 0.04
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (52 bp):
TTGCACACATAGTGCCAATACGAAATTCATAAACTTATTATGAATTCGTAGG
Found at i:3759469 original size:108 final size:108
Alignment explanation
Indices: 3759280--3759516 Score: 325
Period size: 108 Copynumber: 2.2 Consensus size: 108
3759270 TTCTGTGGTT
* * *
3759280 TTGCACACATAGTGCCGATACGATAATTCAAAAACTCATTATGAATTACGTGGGTTGCGCACATA
1 TTGCACACATAGTGCCAATACGATAATTCAAAAACTCATTATGAATTACGTAGGTTGCACACATA
* * *
3759345 GTGTCAATACTGAAATTCATAAACTTATTATGGATTTGTTAGG
66 GTGCCAATACTGAAATTCATAAACTTATTATGAATTTCTTAGG
* * * * * *
3759388 TTGCACTCATAGTGCCAATACGA-ATATTTATAAACTTATTATGAATTTCTTAGGTTGCACACAT
1 TTGCACACATAGTGCCAATACGATA-ATTCAAAAACTCATTATGAATTACGTAGGTTGCACACAT
3759452 AGTGCCAATA-TGAAAATTCATAAACTTATTATGAATTTCTTAGG
65 AGTGCCAATACTG-AAATTCATAAACTTATTATGAATTTCTTAGG
*
3759496 TTGTACACATAGTGCCAATAC
1 TTGCACACATAGTGCCAATAC
3759517 ATACATTAGG
Statistics
Matches: 113, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
107 3 0.03
108 110 0.97
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (108 bp):
TTGCACACATAGTGCCAATACGATAATTCAAAAACTCATTATGAATTACGTAGGTTGCACACATA
GTGCCAATACTGAAATTCATAAACTTATTATGAATTTCTTAGG
Found at i:3766129 original size:4 final size:4
Alignment explanation
Indices: 3766120--3766145 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3766110 TTTTACTTGA
3766120 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
3766146 TTAGATAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:3772115 original size:20 final size:20
Alignment explanation
Indices: 3772086--3772124 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3772076 AGAGCTCATA
*
3772086 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
3772106 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
3772125 GTGGTGAAAT
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:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:3785434 original size:4 final size:4
Alignment explanation
Indices: 3785425--3785463 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
3785415 TAAGTGGGAT
* *
3785425 AAGA AAGA AAGA AAAA AAGA AAGA AAGA AAAA AAGA AAG
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG
3785464 GAAAAGTCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:3785446 original size:16 final size:16
Alignment explanation
Indices: 3785425--3785463 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
3785415 TAAGTGGGAT
3785425 AAGAAAGAAAGAAAAA
1 AAGAAAGAAAGAAAAA
3785441 AAGAAAGAAAGAAAAA
1 AAGAAAGAAAGAAAAA
3785457 AAGAAAG
1 AAGAAAG
3785464 GAAAAGTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAGAAAGAAAGAAAAA
Found at i:3787007 original size:23 final size:23
Alignment explanation
Indices: 3786977--3787096 Score: 145
Period size: 23 Copynumber: 5.3 Consensus size: 23
3786967 TTGAGGGTTC
*
3786977 TATGTGGTCTTTCGGGACAAAAT
1 TATGTGGTCCTTCGGGACAAAAT
3787000 TATGTGGTCCTTCGGGACAAAAT
1 TATGTGGTCCTTCGGGACAAAAT
*
3787023 TATGTGATCCTTCGGGACAAAAT
1 TATGTGGTCCTTCGGGACAAAAT
* *** **
3787046 TATGTAGTCCTTTATGACAAACC
1 TATGTGGTCCTTCGGGACAAAAT
*
3787069 TATGTGGTCCTTCGGTAC--AAT
1 TATGTGGTCCTTCGGGACAAAAT
3787090 TATGTGG
1 TATGTGG
3787097 CACTTCGATG
Statistics
Matches: 81, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
21 8 0.10
23 73 0.90
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (23 bp):
TATGTGGTCCTTCGGGACAAAAT
Found at i:3789159 original size:23 final size:23
Alignment explanation
Indices: 3789122--3789234 Score: 154
Period size: 23 Copynumber: 4.9 Consensus size: 23
3789112 GTCGAGGGTT
* * *
3789122 CTATATGGTCTTTCGAGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
*
3789145 TTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
* * * *
3789168 TTATGTGGTCCTTTGCGACAAAC
1 CTATGTGGTCCTTCGGGACAAAA
3789191 CTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
3789214 CTATGTGGTCCTTCGGGACAA
1 CTATGTGGTCCTTCGGGACAA
3789235 TTATGTTGCA
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 79 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAA
Found at i:3793540 original size:19 final size:19
Alignment explanation
Indices: 3793516--3793559 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
3793506 AATAGTAAGT
3793516 ATAAATAATACTACTA-ATA
1 ATAAATAATA-TACTATATA
3793535 ATAAATAATATACTATATA
1 ATAAATAATATACTATATA
*
3793554 GTAAAT
1 ATAAAT
3793560 GACATATGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (19 bp):
ATAAATAATATACTATATA
Found at i:3794007 original size:6 final size:6
Alignment explanation
Indices: 3793991--3794033 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
3793981 TAAAATATTT
* * * *
3793991 ATAATA GTAATA ATAATA GTAATA ATAAAA ATAAAA ATAATA A
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA A
3794034 GAATGGAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (6 bp):
ATAATA
Found at i:3794008 original size:12 final size:12
Alignment explanation
Indices: 3793991--3794032 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
3793981 TAAAATATTT
3793991 ATAATAGTAATA
1 ATAATAGTAATA
3794003 ATAATAGTAATA
1 ATAATAGTAATA
* * *
3794015 ATAAAAATAAAA
1 ATAATAGTAATA
3794027 ATAATA
1 ATAATA
3794033 AGAATGGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (12 bp):
ATAATAGTAATA
Found at i:3794360 original size:25 final size:25
Alignment explanation
Indices: 3794326--3794374 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
3794316 ATAATAGATT
* * *
3794326 ATTAATAAAATTAAATAAAATTTAG
1 ATTAAAAAAATAAAACAAAATTTAG
3794351 ATTAAAAAAATAAAACAAAATTTA
1 ATTAAAAAAATAAAACAAAATTTA
3794375 ATGGGTTACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (25 bp):
ATTAAAAAAATAAAACAAAATTTAG
Found at i:3795341 original size:2 final size:2
Alignment explanation
Indices: 3795334--3795395 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
3795324 ATTATTTAAA
3795334 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3795376 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
3795396 TATGTGACTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3795426 original size:17 final size:17
Alignment explanation
Indices: 3795404--3795437 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3795394 ATTATGTGAC
3795404 TAATATGAAAA-TAATAA
1 TAATAT-AAAAGTAATAA
3795421 TAATATAAAAGTAATAA
1 TAATATAAAAGTAATAA
3795438 CAAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAATATAAAAGTAATAA
Found at i:3795459 original size:16 final size:16
Alignment explanation
Indices: 3795440--3795475 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
3795430 AGTAATAACA
3795440 AAATAATA-TTATAAAT
1 AAATAATATTTA-AAAT
3795456 AAATAATATTTAAAAT
1 AAATAATATTTAAAAT
3795472 AAAT
1 AAAT
3795476 TTAAAAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.84
17 3 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATAATATTTAAAAT
Found at i:3797533 original size:3 final size:3
Alignment explanation
Indices: 3797525--3797585 Score: 61
Period size: 3 Copynumber: 20.0 Consensus size: 3
3797515 TTTTATTTTT
* **
3797525 TAA TAA TAA TAA TAA T-A TATA TAA TACA TAA TAA TAA TGA TAA TTT
1 TAA TAA TAA TAA TAA TAA TA-A TAA TA-A TAA TAA TAA TAA TAA TAA
*
3797571 TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA
3797586 AATGAAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3798378 original size:73 final size:73
Alignment explanation
Indices: 3797950--3798374 Score: 805
Period size: 73 Copynumber: 5.8 Consensus size: 73
3797940 TCAAAATAAT
3797950 TGTCTCAAGCGAGACAAATCTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTTTC
1 TGTCTCAAGCGAGACAAAT-TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTTTC
3798015 GAGTGAAAC
65 GAGTGAAAC
*
3798024 TGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAATAATCTCAAGTGAGATAAAGTTCTGTTTCG
1 TGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTTTCG
3798089 AGTGAAAC
66 AGTGAAAC
* *
3798097 TGTCTCAAGCGAGACAAATTTTATTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTATGTTTCG
1 TGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTTTCG
3798162 AGTGAAAC
66 AGTGAAAC
3798170 TGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTTTCG
1 TGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTTTCG
3798235 AGTGAAAC
66 AGTGAAAC
*
3798243 TGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTATTTCG
1 TGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTTTCG
3798308 AGTGAAAC
66 AGTGAAAC
3798316 TGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCT
1 TGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCT
3798375 ATTTGAAAAC
Statistics
Matches: 344, Mismatches: 7, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
73 325 0.94
74 19 0.06
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (73 bp):
TGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTTTCG
AGTGAAAC
Found at i:3798736 original size:166 final size:167
Alignment explanation
Indices: 3798413--3798741 Score: 509
Period size: 166 Copynumber: 2.0 Consensus size: 167
3798403 TATGGATGTG
* * * * *
3798413 GGAAATAGTTTACTAAGTAAGATATTATGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
1 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
** * *
3798478 AGAAAAGATTGAATGAGAAACTATGGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGA
66 AGAAAAGATAAAATGAGAAACTATGGAAAATCATTTTCTCATTATTTTTCAAAATAACATATTGA
* *
3798543 TTGGGTAACATGCCCCAATCTCAAGATAATGCTGTTT
131 TTAGGTAACATGACCCAATCTCAAGATAATGCTGTTT
* *
3798580 GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACATTTTTATTTT
1 GGAAATAGTTTACTAAGT-AAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
*
3798645 -AGAAAAGATAAAATGAGAAACTATGG-AAATCATTTTCTCATTATTTTTCAAAATATCATATTG
65 CAGAAAAGATAAAATGAGAAACTATGGAAAATCATTTTCTCATTATTTTTCAAAATAACATATTG
3798708 ATTAGGTAACATGACCCAATCTCAAGATAATGCT
130 ATTAGGTAACATGACCCAATCTCAAGATAATGCT
3798742 CATTCTTGTG
Statistics
Matches: 147, Mismatches: 14, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
166 66 0.45
167 42 0.29
168 39 0.27
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (167 bp):
GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
AGAAAAGATAAAATGAGAAACTATGGAAAATCATTTTCTCATTATTTTTCAAAATAACATATTGA
TTAGGTAACATGACCCAATCTCAAGATAATGCTGTTT
Found at i:3800741 original size:77 final size:76
Alignment explanation
Indices: 3800586--3800764 Score: 191
Period size: 77 Copynumber: 2.4 Consensus size: 76
3800576 GATGTGGGCC
* * * *
3800586 TTCAGCATGTCCCAGCA-TTGCTGATATGAACATTCAAAAATGCATCAACAGTCCTAATTTTGAT
1 TTCAGCATGCCCCAGCATTTGCTGATATAAACATTCAAAAATACATCAACAGTCCTAATTCTGAT
* **
3800650 TGAAATGGGCT
66 TAAAAAAGGCT
** * *
3800661 TTCAGCATGCCCCAGCATTTTGCTGATATAAACATTC-AGGATACATCAACATTCCTGATTCTGA
1 TTCAGCATGCCCCAGCA-TTTGCTGATATAAACATTCAAAAATACATCAACAGTCCTAATTCTGA
*
3800725 TTAAAAAAAGGTT
65 TT-AAAAAAGGCT
* * *
3800738 TTCAGAATGCCCCAACATTCGCTGATA
1 TTCAGCATGCCCCAGCATTTGCTGATA
3800765 CAGATGCTAA
Statistics
Matches: 86, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
75 16 0.19
76 32 0.37
77 38 0.44
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (76 bp):
TTCAGCATGCCCCAGCATTTGCTGATATAAACATTCAAAAATACATCAACAGTCCTAATTCTGAT
TAAAAAAGGCT
Found at i:3809316 original size:132 final size:132
Alignment explanation
Indices: 3809063--3809301 Score: 304
Period size: 132 Copynumber: 1.8 Consensus size: 132
3809053 TAAACATAAA
* * *
3809063 TAAGATATTTACTTATTTAGAAATATCAGAAAAAGACTTCTAGGTGCTTTAAGACAGCTCTTTTC
1 TAAGATATTTACTTATTTAAAAATATCAGAAAAAGACTTCTAGGTACCTTAAGACAGCTCTTTTC
** * * * ** *
3809128 TTTGATATTAAAAAATAGATAAATTACTAAAACATTTTCTTGAGATAAAAAAATTATTTTAATAT
66 TTCAATATTAAAAAAAAAATAAATTACTAAAACATTATAATAAGATAAAAAAATTATTTTAATAT
3809193 AG
131 AG
* * *
3809195 TAAGATATTTATTTATTTAAAAATATCAGAAAATGGCTTCTAGGTACCTTAAGACAGCTCTTTTC
1 TAAGATATTTACTTATTTAAAAATATCAGAAAAAGACTTCTAGGTACCTTAAGACAGCTCTTTTC
*
3809260 TTCAATATTAATAAATAAAAATAAA-TATTAAAA-A-TATAATAA
66 TTCAATATTAA-AAA-AAAAATAAATTACTAAAACATTATAATAA
3809302 TTTAAATTAA
Statistics
Matches: 90, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
131 4 0.04
132 69 0.77
133 10 0.11
134 7 0.08
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (132 bp):
TAAGATATTTACTTATTTAAAAATATCAGAAAAAGACTTCTAGGTACCTTAAGACAGCTCTTTTC
TTCAATATTAAAAAAAAAATAAATTACTAAAACATTATAATAAGATAAAAAAATTATTTTAATAT
AG
Found at i:3809428 original size:2 final size:2
Alignment explanation
Indices: 3809421--3809446 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3809411 TTATTATTTA
3809421 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3809447 TTATGTGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3809476 original size:17 final size:17
Alignment explanation
Indices: 3809456--3809489 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3809446 TTTATGTGAC
3809456 TAATATGAAAA-TAATAA
1 TAATAT-AAAAGTAATAA
3809473 TAATATAAAAGTAATAA
1 TAATATAAAAGTAATAA
3809490 CAAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAATATAAAAGTAATAA
Found at i:3809534 original size:20 final size:20
Alignment explanation
Indices: 3809509--3809546 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3809499 ATTATAAATA
3809509 AATAAT-TTAAATTTAAAAGC
1 AATAATATTAAA-TTAAAAGC
3809529 AATAATATTAAATTAAAA
1 AATAATATTAAATTAAAA
3809547 AATATATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (20 bp):
AATAATATTAAATTAAAAGC
Found at i:3809541 original size:21 final size:20
Alignment explanation
Indices: 3809509--3809547 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3809499 ATTATAAATA
*
3809509 AATAATTTAAATTTAAAAGC
1 AATAATTTAAATTAAAAAGC
3809529 AATAATATTAAATTAAAAA
1 AATAAT-TTAAATTAAAAA
3809548 ATATATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (20 bp):
AATAATTTAAATTAAAAAGC
Found at i:3810813 original size:3 final size:3
Alignment explanation
Indices: 3810805--3810865 Score: 61
Period size: 3 Copynumber: 20.0 Consensus size: 3
3810795 TTTTATTCTT
* **
3810805 TAA TAA TAA TAA TAA T-A TATA TAA TACA TAA TAA TAA TGA TAA TTT
1 TAA TAA TAA TAA TAA TAA TA-A TAA TA-A TAA TAA TAA TAA TAA TAA
*
3810851 TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA
3810866 AATGAAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3815354 original size:45 final size:45
Alignment explanation
Indices: 3815303--3815647 Score: 451
Period size: 45 Copynumber: 7.7 Consensus size: 45
3815293 TAAAACATAT
*
3815303 TTTTCTGTTGATAATGCACCCATATGCATTTCAATTATAGTATAC
1 TTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
*
3815348 TTTTCTGTTGATAATGCACTCC-TATGCATTTCAACTATAGTATAT
1 TTTTCTGTTGATAATGCAC-CCATATGCATTTCAACTATAGTATAC
* *
3815393 TTTTCTATTGATAATGTACCCATATGCATTTCAACTATAGTATAC
1 TTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
* ** * * *
3815438 TCTTCTGTTGATAATGTGCCCATATACATTTCAACTCTAGCATAC
1 TTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
* *
3815483 TTTTCTGTTGATAATCCACCCATATGCATTTCAACTATAGCATAC
1 TTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
* * * *
3815528 TTTTCTGTTGATAATGTACTCATATACATTTCAACTATCGTATAC
1 TTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
* * *
3815573 TTTTCTGTTGATAATGCACCCATATACATTTCAACTATGGCAT-C
1 TTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
* ***
3815617 CTTTCATGCCAATAATGCACCCATATGCATT
1 TTTTC-TGTTGATAATGCACCCATATGCATT
3815648 AGTGATTTCA
Statistics
Matches: 265, Mismatches: 32, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
44 7 0.03
45 256 0.97
46 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.40
Consensus pattern (45 bp):
TTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATAC
Found at i:3816086 original size:20 final size:20
Alignment explanation
Indices: 3816058--3816099 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3816048 TTGGTTCCGA
* *
3816058 AGTATCGATACTACTACCCT
1 AGTACCGATACTACTACACT
*
3816078 AGTACCGATACTTCTACACT
1 AGTACCGATACTACTACACT
3816098 AG
1 AG
3816100 GGTATCGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (20 bp):
AGTACCGATACTACTACACT
Found at i:3818505 original size:12 final size:12
Alignment explanation
Indices: 3818488--3818514 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3818478 TAATAATAAA
3818488 TAATTGAAATTC
1 TAATTGAAATTC
3818500 TAATTGAAATTC
1 TAATTGAAATTC
3818512 TAA
1 TAA
3818515 GTAAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (12 bp):
TAATTGAAATTC
Found at i:3821740 original size:616 final size:615
Alignment explanation
Indices: 3820543--3822028 Score: 2776
Period size: 616 Copynumber: 2.4 Consensus size: 615
3820533 ATGCAATAAG
*
3820543 TTTGCGAGAGCATTTTATTTTTTATTCTTTACTTTTGTATAGTTTACTTTATATTTTACTTTTTC
1 TTTGCGAGAGCATTTTATTTTTTCTTCTTTACTTTTGTATAGTTTACTTTATATTTTACTTTTTC
*
3820608 TTTTTTAGGCTTATTTGGTGTATGCCTAGAAGACGTTCTAATGAGCCATTTGAACCAATTGAACC
66 TTTTTTAGGCTTATTTGGTGTATGCCTAGAAGACGTTCTGATGAGCCATTTGAACCAATTGAACC
*
3820673 TGAGTTTGAAAGACTTCCGAGGTATTCCAAAATGTTGAACCTACTGATAGGCCCCGTGTTATTCG
131 TGAGTTTGAAAGACTTCCGAGGTATTCCAAAATGTTGGACCTACTGATAGGCCCCGTGTTATTCG
3820738 TGATCATTTGAATCCTATACTGGATTATCTGAATCCTAGAATTATGGCACTCAAAATTCAGTATT
196 TGATCATTTGAATCCTATACTGGATTATCTGAATCCTAGAATTATGGCACTCAAAATTCAGTATT
* *
3820803 TACCTTTTTGTTTACCTTTACATTGTCATTTGATTTCACTACACACACTTTATTTTTCCACGGCA
261 TACCTTTTTGTTTACCTTTACATTATCATTTGATTTCACTACACACACTTTATTTTTCCACGACA
* * *
3820868 TCTCTATTTGCTACCACATCACACTATCATTCCCTTCTCACCAATACATATTGCCTTGATATTCT
326 TCTCTATTTGCTACCACATCACACTATCATTCCCTCCTCACCAATAAATATTGCCGTGATATTCT
3820933 CCATTGATATATGTCATCACGCTAACTATACTTAGATAAAGTAGTTGTTTTCTTTTGTTAAACTC
391 CCATTGATATATGTCATCACGCTAACTATACTTAGATAAAGTAGTTGTTTTCTTTTGTTAAACTC
3820998 ATAAATTTCCACCAATCCCTGTGGAGATGATACTCATCATTATATTACTTGATTGATTATGTATA
456 ATAAATTTCCACCAATCCCTGTGGAGATGATACTCATCATTATATTACTTGATTGATTATGTATA
3821063 CTTGCACATTAATTGCATAAAATTTTATATTACTCACAACATGCAATAAGTTTTTAGCATCGTTG
521 CTTGCACATTAATTGCATAAAATTTTATATTACTCACAACATGCAATAAGTTTTTAGCATCGTTG
3821128 TTGGGGATTGGCAACATGAAGTTAATTAGT
586 TTGGGGATTGGCAACATGAAGTTAATTAGT
3821158 TTTGCGAGAGCATTTTATTTTTTTCTTCTTTACTTTTGTATAGTTTACTTTATATTTTACTTTTT
1 TTTGCGAGAGCATTTTA-TTTTTTCTTCTTTACTTTTGTATAGTTTACTTTATATTTTACTTTTT
*
3821223 CTTTTTTAGGCTTATTTGGTGTATGCCTAGAAGGCGTTCTGATGAGCCATTTGAACCAATTGAAC
65 CTTTTTTAGGCTTATTTGGTGTATGCCTAGAAGACGTTCTGATGAGCCATTTGAACCAATTGAAC
3821288 CTGAGTTTGAAAGACTTCCGAGGTATTCCAAAATGTTGGACCTACTGATAGGCCCCGTGTTATTC
130 CTGAGTTTGAAAGACTTCCGAGGTATTCCAAAATGTTGGACCTACTGATAGGCCCCGTGTTATTC
3821353 GTGATCATTTGAATCCTATACTGGATTATCTGAATCCTAGAATTATGGCACTCAAAATTCAGTAT
195 GTGATCATTTGAATCCTATACTGGATTATCTGAATCCTAGAATTATGGCACTCAAAATTCAGTAT
3821418 TTACCTTTTTGTTTACCTTTACATTATCATTTGATTTCACTACACACACTTTATTTTTCCACGAC
260 TTACCTTTTTGTTTACCTTTACATTATCATTTGATTTCACTACACACACTTTATTTTTCCACGAC
3821483 ATCTCTATTTGCTACCACATCACACTATCATTCCCTCCTCACCAATAAATATTGCCGTGATATTC
325 ATCTCTATTTGCTACCACATCACACTATCATTCCCTCCTCACCAATAAATATTGCCGTGATATTC
3821548 TCCATTGATATATGTCATCACGCTAACTATACTTAGATAAAGTAGTTGTTTTCTTTTGTTAAACT
390 TCCATTGATATATGTCATCACGCTAACTATACTTAGATAAAGTAGTTGTTTTCTTTTGTTAAACT
3821613 CATAAATTTCCACCAATCCCTGTGGAGATGATACTCATCATTATATTACTTGATTGATTATGTAT
455 CATAAATTTCCACCAATCCCTGTGGAGATGATACTCATCATTATATTACTTGATTGATTATGTAT
*
3821678 ACTTGCACATTAATTGCATATAATTTTATATTACTCACAACATGCAATAAGTTTTTAGCATCGTT
520 ACTTGCACATTAATTGCATAAAATTTTATATTACTCACAACATGCAATAAGTTTTTAGCATCGTT
3821743 GTTGGGGATTGGCAACATGAAGTTAATTAGT
585 GTTGGGGATTGGCAACATGAAGTTAATTAGT
* *
3821774 TTTGTGAGAGCATTTTCA-TTTTTCTTTTTTACTTTTGTATAGTTTACTTTATATTTTACTTTTT
1 TTTGCGAGAGCATTTT-ATTTTTTCTTCTTTACTTTTGTATAGTTTACTTTATATTTTACTTTTT
* *
3821838 CTTTTTTAGGCTTATTTGGTGTATGTCTAGAAGACGTTCTGATGAGTCATTTGAACCAATTGAAC
65 CTTTTTTAGGCTTATTTGGTGTATGCCTAGAAGACGTTCTGATGAGCCATTTGAACCAATTGAAC
* * *
3821903 CTGAGTTTGAAAGACTTCCAAGGCATTCCAAAATATTGGACCTACTGATAGGCCCCGTGTTATTC
130 CTGAGTTTGAAAGACTTCCGAGGTATTCCAAAATGTTGGACCTACTGATAGGCCCCGTGTTATTC
* *
3821968 GTGATCATTTGAATCCTATATTGGATTATCTGAATCCTGGAATTATGGCACTCAAAATTCA
195 GTGATCATTTGAATCCTATACTGGATTATCTGAATCCTAGAATTATGGCACTCAAAATTCA
3822029 AGCAGCTCAT
Statistics
Matches: 849, Mismatches: 20, Indels: 4
0.97 0.02 0.00
Matches are distributed among these distances:
615 245 0.29
616 603 0.71
617 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (615 bp):
TTTGCGAGAGCATTTTATTTTTTCTTCTTTACTTTTGTATAGTTTACTTTATATTTTACTTTTTC
TTTTTTAGGCTTATTTGGTGTATGCCTAGAAGACGTTCTGATGAGCCATTTGAACCAATTGAACC
TGAGTTTGAAAGACTTCCGAGGTATTCCAAAATGTTGGACCTACTGATAGGCCCCGTGTTATTCG
TGATCATTTGAATCCTATACTGGATTATCTGAATCCTAGAATTATGGCACTCAAAATTCAGTATT
TACCTTTTTGTTTACCTTTACATTATCATTTGATTTCACTACACACACTTTATTTTTCCACGACA
TCTCTATTTGCTACCACATCACACTATCATTCCCTCCTCACCAATAAATATTGCCGTGATATTCT
CCATTGATATATGTCATCACGCTAACTATACTTAGATAAAGTAGTTGTTTTCTTTTGTTAAACTC
ATAAATTTCCACCAATCCCTGTGGAGATGATACTCATCATTATATTACTTGATTGATTATGTATA
CTTGCACATTAATTGCATAAAATTTTATATTACTCACAACATGCAATAAGTTTTTAGCATCGTTG
TTGGGGATTGGCAACATGAAGTTAATTAGT
Found at i:3823538 original size:29 final size:29
Alignment explanation
Indices: 3823471--3823528 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
3823461 AAAGTGTGTG
*
3823471 GACATTCTTGATCAACTCCGTATTAATGT
1 GACATTCTTGATCAACTCCATATTAATGT
3823500 GACATTCTTGATCAACTCCATATTAATGT
1 GACATTCTTGATCAACTCCATATTAATGT
3823529 ACTTTTCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (29 bp):
GACATTCTTGATCAACTCCATATTAATGT
Found at i:3833050 original size:18 final size:17
Alignment explanation
Indices: 3833020--3833057 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
3833010 ATCGATACTG
*
3833020 ACCCCTTGGGTATCGAT
1 ACCCCTTGAGTATCGAT
3833037 ACCCACTTGAGTATCGAT
1 ACCC-CTTGAGTATCGAT
3833055 ACC
1 ACC
3833058 AAAATTAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (17 bp):
ACCCCTTGAGTATCGAT
Found at i:3833236 original size:20 final size:21
Alignment explanation
Indices: 3833193--3833245 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
3833183 AAAAGGCATC
3833193 AGTATCGATACTGACTCTCTG
1 AGTATCGATACTGACTCTCTG
*
3833214 AGTATCGATATTAGAC-C-CTG
1 AGTATCGATACT-GACTCTCTG
3833234 AGTATCGATACT
1 AGTATCGATACT
3833246 CTTTGAAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 14 0.48
21 12 0.41
22 3 0.10
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (21 bp):
AGTATCGATACTGACTCTCTG
Found at i:3836367 original size:32 final size:29
Alignment explanation
Indices: 3836313--3836382 Score: 68
Period size: 32 Copynumber: 2.3 Consensus size: 29
3836303 AAAAAAGAAG
***
3836313 AAAAAATATAAATGGATAAAAATACACATAAA
1 AAAAAATATAAAACAATAAAAAT-CA-A-AAA
* *
3836345 AAAAAATATAAAACAATGAAAATGAAAAA
1 AAAAAATATAAAACAATAAAAATCAAAAA
3836374 AAAAAATAT
1 AAAAAATAT
3836383 GCGTAATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 12 0.36
30 1 0.03
31 1 0.03
32 19 0.58
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (29 bp):
AAAAAATATAAAACAATAAAAATCAAAAA
Found at i:3836588 original size:23 final size:20
Alignment explanation
Indices: 3836554--3836608 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 20
3836544 ACATATACGT
3836554 ATATAATAATAAAAAAATATA
1 ATATAATAATAAAAAAATA-A
*
3836575 ATATAATAGCATAAATAAATAA
1 ATATAATA--ATAAAAAAATAA
3836597 ATAATAATAATA
1 AT-ATAATAATA
3836609 GTAAAAAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 11 0.37
22 3 0.10
23 16 0.53
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (20 bp):
ATATAATAATAAAAAAATAA
Found at i:3838022 original size:12 final size:12
Alignment explanation
Indices: 3837996--3838040 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
3837986 GAAAAAAATG
3837996 TAATA-AATATA
1 TAATATAATATA
*
3838007 TAATATAATTTA
1 TAATATAATATA
3838019 TAATATAAATATA
1 TAATAT-AATATA
3838032 TATATATAA
1 TA-ATATAA
3838041 GGACGAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 9 0.31
14 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATATAATATA
Found at i:3838275 original size:20 final size:20
Alignment explanation
Indices: 3838252--3838293 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3838242 GAATCCTTCG
3838252 TCGTGAAATTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
*
3838272 TCGTGAAGTTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
3838292 TC
1 TC
3838294 AGAGTTCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGTGAAATTGAAATCGAAC
Found at i:3838548 original size:105 final size:105
Alignment explanation
Indices: 3838351--3838879 Score: 950
Period size: 105 Copynumber: 5.0 Consensus size: 105
3838341 CGTTGTGAAG
* * * *
3838351 CTGAAATTGGGTAATTGTTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTG
1 CTGAAATTGAG-AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
*
3838416 CCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
*
3838457 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
3838522 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* *
3838562 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCTTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
3838627 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
3838667 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
3838732 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAATTTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
3838772 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
3838837 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAGATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
3838877 CTG
1 CTG
3838880 GGTAAAACCT
Statistics
Matches: 409, Mismatches: 14, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
105 400 0.98
106 9 0.02
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
Found at i:3850252 original size:15 final size:15
Alignment explanation
Indices: 3850220--3850277 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
3850210 ATAAATGGAT
*
3850220 AAAAAATACACATA-A
1 AAAAAATA-AAATATA
3850235 AAAAAATAAAATATA
1 AAAAAATAAAATATA
* *
3850250 AAACAATGAAAAT-GA
1 AAAAAAT-AAAATATA
3850265 AAAAAA-AAAATAT
1 AAAAAATAAAATAT
3850278 GTGTAATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 5 0.14
14 4 0.11
15 21 0.60
16 5 0.14
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (15 bp):
AAAAAATAAAATATA
Found at i:3850482 original size:23 final size:20
Alignment explanation
Indices: 3850448--3850502 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 20
3850438 ACATATACGT
3850448 ATATAATAATAAAAAAATATA
1 ATATAATAATAAAAAAATA-A
*
3850469 ATATAATAGCATAAATAAATAA
1 ATATAATA--ATAAAAAAATAA
3850491 ATAATAATAATA
1 AT-ATAATAATA
3850503 GTAAAAAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 11 0.37
22 3 0.10
23 16 0.53
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (20 bp):
ATATAATAATAAAAAAATAA
Found at i:3851915 original size:12 final size:12
Alignment explanation
Indices: 3851889--3851935 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
3851879 AAAAAAAATG
3851889 TAATA-AATATA
1 TAATATAATATA
*
3851900 TAATATAATTTA
1 TAATATAATATA
3851912 TAATATAA-ATA
1 TAATATAATATA
3851923 T-ATAT-ATATA
1 TAATATAATATA
3851933 TAA
1 TAA
3851936 GGACGAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
9 1 0.03
10 8 0.26
11 9 0.29
12 13 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAATATAATATA
Found at i:3852439 original size:28 final size:28
Alignment explanation
Indices: 3852370--3852429 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
3852360 GGTATGGGAG
3852370 AGAACAAGAGAATGTAAAATGGCATCTT
1 AGAACAAGAGAATGTAAAATGGCATCTT
3852398 AGAACAAGAGAATGTAAAATGGCATCTT
1 AGAACAAGAGAATGTAAAATGGCATCTT
3852426 AGAA
1 AGAA
3852430 TAAGTTAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.48, C:0.10, G:0.22, T:0.20
Consensus pattern (28 bp):
AGAACAAGAGAATGTAAAATGGCATCTT
Found at i:3852638 original size:22 final size:22
Alignment explanation
Indices: 3852608--3852658 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
3852598 ACTGTTGGTA
* *
3852608 TTTTT-TATTATATTTTTATTT
1 TTTTTATATTACACTTTTATTT
3852629 TTTTTATATTACACTTTTATTT
1 TTTTTATATTACACTTTTATTT
3852651 TATTTTAT
1 T-TTTTAT
3852659 TTTTTAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 5 0.19
22 15 0.58
23 6 0.23
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTATATTACACTTTTATTT
Found at i:3852663 original size:17 final size:17
Alignment explanation
Indices: 3852606--3852664 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
3852596 CAACTGTTGG
*
3852606 TATTTTTTATTATATTT
1 TATTTTTTATTTTATTT
* *
3852623 T-TATTTT-TTTTATAT
1 TATTTTTTATTTTATTT
**
3852638 TACACTTTTATTTTATTT
1 TA-TTTTTTATTTTATTT
3852656 TATTTTTTA
1 TATTTTTTA
3852665 ACTTTTAATA
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
15 7 0.23
16 5 0.16
17 10 0.32
18 9 0.29
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (17 bp):
TATTTTTTATTTTATTT
Found at i:3853649 original size:6 final size:6
Alignment explanation
Indices: 3853638--3853671 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
3853628 TTATTTATTG
3853638 CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CCCA
1 CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CCCA
3853672 CCCGGCTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.47, C:0.53, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCAAA
Found at i:3854320 original size:37 final size:36
Alignment explanation
Indices: 3854261--3854334 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
3854251 TTTTGGTTGG
*
3854261 CTGACCCAAAAATTTTACCCCTCCACCCAACCCGAC
1 CTGACCCAAAAATTCTACCCCTCCACCCAACCCGAC
* *
3854297 CTGACCCGAAAAA-TCTACACCCTCCACCCGACTCGAC
1 CTGACCC-AAAAATTCTAC-CCCTCCACCCAACCCGAC
3854334 C
1 C
3854335 CGATCTCAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 11 0.33
37 22 0.67
ACGTcount: A:0.30, C:0.47, G:0.08, T:0.15
Consensus pattern (36 bp):
CTGACCCAAAAATTCTACCCCTCCACCCAACCCGAC
Found at i:3861673 original size:43 final size:43
Alignment explanation
Indices: 3861606--3861740 Score: 155
Period size: 43 Copynumber: 3.2 Consensus size: 43
3861596 GTTTACATTA
* * * *
3861606 ACAAACGCCGCAAAA-GTTAGGTTCTTTAGCGGCGTTTTAGAT
1 ACAAATGCCGCAAAAGGTCATGTTCTTTAGCAGCGTTTTAGAT
* * * *
3861648 ACAAATGCCGCAAAAGGTCATGTTCTTTAGCAACGATTAATAT
1 ACAAATGCCGCAAAAGGTCATGTTCTTTAGCAGCGTTTTAGAT
* * * *
3861691 ACAAATGTCGCAAAAGGTCATGTTTTTTAGCAGCATTTTAGAG
1 ACAAATGCCGCAAAAGGTCATGTTCTTTAGCAGCGTTTTAGAT
3861734 ACAAATG
1 ACAAATG
3861741 TTGCTAATAA
Statistics
Matches: 76, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
42 14 0.18
43 62 0.82
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (43 bp):
ACAAATGCCGCAAAAGGTCATGTTCTTTAGCAGCGTTTTAGAT
Found at i:3861793 original size:44 final size:43
Alignment explanation
Indices: 3861743--3861827 Score: 125
Period size: 44 Copynumber: 2.0 Consensus size: 43
3861733 GACAAATGTT
*
3861743 GCTAATAATTATATATATAGTGGCATTTTGCATCCAAAAATACC
1 GCTAATAATTATATATATAGTGGCATTTT-CATCAAAAAATACC
* **
3861787 GCTAATAATTATGTATATAGTGGTGTTTTCATCAAAAAATA
1 GCTAATAATTATATATATAGTGGCATTTTCATCAAAAAATA
3861828 TCATTAATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 11 0.30
44 26 0.70
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (43 bp):
GCTAATAATTATATATATAGTGGCATTTTCATCAAAAAATACC
Found at i:3862774 original size:11 final size:11
Alignment explanation
Indices: 3862758--3862789 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
3862748 TTGAGTTTTT
3862758 CCCACCTCGAA
1 CCCACCTCGAA
3862769 CCCACCTCGAA
1 CCCACCTCGAA
3862780 CCCACCTCGA
1 CCCACCTCGA
3862790 TTTTTAGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.25, C:0.56, G:0.09, T:0.09
Consensus pattern (11 bp):
CCCACCTCGAA
Found at i:3864874 original size:20 final size:20
Alignment explanation
Indices: 3864845--3864882 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3864835 TTTCAAAGGA
3864845 ATGCACCGATGCACCAATTC
1 ATGCACCGATGCACCAATTC
*
3864865 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
3864883 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCACCGATGCACCAATTC
Found at i:3864932 original size:19 final size:19
Alignment explanation
Indices: 3864910--3864961 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
3864900 AATACATTTT
*
3864910 ATGCATCGATGCACATACC
1 ATGCATCGATGCACACACC
* *
3864929 ATGCATCAATGCAGACACC
1 ATGCATCGATGCACACACC
3864948 ATGCATCGATGCAC
1 ATGCATCGATGCAC
3864962 TTGATGCTCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.31, G:0.17, T:0.19
Consensus pattern (19 bp):
ATGCATCGATGCACACACC
Found at i:3873006 original size:24 final size:25
Alignment explanation
Indices: 3872978--3873027 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
3872968 AATCGTTTTA
3872978 GAGTC-TTTTTGATTTAACAAAAAT
1 GAGTCTTTTTTGATTTAACAAAAAT
3873002 GAGTCTTTTTTGATTTAACAAAAAT
1 GAGTCTTTTTTGATTTAACAAAAAT
3873027 G
1 G
3873028 GGGAGAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (25 bp):
GAGTCTTTTTTGATTTAACAAAAAT
Found at i:3873528 original size:45 final size:45
Alignment explanation
Indices: 3873472--3873575 Score: 145
Period size: 45 Copynumber: 2.3 Consensus size: 45
3873462 TGCACATATC
* * *
3873472 ATGCATCGATGCACTCAGGTTTAATAAAAACATTGAATGCATTTT
1 ATGCATCGATGCACTCAGGCTTAATAAAAACATCGAATACATTTT
* * * *
3873517 ATGCATTGATGCACTTAGGCTTATTCAAAACATCGAATACATTTT
1 ATGCATCGATGCACTCAGGCTTAATAAAAACATCGAATACATTTT
3873562 ATGCATCGATGCAC
1 ATGCATCGATGCAC
3873576 ATACCATGCA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGCTTAATAAAAACATCGAATACATTTT
Found at i:3873599 original size:109 final size:110
Alignment explanation
Indices: 3873436--3873639 Score: 329
Period size: 109 Copynumber: 1.9 Consensus size: 110
3873426 GAATAAATTG
* *
3873436 AACATCGAATGCATTTTATACACCGATGCACATATCATGCATCGATGCACTCAGG-TTTAATAAA
1 AACATCGAATACATTTTATACACCGATGCACATACCATGCATCGATGCACTCAGGTTTTAATAAA
* * *
3873500 AACATTGAATGCATTTTATGCATTGATGCACTTAGGCTTATTCAA
66 AACATCGAATACATTTTATGCATCGATGCACTTAGGCTTATTCAA
* * *
3873545 AACATCGAATACATTTTATGCATCGATGCACATACCATGCATCGATGTACTCAGGTTTTAATAAA
1 AACATCGAATACATTTTATACACCGATGCACATACCATGCATCGATGCACTCAGGTTTTAATAAA
3873610 AACATCGAATACATTTTATGCATCGATGCA
66 AACATCGAATACATTTTATGCATCGATGCA
3873640 GACACCATGC
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
109 50 0.58
110 36 0.42
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (110 bp):
AACATCGAATACATTTTATACACCGATGCACATACCATGCATCGATGCACTCAGGTTTTAATAAA
AACATCGAATACATTTTATGCATCGATGCACTTAGGCTTATTCAA
Found at i:3873618 original size:65 final size:64
Alignment explanation
Indices: 3873517--3873706 Score: 236
Period size: 65 Copynumber: 3.0 Consensus size: 64
3873507 AATGCATTTT
* * * * *
3873517 ATGCATTGATGCACTTAGGCTTATTCAAAACATCGAATACATTTTATGCATCGATGCACATACC
1 ATGCATCGATGCACTCAGGCTTAATAAAAACATCGAATACATTTTATGCATCGATGCACACACC
* * *
3873581 ATGCATCGATGTACTCAGGTTTTAATAAAAACATCGAATACATTTTATGCATCGATGCAGACACC
1 ATGCATCGATGCACTCAGG-CTTAATAAAAACATCGAATACATTTTATGCATCGATGCACACACC
* * * * * * *
3873646 ATGCATTGATGCACTTAGGCTTATTCAAAACATTGAATGCATTTTATGCATTGATGCACAC
1 ATGCATCGATGCACTCAGGCTTAATAAAAACATCGAATACATTTTATGCATCGATGCACAC
3873707 TTAGTGCACC
Statistics
Matches: 107, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
64 51 0.48
65 56 0.52
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTCAGGCTTAATAAAAACATCGAATACATTTTATGCATCGATGCACACACC
Found at i:3877915 original size:20 final size:21
Alignment explanation
Indices: 3877892--3877933 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3877882 GAGTATCAAT
* *
3877892 ACTGA-GGGTTTGGTATTGAG
1 ACTGAGGGGCTTGGTATCGAG
3877912 ACTGAGGGGCTTGGTATCGAG
1 ACTGAGGGGCTTGGTATCGAG
3877933 A
1 A
3877934 TCGAGATTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.21, C:0.10, G:0.40, T:0.29
Consensus pattern (21 bp):
ACTGAGGGGCTTGGTATCGAG
Found at i:3878019 original size:20 final size:20
Alignment explanation
Indices: 3877996--3878047 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
3877986 CCAGGTCTCG
3877996 GTATCGATACTCCCAAATGA
1 GTATCGATACTCCCAAATGA
3878016 GTATCGATACTCCCAAATGA
1 GTATCGATACTCCCAAATGA
3878036 GTATCGATACTC
1 GTATCGATACTC
3878048 TCCCTTTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (20 bp):
GTATCGATACTCCCAAATGA
Found at i:3879795 original size:21 final size:21
Alignment explanation
Indices: 3879784--3879835 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
3879774 TGAATTTGAT
3879784 ATGGAATTGATTTGAAATTGC
1 ATGGAATTGATTTGAAATTGC
3879805 ATGGAATTGATTTGAAATTGC
1 ATGGAATTGATTTGAAATTGC
3879826 ATGGAATTGA
1 ATGGAATTGA
3879836 AGTTAGGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.37
Consensus pattern (21 bp):
ATGGAATTGATTTGAAATTGC
Found at i:3881011 original size:21 final size:23
Alignment explanation
Indices: 3880980--3881021 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
3880970 ATTGGACATG
*
3880980 TTGATATATATATATG-GATACA
1 TTGATATATATAAATGAGATACA
3881002 TTGA-ATATATAAATGAGATA
1 TTGATATATATAAATGAGATA
3881022 TGATAATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.38
Consensus pattern (23 bp):
TTGATATATATAAATGAGATACA
Found at i:3881244 original size:22 final size:22
Alignment explanation
Indices: 3881218--3881271 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
3881208 TTGCGCACAC
*
3881218 ACGTACCTTGCATTCTCATTTA
1 ACGTACATTGCATTCTCATTTA
3881240 ACGTACATTGCATTCTCATTTA
1 ACGTACATTGCATTCTCATTTA
3881262 ACGTACATTG
1 ACGTACATTG
3881272 GGCTATACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (22 bp):
ACGTACATTGCATTCTCATTTA
Found at i:3881494 original size:2 final size:2
Alignment explanation
Indices: 3881487--3881525 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3881477 ATATGCCTTT
3881487 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3881526 GTGAAAGGAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3884081 original size:49 final size:49
Alignment explanation
Indices: 3883991--3884116 Score: 141
Period size: 49 Copynumber: 2.5 Consensus size: 49
3883981 TTACCCAAAT
* *
3883991 AATATTTTTTATTTAAATTTATCACATTGAGTAGATAAATTTTAATAAAA
1 AATATATTTTA-TTAAATTTATCACATTGAGTAGATAAATTTAAATAAAA
* *
3884041 TATA-ATTTTTCTTAAATTTTATCACATTGAGATA-A-AAATTTAAATAAAA
1 AATATA-TTTTATTAAA-TTTATCACATTGAG-TAGATAAATTTAAATAAAA
*
3884090 AATATATTTTATTAAAATTCATCACAT
1 AATATATTTTATT-AAATTTATCACAT
3884117 CGACATGATG
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
49 36 0.56
50 26 0.41
51 2 0.03
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (49 bp):
AATATATTTTATTAAATTTATCACATTGAGTAGATAAATTTAAATAAAA
Found at i:3887234 original size:17 final size:17
Alignment explanation
Indices: 3887212--3887248 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
3887202 GTGTTATGAA
3887212 CCCCCTCAAACATGCTG
1 CCCCCTCAAACATGCTG
*
3887229 CCCCCTCAATCATGCTG
1 CCCCCTCAAACATGCTG
3887246 CCC
1 CCC
3887249 TGGGCTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.51, G:0.11, T:0.19
Consensus pattern (17 bp):
CCCCCTCAAACATGCTG
Found at i:3888576 original size:14 final size:14
Alignment explanation
Indices: 3888534--3888569 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3888524 CTGAAATTTA
*
3888534 TAAATAATATATAT
1 TAAATATTATATAT
*
3888548 TATATATTATATAT
1 TAAATATTATATAT
3888562 TAAATATT
1 TAAATATT
3888570 TAATATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAATATTATATAT
Found at i:3893097 original size:3 final size:3
Alignment explanation
Indices: 3893084--3893134 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
3893074 GGACCCATTT
**
3893084 TTA TT- TTA TTA TTA TTA TTA TTAA TTA AAA TTA CTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA -TTA TTA TTA TTA
3893130 TTA TT
1 TTA TT
3893135 TTTGATTGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.80
4 6 0.15
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:3894080 original size:16 final size:16
Alignment explanation
Indices: 3894058--3894097 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
3894048 TGCCGGTTTT
*
3894058 AAAAAAAATGAAAAATG
1 AAAAAAAA-GAAAAAAG
3894075 AAAAAAAAGAAAAAAG
1 AAAAAAAAGAAAAAAG
3894091 AAAAAAA
1 AAAAAAA
3894098 GTGATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (16 bp):
AAAAAAAAGAAAAAAG
Found at i:3896911 original size:15 final size:15
Alignment explanation
Indices: 3896891--3896922 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3896881 GGAGAACTTA
3896891 TGGTCTGATGAAGGT
1 TGGTCTGATGAAGGT
3896906 TGGTCTGATGAAGGT
1 TGGTCTGATGAAGGT
3896921 TG
1 TG
3896923 TTCTATGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.41, T:0.34
Consensus pattern (15 bp):
TGGTCTGATGAAGGT
Found at i:3898747 original size:3 final size:3
Alignment explanation
Indices: 3898734--3898779 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
3898724 GTTTTAATTA
* *
3898734 ATT ATT A-T ATT ATT ATT ATT ATT GTT ATT ATT GTT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3898780 CATAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3911182 original size:15 final size:15
Alignment explanation
Indices: 3911153--3911196 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
3911143 CATGCATTTA
*
3911153 TTCATTATTTATTAT
1 TTCATTATATATTAT
3911168 TT-ATGTATATATTAT
1 TTCAT-TATATATTAT
3911183 TTCATTATAT-TTAT
1 TTCATTATATATTAT
3911197 CTTTATATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.23
15 18 0.69
16 2 0.08
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (15 bp):
TTCATTATATATTAT
Found at i:3914819 original size:45 final size:44
Alignment explanation
Indices: 3914735--3914819 Score: 100
Period size: 45 Copynumber: 1.9 Consensus size: 44
3914725 AAAATAAATA
* *
3914735 AAATGGGGCTCAAGATGAAAATCCATAAAGGGAGTCTTGAAACC
1 AAATGGGGCTCAAGATGAAAATCCACAAAGGGAGGCTTGAAACC
* * *
3914779 AAATGAGGTCTCAAGTTGAAAA-CCTACAAAGGGTGGCTTGA
1 AAATG-GGGCTCAAGATGAAAATCC-ACAAAGGGAGGCTTGA
3914820 GTGTCATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
44 7 0.21
45 27 0.79
ACGTcount: A:0.39, C:0.15, G:0.26, T:0.20
Consensus pattern (44 bp):
AAATGGGGCTCAAGATGAAAATCCACAAAGGGAGGCTTGAAACC
Found at i:3920153 original size:15 final size:15
Alignment explanation
Indices: 3920133--3920166 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
3920123 GTTATCTTCA
3920133 GAATATCTTTCTCCT
1 GAATATCTTTCTCCT
3920148 GAATATCTTTCTCCT
1 GAATATCTTTCTCCT
3920163 GAAT
1 GAAT
3920167 CTTCAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.44
Consensus pattern (15 bp):
GAATATCTTTCTCCT
Found at i:3921824 original size:9 final size:9
Alignment explanation
Indices: 3921812--3921837 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3921802 GATAATTAAT
3921812 GAAATGAAA
1 GAAATGAAA
3921821 GAAATGAAA
1 GAAATGAAA
3921830 GAAATGAA
1 GAAATGAA
3921838 TAGAGTTGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.23, T:0.12
Consensus pattern (9 bp):
GAAATGAAA
Found at i:3928231 original size:21 final size:21
Alignment explanation
Indices: 3928155--3928232 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
3928145 TATACATATT
* * *
3928155 CCAAAAGACCAAATATGTGTC
1 CCAAAGGACCACATATATGTC
* ** *
3928176 TCAAAGGACTTCATATATGTT
1 CCAAAGGACCACATATATGTC
**
3928197 CCAAAGGATTACATATATGTC
1 CCAAAGGACCACATATATGTC
*
3928218 CCGAAGGACCACATA
1 CCAAAGGACCACATA
3928233 GACCCTCGAC
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.24
Consensus pattern (21 bp):
CCAAAGGACCACATATATGTC
Found at i:3928889 original size:20 final size:21
Alignment explanation
Indices: 3928864--3928918 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
3928854 ATTCTAAAAA
*
3928864 TGGTATCGATACCTGA-CTTC
1 TGGTATCGATACCTAACCTTC
*
3928884 TGGTATCGATA-CTAACCCTTT
1 TGGTATCGATACCTAA-CCTTC
3928905 TGGTATCGATACCT
1 TGGTATCGATACCT
3928919 CAAGAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 3 0.10
20 11 0.37
21 14 0.47
22 2 0.07
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (21 bp):
TGGTATCGATACCTAACCTTC
Found at i:3932237 original size:21 final size:22
Alignment explanation
Indices: 3932208--3932261 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 22
3932198 TCATGGGGGT
*
3932208 ATCGCTTCCC-TAAAAGAGGAA
1 ATCGGTTCCCATAAAAGAGGAA
* * *
3932229 ATCGGTTCCCATTCAAAGGGGGA
1 ATCGGTTCCCA-TAAAAGAGGAA
3932252 ATCGGTTCCC
1 ATCGGTTCCC
3932262 CTTCAAGGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 9 0.33
23 18 0.67
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (22 bp):
ATCGGTTCCCATAAAAGAGGAA
Found at i:3932272 original size:22 final size:23
Alignment explanation
Indices: 3932228--3932272 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3932218 TAAAAGAGGA
3932228 AATCGGTTCCCATTCAAAGGGGG
1 AATCGGTTCCCATTCAAAGGGGG
*
3932251 AATCGGTTCCCCTTC-AAGGGGG
1 AATCGGTTCCCATTCAAAGGGGG
3932273 TATTGATTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.22
Consensus pattern (23 bp):
AATCGGTTCCCATTCAAAGGGGG
Done.