Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008752.1 Hibiscus syriacus cultivar Beakdansim tig00111843_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: 1143363
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1006431 original size:23 final size:23
Alignment explanation
Indices: 1006385--1006431 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1006375 AAAAAACAGA
*
1006385 AAAAAGAGAGAGAAAATGATGAG
1 AAAAAGAGAGAGAAAAGGATGAG
*
1006408 AAAAAGAGAGAAGAAAGGGA-GAG
1 AAAAAGAGAG-AGAAAAGGATGAG
1006431 A
1 A
1006432 GAGTCATCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.04
Consensus pattern (23 bp):
AAAAAGAGAGAGAAAAGGATGAG
Found at i:1007160 original size:38 final size:38
Alignment explanation
Indices: 1007108--1007182 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
1007098 TCATCGAAAC
*
1007108 TTTAAATTTTCATTTAAATTTCAACTTTCATGATTAAT
1 TTTAAATTTCCATTTAAATTTCAACTTTCATGATTAAT
1007146 TTTAAATTTCCATTTAAATTTCAACTTTCATGATTAA
1 TTTAAATTTCCATTTAAATTTCAACTTTCATGATTAA
1007183 GACAACAAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.51
Consensus pattern (38 bp):
TTTAAATTTCCATTTAAATTTCAACTTTCATGATTAAT
Found at i:1011141 original size:46 final size:44
Alignment explanation
Indices: 1011087--1011176 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 44
1011077 TTGAAAAAGC
* * *
1011087 CTGAGTGCATCGATGCATGGTCTTGTGTATTGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCAT-AAATGCA
1011133 CTGAGTGCATCGATGCATGGTATGTGCATCGATGCATAAATGCA
1 CTGAGTGCATCGATGCATGGTATGTGCATCGATGCATAAATGCA
1011177 TTCGATGTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 7 0.17
45 13 0.32
46 21 0.51
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (44 bp):
CTGAGTGCATCGATGCATGGTATGTGCATCGATGCATAAATGCA
Found at i:1011224 original size:20 final size:20
Alignment explanation
Indices: 1011196--1011234 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1011186 CAAGAAATTA
1011196 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
1011216 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
1011235 CCCTTGAAAA
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:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:1013879 original size:24 final size:24
Alignment explanation
Indices: 1013859--1013926 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
1013849 GCATCAATAT
*
1013859 GATGAATCGATGCACATTCAAAGG
1 GATGCATCGATGCACATTCAAAGG
1013883 GATGCATCGATGCACATTCAAAGG
1 GATGCATCGATGCACATTCAAAGG
1013907 GATGCATCGATGCAC-TTCAA
1 GATGCATCGATGCACATTCAA
1013927 GTGTATCGAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
23 5 0.12
24 38 0.88
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.22
Consensus pattern (24 bp):
GATGCATCGATGCACATTCAAAGG
Found at i:1017577 original size:22 final size:21
Alignment explanation
Indices: 1017535--1017574 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1017525 GAATTTATTT
*
1017535 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1017556 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1017575 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1019653 original size:63 final size:64
Alignment explanation
Indices: 1019534--1019675 Score: 168
Period size: 64 Copynumber: 2.2 Consensus size: 64
1019524 TGCACTAAGA
* *
1019534 GTGCATCAATGCATAAAATGCATTCGATGTTTTGAAAAAGCTTGAGTGCATCGATGCATGG-TAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTAGAAAAA-CTTGAGTGCATCGATGCATGGAT-T
1019598 -
64 G
*
1019598 GTGCATCGATGCAT-AAATGCATTCGATGTTTAAGAAATTAA-TTGA-TGCATTGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTT-AGAAA--AACTTGAGTGCATCGATGCATGGAT
1019660 TG
63 TG
*
1019662 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
1019676 GCCCTTGAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
63 32 0.46
64 35 0.51
66 2 0.03
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTAGAAAAACTTGAGTGCATCGATGCATGGATTG
Found at i:1020039 original size:19 final size:20
Alignment explanation
Indices: 1020001--1020040 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1019991 TTTGAAATTA
*
1020001 CTCCCCCTTACTATAACATTT
1 CTCCCCCTTA-TAAAACATTT
1020022 CTCCCCCTT-TAAAACATTT
1 CTCCCCCTTATAAAACATTT
1020041 TACACTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.38
Consensus pattern (20 bp):
CTCCCCCTTATAAAACATTT
Found at i:1026206 original size:22 final size:21
Alignment explanation
Indices: 1026164--1026203 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1026154 GAGTTTATTT
*
1026164 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1026185 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1026204 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1032625 original size:12 final size:12
Alignment explanation
Indices: 1032608--1032648 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
1032598 GTGTACCTAA
1032608 AAAATAAAAAAT
1 AAAATAAAAAAT
1032620 AAAATAAATAAAT
1 AAAATAAA-AAAT
*
1032633 AAAAT-AATAAT
1 AAAATAAAAAAT
1032644 AAAAT
1 AAAAT
1032649 GAGTTTCCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 8 0.30
12 10 0.37
13 9 0.33
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:1032648 original size:16 final size:16
Alignment explanation
Indices: 1032605--1032648 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 16
1032595 ATGGTGTACC
1032605 TAAAA-AATAA-AAAA
1 TAAAATAATAATAAAA
1032619 TAAAAT-A-AAT-AAA
1 TAAAATAATAATAAAA
1032632 TAAAATAATAATAAAA
1 TAAAATAATAATAAAA
1032648 T
1 T
1032649 GAGTTTCCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.44
14 7 0.28
15 3 0.12
16 4 0.16
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
TAAAATAATAATAAAA
Found at i:1060729 original size:3 final size:3
Alignment explanation
Indices: 1060721--1060814 Score: 125
Period size: 3 Copynumber: 31.0 Consensus size: 3
1060711 CCATATTAAT
* * * *
1060721 TTA TTA TTA TTA TAA TTA TAA TTA TTA TTA TTA TTA TAA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1060769 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
1060815 AATACATTAA
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
3 77 0.99
4 1 0.01
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1060945 original size:15 final size:16
Alignment explanation
Indices: 1060925--1060959 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1060915 TAGCCGCCTA
1060925 TCCAGCC-CCTCTGCC
1 TCCAGCCGCCTCTGCC
1060940 TCCAGCCGCCTCTGCC
1 TCCAGCCGCCTCTGCC
1060956 TCCA
1 TCCA
1060960 CGCTGCCACG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.09, C:0.57, G:0.14, T:0.20
Consensus pattern (16 bp):
TCCAGCCGCCTCTGCC
Found at i:1062786 original size:22 final size:21
Alignment explanation
Indices: 1062738--1062788 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
1062728 TATATTTAAT
*
1062738 TTATAATTTTTTTATATATATA
1 TTAT-ATTTTTATATATATATA
*
1062760 -CATATTTTTATATATATATTA
1 TTATATTTTTATATATATA-TA
1062781 TTATATTT
1 TTATATTT
1062789 CATTCTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 14 0.58
21 4 0.17
22 6 0.25
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATATTTTTATATATATATA
Found at i:1073377 original size:6 final size:6
Alignment explanation
Indices: 1073362--1073413 Score: 58
Period size: 6 Copynumber: 9.2 Consensus size: 6
1073352 ATGCTTGAAG
*
1073362 GAAAAA -AAAAA GAAAAA GAAAAA G--AAA GAAAAA GAGAAAA -AAGAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GA-AAAA GAAAAA
1073407 GAAAAA G
1 GAAAAA G
1073414 GGGGGTCAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 4 0.10
5 8 0.21
6 23 0.59
7 4 0.10
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:1073384 original size:18 final size:16
Alignment explanation
Indices: 1073364--1073413 Score: 73
Period size: 16 Copynumber: 3.0 Consensus size: 16
1073354 GCTTGAAGGA
1073364 AAAAAAAAAGAAAAAG
1 AAAAAAAAAGAAAAAG
*
1073380 AAAAAGAAAGAAAAAG
1 AAAAAAAAAGAAAAAG
1073396 AGAAAAAAGAAGAAAAAG
1 A-AAAAAA-AAGAAAAAG
1073414 GGGGGTCAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 16 0.53
17 5 0.17
18 9 0.30
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAG
Found at i:1073389 original size:10 final size:10
Alignment explanation
Indices: 1073376--1073413 Score: 53
Period size: 9 Copynumber: 4.0 Consensus size: 10
1073366 AAAAAAAGAA
1073376 AAAGAAAAAG
1 AAAGAAAAAG
1073386 AAAGAAAAAG
1 AAAGAAAAAG
*
1073396 AGA-AAAAAG
1 AAAGAAAAAG
1073405 -AAGAAAAAG
1 AAAGAAAAAG
1073414 GGGGGTCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 1 0.04
9 12 0.48
10 12 0.48
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:1073393 original size:22 final size:22
Alignment explanation
Indices: 1073368--1073410 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1073358 GAAGGAAAAA
1073368 AAAAAGA-AAAAGAAAAAGAAAG
1 AAAAAGAGAAAA-AAAAAGAAAG
*
1073390 AAAAAGAGAAAAAAGAAGAAA
1 AAAAAGAGAAAAAAAAAGAAA
1073411 AAGGGGGGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (22 bp):
AAAAAGAGAAAAAAAAAGAAAG
Found at i:1074684 original size:83 final size:83
Alignment explanation
Indices: 1074545--1074773 Score: 406
Period size: 83 Copynumber: 2.8 Consensus size: 83
1074535 AACATTAACC
*
1074545 GAAAGATGAATTTGCCAATAGCGTCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
1 GAAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
1074610 GAACCAATCATTGAATTT
66 GAACCAATCATTGAATTT
1074628 GAAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
1 GAAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
*
1074693 TAACCAATCATTGAATTT
66 GAACCAATCATTGAATTT
* *
1074711 AAAAGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 GAAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1074774 TAAGAACTAC
Statistics
Matches: 141, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
83 140 0.99
84 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (83 bp):
GAAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
GAACCAATCATTGAATTT
Found at i:1075711 original size:113 final size:113
Alignment explanation
Indices: 1075524--1076164 Score: 700
Period size: 113 Copynumber: 5.6 Consensus size: 113
1075514 TGGATTGACA
*
1075524 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGAAAGTTCATAATGAGA
* * *
1075589 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
66 AGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAGCT
*
1075637 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAGAAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGAAAGTTCATAATGAGA
* * * * *
1075702 AGAACTTGTTCAACCTTTTACTTGAATTCATCAATTGATGGATTATCT
66 AGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAGCT
* *
1075750 TTTCCAGAGGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGG-A-AG-AAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGAAAGTTCATAATGAGA
* * * *
1075812 AGAATTTGTTCAACCTTTTGTTTAAATCCATCATTTGATGGATCAGCT
66 AGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAGCT
*
1075860 TTTCC-CAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA-ATAAGTTCATAATGAG
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGA-AAGTTCATAATGAG
* * * * * *
1075923 -A-AATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATTAACA
65 AAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAGCT
* *
1075970 TTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-G-A-AG-AAGTTCATAAT
1 TTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAGAAAGTTCATAAT
* * * * * *
1076030 AAGAAGAGCTTGTTCAACTTTTTGCAT-AATTCTATCACAGAAGGAGATAGATTAGCATCAGCCT
62 GAGAAGAACTTGTTCAACCTTTTGCTTAAATTC-ATCAC---------TTGA-T-GGATCAG-CT
* *
1076094 TTTCTAGAGAAAGTTCATAATGAGAAGAACTCATC-GAAAGAAGGATGA-AGAAGTTCATAATGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG-AAGAAGGAAGAGA-AAGTTCATAATGA
1076157 GAAGAACT
64 GAAGAACT
1076165 CATCAAAAGC
Statistics
Matches: 449, Mismatches: 47, Indels: 52
0.82 0.09 0.09
Matches are distributed among these distances:
109 35 0.08
110 121 0.27
111 30 0.07
112 36 0.08
113 148 0.33
114 12 0.03
120 1 0.00
121 13 0.03
122 3 0.01
123 4 0.01
124 26 0.06
125 20 0.04
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGAAAGTTCATAATGAGA
AGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAGCT
Found at i:1075854 original size:110 final size:111
Alignment explanation
Indices: 1075505--1076054 Score: 711
Period size: 113 Copynumber: 4.9 Consensus size: 111
1075495 ATTCAAATCT
*
1075505 ATCATTTGATGGATT-GACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCATTTGATGGATTAG-CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
1075569 AGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTC
65 AG--AAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTC
* * *
1075618 ATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAA
1 ATCATTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GGA
* * *
1075683 GAGAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTTGAATTC
65 -AGAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTC
* * * *
1075731 ATCAATTGATGGATTATCTTTTCCAGAGGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
1075796 G-AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATCC
66 GAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTC
* *
1075841 ATCATTTGATGGATCAGCTTTTCC-CAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
1075905 GAATAAGTTCATAATGAG-A-AATTTGTTCAACCTTTTGTTTAAATTC
66 G-A-AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTC
* * * *
1075951 ATCATTTGATGGATTAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 ATCATTTGATGGATTAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
* ** *
1076015 -GAAG-AAGTTCATAATAAGAAGAGCTTGTTCAACTTTTTGC
62 GGAAGAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
1076055 ATAATTCTAT
Statistics
Matches: 388, Mismatches: 36, Indels: 27
0.86 0.08 0.06
Matches are distributed among these distances:
109 38 0.10
110 120 0.31
111 23 0.06
112 31 0.08
113 159 0.41
114 15 0.04
115 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.31
Consensus pattern (111 bp):
ATCATTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTC
Found at i:1076009 original size:223 final size:222
Alignment explanation
Indices: 1075505--1076164 Score: 778
Period size: 222 Copynumber: 2.9 Consensus size: 222
1075495 ATTCAAATCT
*
1075505 ATCATTTGATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATTAACATTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
1075570 GAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAG
65 G---AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTAAATCCATCACTTGATGGATCAG
* *
1075635 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAGAAAGTTCATAATGA
127 CTTTTCCACAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGAAAGTTCATAATGA
*
1075700 GAAGAACTTGTTCAACCTTTTACTTGAATTC
192 GAAGAACTTGTTCAACCTTTTACTTAAATTC
* * * *
1075731 ATCAATTGATGGATTATCTTTTCCAGAGGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATTAACATTTCCAGA-GAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
** *
1075796 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATCCATCATTTGATGGATCAGCTT
65 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTAAATCCATCACTTGATGGATCAGCTT
1075861 TTCC-CAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA-ATAAGTTCATAATGAG-
130 TTCCACAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGA-AAGTTCATAATGAGA
* **
1075923 A-AATTTGTTCAACCTTTTGTTTAAATTC
194 AGAACTTGTTCAACCTTTTACTTAAATTC
*
1075951 ATCATTTGATGGATTAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 ATCATTTGATGGATTAACATTTCCAGAG-A-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
* ** * * * * *
1076015 -GAAGAAGTTCATAATAAGAAGAGCTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGAGATA
61 GGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTAAATCCATCAC---------TT
* * * *
1076079 GATTAGCATCAGCCTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATC-GAAAGAAGGATGA-
117 GA-T-GGATCAG-CTTTTCCACAGAAAGTTCATAATGAGAAGAACTCATCTG-AAGAAGGAAGAG
1076142 AGAAGTTCATAATGAGAAGAACT
178 A-AAGTTCATAATGAGAAGAACT
1076165 CATCAAAAGC
Statistics
Matches: 374, Mismatches: 37, Indels: 35
0.84 0.08 0.08
Matches are distributed among these distances:
218 1 0.00
219 1 0.00
220 62 0.17
221 2 0.01
222 99 0.26
223 75 0.20
226 59 0.16
227 1 0.00
231 3 0.01
232 1 0.00
233 6 0.02
234 7 0.02
235 53 0.14
236 1 0.00
237 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (222 bp):
ATCATTTGATGGATTAACATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTAAATCCATCACTTGATGGATCAGCTTT
TCCACAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGAAAGTTCATAATGAGAAG
AACTTGTTCAACCTTTTACTTAAATTC
Found at i:1076159 original size:40 final size:41
Alignment explanation
Indices: 1076104--1076212 Score: 193
Period size: 42 Copynumber: 2.7 Consensus size: 41
1076094 TTTCTAGAGA
*
1076104 AAGTTCATAATGAGAAGAACTCATCGAAA-GAAGGATGAAG
1 AAGTTCATAATGAGAAGAACTCATCAAAACGAAGGATGAAG
1076144 AAGTTCATAATGAGAAGAACTCATCAAAAGCGAAGGATGAAG
1 AAGTTCATAATGAGAAGAACTCATCAAAA-CGAAGGATGAAG
1076186 AAGTTCATAATGAGAAGAACTCATCAA
1 AAGTTCATAATGAGAAGAACTCATCAA
1076213 GAGCTTATTC
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
40 28 0.42
42 38 0.58
ACGTcount: A:0.48, C:0.12, G:0.22, T:0.18
Consensus pattern (41 bp):
AAGTTCATAATGAGAAGAACTCATCAAAACGAAGGATGAAG
Found at i:1076469 original size:3 final size:3
Alignment explanation
Indices: 1076461--1076546 Score: 111
Period size: 3 Copynumber: 29.0 Consensus size: 3
1076451 ACCTATTAAT
* * * *
1076461 TTA TTA TTA TTA TAA TTA TAA TTA TAA TTA TTA TTA TTA TTA -TA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1076508 TTA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1076547 AATACATTAA
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
2 2 0.03
3 69 0.97
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1076478 original size:9 final size:9
Alignment explanation
Indices: 1076461--1076574 Score: 69
Period size: 9 Copynumber: 13.1 Consensus size: 9
1076451 ACCTATTAAT
*
1076461 TTATTATTA
1 TTATTATAA
* *
1076470 TTATAATTA
1 TTATTATAA
*
1076479 TAATTATAA
1 TTATTATAA
*
1076488 TTATTATTA
1 TTATTATAA
1076497 TTATTATAA
1 TTATTATAA
*
1076506 -TATTATTA
1 TTATTATAA
*
1076514 TTATTATTA
1 TTATTATAA
*
1076523 TTA-TAAATA
1 TTATTATA-A
*
1076532 TTATTATTA
1 TTATTATAA
1076541 TTATTA-AA
1 TTATTATAA
*
1076549 TACATTA-AA
1 T-TATTATAA
1076558 -TATTATAA
1 TTATTATAA
*
1076566 -AATTATAA
1 TTATTATAA
1076574 T
1 T
1076575 CCAAATATCC
Statistics
Matches: 83, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
7 4 0.05
8 20 0.24
9 57 0.69
10 2 0.02
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (9 bp):
TTATTATAA
Found at i:1076499 original size:41 final size:42
Alignment explanation
Indices: 1076454--1076544 Score: 125
Period size: 41 Copynumber: 2.2 Consensus size: 42
1076444 ATTTTTTACC
* *
1076454 TATTAATT-TATTATTATTATAATTATAATTATAATTATTAT
1 TATTAATTATAATATTATTATAATTATAATTATAAATATTAT
* *
1076495 TATT-ATTATAATATTATTATTATTATTATTATAAATATTAT
1 TATTAATTATAATATTATTATAATTATAATTATAAATATTAT
1076536 TATT-ATTAT
1 TATTAATTAT
1076545 TAAATACATT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 3 0.07
41 42 0.93
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (42 bp):
TATTAATTATAATATTATTATAATTATAATTATAAATATTAT
Found at i:1076671 original size:15 final size:16
Alignment explanation
Indices: 1076651--1076692 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
1076641 CCTAATCCCT
1076651 AGCCGCCTCT-AATCC
1 AGCCGCCTCTGAATCC
**
1076666 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGAATCC
1076682 AGCCGCCTCTG
1 AGCCGCCTCTG
1076693 CCTCCACCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.12, C:0.50, G:0.19, T:0.19
Consensus pattern (16 bp):
AGCCGCCTCTGAATCC
Found at i:1076684 original size:16 final size:16
Alignment explanation
Indices: 1076663--1076702 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
1076653 CCGCCTCTAA
1076663 TCCAGCCGCCTCTGCC
1 TCCAGCCGCCTCTGCC
1076679 TCCAGCCGCCTCTGCC
1 TCCAGCCGCCTCTGCC
1076695 TCCA-CCGC
1 TCCAGCCGC
1076703 TGCCACGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.07, C:0.57, G:0.17, T:0.17
Consensus pattern (16 bp):
TCCAGCCGCCTCTGCC
Found at i:1078436 original size:6 final size:6
Alignment explanation
Indices: 1078425--1078451 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1078415 CGGTTACGAC
1078425 AATTAT AATTAT AATTAT AATTAT AAT
1 AATTAT AATTAT AATTAT AATTAT AAT
1078452 GAATCATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTAT
Found at i:1078774 original size:19 final size:20
Alignment explanation
Indices: 1078741--1078782 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1078731 AAATTACATA
* *
1078741 AAAACTAAAGTTTATATTCT
1 AAAACTAAAGATTATATTAT
1078761 AAAA-TAAAGATTATATTAT
1 AAAACTAAAGATTATATTAT
1078780 AAA
1 AAA
1078783 TTTTAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTAAAGATTATATTAT
Found at i:1082840 original size:20 final size:20
Alignment explanation
Indices: 1082815--1082854 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1082805 CAACTCTCCT
1082815 GAGATAGGTCATCTATTTTC
1 GAGATAGGTCATCTATTTTC
1082835 GAGATAGGTCATCTATTTTC
1 GAGATAGGTCATCTATTTTC
1082855 TTTCCTCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (20 bp):
GAGATAGGTCATCTATTTTC
Found at i:1083105 original size:16 final size:16
Alignment explanation
Indices: 1083081--1083111 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1083071 CGATTCATTT
1083081 ATTTGTTTTTAAATTA
1 ATTTGTTTTTAAATTA
*
1083097 ATTTTTTTTTAAATT
1 ATTTGTTTTTAAATT
1083112 CATGTTTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
ATTTGTTTTTAAATTA
Found at i:1083328 original size:13 final size:12
Alignment explanation
Indices: 1083301--1083325 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1083291 ATTAATAAAA
1083301 TAAAAGTATAAT
1 TAAAAGTATAAT
1083313 TAAAAGTATAAT
1 TAAAAGTATAAT
1083325 T
1 T
1083326 TAATATAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (12 bp):
TAAAAGTATAAT
Found at i:1084881 original size:22 final size:23
Alignment explanation
Indices: 1084824--1084917 Score: 65
Period size: 22 Copynumber: 4.1 Consensus size: 23
1084814 TGTAGTATTC
* *
1084824 TATATAATATTATTTATATGGTAT
1 TATATATTATTA-TTATATAGTAT
*
1084848 TATACT-TCATTATTA-ATAGTAT
1 TATA-TATTATTATTATATAGTAT
1084870 TATATATTATTATTATTATCA-TAT
1 TATATATTATTATTA-TAT-AGTAT
*
1084894 TGTATA-TA-TA-TATATTAGTAT
1 TATATATTATTATTATA-TAGTAT
1084915 TAT
1 TAT
1084918 GTTATATATT
Statistics
Matches: 57, Mismatches: 6, Indels: 17
0.71 0.08 0.21
Matches are distributed among these distances:
20 3 0.05
21 9 0.16
22 20 0.35
23 5 0.09
24 18 0.32
25 2 0.04
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.54
Consensus pattern (23 bp):
TATATATTATTATTATATAGTAT
Found at i:1084894 original size:24 final size:25
Alignment explanation
Indices: 1084867--1084927 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
1084857 TTATTAATAG
*
1084867 TATTATATATTAT-TATTATTATCA
1 TATTATATATTATATATTAGTATCA
* *
1084891 TATTGTATATATATATATTAGTATTA
1 TATTATATAT-TATATATTAGTATCA
*
1084917 TGTTATATATT
1 TATTATATATT
1084928 TAATATCATT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 9 0.30
25 4 0.13
26 17 0.57
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (25 bp):
TATTATATATTATATATTAGTATCA
Found at i:1084933 original size:29 final size:28
Alignment explanation
Indices: 1084901--1084966 Score: 64
Period size: 29 Copynumber: 2.3 Consensus size: 28
1084891 TATTGTATAT
* *
1084901 ATATATATTAGTATTA-TGTTATATATTTA
1 ATATATATTA-CATTATTCTTATATA-TTA
*
1084930 ATATCATTTTACATTATTCTTATATATTA
1 ATAT-ATATTACATTATTCTTATATATTA
1084959 ATAT-TATT
1 ATATATATT
1084967 TGTGTTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
27 3 0.10
29 15 0.48
30 13 0.42
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (28 bp):
ATATATATTACATTATTCTTATATATTA
Found at i:1086263 original size:24 final size:23
Alignment explanation
Indices: 1086236--1086283 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
1086226 TTCCTTCCCA
*
1086236 TTAATTTT-CTTTATTAGGTTTATT
1 TTAATTTTAATTTATTA--TTTATT
1086260 TTAATTTTAATTTATTATTTATT
1 TTAATTTTAATTTATTATTTATT
1086283 T
1 T
1086284 GATTTTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 8 0.36
25 7 0.32
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (23 bp):
TTAATTTTAATTTATTATTTATT
Found at i:1086406 original size:27 final size:28
Alignment explanation
Indices: 1086376--1086438 Score: 83
Period size: 32 Copynumber: 2.1 Consensus size: 28
1086366 TCATTATATG
1086376 TATTTA-TTTTGTTAGATCTTTGATTTA
1 TATTTATTTTTGTTAGATCTTTGATTTA
1086403 TATTTTATTGCTTTTGTTAGATCTTTGATTTA
1 TA-TTTA-T--TTTTGTTAGATCTTTGATTTA
1086435 TATT
1 TATT
1086439 CCTTTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
27 2 0.06
28 4 0.13
31 2 0.06
32 23 0.74
ACGTcount: A:0.21, C:0.05, G:0.11, T:0.63
Consensus pattern (28 bp):
TATTTATTTTTGTTAGATCTTTGATTTA
Found at i:1089076 original size:75 final size:76
Alignment explanation
Indices: 1088963--1089158 Score: 263
Period size: 75 Copynumber: 2.6 Consensus size: 76
1088953 CCGTTGAACA
* * *
1088963 GGGGGAATCGGTACC-CCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACA
** *
1089026 AAAATGTTTAG
66 AAAACATTCAG
* * *
1089037 GGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACA
*
1089101 AAACCATTCAG
66 AAAACATTCAG
*
1089112 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 GGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCA
1089159 ATCTGTAATT
Statistics
Matches: 107, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
74 14 0.13
75 69 0.64
76 1 0.01
77 23 0.21
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.23
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACA
AAAACATTCAG
Found at i:1091779 original size:21 final size:21
Alignment explanation
Indices: 1091753--1091792 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1091743 CAGAACCCCA
*
1091753 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1091774 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1091793 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1097687 original size:75 final size:75
Alignment explanation
Indices: 1097584--1097782 Score: 247
Period size: 75 Copynumber: 2.6 Consensus size: 75
1097574 GACCGTTGAA
* * *
1097584 CAGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTAT-GGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
**
1097648 ACAAAAATGTT
65 ACAAAAACATT
* * * * *
1097659 TAGGGGGGAATCGGTTTCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAA
* *
1097724 CCAAACCATT
66 CAAAAACATT
* *
1097734 CAGGGGGGAATCAGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGG-ATCGGTTCCCTCCGAGCA
1097783 ATCTGTAATT
Statistics
Matches: 105, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
75 87 0.83
76 18 0.17
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.23
Consensus pattern (75 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAA
CAAAAACATT
Found at i:1099797 original size:21 final size:21
Alignment explanation
Indices: 1099755--1099797 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1099745 TTTCTGGGCT
* *
1099755 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
1099776 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
1099797 A
1 A
1099798 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1100500 original size:102 final size:103
Alignment explanation
Indices: 1100324--1100540 Score: 400
Period size: 102 Copynumber: 2.1 Consensus size: 103
1100314 GTAGAGGGTC
* * *
1100324 TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACGCATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAGGTCTGGTGAGACACATAC
1100389 TTGATCCTTGGCATATGTATATGATTCTTAA-GAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1100426 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAGGTCTGGTGAGACACATAC
1100491 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1100529 TATGTGGTCCTT
1 TATGTGGTCCTT
1100541 ATGGACATTA
Statistics
Matches: 111, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
102 93 0.84
103 18 0.16
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1100591 original size:23 final size:23
Alignment explanation
Indices: 1100556--1100608 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
1100546 CATTATTATA
1100556 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
1100579 TGGCACT-CTGGTGCAATTCTACG
1 TGGCACTAC-GGTGCAATTCTACG
1100602 TGGCACT
1 TGGCACT
1100609 TAAGTGCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:1100615 original size:23 final size:23
Alignment explanation
Indices: 1100566--1100619 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
1100556 TGGCACTACG
*
1100566 GTGCAATTCTACGTGGCACTCTG
1 GTGCAATTCTACGTGGCACTCTA
1100589 GTGCAATTCTACGTGGCACT-TAA
1 GTGCAATTCTACGTGGCACTCT-A
1100612 GTGCAATT
1 GTGCAATT
1100620 ATATGAGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (23 bp):
GTGCAATTCTACGTGGCACTCTA
Found at i:1106738 original size:20 final size:20
Alignment explanation
Indices: 1106713--1106750 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1106703 GAATGCTAGA
*
1106713 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
1106733 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
1106751 TAAAAAAAAG
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:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:1107386 original size:23 final size:23
Alignment explanation
Indices: 1107351--1107413 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
1107341 ATTATTATAT
*
1107351 GGCACTACGGTGCAATTCTACGC
1 GGCACTACAGTGCAATTCTACGC
* * * *
1107374 GGCACTCCAGTGCAATTTTATGT
1 GGCACTACAGTGCAATTCTACGC
1107397 GGCACTTA-AGTGCAATT
1 GGCAC-TACAGTGCAATT
1107414 ATATGAGGCT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (23 bp):
GGCACTACAGTGCAATTCTACGC
Found at i:1112047 original size:19 final size:20
Alignment explanation
Indices: 1112006--1112056 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1111996 GAAACCCCTT
*
1112006 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
1112026 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
1112045 TGAAGATACATG
1 TGAAAATACATG
1112057 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1118589 original size:242 final size:242
Alignment explanation
Indices: 1118164--1118647 Score: 720
Period size: 242 Copynumber: 2.0 Consensus size: 242
1118154 GCATTTAGTC
* * * *
1118164 TTTTACTCAAAGGGATTTAACCTTTCATCTAACTGGCATTATTGACACCTTTCTCTCAAATGCAC
1 TTTTACTCAAAGGGATTTAACCTTTCATCTAACTAGCATGATTGACACATTTCTCTCAAATACAC
* * * * *
1118229 AACTAGGCTATTAATATTTTACTTAAAGGTGTTTAACCTTTCATCTAATTGGCATGATTGACACC
66 AACTAGGCAATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACC
* * *
1118294 TTTTTGTCAAATGTACAGCTAGGTAATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAAC
131 TTTCTGTCAAATGCACAGCTA-GTAATTAATAGTTTACTCAAAGGTATTTAACCTTTCATCTAAC
* *
1118359 TGGCATGATTGACACCTTTCTATC-AATGCACAACTAGACAATTAATA
195 TGGCATGATTAACACATTTCTATCAAATGCACAACTAGACAATTAATA
* *
1118406 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACATTTCTGTCAAATACAC
1 TTTTACTCAAAGGGATTTAACCTTTCATCTAACTAGCATGATTGACACATTTCTCTCAAATACAC
*
1118471 AACTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACC
66 AACTAGGCAATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACC
* * *
1118536 TTTCTGTCAAATGCACATCTA-TACTATTAATCGTTTACTCAAAGGTATTTAACCTTTCATTTAA
131 TTTCTGTCAAATGCACAGCTAGTA--ATTAATAGTTTACTCAAAGGTATTTAACCTTTCATCTAA
* * *
1118600 CTGGCATGATTAACACATTTCTGTCAAATGCACAGCTAGGCAATTAAT
194 CTGGCATGATTAACACATTTCTATCAAATGCACAACTAGACAATTAAT
1118648 CTTTCATCTA
Statistics
Matches: 216, Mismatches: 23, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
240 2 0.01
242 194 0.90
243 20 0.09
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (242 bp):
TTTTACTCAAAGGGATTTAACCTTTCATCTAACTAGCATGATTGACACATTTCTCTCAAATACAC
AACTAGGCAATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACC
TTTCTGTCAAATGCACAGCTAGTAATTAATAGTTTACTCAAAGGTATTTAACCTTTCATCTAACT
GGCATGATTAACACATTTCTATCAAATGCACAACTAGACAATTAATA
Found at i:1118648 original size:81 final size:81
Alignment explanation
Indices: 1118164--1118647 Score: 709
Period size: 81 Copynumber: 6.0 Consensus size: 81
1118154 GCATTTAGTC
* * *
1118164 TTTTACTCAAAGGGATTTAACCTTTCATCTAACTGGCATTATTGACACCTTTCTCTCAAATGCAC
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCAC
*
1118229 AACTAGGCTATTAATA
66 AACTAGGCAATTAATA
* * * * *
1118245 TTTTACTTAAAGGTGTTTAACCTTTCATCTAATTGGCATGATTGACACCTTTTTGTCAAATGTAC
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCAC
* *
1118310 AGCTAGGTAATTAATA
66 AACTAGGCAATTAATA
*
1118326 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTATC-AATGCAC
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCAC
*
1118390 AACTAGACAATTAATA
66 AACTAGGCAATTAATA
* * *
1118406 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACATTTCTGTCAAATACAC
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCAC
*
1118471 AACTAGGCAATTAATC
66 AACTAGGCAATTAATA
*
1118487 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTGTCAAATGCAC
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCAC
* ** * *
1118552 ATCTATACTATTAATC
66 AACTAGGCAATTAATA
* * * *
1118568 GTTTACTCAAAGGTATTTAACCTTTCATTTAACTGGCATGATTAACACATTTCTGTCAAATGCAC
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCAC
*
1118633 AGCTAGGCAATTAAT
66 AACTAGGCAATTAAT
1118648 CTTTCATCTA
Statistics
Matches: 361, Mismatches: 41, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
80 73 0.20
81 288 0.80
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (81 bp):
TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCAC
AACTAGGCAATTAATA
Found at i:1118662 original size:59 final size:59
Alignment explanation
Indices: 1118584--1118710 Score: 184
Period size: 59 Copynumber: 2.2 Consensus size: 59
1118574 TCAAAGGTAT
* * * *
1118584 TTAACCTTTCATTTAACTGGCATGATT-AACACATTTCTGTCAAATGCACAGCTAGGCAA
1 TTAATCTTTCATCTAACTGGCATGATTGAAAAC-TTTCTGTCAAATGCACAACTAGGCAA
* *
1118643 TTAATCTTTCATCTAACTGGCATGATTGAAAACTTTTTGTCAAATGCATAACTAGGCAA
1 TTAATCTTTCATCTAACTGGCATGATTGAAAACTTTCTGTCAAATGCACAACTAGGCAA
1118702 TTAATCTTT
1 TTAATCTTT
1118711 TACTCAAAGG
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 57 0.93
60 4 0.07
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (59 bp):
TTAATCTTTCATCTAACTGGCATGATTGAAAACTTTCTGTCAAATGCACAACTAGGCAA
Found at i:1118716 original size:140 final size:140
Alignment explanation
Indices: 1118503--1118791 Score: 425
Period size: 140 Copynumber: 2.1 Consensus size: 140
1118493 TCAAAGGTAT
* * * * * *
1118503 TTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTGTCAAATGCACATCTATACTATTAATC
1 TTAATCTTTCATCTAACTAGCATGATTGAAAACTTTCTGTCAAATGCACAACTAGACAATTAATC
* *
1118568 GTTTACTCAAAGGTATTTAACCTTTCATTTAACTGGCATGATTAACACATTTCTGTCAAATGCAC
66 GTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTAACACATTTCTATCAAATGCAC
1118633 AGCTAGGCAA
131 AGCTAGGCAA
* * * *
1118643 TTAATCTTTCATCTAACTGGCATGATTGAAAACTTTTTGTCAAATGCATAACTAGGCAATTAATC
1 TTAATCTTTCATCTAACTAGCATGATTGAAAACTTTCTGTCAAATGCACAACTAGACAATTAATC
* * * * *
1118708 TTTTACTCAAAGGTATTTAAGCTTTCATCTAACTGGCATGATTGATACCTTTCTATCAAATGCAC
66 GTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTAACACATTTCTATCAAATGCAC
1118773 AGCTAGGCAA
131 AGCTAGGCAA
1118783 TTAATCTTT
1 TTAATCTTT
1118792 TACTCAAAGG
Statistics
Matches: 132, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
140 132 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36
Consensus pattern (140 bp):
TTAATCTTTCATCTAACTAGCATGATTGAAAACTTTCTGTCAAATGCACAACTAGACAATTAATC
GTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTAACACATTTCTATCAAATGCAC
AGCTAGGCAA
Found at i:1118783 original size:81 final size:81
Alignment explanation
Indices: 1118643--1118955 Score: 491
Period size: 81 Copynumber: 3.9 Consensus size: 81
1118633 AGCTAGGCAA
* * * * * * *
1118643 TTAATCTTTCATCTAACTGGCATGATTGAAAACTTTTTGTCAAATGCATAACTAGGCAATTAATC
1 TTAACCTTTCATCTAACTGACATGATTGATACCTTTCTGTCAAATGCACAGCTAGGCAATTAATC
1118708 TTTTACTCAAAGGTAT
66 TTTTACTCAAAGGTAT
* * *
1118724 TTAAGCTTTCATCTAACTGGCATGATTGATACCTTTCTATCAAATGCACAGCTAGGCAATTAATC
1 TTAACCTTTCATCTAACTGACATGATTGATACCTTTCTGTCAAATGCACAGCTAGGCAATTAATC
1118789 TTTTACTCAAAGGTAT
66 TTTTACTCAAAGGTAT
*
1118805 TTAACCTTTCATCTAACTGACATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATC
1 TTAACCTTTCATCTAACTGACATGATTGATACCTTTCTGTCAAATGCACAGCTAGGCAATTAATC
*
1118870 TTTTACTCAAAAGTAT
66 TTTTACTCAAAGGTAT
* * *
1118886 TTAACCTTTCATCTGACTGACATGATTGATATCTTTCTGTCAAATGCATAGCTAGGCAATTAATC
1 TTAACCTTTCATCTAACTGACATGATTGATACCTTTCTGTCAAATGCACAGCTAGGCAATTAATC
1118951 TTTTA
66 TTTTA
1118956 TTTTAAAATA
Statistics
Matches: 216, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 216 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (81 bp):
TTAACCTTTCATCTAACTGACATGATTGATACCTTTCTGTCAAATGCACAGCTAGGCAATTAATC
TTTTACTCAAAGGTAT
Found at i:1118810 original size:221 final size:221
Alignment explanation
Indices: 1118422--1118872 Score: 715
Period size: 221 Copynumber: 2.0 Consensus size: 221
1118412 TCAAAGGTAT
* *
1118422 TTAACCTTTCATCTAACTAGCATGATTGACACATTTCTGTCAAATACACAACTAGGCAATTAATC
1 TTAATCTTTCATCTAACTAGCATGATTGAAACATTTCTGTCAAATACACAACTAGGCAATTAATC
*
1118487 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTGTCAAATGCAC
66 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTATCAAATGCAC
* * * * *
1118552 ATCTATACTATTAATCGTTTACTCAAAGGTATTTAACCTTTCATTTAACTGGCATGATTAACACA
131 AGCTAGACAATTAATCGTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATGATTAACACA
1118617 TTTCTGTCAAATGCACAGCTAGGCAA
196 TTTCTGTCAAATGCACAGCTAGGCAA
* * * *
1118643 TTAATCTTTCATCTAACTGGCATGATTGAAA-ACTTTTTGTCAAATGCATAACTAGGCAATTAAT
1 TTAATCTTTCATCTAACTAGCATGATTGAAACA-TTTCTGTCAAATACACAACTAGGCAATTAAT
* * *
1118707 CTTTTACTCAAAGGTATTTAAGCTTTCATCTAACTGGCATGATTGATACCTTTCTATCAAATGCA
65 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTATCAAATGCA
* * *
1118772 CAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATGATTGACAC
130 CAGCTAGACAATTAATCGTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATGATTAACAC
*
1118837 CTTTCTGTCAAATGCACAGCTAGGCAA
195 ATTTCTGTCAAATGCACAGCTAGGCAA
1118864 TTAATCTTT
1 TTAATCTTT
1118873 TACTCAAAAG
Statistics
Matches: 210, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
220 1 0.00
221 209 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.36
Consensus pattern (221 bp):
TTAATCTTTCATCTAACTAGCATGATTGAAACATTTCTGTCAAATACACAACTAGGCAATTAATC
TTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTATCAAATGCAC
AGCTAGACAATTAATCGTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATGATTAACACA
TTTCTGTCAAATGCACAGCTAGGCAA
Found at i:1118943 original size:302 final size:301
Alignment explanation
Indices: 1118342--1118953 Score: 940
Period size: 302 Copynumber: 2.0 Consensus size: 301
1118332 TCAAAGGTAT
* * *
1118342 TTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTATCAATGCACAACTAGACAATTAATAT
1 TTAATCTTTCATCTAACTGGCATGATTGAAAACTTTCTATCAATGCACAACTAGACAATTAATAT
*
1118407 TTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACATTTCTGTCAAATACACA
66 TTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACATTTCTATCAAATACACA
1118472 ACTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACCT
131 ACTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACCT
* * * * *
1118537 TTCTGTCAAATGCACATCTATACTATTAATCGTTTACTCAAAGGTATTTAACCTTTCATTTAACT
196 TTCTGTCAAATGCACAGCTAGACAATTAATCGTTTACTCAAAAGTATTTAACCTTTCATCTAACT
*
1118602 GGCATGATTAACACATTTCTGTCAAATGCACAGCTAGGCAA
261 GACATGATTAACACATTTCTGTCAAATGCACAGCTAGGCAA
* * * * *
1118643 TTAATCTTTCATCTAACTGGCATGATTGAAAACTTTTTGTCAAATGCATAACTAGGCAATTAATC
1 TTAATCTTTCATCTAACTGGCATGATTGAAAACTTTCTATC-AATGCACAACTAGACAATTAATA
* * * * *
1118708 TTTTACTCAAAGGTATTTAAGCTTTCATCTAACTGGCATGATTGATACCTTTCTATCAAATGCAC
65 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACATTTCTATCAAATACAC
*
1118773 AGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACT-GACATGATTGACAC
130 AACTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAG-CATGATTGACAC
* * *
1118837 CTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAAGTATTTAACCTTTCATCTGA
194 CTTTCTGTCAAATGCACAGCTAGACAATTAATCGTTTACTCAAAAGTATTTAACCTTTCATCTAA
* * *
1118902 CTGACATGATTGATATC-TTTCTGTCAAATGCATAGCTAGGCAA
259 CTGACATGATTAACA-CATTTCTGTCAAATGCACAGCTAGGCAA
1118945 TTAATCTTT
1 TTAATCTTT
1118954 TATTTTAAAA
Statistics
Matches: 281, Mismatches: 27, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
301 37 0.13
302 243 0.86
303 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (301 bp):
TTAATCTTTCATCTAACTGGCATGATTGAAAACTTTCTATCAATGCACAACTAGACAATTAATAT
TTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACATTTCTATCAAATACACA
ACTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACCT
TTCTGTCAAATGCACAGCTAGACAATTAATCGTTTACTCAAAAGTATTTAACCTTTCATCTAACT
GACATGATTAACACATTTCTGTCAAATGCACAGCTAGGCAA
Found at i:1121073 original size:19 final size:19
Alignment explanation
Indices: 1121046--1121090 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1121036 AGTAAGGGAA
1121046 AAGATATGATATTAATGAG
1 AAGATATGATATTAATGAG
*
1121065 AATATATGATATTAATGAG
1 AAGATATGATATTAATGAG
1121084 AAGATAT
1 AAGATAT
1121091 TTGATCTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (19 bp):
AAGATATGATATTAATGAG
Found at i:1124756 original size:23 final size:22
Alignment explanation
Indices: 1124693--1124788 Score: 122
Period size: 23 Copynumber: 4.3 Consensus size: 22
1124683 CACCGAAATG
* *
1124693 CCACATAGAATGTCTCGAAGGA
1 CCACGTAGAATGTCCCGAAGGA
*
1124715 CCACATAG-ATGTCCCGAAGGA
1 CCACGTAGAATGTCCCGAAGGA
*
1124736 CCACGTAGAATTATCCCGAAGGA
1 CCACGTAGAA-TGTCCCGAAGGA
1124759 CCACGTAGAACTGTCCCGAAGGA
1 CCACGTAGAA-TGTCCCGAAGGA
*
1124782 CCGCGTA
1 CCACGTA
1124789 AAACCCTCGA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.29
22 9 0.14
23 38 0.58
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16
Consensus pattern (22 bp):
CCACGTAGAATGTCCCGAAGGA
Found at i:1125381 original size:3 final size:3
Alignment explanation
Indices: 1125371--1125454 Score: 79
Period size: 3 Copynumber: 29.3 Consensus size: 3
1125361 CATTTTTTTA
* *
1125371 ATT A-T ATT ATT ATT AAT ATT ATT -TT ATT -TT ATT -TAT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
* * *
1125413 ATT TTT ATT TTT A-T ATT ATT ATA ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1125455 AATAATATTT
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
2 9 0.14
3 56 0.86
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1126602 original size:21 final size:21
Alignment explanation
Indices: 1126578--1126617 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1126568 ATTTTAGTCC
* *
1126578 TTTATATAAAATAATAGATAT
1 TTTAGATAAAATAAAAGATAT
*
1126599 TTTAGGTAAAATAAAAGAT
1 TTTAGATAAAATAAAAGAT
1126618 TTAGTCCTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTAGATAAAATAAAAGATAT
Found at i:1126947 original size:3 final size:3
Alignment explanation
Indices: 1126939--1126980 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1126929 AATATATTTA
1126939 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1126981 TAGTCATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1127033 original size:13 final size:13
Alignment explanation
Indices: 1127017--1127047 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1127007 TAATAAATAT
1127017 TTTTTATTTTTTA
1 TTTTTATTTTTTA
*
1127030 TTTTTATTTTTTG
1 TTTTTATTTTTTA
1127043 TTTTT
1 TTTTT
1127048 TTGTTTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:1127054 original size:7 final size:7
Alignment explanation
Indices: 1127014--1127048 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
1127004 ATATAATAAA
1127014 TATTTTT
1 TATTTTT
1127021 TATTTTT
1 TATTTTT
1127028 TA-TTTT
1 TATTTTT
1127034 TATTTTT
1 TATTTTT
*
1127041 TGTTTTT
1 TATTTTT
1127048 T
1 T
1127049 TGTTTTCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (7 bp):
TATTTTT
Found at i:1127891 original size:13 final size:13
Alignment explanation
Indices: 1127873--1127911 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1127863 ACTTATAATA
1127873 TTTATTATATTTT
1 TTTATTATATTTT
*
1127886 TTTATTA-ATGTT
1 TTTATTATATTTT
*
1127898 TTTATTTTATTTT
1 TTTATTATATTTT
1127911 T
1 T
1127912 AGATATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTATTATATTTT
Found at i:1128808 original size:36 final size:36
Alignment explanation
Indices: 1128757--1128828 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
1128747 GAGCTATGCA
* * *
1128757 CACAAAGATCTTGTTATATTAATACCAAAAGTATTC
1 CACAAAGATCATGTTAGATTAATACCAAAAGCATTC
*
1128793 CACAAAGATCATGTTAGATTGATACCAAAAGCATTC
1 CACAAAGATCATGTTAGATTAATACCAAAAGCATTC
1128829 TACTACAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (36 bp):
CACAAAGATCATGTTAGATTAATACCAAAAGCATTC
Found at i:1129347 original size:43 final size:44
Alignment explanation
Indices: 1129282--1129368 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
1129272 TGGCTTTAGA
* * *
1129282 GAAGTTAGGAGAGAAAGTTATCCCTTATAGGT-AAAGTTTTGTT
1 GAAGTTAGGAGAGAAAGCTATCCCCTACAGGTAAAAGTTTTGTT
* *
1129325 GAAGTTAGGAGTGAAAGCTATCCCCTACATGTAAAAGTTTTGTT
1 GAAGTTAGGAGAGAAAGCTATCCCCTACAGGTAAAAGTTTTGTT
1129369 TGATGCACGG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
43 27 0.71
44 11 0.29
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.33
Consensus pattern (44 bp):
GAAGTTAGGAGAGAAAGCTATCCCCTACAGGTAAAAGTTTTGTT
Found at i:1131761 original size:21 final size:20
Alignment explanation
Indices: 1131690--1131807 Score: 146
Period size: 21 Copynumber: 5.8 Consensus size: 20
1131680 CGGTGTTTGA
* *
1131690 GTGCATGGATGCACTTCATG
1 GTGCATGGATGCACTGCAGG
* *
1131710 GTGCATCGATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
*
1131730 GTGCATCGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
*
1131750 GATGCATGGATGCACTGTAGG
1 G-TGCATGGATGCACTGCAGG
*
1131771 GATGCATGGATACACTGCAGAG
1 G-TGCATGGATGCACTGCAG-G
1131793 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1131808 TTGACACCTT
Statistics
Matches: 88, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
20 38 0.43
21 48 0.55
22 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.24
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:1131908 original size:29 final size:29
Alignment explanation
Indices: 1131887--1131944 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
1131877 AAACTTTGAA
1131887 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
1131916 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
1131945 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:1131934 original size:30 final size:30
Alignment explanation
Indices: 1131887--1131946 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
1131877 AAACTTTGAA
1131887 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
1131916 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
1131947 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:1132424 original size:20 final size:20
Alignment explanation
Indices: 1132399--1132436 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1132389 ACTTTATGCA
*
1132399 ATACCAATTGTTTAAATTTG
1 ATACCAATTGTTAAAATTTG
1132419 ATACCAATTGTTAAAATT
1 ATACCAATTGTTAAAATT
1132437 AAGTACATAT
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:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (20 bp):
ATACCAATTGTTAAAATTTG
Found at i:1140405 original size:54 final size:53
Alignment explanation
Indices: 1140316--1140524 Score: 294
Period size: 54 Copynumber: 3.9 Consensus size: 53
1140306 AGAAATCTGT
* * * *
1140316 GCAGAAGCCACAGGAAAGGATAAATGTGTTGTCAAATGCTTTACGAACATCTA
1 GCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTA
* * *
1140369 TGCCGAAACCACATGAAAATATGAATGTGTTGTCAAATGTTTTACGAACATCTAA
1 -GCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCT-A
*
1140424 GCAGAAACCACAGGAAAAGATAAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCT-A
* *
1140478 GAAGAAGCCACAGGAAAAGATGAATGTGTTGTCAAATG-TTTACGAAC
1 GCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
1140525 CAGTGATTAT
Statistics
Matches: 139, Mismatches: 15, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
53 9 0.06
54 129 0.93
55 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (53 bp):
GCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTA
Found at i:1141544 original size:104 final size:103
Alignment explanation
Indices: 1141410--1141613 Score: 322
Period size: 104 Copynumber: 2.0 Consensus size: 103
1141400 TCATCATTCG
*
1141410 ATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGAA
1 ATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAACAACTCATCTGAAG-AG--GAAGAAGAA
1141475 GTTCATAATGAGAAGAACTTATTCAA-CTTTAGCTTGATCA
63 GTTCATAATGAGAAGAACTTATTCAACCTTTAGCTTGATCA
**
1141515 ATGGATCAA-ATTTTCAGGTAGAGTTCATAATGAGAACAACTCATCTGAAGAGGAAGAAGAAGTT
1 ATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAACAACTCATCTGAAGAGGAAGAAGAAGTT
* *
1141579 CATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
66 CATAATGAGAAGAACTTATTCAACCTTTAGCTTGA
1141614 CTCTATTTCC
Statistics
Matches: 93, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
101 34 0.37
102 10 0.11
103 2 0.02
104 38 0.41
105 9 0.10
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (103 bp):
ATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAACAACTCATCTGAAGAGGAAGAAGAAGTT
CATAATGAGAAGAACTTATTCAACCTTTAGCTTGATCA
Found at i:1141802 original size:20 final size:17
Alignment explanation
Indices: 1141755--1141794 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1141745 CAACATTTCC
1141755 AGAAG-AGTTCATAATG
1 AGAAGAAGTTCATAATG
*
1141771 AGAAGAAGTTCATAATT
1 AGAAGAAGTTCATAATG
1141788 AGAAGAA
1 AGAAGAA
1141795 CTTGTTCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.50, C:0.05, G:0.23, T:0.23
Consensus pattern (17 bp):
AGAAGAAGTTCATAATG
Found at i:1142056 original size:3 final size:3
Alignment explanation
Indices: 1142044--1142123 Score: 80
Period size: 3 Copynumber: 28.0 Consensus size: 3
1142034 CATTTGTTTT
*
1142044 TTA TTA -TA TTA TTA TTA TTA TTA TT- TTA TT- TTA TT- TATA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
* * *
1142086 TTA TTT TTA TTT TTA -TA TTA TTA TAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1142124 AATAATATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
2 9 0.14
3 54 0.86
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1142064 original size:17 final size:17
Alignment explanation
Indices: 1142044--1142123 Score: 83
Period size: 17 Copynumber: 4.6 Consensus size: 17
1142034 CATTTGTTTT
1142044 TTATTATATTATTATTA
1 TTATTATATTATTATTA
*
1142061 TTATTATTTTATT-TTA
1 TTATTATATTATTATTA
*
1142077 TT-TATACTATTATTTTTA
1 TTAT-TA-TATTATTATTA
* *
1142095 TTTTTATATTATTATAA
1 TTATTATATTATTATTA
1142112 TTATTATTATTA
1 TTATTA-TATTA
1142124 AATAATATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
15 1 0.02
16 7 0.13
17 32 0.60
18 12 0.23
19 1 0.02
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTATATTATTATTA
Done.