Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006174.1 Hibiscus syriacus cultivar Beakdansim tig00014678_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: 91003
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:8182 original size:125 final size:125
Alignment explanation
Indices: 7960--8201 Score: 457
Period size: 125 Copynumber: 1.9 Consensus size: 125
7950 CTTTACTTTG
* *
7960 TCACCTAAGTAAAGTTAGTGATGGTATATACAAATGAAAATGTTATGACAAAATGGAATGACTGA
1 TCACCTAAGTAAAGTTAGTAATGGTATATACAAAAGAAAATGTTATGACAAAATGGAATGACTGA
8025 TGTGGAAATGGAATGATGGCAGAGTGGTAAAAATTGATTATGTTGTGGCAAATTAAATTA
66 TGTGGAAATGGAATGATGGCAGAGTGGTAAAAATTGATTATGTTGTGGCAAATTAAATTA
*
8085 TCACCTAAGTAAAGTTAGTAATGGTATATGCAAAAGAAAATGTTATGACAAAATGGAATGACTGA
1 TCACCTAAGTAAAGTTAGTAATGGTATATACAAAAGAAAATGTTATGACAAAATGGAATGACTGA
8150 TGTGGAAATGGAATGATGGCAGAGTGGTAAAAATTGATTATGTTGTGGCAAA
66 TGTGGAAATGGAATGATGGCAGAGTGGTAAAAATTGATTATGTTGTGGCAAA
8202 CAAATGGAAA
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
125 114 1.00
ACGTcount: A:0.40, C:0.07, G:0.25, T:0.29
Consensus pattern (125 bp):
TCACCTAAGTAAAGTTAGTAATGGTATATACAAAAGAAAATGTTATGACAAAATGGAATGACTGA
TGTGGAAATGGAATGATGGCAGAGTGGTAAAAATTGATTATGTTGTGGCAAATTAAATTA
Found at i:15450 original size:18 final size:16
Alignment explanation
Indices: 15427--15489 Score: 54
Period size: 18 Copynumber: 3.7 Consensus size: 16
15417 AAGGAGAGAT
15427 AAAAAGAAAAAGATAAGA
1 AAAAAGAAAAA-A-AAGA
15445 AAAAAGAAGAAAAAGAGA
1 AAAAAGAA-AAAAA-AGA
* * *
15463 TAAAACAACAAAAAGA
1 AAAAAGAAAAAAAAGA
*
15479 AAAAGGAAAAA
1 AAAAAGAAAAA
15490 GGAAAAGAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
16 10 0.28
17 5 0.14
18 18 0.50
19 3 0.08
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (16 bp):
AAAAAGAAAAAAAAGA
Found at i:15454 original size:10 final size:11
Alignment explanation
Indices: 15430--15462 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
15420 GAGAGATAAA
*
15430 AAGAAAAAGAT
1 AAGAAAAAGAG
15441 AAGAAAAA-AG
1 AAGAAAAAGAG
15451 AAGAAAAAGAG
1 AAGAAAAAGAG
15462 A
1 A
15463 TAAAACAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (11 bp):
AAGAAAAAGAG
Found at i:15490 original size:13 final size:13
Alignment explanation
Indices: 15427--15512 Score: 57
Period size: 14 Copynumber: 6.1 Consensus size: 13
15417 AAGGAGAGAT
15427 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
15440 TAAGAAA-AAAGAAGA
1 -AA-AAAGAAA-AAGA
*
15455 AAAAGAGATAAAACAA
1 AAAA-AGA-AAAA-GA
*
15471 CAAAAAGAAAAAGG
1 -AAAAAGAAAAAGA
*
15485 AAAAAGGAAAAGA
1 AAAAAGAAAAAGA
*
15498 AAAGAAGAAAGAGA
1 AAA-AAGAAAAAGA
15512 A
1 A
15513 CAAATCAAGT
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
13 16 0.28
14 17 0.30
15 14 0.25
16 6 0.11
17 4 0.07
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:17759 original size:42 final size:42
Alignment explanation
Indices: 17712--17791 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
17702 AATTGGTAAG
** *
17712 TCCTTCGTGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGAACCATCAGTAAGTCTTTCGAGCAAGATGATTAAA
* * *
17754 TCCTTCGAATCATCTGTCAGTCTTTCGAGCAAGATGAT
1 TCCTTCGAACCATCAGTAAGTCTTTCGAGCAAGATGAT
17792 AAGCCCTTCG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.34
Consensus pattern (42 bp):
TCCTTCGAACCATCAGTAAGTCTTTCGAGCAAGATGATTAAA
Found at i:18021 original size:42 final size:41
Alignment explanation
Indices: 17974--18064 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 41
17964 AATTGGTAAG
*
17974 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATGA-TAAA
* * * * *
18016 TCCTTCAGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAG
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATGATAAA
18057 TCCTTCGG
1 TCCTTCGG
18065 TTCATCTATG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 10 0.24
42 32 0.76
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATGATAAA
Found at i:18051 original size:262 final size:261
Alignment explanation
Indices: 17587--18280 Score: 1083
Period size: 262 Copynumber: 2.7 Consensus size: 261
17577 TTATATAATT
* * *
17587 TGAAAAATGTGAAAAGTAATTTTCAAAGTTTCTTATTTAATATTTTCATAAAAT-AAAATATTTG
1 TGAAAAATGAGAAAAGTAATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAAAT-TTTG
* *
17651 AAAAGTAAGAAAGCGATTTTCAAAGTTTCTTACCTAGTAAACAATTTCCAAAATTGGTAAGTCCT
65 AAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCT
*
17716 TCGTGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAATCATCTGTCAGTCTTTCG
130 TCGAGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAATCATCTGTCAGTCTTTCG
* *
17781 AGCAAGATGATAAGCCCTTCGGACT-ATCTATAAGACCTTTGGGTAAGATGTTTTCATATGATAT
195 AGCAAGATGATAAGCCCTTCGG-CTCATCTATAAGACCTTTGGGCAAGATGATTTCATATGATAT
17845 TTA
259 TTA
17848 TGAAAAATGAGAAAAGTAATTTTCAAAGTTTCTCATTTAATATTTTTCAGAAAATGAAAATTTTG
1 TGAAAAATGAGAAAAGTAATTTTCAAAGTTTCTCATTTAATA-TTTTCAGAAAATGAAAATTTTG
* *
17913 AAATGTAAGAAAGCGATTTCCAAAGTTTATTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCT
65 AAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCT
* *
17978 TCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC-AGGTCATCTGTCAGTCTTTC
130 TCGAGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGA-ATCATCTGTCAGTCTTTC
* * * * *
18042 GAGCAAGATGATAAGTCCTTCGGTTCATCTATGAGACGTTTGGGCAAGATGATTTCATATGATGT
194 GAGCAAGATGATAAGCCCTTCGGCTCATCTATAAGACCTTTGGGCAAGATGATTTCATATGATAT
18107 TTA
259 TTA
*
18110 TGAAAAATGAGAAAA-TGAATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTG
1 TGAAAAATGAGAAAAGT-AATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAAATTTTG
* * * * *
18174 AAAAGTAAGAAA-CTAATCTCCAAAGTTTCTTACCTAGTAGACTATTTCTAAAATTGGCAAGTCC
65 AAAAGTAAGAAAGC-GATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCC
*
18238 TTCGAGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCT
129 TTCGAGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCT
18281 CCGGGTTATT
Statistics
Matches: 401, Mismatches: 26, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
260 1 0.00
261 160 0.40
262 235 0.59
263 5 0.01
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (261 bp):
TGAAAAATGAGAAAAGTAATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAAATTTTGA
AAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTT
CGAGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAATCATCTGTCAGTCTTTCGA
GCAAGATGATAAGCCCTTCGGCTCATCTATAAGACCTTTGGGCAAGATGATTTCATATGATATTT
A
Found at i:18447 original size:3 final size:3
Alignment explanation
Indices: 18421--18520 Score: 65
Period size: 3 Copynumber: 31.7 Consensus size: 3
18411 TTTTGCCAGG
* * * * * *
18421 TTA TCA TTA TTA ATA TTTA ATA TTA TTC TTA TTC TTA TTA TTT TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
18467 TTTA ATA TTTA ATA TTTA ATA ATA TTA TTA TTAA TTA TTA TTA TTA TTA
1 -TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
18516 TTA TT
1 TTA TT
18521 TATTGTTACA
Statistics
Matches: 74, Mismatches: 18, Indels: 10
0.73 0.18 0.10
Matches are distributed among these distances:
3 62 0.84
4 12 0.16
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:18498 original size:45 final size:45
Alignment explanation
Indices: 18430--18522 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 45
18420 GTTATCATTA
* * * *
18430 TTAATATTTAATATTATTCTTATT-CTTATTATTTTTATTTAATAT
1 TTAATATTTAATAATATTATTATTAATTATTATTATTA-TTAATAT
*
18475 TTAATATTTAATAATATTATTATTAATTATTATTATTATTATTAT
1 TTAATATTTAATAATATTATTATTAATTATTATTATTATTAATAT
18520 TTA
1 TTA
18523 TTGTTACAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
45 31 0.74
46 11 0.26
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (45 bp):
TTAATATTTAATAATATTATTATTAATTATTATTATTATTAATAT
Found at i:19914 original size:3 final size:3
Alignment explanation
Indices: 19906--19938 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
19896 CCATTTTAAA
*
19906 ATT ATT ATT ATT ATT ATT -GT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
19939 AAAAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 1 0.04
3 26 0.96
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:19930 original size:14 final size:14
Alignment explanation
Indices: 19911--19937 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19901 TTAAAATTAT
19911 TATTATTATTATTG
1 TATTATTATTATTG
19925 TATTATTATTATT
1 TATTATTATTATT
19938 AAAAAAAATA
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:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (14 bp):
TATTATTATTATTG
Found at i:21191 original size:14 final size:17
Alignment explanation
Indices: 21163--21198 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
21153 ATATTTTACA
21163 TTTTAATTCTATATTT-
1 TTTTAATTCTATATTTG
21179 TTTTAATT-T-TATTTG
1 TTTTAATTCTATATTTG
21194 TTTTA
1 TTTTA
21199 GTCATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.26
15 6 0.32
16 8 0.42
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTTAATTCTATATTTG
Found at i:21417 original size:25 final size:25
Alignment explanation
Indices: 21371--21427 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
21361 CCTATTCTGG
21371 TATTTTAAAAATAAATAAATAT-CT
1 TATTTTAAAAATAAATAAATATACT
* *
21395 TATTTATAAAAATATATATATATACT
1 TATTT-TAAAAATAAATAAATATACT
21421 TCATTTT
1 T-ATTTT
21428 TATTATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 5 0.18
25 15 0.54
26 4 0.14
27 4 0.14
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (25 bp):
TATTTTAAAAATAAATAAATATACT
Found at i:22893 original size:16 final size:17
Alignment explanation
Indices: 22856--22898 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
22846 TGGTACTAAC
*
22856 CATTTTATTTTTTCTTA
1 CATTTTATTTTTTCGTA
*
22873 -TTTTTATTTTTT-GTA
1 CATTTTATTTTTTCGTA
22888 CATTTTATTTT
1 CATTTTATTTT
22899 GCTCCAACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 2 0.09
16 20 0.91
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.74
Consensus pattern (17 bp):
CATTTTATTTTTTCGTA
Found at i:27130 original size:22 final size:21
Alignment explanation
Indices: 27094--27137 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
27084 CATTCATTAT
* *
27094 AAGAAAAAAAGAAGAAAGAAG
1 AAGAAAAAAACAAGAAAAAAG
27115 AAGAAGAAAAACAAGAAAAAAG
1 AAGAA-AAAAACAAGAAAAAAG
27137 A
1 A
27138 TGATAAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.00
Consensus pattern (21 bp):
AAGAAAAAAACAAGAAAAAAG
Found at i:29977 original size:108 final size:108
Alignment explanation
Indices: 29838--30112 Score: 338
Period size: 108 Copynumber: 2.5 Consensus size: 108
29828 ACTTCACTGG
* *
29838 CGAACATCTGTGCAGAAGCCACAGGAAAGGATGAACGTGTTATCAAATGTATTACGAACATCTGT
1 CGAACATCTGTGCAGAAGCCACAGGAAAGGATGAACGTGTTATCAAATGTATTACGAACATCAGG
*
29903 GCAGAAGACACA-GAAAATGGTGAATATATTATCAAATATATTA
66 GCAGAAGACACATG-AAATGATGAATATATTATCAAATATATTA
* * * * *
29946 CGAACATCTGTGCTGGAGCCACAGGAAAGGATTAACGTATTGTCAAATGTATTACGAACATCAGG
1 CGAACATCTGTGCAGAAGCCACAGGAAAGGATGAACGTGTTATCAAATGTATTACGAACATCAGG
* * * * * *
30011 GGAGAAGCCACATGAAATGATGAATGTGTTGTCAAATATTTTA
66 GCAGAAGACACATGAAATGATGAATATATTATCAAATATATTA
* * * * * *
30054 CGAACCTCTG-GACAGAAGCTACAGGAAATGATGAATGTGTTCTCAAATGTTTTACGAAC
1 CGAACATCTGTG-CAGAAGCCACAGGAAAGGATGAACGTGTTATCAAATGTATTACGAAC
30113 CAGTGATTAT
Statistics
Matches: 141, Mismatches: 24, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
107 1 0.01
108 139 0.99
109 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (108 bp):
CGAACATCTGTGCAGAAGCCACAGGAAAGGATGAACGTGTTATCAAATGTATTACGAACATCAGG
GCAGAAGACACATGAAATGATGAATATATTATCAAATATATTA
Found at i:30113 original size:54 final size:54
Alignment explanation
Indices: 29838--30112 Score: 300
Period size: 54 Copynumber: 5.1 Consensus size: 54
29828 ACTTCACTGG
* *
29838 CGAACATCTGTGCAGAAGCCACAGGAAAGGATGAACGTGTTATCAAATGTATTA
1 CGAACATCTGTGCAGAAGCCACAGGAAATGATGAATGTGTTATCAAATGTATTA
* * * * * *
29892 CGAACATCTGTGCAGAAGACACAGAAAATGGTGAATATATTATCAAATATATTA
1 CGAACATCTGTGCAGAAGCCACAGGAAATGATGAATGTGTTATCAAATGTATTA
* * * * * * *
29946 CGAACATCTGTGCTGGAGCCACAGGAAAGGATTAACGTATTGTCAAATGTATTA
1 CGAACATCTGTGCAGAAGCCACAGGAAATGATGAATGTGTTATCAAATGTATTA
* * * * * * *
30000 CGAACATCAGGGGAGAAGCCACATGAAATGATGAATGTGTTGTCAAATATTTTA
1 CGAACATCTGTGCAGAAGCCACAGGAAATGATGAATGTGTTATCAAATGTATTA
* * * *
30054 CGAACCTCTG-GACAGAAGCTACAGGAAATGATGAATGTGTTCTCAAATGTTTTA
1 CGAACATCTGTG-CAGAAGCCACAGGAAATGATGAATGTGTTATCAAATGTATTA
30108 CGAAC
1 CGAAC
30113 CAGTGATTAT
Statistics
Matches: 182, Mismatches: 38, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
53 1 0.01
54 181 0.99
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (54 bp):
CGAACATCTGTGCAGAAGCCACAGGAAATGATGAATGTGTTATCAAATGTATTA
Found at i:31343 original size:116 final size:116
Alignment explanation
Indices: 31138--31399 Score: 443
Period size: 116 Copynumber: 2.2 Consensus size: 116
31128 CCCACATCTG
* *
31138 TAAGACCTACAGTGCATGATGTTTTCAAAAAAACCTTCGGGAGCTTTTTGATATTTAAAGCCTTC
1 TAAGACCTACAGTGCAGGATGTTTTC-AAAAAACCTTCGGGAGCTTTTTGATATTTAAAGCCTCC
*
31203 GGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGTCATCCA
65 GGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
*
31255 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAACCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
* *
31320 GGTTATCTGTAAGACCTATAGTGCAAGATGATAAGACCTCAGGGCCATCCA
66 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
* *
31371 TAAGACCTCCAGTACAGGATGTTTTCAAA
1 TAAGACCTACAGTGCAGGATGTTTTCAAA
31400 TGAGATTTTA
Statistics
Matches: 137, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
116 112 0.82
117 25 0.18
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (116 bp):
TAAGACCTACAGTGCAGGATGTTTTCAAAAAACCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
Found at i:31659 original size:3 final size:3
Alignment explanation
Indices: 31653--31708 Score: 71
Period size: 3 Copynumber: 19.3 Consensus size: 3
31643 TTATTTTAAA
* * *
31653 ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT ATT A-T ATT ATT ATT -GT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
31699 ATT ATT ATT A
1 ATT ATT ATT A
31709 ATAAATAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 3 0.07
3 42 0.93
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:31692 original size:11 final size:12
Alignment explanation
Indices: 31653--31708 Score: 71
Period size: 11 Copynumber: 4.8 Consensus size: 12
31643 TTATTTTAAA
31653 ATTATTATTATT
1 ATTATTATTATT
* *
31665 ATTATAAATATT
1 ATTATTATTATT
31677 ATTATTATTA-T
1 ATTATTATTATT
*
31688 ATTATTATT-GT
1 ATTATTATTATT
31699 ATTATTATTA
1 ATTATTATTA
31709 ATAAATAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
11 20 0.53
12 18 0.47
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (12 bp):
ATTATTATTATT
Found at i:33452 original size:2 final size:2
Alignment explanation
Indices: 33445--33481 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
33435 TACAAAACCC
33445 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33482 TTAATACTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34479 original size:15 final size:16
Alignment explanation
Indices: 34451--34483 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
34441 ATATCACTTT
34451 TTATCTTTTAAAATTA
1 TTATCTTTTAAAATTA
*
34467 TTAT-TTTTTAAATTA
1 TTATCTTTTAAAATTA
34482 TT
1 TT
34484 TTAAATGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATCTTTTAAAATTA
Found at i:35677 original size:9 final size:9
Alignment explanation
Indices: 35655--35695 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
35645 CAGTCATGCT
35655 ATCGGTTC-
1 ATCGGTTCA
35663 ATCGGTTCA
1 ATCGGTTCA
*
35672 ATCGGTTAA
1 ATCGGTTCA
35681 ATCGG-TCAA
1 ATCGGTTC-A
35690 ATCGGT
1 ATCGGT
35696 CTGACCGGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 9 0.32
9 19 0.68
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (9 bp):
ATCGGTTCA
Found at i:36375 original size:32 final size:32
Alignment explanation
Indices: 36330--36407 Score: 140
Period size: 32 Copynumber: 2.5 Consensus size: 32
36320 TGTGAGTTTG
*
36330 AGTT-GAGTTGAGCTTACTTTTAAAGTTTTCA
1 AGTTCGAGTCGAGCTTACTTTTAAAGTTTTCA
36361 AGTTCGAGTCGAGCTTACTTTTAAAGTTTTCA
1 AGTTCGAGTCGAGCTTACTTTTAAAGTTTTCA
36393 AGTTCGAGTCGAGCT
1 AGTTCGAGTCGAGCT
36408 CAGCAATATT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 4 0.09
32 41 0.91
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.40
Consensus pattern (32 bp):
AGTTCGAGTCGAGCTTACTTTTAAAGTTTTCA
Found at i:36680 original size:6 final size:6
Alignment explanation
Indices: 36671--36737 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
36661 AATTCGAATT
* * * *
36671 TATTTA TATTAA TTATTTA T-TTTA TTATTAA TATTTA TATTAA AATTT-
1 TATTTA TATTTA -TATTTA TATTTA -TATTTA TATTTA TATTTA TATTTA
*
36719 TATTTG TATTTA T-TTTA TA
1 TATTTA TATTTA TATTTA TA
36738 AATTATTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
5 13 0.28
6 26 0.55
7 8 0.17
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (6 bp):
TATTTA
Found at i:43621 original size:21 final size:21
Alignment explanation
Indices: 43507--43649 Score: 154
Period size: 21 Copynumber: 6.8 Consensus size: 21
43497 TTGTACCAAG
*
43507 GACGAGAAGAGCATTCATCAA
1 GACGAGAAGACCATTCATCAA
*
43528 GACGAGAATG-TCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
43549 GACGAGAATG-CCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
*
43570 GACGAGAAGGCCATTCATCAA
1 GACGAGAAGACCATTCATCAA
*
43591 GACGAGAAGACCTTTCAT-AA
1 GACGAGAAGACCATTCATCAA
43611 CGACGAGAAGACC-TTCAT-AA
1 -GACGAGAAGACCATTCATCAA
43631 CGAC-ATGAAGACCACTTCA
1 -GACGA-GAAGACCA-TTCA
43650 CATTGGAGGT
Statistics
Matches: 112, Mismatches: 4, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
19 1 0.01
20 21 0.19
21 85 0.76
22 5 0.04
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.17
Consensus pattern (21 bp):
GACGAGAAGACCATTCATCAA
Found at i:48553 original size:36 final size:36
Alignment explanation
Indices: 48397--48586 Score: 229
Period size: 36 Copynumber: 5.2 Consensus size: 36
48387 AAGTCAATCC
48397 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* * *
48433 GAAGCCTTCACCGGAGAATAGTGAAGCAATCAATCT
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* *
48469 GAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCA
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* * * *
48505 TAAGTCTTCACCAGAGAGTAGTGAAGTAAACCATCT
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* * * * *
48541 TAAGTCTTCACC-AAAAAGTAGTGAAGCATATCCATTT
1 TAAGCCTTCACCGGAGAA-TAGTGAAGCA-AACCATCT
48578 TAAGCCTTC
1 TAAGCCTTC
48587 TCAGAAGAGT
Statistics
Matches: 133, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
35 2 0.02
36 117 0.88
37 14 0.11
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (36 bp):
TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
Found at i:48865 original size:51 final size:51
Alignment explanation
Indices: 48800--50539 Score: 1988
Period size: 51 Copynumber: 33.8 Consensus size: 51
48790 AAGATTATTT
* * * * *
48800 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTTTGAAGATGTCC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * * * * *
48851 GAGTTCCATACTCCCTAGAGAAGGAAGGAGCGAACCCGTGTGAAGATATGC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * * *
48902 GAGTTCTATACTCCTTAAAGAAAGAATGAGCGAACCCGTTTAAAGATGTCC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * * * * *
48953 GAGTTCCATACTCCCTAGAGAAGGAAGGAGCGAACCCGTGTGAAGATATGC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * * *
49004 GAGTTCTATAATCCTTAAAGAAAGAAGGAGCGAAACCGTTTAAAGATG--C
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * * *
49053 GAGTTCTATACTCCTTAAAGAAAGAATGAGCGAACCCGTTTAAAGATGTCC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * * * * *
49104 GAGTTCCATACTCCCTAGAGAAGGAAGGAGCGAACCCGTGTGAAGATATGC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * * *
49155 GAGTTCTATAATCCTTAAAGAAAGAAGGAGCGAAACCGTTTAAAGATGTTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
*
49206 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAGCCCGTTTGAATAGATG-TC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTTC
* * * * * *
49258 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATGC
1 -GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * * *
49310 GAGTTCTATAATCCTTAAAGAAAGAAGGAGCGAACTCGTTTAAAGATGTTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
49361 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCAG-TTGAAGATGTTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCC-GTTTGAAGATGTTC
* * *
49412 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG--TGAAGAGATGTTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTTC
* * * * *
49463 GAGTTCCATACTCCCTAAAGAAAGAGGGAGCAAACCCATTTGAACATGTTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
*
49514 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
** *
49565 GAGTTTTATACTCCTTAAAGAAGGAAGGAGCGAACCCGTTTGAAGAGATGTTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTTC
* * * ** *
49618 GAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAG-ATGT-TC
* * * * * *
49671 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATGC
1 -GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * * *
49723 GAGTTCTATAATCCTTAAAGAAAGAAGGAGCGAACTCGTTTAAAGATGTTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
49774 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCAG-TTGAAGATGTTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCC-GTTTGAAGATGTTC
* * *
49825 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG--TGAAGAGATGTTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTTC
* * * * *
49876 GAGTTCCATACTCCCTAAAGAAAGAGGGAGCAAACCCATTTGAACATGTTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
*
49927 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
** *
49978 GAGTTTTATACTCCTTAAAGAAGGAAGGAGCGAACCCGTTTGAAGAGATGTTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTTC
* * * ** *
50031 GAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAG-ATGT-TC
* * * * * *
50084 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATGC
1 -GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * * * *
50136 GAGTTCTATAATCCTTAAAGAAAGAATGAGCGAACTCGTTTAAAGATGTTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
*
50187 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCAG-TTGAAGATGTGC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCC-GTTTGAAGATGTTC
* * * ***
50238 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAAAGATGTTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * *
50289 GAGTTCCATACTCCTTAAAGAAAGAGGGAGCAAACCCATTTGAAGATGTTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
*
50340 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
** *
50391 GAGTTTTATACTCCTTAAAGAAGGAAGGAGCGAACCCGTTTGAAGAGATGTTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTTC
* * * ** *
50444 GAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAG-ATGT-TC
* * * * * *
50497 TGAGTTCCATACTCCCTAGAGAAATAGGGAGTGAACCCATTTG
1 -GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG
50540 TTGAAGATTG
Statistics
Matches: 1460, Mismatches: 196, Indels: 63
0.85 0.11 0.04
Matches are distributed among these distances:
49 50 0.03
50 5 0.00
51 1065 0.73
52 27 0.02
53 192 0.13
54 121 0.08
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (51 bp):
GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
Found at i:49748 original size:413 final size:413
Alignment explanation
Indices: 48800--50534 Score: 2869
Period size: 413 Copynumber: 4.2 Consensus size: 413
48790 AAGATTATTT
* * * *
48800 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTTTGAAG---ATGTCCGAGTTCCATAC
1 GAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTCTGAGTTCCATAC
* * *
48862 TCCCTAGAGAAGGAAGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGA
66 TCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATAATCCTTAAAGAAAGA
* * * * * *
48927 ATGAGCGAACCCGTTTAAAGATGTCCGAGTTCCATACTCCCTAGAGAAGGAAGGAGCGAACCC-G
131 AGGAGCGAACTCGTTTAAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCAG
* * * * * * * *
48991 TGTGAAGATATGCGAGTTCTATAATCCTTAAAGAAAGAAGGAGCGAAACCGTTTAA-AGATG--C
196 T-TGAAGATGTGCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TGAAGAGATGTTC
* * ** * * * * * *
49053 GAGTTCTATACTCCTTAAAGAAAGAATGAGCGAACCCGTTTAAAGATGTCCGAGTTCCATACTCC
259 GAGTTCCATACTCCCTAAAGAAAGAGGGAGCAAACCCATTTGAACATGTTCGAGTTCTATACTCC
* * * * * * * * *
49118 CTAGAGAAGGAAGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATAATCCTTAAAGAAAGAAGG
324 TTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTTTATACTCCTTAAAGAAGGAAGG
*
49183 AGCGAAACCGTTT-AA-AGATGTTC
389 AGCGAACCCGTTTGAAGAGATGTTC
* * * ** * * *
49206 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAGCCCGTTTGAA-TAGATGTCTGAGTTCCATAC
1 GAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTCTGAGTTCCATAC
49270 TCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATAATCCTTAAAGAAAGA
66 TCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATAATCCTTAAAGAAAGA
49335 AGGAGCGAACTCGTTTAAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCAG
131 AGGAGCGAACTCGTTTAAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCAG
*
49400 TTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAGAGATGTTCGA
196 TTGAAGATGTGCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAGAGATGTTCGA
49465 GTTCCATACTCCCTAAAGAAAGAGGGAGCAAACCCATTTGAACATGTTCGAGTTCTATACTCCTT
261 GTTCCATACTCCCTAAAGAAAGAGGGAGCAAACCCATTTGAACATGTTCGAGTTCTATACTCCTT
49530 AAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTTTATACTCCTTAAAGAAGGAAGGAG
326 AAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTTTATACTCCTTAAAGAAGGAAGGAG
49595 CGAACCCGTTTGAAGAGATGTTC
391 CGAACCCGTTTGAAGAGATGTTC
49618 GAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTCTGAGTTCCATAC
1 GAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTCTGAGTTCCATAC
49683 TCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATAATCCTTAAAGAAAGA
66 TCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATAATCCTTAAAGAAAGA
49748 AGGAGCGAACTCGTTTAAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCAG
131 AGGAGCGAACTCGTTTAAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCAG
*
49813 TTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAGAGATGTTCGA
196 TTGAAGATGTGCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAGAGATGTTCGA
49878 GTTCCATACTCCCTAAAGAAAGAGGGAGCAAACCCATTTGAACATGTTCGAGTTCTATACTCCTT
261 GTTCCATACTCCCTAAAGAAAGAGGGAGCAAACCCATTTGAACATGTTCGAGTTCTATACTCCTT
49943 AAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTTTATACTCCTTAAAGAAGGAAGGAG
326 AAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTTTATACTCCTTAAAGAAGGAAGGAG
50008 CGAACCCGTTTGAAGAGATGTTC
391 CGAACCCGTTTGAAGAGATGTTC
50031 GAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTCTGAGTTCCATAC
1 GAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTCTGAGTTCCATAC
50096 TCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATAATCCTTAAAGAAAGA
66 TCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATAATCCTTAAAGAAAGA
*
50161 ATGAGCGAACTCGTTTAAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCAG
131 AGGAGCGAACTCGTTTAAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCAG
*
50226 TTGAAGATGTGCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAAAGATGTTCGA
196 TTGAAGATGTGCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAGAGATGTTCGA
* *
50291 GTTCCATACTCCTTAAAGAAAGAGGGAGCAAACCCATTTGAAGATGTTCGAGTTCTATACTCCTT
261 GTTCCATACTCCCTAAAGAAAGAGGGAGCAAACCCATTTGAACATGTTCGAGTTCTATACTCCTT
50356 AAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTTTATACTCCTTAAAGAAGGAAGGAG
326 AAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTTTATACTCCTTAAAGAAGGAAGGAG
50421 CGAACCCGTTTGAAGAGATGTTC
391 CGAACCCGTTTGAAGAGATGTTC
50444 GAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTCTGAGTTCCATAC
1 GAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTCTGAGTTCCATAC
* *
50509 TCCCTAGAGAAATAGGGAGTGAACCC
66 TCCCTAGAGAAAGAGGGAGCGAACCC
50535 ATTTGTTGAA
Statistics
Matches: 1260, Mismatches: 59, Indels: 13
0.95 0.04 0.01
Matches are distributed among these distances:
406 39 0.03
407 3 0.00
408 181 0.14
409 2 0.00
410 124 0.10
411 2 0.00
412 46 0.04
413 863 0.68
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (413 bp):
GAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTCTGAGTTCCATAC
TCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATAATCCTTAAAGAAAGA
AGGAGCGAACTCGTTTAAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCAG
TTGAAGATGTGCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAGAGATGTTCGA
GTTCCATACTCCCTAAAGAAAGAGGGAGCAAACCCATTTGAACATGTTCGAGTTCTATACTCCTT
AAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTTTATACTCCTTAAAGAAGGAAGGAG
CGAACCCGTTTGAAGAGATGTTC
Found at i:50577 original size:53 final size:53
Alignment explanation
Indices: 50516--50641 Score: 132
Period size: 55 Copynumber: 2.3 Consensus size: 53
50506 TACTCCCTAG
* *
50516 AGAAATAGGGAGTGAACCCATTTGTTGAAGATTG-T-GGGTCTTATACTCTCTGA
1 AGAAATAGGGAG-GAACCCA-TAGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
* * *
50569 AGATATAGGG-GGAAGACACGATAGTTGAAGATTGTTCGAGTCTTATACTCTCTGG
1 AGAAATAGGGAGG-A-AC-CCATAGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
50624 AGAAATAGGGAGCGAACC
1 AGAAATAGGGAG-GAACC
50642 TGTTTTTAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
51 1 0.02
52 2 0.03
53 23 0.38
54 4 0.07
55 27 0.45
56 2 0.03
57 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (53 bp):
AGAAATAGGGAGGAACCCATAGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
Found at i:56750 original size:15 final size:15
Alignment explanation
Indices: 56725--56767 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
56715 GTTGTGTTTA
*
56725 TATTTTTTAAAATAT
1 TATTATTTAAAATAT
56740 T-TTAATTTAAAAATAT
1 TATT-ATTT-AAAATAT
56756 TATTATTTAAAA
1 TATTATTTAAAA
56768 AAATATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
14 2 0.08
15 8 0.33
16 12 0.50
17 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTATTTAAAATAT
Found at i:56776 original size:17 final size:18
Alignment explanation
Indices: 56733--56776 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
56723 TATATTTTTT
*
56733 AAAATATTTTAATTTAAA
1 AAAATATATTAATTTAAA
*
56751 AATAT-TATT-ATTTAAA
1 AAAATATATTAATTTAAA
56767 AAAATATATT
1 AAAATATATT
56777 TTCTAAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 11 0.50
17 7 0.32
18 4 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAATATATTAATTTAAA
Found at i:57781 original size:22 final size:22
Alignment explanation
Indices: 57738--57781 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
57728 GCCTCAACTC
* *
57738 CTTAAATCCATAAATTTTTAAA
1 CTTAAATCCATAAATCTCTAAA
57760 CTTAAATTCC-TAAATCTCTAAA
1 CTTAAA-TCCATAAATCTCTAAA
57782 ATCTTTGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (22 bp):
CTTAAATCCATAAATCTCTAAA
Found at i:57844 original size:23 final size:23
Alignment explanation
Indices: 57771--57846 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
57761 TTAAATTCCT
*
57771 AAATCTCTAAAATCTTTGATACCC
1 AAAT-TCTTAAATCTTTGATACCC
* * **
57795 AAATTCCCTAAAT-TCTT-AAACTT
1 AAATT-CTTAAATCT-TTGATACCC
57818 AAATTCTTAAATCTTTGATACCC
1 AAATTCTTAAATCTTTGATACCC
57841 AAATTC
1 AAATTC
57847 CCTAAATTCC
Statistics
Matches: 39, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
22 8 0.21
23 20 0.51
24 11 0.28
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.37
Consensus pattern (23 bp):
AAATTCTTAAATCTTTGATACCC
Found at i:59006 original size:11 final size:10
Alignment explanation
Indices: 58957--59018 Score: 61
Period size: 11 Copynumber: 5.9 Consensus size: 10
58947 TTTACATTAT
*
58957 ATTTTTATTG
1 ATTTTTATTC
*
58967 AATTTTATTC
1 ATTTTTATTC
58977 ATTTTTAATTC
1 ATTTTT-ATTC
*
58988 TTTTTTATTGC
1 ATTTTTATT-C
*
58999 ATTTTTATTT
1 ATTTTTATTC
59009 ATTTTATATT
1 ATTTT-TATT
59019 TTTTATAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
10 21 0.49
11 22 0.51
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (10 bp):
ATTTTTATTC
Found at i:59014 original size:31 final size:31
Alignment explanation
Indices: 58958--59022 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
58948 TTACATTATA
58958 TTTTTATTGAATTTTATTCATTTTTA-ATTCT
1 TTTTTATTGAATTTTATTCATTTTTATATT-T
* *
58989 TTTTTATTGCATTTTTATTTA-TTTTATATTT
1 TTTTTATTG-AATTTTATTCATTTTTATATTT
59020 TTT
1 TTT
59023 ATAATTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 18 0.60
32 12 0.40
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (31 bp):
TTTTTATTGAATTTTATTCATTTTTATATTT
Found at i:67940 original size:35 final size:34
Alignment explanation
Indices: 67855--67941 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
67845 ATTTGGTATT
*
67855 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
67889 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
67927 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
67942 ACTAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:68169 original size:3 final size:3
Alignment explanation
Indices: 68163--68206 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
68153 GTCATCATCA
* * *
68163 TCG TCG TCA TCG TCG TCG TTG TCG TCG TCG TCG TCG TCG CCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
68207 CTGAGCAGGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.02, C:0.34, G:0.30, T:0.34
Consensus pattern (3 bp):
TCG
Found at i:68178 original size:12 final size:12
Alignment explanation
Indices: 68157--68206 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
68147 CTCGCTGTCA
*
68157 TCATCATCGTCG
1 TCATCGTCGTCG
68169 TCATCGTCGTCG
1 TCATCGTCGTCG
**
68181 TTGTCGTCGTCG
1 TCATCGTCGTCG
* *
68193 TCGTCGTCGCCG
1 TCATCGTCGTCG
68205 TC
1 TC
68207 CTGAGCAGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.06, C:0.34, G:0.26, T:0.34
Consensus pattern (12 bp):
TCATCGTCGTCG
Found at i:70241 original size:17 final size:18
Alignment explanation
Indices: 70221--70261 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
70211 GAATTATATT
70221 AGTAAAAT-ATTAAATAA
1 AGTAAAATAATTAAATAA
70238 AGTAAAATAATTAAATAA
1 AGTAAAATAATTAAATAA
*
70256 ATTAAA
1 AGTAAA
70262 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATAATTAAATAA
Found at i:71185 original size:25 final size:25
Alignment explanation
Indices: 71143--71194 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
71133 GACAATTACA
* **
71143 ATATATAAAAATATAAATTTAAAAT
1 ATATATAAAAATAAAAATGAAAAAT
* *
71168 ATATCTAAAATTAAAAATGAAAAAT
1 ATATATAAAAATAAAAATGAAAAAT
71193 AT
1 AT
71195 TTTTTATTCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (25 bp):
ATATATAAAAATAAAAATGAAAAAT
Found at i:71397 original size:18 final size:19
Alignment explanation
Indices: 71357--71400 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
71347 TTTGGTTCAC
* *
71357 GGAATATAAGATTATCAGTG
1 GGAATAAAAGATTACCAG-G
71377 GGAATAAAAGATTACCA-G
1 GGAATAAAAGATTACCAGG
71395 GGAATA
1 GGAATA
71401 GGATTACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.45, C:0.07, G:0.25, T:0.23
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:71589 original size:36 final size:37
Alignment explanation
Indices: 71540--71615 Score: 104
Period size: 36 Copynumber: 2.1 Consensus size: 37
71530 ATAATATTAC
71540 AAATTGTAAAATATTTATAT-ATTTTCTTTA-AAAAGTT
1 AAATTGTAAAATATTTATATAATTTT-TTTACAAAA-TT
*
71577 AAATT-TATAATATTTATATAATTTTTTTACAAAATT
1 AAATTGTAAAATATTTATATAATTTTTTTACAAAATT
71613 AAA
1 AAA
71616 AATATAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 22 0.61
37 14 0.39
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (37 bp):
AAATTGTAAAATATTTATATAATTTTTTTACAAAATT
Found at i:72829 original size:2 final size:2
Alignment explanation
Indices: 72822--72846 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
72812 AAAAAGGAAT
72822 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
72847 TTCGTCTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:75579 original size:2 final size:2
Alignment explanation
Indices: 75572--75615 Score: 72
Period size: 2 Copynumber: 22.0 Consensus size: 2
75562 TGAAAGCAGT
75572 TA TA TA TA TA GT- 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
75614 TA
1 TA
75616 ATTAGAATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 38 0.95
3 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:77252 original size:15 final size:15
Alignment explanation
Indices: 77229--77262 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
77219 GTCATTTGGA
*
77229 TCGGGTCAGGTTATT
1 TCGGATCAGGTTATT
77244 TCGGATCAGGTTATT
1 TCGGATCAGGTTATT
77259 TCGG
1 TCGG
77263 TTTTAGACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.32, T:0.38
Consensus pattern (15 bp):
TCGGATCAGGTTATT
Found at i:78725 original size:19 final size:19
Alignment explanation
Indices: 78701--78737 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
78691 AATTTAAATC
78701 GTAAGTAACATTACTTATA
1 GTAAGTAACATTACTTATA
*
78720 GTAAGTAACGTTACTTAT
1 GTAAGTAACATTACTTAT
78738 CATAGTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (19 bp):
GTAAGTAACATTACTTATA
Found at i:78756 original size:2 final size:2
Alignment explanation
Indices: 78749--78803 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
78739 ATAGTTTCAG
*
78749 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
78790 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
78804 TTCTTTGTTG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:79213 original size:39 final size:39
Alignment explanation
Indices: 79139--79213 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
79129 GTTGAATATG
** *
79139 TTGCAACAAAAAATATTACATTCTTCGTAACATTTTATA
1 TTGCAACAAAAAATATTACATTCTTCACAAAATTTTATA
* *
79178 TTGCAACAAAAAATGTTATATTCTTCACAAAATTTT
1 TTGCAACAAAAAATATTACATTCTTCACAAAATTTT
79214 GGTTGTAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (39 bp):
TTGCAACAAAAAATATTACATTCTTCACAAAATTTTATA
Found at i:81416 original size:19 final size:19
Alignment explanation
Indices: 81392--81451 Score: 88
Period size: 19 Copynumber: 3.3 Consensus size: 19
81382 GCCAGGGAGA
81392 GCATCGATGCATGGTCTGT
1 GCATCGATGCATGGTCTGT
* *
81411 GCATCGATTCATGGTTTGT
1 GCATCGATGCATGGTCTGT
81430 GCATCGATGC-T-GTCTGT
1 GCATCGATGCATGGTCTGT
81447 GCATC
1 GCATC
81452 TACACAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.27
18 1 0.03
19 26 0.70
ACGTcount: A:0.15, C:0.22, G:0.28, T:0.35
Consensus pattern (19 bp):
GCATCGATGCATGGTCTGT
Found at i:81889 original size:13 final size:12
Alignment explanation
Indices: 81867--81894 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
81857 TTTTCTTGGA
81867 AAATCATTTTTG
1 AAATCATTTTTG
81879 AAATCATTTTTG
1 AAATCATTTTTG
81891 AAAT
1 AAAT
81895 TACTCCCCCT
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:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (12 bp):
AAATCATTTTTG
Found at i:84244 original size:44 final size:44
Alignment explanation
Indices: 84181--84283 Score: 136
Period size: 44 Copynumber: 2.4 Consensus size: 44
84171 GATGCATAGC
* * * *
84181 ATGGTGCATTGATTCACATTCAAGGAATGCATCGGTGCACCCTT
1 ATGGTGTATCGATGCACATTCAAGGAATGCATCGGTACACCCTT
* *
84225 ATGGTGTATCGATGCACATTCAAGGGATGCATCGGTACACTCTT
1 ATGGTGTATCGATGCACATTCAAGGAATGCATCGGTACACCCTT
*
84269 -TAGTGTATCGATGCA
1 ATGGTGTATCGATGCA
84284 TGTTGCACAA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
43 14 0.27
44 38 0.73
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (44 bp):
ATGGTGTATCGATGCACATTCAAGGAATGCATCGGTACACCCTT
Found at i:85919 original size:2 final size:2
Alignment explanation
Indices: 85912--85984 Score: 132
Period size: 2 Copynumber: 37.5 Consensus size: 2
85902 ATCACAAACA
85912 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT A- 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
85952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
85985 CATTATTATC
Statistics
Matches: 69, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 67 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:86979 original size:20 final size:23
Alignment explanation
Indices: 86954--87002 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
86944 CCTTGAAGTT
86954 ATGCATTC-T-ACA-GTGCATCG
1 ATGCATTCTTAACATGTGCATCG
86974 ATGCATTCTTTAACATGTGCATCG
1 ATGCATTC-TTAACATGTGCATCG
86998 ATGCA
1 ATGCA
87003 CTACCCATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.32
22 1 0.04
23 3 0.12
24 13 0.52
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (23 bp):
ATGCATTCTTAACATGTGCATCG
Done.