Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007823.1 Hibiscus syriacus cultivar Beakdansim tig00110160_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: 6287495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 33
Found at i:937563 original size:16 final size:16
Alignment explanation
Indices: 937538--937568 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
937528 TGATATCAAT
937538 TTTTTAAATATTTTGG
1 TTTTTAAATATTTTGG
*
937554 TTTTTCAATATTTTG
1 TTTTTAAATATTTTG
937569 ACCTTAAAAT
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:0.23, C:0.03, G:0.10, T:0.65
Consensus pattern (16 bp):
TTTTTAAATATTTTGG
Found at i:939713 original size:23 final size:23
Alignment explanation
Indices: 939683--939762 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 23
939673 CACCTAGACA
*
939683 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCATACCTTGAAT
*
939706 GTGCATCGAT--ATACCATGAA-
1 GTGCATCGATGCATACCTTGAAT
* *
939726 GTTGCACCGATGCATTCCTTGAAT
1 G-TGCATCGATGCATACCTTGAAT
939750 GTGCATCGATGCA
1 GTGCATCGATGCA
939763 CTCTGCTGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
20 1 0.02
21 16 0.34
23 29 0.62
24 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (23 bp):
GTGCATCGATGCATACCTTGAAT
Found at i:939737 original size:44 final size:44
Alignment explanation
Indices: 939663--939759 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
939653 TTGTGCATAA
*
939663 TGCATCGATACACCTAGACAGTGCATCGATGCATCCCTTGAATG
1 TGCATCGATACACCTAGACAGTGCACCGATGCATCCCTTGAATG
* *
939707 TGCATCGATATACC-ATGA-AGTTGCACCGATGCATTCCTTGAATG
1 TGCATCGATACACCTA-GACAG-TGCACCGATGCATCCCTTGAATG
939751 TGCATCGAT
1 TGCATCGAT
939760 GCACTCTGCT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
43 3 0.06
44 45 0.94
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (44 bp):
TGCATCGATACACCTAGACAGTGCACCGATGCATCCCTTGAATG
Found at i:940035 original size:28 final size:28
Alignment explanation
Indices: 940003--940063 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
939993 AAAAACCCCT
*
940003 GTTTTATTGATTTTTGAACTTATGACTA
1 GTTTTATTGATTTTTGAACTTAGGACTA
940031 GTTTTATTGATTTTTGAACTTAGGACTA
1 GTTTTATTGATTTTTGAACTTAGGACTA
940059 GTTTT
1 GTTTT
940064 TGATTAATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.23, C:0.07, G:0.16, T:0.54
Consensus pattern (28 bp):
GTTTTATTGATTTTTGAACTTAGGACTA
Found at i:942553 original size:65 final size:65
Alignment explanation
Indices: 942431--942584 Score: 184
Period size: 65 Copynumber: 2.4 Consensus size: 65
942421 ACCCATTTCG
* * * **
942431 AATGCATTTTATGTACCGATACACAAGCCATGCATCGATGCACTCTTGAATATTTTGAAACATCA
1 AATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCACTCCAGAATATTTTGAAACATCA
** *
942496 AATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCACTCCAGGCT-TGTTTGAAACATT
1 AATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCACTCCAGAATAT-TTTGAAACATC
*
942560 G
65 A
* * *
942561 AATGTAATTAGTGTACCGATGCAC
1 AATGCATTTTGTGTACCGATGCAC
942585 CCCTAGTGTA
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
64 1 0.01
65 75 0.99
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (65 bp):
AATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCACTCCAGAATATTTTGAAACATCA
Found at i:952643 original size:13 final size:13
Alignment explanation
Indices: 952613--952637 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
952603 ATAATAAATA
952613 TTTATTAGTAATC
1 TTTATTAGTAATC
952626 TTTATTAGTAAT
1 TTTATTAGTAAT
952638 TATTATAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (13 bp):
TTTATTAGTAATC
Found at i:952763 original size:24 final size:27
Alignment explanation
Indices: 952736--952785 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 27
952726 ATATTAATAA
*
952736 TAAATCAT-T-ATTAGT-AATCATTAT
1 TAAATCATATCATTACTAAATCATTAT
952760 TAAATCATATCATTACTAAATCATTA
1 TAAATCATATCATTACTAAATCATTA
952786 AATATTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 1 0.05
26 5 0.23
27 8 0.36
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (27 bp):
TAAATCATATCATTACTAAATCATTAT
Found at i:952771 original size:16 final size:16
Alignment explanation
Indices: 952752--952783 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
952742 ATTATTAGTA
*
952752 ATCATTATTAAATCAT
1 ATCATTACTAAATCAT
952768 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
952784 TAAATATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.41
Consensus pattern (16 bp):
ATCATTACTAAATCAT
Found at i:952798 original size:15 final size:15
Alignment explanation
Indices: 952778--952806 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
952768 ATCATTACTA
952778 AATCATTAAATATTG
1 AATCATTAAATATTG
952793 AATCATTAAATATT
1 AATCATTAAATATT
952807 AATAATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (15 bp):
AATCATTAAATATTG
Found at i:955735 original size:10 final size:10
Alignment explanation
Indices: 955720--955748 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
955710 CCTCGCTATT
955720 CTAAGCTTCG
1 CTAAGCTTCG
955730 CTAAGCTTCG
1 CTAAGCTTCG
955740 CTAAGCTTC
1 CTAAGCTTC
955749 AACCTCTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.31
Consensus pattern (10 bp):
CTAAGCTTCG
Found at i:958830 original size:15 final size:15
Alignment explanation
Indices: 958810--958846 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
958800 CATACCAAAA
958810 TCGGGTCCGGTAGTT
1 TCGGGTCCGGTAGTT
958825 TCGGGTCCGGTAGTT
1 TCGGGTCCGGTAGTT
958840 TCGGGTC
1 TCGGGTC
958847 GATAATCGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.05, C:0.22, G:0.41, T:0.32
Consensus pattern (15 bp):
TCGGGTCCGGTAGTT
Found at i:961237 original size:33 final size:34
Alignment explanation
Indices: 961186--961250 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
961176 AATATTTATA
*
961186 TATATTTTCTTTAAAAAATTTAAAATCATAAAATT
1 TATATTTTCTTTAAAAAATTGAAAAT-ATAAAATT
*
961221 TATA-TTT-TTTACAAAATTGAAAATATAAAA
1 TATATTTTCTTTAAAAAATTGAAAATATAAAA
961251 AGGTTTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 6 0.21
33 15 0.54
34 3 0.11
35 4 0.14
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (34 bp):
TATATTTTCTTTAAAAAATTGAAAATATAAAATT
Found at i:961803 original size:24 final size:24
Alignment explanation
Indices: 961776--961835 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
961766 TATTTATAAG
961776 GCCTCATCTTCTCTATTCTTACTT
1 GCCTCATCTTCTCTATTCTTACTT
961800 GCCTCATCTTCTCTATTCTTACTT
1 GCCTCATCTTCTCTATTCTTACTT
961824 GCCTCATCTTCT
1 GCCTCATCTTCT
961836 TTGGCGGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.12, C:0.35, G:0.05, T:0.48
Consensus pattern (24 bp):
GCCTCATCTTCTCTATTCTTACTT
Found at i:962697 original size:17 final size:17
Alignment explanation
Indices: 962675--962709 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
962665 TATTTATCAA
962675 CTTTTTATTCTCTTTTT
1 CTTTTTATTCTCTTTTT
*
962692 CTTTTTATTCTTTTTTT
1 CTTTTTATTCTCTTTTT
962709 C
1 C
962710 ATAGGGGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (17 bp):
CTTTTTATTCTCTTTTT
Found at i:970410 original size:21 final size:21
Alignment explanation
Indices: 970355--970404 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
970345 TTGTGTGCAT
970355 CGATGCACATTCAATGTGTAC
1 CGATGCACATTCAATGTGTAC
970376 CGATGCACATTCAATGTGTAC
1 CGATGCACATTCAATGTGTAC
970397 CGATGCAC
1 CGATGCAC
970405 TCTCAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (21 bp):
CGATGCACATTCAATGTGTAC
Found at i:971136 original size:18 final size:18
Alignment explanation
Indices: 971101--971153 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
971091 GAGGGATTAT
971101 TAGTGGTCCTTC-GGACA
1 TAGTGGTCCTTCGGGACA
971118 TAGTGGTCCTTCGGGACA
1 TAGTGGTCCTTCGGGACA
*
971136 TAGTGGTCATTCGGGACA
1 TAGTGGTCCTTCGGGACA
971154 AATATTCAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 12 0.35
18 22 0.65
ACGTcount: A:0.19, C:0.21, G:0.32, T:0.28
Consensus pattern (18 bp):
TAGTGGTCCTTCGGGACA
Found at i:977323 original size:30 final size:30
Alignment explanation
Indices: 977255--977339 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
977245 GATTTATTTA
* *
977255 GTGACCAAATTATAAATTTGGTAAAGTTTG
1 GTGACCAAAGTATAAATTTGGAAAAGTTTG
977285 GTGACCAAAGTATAAACTTT-GAAAAGTTTAG
1 GTGACCAAAGTATAAA-TTTGGAAAAGTTT-G
* * * *
977316 G-GGCCAAAATGTAATTTTGGAAAA
1 GTGACCAAAGTATAAATTTGGAAAA
977340 ATTACAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
29 3 0.07
30 38 0.83
31 5 0.11
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (30 bp):
GTGACCAAAGTATAAATTTGGAAAAGTTTG
Found at i:979503 original size:45 final size:44
Alignment explanation
Indices: 979439--979532 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 44
979429 ATAAACATAT
* * * *
979439 AAATAAGCTTACGAGCTTATGGGATAAATGTTATGTATATTGGTA
1 AAATAAGCTTACGAGCTTATAGAATAAATGGTAAGTATA-TGGTA
*
979484 AAATAAGCTTATGAGCTTATAGAATAAATGGTAAGTATATGGTA
1 AAATAAGCTTACGAGCTTATAGAATAAATGGTAAGTATATGGTA
979528 AAATA
1 AAATA
979533 TTGGATATGC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 10 0.23
45 34 0.77
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.33
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATAGAATAAATGGTAAGTATATGGTA
Found at i:980503 original size:34 final size:34
Alignment explanation
Indices: 980455--980555 Score: 157
Period size: 34 Copynumber: 3.0 Consensus size: 34
980445 TGAATATATG
* *
980455 TGGACGAGTAGAGTTATCTCGTTGTCTTTATGTA
1 TGGACGAGTGGAGTTATCTCGTTGTCCTTATGTA
980489 TGGACGAGTGGAGTTATCTCGTTGTCCTTATGTA
1 TGGACGAGTGGAGTTATCTCGTTGTCCTTATGTA
* * *
980523 TGGACGGGTGGAGTTATCCCGCTGTCCTTATGT
1 TGGACGAGTGGAGTTATCTCGTTGTCCTTATGT
980556 GTGGTTGATC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 62 1.00
ACGTcount: A:0.17, C:0.16, G:0.30, T:0.38
Consensus pattern (34 bp):
TGGACGAGTGGAGTTATCTCGTTGTCCTTATGTA
Found at i:982598 original size:23 final size:22
Alignment explanation
Indices: 982566--982631 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
982556 ATTTTAAATT
982566 TAAAATATAATAATATTAAAAAA
1 TAAAATATAA-AATATTAAAAAA
* *
982589 TTAAATATAACAATACT-AAAAA
1 TAAAATATAA-AATATTAAAAAA
*
982611 TAAAAT-TAAATTATTAAAAAA
1 TAAAATATAAAATATTAAAAAA
982632 ATCCAAAAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 4 0.11
21 8 0.22
22 10 0.28
23 14 0.39
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAATATAAAATATTAAAAAA
Found at i:982936 original size:23 final size:23
Alignment explanation
Indices: 982879--982936 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
982869 GAACCTAGCT
*
982879 TTATGTATATTTTTATTTTTTTAA
1 TTAT-TATATTTTTATTTTTGTAA
*
982903 TAATT-TAATTTTTATTTTTGGT-A
1 TTATTAT-ATTTTTATTTTT-GTAA
982926 TTATTATATTT
1 TTATTATATTT
982937 ATTTTTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
22 1 0.04
23 22 0.79
24 5 0.18
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (23 bp):
TTATTATATTTTTATTTTTGTAA
Found at i:982949 original size:22 final size:20
Alignment explanation
Indices: 982890--982950 Score: 50
Period size: 21 Copynumber: 2.9 Consensus size: 20
982880 TATGTATATT
*
982890 TTTATTTTTTTAATAATTTAA
1 TTTA-TTTTTTAATATTTTAA
* **
982911 TTTTTATTTTTGGTATTATTATA
1 TTTAT-TTTTTAATATT-TTA-A
982934 TTTATTTTTTAATATTT
1 TTTATTTTTTAATATTT
982951 AACCCATCAG
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
20 1 0.03
21 12 0.40
22 12 0.40
23 5 0.17
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.70
Consensus pattern (20 bp):
TTTATTTTTTAATATTTTAA
Found at i:991708 original size:9 final size:9
Alignment explanation
Indices: 991694--991726 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
991684 CTATGAAGAT
991694 GAAGAGGAA
1 GAAGAGGAA
991703 GAAGAGGAA
1 GAAGAGGAA
991712 GAAGAGGAA
1 GAAGAGGAA
991721 GAAGAG
1 GAAGAG
991727 ACAAAGGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (9 bp):
GAAGAGGAA
Found at i:992353 original size:162 final size:163
Alignment explanation
Indices: 992086--992412 Score: 638
Period size: 162 Copynumber: 2.0 Consensus size: 163
992076 TACAAGGGAA
992086 AATTAGTCTTTTAGCATGGAAGTAATTAAATATTACTTTTGAAGGGATATTTTAATACCCACGTG
1 AATTAGTCTTTTAGCATGGAAGTAATTAAATATTACTTTTGAAGGGATATTTTAATACCCACGTG
992151 GAAGACAACTGGGGAAAACCAAAGTTCCATATTTCTCTTCTTCTTCATTCTTTTTCTCCACCGTG
66 GAAGACAACTGGGGAAAACCAAAGTTCCATATTTCTCTTCTTCTTCATTCTTTTTCTCCACCGTG
992216 AAGCCAAGCTAAAGGTGAGTTTTC-TGTTGATC
131 AAGCCAAGCTAAAGGTGAGTTTTCTTGTTGATC
*
992248 AATTAGTCTTTTGGCATGGAAGTAATTAAATATTACTTTTGAAGGGATATTTTAATACCCACGTG
1 AATTAGTCTTTTAGCATGGAAGTAATTAAATATTACTTTTGAAGGGATATTTTAATACCCACGTG
992313 GAAGACAACTGGGGAAAACCAAAGTTCCATATTTCTCTTCTTCTTCATTCTTTTTCTCCACCGTG
66 GAAGACAACTGGGGAAAACCAAAGTTCCATATTTCTCTTCTTCTTCATTCTTTTTCTCCACCGTG
992378 AAGCCAAGCTAAAGGTGAGTTTTCTTGTTGATC
131 AAGCCAAGCTAAAGGTGAGTTTTCTTGTTGATC
992411 AA
1 AA
992413 ATTCTTGATG
Statistics
Matches: 163, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
162 153 0.94
163 10 0.06
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (163 bp):
AATTAGTCTTTTAGCATGGAAGTAATTAAATATTACTTTTGAAGGGATATTTTAATACCCACGTG
GAAGACAACTGGGGAAAACCAAAGTTCCATATTTCTCTTCTTCTTCATTCTTTTTCTCCACCGTG
AAGCCAAGCTAAAGGTGAGTTTTCTTGTTGATC
Found at i:992610 original size:17 final size:17
Alignment explanation
Indices: 992588--992621 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
992578 ATTTGACTTG
992588 TCATAAGTGGAATTAAA
1 TCATAAGTGGAATTAAA
992605 TCATAAGTGGAATTAAA
1 TCATAAGTGGAATTAAA
992622 GGATATGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (17 bp):
TCATAAGTGGAATTAAA
Found at i:993651 original size:23 final size:23
Alignment explanation
Indices: 993615--993660 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
993605 CAATCTTATA
*
993615 TGGCACTACGGTGCAATTT-TACG
1 TGGCACTACAGTGC-ATTTATACG
*
993638 TGGCACTTCAGTGCATTTATACG
1 TGGCACTACAGTGCATTTATACG
993661 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.33
Consensus pattern (23 bp):
TGGCACTACAGTGCATTTATACG
Found at i:1000430 original size:23 final size:23
Alignment explanation
Indices: 1000404--1000450 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1000394 ACTATGATGT
1000404 AATTCTACGCGGCACTTCGGTGC
1 AATTCTACGCGGCACTTCGGTGC
*
1000427 AATTCTACGTGGCACTTCGGTGC
1 AATTCTACGCGGCACTTCGGTGC
1000450 A
1 A
1000451 TTTATACGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.28
Consensus pattern (23 bp):
AATTCTACGCGGCACTTCGGTGC
Found at i:1000458 original size:23 final size:23
Alignment explanation
Indices: 1000404--1000458 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
1000394 ACTATGATGT
*
1000404 AATTCTACGCGGCACTTCGGTGC
1 AATTATACGCGGCACTTCGGTGC
* *
1000427 AATTCTACGTGGCACTTCGGTGC
1 AATTATACGCGGCACTTCGGTGC
*
1000450 ATTTATACG
1 AATTATACG
1000459 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.31
Consensus pattern (23 bp):
AATTATACGCGGCACTTCGGTGC
Found at i:1005851 original size:364 final size:364
Alignment explanation
Indices: 1005182--1005917 Score: 1278
Period size: 364 Copynumber: 2.0 Consensus size: 364
1005172 AGAGTATTAG
1005182 GCTTAGGTTGGCCCAATAGTTATAGGAAAGTGGTGTTTTTAAAAGTAAGTAAATAGGAAAAGGAC
1 GCTTAGGTTGGCCCAATAGTTATAGGAAAGTGGTGTTTTTAAAAGTAAGTAAATAGGAAAAGGAC
* *
1005247 CTAAAGTGTTGTTCACCCTTTTTGTTAAAGCTAAAAACTTCCCCCCCCTTTTTATATCATTTCAC
66 CTAAAGTGTTGTTCACCCTTTTTCTTAAAGATAAAAACTTCCCCCCCCTTTTTATATCATTTCAC
* * * * *
1005312 TTAACCAAACTCCCTATAATATCTTACCACTCTTCTTCTTCTTCCTCCCATTAGTTTCCATTTCT
131 GTAACCAAAATCCCCATAATATCTCACCACTCTTCTTCTTCTTCCTCCCATTAGTTTCCATTTAT
* * * *
1005377 TCTTCCTTTTAAGAGCCACGTTTCAAGTATTCTAAGCTTAGTTTGTTGTATCCAAGGTAAGAATG
196 TCTTCATTTCAAGAGCCAAGTTTAAAGTATTCTAAGCTTAGTTTGTTGTATCCAAGGTAAGAATG
1005442 TTTTCCTCCATCCTTCAAGCTTTGTTTTAAGCTCCATTTTGTAAGTTTTATAATTTGTTTTCAAA
261 TTTTCCTCCATCCTTCAAGCTTTGTTTTAAGCTCCATTTTGTAAGTTTTATAATTTGTTTTCAAA
1005507 AATGAGTTTTATGGAAGTTAAGGGGATCCATGAATCCAA
326 AATGAGTTTTATGGAAGTTAAGGGGATCCATGAATCCAA
* * *
1005546 GCTTAGGTTGGCCCAATATTTATAGGAAAGTGGTGTTTTTAAAAGTAAGTAAATAGGAGAATGAC
1 GCTTAGGTTGGCCCAATAGTTATAGGAAAGTGGTGTTTTTAAAAGTAAGTAAATAGGAAAAGGAC
* *
1005611 CTAAAGTGTTGTTCACCCTTTTTCTTAAAGATGAAAAA-TTTCCCCCTCTTTTTATATCATTTCA
66 CTAAAGTGTTGTTCACCCTTTTTCTTAAAGAT-AAAAACTTCCCCCCCCTTTTTATATCATTTCA
* * *
1005675 CGTAACCAAAATCCCCATAATATCTCACCATTCTTTTTCTTCTTCCTCCTATTAGTTTCCATTTA
130 CGTAACCAAAATCCCCATAATATCTCACCACTCTTCTTCTTCTTCCTCCCATTAGTTTCCATTTA
1005740 TTCTTCATTTCAAGAGCCAAGTTTAAAGTATTCTAAGCTTAGTTTGTTGTATCCAAGGTAAGAAT
195 TTCTTCATTTCAAGAGCCAAGTTTAAAGTATTCTAAGCTTAGTTTGTTGTATCCAAGGTAAGAAT
1005805 GTTTTCCTCCATCCTTCAAGCTTTGTTTTAAGCTCCATTTTGTAAGTTTTATAATTTGTTTTCAA
260 GTTTTCCTCCATCCTTCAAGCTTTGTTTTAAGCTCCATTTTGTAAGTTTTATAATTTGTTTTCAA
1005870 AAATGAGTTTTATGGAAGTTAAGGGGATCCATGAATCCAA
325 AAATGAGTTTTATGGAAGTTAAGGGGATCCATGAATCCAA
1005910 GCTT-GGTT
1 GCTTAGGTT
1005918 ATAGTGTATT
Statistics
Matches: 352, Mismatches: 19, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
363 4 0.01
364 343 0.97
365 5 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (364 bp):
GCTTAGGTTGGCCCAATAGTTATAGGAAAGTGGTGTTTTTAAAAGTAAGTAAATAGGAAAAGGAC
CTAAAGTGTTGTTCACCCTTTTTCTTAAAGATAAAAACTTCCCCCCCCTTTTTATATCATTTCAC
GTAACCAAAATCCCCATAATATCTCACCACTCTTCTTCTTCTTCCTCCCATTAGTTTCCATTTAT
TCTTCATTTCAAGAGCCAAGTTTAAAGTATTCTAAGCTTAGTTTGTTGTATCCAAGGTAAGAATG
TTTTCCTCCATCCTTCAAGCTTTGTTTTAAGCTCCATTTTGTAAGTTTTATAATTTGTTTTCAAA
AATGAGTTTTATGGAAGTTAAGGGGATCCATGAATCCAA
Found at i:1009625 original size:30 final size:31
Alignment explanation
Indices: 1009527--1009645 Score: 143
Period size: 31 Copynumber: 3.9 Consensus size: 31
1009517 GAGTCGAGGG
* *
1009527 TTACCTATGTCCTTCGGGGCATATGGGCAGT
1 TTACCTATGTCCTTCGGGACATATGGACAGT
* * *
1009558 TTACCTATGT-CTTCCGAGACATATGAATAGT
1 TTACCTATGTCCTT-CGGGACATATGGACAGT
*
1009589 TTACCTATGTCCTTCGGGATATATGGACAG-
1 TTACCTATGTCCTTCGGGACATATGGACAGT
* *
1009619 TTACCTATGTTCTTCGGAACATATGGA
1 TTACCTATGTCCTTCGGGACATATGGA
1009646 TAGGTCCTTC
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
30 27 0.36
31 44 0.59
32 3 0.04
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (31 bp):
TTACCTATGTCCTTCGGGACATATGGACAGT
Found at i:1009633 original size:62 final size:61
Alignment explanation
Indices: 1009527--1009648 Score: 174
Period size: 62 Copynumber: 2.0 Consensus size: 61
1009517 GAGTCGAGGG
* *
1009527 TTACCTATGTCCTTCGGGGCATATGGGCAGTTTACCTATGTCTTCCGAGACATATGAATAGT
1 TTACCTATGTCCTTCGGGACATATGGACAGTTTACCTATGTCTTCCGA-ACATATGAATAGT
* * *
1009589 TTACCTATGTCCTTCGGGATATATGGACAG-TTACCTATGTTCTTCGGAACATATGGATAG
1 TTACCTATGTCCTTCGGGACATATGGACAGTTTACCTATG-TCTTCCGAACATATGAATAG
1009649 GTCCTTCGGG
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
61 20 0.37
62 34 0.63
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (61 bp):
TTACCTATGTCCTTCGGGACATATGGACAGTTTACCTATGTCTTCCGAACATATGAATAGT
Found at i:1010867 original size:19 final size:19
Alignment explanation
Indices: 1010831--1010881 Score: 84
Period size: 19 Copynumber: 2.6 Consensus size: 19
1010821 TTACCATATA
1010831 GTATCGATACCCTACCCAAG
1 GTATCGATA-CCTACCCAAG
*
1010851 GTATCGATACTTACCCAAG
1 GTATCGATACCTACCCAAG
1010870 GTATCGATACCT
1 GTATCGATACCT
1010882 CTGAACCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 20 0.69
20 9 0.31
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25
Consensus pattern (19 bp):
GTATCGATACCTACCCAAG
Found at i:1011834 original size:37 final size:37
Alignment explanation
Indices: 1011790--1011877 Score: 151
Period size: 37 Copynumber: 2.4 Consensus size: 37
1011780 ATTTTGTTCG
1011790 GGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTC-
1 GGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCA
*
1011826 GATTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCA
1 G-GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCA
1011864 GGTCGGGTCGGGTT
1 GGTCGGGTCGGGTT
1011878 CAGGTTTAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
36 1 0.02
37 46 0.96
38 1 0.02
ACGTcount: A:0.11, C:0.11, G:0.40, T:0.38
Consensus pattern (37 bp):
GGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCA
Found at i:1012469 original size:16 final size:18
Alignment explanation
Indices: 1012444--1012488 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1012434 TATGGAATTG
1012444 GATTCTAATTCC-T-ACA
1 GATTCTAATTCCTTCACA
*
1012460 GATTCCAATTCCTTCACA
1 GATTCTAATTCCTTCACA
1012478 GATTCTAATTC
1 GATTCTAATTC
1012489 TCTCATAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.44
17 1 0.04
18 13 0.52
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.38
Consensus pattern (18 bp):
GATTCTAATTCCTTCACA
Found at i:1014291 original size:15 final size:15
Alignment explanation
Indices: 1014258--1014290 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1014248 TAAAATATTG
1014258 TTTTATATAATAAAT
1 TTTTATATAATAAAT
*
1014273 TTTTATAT-TTAAAT
1 TTTTATATAATAAAT
1014287 TTTT
1 TTTT
1014291 TTAAGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTATATAATAAAT
Found at i:1016714 original size:2 final size:2
Alignment explanation
Indices: 1016707--1016735 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1016697 TAAGAATACT
1016707 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1016736 GATAGCTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1020571 original size:22 final size:21
Alignment explanation
Indices: 1020536--1020593 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 21
1020526 TTATAATTAT
1020536 ATTAATATTTATTAAAATAAG
1 ATTAATATTTATTAAAATAAG
*
1020557 ATTAATGTATTATTAAAAT-A-
1 ATTAATAT-TTATTAAAATAAG
1020577 A-TAATA-TTATTAAAATA
1 ATTAATATTTATTAAAATA
1020594 TTAAAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
17 10 0.30
19 4 0.12
20 1 0.03
21 8 0.24
22 10 0.30
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (21 bp):
ATTAATATTTATTAAAATAAG
Found at i:1020597 original size:8 final size:8
Alignment explanation
Indices: 1020567--1020616 Score: 57
Period size: 8 Copynumber: 6.2 Consensus size: 8
1020557 ATTAATGTAT
1020567 TATTAAAA
1 TATTAAAA
* *
1020575 TAATAATAT
1 TATTAA-AA
1020584 TATTAAAA
1 TATTAAAA
1020592 TATTAAAA
1 TATTAAAA
*
1020600 -ATTATAA
1 TATTAAAA
1020607 TATTAAAA
1 TATTAAAA
1020615 TA
1 TA
1020617 AGAATATTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
7 6 0.18
8 22 0.65
9 6 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TATTAAAA
Found at i:1020608 original size:15 final size:15
Alignment explanation
Indices: 1020585--1020614 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1020575 TAATAATATT
1020585 ATTAAAATATTAAAA
1 ATTAAAATATTAAAA
*
1020600 ATTATAATATTAAAA
1 ATTAAAATATTAAAA
1020615 TAAGAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATTAAAATATTAAAA
Found at i:1020650 original size:40 final size:39
Alignment explanation
Indices: 1020563--1020653 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 39
1020553 TAAGATTAAT
*
1020563 GTAT-TATTAAAATAATAATATTATTAAAATATTAAAAA
1 GTATATATTAAAATAAGAATATTATTAAAATATTAAAAA
* * * * *
1020601 TTATAATATTAAAATAAGAATATTATATTATATTTTAAAGA
1 GTAT-ATATTAAAATAAGAATATTAT-TAAAATATTAAAAA
1020642 GTATATATTAAA
1 GTATATATTAAA
1020654 TATTCAATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
38 3 0.07
40 27 0.63
41 13 0.30
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (39 bp):
GTATATATTAAAATAAGAATATTATTAAAATATTAAAAA
Found at i:1021264 original size:163 final size:163
Alignment explanation
Indices: 1020995--1021295 Score: 462
Period size: 163 Copynumber: 1.8 Consensus size: 163
1020985 TTTGTTTGCT
* * * * *
1020995 AATCAAACACTTAAAAAACGAGAAAAATATTTTCCGAAAAAGCAATTACAAGAAAACACATATCC
1 AATCAAACACTTAAAAAACCAAAAAAATATTTTCCGAAAAAGCAATTACAAAAAAAAACATACCC
*
1021060 TTATTATCATATGGTGTTTACTTCGCTGTTTCTTTATGGAAAAACAATTCACCTGTTTCCATT-C
66 TTATTATCATATGGTGTTTACTTCGCTGTCTCTTTATGGAAAAACAATTCACCTGTTTCCATTAC
1021124 AAAAAAAATTACATCGACTATATATTTTCCGCC
131 AAAAAAAATTACATCGACTATATATTTTCCGCC
* * *
1021157 AATCAAACACTTAAAAGACCAAAAAAATATTTTCTG-AAAAGCCAATTACAATAAAAAAACATGC
1 AATCAAACACTTAAAAAACCAAAAAAATATTTTCCGAAAAAG-CAATTACAA-AAAAAAACATAC
* *
1021221 CCTTATTGTCATATGGTGTTTGCTTCGCTGTCTCTTTATGGAAAAACAATTCACCTGTTTCCATT
64 CCTTATTATCATATGGTGTTTACTTCGCTGTCTCTTTATGGAAAAACAATTCACCTGTTTCCATT
*
1021286 AGAAAAAAAA
129 ACAAAAAAAA
1021296 CCCATAGAAT
Statistics
Matches: 124, Mismatches: 12, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
161 5 0.04
162 41 0.33
163 70 0.56
164 8 0.06
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.31
Consensus pattern (163 bp):
AATCAAACACTTAAAAAACCAAAAAAATATTTTCCGAAAAAGCAATTACAAAAAAAAACATACCC
TTATTATCATATGGTGTTTACTTCGCTGTCTCTTTATGGAAAAACAATTCACCTGTTTCCATTAC
AAAAAAAATTACATCGACTATATATTTTCCGCC
Found at i:1027236 original size:20 final size:21
Alignment explanation
Indices: 1027211--1027251 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1027201 TTTATTATGT
**
1027211 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
1027231 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
1027252 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:1028649 original size:3 final size:3
Alignment explanation
Indices: 1028641--1028707 Score: 100
Period size: 3 Copynumber: 22.7 Consensus size: 3
1028631 AATATATATT
* *
1028641 TAA TAA TAA TAA TAA TAA TAA TGA TGA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1028688 TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
1028708 TGGATAAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1029033 original size:115 final size:117
Alignment explanation
Indices: 1028897--1030052 Score: 1797
Period size: 117 Copynumber: 10.1 Consensus size: 117
1028887 GGGGATGATG
*
1028897 ATCCATCAA-ATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
1 ATCCATCAACTTGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
* * *
1028961 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT-GCAATGTTG
66 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
* *
1029012 ATCCATCAA-ATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
1 ATCCATCAACTTGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
1029076 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
66 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
* *
1029128 ATCCATTAACTTGATGAATTCAGGCAAAAGATTGAACAAG-TCTTCTCATTATGAACTTCTTCTT
1 ATCCATCAACTTGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
1029192 CCTTCTTCAGATGACGAG---TTCTCATTATGAACTCTACCTGGCAAAGATA
66 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
* *
1029241 ATCCATTAACTTGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
1 ATCCATCAACTTGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
* * *
1029306 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT-GCAATGTTG
66 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
* *
1029357 ATCCATCAA-ATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
1 ATCCATCAACTTGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
1029421 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGC-AAGATA
66 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
* *
1029472 ATCCATTAACTTGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
1 ATCCATCAACTTGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
1029537 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
66 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
* *
1029589 ATCCATTAACTTGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
1 ATCCATCAACTTGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
1029654 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
66 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
* * *
1029706 ATCCATCAACTTGATGAATTC-AGAAAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCT
1 ATCCATCAACTTGATGAATTCAAG-CAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCT
*
1029770 CCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
65 TCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
* * *
1029823 ATCCATTAACTTGATGAATTC-AG-AAAAAAGGTGAACAAGTTCTTCTCATTATGAACTTCTTCT
1 ATCCATCAACTTGATGAATTCAAGCAAAAGA-TTGAACAAGTTCTTCTCATTATGAACTTCTTCT
* *
1029886 T-CTTCTTCAGAT-A--AG-TC-T-TCATTATGAACT-TTCTCTGGAAAAGAT-
65 TCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGATA
* * * *
1029931 ATCCATCAA-TTGATGAATTCATGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT
1 ATCCATCAACTTGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
* *
1029995 CCTTCTTCA-A--ATGAGTTCTTCTCATTATGAACTTTACCTGGCAAAGATA
66 CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
1030044 ATCCATCAA
1 ATCCATCAA
1030053 ATGATAGATT
Statistics
Matches: 975, Mismatches: 44, Indels: 46
0.92 0.04 0.04
Matches are distributed among these distances:
107 12 0.01
108 44 0.05
109 36 0.04
110 3 0.00
111 3 0.00
112 24 0.02
113 82 0.08
114 43 0.04
115 225 0.23
116 200 0.21
117 303 0.31
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (117 bp):
ATCCATCAACTTGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
CCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
Found at i:1029519 original size:345 final size:347
Alignment explanation
Indices: 1028907--1030057 Score: 1913
Period size: 345 Copynumber: 3.3 Consensus size: 347
1028897 ATCCATCAAA
*
1028907 TGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* * *
1028972 TGACGAGTTCTTCTCATTATGAACTCTACCT-GCAATGTTGATCCATCAAATGATGAATTCAAGC
66 TGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAAATGATGAATTCAAGC
1029036 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTCTTCAGATGACGAGTTCTTCT
131 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTCTTCAGATGACGAGTTCTTCT
1029101 CATTATGAACTCTACCTGGCAAAGATAATCCATTAACTTGATGAATTCAGGCAAAAGATTGAACA
196 CATTATGAACTCTACCTGGCAAAGATAATCCATTAACTTGATGAATTCAGGCAAAAGATTGAACA
1029166 AG-TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTCATTATGAACTCTACC
261 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTCATTATGAACTCTACC
1029230 TGGCAAAGATAATCCATTAACT
326 TGGCAAAGATAATCCATTAACT
1029252 TGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* * *
1029317 TGACGAGTTCTTCTCATTATGAACTCTACCT-GCAATGTTGATCCATCAAATGATGAATTCAAGC
66 TGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAAATGATGAATTCAAGC
1029381 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTCTTCAGATGACGAGTTCTTCT
131 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTCTTCAGATGACGAGTTCTTCT
1029446 CATTATGAACTCTACCTGGC-AAGATAATCCATTAACTTGATGAATTCAGGCAAAAGATTGAACA
196 CATTATGAACTCTACCTGGCAAAGATAATCCATTAACTTGATGAATTCAGGCAAAAGATTGAACA
1029510 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
261 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAG---TTCTCATTATGAACTCT
1029575 ACCTGGCAAAGATAATCCATTAACT
323 ACCTGGCAAAGATAATCCATTAACT
1029600 TGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*
1029665 TGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAACTTGATGAATTC-AG
66 TGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAA-ATGATGAATTCAAG
* * *
1029729 AAAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTCCCTTCTTCAGATGACGAGTTCTT
130 -CAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTCTTCAGATGACGAGTTCTT
** *
1029794 CTCATTATGAACTCTACCTGGCAAAGATAATCCATTAACTTGATGAATTCAGAAAAAAG-GTGAA
194 CTCATTATGAACTCTACCTGGCAAAGATAATCCATTAACTTGATGAATTCAGGCAAAAGATTGAA
1029858 CAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGAT-A--AG-TCTTCATTATGAACT-T
259 CAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTC-TCATTATGAACTCT
* * *
1029917 TCTCTGGAAAAGAT-ATCCATCAA-T
323 AC-CTGGCAAAGATAATCCATTAACT
* * * *
1029941 TGATGAATTCATGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-A
1 TGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* *
1030005 --ATGAGTTCTTCTCATTATGAACTTTACCTGGCAAAGATAATCCATCAAATGAT
66 TGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAAATGAT
1030058 AGATTTGAAT
Statistics
Matches: 775, Mismatches: 21, Indels: 28
0.94 0.03 0.03
Matches are distributed among these distances:
337 4 0.01
338 46 0.06
340 1 0.00
341 60 0.08
342 12 0.02
343 22 0.03
344 46 0.06
345 255 0.33
346 2 0.00
348 139 0.18
349 28 0.04
350 126 0.16
351 34 0.04
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.35
Consensus pattern (347 bp):
TGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
TGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAAATGATGAATTCAAGC
AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTCTTCAGATGACGAGTTCTTCT
CATTATGAACTCTACCTGGCAAAGATAATCCATTAACTTGATGAATTCAGGCAAAAGATTGAACA
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTCATTATGAACTCTACC
TGGCAAAGATAATCCATTAACT
Found at i:1031004 original size:83 final size:83
Alignment explanation
Indices: 1030777--1031155 Score: 620
Period size: 83 Copynumber: 4.6 Consensus size: 83
1030767 TTCCTACTGA
* * * * *
1030777 ATCAGATCAGACTCAAAGAAAACTTCCATAAGATGCTATGAACACATTCATCTTTTAAACTCAA-
1 ATCAGAT-A-ACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAAT
1030841 GATT-GTTCTGTCCAACCAG
64 GATTGGTTCTGTCCAACCAG
1030860 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTCAATG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTCTAAATTCAATG
*
1030925 ATTGGTTTTGTCCAACCAG
65 ATTGGTTCTGTCCAACCAG
*
1030944 ATCAGATAACTTAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAATGA
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAATGA
1031009 TTGGTTCTGTCCAACCAG
66 TTGGTTCTGTCCAACCAG
*
1031027 ATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTCAATG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTCTAAATTCAATG
*
1031092 ATTGGTTTTGTCCAACCA-
65 ATTGGTTCTGTCCAACCAG
1031110 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
1031156 ATATTTGTTC
Statistics
Matches: 280, Mismatches: 12, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
81 26 0.09
82 34 0.12
83 126 0.45
84 94 0.34
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAATGA
TTGGTTCTGTCCAACCAG
Found at i:1031053 original size:167 final size:164
Alignment explanation
Indices: 1030776--1031155 Score: 652
Period size: 167 Copynumber: 2.3 Consensus size: 164
1030766 GTTCCTACTG
* * * *
1030776 AATCAGATCAGACTCAAAGAAAACTTCCATAAGATGCTATGAACACATTCATCTTTTAAACTCAA
1 AATCAGAT-A-ACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAACTCAA
1030841 GATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACAT
64 GATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACAT
1030906 TCATCTTCTAAATTCAATGATTGGTTTTGTCCAACC
129 TCATCTTCTAAATTCAATGATTGGTTTTGTCCAACC
* *
1030942 AGATCAGATAACTTAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAAT
1 A-ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAACTCAA-
*
1031007 GATTGGTTCTGTCCAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACA
64 GATT-GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACA
1031072 TTCATCTTCTAAATTCAATGATTGGTTTTGTCCAACC
128 TTCATCTTCTAAATTCAATGATTGGTTTTGTCCAACC
1031109 AATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
1 AATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
1031156 ATATTTGTTC
Statistics
Matches: 203, Mismatches: 8, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
165 48 0.24
166 51 0.25
167 104 0.51
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (164 bp):
AATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAACTCAAGA
TTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTC
ATCTTCTAAATTCAATGATTGGTTTTGTCCAACC
Found at i:1032292 original size:11 final size:10
Alignment explanation
Indices: 1032271--1032335 Score: 58
Period size: 11 Copynumber: 6.1 Consensus size: 10
1032261 CCTTGACCCC
*
1032271 CTTTCTTTTT
1 CTTTTTTTTT
1032281 CTTCTTTTTTT
1 CTT-TTTTTTT
*
1032292 CTTTTTCTTT
1 CTTTTTTTTT
* *
1032302 CATTTTTCTT
1 CTTTTTTTTT
1032312 CTTTTTTTTCTT
1 C-TTTTTTT-TT
1032324 CTCTTTTTTTT
1 CT-TTTTTTTT
1032335 C
1 C
1032336 AAGCATATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
10 17 0.39
11 18 0.41
12 9 0.20
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:1032294 original size:17 final size:17
Alignment explanation
Indices: 1032272--1032323 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 17
1032262 CTTGACCCCC
1032272 TTTCTTTTTCTTCTTTT
1 TTTCTTTTTCTTCTTTT
1032289 TTTCTTTTTCTTTCATTTT
1 TTTCTTTTTC-TTC-TTTT
*
1032308 TCTTCTTTTTTTTCTT
1 T-TTCTTTTTCTTCTT
1032324 CTCTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 10 0.32
18 5 0.16
19 8 0.26
20 8 0.26
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTCTTTTTCTTCTTTT
Found at i:1032328 original size:17 final size:17
Alignment explanation
Indices: 1032273--1032334 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
1032263 TTGACCCCCT
* *
1032273 TTCTTTTTCTTCTTTTT
1 TTCTTTTTTTTCTTTTC
1032290 TTCTTTTTCTTTCATTTTTC
1 TTCTTTTT-TTTC--TTTTC
*
1032310 TTCTTTTTTTTCTTCTC
1 TTCTTTTTTTTCTTTTC
1032327 TT-TTTTTT
1 TTCTTTTTT
1032335 CAAGCATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
16 6 0.15
17 14 0.36
18 3 0.08
19 4 0.10
20 12 0.31
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81
Consensus pattern (17 bp):
TTCTTTTTTTTCTTTTC
Found at i:1032328 original size:28 final size:27
Alignment explanation
Indices: 1032271--1032335 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 27
1032261 CCTTGACCCC
*
1032271 CTTTCTTTTTCTTCTTTTTTTCTTTTT
1 CTTTCTTTTTCTTCTTTTTTTCTTTCT
1032298 CTTTCATTTTTCTTCTTTTTTT-TCTTCT
1 CTTTC-TTTTTCTTCTTTTTTTCT-TTCT
1032326 CTTT-TTTTTC
1 CTTTCTTTTTC
1032336 AAGCATATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 6 0.17
27 6 0.17
28 23 0.66
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (27 bp):
CTTTCTTTTTCTTCTTTTTTTCTTTCT
Found at i:1032335 original size:14 final size:13
Alignment explanation
Indices: 1032271--1032335 Score: 64
Period size: 14 Copynumber: 5.1 Consensus size: 13
1032261 CCTTGACCCC
*
1032271 CTTTCTTTTTCTT
1 CTTTCTTTTTTTT
*
1032284 CTTTTTTTCTTTTT
1 CTTTCTTT-TTTTT
*
1032298 CTTTC--ATTTTT
1 CTTTCTTTTTTTT
1032309 C-TTCTTTTTTTT
1 CTTTCTTTTTTTT
1032321 CTTCTCTTTTTTTT
1 CTT-TCTTTTTTTT
1032335 C
1 C
1032336 AAGCATATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
10 3 0.07
11 6 0.14
12 6 0.14
13 8 0.19
14 19 0.45
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (13 bp):
CTTTCTTTTTTTT
Found at i:1042174 original size:17 final size:17
Alignment explanation
Indices: 1042131--1042174 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1042121 TTTCTGAATT
*
1042131 TAAATAAATTTAAATAA
1 TAAATAAATTTAAACAA
*
1042148 -AAATGTAATTTAAACAA
1 TAAAT-AAATTTAAACAA
1042165 TAAATAAATT
1 TAAATAAATT
1042175 AACAGAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
16 4 0.18
17 14 0.64
18 4 0.18
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (17 bp):
TAAATAAATTTAAACAA
Found at i:1042671 original size:18 final size:17
Alignment explanation
Indices: 1042624--1042673 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
1042614 AAATACTTGC
*
1042624 AAATAAATAAAACATAT
1 AAATAAATAAAAAATAT
*
1042641 AAAT-ATTATAAAAATAAT
1 AAATAAATA-AAAAAT-AT
1042659 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
1042674 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 3 0.11
17 9 0.33
18 12 0.44
19 3 0.11
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:1044253 original size:16 final size:16
Alignment explanation
Indices: 1044232--1044262 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1044222 TGTTGTTGTT
1044232 TTTTTTTCTTTCTCTG
1 TTTTTTTCTTTCTCTG
*
1044248 TTTTTTTTTTTCTCT
1 TTTTTTTCTTTCTCT
1044263 CGGTTCTATC
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:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTTTTCTTTCTCTG
Found at i:1044759 original size:3 final size:3
Alignment explanation
Indices: 1044751--1044823 Score: 130
Period size: 3 Copynumber: 24.7 Consensus size: 3
1044741 TTTAATATTT
1044751 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1044798 TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
1044824 TGGATAAAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1046270 original size:2 final size:2
Alignment explanation
Indices: 1046263--1046333 Score: 128
Period size: 2 Copynumber: 36.5 Consensus size: 2
1046253 TAACTTAACA
1046263 AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT -T 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
1046303 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1046334 ATTCATATCA
Statistics
Matches: 67, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 65 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1048296 original size:29 final size:26
Alignment explanation
Indices: 1048264--1048345 Score: 96
Period size: 25 Copynumber: 3.1 Consensus size: 26
1048254 TATACACTTA
*
1048264 AAAGTACCTCGTAGATATATTTGCACTCG
1 AAAGTGCCTCGTAGA-A-A-TTGCACTCG
*
1048293 AAAGTGTCTCGTAG-AATTGCACTCG
1 AAAGTGCCTCGTAGAAATTGCACTCG
*
1048318 AAAGTGCCTCATAG-AATTGCACTCG
1 AAAGTGCCTCGTAGAAATTGCACTCG
1048343 AAA
1 AAA
1048346 CTCATAGAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
25 35 0.71
26 1 0.02
27 1 0.02
29 12 0.24
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (26 bp):
AAAGTGCCTCGTAGAAATTGCACTCG
Found at i:1048318 original size:25 final size:25
Alignment explanation
Indices: 1048284--1048360 Score: 108
Period size: 25 Copynumber: 3.2 Consensus size: 25
1048274 GTAGATATAT
* *
1048284 TTGCACTCGAAAGTGTCTCGTAGAA
1 TTGCACTCGAAAGTGCCTCATAGAA
1048309 TTGCACTCGAAAGTGCCTCATAGAA
1 TTGCACTCGAAAGTGCCTCATAGAA
1048334 TTGCACTCGAAA----CTCATAGAA
1 TTGCACTCGAAAGTGCCTCATAGAA
1048355 TTGCAC
1 TTGCAC
1048361 CATAGGTGCC
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
21 15 0.30
25 35 0.70
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (25 bp):
TTGCACTCGAAAGTGCCTCATAGAA
Found at i:1050006 original size:71 final size:71
Alignment explanation
Indices: 1049890--1050031 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
1049880 AGAATAAATG
1049890 TAATCATAGTTTAAAAATAGTAGTATTTTATTTAAGTAAAACAAGTTTCTAAAATCACTATAATA
1 TAATCATAGTTTAAAAATAGTAGTATTTTATTTAAGTAAAACAAGTTTCTAAAATCACTATAATA
1049955 CCCTCC
66 CCCTCC
1049961 TAATCATAGTTTAAAAATAGTAGTATTTTATTTAAGTAAAACAAGTTTCTAAAATCACTATAATA
1 TAATCATAGTTTAAAAATAGTAGTATTTTATTTAAGTAAAACAAGTTTCTAAAATCACTATAATA
1050026 CCCTCC
66 CCCTCC
1050032 AACCGAACAC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (71 bp):
TAATCATAGTTTAAAAATAGTAGTATTTTATTTAAGTAAAACAAGTTTCTAAAATCACTATAATA
CCCTCC
Found at i:1050107 original size:45 final size:45
Alignment explanation
Indices: 1050043--1050132 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
1050033 ACCGAACACC
1050043 GATATGTAGTTCCCCATAACTGCATCCATAAGGACTTACCCTAGG
1 GATATGTAGTTCCCCATAACTGCATCCATAAGGACTTACCCTAGG
1050088 GATATGTAGTTCCCCATAACTGCATCCATAAGGACTTACCCTAGG
1 GATATGTAGTTCCCCATAACTGCATCCATAAGGACTTACCCTAGG
1050133 CCCATTGGGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (45 bp):
GATATGTAGTTCCCCATAACTGCATCCATAAGGACTTACCCTAGG
Found at i:1050202 original size:31 final size:33
Alignment explanation
Indices: 1050167--1050253 Score: 126
Period size: 31 Copynumber: 2.7 Consensus size: 33
1050157 AAAGGAATGT
* *
1050167 CTTGGGGCCTGAGAGCTTACCCAAA-GAA-TAC
1 CTTGGGGCCTGAGAGCCTACCCAAATGAAGCAC
*
1050198 CTTGGGGCCTTAGAGCCTA-CCAAATGAAGCAC
1 CTTGGGGCCTGAGAGCCTACCCAAATGAAGCAC
1050230 CTTGGGGCCTGAGAGCCTACCCAA
1 CTTGGGGCCTGAGAGCCTACCCAA
1050254 GGGAACATCG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
30 5 0.10
31 20 0.41
32 20 0.41
33 4 0.08
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (33 bp):
CTTGGGGCCTGAGAGCCTACCCAAATGAAGCAC
Found at i:1050237 original size:32 final size:30
Alignment explanation
Indices: 1050167--1050250 Score: 114
Period size: 32 Copynumber: 2.7 Consensus size: 30
1050157 AAAGGAATGT
* *
1050167 CTTGGGGCCTGAGAGCTTACCCAAAGAATAC
1 CTTGGGGCCTGAGAGCCTA-CCAAAGAACAC
*
1050198 CTTGGGGCCTTAGAGCCTACCAAATGAAGCAC
1 CTTGGGGCCTGAGAGCCTACCAAA-GAA-CAC
1050230 CTTGGGGCCTGAGAGCCTACC
1 CTTGGGGCCTGAGAGCCTACC
1050251 CAAGGGAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
30 5 0.11
31 20 0.43
32 22 0.47
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.19
Consensus pattern (30 bp):
CTTGGGGCCTGAGAGCCTACCAAAGAACAC
Found at i:1050607 original size:32 final size:32
Alignment explanation
Indices: 1050563--1050647 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 32
1050553 TAATGCCTTG
* * *
1050563 GGGGCCTCAGAGCCTACCCAAT-GAAGTACCTT
1 GGGGCCTAAGAGCCTACCCAATAGAACT-CCTA
* * * *
1050595 GGGGCTTGAGAGCATACCCAATAGAACTTCTA
1 GGGGCCTAAGAGCCTACCCAATAGAACTCCTA
1050627 GGGGCCTAAGAGCCTACCCAA
1 GGGGCCTAAGAGCCTACCCAA
1050648 GGGTCACCTT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
32 39 0.91
33 4 0.09
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (32 bp):
GGGGCCTAAGAGCCTACCCAATAGAACTCCTA
Found at i:1054921 original size:2 final size:2
Alignment explanation
Indices: 1054835--1054908 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
1054825 GAGGGAACGA
*
1054835 AT AT AT AT AC 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
1054877 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
1054909 TTTGAATATA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1057036 original size:27 final size:27
Alignment explanation
Indices: 1056984--1057036 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1056974 TTTATTGTTG
* * *
1056984 TCTCAAGTGAGAATGAAAATGGTTTTA
1 TCTCAAGGGAGAAGGAAAATGATTTTA
*
1057011 TCTCAAGGGAGAAGGAATATGATTTT
1 TCTCAAGGGAGAAGGAAAATGATTTT
1057037 CAAAGGAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.32
Consensus pattern (27 bp):
TCTCAAGGGAGAAGGAAAATGATTTTA
Found at i:1057145 original size:42 final size:38
Alignment explanation
Indices: 1057098--1057231 Score: 159
Period size: 36 Copynumber: 3.5 Consensus size: 38
1057088 AATAGAATTG
* *
1057098 TCTCAAGTGAGACAAAATTTGTTTTTTAGAAGAAAAAAACAA
1 TCTCAAGTGAGATAAAATCTGTTTTTT--AAG--AAAAACAA
1057140 TCTCAAGTGAGATAAAATCTG--TTTTAAGAAAAACAA
1 TCTCAAGTGAGATAAAATCTGTTTTTTAAGAAAAACAA
* *
1057176 TCTCGAGTGAGATAAAATCTG--TTTTAAGAAAAATAA
1 TCTCAAGTGAGATAAAATCTGTTTTTTAAGAAAAACAA
*
1057212 TCTTAAGTGAGATAAAATCT
1 TCTCAAGTGAGATAAAATCT
1057232 TGTGTGAAAT
Statistics
Matches: 86, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
36 60 0.70
38 3 0.03
40 4 0.05
42 19 0.22
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.30
Consensus pattern (38 bp):
TCTCAAGTGAGATAAAATCTGTTTTTTAAGAAAAACAA
Found at i:1057175 original size:36 final size:36
Alignment explanation
Indices: 1057132--1057231 Score: 173
Period size: 36 Copynumber: 2.8 Consensus size: 36
1057122 TTTAGAAGAA
1057132 AAAAACAATCTCAAGTGAGATAAAATCTGTTTTAAG
1 AAAAACAATCTCAAGTGAGATAAAATCTGTTTTAAG
*
1057168 AAAAACAATCTCGAGTGAGATAAAATCTGTTTTAAG
1 AAAAACAATCTCAAGTGAGATAAAATCTGTTTTAAG
* *
1057204 AAAAATAATCTTAAGTGAGATAAAATCT
1 AAAAACAATCTCAAGTGAGATAAAATCT
1057232 TGTGTGAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (36 bp):
AAAAACAATCTCAAGTGAGATAAAATCTGTTTTAAG
Found at i:1066141 original size:20 final size:20
Alignment explanation
Indices: 1066116--1066153 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1066106 TGAAAAAATA
1066116 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
1066136 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
1066154 CACTTTGAAA
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:1072743 original size:20 final size:20
Alignment explanation
Indices: 1072701--1072743 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1072691 TTATTTTCAT
* *
1072701 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAAAATAA
1072721 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
1072741 TTT
1 TTT
1072744 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:1074431 original size:21 final size:21
Alignment explanation
Indices: 1074407--1074450 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1074397 CTTTGATGCT
1074407 TTCTCT-TTGATTCTCTCTTGA
1 TTCTCTCTTGATTCT-TCTTGA
*
1074428 TTCTCTCTTGATTCTTGTTGA
1 TTCTCTCTTGATTCTTCTTGA
1074449 TT
1 TT
1074451 GTTGTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.09, C:0.20, G:0.11, T:0.59
Consensus pattern (21 bp):
TTCTCTCTTGATTCTTCTTGA
Found at i:1074450 original size:10 final size:11
Alignment explanation
Indices: 1074407--1074442 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
1074397 CTTTGATGCT
1074407 TTCTCT-TTGA
1 TTCTCTCTTGA
1074417 TTCTCTCTTGA
1 TTCTCTCTTGA
1074428 TTCTCTCTTGA
1 TTCTCTCTTGA
1074439 TTCT
1 TTCT
1074443 TGTTGATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.08, C:0.25, G:0.08, T:0.58
Consensus pattern (11 bp):
TTCTCTCTTGA
Found at i:1074811 original size:45 final size:46
Alignment explanation
Indices: 1074723--1074813 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 46
1074713 TTGAAAAAGC
* *
1074723 CTGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
1074769 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
1074814 TTCGATGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 22 0.51
46 21 0.49
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:1080599 original size:58 final size:57
Alignment explanation
Indices: 1080496--1080637 Score: 194
Period size: 58 Copynumber: 2.4 Consensus size: 57
1080486 TAATGATGTA
* * * * *
1080496 ATTTTGTATTCATGTTTTGGTTCTTCTTCGGAGGGTAATGCCCCCATCTTGTTTCCTG
1 ATTTTGTATT-ATGTTTGGGTTCCTCTTCAGAGAGTAACGCCCCCATCTTGTTTCCTG
* *
1080554 ATATTTGTATTATGTTTGGGTTCCTCTTTAGAGAGTAACGTCCCCATCTTGTTTCCTG
1 AT-TTTGTATTATGTTTGGGTTCCTCTTCAGAGAGTAACGCCCCCATCTTGTTTCCTG
1080612 ATTATTGTATTATGTTTGGGTTCCTC
1 ATT-TTGTATTATGTTTGGGTTCCTC
1080638 ATCGGATGTT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
57 1 0.01
58 66 0.88
59 8 0.11
ACGTcount: A:0.15, C:0.18, G:0.20, T:0.47
Consensus pattern (57 bp):
ATTTTGTATTATGTTTGGGTTCCTCTTCAGAGAGTAACGCCCCCATCTTGTTTCCTG
Found at i:1081533 original size:21 final size:21
Alignment explanation
Indices: 1081490--1081533 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1081480 TTACCGTACG
* *
1081490 AATGACCAATCTTTTTATGAA
1 AATGACCAATCCTTTTATAAA
* *
1081511 AATGATCAATCCTTTTCTAAA
1 AATGACCAATCCTTTTATAAA
1081532 AA
1 AA
1081534 ATGGAACATT
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:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (21 bp):
AATGACCAATCCTTTTATAAA
Found at i:1082605 original size:13 final size:13
Alignment explanation
Indices: 1082571--1082611 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1082561 ACATTTATAT
1082571 ATATATATATATT-
1 ATAT-TATATATTA
*
1082584 ATGTTATATATTA
1 ATATTATATATTA
1082597 ATATTATATATTA
1 ATATTATATATTA
1082610 AT
1 AT
1082612 TCAAATGACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (13 bp):
ATATTATATATTA
Found at i:1086484 original size:28 final size:29
Alignment explanation
Indices: 1086452--1086521 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 29
1086442 ATCTTATGTA
* *
1086452 ATTTAAATAATTTATGTT-TATAATTTAT
1 ATTTAAATAATTAATGTTAAATAATTTAT
1086480 ATTTAAATAATTAATGTTCAAATAATTTAT
1 ATTTAAATAATTAATGTT-AAATAATTTAT
1086510 ATTTAAATAATT
1 ATTTAAATAATT
1086522 GATAAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 17 0.45
30 21 0.55
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (29 bp):
ATTTAAATAATTAATGTTAAATAATTTAT
Found at i:1086489 original size:15 final size:15
Alignment explanation
Indices: 1086452--1086521 Score: 90
Period size: 15 Copynumber: 4.8 Consensus size: 15
1086442 ATCTTATGTA
1086452 ATTTAAATAATTTAT
1 ATTTAAATAATTTAT
*
1086467 GTTT--ATAATTTAT
1 ATTTAAATAATTTAT
*
1086480 ATTTAAATAATTAAT
1 ATTTAAATAATTTAT
* *
1086495 GTTCAAATAATTTAT
1 ATTTAAATAATTTAT
1086510 ATTTAAATAATT
1 ATTTAAATAATT
1086522 GATAAAAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
13 12 0.27
15 33 0.73
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (15 bp):
ATTTAAATAATTTAT
Found at i:1088434 original size:12 final size:12
Alignment explanation
Indices: 1088407--1088440 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
1088397 CTATTTTCGG
1088407 AAAATTAATTTA
1 AAAATTAATTTA
1088419 AAAAGTTAATTTAA
1 AAAA-TTAATTT-A
1088433 AAAATTAA
1 AAAATTAA
1088441 AGATTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 11 0.55
14 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (12 bp):
AAAATTAATTTA
Found at i:1088467 original size:14 final size:13
Alignment explanation
Indices: 1088408--1088473 Score: 62
Period size: 14 Copynumber: 4.8 Consensus size: 13
1088398 TATTTTCGGA
*
1088408 AAATTAATTTAA-
1 AAATTAAATTAAT
* *
1088420 AAAGTTAATTTAAA
1 AAA-TTAAATTAAT
1088434 AAATTAAAGATTAAT
1 AAATT-AA-ATTAAT
1088449 AAATTAAATTAATT
1 AAATTAAATTAA-T
1088463 AAATTAAATTA
1 AAATTAAATTA
1088474 TTATAAACGT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
12 3 0.06
13 16 0.34
14 19 0.40
15 9 0.19
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (13 bp):
AAATTAAATTAAT
Found at i:1089735 original size:17 final size:17
Alignment explanation
Indices: 1089715--1089747 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1089705 ATTTTAGAAC
1089715 TAATAAAATTTAAAATA
1 TAATAAAATTTAAAATA
*
1089732 TAATAGAATTTAAAAT
1 TAATAAAATTTAAAAT
1089748 TTTAGTTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TAATAAAATTTAAAATA
Found at i:1099001 original size:15 final size:16
Alignment explanation
Indices: 1098970--1099002 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1098960 AGTTACTATA
1098970 AAATATATTTTCATTAT
1 AAATATATTTT-ATTAT
1098987 AAATATATTTT-TTAT
1 AAATATATTTTATTAT
1099002 A
1 A
1099003 TTTACTATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
17 11 0.69
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
AAATATATTTTATTAT
Found at i:1100515 original size:11 final size:11
Alignment explanation
Indices: 1100487--1100525 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
1100477 AGCACTCAAA
1100487 AATATATTATTT
1 AATAT-TTATTT
1100499 --TATTTATTT
1 AATATTTATTT
1100508 AATATTTATTT
1 AATATTTATTT
1100519 AATATTT
1 AATATTT
1100526 TAGTATCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 6 0.24
10 3 0.12
11 16 0.64
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
AATATTTATTT
Found at i:1100629 original size:10 final size:10
Alignment explanation
Indices: 1100552--1100635 Score: 52
Period size: 11 Copynumber: 8.5 Consensus size: 10
1100542 AAAAATTAAT
*
1100552 TATTAAAATA
1 TATTAATATA
1100562 T-TTAATAT-
1 TATTAATATA
1100570 TATTATAATATAA
1 TA-T-TAATAT-A
*
1100583 TTTTAATA-A
1 TATTAATATA
1100592 TATT-ATAT-
1 TATTAATATA
*
1100600 TTTTAATATTA
1 TATTAATA-TA
*
1100611 TATTAATATG
1 TATTAATATA
*
1100621 TATTCATATA
1 TATTAATATA
1100631 TATTA
1 TATTA
1100636 TAATAATATA
Statistics
Matches: 56, Mismatches: 9, Indels: 18
0.67 0.11 0.22
Matches are distributed among these distances:
8 7 0.12
9 13 0.23
10 16 0.29
11 18 0.32
12 1 0.02
13 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (10 bp):
TATTAATATA
Found at i:1100655 original size:50 final size:50
Alignment explanation
Indices: 1100563--1100657 Score: 115
Period size: 50 Copynumber: 1.9 Consensus size: 50
1100553 ATTAAAATAT
* * *
1100563 TTAATATTATTATAATATAATTTTAATAATATTATATTTTTAATATTATA
1 TTAATATTATTATAATATAATTATAATAATATTACATGTTTAATATTATA
1100613 TTAATATGTATTCAT-ATAT-ATTATAATAATA-TAGCATGTTTAATA
1 TTAATAT-TATT-ATAATATAATTATAATAATATTA-CATGTTTAATA
1100658 ATTTAGTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
49 2 0.05
50 27 0.69
51 8 0.21
52 2 0.05
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (50 bp):
TTAATATTATTATAATATAATTATAATAATATTACATGTTTAATATTATA
Found at i:1101000 original size:29 final size:30
Alignment explanation
Indices: 1100947--1101027 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 30
1100937 TTCAGGAAAT
* * *
1100947 GTAATTTATTTTACGTAAAATAATTAT-AG
1 GTAATTCATTTTACGTAAAACAATTATCAC
* * *
1100976 GTTATTCATTTTATGTAAAACAATTTTCAC
1 GTAATTCATTTTACGTAAAACAATTATCAC
*
1101006 GTAATTTATTTTACGTAAAACA
1 GTAATTCATTTTACGTAAAACA
1101028 TTTTTGATGA
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 22 0.52
30 20 0.48
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (30 bp):
GTAATTCATTTTACGTAAAACAATTATCAC
Found at i:1101024 original size:30 final size:29
Alignment explanation
Indices: 1100947--1101032 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 29
1100937 TTCAGGAAAT
* * *
1100947 GTAATTTATTTTACGTAAAATAATTATAG
1 GTAATTTATTTTACGTAAAACAATTTTAC
* * *
1100976 GTTATTCATTTTATGTAAAACAATTTTCAC
1 GTAATTTATTTTACGTAAAACAATTTT-AC
*
1101006 GTAATTTATTTTACGTAAAACATTTTT
1 GTAATTTATTTTACGTAAAACAATTTT
1101033 GATGAAAACA
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
29 22 0.48
30 24 0.52
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (29 bp):
GTAATTTATTTTACGTAAAACAATTTTAC
Found at i:1102907 original size:15 final size:15
Alignment explanation
Indices: 1102887--1102923 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1102877 ATATTTAGCT
*
1102887 GGGCGGGCAGATGTG
1 GGGCGGGCAGATGCG
*
1102902 GGGCGGGCGGATGCG
1 GGGCGGGCAGATGCG
1102917 GGGCGGG
1 GGGCGGG
1102924 TAATGTCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.16, G:0.68, T:0.08
Consensus pattern (15 bp):
GGGCGGGCAGATGCG
Found at i:1109680 original size:28 final size:28
Alignment explanation
Indices: 1109587--1109674 Score: 158
Period size: 28 Copynumber: 3.1 Consensus size: 28
1109577 GATGACTGCG
*
1109587 AACAATAAGTAAAACTTGTTGTTTCTAC
1 AACAGTAAGTAAAACTTGTTGTTTCTAC
*
1109615 AACAGTAAGTAAAACTTGTTGTTTCTAT
1 AACAGTAAGTAAAACTTGTTGTTTCTAC
1109643 AACAGTAAGTAAAACTTGTTGTTTCTAC
1 AACAGTAAGTAAAACTTGTTGTTTCTAC
1109671 AACA
1 AACA
1109675 AGAAGTTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (28 bp):
AACAGTAAGTAAAACTTGTTGTTTCTAC
Found at i:1111777 original size:11 final size:12
Alignment explanation
Indices: 1111761--1111791 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1111751 ATAGAAAAAT
1111761 ACCTAACTC-TC
1 ACCTAACTCTTC
1111772 ACCTAACTCTTC
1 ACCTAACTCTTC
1111784 ACCTAACT
1 ACCTAACT
1111792 AAATTGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.29, C:0.42, G:0.00, T:0.29
Consensus pattern (12 bp):
ACCTAACTCTTC
Found at i:1122308 original size:66 final size:62
Alignment explanation
Indices: 1122155--1122274 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 62
1122145 AAGTATTTTC
* * *
1122155 ATCTTTTTAACTTTGAATATTAAATATAATTGTATACTTTTGTATATTTCAAATTAAAATAAT
1 ATCTATTTAAGTTTGAATATTAAA-ATAATTGTATACTTTTGAATATTTCAAATTAAAATAAT
* *
1122218 ATCTATTTAAGTTTGAATGA-TAAAATGAGTT-TAT-CTTTTGAATATTTTAAATTAAAA
1 ATCTATTTAAGTTTGAAT-ATTAAAAT-AATTGTATACTTTTGAATATTTCAAATTAAAA
1122275 GATATTATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
61 21 0.42
62 5 0.10
63 23 0.46
64 1 0.02
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (62 bp):
ATCTATTTAAGTTTGAATATTAAAATAATTGTATACTTTTGAATATTTCAAATTAAAATAAT
Found at i:1123889 original size:26 final size:27
Alignment explanation
Indices: 1123846--1123901 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
1123836 TAAATTTACT
* * *
1123846 TTATATATATTAATTATAATTATTATA
1 TTATAAATATTAATTATAATCATTAAA
*
1123873 TTATAAATCTTAA-TATAATCATTAAA
1 TTATAAATATTAATTATAATCATTAAA
1123899 TTA
1 TTA
1123902 ATTTTATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (27 bp):
TTATAAATATTAATTATAATCATTAAA
Found at i:1124029 original size:23 final size:25
Alignment explanation
Indices: 1123994--1124039 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
1123984 TGTGTACTAA
1123994 TTAATTAATAA-TTT-AAATATAAT
1 TTAATTAATAATTTTAAAATATAAT
1124017 TTAACTTAA-AATTTTAAAATATA
1 TTAA-TTAATAATTTTAAAATATA
1124040 TATAAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAATTAATAATTTTAAAATATAAT
Found at i:1124544 original size:19 final size:19
Alignment explanation
Indices: 1124520--1124567 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
1124510 ATTTTAATTA
1124520 TTTTTAATGTTCTCTTCTT
1 TTTTTAATGTTCTCTTCTT
1124539 TTTTTAATGTTCTCTTCTT
1 TTTTTAATGTTCTCTTCTT
1124558 TTTTTAATGT
1 TTTTTAATGT
1124568 GCACAATTAT
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:0.12, C:0.12, G:0.06, T:0.69
Consensus pattern (19 bp):
TTTTTAATGTTCTCTTCTT
Found at i:1124687 original size:14 final size:15
Alignment explanation
Indices: 1124663--1124705 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 15
1124653 ATATACTTAC
1124663 ATACATTATATATAT
1 ATACATTATATATAT
1124678 ATAC-TTATATATACTT
1 ATACATTATATATA--T
1124694 ATACATGTATAT
1 ATACAT-TATAT
1124706 TTTTTTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.38
15 4 0.17
16 5 0.21
17 1 0.04
18 5 0.21
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (15 bp):
ATACATTATATATAT
Found at i:1130597 original size:2 final size:2
Alignment explanation
Indices: 1130592--1130800 Score: 79
Period size: 2 Copynumber: 109.0 Consensus size: 2
1130582 TTATATTACT
* * * *
1130592 TA TA TA TA TT TA TA TA TA T- TA TA CA TA CT- TA TA TA GA TC T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * * *
1130632 TT TA TA TA CA TA TA TA TA TA TG TG TG TG TA -A T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1130672 TA -A GTA TA CA TA TA CA TA AA TA TA -A TG TA TA CT- TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * *
1130713 TA T- TA TA CA TA TA CT- TA TG TA TA -A TG TA TA -A TA TA TA CCA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* *
1130753 TA -A TG TA TA -A TG TA TA CT- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
1130793 TA TA TA TA
1 TA TA TA TA
1130801 CACACACACT
Statistics
Matches: 154, Mismatches: 32, Indels: 42
0.68 0.14 0.18
Matches are distributed among these distances:
1 15 0.10
2 133 0.86
3 6 0.04
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1130598 original size:19 final size:19
Alignment explanation
Indices: 1130574--1130650 Score: 75
Period size: 19 Copynumber: 3.9 Consensus size: 19
1130564 TACATCATAC
1130574 ATATATACTTATAT-TACTT
1 ATATATACTTATATATA-TT
*
1130593 ATATATATTTATATATATT
1 ATATATACTTATATATATT
* *
1130612 ATACATACTTATATAGATCTT
1 ATATATACTTATAT--ATATT
* *
1130633 TTATATACATATATATAT
1 ATATATACTTATATATAT
1130651 ATGTGTGTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 30 0.64
20 2 0.04
21 15 0.32
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.51
Consensus pattern (19 bp):
ATATATACTTATATATATT
Found at i:1130640 original size:21 final size:21
Alignment explanation
Indices: 1130574--1130650 Score: 81
Period size: 21 Copynumber: 3.9 Consensus size: 21
1130564 TACATCATAC
1130574 ATATATACTTATAT-TA-CTT
1 ATATATACTTATATATATCTT
*
1130593 ATATATA-TT-TATATATATT
1 ATATATACTTATATATATCTT
* *
1130612 ATACATACTTATATAGATCTT
1 ATATATACTTATATATATCTT
* *
1130633 TTATATACATATATATAT
1 ATATATACTTATATATAT
1130651 ATGTGTGTGT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
17 3 0.07
18 4 0.09
19 15 0.33
20 2 0.04
21 22 0.48
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.51
Consensus pattern (21 bp):
ATATATACTTATATATATCTT
Found at i:1130726 original size:40 final size:41
Alignment explanation
Indices: 1130663--1130742 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 41
1130653 GTGTGTGTAA
1130663 TTATATATATAAGTATACATATACATAAATATAATGTATAC
1 TTATATATATAAGTATACATATACATAAATATAATGTATAC
* * **
1130704 TTATATATAT-ATTATACATATACTTATGTATAATGTATA
1 TTATATATATAAGTATACATATACATAAATATAATGTATA
1130743 ATATATACCA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
40 25 0.71
41 10 0.29
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (41 bp):
TTATATATATAAGTATACATATACATAAATATAATGTATAC
Found at i:1130757 original size:19 final size:19
Alignment explanation
Indices: 1130733--1130769 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1130723 ATACTTATGT
1130733 ATAATGTATAATATATACC
1 ATAATGTATAATATATACC
*
1130752 ATAATGTATAATGTATAC
1 ATAATGTATAATATATAC
1130770 TTATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (19 bp):
ATAATGTATAATATATACC
Found at i:1130845 original size:20 final size:21
Alignment explanation
Indices: 1130811--1130874 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 21
1130801 CACACACACT
* *
1130811 TATAGTTACAAGTATAATGTA
1 TATACTTAAAAGTATAATGTA
*
1130832 TATA-TTATAAGTATAA--TA
1 TATACTTAAAAGTATAATGTA
*
1130850 TATACTTAAAAGTATTATGTA
1 TATACTTAAAAGTATAATGTA
1130871 TATA
1 TATA
1130875 GTTTTATGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 6 0.16
19 10 0.27
20 11 0.30
21 10 0.27
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (21 bp):
TATACTTAAAAGTATAATGTA
Found at i:1130863 original size:39 final size:40
Alignment explanation
Indices: 1130811--1130893 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 40
1130801 CACACACACT
* *
1130811 TATAGTTACAAGTATAATGTATATA-TTATAAGTATAATA
1 TATACTTAAAAGTATAATGTATATAGTTATAAGTATAATA
* * * *
1130850 TATACTTAAAAGTATTATGTATATAGTTTTATGTATTATA
1 TATACTTAAAAGTATAATGTATATAGTTATAAGTATAATA
1130890 TATA
1 TATA
1130894 TATATATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 22 0.59
40 15 0.41
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (40 bp):
TATACTTAAAAGTATAATGTATATAGTTATAAGTATAATA
Found at i:1130872 original size:19 final size:20
Alignment explanation
Indices: 1130820--1130874 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
1130810 TTATAGTTAC
*
1130820 AAGTATAATGTATATATTAT
1 AAGTATAATGTATATATTAA
1130840 AAGTATAA--TATATACTTAA
1 AAGTATAATGTATATA-TTAA
*
1130859 AAGTATTATGTATATA
1 AAGTATAATGTATATA
1130875 GTTTTATGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 6 0.20
19 10 0.33
20 8 0.27
21 6 0.20
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (20 bp):
AAGTATAATGTATATATTAA
Found at i:1131168 original size:71 final size:70
Alignment explanation
Indices: 1131033--1131170 Score: 213
Period size: 71 Copynumber: 2.0 Consensus size: 70
1131023 AGTTAAATAT
*
1131033 TAATTTATGCAATTTAGTCTTTAAAATTATATTTGTATATGAAATTAACACATACTTATTTATAT
1 TAATTTATGCAATTTAGTCCTTAAAATTATATTTGTATATGAAATTAACACATACTTATTTATAT
1131098 TTTTG
66 TTTTG
* * * * *
1131103 TAATTTACTTCAATTTTGTCCTTAAAATTATTTTTGTATATGAAATTGACCCATACTTATTTATA
1 TAATTTA-TGCAATTTAGTCCTTAAAATTATATTTGTATATGAAATTAACACATACTTATTTATA
1131168 TTT
65 TTT
1131171 CGATTTAGTC
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
70 7 0.11
71 54 0.89
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (70 bp):
TAATTTATGCAATTTAGTCCTTAAAATTATATTTGTATATGAAATTAACACATACTTATTTATAT
TTTTG
Found at i:1138604 original size:49 final size:49
Alignment explanation
Indices: 1138510--1138604 Score: 113
Period size: 49 Copynumber: 1.9 Consensus size: 49
1138500 AAGTTTAACA
* * * *
1138510 AATTTAACAAAATAAAGTAAGTATTAAATGAGAAATAATAAAAAATTAC
1 AATTTAACAAAATAAAGTAAATATCAAATGAGAAAAAAAAAAAAATTAC
*
1138559 AATTTAACAAAATAAAGTAAATA-CAAAT-ATAATAAAAAAACAAAAT
1 AATTTAACAAAATAAAGTAAATATCAAATGAGAA-AAAAAAA-AAAAT
1138605 CTATCGATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
47 3 0.08
48 9 0.23
49 27 0.69
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.24
Consensus pattern (49 bp):
AATTTAACAAAATAAAGTAAATATCAAATGAGAAAAAAAAAAAAATTAC
Found at i:1140723 original size:17 final size:17
Alignment explanation
Indices: 1140703--1140742 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1140693 AATTTATATT
*
1140703 AGTAAAATATTAAATAA
1 AGTAAAATACTAAATAA
1140720 AGTAAAATACTAAATAA
1 AGTAAAATACTAAATAA
*
1140737 ATTAAA
1 AGTAAA
1140743 CTAATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (17 bp):
AGTAAAATACTAAATAA
Found at i:1141301 original size:72 final size:74
Alignment explanation
Indices: 1141189--1141337 Score: 241
Period size: 73 Copynumber: 2.0 Consensus size: 74
1141179 CAGGCTTGTG
* *
1141189 TATGCAAATATGCCCAAAAAACCCTACCCTAGAAAAGAAAGTGATTTGCAGAGAAA-ATAAGCAA
1 TATGCAAATATGCCCAAAAAACCATACCCTAGAAAAGAAAGTGATTTGCAGAGAAATA-AAGAAA
1141253 -TTATTAATA
65 TTTATTAATA
*
1141262 TATGCAAATATGCCCAAAAAACCATGCCCT-GAAAAGAAAGTGATTTGCAGAGAAATAAAGAAAT
1 TATGCAAATATGCCCAAAAAACCATACCCTAGAAAAGAAAGTGATTTGCAGAGAAATAAAGAAAT
1141326 TTATTAATA
66 TTATTAATA
1141335 TAT
1 TAT
1141338 ATATTACTAC
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
72 30 0.42
73 41 0.58
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (74 bp):
TATGCAAATATGCCCAAAAAACCATACCCTAGAAAAGAAAGTGATTTGCAGAGAAATAAAGAAAT
TTATTAATA
Found at i:1143327 original size:103 final size:97
Alignment explanation
Indices: 1143131--1143334 Score: 246
Period size: 103 Copynumber: 2.0 Consensus size: 97
1143121 ACCGACCCGA
* ***
1143131 ATCACACTTAAAAAACCCGAACAGACCCGACCCGAACCCGAAATTTTTTAAAAAATCTGTCCGAT
1 ATCACACTTAAAAAACCCGAACAGACCCGACCCAAACCCGAAATTTTTTAAAAAATCCAACCGAT
* *
1143196 CAGGAATTTTTTGAAAAAAACCCGACCCGAAT
66 CACGAATTTTTTGAAAAAAACCCAACCCGAAT
* * *
1143228 ATCACACTTACAAAAACCCGACCTGACCCGACCCAAACCCGAATTTTTTTTTATAAAAAAGTCCA
1 ATCACACTTA-AAAAACCCGAACAGACCCGACCCAAACCCGAA---ATTTTT-TAAAAAA-TCCA
* * *
1143293 ACCGATCCCGAATTTTTTTAAAAAAATCCAACCCGAAT
60 ACCGATCACGAATTTTTTGAAAAAAACCCAACCCGAAT
1143331 ATCA
1 ATCA
1143335 AAAGATTGAT
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
97 10 0.11
98 29 0.33
101 5 0.06
102 7 0.08
103 38 0.43
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.23
Consensus pattern (97 bp):
ATCACACTTAAAAAACCCGAACAGACCCGACCCAAACCCGAAATTTTTTAAAAAATCCAACCGAT
CACGAATTTTTTGAAAAAAACCCAACCCGAAT
Found at i:1148296 original size:26 final size:26
Alignment explanation
Indices: 1148266--1148325 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
1148256 ATAACCAATG
1148266 CCATAAAATAATGAAAGGGTCAAACC
1 CCATAAAATAATGAAAGGGTCAAACC
*
1148292 CCATAAAATAATGAAAGGGTCAAACT
1 CCATAAAATAATGAAAGGGTCAAACC
1148318 CCATAAAA
1 CCATAAAA
1148326 CAAATACAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.52, C:0.18, G:0.13, T:0.17
Consensus pattern (26 bp):
CCATAAAATAATGAAAGGGTCAAACC
Found at i:1149655 original size:14 final size:14
Alignment explanation
Indices: 1149636--1149678 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
1149626 ATGACTGTAT
1149636 GAGACAGTGCAGTA
1 GAGACAGTGCAGTA
1149650 GAGACAGTGCAGTA
1 GAGACAGTGCAGTA
*
1149664 GAGACAGGGCAGTA
1 GAGACAGTGCAGTA
1149678 G
1 G
1149679 GGACGGTCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.35, C:0.14, G:0.40, T:0.12
Consensus pattern (14 bp):
GAGACAGTGCAGTA
Found at i:1149912 original size:21 final size:21
Alignment explanation
Indices: 1149886--1149930 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1149876 GAAACACTGC
1149886 CCATTGCCCTTTGCCCAAAAG
1 CCATTGCCCTTTGCCCAAAAG
1149907 CCATTGCCCTTTGCCCAAAAG
1 CCATTGCCCTTTGCCCAAAAG
1149928 CCA
1 CCA
1149931 AAAAAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.40, G:0.13, T:0.22
Consensus pattern (21 bp):
CCATTGCCCTTTGCCCAAAAG
Found at i:1157388 original size:12 final size:12
Alignment explanation
Indices: 1157371--1157396 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1157361 AATCTCTCAT
1157371 ATAGGTATTACA
1 ATAGGTATTACA
1157383 ATAGGTATTACA
1 ATAGGTATTACA
1157395 AT
1 AT
1157397 TTGACAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (12 bp):
ATAGGTATTACA
Found at i:1160158 original size:3 final size:3
Alignment explanation
Indices: 1160150--1160175 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1160140 ACTAGGCAGC
1160150 GCT GCT GCT GCT GCT GCT GCT GCT GC
1 GCT GCT GCT GCT GCT GCT GCT GCT GC
1160176 CTCCTGGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.35, T:0.31
Consensus pattern (3 bp):
GCT
Found at i:1162763 original size:29 final size:29
Alignment explanation
Indices: 1162708--1162836 Score: 143
Period size: 29 Copynumber: 4.4 Consensus size: 29
1162698 ACAAAATGGA
* * * *
1162708 GATATAATCACATGCAGAGTCAGGACGGG
1 GATATAATCCCATACAAAATCAGGACGGG
* * *
1162737 GATATCATCTCATACAAAATCAAGACGGG
1 GATATAATCCCATACAAAATCAGGACGGG
* * *
1162766 GATATAATCCCACACAGAA-CTAGGACGAG
1 GATATAATCCCATACAAAATC-AGGACGGG
*
1162795 GATATAATCCCATACAAAATCAGGGCGGG
1 GATATAATCCCATACAAAATCAGGACGGG
1162824 GATATAATCCCAT
1 GATATAATCCCAT
1162837 GCAGAATAAA
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
28 1 0.01
29 80 0.98
30 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.19
Consensus pattern (29 bp):
GATATAATCCCATACAAAATCAGGACGGG
Found at i:1162773 original size:58 final size:58
Alignment explanation
Indices: 1162708--1162842 Score: 173
Period size: 58 Copynumber: 2.3 Consensus size: 58
1162698 ACAAAATGGA
* * * * *
1162708 GATATAATCACATGCAG-AGTCAGGACGGGGATATCATCTCATACAAAATCAAGACGGG
1 GATATAATCCCATGCAGAACT-AGGACGAGGATATAATCCCATACAAAATCAAGACGGG
** * *
1162766 GATATAATCCCACACAGAACTAGGACGAGGATATAATCCCATACAAAATCAGGGCGGG
1 GATATAATCCCATGCAGAACTAGGACGAGGATATAATCCCATACAAAATCAAGACGGG
1162824 GATATAATCCCATGCAGAA
1 GATATAATCCCATGCAGAA
1162843 TAAAAAAATG
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 63 0.97
59 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.18
Consensus pattern (58 bp):
GATATAATCCCATGCAGAACTAGGACGAGGATATAATCCCATACAAAATCAAGACGGG
Found at i:1166482 original size:29 final size:29
Alignment explanation
Indices: 1166429--1166557 Score: 118
Period size: 29 Copynumber: 4.5 Consensus size: 29
1166419 TCCGAAGATG
* *
1166429 ATCCCAAACAGAAAT-ATGATAGGGATATA
1 ATCCCATACAG-AATCAGGATAGGGATATA
* * *
1166458 AACCCATACAGAATGAGGATGGGGATATA
1 ATCCCATACAGAATCAGGATAGGGATATA
* * *
1166487 ATCCCATGCAGAATCAGGTTAGGGAAATA
1 ATCCCATACAGAATCAGGATAGGGATATA
* * *
1166516 ATCTCATACAGAATCAGGA-CGTGATATA
1 ATCCCATACAGAATCAGGATAGGGATATA
* *
1166544 ATCTCATGCAGAAT
1 ATCCCATACAGAAT
1166558 AAAAAATGTA
Statistics
Matches: 82, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
28 22 0.27
29 60 0.73
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (29 bp):
ATCCCATACAGAATCAGGATAGGGATATA
Found at i:1166557 original size:57 final size:58
Alignment explanation
Indices: 1166448--1166557 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 58
1166438 AGAAATATGA
* * *
1166448 TAGGGATATAAACCCATACAGAATGAGGATGGGGATATAATCCCATGCAGAATCAGGT
1 TAGGGAAATAAACCCATACAGAATCAGGATCGGGATATAATCCCATGCAGAATCAGGT
* * * *
1166506 TAGGGAAATAATCTCATACAGAATCAGGA-CGTGATATAATCTCATGCAGAAT
1 TAGGGAAATAAACCCATACAGAATCAGGATCGGGATATAATCCCATGCAGAAT
1166558 AAAAAATGTA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 20 0.44
58 25 0.56
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (58 bp):
TAGGGAAATAAACCCATACAGAATCAGGATCGGGATATAATCCCATGCAGAATCAGGT
Found at i:1174373 original size:21 final size:21
Alignment explanation
Indices: 1174335--1174374 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1174325 AAAAAATTAT
*
1174335 TTAAAAAATTATTATTTTTAC
1 TTAAAAAATTAATATTTTTAC
* *
1174356 TTAAAACATTAATGTTTTT
1 TTAAAAAATTAATATTTTT
1174375 TAATATTTTC
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:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (21 bp):
TTAAAAAATTAATATTTTTAC
Found at i:1179717 original size:44 final size:44
Alignment explanation
Indices: 1179654--1179743 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
1179644 CTGGTTTATG
1179654 AAGATTTCATAATTGTCGATCTGCATTGGAAATCTCATCGATTT
1 AAGATTTCATAATTGTCGATCTGCATTGGAAATCTCATCGATTT
1179698 AAGATTTCATAATTGTCGATCTGCATTGGAAATCTCATCGATTT
1 AAGATTTCATAATTGTCGATCTGCATTGGAAATCTCATCGATTT
1179742 AA
1 AA
1179744 TGAGAGTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (44 bp):
AAGATTTCATAATTGTCGATCTGCATTGGAAATCTCATCGATTT
Found at i:1179738 original size:22 final size:22
Alignment explanation
Indices: 1179669--1179739 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
1179659 TTCATAATTG
1179669 TCGATCTGCATTGGAAATCTCA
1 TCGATCTGCATTGGAAATCTCA
* ** *
1179691 TCGATTTAAG-ATTTCATAAT-T-G
1 TCGATCT--GCATTGGA-AATCTCA
1179713 TCGATCTGCATTGGAAATCTCA
1 TCGATCTGCATTGGAAATCTCA
1179735 TCGAT
1 TCGAT
1179740 TTAATGAGAG
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
20 4 0.11
21 5 0.14
22 17 0.49
23 5 0.14
24 4 0.11
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (22 bp):
TCGATCTGCATTGGAAATCTCA
Done.