Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001523.1 Hibiscus syriacus cultivar Beakdansim tig00002982_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: 1321709
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:935815 original size:113 final size:113
Alignment explanation
Indices: 935043--935808 Score: 1074
Period size: 113 Copynumber: 6.8 Consensus size: 113
935033 GATTCAAATC
* *
935043 CATCACTTGATGGATCAGCTTTTCTAGAAAAAGTTCATAAT--G-AGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
935105 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATT
*
935153 CATCATTTGATGGATCAGGTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
935218 AGAAGAAATTCATAATGAGAATAATTTGTTCAACCTTTTGCTC-AAAT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATT
*
935265 CTATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAATAAGG
1 C-ATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * *
935330 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
65 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATT
*
935379 CATCACTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * *
935444 AAGAAGAAGTTCATAATGAAAAGAATTTGTTCAACCTTTTGTTTGAATT
65 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATT
* * ** * *
935493 CATCATTTGATGGATCAACATCCCCAGTGAAAGAGTTCATAATGAGAAAAACTCATCTGAAGAAG
1 CATCATTTGATGGATCAGCTTTTCCA--GAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
* *
935558 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTGAATT
64 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GCTCGAATT
* * **** *
935608 CATCATTTGATGGATCAGCATTGCCAGGGCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
935673 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATT
* * * * ** * * *
935721 CATCACTCGATAGATCAACTTTTTTAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
935786 AGAAGAAGTTCATAATGAGAAGA
66 AGAAGAAGTTCATAATGAGAAGA
935809 GCTTGTTTGA
Statistics
Matches: 599, Mismatches: 47, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
110 38 0.06
112 4 0.01
113 341 0.57
114 117 0.20
115 98 0.16
116 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATT
Found at i:935928 original size:17 final size:17
Alignment explanation
Indices: 935870--935928 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
935860 CAACATTTCC
*
935870 AGAAGGAGTTCACAATG
1 AGAAGAAGTTCACAATG
*
935887 AGAAGAA-CTCATCTGAA-G
1 AGAAGAAGTTCA-C--AATG
935905 AAGAAGAAGTTCACAATG
1 -AGAAGAAGTTCACAATG
935923 AGAAGA
1 AGAAGA
935929 GCTTGTTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
16 3 0.09
17 15 0.45
18 2 0.06
19 10 0.30
20 3 0.09
ACGTcount: A:0.47, C:0.12, G:0.25, T:0.15
Consensus pattern (17 bp):
AGAAGAAGTTCACAATG
Found at i:936175 original size:9 final size:10
Alignment explanation
Indices: 936166--936236 Score: 55
Period size: 9 Copynumber: 7.5 Consensus size: 10
936156 TTTACCCATT
936166 TTATTTA-T-
1 TTATTTATTA
936174 TTATTTATTA
1 TTATTTATTA
936184 TTA-TTATTA
1 TTATTTATTA
936193 TTA-TTA-TA
1 TTATTTATTA
* *
936201 ATAATTATTA
1 TTATTTATTA
*
936211 TTAATATATATA
1 TT-ATTTAT-TA
936223 TTA-TTATTA
1 TTATTTATTA
936232 TTATT
1 TTATT
936237 AAAAAATAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
8 11 0.22
9 21 0.41
10 10 0.20
11 5 0.10
12 4 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TTATTTATTA
Found at i:936186 original size:3 final size:3
Alignment explanation
Indices: 936178--936237 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
936168 ATTTATTTAT
* * *
936178 TTA TTA TTA TTA TTA TTA TTA TAA TAA TTA TTA TTA ATA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
936223 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
936238 AAAAATAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:937518 original size:3 final size:3
Alignment explanation
Indices: 937505--937561 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
937495 TTATTTGCAA
* * *
937505 TAT TAT T-T TAT TAT TAT TGT TTT TAAT TAT TAT T-T CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
*
937549 TAT TTT TAT TAT T
1 TAT TAT TAT TAT T
937562 TATATAAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
2 3 0.07
3 39 0.89
4 2 0.05
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:937529 original size:39 final size:39
Alignment explanation
Indices: 937486--937561 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
937476 TTTCCTTTTA
937486 TTTTAATCATTATTTGCAATATTATT-TTATTATTATTGT
1 TTTTAATCATTATTT-CAATATTATTATTATTATTATTGT
* * *
937525 TTTTAATTATTATTTCATTATTATTATTTTTATTATT
1 TTTTAATCATTATTTCAATATTATTATTATTATTATT
937562 TATATAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 9 0.27
39 24 0.73
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.66
Consensus pattern (39 bp):
TTTTAATCATTATTTCAATATTATTATTATTATTATTGT
Found at i:937564 original size:27 final size:27
Alignment explanation
Indices: 937505--937561 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
937495 TTATTTGCAA
* *
937505 TATTATTTTATTATTATTGTTTTTAAT
1 TATTATTTCATTATTATTATTTTTAAT
937532 TATTATTTCATTATTATTATTTTT-AT
1 TATTATTTCATTATTATTATTTTTAAT
937558 TATT
1 TATT
937562 TATATAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (27 bp):
TATTATTTCATTATTATTATTTTTAAT
Found at i:939774 original size:19 final size:20
Alignment explanation
Indices: 939736--939778 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
939726 TAGGTACTAA
*
939736 AATA-TAAATATTATACAAT
1 AATATTAAATATTATAAAAT
939755 AATATTAAATATTA-AAAAT
1 AATATTAAATATTATAAAAT
939774 AATAT
1 AATAT
939779 ATTAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
AATATTAAATATTATAAAAT
Found at i:942073 original size:131 final size:130
Alignment explanation
Indices: 941834--942198 Score: 444
Period size: 131 Copynumber: 2.8 Consensus size: 130
941824 TCGATATTGA
* *
941834 AAATAATAATATCTCATCATTTCAGTTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
1 AAATAGTAATATCTCTTCATTTCAGTTGGAGTAATAAATG-ATGCTTTAAGGCATGAGAGGTCAT
* * * * *
941899 TTATTATCAATTGGAAATAATTCGATATTAGCGTTTTCTCTCGAATCAATATTG-ATCTTTAAGA
65 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAAT-TTTAAGA
941963 CG
129 CG
* * * * * *
941965 AAATATTGATATCTCTTCATTTCAATTGGAGCAATAAATGACTACTTTAAGGCATGAGAGGTCCT
1 AAATAGTAATATCTCTTCATTTCAGTTGGAGTAATAAATGA-TGCTTTAAGGCATGAGAGGTCAT
* * * * *
942030 TTATTCTCGATTAGAAATCATTAAATATTATCTTTTTCACTCGAATCGATATTGAATTTTAAGAC
65 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAGAC
942095 G
130 G
* * ** * ** *
942096 AAATAGTAATATCCCTTTATTTTGGTTGGAGTAATAAATGGATGTTTTAAGGCACCAAAGGTCAT
1 AAATAGTAATATCTCTTCATTTCAGTTGGAGTAATAAAT-GATGCTTTAAGGCATGAGAGGTCAT
*
942161 TTATTCTCGATTGGAAATAATTAGATATTATTGTTTTC
65 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTC
942199 TCTCTTAAAA
Statistics
Matches: 195, Mismatches: 36, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
130 1 0.01
131 190 0.97
132 4 0.02
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (130 bp):
AAATAGTAATATCTCTTCATTTCAGTTGGAGTAATAAATGATGCTTTAAGGCATGAGAGGTCATT
TATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAGACG
Found at i:944122 original size:11 final size:11
Alignment explanation
Indices: 944106--944139 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
944096 CAATACCTTG
944106 CATTGCATTTA
1 CATTGCATTTA
*
944117 CATTGCATCTA
1 CATTGCATTTA
944128 CATTGCATTTA
1 CATTGCATTTA
944139 C
1 C
944140 TTTTTGCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (11 bp):
CATTGCATTTA
Found at i:949280 original size:6 final size:7
Alignment explanation
Indices: 949262--949315 Score: 58
Period size: 7 Copynumber: 8.0 Consensus size: 7
949252 GTACTTCGCT
949262 TGAAAAA
1 TGAAAAA
949269 TGAAAAA
1 TGAAAAA
*
949276 TAAAAAA
1 TGAAAAA
949283 TGAAAAA
1 TGAAAAA
* *
949290 AGAGAAA
1 TGAAAAA
949297 TG--AAA
1 TGAAAAA
949302 TGAAAAA
1 TGAAAAA
*
949309 AGAAAAA
1 TGAAAAA
949316 AAGAAAAGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
5 5 0.13
7 34 0.87
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (7 bp):
TGAAAAA
Found at i:949304 original size:19 final size:19
Alignment explanation
Indices: 949280--949337 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
949270 GAAAAATAAA
949280 AAATGAAAAAAGAGAAATG
1 AAATGAAAAAAGAGAAATG
949299 AAATGAAAAAAGA-AAA--
1 AAATGAAAAAAGAGAAATG
949315 AAA-G--AAAAG-GAAATG
1 AAATGAAAAAAGAGAAATG
949330 AAATGAAA
1 AAATGAAA
949338 GAGATCAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
13 8 0.24
15 4 0.12
16 4 0.12
18 4 0.12
19 13 0.39
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (19 bp):
AAATGAAAAAAGAGAAATG
Found at i:949307 original size:26 final size:26
Alignment explanation
Indices: 949273--949332 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
949263 GAAAAATGAA
*
949273 AAAT-AAAAAATG-AAAAAAGAGAAATG
1 AAATGAAAAAA-GAAAAAAAGA-AAAGG
949299 AAATGAAAAAAGAAAAAAAGAAAAGG
1 AAATGAAAAAAGAAAAAAAGAAAAGG
949325 AAATGAAA
1 AAATGAAA
949333 TGAAAGAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 17 0.55
27 14 0.45
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (26 bp):
AAATGAAAAAAGAAAAAAAGAAAAGG
Found at i:950830 original size:134 final size:134
Alignment explanation
Indices: 950573--950892 Score: 379
Period size: 134 Copynumber: 2.4 Consensus size: 134
950563 ATCGAACTAA
* * * * *
950573 ATTCAATCTTTCTTGAAGAGCAGTGGAATGAATCAACATTTCTAGATTTGATTTTCCCTCAAAAA
1 ATTCAATCTTCCCTGAAGAACAGGGGAATGAATCAACATTTCTAGATCTGATTTTCCCTCAAAAA
* ** * * * *
950638 ACAACGAAACATATCCCTCTCTTTCCAGATTTGTTCTTCCCTAAGGAATAATGTAACAAGTCTAC
66 ACAACAAAACATATCCCTCTCTTTCCAGATTTGACCTTCCCTAAGCAACAATGGAACAAGTATAC
*
950703 TTCG
131 CTCG
* * * *
950707 ATTCAATCTTCCCTGAAGAACAGGGGATTGAATTAACATTTCTAGATCTGATTTTCCCTCTAGAA
1 ATTCAATCTTCCCTGAAGAACAGGGGAATGAATCAACATTTCTAGATCTGATTTTCCCTCAAAAA
* * * *
950772 ACAACAAAACATATCCTTCTCTTTCCAGATTTGACCTTCCTTGAGCAACAATGGAACAAGTATGC
66 ACAACAAAACATATCCCTCTCTTTCCAGATTTGACCTTCCCTAAGCAACAATGGAACAAGTATAC
950837 CTCG
131 CTCG
* * ** * ** *
950841 ATTCGATCTTCCCTGAATAACAATGGAATAAATCAATGTTTCTCGATCTGAT
1 ATTCAATCTTCCCTGAAGAACAGGGGAATGAATCAACATTTCTAGATCTGAT
950893 ATACCCAGAA
Statistics
Matches: 155, Mismatches: 31, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
134 155 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (134 bp):
ATTCAATCTTCCCTGAAGAACAGGGGAATGAATCAACATTTCTAGATCTGATTTTCCCTCAAAAA
ACAACAAAACATATCCCTCTCTTTCCAGATTTGACCTTCCCTAAGCAACAATGGAACAAGTATAC
CTCG
Found at i:951060 original size:3 final size:3
Alignment explanation
Indices: 951052--951151 Score: 62
Period size: 3 Copynumber: 33.7 Consensus size: 3
951042 CCCAACATTT
* * *
951052 TTA TTA TTAA TAA TAA TTA TAA TTA TTTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
* * * * * * * *
951099 TTG TTG TTG TTG TTG TTG TTA TTA TTA TTA -TA CTA ATA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
951145 TT- TTA TT
1 TTA TTA TT
951152 TTTCAGGTCT
Statistics
Matches: 84, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
2 6 0.07
3 73 0.87
4 5 0.06
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:951078 original size:19 final size:19
Alignment explanation
Indices: 951054--951098 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
951044 CAACATTTTT
951054 ATTATTAATAATAATTATA
1 ATTATTAATAATAATTATA
* * * *
951073 ATTATTTATTATTATTATT
1 ATTATTAATAATAATTATA
951092 ATTATTA
1 ATTATTA
951099 TTGTTGTTGT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTATTAATAATAATTATA
Found at i:953492 original size:130 final size:130
Alignment explanation
Indices: 953246--953607 Score: 394
Period size: 130 Copynumber: 2.8 Consensus size: 130
953236 TCGATATTGA
* * * * * *
953246 AAATAGTAATATCTCA-TCGTTTTGGTTGGAGTAATAAATGACTGCTTTAAGGATGAGAGGTCAT
1 AAATAGTAATATC-CATTCATTTCGATTAGAGCAATAAATGACTGCTTTAAGGATGAGAAGTCAT
* * * * *
953310 TTATTTTCGATTGGAAATAATTCGATATTATCGTTTTCTCTCGAATCAATATTGATTTTTAAGAA
65 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCAAATCAATATTGAATTTTAAGAA
953375 G
130 G
* ** *
953376 GAATAGTGTTATCTC-TTCATTTCGATTAGAGCAATAAATGACCGCTTTAAGGTATGAGAAGT-A
1 AAATAGTAATATC-CATTCATTTCGATTAGAGCAATAAATGACTGCTTTAAGG-ATGAGAAGTCA
* * **
953439 TTTATTCTCGATTGGAAATCATTAGATATTATCATTTTCACTCAAATTGATATTGAATTTTAAGA
64 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCAAATCAATATTGAATTTTAAGA
*
953504 CG
129 AG
* * * * **
953506 AAATAGTAATATCCATTCATTTTGATTGGAGTAATAAATGGCTATTTTAAGGCACT-A-AAGGTC
1 AAATAGTAATATCCATTCATTTCGATTAGAGCAATAAATGACTGCTTTAAGG-A-TGAGAA-GTC
953569 ATTT-TTCTCGATTGGAAATAATTAGATATTATCGTTTTC
63 ATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTC
953608 TCTCTTAAAA
Statistics
Matches: 193, Mismatches: 33, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
129 3 0.02
130 177 0.92
131 13 0.07
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.40
Consensus pattern (130 bp):
AAATAGTAATATCCATTCATTTCGATTAGAGCAATAAATGACTGCTTTAAGGATGAGAAGTCATT
TATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCAAATCAATATTGAATTTTAAGAAG
Found at i:956126 original size:21 final size:22
Alignment explanation
Indices: 956091--956132 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
956081 AATCTGAAAA
*
956091 TGCTTAGTGTTTTTAGCATTTT
1 TGCTTAATGTTTTTAGCATTTT
*
956113 TGCTTAAT-TTTTTAGGATTT
1 TGCTTAATGTTTTTAGCATTT
956133 GATTATGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.17, C:0.07, G:0.17, T:0.60
Consensus pattern (22 bp):
TGCTTAATGTTTTTAGCATTTT
Found at i:956760 original size:39 final size:38
Alignment explanation
Indices: 956717--956844 Score: 139
Period size: 39 Copynumber: 3.3 Consensus size: 38
956707 TCTTTGACTT
* *
956717 GTAAGTGCTTACCACAGGCTCCTGGACTTTGTGCTCAGG
1 GTAAGTCCTTACCGCAGGCTCCTGG-CTTTGTGCTCAGG
* * * *
956756 GTAAGTCCTTACTGTAGGCTTCTTGGCTTTGTGCTCAGC
1 GTAAGTCCTTACCGCAGGC-TCCTGGCTTTGTGCTCAGG
* * * *
956795 ATAAGACCTTACCGCAGGCTCCTCTGCTTTGTGCACAGG
1 GTAAGTCCTTACCGCAGGCTCCT-GGCTTTGTGCTCAGG
956834 GTAAGTCCTTA
1 GTAAGTCCTTA
956845 ATGTAGATTC
Statistics
Matches: 71, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
38 3 0.04
39 63 0.89
40 5 0.07
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (38 bp):
GTAAGTCCTTACCGCAGGCTCCTGGCTTTGTGCTCAGG
Found at i:963679 original size:51 final size:51
Alignment explanation
Indices: 963618--963732 Score: 160
Period size: 51 Copynumber: 2.3 Consensus size: 51
963608 AGAATTAGAT
* *
963618 TTATTATTTTATTAGGAACAAAGATAGAGTTAAAACATTAT-TCTTAGTTTA
1 TTATTATTTTATTAGGAACAAAGATAGAATCAAAACATTATCT-TTAGTTTA
** * *
963669 TTATTATTTTATTAGGAATTATGATAGAATCGAAACATTATCTTTAGTTTA
1 TTATTATTTTATTAGGAACAAAGATAGAATCAAAACATTATCTTTAGTTTA
963720 TTATTATTTTATT
1 TTATTATTTTATT
963733 CATTAGTCAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 56 0.98
52 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (51 bp):
TTATTATTTTATTAGGAACAAAGATAGAATCAAAACATTATCTTTAGTTTA
Found at i:966788 original size:17 final size:19
Alignment explanation
Indices: 966760--966808 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
966750 TATTTTGAAA
966760 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
966778 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
966797 CACCGATGCACT
1 CATCGATGCACT
966809 AAGGGTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:975429 original size:46 final size:46
Alignment explanation
Indices: 975378--975477 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 46
975368 TGCACATACC
* * *
975378 ATGCAC-CGAGGATGTTATGAAAACATC-GAATGCATTTGATGCATCG
1 ATGCACTC-AGGATATT-TGAAAACATCAAAATGCACTTGATGCATCG
* * *
975424 ATGCACTCTGGCTATTTTAAAACATCAAAATGCACTTGATGCATCG
1 ATGCACTCAGGATATTTGAAAACATCAAAATGCACTTGATGCATCG
975470 ATGCACTC
1 ATGCACTC
975478 TTAGTGCACC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
45 9 0.20
46 36 0.78
47 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (46 bp):
ATGCACTCAGGATATTTGAAAACATCAAAATGCACTTGATGCATCG
Found at i:975475 original size:17 final size:19
Alignment explanation
Indices: 975453--975495 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
975443 AAACATCAAA
*
975453 ATGCACT-TGA-TGCATCG
1 ATGCACTCTGAGTGCACCG
*
975470 ATGCACTCTTAGTGCACCG
1 ATGCACTCTGAGTGCACCG
975489 ATGCACT
1 ATGCACT
975496 AAGGGTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (19 bp):
ATGCACTCTGAGTGCACCG
Found at i:981838 original size:17 final size:17
Alignment explanation
Indices: 981796--981866 Score: 72
Period size: 17 Copynumber: 4.1 Consensus size: 17
981786 TTCATGAATT
*
981796 TAGTTCATTGAA-TAAAGT
1 TAGTTCATT-AATTAAA-C
981814 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* * *
981831 TGGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
981848 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
981865 TA
1 TA
981867 ACTCTTAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
17 32 0.71
18 13 0.29
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.41
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:985365 original size:17 final size:17
Alignment explanation
Indices: 985343--985431 Score: 106
Period size: 17 Copynumber: 5.2 Consensus size: 17
985333 AATTAAGAGA
985343 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
*
985360 TAGTTTGATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
985377 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
985394 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* * *
985411 TAACTTTATTCAATGAAC
1 T-AGTTTAATAAATGAAC
985429 TAG
1 TAG
985432 ATGCTTTAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
17 49 0.78
18 14 0.22
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:986399 original size:17 final size:17
Alignment explanation
Indices: 986377--986413 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
986367 AATTAAGAGT
986377 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
*
986394 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
986411 TAG
1 TAG
986414 ATGCATGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:990241 original size:14 final size:14
Alignment explanation
Indices: 990222--990252 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
990212 CGGACAGCAA
990222 ATTCTGCAAAACAG
1 ATTCTGCAAAACAG
990236 ATTCTGCAAAACAG
1 ATTCTGCAAAACAG
990250 ATT
1 ATT
990253 ATGTTGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (14 bp):
ATTCTGCAAAACAG
Found at i:991216 original size:40 final size:40
Alignment explanation
Indices: 991161--991242 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
991151 TGTAGGTTTA
*
991161 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
*
991201 TAATATACTTCGGTGTATATGGTGGGCACAACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
991241 TA
1 TA
991243 GCACTACGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
Found at i:991394 original size:44 final size:47
Alignment explanation
Indices: 991346--991456 Score: 147
Period size: 44 Copynumber: 2.4 Consensus size: 47
991336 GTAACCATGC
991346 AAATAAGCTTATGAGCTTACAGAA-T-AATGGCAAGTATATTGG-AA
1 AAATAAGCTTATGAGCTTACAGAATTAAATGGCAAGTATATTGGTAA
* ** * *
991390 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTACAGAA-TTAAATGGCAAGTATATTGGTAA
991438 AAATAAGCTTATGAGCTTA
1 AAATAAGCTTATGAGCTTA
991457 TGGGATAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
44 21 0.37
46 1 0.02
47 15 0.26
48 20 0.35
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.32
Consensus pattern (47 bp):
AAATAAGCTTATGAGCTTACAGAATTAAATGGCAAGTATATTGGTAA
Found at i:991446 original size:48 final size:45
Alignment explanation
Indices: 991346--991472 Score: 166
Period size: 48 Copynumber: 2.8 Consensus size: 45
991336 GTAACCATGC
** *
991346 AAATAAGCTTATGAGCTTACAGAAT-AATGGCAAGTATATTGGAA
1 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATATTGGAA
* *
991390 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA--TAAATGGTAAGTATATTGG-AA
*
991438 AAATAAGCTTATGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAG
991473 AAATTTTATA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
44 21 0.29
46 12 0.17
47 15 0.21
48 24 0.33
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATATTGGAA
Found at i:992700 original size:17 final size:17
Alignment explanation
Indices: 992678--992717 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
992668 TGAACACTTA
992678 AAGTCACGAAGTTTGTT
1 AAGTCACGAAGTTTGTT
992695 AAGTCACGAAGTTTGTT
1 AAGTCACGAAGTTTGTT
992712 AAGTCA
1 AAGTCA
992718 TATAGCACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (17 bp):
AAGTCACGAAGTTTGTT
Found at i:993461 original size:18 final size:17
Alignment explanation
Indices: 993438--993506 Score: 59
Period size: 17 Copynumber: 4.0 Consensus size: 17
993428 ATTCATGCAT
993438 TTAGTTTATTGAA-TAAA
1 TTAGTTTATT-AATTAAA
993455 GTTAGTTTATTAATTAAA
1 -TTAGTTTATTAATTAAA
* * *
993473 TTGGTTTATTCATCAAA
1 TTAGTTTATTAATTAAA
* * *
993490 CTAGTTCATTTATTAAA
1 TTAGTTTATTAATTAAA
993507 CTAACTCTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
17 28 0.67
18 14 0.33
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.48
Consensus pattern (17 bp):
TTAGTTTATTAATTAAA
Found at i:993481 original size:17 final size:18
Alignment explanation
Indices: 993438--993482 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
993428 ATTCATGCAT
993438 TTAGTTTATTGAATAAAG
1 TTAGTTTATTGAATAAAG
993456 TTAGTTTATT-AATTAAA-
1 TTAGTTTATTGAA-TAAAG
*
993473 TTGGTTTATT
1 TTAGTTTATT
993483 CATCAAACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (18 bp):
TTAGTTTATTGAATAAAG
Found at i:996934 original size:17 final size:17
Alignment explanation
Indices: 996904--997034 Score: 122
Period size: 17 Copynumber: 7.7 Consensus size: 17
996894 AATTAAGAGT
* *
996904 TAGTCTAATAAATGAAC
1 TAGTTTAATGAATGAAC
*
996921 TAGTTTCATGAATGAAC
1 TAGTTTAATGAATGAAC
*
996938 TAGTTTAATTAATGAAC
1 TAGTTTAATGAATGAAC
* * *
996955 TAACTTTATTCAATGAAC
1 T-AGTTTAATGAATGAAC
*
996973 T--TGTAATTGAATGAAC
1 TAGTTTAA-TGAATGAAC
* * *
996989 TACTTTGATGAATGAAT
1 TAGTTTAATGAATGAAC
997006 TAGTTTAATGAATGAAC
1 TAGTTTAATGAATGAAC
*
997023 TAGTTCAATGAA
1 TAGTTTAATGAA
997035 CTACTTAGTT
Statistics
Matches: 92, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
15 3 0.03
16 9 0.10
17 63 0.68
18 17 0.18
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.37
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:997034 original size:34 final size:34
Alignment explanation
Indices: 996903--997051 Score: 101
Period size: 34 Copynumber: 4.4 Consensus size: 34
996893 CAATTAAGAG
* * *
996903 TTAGTCTAATAAATGAACTAGTTTC-ATGAATGAA
1 TTAGTTTAATGAATGAACTA-CTTCAATGAATGAA
* * * * *
996937 CTAGTTTAATTAATGAACTAACTTTATTCAATGAA
1 TTAGTTTAATGAATGAACT-ACTTCAATGAATGAA
**
996972 CTT-G--TAATTGAATGAACTACTTTGATGAATGAA
1 -TTAGTTTAA-TGAATGAACTACTTCAATGAATGAA
* *
997005 TTAGTTTAATGAATGAACTAGTTCAATGAACT-AC
1 TTAGTTTAATGAATGAACTACTTCAATGAA-TGAA
*
997039 TTAGTTAAATGAA
1 TTAGTTTAATGAA
997052 GTGCATAGCT
Statistics
Matches: 90, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
32 2 0.02
33 16 0.18
34 58 0.64
35 13 0.14
36 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (34 bp):
TTAGTTTAATGAATGAACTACTTCAATGAATGAA
Found at i:997101 original size:34 final size:34
Alignment explanation
Indices: 997029--997103 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
997019 GAACTAGTTC
* * *
997029 AATGAACTACTTAGTTAAATGAAGTGCATAGCTA
1 AATGAACTACATAGTTAAATGAAATGCAAAGCTA
*
997063 AATGAACTACAT-GTTTAAATGAAATG-AAAGCTTT
1 AATGAACTACATAG-TTAAATGAAATGCAAAGC-TA
997097 AATGAAC
1 AATGAAC
997104 AACACACTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
33 5 0.14
34 30 0.86
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (34 bp):
AATGAACTACATAGTTAAATGAAATGCAAAGCTA
Found at i:1000407 original size:17 final size:17
Alignment explanation
Indices: 1000369--1000446 Score: 66
Period size: 17 Copynumber: 4.5 Consensus size: 17
1000359 TGAAACAATT
* *
1000369 ATGAGCTAGTTTAACAA
1 ATGAACTAGTTTAATAA
* * *
1000386 TTGAACTAGTTTGATGA
1 ATGAACTAGTTTAATAA
*
1000403 ATGAACTATTTTAATAA
1 ATGAACTAGTTTAATAA
* * *
1000420 ATGAACTAACTTTATTCA
1 ATGAACT-AGTTTAATAA
1000438 ATGAACTAG
1 ATGAACTAG
1000447 ATGCATGAAT
Statistics
Matches: 47, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
17 33 0.70
18 14 0.30
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (17 bp):
ATGAACTAGTTTAATAA
Found at i:1002966 original size:14 final size:14
Alignment explanation
Indices: 1002947--1002975 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1002937 TACGAGTTAG
1002947 TTTAATAAATGAAC
1 TTTAATAAATGAAC
1002961 TTTAATAAATGAAC
1 TTTAATAAATGAAC
1002975 T
1 T
1002976 AGTTCGATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (14 bp):
TTTAATAAATGAAC
Found at i:1003005 original size:17 final size:17
Alignment explanation
Indices: 1002944--1003007 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 17
1002934 AATTACGAGT
1002944 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
1002961 ---TTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
** *
1002975 TAGTTCGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
1002992 TAGTTTAATTAATGAA
1 TAGTTTAATAAATGAA
1003008 TTAACTTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 14 0.37
17 24 0.63
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:1005960 original size:17 final size:18
Alignment explanation
Indices: 1005938--1006009 Score: 60
Period size: 17 Copynumber: 4.2 Consensus size: 18
1005928 AATTAAGAGT
1005938 TAGTTTTA-TAAATGAAC
1 TAGTTTTATTAAATGAAC
* *
1005955 TAGTTTGA-TGAATGAAC
1 TAGTTTTATTAAATGAAC
* *
1005972 TTGTTTAATTAAA-GAAC
1 TAGTTTTATTAAATGAAC
** *
1005989 TAACTTTATTCAATGAAC
1 TAGTTTTATTAAATGAAC
1006007 TAG
1 TAG
1006010 ATGCTTTAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
17 33 0.79
18 9 0.21
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (18 bp):
TAGTTTTATTAAATGAAC
Found at i:1012667 original size:40 final size:40
Alignment explanation
Indices: 1012622--1012697 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
1012612 ACCTAAGTAC
*
1012622 GACTAGACGTTCTCAACAAGAAGGAACAATGTCATCCCCA
1 GACTAGACCTTCTCAACAAGAAGGAACAATGTCATCCCCA
* *
1012662 GACTAGACCTTCTCAACACGAAGGAGCAATGTCATC
1 GACTAGACCTTCTCAACAAGAAGGAACAATGTCATC
1012698 TTTGGATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.18
Consensus pattern (40 bp):
GACTAGACCTTCTCAACAAGAAGGAACAATGTCATCCCCA
Found at i:1013235 original size:36 final size:39
Alignment explanation
Indices: 1013170--1013241 Score: 105
Period size: 36 Copynumber: 1.9 Consensus size: 39
1013160 ATCATTTCAT
* *
1013170 TTGAAACAAAAGTTTTATCTCACTTGAGAT-TATTTTCC
1 TTGAAACAAAAGTTTCATCTCACTCGAGATATATTTTCC
1013208 TTGAAAC-AAA-TTTCATCTCACTCGAGATATATTT
1 TTGAAACAAAAGTTTCATCTCACTCGAGATATATTT
1013242 CTCTGGAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 16 0.52
37 8 0.26
38 7 0.23
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (39 bp):
TTGAAACAAAAGTTTCATCTCACTCGAGATATATTTTCC
Found at i:1013251 original size:37 final size:37
Alignment explanation
Indices: 1013172--1013252 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 37
1013162 CATTTCATTT
* * *
1013172 GAAACAAAAGTTTTATCTCACTTGAGATTATTTTCCTT
1 GAAAC-AAAGTTTCATCTCACTCGAGATTATTTTCCTG
1013210 GAAACAAA-TTTCATCTCACTCGAGA-TATATTTCTCTG
1 GAAACAAAGTTTCATCTCACTCGAGATTAT-TTTC-CTG
1013247 GAAACA
1 GAAACA
1013253 CAACTTTAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
35 3 0.08
36 19 0.50
37 11 0.29
38 5 0.13
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.36
Consensus pattern (37 bp):
GAAACAAAGTTTCATCTCACTCGAGATTATTTTCCTG
Found at i:1015170 original size:42 final size:43
Alignment explanation
Indices: 1015123--1015250 Score: 150
Period size: 42 Copynumber: 3.0 Consensus size: 43
1015113 AATTTGGAAC
* *
1015123 TTTGTTGTTCTTCTGGGGAAAGTGGATGAATCATATTTG-GGG
1 TTTGTTGTTCTTCTGGGGAAAGTGGATGAATCAAATTTGAAGG
* * **
1015165 TTTGTTGTTCTTATGGGGAAAGTGGATGAATCACAAGTTGACATT
1 TTTGTTGTTCTTCTGGGGAAAGTGGATGAATCA-AATTTGA-AGG
* * *
1015210 TTTCTTGTTCTTCTAGGGAAAGTGGATGAATCACATTTGAA
1 TTTGTTGTTCTTCTGGGGAAAGTGGATGAATCAAATTTGAA
1015251 TGCAAAACAT
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
42 32 0.44
43 5 0.07
44 5 0.07
45 30 0.42
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.39
Consensus pattern (43 bp):
TTTGTTGTTCTTCTGGGGAAAGTGGATGAATCAAATTTGAAGG
Found at i:1015233 original size:45 final size:43
Alignment explanation
Indices: 1015127--1015244 Score: 139
Period size: 45 Copynumber: 2.7 Consensus size: 43
1015117 TGGAACTTTG
* * * *
1015127 TTGTTCTTCTGGGGAAAGTGGATGAATCA-TATTTGGGGTTTG
1 TTGTTCTTCTGGGGAAAGTGGATGAATCACAAGTTGAGGTTTC
* **
1015169 TTGTTCTTATGGGGAAAGTGGATGAATCACAAGTTGACATTTTTC
1 TTGTTCTTCTGGGGAAAGTGGATGAATCACAAGTTG--AGGTTTC
*
1015214 TTGTTCTTCTAGGGAAAGTGGATGAATCACA
1 TTGTTCTTCTGGGGAAAGTGGATGAATCACA
1015245 TTTGAATGCA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 28 0.44
43 4 0.06
45 32 0.50
ACGTcount: A:0.25, C:0.10, G:0.28, T:0.37
Consensus pattern (43 bp):
TTGTTCTTCTGGGGAAAGTGGATGAATCACAAGTTGAGGTTTC
Found at i:1017514 original size:2 final size:2
Alignment explanation
Indices: 1017507--1017551 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1017497 TTGTAACTTT
1017507 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1017549 TA T
1 TA T
1017552 TCCATCTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1021624 original size:22 final size:22
Alignment explanation
Indices: 1021593--1021638 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1021583 TTTTGTTTTA
*
1021593 TTTTAGTTTAGTCACTATTAGTT
1 TTTTAGTTTAGCCACTATTA-TT
*
1021616 TTTTA-TTTAGCCACTGTTATT
1 TTTTAGTTTAGCCACTATTATT
1021637 TT
1 TT
1021639 AATTTTTGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 12 0.57
23 5 0.24
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.59
Consensus pattern (22 bp):
TTTTAGTTTAGCCACTATTATT
Found at i:1021984 original size:36 final size:34
Alignment explanation
Indices: 1021942--1022012 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 34
1021932 ATTTGATCCA
*
1021942 TGAATTTTAATTCTTTCCAATTTAATTTTTTTAATT
1 TGAATTTTAATTCATTCC--TTTAATTTTTTTAATT
** *
1021978 TGAATTTTCTTTCATTCCTTTTATTTTTTTAATT
1 TGAATTTTAATTCATTCCTTTAATTTTTTTAATT
1022012 T
1 T
1022013 TTATTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 16 0.52
36 15 0.48
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.65
Consensus pattern (34 bp):
TGAATTTTAATTCATTCCTTTAATTTTTTTAATT
Found at i:1024055 original size:43 final size:43
Alignment explanation
Indices: 1024000--1024087 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
1023990 GTAGGACTAA
* *
1024000 GCCTGCGAGGATGATCTAAGAAAAGAGTCCTCATATCCTAAGG
1 GCCTGCCAGGATGATCTAAGAAAAGAGTCCCCATATCCTAAGG
1024043 GCCTGCCAGGATGATCTAAGAAAAGAGTCCCCATATCCTAAGG
1 GCCTGCCAGGATGATCTAAGAAAAGAGTCCCCATATCCTAAGG
1024086 GC
1 GC
1024088 TACGATGTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (43 bp):
GCCTGCCAGGATGATCTAAGAAAAGAGTCCCCATATCCTAAGG
Found at i:1025070 original size:12 final size:12
Alignment explanation
Indices: 1025055--1025112 Score: 55
Period size: 12 Copynumber: 4.6 Consensus size: 12
1025045 TGAAGAAAAG
1025055 AAAAAAAAGAGA
1 AAAAAAAAGAGA
*
1025067 AAAACAAAGA-A
1 AAAAAAAAGAGA
*
1025078 AAAAGCAAAGAGAA
1 AAAA-AAAAGAG-A
1025092 AATAAAAAAGAGA
1 AA-AAAAAAGAGA
1025105 AACAAAAA
1 AA-AAAAA
1025113 CAAAGGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
11 5 0.13
12 15 0.38
13 8 0.21
14 9 0.23
15 2 0.05
ACGTcount: A:0.79, C:0.05, G:0.14, T:0.02
Consensus pattern (12 bp):
AAAAAAAAGAGA
Found at i:1025112 original size:19 final size:18
Alignment explanation
Indices: 1025057--1025112 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 18
1025047 AAGAAAAGAA
1025057 AAAAAAGAGAAAAACAAAG
1 AAAAAAGAGAAAAA-AAAG
* *
1025076 AAAAAAGCA-AAGAGAAAAT
1 AAAAAAG-AGAA-AAAAAAG
1025095 AAAAAAGAGAAACAAAAA
1 AAAAAAGAGAAA-AAAAA
1025113 CAAAGGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
18 2 0.07
19 25 0.83
20 3 0.10
ACGTcount: A:0.79, C:0.05, G:0.14, T:0.02
Consensus pattern (18 bp):
AAAAAAGAGAAAAAAAAG
Found at i:1026260 original size:31 final size:32
Alignment explanation
Indices: 1026213--1026279 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
1026203 ATCTTTGAAT
*
1026213 CATCAAATGTTGGGGCATCTTTGGAGATT-AA
1 CATCAAATATTGGGGCATCTTTGGAGATTCAA
* *
1026244 CATCGAATATTGGGGCATCTTTGGGGATTCAA
1 CATCAAATATTGGGGCATCTTTGGAGATTCAA
1026276 CATC
1 CATC
1026280 CATATGTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 26 0.81
32 6 0.19
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.31
Consensus pattern (32 bp):
CATCAAATATTGGGGCATCTTTGGAGATTCAA
Found at i:1027103 original size:61 final size:61
Alignment explanation
Indices: 1026941--1027116 Score: 201
Period size: 65 Copynumber: 2.8 Consensus size: 61
1026931 GACGCAACTT
* * *
1026941 ACAAAAGA-TTGAATTTCAACTTTACAACGAAGGATATCCAACTTAAAGCCAATTCAGTCAA
1 ACAAAAGATTTG-ATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCTAATTCAGTCAA
* * * ** *
1027002 ACTTACTCAATATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCTAATTTGGTGAA
1 AC--A--AAAGATTTGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCTAATTCAGTCAA
* *
1027067 ACAAAAGATTTGATTTCAACTTGACAACGAAGGATATCCAATTCAAAGCT
1 ACAAAAGATTTGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCT
1027117 CAACTTCTCA
Statistics
Matches: 96, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
61 44 0.46
63 2 0.02
65 48 0.50
66 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (61 bp):
ACAAAAGATTTGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCTAATTCAGTCAA
Found at i:1027387 original size:85 final size:85
Alignment explanation
Indices: 1027244--1027651 Score: 446
Period size: 85 Copynumber: 4.8 Consensus size: 85
1027234 TCCCAGCCTA
* * *
1027244 TTACAACATAGCTCAAGGCGAGAAGGGCTATATGTAAACAAAGACCTTCAAGTTCGATTACATTC
1 TTACAACATAGCTCAAGACGAGAAGGGCTATCTGTCAACAAAGACCTTCAAGTTCGATTACATTC
1027309 AGCTCAAAGGCATATCAAAT
66 AGCTCAAAGGCATATCAAAT
* * * * *
1027329 TTACATCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTC
1 TTACAACATAGCTCAAGACGAGAAGGGCTATCTGTCAACAAAGACCTTCAAGTTCGATTACATTC
*
1027394 ATCT-AAGAGGCATATCAAAT
66 AGCTCAA-AGGCATATCAAAT
* * * * *
1027414 TTACAACATAACTCAAGACGAGAAGGGTTATCTGTCAATAAATACCTTCAAGTTCGGTTACATTC
1 TTACAACATAGCTCAAGACGAGAAGGGCTATCTGTCAACAAAGACCTTCAAGTTCGATTACATTC
1027479 AGCTCAAAGGCATATCAAAT
66 AGCTCAAAGGCATATCAAAT
** * * * * * *
1027499 TTACAGTATAGCTCAAGACAAGAAGGGCCAACTATCAACAAATACCTTCGAGTTCGATT-CTATT
1 TTACAACATAGCTCAAGACGAGAAGGGCTATCTGTCAACAAAGACCTTCAAGTTCGATTAC-ATT
* *
1027563 CAGCTCAAGGGCATGTCAAAT
65 CAGCTCAAAGGCATATCAAAT
* * * * *** * * * *
1027584 TTACAGCATAACTTAAGTCGAGAAAATCTATCTGT-AA-AAAAAACTGTCGAGTTCGATTCCATT
1 TTACAACATAGCTCAAGACGAGAAGGGCTATCTGTCAACAAAGACCT-TCAAGTTCGATTACATT
1027647 CAGCT
65 CAGCT
1027652 TGATGACATA
Statistics
Matches: 276, Mismatches: 42, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
83 6 0.02
84 25 0.09
85 243 0.88
86 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (85 bp):
TTACAACATAGCTCAAGACGAGAAGGGCTATCTGTCAACAAAGACCTTCAAGTTCGATTACATTC
AGCTCAAAGGCATATCAAAT
Found at i:1027548 original size:170 final size:170
Alignment explanation
Indices: 1027244--1027651 Score: 493
Period size: 170 Copynumber: 2.4 Consensus size: 170
1027234 TCCCAGCCTA
* *
1027244 TTACAACATAGCTCAAGGCGAGAAGGGCTATATGTAAACAAAGACCTTCAAGTTCGATTACATTC
1 TTACAACATAACTCAAGACGAGAAGGGCTATATGTAAACAAAGACCTTCAAGTTCGATTACATTC
* * ** * * *
1027309 AGCTCAAAGGCATATCAAATTTACATCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGAC
66 AGCTCAAAGGCATATCAAATTTACATCATAGCTCAAGACAAGAAGGGCCAACTATCAACAAAGAC
*
1027374 CTTCGAGTTCGATTAC-ATTCATCT-AAGAGGCATATCAAAT
131 CTTCGAGTTCGATT-CTATTCAGCTCAAG-GGCATATCAAAT
* * * * * *
1027414 TTACAACATAACTCAAGACGAGAAGGGTTATCTGTCAATAAATACCTTCAAGTTCGGTTACATTC
1 TTACAACATAACTCAAGACGAGAAGGGCTATATGTAAACAAAGACCTTCAAGTTCGATTACATTC
*
1027479 AGCTCAAAGGCATATCAAATTTACAGT-ATAGCTCAAGACAAGAAGGGCCAACTATCAACAAATA
66 AGCTCAAAGGCATATCAAATTTACA-TCATAGCTCAAGACAAGAAGGGCCAACTATCAACAAAGA
*
1027543 CCTTCGAGTTCGATTCTATTCAGCTCAAGGGCATGTCAAAT
130 CCTTCGAGTTCGATTCTATTCAGCTCAAGGGCATATCAAAT
* * * *** * * * *
1027584 TTACAGCATAACTTAAGTCGAGAAAATCTATCTGTAAA-AAA-AACTGTCGAGTTCGATTCCATT
1 TTACAACATAACTCAAGACGAGAAGGGCTATATGTAAACAAAGACCT-TCAAGTTCGATTACATT
1027647 CAGCT
65 CAGCT
1027652 TGATGACATA
Statistics
Matches: 204, Mismatches: 30, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
168 3 0.01
169 23 0.11
170 174 0.85
171 4 0.02
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (170 bp):
TTACAACATAACTCAAGACGAGAAGGGCTATATGTAAACAAAGACCTTCAAGTTCGATTACATTC
AGCTCAAAGGCATATCAAATTTACATCATAGCTCAAGACAAGAAGGGCCAACTATCAACAAAGAC
CTTCGAGTTCGATTCTATTCAGCTCAAGGGCATATCAAAT
Found at i:1029273 original size:11 final size:11
Alignment explanation
Indices: 1029257--1029301 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
1029247 GGACCATTCG
1029257 TTTTTATTTTA
1 TTTTTATTTTA
1029268 TTTTTATTTTA
1 TTTTTATTTTA
*
1029279 TTATTCATTTT-
1 TT-TTTATTTTA
1029290 TGTTTTATTTTA
1 T-TTTTATTTTA
1029302 GTTAAGTCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 21 0.72
12 8 0.28
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:1029290 original size:18 final size:16
Alignment explanation
Indices: 1029258--1029301 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 16
1029248 GACCATTCGT
1029258 TTTTATTTTATTTTTA
1 TTTTATTTTATTTTTA
*
1029274 TTTTATTATTCATTTTTG
1 TTTTATT-TT-ATTTTTA
1029292 TTTTATTTTA
1 TTTTATTTTA
1029302 GTTAAGTCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 8 0.32
17 4 0.16
18 13 0.52
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTTATTTTATTTTTA
Found at i:1029558 original size:30 final size:31
Alignment explanation
Indices: 1029524--1029605 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 31
1029514 TTTGTTAATA
1029524 CTATTTTAATCCTTTAAATTTCTA-TCTGTG
1 CTATTTTAATCCTTTAAATTTCTATTCTGTG
** * * *
1029554 CTATTTTGGTACTTTAAA-TTCTATTTTTTG
1 CTATTTTAATCCTTTAAATTTCTATTCTGTG
* *
1029584 CTA-TTTAATCCCTTAAGTTTCT
1 CTATTTTAATCCTTTAAATTTCT
1029606 GTTTTTCTCA
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
29 14 0.35
30 26 0.65
ACGTcount: A:0.22, C:0.16, G:0.07, T:0.55
Consensus pattern (31 bp):
CTATTTTAATCCTTTAAATTTCTATTCTGTG
Found at i:1029724 original size:17 final size:17
Alignment explanation
Indices: 1029673--1029733 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
1029663 CAATTTAATC
**
1029673 TTTTTTTAATTTGATT-
1 TTTTTTTAATTTTTTTA
* *
1029689 TTTCTTTCATTTCTTTTA
1 TTTTTTTAATTT-TTTTA
1029707 TTTTTTTAATTTTTTTA
1 TTTTTTTAATTTTTTTA
1029724 TTTTTTTAAT
1 TTTTTTTAAT
1029734 ACTAACTCTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
16 10 0.27
17 17 0.46
18 10 0.27
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTTTTAATTTTTTTA
Found at i:1029730 original size:8 final size:8
Alignment explanation
Indices: 1029697--1029731 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
1029687 TTTTTCTTTC
1029697 ATTTCTTTT
1 ATTT-TTTT
1029706 ATTTTTTT
1 ATTTTTTT
1029714 AATTTTTTT
1 -ATTTTTTT
1029723 ATTTTTTT
1 ATTTTTTT
1029731 A
1 A
1029732 ATACTAACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 13 0.52
9 12 0.48
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (8 bp):
ATTTTTTT
Found at i:1031819 original size:29 final size:31
Alignment explanation
Indices: 1031787--1031856 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 31
1031777 TATTTATACT
1031787 TTATACCACTGAACTTTTA-ATTT-TATCAA
1 TTATACCACTGAACTTTTATATTTGTATCAA
* * * *
1031816 TTATAGCACTGAATTTTTATTTTTGTTTCAA
1 TTATACCACTGAACTTTTATATTTGTATCAA
1031847 TTATACCACT
1 TTATACCACT
1031857 AGATCGTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 17 0.50
30 3 0.09
31 14 0.41
ACGTcount: A:0.30, C:0.16, G:0.06, T:0.49
Consensus pattern (31 bp):
TTATACCACTGAACTTTTATATTTGTATCAA
Found at i:1032263 original size:33 final size:33
Alignment explanation
Indices: 1032221--1032322 Score: 177
Period size: 33 Copynumber: 3.1 Consensus size: 33
1032211 ATGTATAAGT
*
1032221 TTTCCCCTTTTTCTCGTTGTACTGTACAAATAA
1 TTTCCCCTTTTTCTTGTTGTACTGTACAAATAA
*
1032254 TTTCCCCTTTTTCTTTTTGTACTGTACAAATAA
1 TTTCCCCTTTTTCTTGTTGTACTGTACAAATAA
*
1032287 TTTCCCCTTTTTCTTGTTGCACTGTACAAATAA
1 TTTCCCCTTTTTCTTGTTGTACTGTACAAATAA
1032320 TTT
1 TTT
1032323 TCCGCCCCGT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 65 1.00
ACGTcount: A:0.21, C:0.23, G:0.08, T:0.49
Consensus pattern (33 bp):
TTTCCCCTTTTTCTTGTTGTACTGTACAAATAA
Found at i:1033272 original size:13 final size:13
Alignment explanation
Indices: 1033254--1033279 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1033244 AAGTATATGA
1033254 CATATGGATTGAT
1 CATATGGATTGAT
1033267 CATATGGATTGAT
1 CATATGGATTGAT
1033280 GATTGATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
CATATGGATTGAT
Found at i:1037171 original size:31 final size:31
Alignment explanation
Indices: 1037135--1037212 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
1037125 TAAGTTATAT
*
1037135 ATTTAATACTTAAATTATTAATTTTATTTTA
1 ATTTAATACTTAAATTATTAATTTTATCTTA
* *
1037166 ATTTAATACGTAAACTATTAATTTTATCTTA
1 ATTTAATACTTAAATTATTAATTTTATCTTA
* * *
1037197 TTTTAGTATTTAAATT
1 ATTTAATACTTAAATT
1037213 TTCATTTGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (31 bp):
ATTTAATACTTAAATTATTAATTTTATCTTA
Found at i:1043431 original size:22 final size:21
Alignment explanation
Indices: 1043392--1043440 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
1043382 AATATTATAA
* *
1043392 TAAAAAATAAATTTAAAACTAT
1 TAAAATATAAATTAAAAAC-AT
* *
1043414 TAAAATATACATTAAAAACCT
1 TAAAATATAAATTAAAAACAT
1043435 TAAAAT
1 TAAAAT
1043441 TAATATTCTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAAATATAAATTAAAAACAT
Found at i:1045334 original size:4 final size:4
Alignment explanation
Indices: 1045211--1045317 Score: 214
Period size: 4 Copynumber: 26.8 Consensus size: 4
1045201 TTATTATATA
1045211 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1045259 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1045307 TATG TATG TAT
1 TATG TATG TAT
1045318 ATATATTTTG
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 103 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:1051303 original size:83 final size:84
Alignment explanation
Indices: 1051174--1051388 Score: 222
Period size: 83 Copynumber: 2.5 Consensus size: 84
1051164 AAAAGAGAAT
* * * * *
1051174 ATCAATCATTGATTAC-AACCTGGTGTCATTTAGAGAAAGAATCAAGAACATTCTTCAATTTGGC
1 ATCAACCATTGATTACGAA-TTGGTGTC-TTTAGAGAAATAAGCAAGAACATTCTCCAATTTGGC
*
1051238 ATCCTTTAGAGA-AATGACCAA
64 ATCCTTAAGAGATAA-GACCAA
* *
1051259 AT-AACCATTG-TTACGAATTGGTGTCTTTAAGAGAAATAAGCAAGACCATTCTCCGATTTGGCA
1 ATCAACCATTGATTACGAATTGGTGTCTTT-AGAGAAATAAGCAAGAACATTCTCCAATTTGGCA
* * *
1051322 TCCTTAATAGATAAGAGCAT
65 TCCTTAAGAGATAAGACCAA
* * * *
1051342 ATCAACCATTGATTATGACTTGGTATCTTTTAGAGAAATGAGCAAGA
1 ATCAACCATTGATTACGAATTGGTGTC-TTTAGAGAAATAAGCAAGA
1051389 TCGTTCTTTG
Statistics
Matches: 109, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
82 3 0.03
83 55 0.50
84 19 0.17
85 29 0.27
86 3 0.03
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (84 bp):
ATCAACCATTGATTACGAATTGGTGTCTTTAGAGAAATAAGCAAGAACATTCTCCAATTTGGCAT
CCTTAAGAGATAAGACCAA
Found at i:1051402 original size:85 final size:85
Alignment explanation
Indices: 1050848--1051395 Score: 369
Period size: 85 Copynumber: 6.5 Consensus size: 85
1050838 TTCATTTATC
* * * ** * * * *
1050848 ACGACTTGGCGTCCTTCAGAGAAA-GAAGCAAGATTGTTCCCCGATTTGGCGTCCTTCAAAGAAA
1 ACGACTTGGTGTCTTTTAGAGAAATG-AGCAAGACCGTTCTCCGATTTGGCATCCTTTATAGAAA
*
1050912 GGAG-AAGATCAACCATTGATT
65 AGAGCAA-ATCAACCATTGATT
* ** * * * * * *
1050933 ACGATTTGGAATCCTTTAAAGAAAGGAGAAAGACCGTTC-CTCGATTTGGCATCCTATAGAGAAA
1 ACGACTTGGTGTCTTTTAGAGAAATGAGCAAGACCGTTCTC-CGATTTGGCATCCTTTATAGAAA
* * *
1050997 GGAACAAATCAACCACTGATT
65 AGAGCAAATCAACCATTGATT
* * * * * * * * * * *
1051018 ATGACTTCGCGTCCTTCAGAGAAAGGAGCAAGATCTTTC-CCTGATTTGGCGTTCTTTAGAGAAA
1 ACGACTTGGTGTCTTTTAGAGAAATGAGCAAGACCGTTCTCC-GATTTGGCATCCTTTATAGAAA
** *
1051082 AGATTAGATCAACCATTGATT
65 AGAGCAAATCAACCATTGATT
* ** * * * *
1051103 ACTACTTGACGTCTTTTAGAG-GATGGAGTAAGACCGTTATCCGATTTGGCAT-CTATCATAGAA
1 ACGACTTGGTGTCTTTTAGAGAAAT-GAGCAAGACCGTTCTCCGATTTGGCATCCT-TTATAGAA
*
1051166 AAGAG-AATATCAATCATTGATT
64 AAGAGCAA-ATCAACCATTGATT
* * * * * * * * *
1051188 ACAACCTGGTGTCATTTAGAGAAA-GAATCAAGAACATTCTTCAATTTGGCATCCTTTAGAGAAA
1 ACGACTTGGTGTCTTTTAGAGAAATG-AGCAAGACCGTTCTCCGATTTGGCATCCTTTATAGAAA
* *
1051252 TGACCAAAT-AACCATTG-TT
65 AGAGCAAATCAACCATTGATT
* * * * * *
1051271 ACGAATTGGTGTCTTTAAGAGAAATAAGCAAGACCATTCTCCGATTTGGCATCCTTAATAGATAA
1 ACGACTTGGTGTCTTTTAGAGAAATGAGCAAGACCGTTCTCCGATTTGGCATCCTTTATAGAAAA
*
1051336 GAGCATATCAACCATTGATT
66 GAGCAAATCAACCATTGATT
* * *
1051356 ATGACTTGGTATCTTTTAGAGAAATGAGCAAGATCGTTCT
1 ACGACTTGGTGTCTTTTAGAGAAATGAGCAAGACCGTTCT
1051396 TTGATTTAGT
Statistics
Matches: 357, Mismatches: 91, Indels: 30
0.75 0.19 0.06
Matches are distributed among these distances:
83 58 0.16
84 22 0.06
85 267 0.75
86 10 0.03
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (85 bp):
ACGACTTGGTGTCTTTTAGAGAAATGAGCAAGACCGTTCTCCGATTTGGCATCCTTTATAGAAAA
GAGCAAATCAACCATTGATT
Found at i:1052792 original size:24 final size:23
Alignment explanation
Indices: 1052765--1052812 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1052755 AAAATTTTAG
*
1052765 TGTAATTTAAATTCTCTTTGTTTT
1 TGTAAATT-AATTCTCTTTGTTTT
* *
1052789 TGTAAATTAATTTTTTTTGTTTT
1 TGTAAATTAATTCTCTTTGTTTT
1052812 T
1 T
1052813 ATTCTTTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.21, C:0.04, G:0.08, T:0.67
Consensus pattern (23 bp):
TGTAAATTAATTCTCTTTGTTTT
Found at i:1055696 original size:12 final size:12
Alignment explanation
Indices: 1055681--1055716 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1055671 ATTAGTTTAA
1055681 ATATTATATTAT
1 ATATTATATTAT
1055693 ATATTATATTAT
1 ATATTATATTAT
* *
1055705 ATTTTCTATTAT
1 ATATTATATTAT
1055717 CTTTGTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (12 bp):
ATATTATATTAT
Found at i:1055919 original size:21 final size:22
Alignment explanation
Indices: 1055893--1055934 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1055883 AGTTTTAATA
* *
1055893 AAAGTT-TTTCTTTTCTTTTTC
1 AAAGTTCTTTATTTTATTTTTC
1055914 AAAGTTCTTTATTTTATTTTT
1 AAAGTTCTTTATTTTATTTTT
1055935 ATTTTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.19, C:0.10, G:0.05, T:0.67
Consensus pattern (22 bp):
AAAGTTCTTTATTTTATTTTTC
Found at i:1060825 original size:27 final size:27
Alignment explanation
Indices: 1060792--1060849 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
1060782 ATGGTTAATT
*
1060792 ATTTGTCCATATGTAAGTTACCATTAG
1 ATTTGTCCACATGTAAGTTACCATTAG
*
1060819 ATTTGTCCACATGTAAGTTACCATTTG
1 ATTTGTCCACATGTAAGTTACCATTAG
1060846 ATTT
1 ATTT
1060850 TTTGAGAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (27 bp):
ATTTGTCCACATGTAAGTTACCATTAG
Found at i:1065156 original size:25 final size:25
Alignment explanation
Indices: 1065113--1065176 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
1065103 ACAGTGCCAC
* *
1065113 GTAGAATATACACATGAATGTACCAA
1 GTAGAAT-TGCACACGAATGTACCAA
** *
1065139 GTAGAATTGCACACGAATGTGTCAT
1 GTAGAATTGCACACGAATGTACCAA
*
1065164 GTAGATTTGCACA
1 GTAGAATTGCACA
1065177 TATAATACTC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 25 0.78
26 7 0.22
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (25 bp):
GTAGAATTGCACACGAATGTACCAA
Found at i:1068464 original size:8 final size:9
Alignment explanation
Indices: 1068443--1068475 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1068433 CGTGTTAGTA
1068443 AAAAAATTC
1 AAAAAATTC
1068452 AAAAAATTC
1 AAAAAATTC
*
1068461 AAAAAATAC
1 AAAAAATTC
1068470 AAAAAA
1 AAAAAA
1068476 AAAATTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAAAATTC
Found at i:1072047 original size:81 final size:81
Alignment explanation
Indices: 1071952--1072129 Score: 266
Period size: 81 Copynumber: 2.2 Consensus size: 81
1071942 ACAAAAAGGG
* * *
1071952 TAATTGACACATTTCTGTCAAATGCACGACTAGGCCATTAATTTTTTACTCAAAGGTATTTAACC
1 TAATTGACACATTTCTGTCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGATATTTAACC
1072017 TTTCATATAAATGTCA
66 TTTCATATAAATGTCA
* * * *
1072033 TAATTGACATATTTCTGTTAAATGCACAACTAGGTCATTAATCTTTTACTCAATGATATTTAACC
1 TAATTGACACATTTCTGTCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGATATTTAACC
* *
1072098 TTTCATCTAACTGTCA
66 TTTCATATAAATGTCA
*
1072114 TAATTGACACCTTTCT
1 TAATTGACACATTTCT
1072130 ATCAGATAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 86 1.00
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (81 bp):
TAATTGACACATTTCTGTCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGATATTTAACC
TTTCATATAAATGTCA
Found at i:1072147 original size:81 final size:81
Alignment explanation
Indices: 1071952--1072163 Score: 226
Period size: 81 Copynumber: 2.6 Consensus size: 81
1071942 ACAAAAAGGG
* ** * * *
1071952 TAATTGACACATTTCTGTCAAATGCACGACTAGGCCATTAATTTTTTACTCAAAGGTATTTAACC
1 TAATTGACACATTTCTATCAAATAAACAACTAGGCCATTAATCTTTTACTCAAAGATATTTAACC
1072017 TTTCATATAAATGTCA
66 TTTCATATAAATGTCA
* * * ** * *
1072033 TAATTGACATATTTCTGTTAAATGCACAACTAGGTCATTAATCTTTTACTCAATGATATTTAACC
1 TAATTGACACATTTCTATCAAATAAACAACTAGGCCATTAATCTTTTACTCAAAGATATTTAACC
* *
1072098 TTTCATCTAACTGTCA
66 TTTCATATAAATGTCA
* * * * ** *
1072114 TAATTGACACCTTTCTATCAGATAAAGAGCTAGGCTTTTAGTCTTTTACT
1 TAATTGACACATTTCTATCAAATAAACAACTAGGCCATTAATCTTTTACT
1072164 TTAGAACAAT
Statistics
Matches: 109, Mismatches: 22, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
81 109 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (81 bp):
TAATTGACACATTTCTATCAAATAAACAACTAGGCCATTAATCTTTTACTCAAAGATATTTAACC
TTTCATATAAATGTCA
Found at i:1073384 original size:14 final size:15
Alignment explanation
Indices: 1073360--1073392 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1073350 AATTTTGTGT
1073360 TTTTCCCCTTTCCCC
1 TTTTCCCCTTTCCCC
*
1073375 TTTT-CCCTTTTCCC
1 TTTTCCCCTTTCCCC
1073389 TTTT
1 TTTT
1073393 TTCCTATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTCCCCTTTCCCC
Found at i:1073393 original size:15 final size:15
Alignment explanation
Indices: 1073359--1073393 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1073349 AAATTTTGTG
1073359 TTTTTCCCCTTTCCC
1 TTTTTCCCCTTTCCC
* *
1073374 CTTTTCCCTTTTCCC
1 TTTTTCCCCTTTCCC
1073389 TTTTT
1 TTTTT
1073394 TCCTATACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTCCCCTTTCCC
Found at i:1074948 original size:12 final size:12
Alignment explanation
Indices: 1074926--1074964 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1074916 ATCAATGCCT
1074926 TTTTGGCATTACA
1 TTTT-GCATTACA
1074939 TTTTGCATTACA
1 TTTTGCATTACA
**
1074951 CATTGCATTACA
1 TTTTGCATTACA
1074963 TT
1 TT
1074965 CATATTTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (12 bp):
TTTTGCATTACA
Found at i:1077524 original size:125 final size:125
Alignment explanation
Indices: 1077374--1077653 Score: 332
Period size: 125 Copynumber: 2.2 Consensus size: 125
1077364 GTTCCCTGAT
* * * *
1077374 TTGACA-CTCTTCAGAGAAATGAGCAAGATCATTCCCCAATTTGGTGTCCTTCAAAGGAATGAGA
1 TTGACATC-CTTCAGAGAAAGGAGCAAGATCATTCCCCAATTTGGCGTCCTTCAAAGAAAGGAGA
* * * *
1077438 AAAATCATTATTTGATTTGACATCATTTAGAGAAAGGATCAG-ATCAACCATTGATTATGAC
65 AAAACCATTATTTGATTTGACATCATTCAGAGAAAGGAAC-GTATCAACCATTGATTAGGAC
* * * ** *
1077499 TTGGCATCCTTTAGAGAAAGGAGCAAGATCATTCTCTGATTTGGCGTCCTTCAGAGAAAGGAGAA
1 TTGACATCCTTCAGAGAAAGGAGCAAGATCATTCCCCAATTTGGCGTCCTTCAAAGAAAGGAGAA
* * ***
1077564 ATACCATTCTTTGATTTGGTGTCATTCAGAGAAAGGAACGTATCAACCATTGATTAGGAC
66 AAACCATTATTTGATTTGACATCATTCAGAGAAAGGAACGTATCAACCATTGATTAGGAC
* *
1077624 TTGACGTCCTTCAGAGAAAGAAG-AAGATCA
1 TTGACATCCTTCAGAGAAAGGAGCAAGATCA
1077654 ACCATTGATT
Statistics
Matches: 130, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
124 8 0.06
125 121 0.93
126 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (125 bp):
TTGACATCCTTCAGAGAAAGGAGCAAGATCATTCCCCAATTTGGCGTCCTTCAAAGAAAGGAGAA
AAACCATTATTTGATTTGACATCATTCAGAGAAAGGAACGTATCAACCATTGATTAGGAC
Found at i:1077541 original size:85 final size:84
Alignment explanation
Indices: 1077441--1077931 Score: 304
Period size: 85 Copynumber: 5.8 Consensus size: 84
1077431 AATGAGAAAA
* * * *
1077441 ATCATTATTTGATTTGACATCATTTAGAGAAAGGATCAGATCAACCATTGATTATGACTTGGCAT
1 ATCATTCTTTGATTTGGCATCCTTCAGAGAAAGGAT-AGATCAACCATTGATTATGACTTGGCAT
*
1077506 CCTTTAGAGAAAGGAGCAAG
65 CCTTCAGAGAAAGGAGCAAG
* * * * * * **
1077526 ATCATTCTCTGATTTGGCGTCCTTCAGAGAAAGGAGAAAT--ACCATT-CTT-TGATTTGGTGTC
1 ATCATTCTTTGATTTGGCATCCTTCAGAGAAAGGATAGATCAACCATTGATTATGACTTGGCATC
* *
1077587 ATTCAGAGAAAGGA--ACG
66 CTTCAGAGAAAGGAGCAAG
** * *
1077604 TATCAACCATTGATTAGGACTTGACGTCCTTCAGAGAAAGAAGA-AGATCAACCATTGATTACT-
1 -ATCATTCTTTGATTTGG-C---A--TCCTTCAGAGAAAG--GATAGATCAACCATTGATTA-TG
* * *
1077667 ACTTAGCGTCCTTCAGACAATA--ACGCAAG
56 ACTTGGCATCCTTCAGAGAA-AGGA-GCAAG
* * * * * * * *
1077696 ATCGTTCTCTGATTTGGCATTCTTCAGAGAAATGAGTAGATCAACAATTGATTA-CAATATGTCA
1 ATCATTCTTTGATTTGGCATCCTTCAGAGAAAGGA-TAGATCAACCATTGATTATGACT-TGGCA
* *
1077760 TCCTTAAGAGAAAGGATCAAG
64 TCCTTCAGAGAAAGGAGCAAG
* * ** * * * **
1077781 ATCA-TCTTTGATTTGGCATCCTTCATAGATAGGGGCATATCAACTATTGATTACGACTTGGTGT
1 ATCATTCTTTGATTTGGCATCCTTCAGAGA-AAGGATAGATCAACCATTGATTATGACTTGGCAT
* *
1077845 CCTTTAGAGAAAAGAGCAAG
65 CCTTCAGAGAAAGGAGCAAG
* * * * * *
1077865 ATCGTTCTTTGATTTGGCATACTTTAGAGAAATGAGTAGATCAACTATTGATGATGACTTGGCAT
1 ATCATTCTTTGATTTGGCATCCTTCAGAGAAAGGA-TAGATCAACCATTGATTATGACTTGGCAT
1077930 CC
65 CC
1077932 CCATTCTAAG
Statistics
Matches: 302, Mismatches: 76, Indels: 56
0.70 0.18 0.13
Matches are distributed among these distances:
78 2 0.01
79 12 0.04
80 22 0.07
81 2 0.01
82 6 0.02
83 2 0.01
84 68 0.23
85 141 0.47
86 4 0.01
87 3 0.01
88 6 0.02
89 3 0.01
90 16 0.05
91 13 0.04
92 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Consensus pattern (84 bp):
ATCATTCTTTGATTTGGCATCCTTCAGAGAAAGGATAGATCAACCATTGATTATGACTTGGCATC
CTTCAGAGAAAGGAGCAAG
Found at i:1077555 original size:40 final size:40
Alignment explanation
Indices: 1077346--1077600 Score: 136
Period size: 40 Copynumber: 6.2 Consensus size: 40
1077336 ATCATTCTTT
** * * *
1077346 AGAGAAAGGAGCAAGATTGTTCCCTGATTTGAC-ACTCTTC
1 AGAGAAAGGAGCAAGATCATTCTCTGATTTGGCGTC-CTTC
* * ** *
1077386 AGAGAAATGAGCAAGATCATTCCCCAATTTGGTGTCCTTC
1 AGAGAAAGGAGCAAGATCATTCTCTGATTTGGCGTCCTTC
* * * * * * * * * * *
1077426 AAAGGAATGAGAAAAATCATTATTTGATTTGACATCATTT
1 AGAGAAAGGAGCAAGATCATTCTCTGATTTGGCGTCCTTC
* * * * * *
1077466 AGAGAAAGGATC-AGATCAACCATTGATTATGACTTGGCATCCTTT
1 AGAGAAAGGAGCAAGAT----CATT--CTCTGATTTGGCGTCCTTC
1077511 AGAGAAAGGAGCAAGATCATTCTCTGATTTGGCGTCCTTC
1 AGAGAAAGGAGCAAGATCATTCTCTGATTTGGCGTCCTTC
* * * * * *
1077551 AGAGAAAGGAGAAATACCATTCTTTGATTTGGTGTCATTC
1 AGAGAAAGGAGCAAGATCATTCTCTGATTTGGCGTCCTTC
1077591 AGAGAAAGGA
1 AGAGAAAGGA
1077601 ACGTATCAAC
Statistics
Matches: 162, Mismatches: 45, Indels: 16
0.73 0.20 0.07
Matches are distributed among these distances:
39 3 0.02
40 121 0.75
41 1 0.01
42 4 0.02
43 4 0.02
45 25 0.15
46 4 0.02
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.29
Consensus pattern (40 bp):
AGAGAAAGGAGCAAGATCATTCTCTGATTTGGCGTCCTTC
Found at i:1077638 original size:45 final size:44
Alignment explanation
Indices: 1077588--1077683 Score: 124
Period size: 45 Copynumber: 2.1 Consensus size: 44
1077578 TTTGGTGTCA
*
1077588 TTCAGAGAAAG-GAACGTATCAACCATTGATTAGGACTT-GACGTCC
1 TTCAGAGAAAGAGAA-G-ATCAACCATTGATTACGACTTAG-CGTCC
*
1077633 TTCAGAGAAAGAAGAAGATCAACCATTGATTACTACTTAGCGTCC
1 TTCAGAGAAAG-AGAAGATCAACCATTGATTACGACTTAGCGTCC
1077678 TTCAGA
1 TTCAGA
1077684 CAATAACGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
45 41 0.89
46 2 0.04
47 3 0.07
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (44 bp):
TTCAGAGAAAGAGAAGATCAACCATTGATTACGACTTAGCGTCC
Found at i:1081353 original size:39 final size:39
Alignment explanation
Indices: 1081299--1081376 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
1081289 ATCAGAAGAG
1081299 TTTTAAAGTTCATTTTCTCATATTCTTTGTAACACACTT
1 TTTTAAAGTTCATTTTCTCATATTCTTTGTAACACACTT
*
1081338 TTTTAAAGCTT-ATTTTGTCATATTCTTTGTAACACACTT
1 TTTTAAAG-TTCATTTTCTCATATTCTTTGTAACACACTT
1081377 GTCGAGCTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
39 35 0.95
40 2 0.05
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (39 bp):
TTTTAAAGTTCATTTTCTCATATTCTTTGTAACACACTT
Found at i:1083709 original size:23 final size:21
Alignment explanation
Indices: 1083687--1083735 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1083677 CTTTAATTTA
*
1083687 TTTATTTAATTA-T-TTTTCT
1 TTTATTTAATTATTATTTTTT
*
1083706 TTTATTTAATTCTTATTTTTT
1 TTTATTTAATTATTATTTTTT
*
1083727 ATTATTTAA
1 TTTATTTAA
1083736 AAAACAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 11 0.44
20 1 0.04
21 13 0.52
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTATTTAATTATTATTTTTT
Found at i:1083711 original size:19 final size:20
Alignment explanation
Indices: 1083687--1083735 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1083677 CTTTAATTTA
1083687 TTTATTTAATTATT-TTTCT
1 TTTATTTAATTATTATTTCT
* *
1083706 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTCT
1083726 TATTATTTAA
1 T-TTATTTAA
1083736 AAAACAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 13 0.50
20 5 0.19
21 8 0.31
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATTTAATTATTATTTCT
Found at i:1085344 original size:18 final size:18
Alignment explanation
Indices: 1085298--1085348 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
1085288 AATCTCTTTA
1085298 ATTTGTTTATTTAATTATT
1 ATTT-TTTATTTAATTATT
* *
1085317 TTTCTTTTATTTAATTCTT
1 ATT-TTTTATTTAATTATT
1085336 ATTTTTTATTTAA
1 ATTTTTTATTTAA
1085349 AAAACAACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 10 0.36
19 17 0.61
20 1 0.04
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:1096535 original size:47 final size:48
Alignment explanation
Indices: 1096435--1096537 Score: 120
Period size: 48 Copynumber: 2.2 Consensus size: 48
1096425 ACCTAAATTT
* * * * *
1096435 CATTAATGGCAACTTCTGCCAAAAGTGCACCGTTAGACTTCTAATTTG
1 CATTAATGGCAACTTCTGCCAAAAGAGCACAGTTAGACATCTAACTTA
* *
1096483 CATTAATGGCACCTTTCTGCCAAAA-AGCACATTTAG-CATCTAACTTA
1 CATTAATGGCAAC-TTCTGCCAAAAGAGCACAGTTAGACATCTAACTTA
1096530 CATTAATG
1 CATTAATG
1096538 ACATTTTTCT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
47 16 0.34
48 20 0.43
49 11 0.23
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (48 bp):
CATTAATGGCAACTTCTGCCAAAAGAGCACAGTTAGACATCTAACTTA
Found at i:1108387 original size:19 final size:19
Alignment explanation
Indices: 1108363--1108402 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1108353 TAGATATCTG
1108363 AGATCATAACAGAAATCAA
1 AGATCATAACAGAAATCAA
* *
1108382 AGATCATAACATATATCAA
1 AGATCATAACAGAAATCAA
1108401 AG
1 AG
1108403 TTCAGAGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.55, C:0.15, G:0.10, T:0.20
Consensus pattern (19 bp):
AGATCATAACAGAAATCAA
Found at i:1108413 original size:19 final size:19
Alignment explanation
Indices: 1108363--1108418 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
1108353 TAGATATCTG
* *
1108363 AGATCATAACAGAAATCAA
1 AGATCAGAACATAAATCAA
* *
1108382 AGATCATAACATATATCAA
1 AGATCAGAACATAAATCAA
* *
1108401 AGTTCAGAGCATAAATCA
1 AGATCAGAACATAAATCA
1108419 GAGGTCAGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.52, C:0.16, G:0.11, T:0.21
Consensus pattern (19 bp):
AGATCAGAACATAAATCAA
Found at i:1113166 original size:20 final size:21
Alignment explanation
Indices: 1113143--1113184 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
1113133 GAAAATTCAA
1113143 AGAAAAATAAAA-AAAAAATC
1 AGAAAAATAAAATAAAAAATC
*
1113163 AGAAAAATAAAATTAAAAATC
1 AGAAAAATAAAATAAAAAATC
1113184 A
1 A
1113185 AAATCAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (21 bp):
AGAAAAATAAAATAAAAAATC
Found at i:1114661 original size:21 final size:21
Alignment explanation
Indices: 1114637--1114683 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1114627 GCTTTGGAAT
*
1114637 TTTTCATGGGATGCATCCAGC
1 TTTTCATGGGATGCAACCAGC
* *
1114658 TTTTCCTGGGATGTAACCAGC
1 TTTTCATGGGATGCAACCAGC
1114679 TTTTC
1 TTTTC
1114684 TTGTGAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.38
Consensus pattern (21 bp):
TTTTCATGGGATGCAACCAGC
Found at i:1116160 original size:21 final size:20
Alignment explanation
Indices: 1116127--1116165 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1116117 AAATTTAAGG
*
1116127 TAAAAAAATAAATAAAAATT
1 TAAAAAAAAAAATAAAAATT
1116147 TAAAAATAAAAAATAAAAA
1 TAAAAA-AAAAAATAAAAA
1116166 ATGGTATGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (20 bp):
TAAAAAAAAAAATAAAAATT
Found at i:1119314 original size:131 final size:131
Alignment explanation
Indices: 1119079--1119316 Score: 286
Period size: 131 Copynumber: 1.8 Consensus size: 131
1119069 TCCACCGCTC
* * * * *
1119079 TTCAGGAAGAACAAATAAGAAAAATGAAGATATGCTCTGCTACTCTTTAGGGGAGATCAAACTTG
1 TTCAGAAAGAACAAATAAGAAAAATGAAGATATGCTCCGCTAATCTTTAGGAGAGACCAAACTTG
* * *
1119144 GAAATTTTGATTCATTTCACTGTTCTTTAGGAATCATTGAATCAAGTTTGACTTGCTTCGCTGCT
66 GAAATTCTGATTCATTCCACTCTTCTTTAGGAATCATTGAATCAAGTTTGACTTGCTTCGCTGCT
1119209 A
131 A
* * * * *
1119210 TTCAGAAAGACCAAATATA-AAAAATGAGGATTTTCTCCGCTAATCTTTAGGAGAGACCATATCT
1 TTCAGAAAGAACAAATA-AGAAAAATGAAGATATGCTCCGCTAATCTTTAGGAGAGACCA-AACT
*
1119274 T-GAAATTCTGATTCATTCCACCTCTT-TTTGGGGAAT-ATTGAAT
64 TGGAAATTCTGATTCATTCCA-CTCTTCTTT-AGGAATCATTGAAT
1119317 TAGGGTCGAT
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
131 75 0.84
132 14 0.16
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Consensus pattern (131 bp):
TTCAGAAAGAACAAATAAGAAAAATGAAGATATGCTCCGCTAATCTTTAGGAGAGACCAAACTTG
GAAATTCTGATTCATTCCACTCTTCTTTAGGAATCATTGAATCAAGTTTGACTTGCTTCGCTGCT
A
Found at i:1131290 original size:23 final size:23
Alignment explanation
Indices: 1131245--1131291 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1131235 AATAATAGCT
**
1131245 TAAAATTCATATTATAATGAAAG
1 TAAAATTCATATTATAACCAAAG
1131268 TAAAATT-ATCATTATAACCAAAG
1 TAAAATTCAT-ATTATAACCAAAG
1131291 T
1 T
1131292 CATAATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (23 bp):
TAAAATTCATATTATAACCAAAG
Found at i:1131557 original size:21 final size:21
Alignment explanation
Indices: 1131518--1131557 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1131508 GTCCATATAA
*
1131518 GTTGTCTTTATTCCGAAAGTT
1 GTTGTCTTTATTCCAAAAGTT
1131539 GTTGT-TTTATCTCCAAAAG
1 GTTGTCTTTAT-TCCAAAAG
1131558 CAATCTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (21 bp):
GTTGTCTTTATTCCAAAAGTT
Found at i:1134736 original size:6 final size:7
Alignment explanation
Indices: 1134721--1134748 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1134711 CTTGAGTTAG
1134721 AAAATAA
1 AAAATAA
1134728 AAAATAA
1 AAAATAA
1134735 AAAATAA
1 AAAATAA
1134742 AAAATAA
1 AAAATAA
1134749 TTCATGTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAATAA
Found at i:1136242 original size:42 final size:41
Alignment explanation
Indices: 1136193--1136332 Score: 136
Period size: 42 Copynumber: 3.3 Consensus size: 41
1136183 CATATTTGAT
*
1136193 ATTTAGCGGCGTTTCGGGCTCAAACGCCGCAATAGGTTGGTC
1 ATTTAGCGGCGTTTCGGGC-CAAACGCCGCAATAGGTTGGAC
* ** * * * * *
1136235 ATTTAGCGGCATTTTTAGTCACAAACGCCGCATTAGATTTGAA
1 ATTTAGCGGC-GTTTCGGGC-CAAACGCCGCAATAGGTTGGAC
* * *
1136278 ATTTAGCGGCGTTTCGGGCAACAATGCCGCAATAGGTTGGGC
1 ATTTAGCGGCGTTTCGGGCCA-AACGCCGCAATAGGTTGGAC
1136320 ATTTAGCGGCGTT
1 ATTTAGCGGCGTT
1136333 GTTAGTCACA
Statistics
Matches: 75, Mismatches: 21, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
41 1 0.01
42 42 0.56
43 32 0.43
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.29
Consensus pattern (41 bp):
ATTTAGCGGCGTTTCGGGCCAAACGCCGCAATAGGTTGGAC
Found at i:1136282 original size:85 final size:85
Alignment explanation
Indices: 1136134--1136420 Score: 353
Period size: 85 Copynumber: 3.4 Consensus size: 85
1136124 AGGCGTTTTC
** *
1136134 CCGCAATAGGTTGGTCATTTAGCGACATTTTTAGTCACAAATACCACAACATATTTGATATTTAG
1 CCGCAATAGGTTGGTCATTTAGCGACATTTTTAGTCACAAACGCCGCAACATATTTGATATTTAG
1136199 CGGCGTTTCGGGCTCAAACG
66 CGGCGTTTCGGGCTCAAACG
* ** * *
1136219 CCGCAATAGGTTGGTCATTTAGCGGCATTTTTAGTCACAAACGCCGCATTAGATTTGAAATTTAG
1 CCGCAATAGGTTGGTCATTTAGCGACATTTTTAGTCACAAACGCCGCAACATATTTGATATTTAG
* *
1136284 CGGCGTTTCGGGC-AACAATG
66 CGGCGTTTCGGGCTCA-AACG
* * * * * * *
1136304 CCGCAATAGGTTGGGCATTTAGCGGCGTTGTTAGTCACAAACGCCGTAACATATATGATATTTAT
1 CCGCAATAGGTTGGTCATTTAGCGACATTTTTAGTCACAAACGCCGCAACATATTTGATATTTAG
* *
1136369 CGGCATTTCAGG-TACAAACG
66 CGGCGTTTCGGGCT-CAAACG
* *
1136389 CCACAATATGTTGGTCATTTAGCGACATTTTT
1 CCGCAATAGGTTGGTCATTTAGCGACATTTTT
1136421 TTCTAAAATC
Statistics
Matches: 169, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
84 1 0.01
85 167 0.99
86 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (85 bp):
CCGCAATAGGTTGGTCATTTAGCGACATTTTTAGTCACAAACGCCGCAACATATTTGATATTTAG
CGGCGTTTCGGGCTCAAACG
Found at i:1136809 original size:12 final size:12
Alignment explanation
Indices: 1136792--1136826 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1136782 TCCTGAAATG
1136792 TTGCTTCTCTCT
1 TTGCTTCTCTCT
*
1136804 TTGCTTCTCTCG
1 TTGCTTCTCTCT
1136816 TTG-TTCTCTCT
1 TTGCTTCTCTCT
1136827 GCAATAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.00, C:0.31, G:0.11, T:0.57
Consensus pattern (12 bp):
TTGCTTCTCTCT
Found at i:1141603 original size:34 final size:34
Alignment explanation
Indices: 1141535--1141617 Score: 123
Period size: 35 Copynumber: 2.4 Consensus size: 34
1141525 ATACGATTAT
*
1141535 TACAACATCATAACATATCACCAAAACGTAAATA
1 TACAACATCATAACATATCACCAAAACATAAATA
* *
1141569 TACAATATACATAACATATCACCGAAACAT-AATA
1 TACAACAT-CATAACATATCACCAAAACATAAATA
1141603 TACAACATCATAACA
1 TACAACATCATAACA
1141618 CACATGCAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
33 7 0.16
34 18 0.41
35 19 0.43
ACGTcount: A:0.53, C:0.23, G:0.02, T:0.22
Consensus pattern (34 bp):
TACAACATCATAACATATCACCAAAACATAAATA
Found at i:1142170 original size:235 final size:235
Alignment explanation
Indices: 1141759--1142228 Score: 931
Period size: 235 Copynumber: 2.0 Consensus size: 235
1141749 TACAAGTGTG
1141759 ATCCAGCAGGCCATTTTTACAGTAACAAGGTGTTTGCAAGTTAATTTTATTGCACATCAAGTTTG
1 ATCCAGCAGGCCATTTTTACAGTAACAAGGTGTTTGCAAGTTAATTTTATTGCACATCAAGTTTG
1141824 GATTCTTGATTTTAGTTCTAAATGCCTGGATTCCATAAGTCGTATATTATTACTATGGTTATGAT
66 GATTCTTGATTTTAGTTCTAAATGCCTGGATTCCATAAGTCGTATATTATTACTATGGTTATGAT
*
1141889 TCATCACTAATTGTACTAATATCATGTTCGAGGAGGCATCTTAAGTTCCTAACGCTAATTGTGCT
131 TCATCAATAATTGTACTAATATCATGTTCGAGGAGGCATCTTAAGTTCCTAACGCTAATTGTGCT
1141954 AAAATCTCATGTTAATGGAGGTTCTAAATATCATGTTCAA
196 AAAATCTCATGTTAATGGAGGTTCTAAATATCATGTTCAA
1141994 ATCCAGCAGGCCATTTTTACAGTAACAAGGTGTTTGCAAGTTAATTTTATTGCACATCAAGTTTG
1 ATCCAGCAGGCCATTTTTACAGTAACAAGGTGTTTGCAAGTTAATTTTATTGCACATCAAGTTTG
1142059 GATTCTTGATTTTAGTTCTAAATGCCTGGATTCCATAAGTCGTATATTATTACTATGGTTATGAT
66 GATTCTTGATTTTAGTTCTAAATGCCTGGATTCCATAAGTCGTATATTATTACTATGGTTATGAT
1142124 TCATCAATAATTGTACTAATATCATGTTCGAGGAGGCATCTTAAGTTCCTAACGCTAATTGTGCT
131 TCATCAATAATTGTACTAATATCATGTTCGAGGAGGCATCTTAAGTTCCTAACGCTAATTGTGCT
1142189 AAAATCTCATGTTAATGGAGGTTCTAAATATCATGTTCAA
196 AAAATCTCATGTTAATGGAGGTTCTAAATATCATGTTCAA
1142229 GGAGGTATCT
Statistics
Matches: 234, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
235 234 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Consensus pattern (235 bp):
ATCCAGCAGGCCATTTTTACAGTAACAAGGTGTTTGCAAGTTAATTTTATTGCACATCAAGTTTG
GATTCTTGATTTTAGTTCTAAATGCCTGGATTCCATAAGTCGTATATTATTACTATGGTTATGAT
TCATCAATAATTGTACTAATATCATGTTCGAGGAGGCATCTTAAGTTCCTAACGCTAATTGTGCT
AAAATCTCATGTTAATGGAGGTTCTAAATATCATGTTCAA
Found at i:1142518 original size:49 final size:49
Alignment explanation
Indices: 1142325--1142596 Score: 171
Period size: 49 Copynumber: 5.5 Consensus size: 49
1142315 AATGTAAAGG
* ** *
1142325 TCAATGAAGTACTTTGTGTGCCTAAAACTAATTGTGTTAAATATCAAGT
1 TCAAGGAAGTACTTTGTGTGCCTAGCACTAATTATGTTAAATATCAAGT
* * * * * *
1142374 TCAAGGAAGTACTTTATATTCCTAACATTAATTGTGTTAAATATCATA-T
1 TCAAGGAAGTACTTTGTGTGCCTAGCACTAATTATGTTAAATATCA-AGT
* * * * * * *
1142423 TTAA-TAACGTATCTTAAGTGT--CTAGTATTGATTATGCTCAAATATCAAGT
1 TCAAGGAA-GTA-CTT-TGTGTGCCTAGCACTAATTATG-TTAAATATCAAGT
* *
1142473 TCAAGGAAGTACTTTGTGTGCCTAGCACTAATTCTGTTAAATATCATG-
1 TCAAGGAAGTACTTTGTGTGCCTAGCACTAATTATGTTAAATATCAAGT
* ** * *
1142521 TCTAGTGACTTATCTTAAGTGT--CTAGCACTAATTATGCTAAAATATCAAGT
1 TCAAG-GAAGTA-CTT-TGTGTGCCTAGCACTAATTATG-TTAAATATCAAGT
* * *
1142572 TTAAGGGAGTACTTTGTGTGACTAG
1 TCAAGGAAGTACTTTGTGTGCCTAG
1142597 TTGTATATTC
Statistics
Matches: 169, Mismatches: 38, Indels: 31
0.71 0.16 0.13
Matches are distributed among these distances:
48 14 0.08
49 93 0.55
50 51 0.30
51 11 0.07
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (49 bp):
TCAAGGAAGTACTTTGTGTGCCTAGCACTAATTATGTTAAATATCAAGT
Found at i:1142535 original size:99 final size:99
Alignment explanation
Indices: 1142363--1142596 Score: 306
Period size: 99 Copynumber: 2.4 Consensus size: 99
1142353 TAATTGTGTT
* * * * * * *
1142363 AAATATCAAGTTCAAGGAAGTACTTTATATTCCTAACATTAATTGTGTTAAATATCATATTTAAT
1 AAATATCAAGTTCAAGGAAGTACTTTGTGTGCCTAGCACTAATTCTGTTAAATATCATATCTAAT
* * * *
1142428 AACGTATCTTAAGTGTCTAGTATTGATTATGCTC
66 AACGTATCTTAAGTGTCTAGCACTAATTATGCTA
* *
1142462 AAATATCAAGTTCAAGGAAGTACTTTGTGTGCCTAGCACTAATTCTGTTAAATATCATGTCTAGT
1 AAATATCAAGTTCAAGGAAGTACTTTGTGTGCCTAGCACTAATTCTGTTAAATATCATATCTAAT
* *
1142527 GACTTATCTTAAGTGTCTAGCACTAATTATGCTA
66 AACGTATCTTAAGTGTCTAGCACTAATTATGCTA
* * *
1142561 AAATATCAAGTTTAAGGGAGTACTTTGTGTGACTAG
1 AAATATCAAGTTCAAGGAAGTACTTTGTGTGCCTAG
1142597 TTGTATATTC
Statistics
Matches: 117, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
99 117 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (99 bp):
AAATATCAAGTTCAAGGAAGTACTTTGTGTGCCTAGCACTAATTCTGTTAAATATCATATCTAAT
AACGTATCTTAAGTGTCTAGCACTAATTATGCTA
Found at i:1142554 original size:148 final size:149
Alignment explanation
Indices: 1142213--1142568 Score: 382
Period size: 148 Copynumber: 2.4 Consensus size: 149
1142203 ATGGAGGTTC
* * * * * * *
1142213 TAAATATCATGTTCAAGGAGGTATCTTGAGTGCCTAGCCCTAATTGTGCTAAAATATTATGTTCA
1 TAAATATCAAGTTCAAGGAAGTATCTTAAGTGTCTAGCACTAATTGTGCTAAAATATCATATTCA
* * *
1142278 AAGAACTATCTTAAGTGTCTATTACTGATTATGCTAAAATGTAAAGGTCAATGAAGTACTTTGTG
66 AAGAACTATCTTAAGTGTCTAGTACTGATTATGCTAAAATATAAAGGTCAAGGAAGTACTTTGTG
*
1142343 TGCCTAAAACTAATTGTGT
131 TGCCTAAAACTAATTCTGT
* * *
1142362 TAAATATCAAGTTCAAGGAAGTA-CTTTATA-T-TCCTAACATTAATTGTG-TTAAATATCATAT
1 TAAATATCAAGTTCAAGGAAGTATC-TTA-AGTGT-CTAGCACTAATTGTGCTAAAATATCATAT
* * * * * *
1142423 T-TAATAACGTATCTTAAGTGTCTAGTATTGATTATGCTCAAATATCAAGTTCAAGGAAGTACTT
63 TCAAAGAAC-TATCTTAAGTGTCTAGTACTGATTATGCTAAAATATAAAGGTCAAGGAAGTACTT
**
1142487 TGTGTGCCTAGCACTAATTCTGT
127 TGTGTGCCTAAAACTAATTCTGT
* * ** *
1142510 TAAATATCATG-TCTAGTGACTTATCTTAAGTGTCTAGCACTAATTATGCTAAAATATCA
1 TAAATATCAAGTTCAAG-GAAGTATCTTAAGTGTCTAGCACTAATTGTGCTAAAATATCA
1142569 AGTTTAAGGG
Statistics
Matches: 168, Mismatches: 30, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
147 10 0.06
148 110 0.65
149 47 0.28
150 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (149 bp):
TAAATATCAAGTTCAAGGAAGTATCTTAAGTGTCTAGCACTAATTGTGCTAAAATATCATATTCA
AAGAACTATCTTAAGTGTCTAGTACTGATTATGCTAAAATATAAAGGTCAAGGAAGTACTTTGTG
TGCCTAAAACTAATTCTGT
Found at i:1144244 original size:10 final size:9
Alignment explanation
Indices: 1144231--1144262 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
1144221 AATTATATTA
1144231 TTTAAATTAT
1 TTTAAA-TAT
1144241 TTTAAATAT
1 TTTAAATAT
1144250 TTTAAATAT
1 TTTAAATAT
1144259 TTTA
1 TTTA
1144263 TAATGTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTAAATAT
Found at i:1152423 original size:18 final size:17
Alignment explanation
Indices: 1152402--1152443 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1152392 TATTTTGGTC
1152402 ATTTTTTATTG-CCATTTT
1 ATTTTTTATTGTCC--TTT
1152420 ATTTTATTATTGTCCTTT
1 ATTTT-TTATTGTCCTTT
1152438 ATTTTT
1 ATTTTT
1152444 CAATACTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.05
18 13 0.59
19 6 0.27
20 2 0.09
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.69
Consensus pattern (17 bp):
ATTTTTTATTGTCCTTT
Found at i:1152699 original size:18 final size:18
Alignment explanation
Indices: 1152676--1152714 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1152666 TTTTAGGAAA
1152676 ATTTATCATA-TTTTTAAT
1 ATTTAT-ATATTTTTTAAT
*
1152694 ATTTATTTATTTTTTAAT
1 ATTTATATATTTTTTAAT
1152712 ATT
1 ATT
1152715 AAATAAATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTATATATTTTTTAAT
Found at i:1152778 original size:143 final size:143
Alignment explanation
Indices: 1152528--1152787 Score: 379
Period size: 143 Copynumber: 1.8 Consensus size: 143
1152518 AATATAATTT
1152528 GAAAATTTTCATAATTTAATTAAATTTATTTATTTTTTTAATATTAAGAAAAGGGTTGTCTTAAA
1 GAAAATTTTCATAATTT-ATTAAATTTATTTATTTTTTTAATATTAAGAAAAGGGTTGTCTTAAA
** *
1152593 GTAACTAGATGTCATTTTCTGATATTTTTAAATAAATAAAATA-TTATATTTAATCTAGTTTTAT
65 ACAACTAGATGTCATTTTCTAATATTTTTAAATAAATAAAATACTT-TATTTAATCTAGTTTTAT
1152657 TTAAATCATTTTTAG
129 TTAAATCATTTTTAG
1152672 GAAAATTTATCAT-ATTT-TTAATATTTATTTA-TTTTTTAATATTAA-ATAAATGGGTTGTCTT
1 GAAAATTT-TCATAATTTATTAA-ATTTATTTATTTTTTTAATATTAAGA-AAA-GGGTTGTCTT
*
1152733 AAAACAATTAGATGTCATTTTCTAATATTTTTTAAATAAAT-AAATACTTTATTTA
62 AAAACAACTAGATGTCATTTTCTAATA-TTTTTAAATAAATAAAATACTTTATTTA
1152788 TAATTTATAA
Statistics
Matches: 106, Mismatches: 4, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
141 1 0.01
142 21 0.20
143 53 0.50
144 27 0.25
145 4 0.04
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.49
Consensus pattern (143 bp):
GAAAATTTTCATAATTTATTAAATTTATTTATTTTTTTAATATTAAGAAAAGGGTTGTCTTAAAA
CAACTAGATGTCATTTTCTAATATTTTTAAATAAATAAAATACTTTATTTAATCTAGTTTTATTT
AAATCATTTTTAG
Found at i:1155726 original size:20 final size:19
Alignment explanation
Indices: 1155703--1155766 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 19
1155693 TTTTCGTTAC
1155703 ATTTGCATTTTTATGTTTTT
1 ATTTGCATTTTTAT-TTTTT
* *
1155723 ATTTTCATTTTTATATTTTC
1 ATTTGCATTTTTAT-TTTTT
* * *
1155743 ATTTTCATTTTCATTTTAT
1 ATTTGCATTTTTATTTTTT
1155762 ATTTG
1 ATTTG
1155767 TATCTTTGCA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 7 0.19
20 30 0.81
ACGTcount: A:0.19, C:0.08, G:0.05, T:0.69
Consensus pattern (19 bp):
ATTTGCATTTTTATTTTTT
Found at i:1155735 original size:12 final size:13
Alignment explanation
Indices: 1155718--1155765 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
1155708 CATTTTTATG
1155718 TTTT-TATTTTCA
1 TTTTATATTTTCA
1155730 TTTTTATATTTTCA
1 -TTTTATATTTTCA
*
1155744 TTTT-CATTTTCA
1 TTTTATATTTTCA
1155756 TTTTATATTT
1 TTTTATATTT
1155766 GTATCTTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 11 0.35
13 12 0.39
14 8 0.26
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTATATTTTCA
Found at i:1158998 original size:76 final size:75
Alignment explanation
Indices: 1158872--1159019 Score: 226
Period size: 76 Copynumber: 2.0 Consensus size: 75
1158862 TAAACTCAAA
1158872 TTTAGGATAATATTTTAAACATTATATTTTATCTTTGTATTTTAATTTAAATAGGTTTTTAGTAT
1 TTTAGGATAATATTTTAAACATTATATTTTATCTTTGTATTTTAATTTAAATAGG-TTTTAGTAT
1158937 TTTAATTAAGT
65 TTTAATTAAGT
* * * * *
1158948 TTTAGGATATTATTTT-TATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 TTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAATTTAAATAGGTTTTAGTAT
1159012 TTTAATTA
65 TTTAATTA
1159020 GGATTTAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
75 24 0.36
76 42 0.64
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.58
Consensus pattern (75 bp):
TTTAGGATAATATTTTAAACATTATATTTTATCTTTGTATTTTAATTTAAATAGGTTTTAGTATT
TTAATTAAGT
Found at i:1159703 original size:21 final size:22
Alignment explanation
Indices: 1159677--1159717 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1159667 TTATATTTTG
1159677 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
1159698 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
1159718 TATTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:1159774 original size:16 final size:16
Alignment explanation
Indices: 1159753--1159783 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1159743 TCCCCCTTTT
1159753 ATATTTATTACTATTA
1 ATATTTATTACTATTA
*
1159769 ATATTTATTATTATT
1 ATATTTATTACTATT
1159784 TTTCTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTTATTACTATTA
Found at i:1165403 original size:20 final size:20
Alignment explanation
Indices: 1165380--1165440 Score: 81
Period size: 19 Copynumber: 3.1 Consensus size: 20
1165370 ACCCATTTCG
1165380 TTATATTTTTTTTTATTTTT
1 TTATATTTTTTTTTATTTTT
**
1165400 TTAT-TTTCGTTTTATTTTT
1 TTATATTTTTTTTTATTTTT
1165419 TT-TATTTTTGTTTTATTTTT
1 TTATATTTTT-TTTTATTTTT
1165439 TT
1 TT
1165441 TAATTTTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
18 1 0.03
19 18 0.51
20 16 0.46
ACGTcount: A:0.11, C:0.02, G:0.03, T:0.84
Consensus pattern (20 bp):
TTATATTTTTTTTTATTTTT
Found at i:1165415 original size:29 final size:31
Alignment explanation
Indices: 1165375--1165437 Score: 94
Period size: 29 Copynumber: 2.1 Consensus size: 31
1165365 AGGCAACCCA
1165375 TTTCGTTATATTTTTTTT-TATTT-TTTTAT
1 TTTCGTTATATTTTTTTTATATTTGTTTTAT
* *
1165404 TTTCGTTTTATTTTTTTTATTTTTGTTTTAT
1 TTTCGTTATATTTTTTTTATATTTGTTTTAT
1165435 TTT
1 TTT
1165438 TTTTAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 17 0.57
30 4 0.13
31 9 0.30
ACGTcount: A:0.11, C:0.03, G:0.05, T:0.81
Consensus pattern (31 bp):
TTTCGTTATATTTTTTTTATATTTGTTTTAT
Found at i:1165441 original size:20 final size:20
Alignment explanation
Indices: 1165383--1165448 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
1165373 CATTTCGTTA
1165383 TATTTTT-TTTTA-TTTTTT
1 TATTTTTGTTTTATTTTTTT
*
1165401 TATTTTCGTTTTATTTTTTT
1 TATTTTTGTTTTATTTTTTT
1165421 TATTTTTGTTTTATTTTTTT
1 TATTTTTGTTTTATTTTTTT
1165441 TAATTTTT
1 T-ATTTTT
1165449 AGCGAACTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
18 6 0.14
19 5 0.12
20 26 0.60
21 6 0.14
ACGTcount: A:0.12, C:0.02, G:0.03, T:0.83
Consensus pattern (20 bp):
TATTTTTGTTTTATTTTTTT
Found at i:1167353 original size:76 final size:75
Alignment explanation
Indices: 1167262--1167426 Score: 242
Period size: 76 Copynumber: 2.2 Consensus size: 75
1167252 TTAAACTCAA
*
1167262 ATTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGGATATTATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGT
1167326 ATTTTAATTAAG
64 ATTTTAATTAAG
* * * *
1167338 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
*
1167403 TTTAATTAGG
66 TTTAATTAAG
*
1167413 ATTTAGAATATTAT
1 ATTTAGGATATTAT
1167427 ATTATATTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 37 0.46
76 43 0.54
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.56
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
TTTAATTAAG
Found at i:1167438 original size:75 final size:76
Alignment explanation
Indices: 1167290--1167438 Score: 239
Period size: 75 Copynumber: 2.0 Consensus size: 76
1167280 AACATTATAT
* * *
1167290 TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTT
1 TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATTATTTA
1167355 TATATTTTATC
66 TATATTTTATC
*
1167366 TTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTATTTTAATTAGGATTTAGAATATTATATT
1 TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATTAT-TT
1167430 ATAT-TTTTA
65 ATATATTTTA
1167439 GGTATTTTAG
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
75 35 0.51
76 33 0.49
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (76 bp):
TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATTATTTA
TATATTTTATC
Found at i:1168100 original size:22 final size:23
Alignment explanation
Indices: 1168075--1168123 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
1168065 CTTTAATTTG
*
1168075 TTTATTTAATTATT-TTTTTTCT
1 TTTATTTAATTATTATTTTTTAT
*
1168097 TTTATTTAATTCTTATTTTTTAT
1 TTTATTTAATTATTATTTTTTAT
1168120 TTTA
1 TTTA
1168124 ACCACAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTATTTAATTATTATTTTTTAT
Done.