Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008926.1 Hibiscus syriacus cultivar Beakdansim tig00112231_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: 4069050
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 20
Found at i:1138707 original size:35 final size:34
Alignment explanation
Indices: 1138660--1138755 Score: 104
Period size: 35 Copynumber: 2.7 Consensus size: 34
1138650 TATCGCACTT
1138660 GAAAAAAGAAAAAGAAAGAAAAATAAAAGAAAGAA
1 GAAAAAAGAAAAAGAAAGAAAAAT-AAAGAAAGAA
*
1138695 GAAAAGAA-AAAAAGGAAGAAAAATAAAGAAAGAAAAA
1 GAAAA-AAGAAAAAGAAAGAAAAATAAAGAAAG---AA
* *
1138732 GAATAAAGAATAAAAAAAGAAAAA
1 GAAAAAAGAA-AAAGAAAGAAAAA
1138756 AGATAGATAG
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
34 8 0.16
35 20 0.39
36 4 0.08
37 8 0.16
38 11 0.22
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (34 bp):
GAAAAAAGAAAAAGAAAGAAAAATAAAGAAAGAA
Found at i:1138713 original size:24 final size:22
Alignment explanation
Indices: 1138661--1138756 Score: 73
Period size: 20 Copynumber: 4.5 Consensus size: 22
1138651 ATCGCACTTG
1138661 AAAA-AAGAAAAAG-AAAGAAA
1 AAAAGAAGAAAAAGAAAAGAAA
1138681 AATAA-AAGAAAGAAGAAAAGAAA
1 AA-AAGAAGAAA-AAGAAAAGAAA
*
1138704 AAAAGGAAGAAAAA-TAAAGAAA
1 AAAA-GAAGAAAAAGAAAAGAAA
* *
1138726 GAAA-AAGAATAAAG--AATAAA
1 AAAAGAAGAA-AAAGAAAAGAAA
1138746 AAAAGAA-AAAA
1 AAAAGAAGAAAA
1138757 GATAGATAGA
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
19 2 0.03
20 17 0.27
21 13 0.20
22 15 0.23
23 11 0.17
24 6 0.09
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (22 bp):
AAAAGAAGAAAAAGAAAAGAAA
Found at i:1138723 original size:27 final size:27
Alignment explanation
Indices: 1138664--1138756 Score: 76
Period size: 24 Copynumber: 3.6 Consensus size: 27
1138654 GCACTTGAAA
1138664 AAAGAAAAAGAAAGAAAA-ATA-AAAGAA-
1 AAAG-AAAAGAAA-AAAAGA-AGAAAGAAT
1138691 AGAAGAAAAGAAAAAAAGGAAGAAA-AAT
1 A-AAGAAAAGAAAAAAA-GAAGAAAGAAT
*
1138719 AAAG-AAAG--AAAAAGAATAAAGAAT
1 AAAGAAAAGAAAAAAAGAAGAAAGAAT
1138743 AAA-AAAAGAAAAAA
1 AAAGAAAAGAAAAAA
1138757 GATAGATAGA
Statistics
Matches: 56, Mismatches: 1, Indels: 19
0.74 0.01 0.25
Matches are distributed among these distances:
23 6 0.11
24 15 0.27
26 12 0.21
27 15 0.27
28 8 0.14
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (27 bp):
AAAGAAAAGAAAAAAAGAAGAAAGAAT
Found at i:1141443 original size:42 final size:42
Alignment explanation
Indices: 1141396--1142328 Score: 481
Period size: 42 Copynumber: 21.7 Consensus size: 42
1141386 AATCTTCAAA
* * *
1141396 TTGACTTCCTCGTAAATAGGAGCCAATCTTTCAATGTTATTC
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTC
* * * * * *
1141438 TTGACTTTCTTGTAAAGAGAAGACAATCTTTCAGTATTGTCATTC
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCA--A-TGTTATTC
* * * ** * *
1141483 TTAACTCCCTCTTGAAGAGGAGTCAATAATTCAATATTATTT
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTC
* * *
1141525 TTGATTTCCTCATGAAGAGGAGTCAATCTTTTAATGTTATTC
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTC
* * * * * *
1141567 CTAAC-TCCTTCATGAAAAAGAGTCAATCTTTCAATATTATTC
1 TTGACTTCC-TCGTGAAGAGGAGTCAATCTTTCAATGTTATTC
* * * *
1141609 TTGACTTTCTCGCGAAGA-GACATCAATCTTTCAGTATCGTCATTC
1 TTGACTTCCTCGTGAAGAGGA-GTCAATCTTTCA--AT-GTTATTC
* * ** * *
1141654 CTGACTTTCTCGTGAAGAAAAATCAATCTTGCTGTAATGTTATTC
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTT--T-CAATGTTATTC
* * * * *
1141699 TTGAATTTCTAGTGAAGAGAAGTTAATCTTTCAGTATTGTCT-TTC
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCA--A-TGT-TATTC
* * * *
1141744 TTGACTCCCTCATTAAGAGGACTCAATCTTTCAATGTTATTC
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTC
* * *
1141786 TTGACTTCCTCGTGAATAGGAGTCAATATTTCAATGCTATTC
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTC
* * * *
1141828 TTGACTTTCTCGTGAAGAGAAGTAAATCTTTCAGTATTGTCATTC
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCA--A-TGTTATTC
* * * * *
1141873 TTGACTCCCTCGTAAAGAGAATTCAATCTTTCAATATTATTC
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTC
*
1141915 TTCACTTCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTC
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTC
* * ** * *
1141957 TTAACTACCTCACGAAGAGGAGTTAATCTTTCAATATTATTC
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTC
* * * * **
1141999 TTGACTGT-TTTGCGATGATAAGTCAATCTTTCAGTATTGTCT-TTC
1 TTGACT-TCCTCGTGAAGAGGAGTCAATCTTTCA--A-TGT-TATTC
* * * ** ** *
1142044 TTAACTTTCTC--G--CA--A-TCTTTC-AGCAATGTCATTC
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTC
* * *
1142078 TTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAATATTGTCATTC
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTC-A-A-TGTTATTC
* * * * *
1142123 TTGACTTTCTCGTGAAGAGAAATCAATATTTCAATGTTATAC
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTC
* * *
1142165 TTGAC-TCTCTCGTGAAGAGAATTCAATCTTTTAGCAATGTGATTC
1 TTGACTTC-CTCGTGAAGAGGAGTCAATC-TTT--CAATGTTATTC
* * * * * * * * *
1142210 ATAAATTTCTCGTGAAGAGAAGTAAATCTTCTAATATTGTCATTT
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTT-TCA-A-TGTTATTC
* * * * * *
1142255 TTTACTTTCTCATGAAAAAGAGTCAATCTTTTAGTGATGTTATTC
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCA---ATGTTATTC
* * * *
1142300 TTGATTTTCTTGCGAAGAGGAGTCAATCT
1 TTGACTTCCTCGTGAAGAGGAGTCAATCT
1142329 AATGGTGTTG
Statistics
Matches: 682, Mismatches: 160, Indels: 95
0.73 0.17 0.10
Matches are distributed among these distances:
34 16 0.02
35 1 0.00
36 1 0.00
37 2 0.00
38 5 0.01
39 1 0.00
40 1 0.00
41 12 0.02
42 318 0.47
43 13 0.02
44 14 0.02
45 289 0.42
46 7 0.01
47 1 0.00
48 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (42 bp):
TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTC
Found at i:1141501 original size:45 final size:44
Alignment explanation
Indices: 1141396--1142375 Score: 492
Period size: 45 Copynumber: 22.7 Consensus size: 44
1141386 AATCTTCAAA
* * * * *
1141396 TTGACTTCCTCGTAAATAGGAGCCAATCTTTCA--ATGTTATTC
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATGTCATTC
* * * *
1141438 TTGACTTTCTTGTAAAGAGAAGACAATCTTTCAGTATTGTCATTC
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTA-TGTCATTC
* * * * ** * *
1141483 TTAACTCCCTCTTGAAGAGGAGTCAATAATTCAATAT-T-ATTT
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATGTCATTC
* * * * *
1141525 TTGATTTCCTCATGAAGAGGAGTCAATCTTTTA--ATGTTATTC
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATGTCATTC
* * * * *
1141567 CTAAC-TCCTTCATGAA-AAAGAGTCAATCTTTCAATAT-T-ATTC
1 TTGACTTCC-TCGTGAAGAGA-AGTCAATCTTTCAGTATGTCATTC
* *
1141609 TTGACTTTCTCGCGAAGAGACA-TCAATCTTTCAGTATCGTCATTC
1 TTGACTTCCTCGTGAAGAGA-AGTCAATCTTTCAGTAT-GTCATTC
* * * * * * *
1141654 CTGACTTTCTCGTGAAGAAAAATCAATCTTGCTGTAATGTTATTC
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGT-ATGTCATTC
* * * * *
1141699 TTGAATTTCTAGTGAAGAGAAGTTAATCTTTCAGTATTGTCTTTC
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTA-TGTCATTC
* * * * * *
1141744 TTGACTCCCTCATTAAGAGGACTCAATCTTTCA--ATGTTATTC
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATGTCATTC
* * *
1141786 TTGACTTCCTCGTGAATAGGAGTCAATATTTCA--ATG-CTATTC
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATGTC-ATTC
* *
1141828 TTGACTTTCTCGTGAAGAGAAGTAAATCTTTCAGTATTGTCATTC
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTA-TGTCATTC
* * * *
1141873 TTGACTCCCTCGTAAAGAGAATTCAATCTTTCAATAT-T-ATTC
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATGTCATTC
* * *
1141915 TTCACTTCCTCGTGAAGAGGAGTCAATCTTTCA--ATGTTATTC
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATGTCATTC
* * ** * * *
1141957 TTAACTACCTCACGAAGAGGAGTTAATCTTTCAATAT-T-ATTC
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATGTCATTC
* * * * * *
1141999 TTGACTGT-TTTGCGATGATAAGTCAATCTTTCAGTATTGTCTTTC
1 TTGACT-TCCTCGTGAAGAGAAGTCAATCTTTCAGTA-TGTCATTC
* * *
1142044 TTAACTT--TC-T-------CG-CAATCTTTCAGCAATGTCATTC
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAG-TATGTCATTC
* *
1142078 TTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAATATTGTCATTC
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTA-TGTCATTC
* * * * *
1142123 TTGACTTTCTCGTGAAGAGAAATCAATATTTCA--ATGTTATAC
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATGTCATTC
* * * *
1142165 TTGAC-TCTCTCGTGAAGAGAATTCAATCTTTTAGCAATGTGATTC
1 TTGACTTC-CTCGTGAAGAGAAGTCAATCTTTCAG-TATGTCATTC
* * * * * * *
1142210 ATAAATTTCTCGTGAAGAGAAGTAAATC-TTCTAATATTGTCATTT
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTTC-AGTA-TGTCATTC
* * * * * *
1142255 TTTACTTTCTCATGAA-AAAGAGTCAATCTTTTAGTGATGTTATTC
1 TTGACTTCCTCGTGAAGAGA-AGTCAATCTTTCAGT-ATGTCATTC
* * * * * * * * *
1142300 TTGATTTTCTTGCGAAGAGGAGTCAATCTAAT-GGTGTTGTCATCC
1 TTGACTTCCTCGTGAAGAGAAGTCAATCT-TTCAGT-ATGTCATTC
* * *
1142345 TTGACTTCCTCTTAAAGAGAATTCAATCTTT
1 TTGACTTCCTCGTGAAGAGAAGTCAATCTTT
1142376 TATTTTTATC
Statistics
Matches: 715, Mismatches: 168, Indels: 108
0.72 0.17 0.11
Matches are distributed among these distances:
34 24 0.03
35 2 0.00
36 2 0.00
37 1 0.00
40 4 0.01
41 7 0.01
42 301 0.42
43 13 0.02
44 21 0.03
45 331 0.46
46 9 0.01
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (44 bp):
TTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAGTATGTCATTC
Found at i:1141873 original size:87 final size:87
Alignment explanation
Indices: 1141396--1142232 Score: 420
Period size: 87 Copynumber: 9.8 Consensus size: 87
1141386 AATCTTCAAA
* * * * * * * * *
1141396 TTGACTTCCTCGTAAATAGGAGCCAATCTTTCA--A-TGTTATTCTTGACTTTCTTGTAAAGAGA
1 TTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTCCTCGTGAAGAGA
* * *
1141458 AGACAATCTTTCAGTATTGTCATTC
66 AGTCAATATTTCA--A-TGTTATTC
* ** * * ** * * * * *
1141483 TTAACTCCCTCTTGAAGAGGAGTCAATAATTCAATA-T-T-ATTTTTGATTTCCTCATGAAGAGG
1 TTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTCCTCGTGAAGAGA
* *
1141545 AGTCAATCTTTTAATGTTATTC
66 AGTCAATATTTCAATGTTATTC
* * * * * * * *
1141567 CTAAC-TCCTTCATGAA-AAAGAGTCAATCTTTCAATA-T-T-ATTCTTGACTTTCTCGCGAAGA
1 TTGACTTTC-TCGTGAAGAGA-AGTCAATCTTTCAGTATTGTCATTCTTGACTTCCTCGTGAAGA
* *
1141627 GACA-TCAATCTTTCAGTATCGTCATTC
64 GA-AGTCAATATTTCA--AT-GTTATTC
* * * * * * * * * *
1141654 CTGACTTTCTCGTGAAGAAAAATCAATCTTGCTGTAATGTTATTCTTGAATTTCTAGTGAAGAGA
1 TTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTCCTCGTGAAGAGA
* *
1141719 AGTTAATCTTTCAGTATTGTCT-TTC
66 AGTCAATATTTCA--A-TGT-TATTC
** * * * * * * *
1141744 TTGACTCCCTCATTAAGAGGACTCAATCTTTCA--A-TGTTATTCTTGACTTCCTCGTGAATAGG
1 TTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTCCTCGTGAAGAGA
*
1141806 AGTCAATATTTCAATGCTATTC
66 AGTCAATATTTCAATGTTATTC
* * *
1141828 TTGACTTTCTCGTGAAGAGAAGTAAATCTTTCAGTATTGTCATTCTTGACTCCCTCGTAAAGAGA
1 TTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTCCTCGTGAAGAGA
* * *
1141893 ATTCAATCTTTCAATATTATTC
66 AGTCAATATTTCAATGTTATTC
* * * * * * ** *
1141915 TTCACTTCCTCGTGAAGAGGAGTCAATCTTTCA--A-TGTTATTCTTAACTACCTCACGAAGAGG
1 TTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTCCTCGTGAAGAGA
* * *
1141977 AGTTAATCTTTCAATATTATTC
66 AGTCAATATTTCAATGTTATTC
* * * * * * * *
1141999 TTGACTGTT-TTGCGATGATAAGTCAATCTTTCAGTATTGTCTTTCTTAACTT--TC-T--CG-C
1 TTGACT-TTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTCCTCGTGAAGAG
* *
1142057 AA-TC--T-TTCAGCAATGTCATTC
65 AAGTCAATATT--TCAATGTTATTC
* *
1142078 TTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAATATTGTCATTCTTGACTTTCTCGTGAAGAGA
1 TTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTCCTCGTGAAGAGA
* *
1142143 AATCAATATTTCAATGTTATAC
66 AGTCAATATTTCAATGTTATTC
* * * * * * * * * *
1142165 TTGACTCTCTCGTGAAGAGAATTCAATCTTTTAGCAATGTGATTCATAAATTTCTCGTGAAGAGA
1 TTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTCCTCGTGAAGAGA
1142230 AGT
66 AGT
1142233 AAATCTTCTA
Statistics
Matches: 580, Mismatches: 133, Indels: 74
0.74 0.17 0.09
Matches are distributed among these distances:
77 2 0.00
78 3 0.01
79 51 0.09
80 1 0.00
81 3 0.01
82 2 0.00
83 4 0.01
84 158 0.27
85 9 0.02
86 6 0.01
87 263 0.45
88 9 0.02
89 6 0.01
90 62 0.11
91 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (87 bp):
TTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTCCTCGTGAAGAGA
AGTCAATATTTCAATGTTATTC
Found at i:1141929 original size:261 final size:260
Alignment explanation
Indices: 1141428--1141932 Score: 599
Period size: 261 Copynumber: 1.9 Consensus size: 260
1141418 CCAATCTTTC
* *
1141428 AATGTTATTCTTGACTTTCTTGTAAAGAGAAGACAATCTTTCAGTATTGTCATTCTTAACTCCCT
1 AATGTTATTCTTGAATTTCTAGTAAAGAGAAGACAATCTTTCAGTATTGTCATTCTTAACTCCCT
* * * * *
1141493 CTTGAAGAGGAGTCAATAATTCAATATTATTTTTGATTTCCTCATGAAGAGGAGTCAATCTTTTA
66 CTTGAAGAGGACTCAATAATTCAATATTATTCTTGACTTCCTCATGAAGAGGAGTCAATATTTCA
* * ** *
1141558 ATGTTATTCCTAACTCCTTCATGAAAAAGAGTCAATCTTTCAATATTATTCTTGACTTTCTCGCG
131 ATGCTATTCCTAACTCCTTCATGAAAAAGAGTAAATCTTTCAATATTATTCTTGACTCCCTCGCA
* * *
1141623 AAGAGACATCAATCTTTCAGTATCGTCATTCCTGACTTTCTCGTGAAGAAAAATCAATCTTGCTG
196 AAGAGACATCAATCTTTCAATATC-TCATTCCTCACTTCCTCGTGAAGAAAAATCAATCTTGCTG
1141688 T
260 T
* ** * *
1141689 AATGTTATTCTTGAATTTCTAGTGAAGAGAAGTTAATCTTTCAGTATTGTCTTTCTTGACTCCCT
1 AATGTTATTCTTGAATTTCTAGTAAAGAGAAGACAATCTTTCAGTATTGTCATTCTTAACTCCCT
** * * *
1141754 CATT-AAGAGGACTCAATCTTTCAATGTTATTCTTGACTTCCTCGTGAATAGGAGTCAATATTTC
66 C-TTGAAGAGGACTCAATAATTCAATATTATTCTTGACTTCCTCATGAAGAGGAGTCAATATTTC
* * * * * *
1141818 AATGCTATTCTTGACT-TTCTCGTG-AAGAGAAGTAAATCTTTCAGTATTGTCATTCTTGACTCC
130 AATGCTATTCCTAACTCCT-TCATGAAAAAG-AGTAAATCTTTCAATA-T-T-ATTCTTGACTCC
* *
1141881 CTCGTAAAGAGA-ATTCAATCTTTCAATAT-T-ATTCTTCACTTCCTCGTGAAGA
190 CTCGCAAAGAGACA-TCAATCTTTCAATATCTCATTCCTCACTTCCTCGTGAAGA
1141933 GGAGTCAATC
Statistics
Matches: 204, Mismatches: 33, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
260 5 0.02
261 159 0.78
262 4 0.02
263 2 0.01
264 34 0.17
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (260 bp):
AATGTTATTCTTGAATTTCTAGTAAAGAGAAGACAATCTTTCAGTATTGTCATTCTTAACTCCCT
CTTGAAGAGGACTCAATAATTCAATATTATTCTTGACTTCCTCATGAAGAGGAGTCAATATTTCA
ATGCTATTCCTAACTCCTTCATGAAAAAGAGTAAATCTTTCAATATTATTCTTGACTCCCTCGCA
AAGAGACATCAATCTTTCAATATCTCATTCCTCACTTCCTCGTGAAGAAAAATCAATCTTGCTGT
Found at i:1141974 original size:129 final size:128
Alignment explanation
Indices: 1141396--1142253 Score: 597
Period size: 129 Copynumber: 6.7 Consensus size: 128
1141386 AATCTTCAAA
* * * * ** *
1141396 TTGACTTCCTCGTAAATAGGAGCCAATCTTTCAATGTTATTCTTGACTTTCTTGTAAAGAGAAG-
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTAACTTTCTCATGAAGAGAAGT
* * * ** *
1141460 ACAATCTTTCAGTATTGTCATTCTTAACTCCCTCTTGAAGAGGAGTCAATAATTCAATATTATTT
66 A-AATCTTTCAGTATTGTCATTCTTGACTCCCTCGTGAAGA-GAATCAATCTTTCAATATTATTC
* * * * * *
1141525 TTGATTTCCTCATGAAGAGGAGTCAATCTTTTAATGTTATTCCTAAC-TCCTTCATGAA-AAAGA
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTAACTTTC-TCATGAAGAGA-A
* * ** * *
1141588 GTCAATCTTTCAATA-T-T-ATTCTTGACTTTCTCGCGAAGAGACATCAATCTTTCAGTATCGTC
64 GTAAATCTTTCAGTATTGTCATTCTTGACTCCCTCGTGAAGAGA-ATCAATCTTTCAATAT--T-
1141650 ATTC
125 ATTC
* * ** * *
1141654 CTGACTTTCTCGTGAAGAAAAATCAATCTTGCTGTAATGTTATTCTTGAA-TTTCT-AGTGAAGA
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTT--T-CAATGTTATTCTT-AACTTTCTCA-TGAAGA
* * * * * *
1141717 GAAGTTAATCTTTCAGTATTGTCTTTCTTGACTCCCTCATTAAGAGGACTCAATCTTTCAATGTT
61 GAAGTAAATCTTTCAGTATTGTCATTCTTGACTCCCTCGTGAAGA-GAATCAATCTTTCAATATT
1141782 ATTC
125 ATTC
* * * * *
1141786 TTGACTTCCTCGTGAATAGGAGTCAATATTTCAATGCTATTCTTGACTTTCTCGTGAAGAGAAGT
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTAACTTTCTCATGAAGAGAAGT
*
1141851 AAATCTTTCAGTATTGTCATTCTTGACTCCCTCGTAAAGAGAATTCAATCTTTCAATATTATTC
66 AAATCTTTCAGTATTGTCATTCTTGACTCCCTCGTGAAGAGAA-TCAATCTTTCAATATTATTC
* ** * *
1141915 TTCACTTCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTAACTACCTCACGAAGAGGAGT
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTAACTTTCTCATGAAGAGAAGT
* * *** * * * * * *
1141980 TAATCTTTCAATA-T-T-ATTCTTGACTGTTTTGCGATGATAAGTCAATCTTTCAGTATTGTCTT
66 AAATCTTTCAGTATTGTCATTCTTGACTCCCTCGTGAAGAGAA-TCAATCTTTCAATA-T-T-AT
1142042 TC
127 TC
* * * ** ** * * *
1142044 TTAACTTTCTC--G--CA--A-TCTTTC-AGCAATGTCATTCTTGACTTTCTCGTGAAGAGAAGT
1 TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTAACTTTCTCATGAAGAGAAGT
* * ** * * *
1142101 CAATCTTTCAATATTGTCATTCTTGACTTTCTCGTGAAGAGAAATCAATATTTCAATGTTATAC
66 AAATCTTTCAGTATTGTCATTCTTGACTCCCTCGTGAAGAG-AATCAATCTTTCAATATTATTC
* * * * * *
1142165 TTGAC-TCTCTCGTGAAGAGAATTCAATCTTTTAGCAATGTGATTCATAAATTTCTCGTGAAGAG
1 TTGACTTC-CTCGTGAAGAGGAGTCAATC-TTT--CAATGTTATTCTTAACTTTCTCATGAAGAG
*
1142229 AAGTAAATC-TTCTAATATTGTCATT
62 AAGTAAATCTTTC-AGTATTGTCATT
1142254 TTTTACTTTC
Statistics
Matches: 564, Mismatches: 124, Indels: 79
0.74 0.16 0.10
Matches are distributed among these distances:
120 1 0.00
121 48 0.09
122 6 0.01
123 4 0.01
124 28 0.05
125 6 0.01
126 59 0.10
127 5 0.01
128 15 0.03
129 242 0.43
130 1 0.00
131 5 0.01
132 104 0.18
133 8 0.01
134 1 0.00
135 29 0.05
136 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (128 bp):
TTGACTTCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTAACTTTCTCATGAAGAGAAGT
AAATCTTTCAGTATTGTCATTCTTGACTCCCTCGTGAAGAGAATCAATCTTTCAATATTATTC
Found at i:1142065 original size:34 final size:34
Alignment explanation
Indices: 1142022--1142089 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
1142012 GATGATAAGT
* * *
1142022 CAATCTTTCAGTATTGTCTTTCTTAACTTTCTCG
1 CAATCTTTCAGCAATGTCATTCTTAACTTTCTCG
*
1142056 CAATCTTTCAGCAATGTCATTCTTGACTTTCTCG
1 CAATCTTTCAGCAATGTCATTCTTAACTTTCTCG
1142090 TGAAGAGAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.19, C:0.25, G:0.10, T:0.46
Consensus pattern (34 bp):
CAATCTTTCAGCAATGTCATTCTTAACTTTCTCG
Found at i:1142657 original size:20 final size:20
Alignment explanation
Indices: 1142632--1142687 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1142622 ATAAGACCTT
1142632 TTTTGTCTTTCTCAAAGACA
1 TTTTGTCTTTCTCAAAGACA
*
1142652 TTTTGTCTTTCTCAAAGACC
1 TTTTGTCTTTCTCAAAGACA
**
1142672 TTTTCACTTTCTCAAA
1 TTTTGTCTTTCTCAAA
1142688 AGGTTAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.46
Consensus pattern (20 bp):
TTTTGTCTTTCTCAAAGACA
Found at i:1149142 original size:14 final size:16
Alignment explanation
Indices: 1149123--1149156 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1149113 TTTATTCACA
1149123 ATTTC-ATTTTTTT-C
1 ATTTCAATTTTTTTCC
1149137 ATTTCAATTTTTTTCC
1 ATTTCAATTTTTTTCC
1149153 ATTT
1 ATTT
1149157 TCAGGAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 8 0.44
16 5 0.28
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTCAATTTTTTTCC
Found at i:1152118 original size:5 final size:5
Alignment explanation
Indices: 1152108--1152162 Score: 67
Period size: 5 Copynumber: 10.8 Consensus size: 5
1152098 AACGGTCAAT
* *
1152108 GGTCG GGTCG GGTCAG CGGTCG GGTAG GGTCG GGTC- GGTCG AGTCG GGTCG
1 GGTCG GGTCG GGTC-G -GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG
1152159 GGTC
1 GGTC
1152163 AGACCGGTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
4 4 0.09
5 33 0.77
6 2 0.05
7 4 0.09
ACGTcount: A:0.05, C:0.20, G:0.55, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:1152148 original size:19 final size:19
Alignment explanation
Indices: 1152124--1152162 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1152114 GTCGGGTCAG
*
1152124 CGGTCGGGTAGGGTCGGGT
1 CGGTCGAGTAGGGTCGGGT
*
1152143 CGGTCGAGTCGGGTCGGGT
1 CGGTCGAGTAGGGTCGGGT
1152162 C
1 C
1152163 AGACCGGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.21, G:0.54, T:0.21
Consensus pattern (19 bp):
CGGTCGAGTAGGGTCGGGT
Found at i:1158236 original size:21 final size:22
Alignment explanation
Indices: 1158212--1158256 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
1158202 AAAATAGAAG
1158212 AAAAAT-AACAAGTAAAACAAA
1 AAAAATGAACAAGTAAAACAAA
* *
1158233 AAAAATGAAGAAGTAAAATAAA
1 AAAAATGAACAAGTAAAACAAA
1158255 AA
1 AA
1158257 TGCTATGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.76, C:0.04, G:0.09, T:0.11
Consensus pattern (22 bp):
AAAAATGAACAAGTAAAACAAA
Found at i:1158801 original size:64 final size:64
Alignment explanation
Indices: 1158682--1158990 Score: 421
Period size: 64 Copynumber: 4.9 Consensus size: 64
1158672 TACATAATTT
*
1158682 TTTTCAG-TTC-TT-AGAGTCAATTTCAACTTCACAATGAAGGATATTGGACTCAACAAACAAC
1 TTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAATGAAGGATATTGAACTCAACAAACAAC
* * * *
1158743 -TTTCTAGTTTCATTCGGAGTTAATTTCAACTTCACAATGAATGATATTGAACTTAACAAACAAC
1 TTTTC-AGTTTCATTCAGAGTCAATTTCAACTTCACAATGAAGGATATTGAACTCAACAAACAAC
* * * * ** *
1158807 TTTCCAGTTTTATTCATAGTCAATTTCAACTTCCCAGCGAAGGATATTGGACTCAACAAACAAC
1 TTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAATGAAGGATATTGAACTCAACAAACAAC
* *
1158871 TTTTCAGTTTCACTCAGAGTCAATTTCAACTTAACAATGAAGGATATT-AGACTCAACAAACAAC
1 TTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAATGAAGGATATTGA-ACTCAACAAACAAC
**
1158935 TTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCAA
1 TTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAATGAAGGATATTGAACTCAA
1158991 AGCGGCACAA
Statistics
Matches: 212, Mismatches: 29, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
60 4 0.02
61 2 0.01
62 3 0.01
63 2 0.01
64 197 0.93
65 4 0.02
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.32
Consensus pattern (64 bp):
TTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAATGAAGGATATTGAACTCAACAAACAAC
Found at i:1159111 original size:65 final size:63
Alignment explanation
Indices: 1159002--1159177 Score: 216
Period size: 65 Copynumber: 2.8 Consensus size: 63
1158992 GCGGCACAAT
*
1159002 TTACTCGAGATTGGATTTCACGTTCACGACGAAGGATATTCAACTCAAAGCCAATTTGGTGAAAC
1 TTACTC-AGATTGGATTTCAC-TTCACGACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAAC
*
1159067 TTACTCAAGATTGGATTTCGACTTCACGACGAAGGATATCCAACTCAAAACCAATTTGGTGAAAC
1 TTACTC-AGATTGGATTTC-ACTTCACGACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAAC
* * * * *
1159132 -AAC-C--CTTGGATTTCAACTTCACAACAAAGGATATCCAATTCAAAGC
1 TTACTCAGATTGGATTTC-ACTTCACGACGAAGGATATCCAACTCAAAGC
1159178 TTAACTTCAT
Statistics
Matches: 100, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
60 36 0.36
63 1 0.01
64 2 0.02
65 59 0.59
66 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.26
Consensus pattern (63 bp):
TTACTCAGATTGGATTTCACTTCACGACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAAC
Found at i:1159266 original size:125 final size:124
Alignment explanation
Indices: 1159137--1159415 Score: 432
Period size: 125 Copynumber: 2.2 Consensus size: 124
1159127 GAAACAACCC
* * *
1159137 TTGGATTTCAACTTCACAACAAAGGATATCCAATTCAAAGCTTAACTTCATAACGAATGAGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
* *
1159202 CCACGATTTCAAATTCACGACGAATGATATCGTGACCACAAACAACAATATAACTCTAGA
66 CCACGATTTCAAATTCACGACGAAGGATATCATGACCACAAACAAC-ATATAACTCTAGA
* *
1159262 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCCAAGCTCAACTTCACAACGAATGAGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
* * * * *
1159327 CCACGATTTCAACTTTACGACGAAGGATATCATGCCCACAAACAACATCTATCTCTAGA
66 CCACGATTTCAAATTCACGACGAAGGATATCATGACCACAAACAACATATAACTCTAGA
*
1159386 TTGGATTTCAACTTTACAACGAAGGATATC
1 TTGGATTTCAACTTCACAACGAAGGATATC
1159416 TGTTGAAAAC
Statistics
Matches: 140, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
124 39 0.28
125 101 0.72
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.25
Consensus pattern (124 bp):
TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
CCACGATTTCAAATTCACGACGAAGGATATCATGACCACAAACAACATATAACTCTAGA
Found at i:1165394 original size:19 final size:19
Alignment explanation
Indices: 1165370--1165406 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1165360 CCCCCTTTGA
*
1165370 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATACCCCCT
*
1165389 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
1165407 ATGGGGTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.35, G:0.27, T:0.14
Consensus pattern (19 bp):
AGGGGAACCGATACCCCCT
Found at i:1165412 original size:19 final size:19
Alignment explanation
Indices: 1165329--1165412 Score: 53
Period size: 19 Copynumber: 4.2 Consensus size: 19
1165319 TTGGTACAGA
* *
1165329 GGGAATCGATACCCTCATG
1 GGGAACCGATACCCCCATG
* *
1165348 AGGGAACCGATCCCCCCTTTGAAG
1 -GGGAACCGATACCCCC----ATG
*
1165372 GGGAACCGATTCCCCC-TAG
1 GGGAACCGATACCCCCAT-G
*
1165391 GGGAATCGATACCCCCATG
1 GGGAACCGATACCCCCATG
1165410 GGG
1 GGG
1165413 TTTTGGATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
19 19 0.38
20 14 0.28
23 15 0.30
24 2 0.04
ACGTcount: A:0.24, C:0.31, G:0.29, T:0.17
Consensus pattern (19 bp):
GGGAACCGATACCCCCATG
Found at i:1168160 original size:21 final size:21
Alignment explanation
Indices: 1168135--1168185 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
1168125 CGAAGGGAAC
1168135 CGATTCCCCCCCAGGGGATA-
1 CGATTCCCCCCCAGGGGATAT
1168155 CTGATT-CCCCCCAGGGGATAT
1 C-GATTCCCCCCCAGGGGATAT
1168176 CGATTCCCCC
1 CGATTCCCCC
1168186 TACTGTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.18, C:0.41, G:0.22, T:0.20
Consensus pattern (21 bp):
CGATTCCCCCCCAGGGGATAT
Found at i:1185441 original size:31 final size:31
Alignment explanation
Indices: 1185396--1185484 Score: 124
Period size: 31 Copynumber: 2.9 Consensus size: 31
1185386 TACATTGGGC
* * *
1185396 TATACAAATAAATATGAAAGTTATGAAAGAT
1 TATAAAAATGAATATGAAAGTTATGAAAGAA
*
1185427 TATAAAAATGAATATGAAAGTTAAGAAAGAA
1 TATAAAAATGAATATGAAAGTTATGAAAGAA
* *
1185458 TATAAAAATGAATTTGAAAGGTATGAA
1 TATAAAAATGAATATGAAAGTTATGAA
1185485 TGACATCCAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.56, C:0.01, G:0.16, T:0.27
Consensus pattern (31 bp):
TATAAAAATGAATATGAAAGTTATGAAAGAA
Found at i:1187478 original size:22 final size:24
Alignment explanation
Indices: 1187434--1187478 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
1187424 TTTTACTTAC
*
1187434 ATTTTATTTTATTGCTTTAAATTT
1 ATTTTATTTAATTGCTTTAAATTT
*
1187458 ATTTTA-TTAATT-CTTTCAATT
1 ATTTTATTTAATTGCTTTAAATT
1187479 AATTGGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 5 0.26
24 6 0.32
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (24 bp):
ATTTTATTTAATTGCTTTAAATTT
Found at i:1190058 original size:95 final size:92
Alignment explanation
Indices: 1189905--1190129 Score: 238
Period size: 95 Copynumber: 2.4 Consensus size: 92
1189895 CAAGCAATGT
* *
1189905 GGTATCGATACCATGGTAAGGGTATCGATACC-AGTAAACATCGAATCTACTTTGGGTATCGATA
1 GGTATCGATACCATGGT-AGGGTATCGATACCAAGT-AACATCGAAGCTAATTTGGGTATCGATA
* * *
1189969 CCTAAAGAGGGTATTGGTACCATAGCATAGG
64 CATAAAGAGGGTATCGATACCATA--ATAGG
* * *
1190000 GGTATTGATACCATGGTGAGGGTATCGATACCAAGCT-ACATCGAAGCTAATTTTGGTATTGATA
1 GGTATCGATACCATGGT-AGGGTATCGATACCAAG-TAACATCGAAGCTAATTTGGGTATCGATA
* * *
1190064 CATGAAGGGGGTATCGATACCCTAATAGG
64 CATAAAGAGGGTATCGATACCATAATAGG
*
1190093 GTAGTATCGATACCATAAGTAGGGGTATCGATACCAA
1 G--GTATCGATACCAT-GGTA-GGGTATCGATACCAA
1190130 AGGGCCAGAA
Statistics
Matches: 110, Mismatches: 14, Indels: 11
0.81 0.10 0.08
Matches are distributed among these distances:
93 6 0.05
95 84 0.76
96 19 0.17
97 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.27
Consensus pattern (92 bp):
GGTATCGATACCATGGTAGGGTATCGATACCAAGTAACATCGAAGCTAATTTGGGTATCGATACA
TAAAGAGGGTATCGATACCATAATAGG
Found at i:1190102 original size:22 final size:21
Alignment explanation
Indices: 1190071--1190128 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 21
1190061 ATACATGAAG
*
1190071 GGGGTATCGATACCCTAA-TA
1 GGGGTATCGATACCATAAGTA
1190091 GGGTAGTATCGATACCATAAGTA
1 GGG--GTATCGATACCATAAGTA
1190114 GGGGTATCGATACCA
1 GGGGTATCGATACCA
1190129 AAGGGCCAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 3 0.09
21 12 0.35
22 14 0.41
23 5 0.15
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (21 bp):
GGGGTATCGATACCATAAGTA
Found at i:1190642 original size:79 final size:79
Alignment explanation
Indices: 1190511--1190821 Score: 482
Period size: 79 Copynumber: 3.9 Consensus size: 79
1190501 ACTAATGAAT
* *
1190511 AAAAGAATAATGCATATGGGCGCATTAGTGGCATGAAAGGATGTCTTAGCTGATATGTATATGGG
1 AAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATGGG
1190576 TACATTATCGGCAA
66 TACATTATCGGCAA
1190590 AAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATGGG
1 AAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATGGG
*
1190655 TGCATTATCGG-AA
66 TACATTATCGGCAA
*
1190668 TAAAAGAATAATGCATATGGTTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATGG
1 -AAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATGG
1190733 GTACATTATCGGCATA
65 GTACATTATCGGCA-A
* * ** * * *
1190749 ACAA-AATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAGTTGAAATGCATATGGG
1 AAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATGGG
*
1190813 TGCATTATC
66 TACATTATC
1190822 AACATAAAAG
Statistics
Matches: 215, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
78 2 0.01
79 208 0.97
80 4 0.02
81 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (79 bp):
AAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATGGG
TACATTATCGGCAA
Found at i:1191588 original size:44 final size:45
Alignment explanation
Indices: 1191503--1191615 Score: 133
Period size: 45 Copynumber: 2.5 Consensus size: 45
1191493 GTATGAATGA
* *
1191503 ATGTTATAAAGGAACATATA-AACAGAACATAAAAGGCATGAAAGG
1 ATGTCATAAAGGAA-ATATATAATAGAACATAAAAGGCATGAAAGG
* *
1191548 ATGTCATAAAGGAAATATATAATAGTATATAAAA-GCATGAAAGG
1 ATGTCATAAAGGAAATATATAATAGAACATAAAAGGCATGAAAGG
*
1191592 ATGACATAATA-GAAATAGTATAAT
1 ATGTCATAA-AGGAAATA-TATAAT
1191616 GGTGTATTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
44 29 0.48
45 31 0.52
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.23
Consensus pattern (45 bp):
ATGTCATAAAGGAAATATATAATAGAACATAAAAGGCATGAAAGG
Found at i:1193399 original size:2 final size:2
Alignment explanation
Indices: 1193392--1193462 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
1193382 ATGATGTCAA
1193392 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1193434 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 A
1193463 GCTTTTATGG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1194954 original size:19 final size:19
Alignment explanation
Indices: 1194930--1194972 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1194920 GTAAAGTGTA
1194930 TTTTCGACACTTCTTCTTC
1 TTTTCGACACTTCTTCTTC
1194949 TTTTCGACACTTCTTCTTC
1 TTTTCGACACTTCTTCTTC
1194968 TTTTC
1 TTTTC
1194973 ATTCTTCACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.30, G:0.05, T:0.56
Consensus pattern (19 bp):
TTTTCGACACTTCTTCTTC
Found at i:1195659 original size:20 final size:20
Alignment explanation
Indices: 1195593--1195667 Score: 82
Period size: 20 Copynumber: 3.7 Consensus size: 20
1195583 AATCTAATTT
*
1195593 GGGTATCGATACC-TAGAGA
1 GGGTATCGATACCATAGTGA
* *
1195612 GGGTATTGGTACCATAGCAT-A
1 GGGTATCGATACCATAG--TGA
1195633 GGGGTATCGATACCATAGTGA
1 -GGGTATCGATACCATAGTGA
1195654 GGGTATCGATACCA
1 GGGTATCGATACCA
1195668 GGCTACATCG
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
19 11 0.24
20 18 0.39
21 2 0.04
22 15 0.33
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (20 bp):
GGGTATCGATACCATAGTGA
Found at i:1195687 original size:95 final size:94
Alignment explanation
Indices: 1195542--1195764 Score: 234
Period size: 95 Copynumber: 2.3 Consensus size: 94
1195532 AGCAATTTGA
* * * * * * *
1195542 TATCGATACCATGGTAAGAGTATCGATACCAATAAACATTGAATCTAATTTGGGTATCGATACCT
1 TATCGATACCATAGTAAGGGTATCGATACCAAGAAACATCGAAGCTAATTTCGGTATCGATACAT
* *
1195607 -AGAGAGGGTATTGGTACCATAGCATAGGG-G
66 GA-AGAGGGTATCGATACCATA--ATAGGGAG
* * ** *
1195637 TATCGATACCATAGTGAGGGTATCGATACCAGGCTACATCGAAGCTAATTTCGGTATTGATACAT
1 TATCGATACCATAGTAAGGGTATCGATACCAAGAAACATCGAAGCTAATTTCGGTATCGATACAT
* *
1195702 GAAGGGGGTATCGATACCCTAATAGGGTAG
66 GAAGAGGGTATCGATACCATAATAGGG-AG
*
1195732 TATCGATACCATAAGCAAGGGTATCGATACCAA
1 TATCGATACCAT-AGTAAGGGTATCGATACCAA
1195765 AGGGCCAGAA
Statistics
Matches: 105, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
93 6 0.06
95 81 0.77
96 18 0.17
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (94 bp):
TATCGATACCATAGTAAGGGTATCGATACCAAGAAACATCGAAGCTAATTTCGGTATCGATACAT
GAAGAGGGTATCGATACCATAATAGGGAG
Found at i:1196276 original size:79 final size:79
Alignment explanation
Indices: 1196145--1196466 Score: 441
Period size: 79 Copynumber: 4.1 Consensus size: 79
1196135 AAACTAATGA
* * * *
1196145 ATAAAAGAATAATGCATATAGGTGCATTAGTGGCATGAAATGATGTCTTAGCTGATATGTATATA
1 ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATG
*
1196210 GGTACATTATCGGC
66 GGTACATTATCAGC
* * *
1196224 ATAAAAGAATAATGTATATGGGTGTATTAGTGGTATGAAAGGATGCCTTAGCTGATATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATG
*
1196289 GGTACATTATCGGC
66 GGTACATTATCAGC
*
1196303 ATAAAA-AATAATGCATATGGGTGCATTAGTGGCATTAAAGGATGCCTTAGCTGATATGT-TAAT
1 ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTAT-AT
1196366 GGGTACATTATCAGC
65 GGGTACATTATCAGC
* * * * ** * *
1196381 ATAACAGAATAATGCATATGGGTGCATTATTGTCATGAAAGGTTGCCAAAGTTGAAATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATG
* *
1196446 GGTGCATTATCAAC
66 GGTACATTATCAGC
1196460 ATAAAAG
1 ATAAAAG
1196467 TATGCTATAA
Statistics
Matches: 216, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
77 1 0.00
78 70 0.32
79 144 0.67
80 1 0.00
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATG
GGTACATTATCAGC
Found at i:1196441 original size:157 final size:158
Alignment explanation
Indices: 1196145--1196466 Score: 443
Period size: 157 Copynumber: 2.0 Consensus size: 158
1196135 AAACTAATGA
* *
1196145 ATAAAAGAATAATGCATATAGGTGCATTAGTGGCATGAAATGATGTCTTAGCTGATATGTATATA
1 ATAAAAGAATAATGCATATAGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATA
* * * **
1196210 GGTACATTATCGGCATAAAAGAATAATGTATATGGGTGTATTAGTGGTATGAAAGGATGCCTTAG
66 GGTACATTATCAGCATAAAAGAATAATGCATATGGGTGCATTAGTGGTATGAAAGGATGCCAAAG
* **
1196275 CTGATATGTATATGGGTACATTATCGGC
131 CTGAAATGTATATGGGTACATTATCAAC
* *
1196303 ATAAAA-AATAATGCATATGGGTGCATTAGTGGCATTAAAGGATGCCTTAGCTGATATGT-TAAT
1 ATAAAAGAATAATGCATATAGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTAT-AT
* * * *
1196366 GGGTACATTATCAGCATAACAGAATAATGCATATGGGTGCATTA-TTGTCATGAAAGGTTGCCAA
65 AGGTACATTATCAGCATAAAAGAATAATGCATATGGGTGCATTAGTGGT-ATGAAAGGATGCCAA
* *
1196430 AGTTGAAATGTATATGGGTGCATTATCAAC
129 AGCTGAAATGTATATGGGTACATTATCAAC
1196460 ATAAAAG
1 ATAAAAG
1196467 TATGCTATAA
Statistics
Matches: 143, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
156 4 0.03
157 133 0.93
158 6 0.04
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (158 bp):
ATAAAAGAATAATGCATATAGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATA
GGTACATTATCAGCATAAAAGAATAATGCATATGGGTGCATTAGTGGTATGAAAGGATGCCAAAG
CTGAAATGTATATGGGTACATTATCAAC
Found at i:1197199 original size:45 final size:44
Alignment explanation
Indices: 1197150--1197242 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
1197140 AATGAATGTT
*
1197150 ATAAAGGAACACGTA-AACAGAACATAAAAGGCATGAAAGGATGCC
1 ATAAAGGAA-ACATATAACAGAACATAAAA-GCATGAAAGGATGCC
* ***
1197195 ATAAAGGAAACATATAATAGTTTATAAAAGCATGAAAGGATGCC
1 ATAAAGGAAACATATAACAGAACATAAAAGCATGAAAGGATGCC
1197239 ATAA
1 ATAA
1197243 TAGAAATGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
44 23 0.55
45 19 0.45
ACGTcount: A:0.52, C:0.12, G:0.19, T:0.17
Consensus pattern (44 bp):
ATAAAGGAAACATATAACAGAACATAAAAGCATGAAAGGATGCC
Found at i:1199515 original size:81 final size:81
Alignment explanation
Indices: 1197903--1199502 Score: 2094
Period size: 81 Copynumber: 19.8 Consensus size: 81
1197893 TTTTTAAAAA
* * *
1197903 AAAAGATTAACTGCCTAGCTATGCATTTGCCAGAAAGGTGCCAATTATGCCAGTTTGATGAAAGG
1 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGG
*
1197968 TTAAATGCCTTTGAGT
66 TTAAATACCTTTGAGT
* * * * *
1197984 AAAAGATTAACT-CCTTAGTTGTGTATTTGGTAAAAAGGTGCCAATTATGCCAATTAGATGAAAG
1 AAAAGATTAACTGCC-TAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAG
*
1198048 ATTAAATACCTTTGAGT
65 GTTAAATACCTTTGAGT
* * * * * *
1198065 AAAAGATTAACTGCCTCGTTGTGTATTTGGTAGAAAGGTGCCAATTATGCTAGTTATATGAAAGG
1 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGG
1198130 TTAAATACCTTTGAGT
66 TTAAATACCTTTGAGT
* * * * *
1198146 AAAATATTATCTACCTAGTTGTGCATTTGGCAGAAAGGTGACAATTATGCCAGTTAGATGAAAGG
1 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGG
** *
1198211 -TATTTAACCTTTCAGT
66 TTAAAT-ACCTTTGAGT
* *
1198227 AAAAGATTAACTGCCTAGTTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTATATGAAAGG
1 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGG
1198292 TTAAATACCTTTGAGT
66 TTAAATACCTTTGAGT
* * * *
1198308 AAAAGATTAATTGCCTAGCTGTGCATTAGGTAGCAAGGTGCCAATTATGCCAGTTAGATGAAAGG
1 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGG
1198373 TTAAATACCTTT-ATGT
66 TTAAATACCTTTGA-GT
** * * * *
1198389 AAAAGATTAACTATCTAGTTGTGCATTTGGTAGAAAGGTGACAATTATGCTAGTTAGATGAAAGG
1 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGG
**
1198454 TTAAATATGTTTGAGT
66 TTAAATACCTTTGAGT
* *
1198470 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGTCAGTTAGATGAAAGA
1 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGG
1198535 TTAAATACCTTTGAGT
66 TTAAATACCTTTGAGT
* * * * * * *
1198551 AAAAGCTTAACTGCCTAGTTGTACATTTGGTAGAAAGGTGTCGATTATGTCAGTTAGATGAAAGG
1 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGG
1198616 TTAAATACCTTTGAGT
66 TTAAATACCTTTGAGT
* * * * * * *
1198632 AAAAGATTAACTGCCAAGTTGTGCATTTGGAAAAAATGTGCCAATTATGTCAGTTAGATGAAATG
1 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGG
* *
1198697 TTAAATGCTTTTGAGT
66 TTAAATACCTTTGAGT
* * *
1198713 AAAAGATTAACTGGCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCATTTAGATAAAAGG
1 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGG
* *
1198778 TTAAATGCCTTTGGGT
66 TTAAATACCTTTGAGT
* * * * * * * *
1198794 AAACGATTAAATGCATAACTGTGCATTTGGCATAAAGGTGCCAATCATGCAAGTTAGATGAAAAG
1 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGG
1198859 TTAAATACCTTTGAGT
66 TTAAATACCTTTGAGT
* ** **
1198875 AAAAGATTAATTATCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGTTAGTTAGATGAAAGG
1 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGG
1198940 TTAAATACCTTTGAGT
66 TTAAATACCTTTGAGT
* * * * ** * *
1198956 AAAAGATTAATTGCCTAGTTGTGCATTTGGTAGAAATGTGTAAAATATGTCAGTTAGATGAAAGG
1 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGG
1199021 TTAAATACCTTTGAGT
66 TTAAATACCTTTGAGT
* * *
1199037 AAAAGATTAACTGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGACAGTTAGATGAAAGG
1 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGG
1199102 TTAAATACCTTTGAGT
66 TTAAATACCTTTGAGT
* * * * *
1199118 AAAAGATTAACTGTCTAACTGTTCATTTGGCAGAAAGGTGTCAATTATGCCAGTTATATGAAAGG
1 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGG
*
1199183 TTAAATACCTTTAAGT
66 TTAAATACCTTTGAGT
* * *
1199199 AAAAGATTAACTACCTAGATGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGA
1 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGG
* *
1199264 TTAAAT-GCTTTGAGC
66 TTAAATACCTTTGAGT
* * * *
1199279 AAAAGATTAAATGTCTAGCTGTGCATTTGGCATAAAGGTGCCAATTATGCCAATTAGATGAAAGG
1 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGG
*
1199344 TTAAATGCCTTTGAGT
66 TTAAATACCTTTGAGT
* * * *
1199360 AAAAGATTAACTGCCTAGCTGTGCATTTAGCAAAAATGTGCCAATTATGCCATTTAGATGAAAGA
1 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAG-
* *
1199425 G-TAAATGCCTTTGGGT
65 GTTAAATACCTTTGAGT
* * ** * * * *
1199441 AAAAGATTAAATGCCTAACTGTATATTTGGAAGAAAGGTGTCAATCATGCAAGTTAGATGAA
1 AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAA
1199503 CAATTAAATG
Statistics
Matches: 1334, Mismatches: 177, Indels: 16
0.87 0.12 0.01
Matches are distributed among these distances:
80 76 0.06
81 1251 0.94
82 7 0.01
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.32
Consensus pattern (81 bp):
AAAAGATTAACTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGG
TTAAATACCTTTGAGT
Found at i:1199605 original size:49 final size:49
Alignment explanation
Indices: 1199510--1199606 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 49
1199500 GAACAATTAA
* * * *
1199510 ATGCCTAATTGTGGTTTTTGGCAGAAAGGTGCCATTAAATGTAAGTTAT
1 ATGCCTAATGGTGATTTTTGGCAGAAAGGTGCCACTAAATGCAAGTTAT
1199559 ATGCCTAATGGTGCATTTTTGGCAGAAAGGTGCCACT-AATGCAAGTTA
1 ATGCCTAATGGTG-ATTTTTGGCAGAAAGGTGCCACTAAATGCAAGTTA
1199607 GATGAAGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 22 0.51
50 21 0.49
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (49 bp):
ATGCCTAATGGTGATTTTTGGCAGAAAGGTGCCACTAAATGCAAGTTAT
Found at i:1199673 original size:46 final size:46
Alignment explanation
Indices: 1199621--1199794 Score: 231
Period size: 46 Copynumber: 3.8 Consensus size: 46
1199611 AAGAATAGTT
*
1199621 CATAATTGACATGAAAGGATGCCATAAATAAAAATGTATAATAATG
1 CATAATTGACATGAAAGGATGCCATAAATAAAAATGTATAACAATG
*
1199667 CATAATTGACATGAAAGGATGTCATAAATAAAAATGTATAACAATG
1 CATAATTGACATGAAAGGATGCCATAAATAAAAATGTATAACAATG
** * * * * * *
1199713 CATAATTGGTATGAAATGATGTCATAGATGAAAATGTATACCAGTG
1 CATAATTGACATGAAAGGATGCCATAAATAAAAATGTATAACAATG
* *
1199759 CATAATTGGCATGAAAGGATGCCACAAATGAAAAAT
1 CATAATTGACATGAAAGGATGCCATAAAT-AAAAAT
1199795 ACATAACGGT
Statistics
Matches: 112, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
46 107 0.96
47 5 0.04
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.26
Consensus pattern (46 bp):
CATAATTGACATGAAAGGATGCCATAAATAAAAATGTATAACAATG
Found at i:1203829 original size:19 final size:19
Alignment explanation
Indices: 1203805--1203860 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1203795 GAACGCTGGA
1203805 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
1203824 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
1203845 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
1203861 CACGACCCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 9 0.26
21 8 0.24
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:1203840 original size:11 final size:11
Alignment explanation
Indices: 1203805--1203853 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
1203795 GAACGCTGGA
1203805 AACCGGTTTTG
1 AACCGGTTTTG
1203816 -ACCGG-TTT-
1 AACCGGTTTTG
1203824 AACCGGTTTTG
1 AACCGGTTTTG
1203835 AACCGGTTTTG
1 AACCGGTTTTG
1203846 -ACCGGTTT
1 AACCGGTTT
1203854 GACCGGTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:1203856 original size:9 final size:10
Alignment explanation
Indices: 1203806--1203860 Score: 78
Period size: 9 Copynumber: 5.6 Consensus size: 10
1203796 AACGCTGGAA
1203806 ACCGGTTTTG
1 ACCGGTTTTG
*
1203816 ACCGG-TTTA
1 ACCGGTTTTG
1203825 ACCGGTTTTG
1 ACCGGTTTTG
1203835 AACCGGTTTTG
1 -ACCGGTTTTG
1203846 ACCGG-TTTG
1 ACCGGTTTTG
1203855 ACCGGT
1 ACCGGT
1203861 CACGACCCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:1203914 original size:13 final size:13
Alignment explanation
Indices: 1203873--1203903 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1203863 CGACCCGTTT
*
1203873 ACCCGTTTACCCG
1 ACCCGTTGACCCG
1203886 ACCCGTTGACCCG
1 ACCCGTTGACCCG
1203899 ACCCG
1 ACCCG
1203904 ACCCGTTGAC
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:0.16, C:0.48, G:0.19, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:1203918 original size:7 final size:7
Alignment explanation
Indices: 1203906--1203936 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1203896 CCGACCCGAC
1203906 CCGTTGA
1 CCGTTGA
1203913 CCGTTGA
1 CCGTTGA
1203920 CCGTTGA
1 CCGTTGA
1203927 CCGTTGA
1 CCGTTGA
1203934 CCG
1 CCG
1203937 GTGCTATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.32, G:0.29, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:1203997 original size:29 final size:29
Alignment explanation
Indices: 1203936--1204011 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
1203926 ACCGTTGACC
*** *
1203936 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
1203965 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
1203994 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
1204012 TTTTTAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.21, C:0.09, G:0.28, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:1211111 original size:19 final size:19
Alignment explanation
Indices: 1211087--1211142 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1211077 GAACGCTGGA
1211087 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
1211106 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
1211127 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
1211143 CACGACCCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 9 0.26
21 8 0.24
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:1211122 original size:11 final size:11
Alignment explanation
Indices: 1211087--1211135 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
1211077 GAACGCTGGA
1211087 AACCGGTTTTG
1 AACCGGTTTTG
1211098 -ACCGG-TTT-
1 AACCGGTTTTG
1211106 AACCGGTTTTG
1 AACCGGTTTTG
1211117 AACCGGTTTTG
1 AACCGGTTTTG
1211128 -ACCGGTTT
1 AACCGGTTT
1211136 GACCGGTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:1211138 original size:9 final size:10
Alignment explanation
Indices: 1211088--1211142 Score: 78
Period size: 9 Copynumber: 5.6 Consensus size: 10
1211078 AACGCTGGAA
1211088 ACCGGTTTTG
1 ACCGGTTTTG
*
1211098 ACCGG-TTTA
1 ACCGGTTTTG
1211107 ACCGGTTTTG
1 ACCGGTTTTG
1211117 AACCGGTTTTG
1 -ACCGGTTTTG
1211128 ACCGG-TTTG
1 ACCGGTTTTG
1211137 ACCGGT
1 ACCGGT
1211143 CACGACCCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:1211160 original size:8 final size:8
Alignment explanation
Indices: 1211146--1211217 Score: 57
Period size: 7 Copynumber: 9.5 Consensus size: 8
1211136 GACCGGTCAC
1211146 GACCCGTT
1 GACCCGTT
*
1211154 TACCCGTT
1 GACCCGTT
1211162 GACCC---
1 GACCCGTT
1211167 GACCCGTT
1 GACCCGTT
**
1211175 GACCCGACCC
1 GACCCG--TT
1211185 GACCCGTT
1 GACCCGTT
1211193 GA-CCGTT
1 GACCCGTT
1211200 GA-CCGTT
1 GACCCGTT
1211207 GA-CCGTT
1 GACCCGTT
1211214 GACC
1 GACC
1211218 GGTGCTATTC
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
5 5 0.10
7 21 0.40
8 20 0.38
10 6 0.12
ACGTcount: A:0.15, C:0.40, G:0.24, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:1211177 original size:39 final size:38
Alignment explanation
Indices: 1211134--1211220 Score: 95
Period size: 39 Copynumber: 2.2 Consensus size: 38
1211124 TTTGACCGGT
*
1211134 TTGACCGGTCACGACCCGTTTACCCGTTGACC-CGACCCG
1 TTGACCGGTCACGACCCGTTGA-CCGTTGACCGCGA-CCG
* * * *
1211173 TTGACCCGACCCGACCCGTTGACCGTTGACCGTTGACCG
1 TTGACCGGTCACGACCCGTTGACCGTTGACCG-CGACCG
1211212 TTGACCGGT
1 TTGACCGGT
1211221 GCTATTCTGG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
38 9 0.23
39 28 0.72
40 2 0.05
ACGTcount: A:0.15, C:0.38, G:0.25, T:0.22
Consensus pattern (38 bp):
TTGACCGGTCACGACCCGTTGACCGTTGACCGCGACCG
Found at i:1211185 original size:18 final size:18
Alignment explanation
Indices: 1211162--1211196 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1211152 TTTACCCGTT
1211162 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
1211180 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
1211197 GTTGACCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.49, G:0.23, T:0.11
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:1211196 original size:13 final size:13
Alignment explanation
Indices: 1211155--1211185 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1211145 CGACCCGTTT
1211155 ACCCGTTGACCCG
1 ACCCGTTGACCCG
1211168 ACCCGTTGACCCG
1 ACCCGTTGACCCG
1211181 ACCCG
1 ACCCG
1211186 ACCCGTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.48, G:0.23, T:0.13
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:1211200 original size:7 final size:7
Alignment explanation
Indices: 1211188--1211218 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1211178 CCGACCCGAC
1211188 CCGTTGA
1 CCGTTGA
1211195 CCGTTGA
1 CCGTTGA
1211202 CCGTTGA
1 CCGTTGA
1211209 CCGTTGA
1 CCGTTGA
1211216 CCG
1 CCG
1211219 GTGCTATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.32, G:0.29, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:1211279 original size:29 final size:29
Alignment explanation
Indices: 1211218--1211293 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
1211208 ACCGTTGACC
*** *
1211218 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
1211247 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
1211276 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
1211294 TTTTTAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.21, C:0.09, G:0.28, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:1217732 original size:12 final size:12
Alignment explanation
Indices: 1217715--1217739 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1217705 TGGTTCATAT
1217715 CCAACCATATAC
1 CCAACCATATAC
1217727 CCAACCATATAC
1 CCAACCATATAC
1217739 C
1 C
1217740 AAATTTTCCT
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:0.40, C:0.44, G:0.00, T:0.16
Consensus pattern (12 bp):
CCAACCATATAC
Found at i:1221170 original size:23 final size:24
Alignment explanation
Indices: 1221144--1221188 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1221134 AGAAGAAAAA
*
1221144 AATAAAAATG-AAAAGAAAAAATG
1 AATAAAAAAGAAAAAGAAAAAATG
1221167 AATAAAAAAGAAAAAGAAAAAA
1 AATAAAAAAGAAAAAGAAAAAA
1221189 GAGGTTCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (24 bp):
AATAAAAAAGAAAAAGAAAAAATG
Found at i:1222292 original size:115 final size:115
Alignment explanation
Indices: 1222072--1222451 Score: 467
Period size: 116 Copynumber: 3.3 Consensus size: 115
1222062 ATGATTACAG
* * * *
1222072 CAAAGACTCGACAATATCCATCGCACAAGGAGGTGGATCATCATTTCTAAGGAATGGTTCATAAT
1 CAAA-ACTCAACAACATCCATCGCACAAGGAGGTGGATCAACATTTCTAAGGAAGGGTTCATAAT
* * *
1222137 GAGAAGAAGTCATCTAACGAGGGAGAAGAAGTTCATAATGAATAACTTGTT
65 GAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAAAAACTTGTT
* *
1222188 CAAAACTCAACAACATCCATCGCACAAGGAGGTGGATTAACATTTCTGAGGAAGGGTTCATAATG
1 CAAAACTCAACAACATCCATCGCACAAGGAGGTGGATCAACATTTCTAAGGAAGGGTTCATAATG
* **
1222253 AGAAGAACTCATCCAATGAGGGAGAAGAAGTTCCCAATGAGAAAAACTTGTT
66 AGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAAT--GAAAAACTTGTT
* * * * * * * * *
1222305 CAGAACTCGAC-ACATCCATTGTACAATGAGATGAATCAATATTTCTTAGGAAGGGTTCATAATG
1 CAAAACTCAACAACATCCATCGCACAAGGAGGTGGATCAACATTTCTAAGGAAGGGTTCATAATG
* *
1222369 AGAAGAACTCATCCAACGAGGGAGAATAAGTTCATAATGAAAAGAACTTATT
66 AGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATG-AAA-AACTTGTT
* * *
1222421 TAAAACTCAA-AACATCCACCACACAAGGAGG
1 CAAAACTCAACAACATCCATCGCACAAGGAGG
1222452 AAGATCAATA
Statistics
Matches: 223, Mismatches: 36, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
114 1 0.00
115 91 0.41
116 111 0.50
117 20 0.09
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (115 bp):
CAAAACTCAACAACATCCATCGCACAAGGAGGTGGATCAACATTTCTAAGGAAGGGTTCATAATG
AGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAAAAACTTGTT
Found at i:1222602 original size:3 final size:3
Alignment explanation
Indices: 1222594--1222675 Score: 164
Period size: 3 Copynumber: 27.3 Consensus size: 3
1222584 ATTTTCAGCC
1222594 ATT ATT 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 ATT ATT
1222642 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1222676 CAAAACAAAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1223021 original size:19 final size:18
Alignment explanation
Indices: 1222999--1223061 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 18
1222989 ATAAATAATT
1222999 ATAATTAAAAAAAAGAAAA
1 ATAA-TAAAAAAAAGAAAA
* *
1223018 ATAAT--AAAATA-AATA
1 ATAATAAAAAAAAGAAAA
1223033 ATAATAAATAAAAAGATAAA
1 ATAATAAA-AAAAAGA-AAA
1223053 ATAATAAAA
1 ATAATAAAA
1223062 TAATAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
15 8 0.23
16 5 0.14
17 1 0.03
18 5 0.14
19 6 0.17
20 10 0.29
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (18 bp):
ATAATAAAAAAAAGAAAA
Found at i:1223023 original size:3 final size:3
Alignment explanation
Indices: 1222976--1223081 Score: 57
Period size: 3 Copynumber: 36.0 Consensus size: 3
1222966 TTGAAAAGAT
* * * * *
1222976 ATA ATA A-A ATA A-A ATAA ATA ATT ATA ATTA AAA AAA AGA AAA ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA A-TA ATA ATA ATA ATA ATA
1223021 ATA A-A ATAA ATA ATA ATAA ATA A-A A-A GATA A-A ATA ATA A-A ATA
1 ATA ATA AT-A ATA ATA AT-A ATA ATA ATA -ATA ATA ATA ATA ATA ATA
1223064 ATA A-A ATA ATAA ATA ATA
1 ATA ATA ATA AT-A ATA ATA
1223082 GTAGTAAAGA
Statistics
Matches: 84, Mismatches: 6, Indels: 26
0.72 0.05 0.22
Matches are distributed among these distances:
2 15 0.18
3 53 0.63
4 16 0.19
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (3 bp):
ATA
Found at i:1223026 original size:8 final size:8
Alignment explanation
Indices: 1222976--1223081 Score: 85
Period size: 8 Copynumber: 12.8 Consensus size: 8
1222966 TTGAAAAGAT
1222976 ATAATAAA
1 ATAATAAA
*
1222984 ATAAAATAA
1 ATAATA-AA
1222993 ATAATTATAA
1 ATAA-TA-AA
*
1223003 TTAA-AAA
1 ATAATAAA
*
1223010 A-AAGAAAA
1 ATAA-TAAA
1223018 ATAATAAA
1 ATAATAAA
1223026 ATAAATAATA
1 AT-AATAA-A
1223036 ATAAATAAA
1 AT-AATAAA
1223045 A-AGATAAA
1 ATA-ATAAA
1223053 ATAATAAA
1 ATAATAAA
1223061 ATAATAAA
1 ATAATAAA
1223069 ATAAT-AA
1 ATAATAAA
1223076 ATAATA
1 ATAATA
1223082 GTAGTAAAGA
Statistics
Matches: 83, Mismatches: 5, Indels: 20
0.77 0.05 0.19
Matches are distributed among these distances:
6 2 0.02
7 10 0.12
8 39 0.47
9 16 0.19
10 16 0.19
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (8 bp):
ATAATAAA
Found at i:1223026 original size:37 final size:35
Alignment explanation
Indices: 1222979--1223079 Score: 127
Period size: 34 Copynumber: 2.9 Consensus size: 35
1222969 AAAAGATATA
* *
1222979 ATAAAATAAAATAAAT-AATTATAATTAAA-AAAAAG
1 ATAAAATAATA-AAATAAATAATAA-TAAATAAAAAG
1223014 A-AAAATAATAAAATAAATAATAATAAATAAAAAG
1 ATAAAATAATAAAATAAATAATAATAAATAAAAAG
*
1223048 ATAAAATAATAAAATAATAAAATAATAAATAA
1 ATAAAATAATAAAATAA-ATAATAATAAATAA
1223080 TAGTAGTAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
33 8 0.14
34 22 0.37
35 16 0.27
36 13 0.22
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (35 bp):
ATAAAATAATAAAATAAATAATAATAAATAAAAAG
Found at i:1223029 original size:27 final size:25
Alignment explanation
Indices: 1223009--1223061 Score: 52
Period size: 28 Copynumber: 2.0 Consensus size: 25
1222999 ATAATTAAAA
1223009 AAAAGAAAAATAATAAAATAAATAATAA
1 AAAAGAAAAA-AATAAAAT-AATAA-AA
* * *
1223037 TAAATAAAAAGATAAAATAATAAAA
1 AAAAGAAAAAAATAAAATAATAAAA
1223062 TAATAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
25 2 0.09
26 5 0.23
27 7 0.32
28 8 0.36
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (25 bp):
AAAAGAAAAAAATAAAATAATAAAA
Found at i:1223142 original size:18 final size:18
Alignment explanation
Indices: 1223121--1223163 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1223111 GTTATTTTTA
* *
1223121 AAATAAAATATAAGAATT
1 AAATAAAAGAGAAGAATT
*
1223139 AAATAAAAGAGAATAATT
1 AAATAAAAGAGAAGAATT
1223157 AAATAAA
1 AAATAAA
1223164 TAATTTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAGAAGAATT
Found at i:1223804 original size:24 final size:24
Alignment explanation
Indices: 1223768--1223871 Score: 58
Period size: 24 Copynumber: 4.4 Consensus size: 24
1223758 AAATCCTAAT
* *
1223768 TAAAACACTTAAAACTATTTAAAC
1 TAAAATACCTAAAACTATTTAAAC
* *
1223792 TAAAATACCTAAAAATAATATTTAAAA
1 TAAAATACCT--AAA-ACTATTTAAAC
* * **
1223819 TAATAT-TCT-AAA-T-CCTAAA-
1 TAAAATACCTAAAACTATTTAAAC
1223838 TAAAATA-CTAAAACCTATTTAAAC
1 TAAAATACCTAAAA-CTATTTAAAC
1223862 TAAAATACCT
1 TAAAATACCT
1223872 GACATAAAGA
Statistics
Matches: 59, Mismatches: 11, Indels: 19
0.66 0.12 0.21
Matches are distributed among these distances:
19 7 0.12
20 7 0.12
21 1 0.02
22 2 0.03
23 6 0.10
24 15 0.25
25 2 0.03
26 5 0.08
27 14 0.24
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (24 bp):
TAAAATACCTAAAACTATTTAAAC
Found at i:1223834 original size:70 final size:73
Alignment explanation
Indices: 1223757--1223945 Score: 242
Period size: 76 Copynumber: 2.6 Consensus size: 73
1223747 TAAAACATCT
* * *
1223757 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCT-A-AAA-ATAATAT-TTAAA
1 TAAATCCTAATTAAAATAC-TAAAACTATTTAAACTAAAATACCTAATAAAGATAAAATATAAAA
*
1223818 ATAATATTC
65 ATAATATCC
*
1223827 TAAATCCTAAATAAAATACTAAAACCTATTTAAACTAAAATACCTGACATAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAA-CTATTTAAACTAAAATACCT-A-ATAAAGATAAAATATAA
1223892 AAATAATATCC
63 AAATAATATCC
* *
1223903 TAAAACTTAATTAAAATACTAAAACATATTTAAACTAAAATAC
1 TAAATCCTAATTAAAATACTAAAAC-TATTTAAACTAAAATAC
1223946 AAAGATAAAA
Statistics
Matches: 103, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
69 5 0.05
70 37 0.36
73 1 0.01
74 3 0.03
75 7 0.07
76 50 0.49
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.30
Consensus pattern (73 bp):
TAAATCCTAATTAAAATACTAAAACTATTTAAACTAAAATACCTAATAAAGATAAAATATAAAAA
TAATATCC
Found at i:1223840 original size:19 final size:19
Alignment explanation
Indices: 1223816--1223854 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1223806 ATAATATTTA
* * *
1223816 AAATAATATTCTAAATCCT
1 AAATAAAATACTAAAACCT
1223835 AAATAAAATACTAAAACCT
1 AAATAAAATACTAAAACCT
1223854 A
1 A
1223855 TTTAAACTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATAAAATACTAAAACCT
Found at i:1223969 original size:76 final size:71
Alignment explanation
Indices: 1223757--1223981 Score: 231
Period size: 76 Copynumber: 3.1 Consensus size: 71
1223747 TAAAACATCT
* * *
1223757 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATAC-CTAAAA-ATAATATTTAAAAT
1 TAAAACCTAATTAAAATAC-TAAAACTATTTAAACTAAAATACAATAAAATATAATATTTAAAAT
*
1223820 AATATTC
65 AATATCC
* * * *
1223827 TAAATCCTAAATAAAATACTAAAACCTATTTAAACTAAAATACCTGACATAAAGATAAAATA-TA
1 TAAAACCTAATTAAAATACTAAAA-CTATTTAAACTAAAATA-C--A-ATAAA-ATATAATATTT
1223891 AAAATAATATCC
60 AAAATAATATCC
* *
1223903 TAAAACTTAATTAAAATACTAAAACATATTTAAACTAAAATACAAAGATAAAATATAATGTTTAA
1 TAAAACCTAATTAAAATACTAAAAC-TATTTAAACTAAAATAC--A-ATAAAATATAATATTTAA
*
1223968 AATATTATCC
62 AATAATATCC
1223978 TAAA
1 TAAA
1223982 CTTGAGTTTA
Statistics
Matches: 129, Mismatches: 16, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
69 5 0.04
70 34 0.26
71 1 0.01
74 6 0.05
75 28 0.22
76 50 0.39
77 5 0.04
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.30
Consensus pattern (71 bp):
TAAAACCTAATTAAAATACTAAAACTATTTAAACTAAAATACAATAAAATATAATATTTAAAATA
ATATCC
Found at i:1225427 original size:5 final size:5
Alignment explanation
Indices: 1225417--1225529 Score: 68
Period size: 5 Copynumber: 21.8 Consensus size: 5
1225407 TGTTGAAAGA
* * * *
1225417 AAAAT AAAAT AAAAT TAATT AAAAT AAAAT -AAAT AGAAT GAAAAT AAAGTTT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAA--AT
** * * *
1225469 GCTAA- AAAAT AAAAT AAAAAT AAAAC GAAAT AAAGT GAAAAT AAAAT
1 -AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT
*
1225516 GAAAT AAAAT AAAA
1 AAAAT AAAAT AAAA
1225530 AATAGAACGA
Statistics
Matches: 80, Mismatches: 20, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
4 6 0.08
5 59 0.74
6 13 0.16
7 1 0.01
8 1 0.01
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:1225489 original size:11 final size:11
Alignment explanation
Indices: 1225473--1225530 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
1225463 AAGTTTGCTA
1225473 AAAAATAAAAT
1 AAAAATAAAAT
1225484 AAAAATAAAA-
1 AAAAATAAAAT
** *
1225494 CGAAATAAAGT
1 AAAAATAAAAT
*
1225505 GAAAATAAAAT
1 AAAAATAAAAT
*
1225516 -GAAATAAAAT
1 AAAAATAAAAT
1225526 AAAAA
1 AAAAA
1225531 ATAGAACGAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
10 16 0.43
11 21 0.57
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:1225501 original size:21 final size:21
Alignment explanation
Indices: 1225475--1225542 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
1225465 GTTTGCTAAA
1225475 AAATAAAATAAAAATAAAACG
1 AAATAAAATAAAAATAAAACG
* * *
1225496 AAATAAAGTGAAAATAAAATG
1 AAATAAAATAAAAATAAAACG
*
1225517 AAATAAAATAAAAAATAGAACG
1 AAATAAAAT-AAAAATAAAACG
1225539 AAAT
1 AAAT
1225543 GGGTTGCCTC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 26 0.67
22 13 0.33
ACGTcount: A:0.72, C:0.03, G:0.09, T:0.16
Consensus pattern (21 bp):
AAATAAAATAAAAATAAAACG
Found at i:1229596 original size:35 final size:38
Alignment explanation
Indices: 1229532--1229610 Score: 101
Period size: 35 Copynumber: 2.2 Consensus size: 38
1229522 TATATAATAA
*
1229532 AATAAAATAAATAATTAGATTTAAGAAAAAGAAAAAAT
1 AATAAAATAAATAATTAGATTAAAGAAAAAGAAAAAAT
* **
1229570 AATAAAATAAATAA-TA-A-TAAATAAAAAGGGAAAAT
1 AATAAAATAAATAATTAGATTAAAGAAAAAGAAAAAAT
1229605 AATAAA
1 AATAAA
1229611 TAGTAGTAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 20 0.54
36 1 0.03
37 2 0.05
38 14 0.38
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.22
Consensus pattern (38 bp):
AATAAAATAAATAATTAGATTAAAGAAAAAGAAAAAAT
Found at i:1229609 original size:38 final size:39
Alignment explanation
Indices: 1229527--1229609 Score: 95
Period size: 38 Copynumber: 2.2 Consensus size: 39
1229517 GAAAATATAT
*
1229527 AATAA-AATAAAATAAATAATTAGATTTAAGAAAAAGAA
1 AATAATAATAAAATAAATAATTAGATTAAAGAAAAAGAA
*
1229565 AA-AATAATAAAATAAATAA-TA-A-TAAATAAAAAGGGAA
1 AATAATAATAAAATAAATAATTAGATTAAAGAAAAA--GAA
1229602 AATAATAA
1 AATAATAA
1229610 ATAGTAGTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
35 8 0.21
36 1 0.03
37 9 0.23
38 21 0.54
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (39 bp):
AATAATAATAAAATAAATAATTAGATTAAAGAAAAAGAA
Found at i:1229689 original size:17 final size:18
Alignment explanation
Indices: 1229655--1229696 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
1229645 GTTATTTTTA
1229655 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
*
1229673 AAATAAAA-ATAATAATT
1 AAATAAAAGATAAGAATT
1229690 AAATAAA
1 AAATAAA
1229697 TAATTTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:1230351 original size:12 final size:12
Alignment explanation
Indices: 1230336--1230363 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1230326 ATACCTAAAA
1230336 AAATAATATTCT
1 AAATAATATTCT
1230348 AAATAATATTCT
1 AAATAATATTCT
1230360 AAAT
1 AAAT
1230364 CCTAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATAATATTCT
Found at i:1230375 original size:72 final size:75
Alignment explanation
Indices: 1230290--1230476 Score: 238
Period size: 76 Copynumber: 2.5 Consensus size: 75
1230280 AAAACATCTT
* **
1230290 ATCCTAATTAAAATACATAAAACTATTTAAACTAAAATACCT-AAA-AAA-ATAATAT-TCTAAA
1 ATCCTAATTAAAATAC-TAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAA
*
1230351 TAATATTCTAA
65 TAATATCCTAA
* * *
1230362 ATCCTAATTAAAATAGTAAAACCTATTTAAACTAAAGTACGTAAAACAAAGATAAAATATAAAAA
1 ATCCTAATTAAAATACTAAAA-CTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAA
1230427 TAATATCCTAA
65 TAATATCCTAA
* *
1230438 AACTTAATTAAAATACTAAAACATATTTAAACTAAAATA
1 ATCCTAATTAAAATACTAAAAC-TATTTAAACTAAAATA
1230477 AAAAGATAAA
Statistics
Matches: 98, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
71 5 0.05
72 33 0.34
73 3 0.03
74 3 0.03
75 7 0.07
76 47 0.48
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (75 bp):
ATCCTAATTAAAATACTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAAT
AATATCCTAA
Found at i:1230501 original size:76 final size:73
Alignment explanation
Indices: 1230292--1230501 Score: 201
Period size: 76 Copynumber: 2.8 Consensus size: 73
1230282 AACATCTTAT
***
1230292 CCTAATTAAAATACATAAAACTATTTAAACTAAAATACCTAAAAAA-ATAATATTCT--AAATAA
1 CCTAATTAAAATAC-TAAAACTATTTAAACTAAAATAAAAAAAAAATATAATATT-TAAAAATAA
* *
1230354 TATTCTAAAT
64 TATCCTAAAA
* * * * * * *
1230364 CCTAATTAAAATAGTAAAACCTATTTAAACTAAAGTACGTAAAACAAAGATAAAATATAAAAATA
1 CCTAATTAAAATACTAAAA-CTATTTAAACTAAAATA--AAAAAAAAATATAATATTTAAAAATA
1230429 ATATCCTAAAA
63 ATATCCTAAAA
* *
1230440 CTTAATTAAAATACTAAAACATATTTAAACTAAAATAAAAAGATAAAATATAATGTTTAAAA
1 CCTAATTAAAATACTAAAAC-TATTTAAACTAAAATAAAAA-A-AAAATATAATATTTAAAA
1230502 TATTAAAACT
Statistics
Matches: 110, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
71 5 0.05
72 29 0.26
74 9 0.08
75 8 0.07
76 59 0.54
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (73 bp):
CCTAATTAAAATACTAAAACTATTTAAACTAAAATAAAAAAAAAATATAATATTTAAAAATAATA
TCCTAAAA
Found at i:1231849 original size:19 final size:20
Alignment explanation
Indices: 1231799--1231854 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 20
1231789 TGATTTTGGT
*
1231799 TTATCATTTTATTTTAATTA
1 TTATCATTTCATTTTAATTA
* * *
1231819 AT-TCCTTGCATTTT-ATTA
1 TTATCATTTCATTTTAATTA
1231837 TTATCATTTCA-TTTAATT
1 TTATCATTTCATTTTAATT
1231855 GTTCCGTTTA
Statistics
Matches: 27, Mismatches: 7, Indels: 5
0.69 0.18 0.13
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.27, C:0.11, G:0.02, T:0.61
Consensus pattern (20 bp):
TTATCATTTCATTTTAATTA
Found at i:1232309 original size:22 final size:24
Alignment explanation
Indices: 1232265--1232309 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
1232255 TTTTACTTAC
*
1232265 ATTTTATTTTATTGCTTTAAATTT
1 ATTTTATTTAATTGCTTTAAATTT
*
1232289 ATTTTA-TTAATT-CTTTCAATT
1 ATTTTATTTAATTGCTTTAAATT
1232310 AACTGGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 5 0.26
24 6 0.32
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (24 bp):
ATTTTATTTAATTGCTTTAAATTT
Found at i:1232409 original size:3 final size:3
Alignment explanation
Indices: 1232401--1232466 Score: 66
Period size: 3 Copynumber: 22.3 Consensus size: 3
1232391 TTTTACTTAA
** *
1232401 ATT ATT ATT AAA ATT ATT ATT ATT ATT AAAT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT
1232446 A-T ATAT ATT A-T ATT ATT ATT A
1 ATT AT-T ATT ATT ATT ATT ATT A
1232467 AATAATAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
2 6 0.12
3 41 0.79
4 5 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:1232434 original size:25 final size:22
Alignment explanation
Indices: 1232412--1232466 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1232402 TTATTATTAA
1232412 AATTATTATTATTATTAAATATT
1 AATTATTATTATTA-TAAATATT
*
1232435 -ATTATTA-TATTATATATATT
1 AATTATTATTATTATAAATATT
1232455 ATATTATTATTA
1 A-ATTATTATTA
1232467 AATAATAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 7 0.25
21 5 0.18
22 14 0.50
23 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AATTATTATTATTATAAATATT
Found at i:1232441 original size:22 final size:21
Alignment explanation
Indices: 1232401--1232466 Score: 79
Period size: 19 Copynumber: 3.3 Consensus size: 21
1232391 TTTTACTTAA
1232401 ATTATTATTAAA-ATTATTATT
1 ATTATTA-TAAATATTATTATT
1232422 ATTA-T-TAAATATTATTATT
1 ATTATTATAAATATTATTATT
*
1232441 A-TATTATATATATTA-TATT
1 ATTATTATAAATATTATTATT
1232460 ATTATTA
1 ATTATTA
1232467 AATAATAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
18 6 0.15
19 16 0.40
20 14 0.35
21 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTATTATAAATATTATTATT
Found at i:1233897 original size:20 final size:18
Alignment explanation
Indices: 1233872--1233908 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1233862 TATTTTTATT
1233872 TATATA-AATAAATATATA
1 TATATATAATAAATA-ATA
1233890 TATATATAATAAATAATA
1 TATATATAATAAATAATA
1233908 T
1 T
1233909 TTGTTTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TATATATAATAAATAATA
Found at i:1234186 original size:27 final size:27
Alignment explanation
Indices: 1234156--1234210 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
1234146 ATATTTCTAA
1234156 ATAAATAAATATTTTATTT-ATAAATAT
1 ATAAATAAATA-TTTATTTCATAAATAT
* *
1234183 ATAAATTAATATTTATTTCATAATTAT
1 ATAAATAAATATTTATTTCATAAATAT
1234210 A
1 A
1234211 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
ATAAATAAATATTTATTTCATAAATAT
Found at i:1234712 original size:11 final size:11
Alignment explanation
Indices: 1234696--1234737 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
1234686 TTTTATTACT
1234696 TATTATTTTTA
1 TATTATTTTTA
1234707 TATTA-TTTTA
1 TATTATTTTTA
*
1234717 TTAATATTTTTA
1 -TATTATTTTTA
*
1234729 TTTTATTTT
1 TATTATTTT
1234738 ATGAAGGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 5 0.19
11 16 0.62
12 5 0.19
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TATTATTTTTA
Found at i:1236889 original size:36 final size:36
Alignment explanation
Indices: 1236805--1236889 Score: 120
Period size: 36 Copynumber: 2.4 Consensus size: 36
1236795 TTACATTCTT
* *
1236805 ATTCTTACTTTTTACATCTTTGCATTTCCATCTTGT
1 ATTCTTACTTTTTACATCTTTGCATTACCATCTTGC
1236841 ATTCTTACTTTTTACATCTTTGCATTACACAGT-TTGC
1 ATTCTTACTTTTTACATCTTTGCATTAC-CA-TCTTGC
1236878 ATTCTTA-TTTTT
1 ATTCTTACTTTTT
1236890 GAATTTATGC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
36 32 0.71
37 12 0.27
38 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.55
Consensus pattern (36 bp):
ATTCTTACTTTTTACATCTTTGCATTACCATCTTGC
Found at i:1241241 original size:114 final size:114
Alignment explanation
Indices: 1241030--1241243 Score: 340
Period size: 114 Copynumber: 1.9 Consensus size: 114
1241020 CTCGTAGTAG
* * *
1241030 AAATAAGGAGGCCCAATAGTATTTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTCGGTAGG
1 AAATAAGGAGCCCCAATAGCATTTTCTGGAAGTATTCTTTGAGTTATCTAATCTGGTTCGGTAGG
*
1241095 AACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTACTCATAGAAA
66 AACCCCAAAACCAATCATTGGAATTAAAAGATGAATTTACTCATAGAAA
*
1241144 AAATAAGGAGCCCCAATAGCATCTTT-TGGAAGTATTCTTTGAGTTATCTGATCTGGTTCGGTAG
1 AAATAAGGAGCCCCAATAGCAT-TTTCTGGAAGTATTCTTTGAGTTATCTAATCTGGTTCGGTAG
* * *
1241208 GAACCCCAGAACCAATCATTGGAATTGACAGATGAA
65 GAACCCCAAAACCAATCATTGGAATTAAAAGATGAA
1241244 CTGCATGATC
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
114 88 0.97
115 3 0.03
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (114 bp):
AAATAAGGAGCCCCAATAGCATTTTCTGGAAGTATTCTTTGAGTTATCTAATCTGGTTCGGTAGG
AACCCCAAAACCAATCATTGGAATTAAAAGATGAATTTACTCATAGAAA
Found at i:1243423 original size:54 final size:51
Alignment explanation
Indices: 1243355--1243495 Score: 169
Period size: 50 Copynumber: 2.7 Consensus size: 51
1243345 CAGAAGCCAC
*
1243355 AGAAAAGGATGAATGTGTTGTCAAATGCTTTACGAACATCTGAGCAGAAACAACA
1 AGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC-TC-GA-CAGAAACAA-A
* * * *
1243410 AG-AAAGGAAGAATGTGTTTTCAAATGTTTTAC-ATCTCGACAGAAACCAA
1 AGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAACTCGACAGAAACAAA
* *
1243459 AGAAAAAGATGAATGTATTGTCAAATGTTTTACGAAC
1 AGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
1243496 CAGTGATTAT
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
49 3 0.04
50 34 0.46
51 4 0.05
52 2 0.03
53 2 0.03
54 27 0.36
55 2 0.03
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.26
Consensus pattern (51 bp):
AGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAACTCGACAGAAACAAA
Found at i:1243473 original size:50 final size:54
Alignment explanation
Indices: 1243338--1243495 Score: 182
Period size: 54 Copynumber: 3.0 Consensus size: 54
1243328 TAATTGAGAA
* * * *
1243338 ATCTGGGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGCTTTACGAAC
1 ATCTGAGCAGAAACCAAAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* * * *
1243392 ATCTGAGCAGAAACAACAAG-AAAGGAAGAATGTGTTTTCAAATGTTTTAC-ATC
1 ATCTGAGCAGAAACCA-AAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* *
1243445 -TC-GA-CAGAAACCAAAGAAAAAGATGAATGTATTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAACCAAAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
1243496 CAGTGATTAT
Statistics
Matches: 87, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
49 3 0.03
50 34 0.39
51 4 0.05
52 2 0.02
53 2 0.02
54 40 0.46
55 2 0.02
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.24
Consensus pattern (54 bp):
ATCTGAGCAGAAACCAAAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:1243893 original size:22 final size:22
Alignment explanation
Indices: 1243862--1243916 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1243852 ATCTACACTC
*
1243862 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* * *
1243884 TTTAAAGATGACATATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
1243906 TTCAAAGATGA
1 TTCAAAGATGA
1243917 AATCTTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:1244717 original size:76 final size:76
Alignment explanation
Indices: 1244590--1245076 Score: 893
Period size: 76 Copynumber: 6.4 Consensus size: 76
1244580 CTATTTCCCA
1244590 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1244655 AACCTTAGGGT
66 AGCCTTAGGGT
* * *
1244666 TATCTGTAAGTCCTGCAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1244731 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1244742 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGAAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1244807 AGCCTTAGGGT
66 AGCCTTAGGGT
1244818 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1244883 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1244894 CATCTGTAAGTCCTGCAATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1244959 AACCTTAGGGT
66 AGCCTTAGGGT
*
1244970 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGGATGTTTTCA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT-GATGTTTTCA
1245035 AAGCCTTAGGGT
65 AAGCCTTAGGGT
1245047 CATCTGTAAGTCCTGCAGTGCATGATGTTT
1 CATCTGTAAGTCCTGCAGTGCATGATGTTT
1245077 TTAAGACCTC
Statistics
Matches: 396, Mismatches: 14, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
76 345 0.87
77 51 0.13
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:1245238 original size:3 final size:3
Alignment explanation
Indices: 1245230--1245303 Score: 80
Period size: 3 Copynumber: 24.3 Consensus size: 3
1245220 TTTTACTTAA
** *
1245230 ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT ATT AAAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
1245276 A-T ATT ATAT ATAT ATT A-T ATT ATT ATT A
1 ATT ATT AT-T AT-T ATT ATT ATT ATT ATT A
1245304 AATAATAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
2 4 0.07
3 48 0.79
4 9 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:1245262 original size:24 final size:24
Alignment explanation
Indices: 1245230--1245303 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
1245220 TTTTACTTAA
1245230 ATTATTATTAAAATTATTATTATT
1 ATTATTATTAAAATTATTATTATT
1245254 ATTATTATT-AAA-TATTATTATT
1 ATTATTATTAAAATTATTATTATT
*
1245276 A-TATTATATATATATTA-TATTATT
1 ATTATTAT-TA-AAATTATTATTATT
1245300 ATTA
1 ATTA
1245304 AATAATAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
21 6 0.14
22 12 0.27
23 3 0.07
24 19 0.43
25 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTATTATTAAAATTATTATTATT
Found at i:1246693 original size:3 final size:3
Alignment explanation
Indices: 1246685--1246722 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
1246675 TTATTTACAA
1246685 TAT TAT TAT TAT TAT TATT TAT TAT TAT T-T ATAT TAT T
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT -TAT TAT T
1246723 TATATAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 1 0.03
3 27 0.84
4 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1246709 original size:19 final size:19
Alignment explanation
Indices: 1246685--1246725 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1246675 TTATTTACAA
1246685 TATTATTA-TTATTATTATT
1 TATTATTATTTA-TATTATT
1246704 TATTATTATTTATATTATT
1 TATTATTATTTATATTATT
1246723 TAT
1 TAT
1246726 ATAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTATTATTTATATTATT
Found at i:1246725 original size:16 final size:14
Alignment explanation
Indices: 1246688--1246722 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
1246678 TTTACAATAT
1246688 TATTATTATTATTA
1 TATTATTATTATTA
1246702 T-TTATTATTATTTA
1 TATTATTATTA-TTA
1246716 TATTATT
1 TATTATT
1246723 TATATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 9 0.47
14 5 0.26
15 5 0.26
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:1246727 original size:9 final size:10
Alignment explanation
Indices: 1246685--1246725 Score: 68
Period size: 9 Copynumber: 4.3 Consensus size: 10
1246675 TTATTTACAA
1246685 TATTATTA-T
1 TATTATTATT
1246694 TATTATTATT
1 TATTATTATT
1246704 TATTATTATT
1 TATTATTATT
1246714 TA-TATTATT
1 TATTATTATT
1246723 TAT
1 TAT
1246726 ATAAATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 17 0.57
10 13 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TATTATTATT
Found at i:1246984 original size:27 final size:27
Alignment explanation
Indices: 1246954--1247008 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
1246944 ATATTTCTAA
1246954 ATAAATAAATATTTTATTT-ATAAATAT
1 ATAAATAAATA-TTTATTTCATAAATAT
* *
1246981 ATAAATTAATATTTATTTCATAATTAT
1 ATAAATAAATATTTATTTCATAAATAT
1247008 A
1 A
1247009 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
ATAAATAAATATTTATTTCATAAATAT
Found at i:1249634 original size:39 final size:38
Alignment explanation
Indices: 1249591--1249672 Score: 94
Period size: 40 Copynumber: 2.1 Consensus size: 38
1249581 TAGTTGAACT
* *
1249591 GAAAATGTTACATT-TTCATAATATTTTCGGTTGGCAACC
1 GAAAATGCTACATTATTCATAATATTTTCGATT--CAACC
* * *
1249630 GAAAATGCTACCTTATTCGTAGTATTTTCGATTCAACC
1 GAAAATGCTACATTATTCATAATATTTTCGATTCAACC
1249668 GAAAA
1 GAAAA
1249673 ATATTAGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
38 10 0.27
39 12 0.32
40 15 0.41
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (38 bp):
GAAAATGCTACATTATTCATAATATTTTCGATTCAACC
Found at i:1250054 original size:19 final size:19
Alignment explanation
Indices: 1250026--1250064 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1250016 TTTAAAAAAA
1250026 TTTAAATTATCATATATTT
1 TTTAAATTATCATATATTT
* * *
1250045 TTTAATTTATTATGTATTT
1 TTTAAATTATCATATATTT
1250064 T
1 T
1250065 ACTAAAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTAAATTATCATATATTT
Found at i:1251907 original size:33 final size:32
Alignment explanation
Indices: 1251848--1251916 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
1251838 CCTTTACAAC
* *
1251848 TCCCTAGTTTTTACGGGCTAAACTAGAACATT
1 TCCCTAGTTTTCACGGGATAAACTAGAACATT
* * *
1251880 TCCCTAGATTTTCACGGGATCAGCTAGAACCTT
1 TCCCTAG-TTTTCACGGGATAAACTAGAACATT
1251913 TCCC
1 TCCC
1251917 CTTTACAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
32 7 0.23
33 24 0.77
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.32
Consensus pattern (32 bp):
TCCCTAGTTTTCACGGGATAAACTAGAACATT
Found at i:1252460 original size:20 final size:20
Alignment explanation
Indices: 1252435--1252493 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
1252425 CTCTTGCCTA
1252435 GGGTATCGATACTACATGAT
1 GGGTATCGATACTACATGAT
*
1252455 GGGTATCGATAC--CATTCAT
1 GGGTATCGATACTACA-TGAT
1252474 GTGGTATCGATACTACATGA
1 G-GGTATCGATACTACATGA
1252494 AGCAGTATCG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 2 0.06
19 4 0.12
20 23 0.70
21 2 0.06
22 2 0.06
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (20 bp):
GGGTATCGATACTACATGAT
Found at i:1252751 original size:21 final size:19
Alignment explanation
Indices: 1252722--1252778 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 19
1252712 ATGTTTAATG
1252722 AAAAAGATACCAATTGTTT
1 AAAAAGATACCAATTGTTT
*
1252741 ACAAAATGATACCTATTG-TT
1 A-AAAA-GATACCAATTGTTT
*
1252761 AAAAAGATAACAATTGTT
1 AAAAAGATACCAATTGTT
1252779 AGCAATTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 9 0.28
19 6 0.19
20 7 0.22
21 10 0.31
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTT
Found at i:1252769 original size:18 final size:18
Alignment explanation
Indices: 1252722--1252779 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
1252712 ATGTTTAATG
1252722 AAAAAGATACCAATTGTTT
1 AAAAAGATACCAATTG-TT
*
1252741 ACAAAATGATACCTATTGTT
1 A-AAAA-GATACCAATTGTT
*
1252761 AAAAAGATAACAATTGTT
1 AAAAAGATACCAATTGTT
1252779 A
1 A
1252780 GCAATTGTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 12 0.35
19 5 0.15
20 7 0.21
21 10 0.29
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.31
Consensus pattern (18 bp):
AAAAAGATACCAATTGTT
Found at i:1253967 original size:20 final size:20
Alignment explanation
Indices: 1253939--1253987 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1253929 TCTAAATCAT
*
1253939 TTTTTAAAATTTCA-TTTTGA
1 TTTTCAAAATTTCACTTTT-A
*
1253959 TTTTCAAAA-TTGACTTTTA
1 TTTTCAAAATTTCACTTTTA
1253978 TTTTCAAAAT
1 TTTTCAAAAT
1253988 CGATTTATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTCAAAATTTCACTTTTA
Found at i:1256105 original size:20 final size:20
Alignment explanation
Indices: 1256080--1256139 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
1256070 CTCTTGCCTA
1256080 GGGTATCGATACTACATGAT
1 GGGTATCGATACTACATGAT
* * *
1256100 GGGTATTGGTACT-CATTCAT
1 GGGTATCGATACTACA-TGAT
1256120 GTGGTATCGATACTACATGA
1 G-GGTATCGATACTACATGA
1256140 AGCAGTATCG
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 2 0.06
20 15 0.48
21 12 0.39
22 2 0.06
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (20 bp):
GGGTATCGATACTACATGAT
Found at i:1256555 original size:12 final size:13
Alignment explanation
Indices: 1256526--1256558 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1256516 CTTAATAATT
*
1256526 ATTTATATTTATA
1 ATTTAAATTTATA
1256539 ATTTAAATTTA-A
1 ATTTAAATTTATA
1256551 ATTTAAAT
1 ATTTAAAT
1256559 AATACCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTTAAATTTATA
Found at i:1257350 original size:15 final size:16
Alignment explanation
Indices: 1257312--1257352 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1257302 ACAGAGCCTC
*
1257312 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
1257328 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
1257344 T-AATCATTC
1 TGAATCATTC
1257353 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:1267976 original size:2 final size:2
Alignment explanation
Indices: 1267969--1267999 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1267959 AAGGAAGAGG
1267969 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1268000 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1268035 original size:14 final size:14
Alignment explanation
Indices: 1268018--1268044 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1268008 ATATATATAT
1268018 ATATACACACACAC
1 ATATACACACACAC
1268032 ATATACACACACA
1 ATATACACACACA
1268045 TTCACATACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.15
Consensus pattern (14 bp):
ATATACACACACAC
Found at i:1268995 original size:14 final size:14
Alignment explanation
Indices: 1268976--1269022 Score: 78
Period size: 14 Copynumber: 3.4 Consensus size: 14
1268966 TTAGTGATTC
1268976 AAATTTGTAAAGTT
1 AAATTTGTAAAGTT
*
1268990 AAATTTGTCAAGTT
1 AAATTTGTAAAGTT
1269004 -AATTTGTAAAGTT
1 AAATTTGTAAAGTT
1269017 AAATTT
1 AAATTT
1269023 ACAATTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 12 0.40
14 18 0.60
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.45
Consensus pattern (14 bp):
AAATTTGTAAAGTT
Found at i:1269009 original size:13 final size:13
Alignment explanation
Indices: 1268977--1269018 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
1268967 TAGTGATTCA
1268977 AATTTGTAAAGTT
1 AATTTGTAAAGTT
*
1268990 AAATTTGTCAAGTT
1 -AATTTGTAAAGTT
1269004 AATTTGTAAAGTT
1 AATTTGTAAAGTT
1269017 AA
1 AA
1269019 ATTTACAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.43
Consensus pattern (13 bp):
AATTTGTAAAGTT
Found at i:1269687 original size:20 final size:20
Alignment explanation
Indices: 1269577--1269700 Score: 101
Period size: 20 Copynumber: 6.2 Consensus size: 20
1269567 CAATATAACA
*
1269577 GGTTGAAATTTGACAAATCC
1 GGTTGAAATTTGACAAAACC
*
1269597 GGTTGAAATTTGACAAAACA
1 GGTTGAAATTTGACAAAACC
*
1269617 GG-T-AACGGATTTGACTAAACC
1 GGTTGAA---ATTTGACAAAACC
* *
1269638 GATTAGAAATTT-ACAAAACT
1 GGTT-GAAATTTGACAAAACC
*
1269658 AGTTGAAATTTGACAAAACC
1 GGTTGAAATTTGACAAAACC
** * *
1269678 GGTTTCAATTTAACAAAATC
1 GGTTGAAATTTGACAAAACC
1269698 GGT
1 GGT
1269701 AAAGAGCTAC
Statistics
Matches: 82, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
18 2 0.02
19 8 0.10
20 53 0.65
21 16 0.20
22 1 0.01
24 2 0.02
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (20 bp):
GGTTGAAATTTGACAAAACC
Found at i:1275023 original size:15 final size:15
Alignment explanation
Indices: 1275003--1275031 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1274993 AAAAAAAGTT
1275003 TGGTTAATTCGGTTA
1 TGGTTAATTCGGTTA
1275018 TGGTTAATTCGGTT
1 TGGTTAATTCGGTT
1275032 CGGTCGGCCA
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:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (15 bp):
TGGTTAATTCGGTTA
Found at i:1282159 original size:30 final size:30
Alignment explanation
Indices: 1282106--1282188 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
1282096 TTTATCTAGT
1282106 GACTAAAATAT-AAGTTTTG-AAAGTTTAGA
1 GACTAAAATATAAAG-TTTGAAAAGTTTAGA
* *
1282135 GGCTAAAGTATAAAGTTTGAAAAGTTTAGA
1 GACTAAAATATAAAGTTTGAAAAGTTTAGA
* * *
1282165 GACCAAAATAGAAATTTTGAAAAG
1 GACTAAAATATAAAGTTTGAAAAG
1282189 GTATAGATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
29 13 0.29
30 32 0.71
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.29
Consensus pattern (30 bp):
GACTAAAATATAAAGTTTGAAAAGTTTAGA
Found at i:1286297 original size:12 final size:12
Alignment explanation
Indices: 1286280--1286319 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1286270 TGCTGATATG
*
1286280 TTTTTTTTTGTT
1 TTTTTTTTTATT
1286292 TTTTTTTTTATT
1 TTTTTTTTTATT
* *
1286304 TTTATTATTATT
1 TTTTTTTTTATT
1286316 TTTT
1 TTTT
1286320 CGTATTGTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTATT
Found at i:1287825 original size:227 final size:225
Alignment explanation
Indices: 1287392--1288219 Score: 1246
Period size: 227 Copynumber: 3.7 Consensus size: 225
1287382 TAACATAACC
* * * * *
1287392 GGTTAATTACTAGAAATATTATCAACCATAATAACATAACAAGTAGTGCTTATGTAACGTAATAG
1 GGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAG
* * * *
1287457 GTAGCGCCTTTTTAAAGCTGATGGAGCCTTAGAAATCCGATGATAACAAAATATGTTAATTACTT
66 GTAGCGCCTGTTTAAAGCTGATGG-GCCTTAGAAATACGACGATAACAAAATAGGTTAATTACTT
* * * *
1287522 AATTTGTTAACAATTTTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGTTGAT
130 GATTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCTGAT
*
1287587 AGAGCCTTAGAAATCCGACGATAACAAAATA
195 AGAGCCTTAGAAATCTGACGATAACAAAATA
* * *
1287618 GATTAATTATTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAT
1 GGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAG
* * * *
1287683 GTAGCGCCTGTTTAAAGTTGATGAGGTCTTAGAAGTACGACGATAACAAAAATAGGTTAATTAAT
66 GTAGCGCCTGTTTAAAGCTGATG-GGCCTTAGAAATACGACGATAAC-AAAATAGGTTAATTACT
* *
1287748 TGATTTGTTATCAATATTATCAACATATTAAGTAGCGCCTAAAATGTTACCAAAATTTAAGCTGA
129 TGATTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCTGA
1287813 TAGAGCCTTAGAAATCTGACGATAACAAAATA
194 TAGAGCCTTAGAAATCTGACGATAACAAAATA
* *
1287845 GGTTAATTATTGGAAACATTATCAACCATAATAACATAACAAGTATCGCTTATTTAATGTAATAG
1 GGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAG
* *
1287910 GTAGCGTCTGTTTAAAGCTAATGGGCCTT--AAATACGACGATAACAAAATAGGTTAATTACTTG
66 GTAGCGCCTGTTTAAAGCTGATGGGCCTTAGAAATACGACGATAACAAAATAGGTTAATTACTTG
* * *
1287973 ATTTGGTATTAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCTGATG
131 ATTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCTGATA
* *
1288038 GAGCCATAGGAATCTGACGATAACAAAATA
196 GAGCCTTAGAAATCTGACGATAACAAAATA
* *
1288068 GGTTAATTACTGGAAACATTATCAACCATAATAACATAACCAGTAGTGCTTATTTAATGTAATAG
1 GGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAG
* * * * *
1288133 GTAGCGCTTGTTTAAAGCTGGTGATGCATTAGAAATCCGACGATAACAAAATAGGTTAATTACTT
66 GTAGCGCCTGTTTAAAGCTGATG-GGCCTTAGAAATACGACGATAACAAAATAGGTTAATTACTT
*
1288198 GATTTGTTTTCAATATTATCAA
130 GATTTGTTATCAATATTATCAA
1288220 TATCTTACCG
Statistics
Matches: 544, Mismatches: 53, Indels: 10
0.90 0.09 0.02
Matches are distributed among these distances:
223 186 0.34
224 18 0.03
226 152 0.28
227 188 0.35
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (225 bp):
GGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAG
GTAGCGCCTGTTTAAAGCTGATGGGCCTTAGAAATACGACGATAACAAAATAGGTTAATTACTTG
ATTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCTGATA
GAGCCTTAGAAATCTGACGATAACAAAATA
Found at i:1287967 original size:115 final size:113
Alignment explanation
Indices: 1287806--1288194 Score: 298
Period size: 115 Copynumber: 3.4 Consensus size: 113
1287796 ACCAAAATTT
*
1287806 AAGCTGATAGAGCCTTAGAAATCTGACGATAACAAAATAGGTTAATTATTGGAAACATTATCAAC
1 AAGCTGAT-GGGCCTT--AAATC-GACGATAACAAAATAGGTTAATTATTGGAAACATTATCAAC
1287871 CATAATAACATAACAAGTATCGCTTATTTAATGTAATAGGTAGCGTCTGTTTA
62 CATAATAACATAACAAGTATCGCTTATTTAATGTAATAGGTAGCG-CTGTTTA
* ***** * *
1287924 AAGCTAATGGGCCTTAAATACGACGATAACAAAATAGGTTAATTACTT-GATTTGGTATTAA-TA
1 AAGCTGATGGGCCTTAAAT-CGACGATAACAAAATAGGTTAATTA-TTGGAAACATTATCAACCA
* ** * * * * * ***
1287987 TTATCAACATATTAGGTAGCGCCTA--AAATGT--T----ACCAAAGTTT-
64 TAAT-AACATAACAAGTATCGCTTATTTAATGTAATAGGTAGCGCTGTTTA
* *
1288029 AAGCTGATGGAGCCATAGGAATCTGACGATAACAAAATAGGTTAATTACTGGAAACATTATCAAC
1 AAGCTGATGG-GCCTTA--AATC-GACGATAACAAAATAGGTTAATTATTGGAAACATTATCAAC
*
1288094 CATAATAACATAACCAGTAGT-GCTTATTTAATGTAATAGGTAGCGCTTGTTTA
62 CATAATAACATAACAAGTA-TCGCTTATTTAATGTAATAGGTAGCGC-TGTTTA
* * *
1288147 AAGCTGGTGATGCATTAGAAATCCGACGATAACAAAATAGGTTAATTA
1 AAGCTGATG-GGCCTT--AAAT-CGACGATAACAAAATAGGTTAATTA
1288195 CTTGATTTGT
Statistics
Matches: 201, Mismatches: 46, Indels: 48
0.68 0.16 0.16
Matches are distributed among these distances:
105 9 0.04
106 9 0.04
107 4 0.02
108 47 0.23
109 4 0.02
110 5 0.02
111 1 0.00
112 1 0.00
113 5 0.02
114 4 0.02
115 50 0.25
116 5 0.02
117 10 0.05
118 45 0.22
119 1 0.00
120 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (113 bp):
AAGCTGATGGGCCTTAAATCGACGATAACAAAATAGGTTAATTATTGGAAACATTATCAACCATA
ATAACATAACAAGTATCGCTTATTTAATGTAATAGGTAGCGCTGTTTA
Found at i:1288554 original size:20 final size:21
Alignment explanation
Indices: 1288519--1288569 Score: 95
Period size: 20 Copynumber: 2.5 Consensus size: 21
1288509 GAAATTATAA
1288519 GTATCGATACTTTATATATGT
1 GTATCGATACTTTATATATGT
1288540 GTATCGATA-TTTATATATGT
1 GTATCGATACTTTATATATGT
1288560 GTATCGATAC
1 GTATCGATAC
1288570 GTTTTGCGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 20 0.69
21 9 0.31
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (21 bp):
GTATCGATACTTTATATATGT
Found at i:1288765 original size:21 final size:21
Alignment explanation
Indices: 1288739--1288793 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
1288729 GAAATTACCA
1288739 GTATCGATACTTTATATATGG
1 GTATCGATACTTTATATATGG
1288760 GTATCGATACTTTATATATGG
1 GTATCGATACTTTATATATGG
*
1288781 GTATCAATACTTT
1 GTATCGATACTTT
1288794 GTTGCGTACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (21 bp):
GTATCGATACTTTATATATGG
Found at i:1288916 original size:222 final size:221
Alignment explanation
Indices: 1288437--1288995 Score: 747
Period size: 222 Copynumber: 2.5 Consensus size: 221
1288427 TTTTATGCCT
* *
1288437 ATTATCATTATACTGGTAGACTTTT-ACTGTTTTCTTTGTAAA-TTAACCTATTACTTTAAAGTA
1 ATTATCATTATACTGGTAGACTTTTAACT-TTTACATTGTAAATTTAA-CTATTACTTTAAAGTA
** *
1288500 ATAGGTTTCGAAATTATAAGTATCGATACTTTATATATGTGTATCGATA-TTTATATATGTGTAT
64 ATAGGTTTCGAAATTACCAGTATCGATACTTTATATATGTGTATCGATACTTTATATATGGGTAT
* * * *
1288564 CGATACGTTTTGCGTACAAATTGTTTGAGAAGCATACTGGAATAAAAGTATTGATACCGATATAA
129 CAATACGTTTTGCGTACAAATTGTTTGAGAAACATACTGGAATAAAAATATCGATACCGATATAA
**
1288629 AACGTACCGATACTTATAATTTACGATA
194 AACGTACAAATACTTATAATTTACGATA
* * * * *
1288657 ATTATCATTATATTTGTAGATTTTTACCGTTTACATTGTAAATTTAACTATTACTTTAAAGTAAT
1 ATTATCATTATACTGGTAGACTTTTAACTTTTACATTGTAAATTTAACTATTACTTTAAAGTAAT
*
1288722 AGGTTTCGAAATTACCAGTATCGATACTTTATATATGGGTATCGATACTTTATATATGGGTATCA
66 AGGTTTCGAAATTACCAGTATCGATACTTTATATATGTGTATCGATACTTTATATATGGGTATCA
*
1288787 ATACTTTGTTGCGTACAAATTGTTTGAGAAACATACTGGAATAAAAATATCGATACCGATAT-AA
131 ATACGTT-TTGCGTACAAATTGTTTGAGAAACATACTGGAATAAAAATATCGATACCGATATAAA
* * *
1288851 ACATTATAAATACTT-TATGTTTAC-ACCT-
195 AC-GTACAAATACTTATA-ATTTACGA--TA
*
1288879 GTTATCATTATACTGGTAGACTTTTAACTTTTACATTGTAAATTTAACTATTACTTTTAAAGTAA
1 ATTATCATTATACTGGTAGACTTTTAACTTTTACATTGTAAATTTAACTATTAC-TTTAAAGTAA
* * * *
1288944 TAGGTTTTGAAATT-CCAAGTATTGGTACTTTATATAAGTGTATCGATACTTT
65 TAGGTTTCGAAATTACC-AGTATCGATACTTTATATATGTGTATCGATACTTT
1288996 TTGCGTTCAA
Statistics
Matches: 297, Mismatches: 32, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
220 95 0.32
221 33 0.11
222 114 0.38
223 55 0.19
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.41
Consensus pattern (221 bp):
ATTATCATTATACTGGTAGACTTTTAACTTTTACATTGTAAATTTAACTATTACTTTAAAGTAAT
AGGTTTCGAAATTACCAGTATCGATACTTTATATATGTGTATCGATACTTTATATATGGGTATCA
ATACGTTTTGCGTACAAATTGTTTGAGAAACATACTGGAATAAAAATATCGATACCGATATAAAA
CGTACAAATACTTATAATTTACGATA
Found at i:1289087 original size:201 final size:201
Alignment explanation
Indices: 1288767--1289155 Score: 539
Period size: 201 Copynumber: 1.9 Consensus size: 201
1288757 TGGGTATCGA
* *
1288767 TACTTTATATATGGGTATCAATACTTTGTTGCGTACAAATTGTTTGAGAAACATACTGGAATAAA
1 TACTTTATATAAGGGTATCAATACTTTGTTGCGTACAAATTGTTAGAGAAACATACTGGAATAAA
* * * * * * *
1288832 AATATCGATACCGATATAAACATTATAAATACTTTATGTTTACACCTGTTATCATTATACTGGTA
66 AATATCGATACCGAGATAAAAAGTATAAATACTTGATGGTTACACCTATTATCATTATACCGGTA
*
1288897 GACTTTTAAC-TTTTACATTGTAAATTTAACTATTACTTTTAAAGTAATAGGTTTTGAAATTCCA
131 GACTTTTAACGTTTT-CATTGTAAATTTAACTATTAC-TTTAAAGTAATAGGTTTCGAAATTCCA
1288961 AGTATTGG
194 AGTATTGG
* * * * *
1288969 TACTTTATATAAGTGTATCGATACTTT-TTGCGTTCAAATTGTTAGATAAGCATACTGGAATAAA
1 TACTTTATATAAGGGTATCAATACTTTGTTGCGTACAAATTGTTAGAGAAACATACTGGAATAAA
* * ** **
1289033 AGTATCGATACTGAGATAAAAAGTATCGATACTTGATGGTTATGCCTATTATCATTATACCGGTA
66 AATATCGATACCGAGATAAAAAGTATAAATACTTGATGGTTACACCTATTATCATTATACCGGTA
* *
1289098 GACTTTTATCGTTTTCATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAA
131 GACTTTTAACGTTTTCATTGTAAATTTAACTATTACTTTAAAGTAATAGGTTTCGAAA
1289156 GATTCTTTTT
Statistics
Matches: 163, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
200 21 0.13
201 114 0.70
202 28 0.17
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (201 bp):
TACTTTATATAAGGGTATCAATACTTTGTTGCGTACAAATTGTTAGAGAAACATACTGGAATAAA
AATATCGATACCGAGATAAAAAGTATAAATACTTGATGGTTACACCTATTATCATTATACCGGTA
GACTTTTAACGTTTTCATTGTAAATTTAACTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAG
TATTGG
Found at i:1289339 original size:76 final size:74
Alignment explanation
Indices: 1289246--1289406 Score: 252
Period size: 76 Copynumber: 2.1 Consensus size: 74
1289236 ATTTACGTCT
* * *
1289246 ATTTTATTTTACTGTTTACATTATTAGTAACCTTTTATACAAACCTGTAGGT-ATTATAATGTAA
1 ATTTTATTTTACCGTTTACATTATTAGTAACC-TTTAAACAAACCGGTAGGTGA-T-TAATGTAA
1289310 TAAGTAGCGCCA
63 TAAGTAGCGCCA
1289322 ATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACCGGTAGGTGATTAATGTAATAA
1 ATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACCGGTAGGTGATTAATGTAATAA
*
1289387 GTAGCGCCT
66 GTAGCGCCA
1289396 ATTTTATTTTA
1 ATTTTATTTTA
1289407 ATTGGTTAAG
Statistics
Matches: 80, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
74 30 0.38
75 18 0.22
76 32 0.40
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.42
Consensus pattern (74 bp):
ATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACCGGTAGGTGATTAATGTAATAA
GTAGCGCCA
Done.