Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002437.1 Hibiscus syriacus cultivar Beakdansim tig00004989_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: 91461
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:10368 original size:29 final size:29
Alignment explanation
Indices: 10343--10498 Score: 112
Period size: 29 Copynumber: 5.6 Consensus size: 29
10333 TTTAAAAAAT
10343 TTACAAAAATATCACCCTTTTCAAAATAA
1 TTACAAAAATATCACCCTTTTCAAAATAA
* **
10372 TTACTAAAATATCA---TTTTCTTTAA-AA
1 TTACAAAAATATCACCCTTTTC-AAAATAA
* *
10398 TTACAAAATTATCACTC-TTT-AAAA-AA
1 TTACAAAAATATCACCCTTTTCAAAATAA
* * * **
10424 TTACGAAAATAGCGCTATTTTCAAAATAA
1 TTACAAAAATATCACCCTTTTCAAAATAA
* * *
10453 TTACCAAAATACCACCAATTTT-AAAATAA
1 TTACAAAAATATCACC-CTTTTCAAAATAA
*
10482 TTACTAAAATATCACCC
1 TTACAAAAATATCACCC
10499 AGTCAACGAT
Statistics
Matches: 100, Mismatches: 19, Indels: 17
0.74 0.14 0.12
Matches are distributed among these distances:
26 35 0.35
27 5 0.05
28 7 0.07
29 48 0.48
30 5 0.05
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (29 bp):
TTACAAAAATATCACCCTTTTCAAAATAA
Found at i:10423 original size:26 final size:27
Alignment explanation
Indices: 10333--10433 Score: 77
Period size: 26 Copynumber: 3.7 Consensus size: 27
10323 AACACCTTTT
* *
10333 TTTAAAAAATTTAC-AAAAATATCACCC
1 TTTAAAAAA-TTACGAAAATTATCACTC
* *
10360 TTTTCAAAATAATTACTAAAA-TATCATTTTC
1 -TTT-AAAA-AATTACGAAAATTATCA--CTC
10391 TTT--AAAATTAC-AAAATTATCACTC
1 TTTAAAAAATTACGAAAATTATCACTC
10415 TTTAAAAAATTACGAAAAT
1 TTTAAAAAATTACGAAAAT
10434 AGCGCTATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
24 5 0.08
25 4 0.07
26 19 0.31
27 7 0.11
28 3 0.05
29 13 0.21
30 9 0.15
31 1 0.02
ACGTcount: A:0.49, C:0.14, G:0.01, T:0.37
Consensus pattern (27 bp):
TTTAAAAAATTACGAAAATTATCACTC
Found at i:10553 original size:20 final size:19
Alignment explanation
Indices: 10530--10567 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
10520 GTTACAACCA
*
10530 GTCAAATCGGTTCAAAATCG
1 GTCAAACCGG-TCAAAATCG
10550 GTCAAACCGGTCAAAATC
1 GTCAAACCGGTCAAAATC
10568 TGTGTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (19 bp):
GTCAAACCGGTCAAAATCG
Found at i:17386 original size:29 final size:29
Alignment explanation
Indices: 17354--17495 Score: 150
Period size: 29 Copynumber: 5.0 Consensus size: 29
17344 AAAATTTATG
17354 AAAATATCATCATTTTCAAAATAATTACT
1 AAAATATCATCATTTTCAAAATAATTACT
*
17383 AAAATAAC-TCTATTTTCAAAATAATTACT
1 AAAATATCATC-ATTTTCAAAATAATTACT
** *
17412 AAAATATCATTTTTTTTAAAA-AATTA-T
1 AAAATATCATCATTTTCAAAATAATTACT
* *
17439 AAAATTATCATTC-TTTT-AAAAAAATTACA
1 AAAA-TATCA-TCATTTTCAAAATAATTACT
* *
17468 AAAATAGCACCATTTTCAAAATAATTAC
1 AAAATATCATCATTTTCAAAATAATTAC
17496 CACCACTAAT
Statistics
Matches: 95, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
27 10 0.11
28 29 0.31
29 55 0.58
30 1 0.01
ACGTcount: A:0.49, C:0.12, G:0.01, T:0.38
Consensus pattern (29 bp):
AAAATATCATCATTTTCAAAATAATTACT
Found at i:17437 original size:28 final size:28
Alignment explanation
Indices: 17337--17495 Score: 135
Period size: 29 Copynumber: 5.5 Consensus size: 28
17327 TTAACACCTT
* *
17337 TTTTTAAAAAATTTA-TGAAAATATCATCA
1 TTTTCAAAAAA-TTACT-AAAATATCATTA
*
17366 TTTTCAAAATAATTACTAAAATAAC-TCTA
1 TTTTCAAAA-AATTACTAAAATATCAT-TA
*
17395 TTTTCAAAATAATTACTAAAATATCATTT
1 TTTTCAAAA-AATTACTAAAATATCATTA
* *
17424 TTTTTAAAAAATTA-TAAAATTATCATTC
1 TTTTCAAAAAATTACTAAAA-TATCATTA
* * * **
17452 TTTTAAAAAAATTACAAAAATAGCACCA
1 TTTTCAAAAAATTACTAAAATATCATTA
17480 TTTTCAAAATAATTAC
1 TTTTCAAAA-AATTAC
17496 CACCACTAAT
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
27 5 0.05
28 38 0.35
29 62 0.57
30 4 0.04
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.40
Consensus pattern (28 bp):
TTTTCAAAAAATTACTAAAATATCATTA
Found at i:17483 original size:85 final size:87
Alignment explanation
Indices: 17335--17495 Score: 231
Period size: 85 Copynumber: 1.9 Consensus size: 87
17325 AATTAACACC
* * * *
17335 TTTTTTTAAAAAATTTATGAAAATATCATCATTTTCAAAATAATTACTAAAATAACTCTATTTTC
1 TTTTTTTAAAAAATTTATGAAAATATCATCATTTTCAAAAAAATTACAAAAATAACACCATTTTC
17400 AAAATAATTACTAAAATATCAT
66 AAAATAATTACTAAAATATCAT
*
17422 TTTTTTTAAAAAA-TTAT-AAAATTATCATTC-TTTT-AAAAAAATTACAAAAATAGCACCATTT
1 TTTTTTTAAAAAATTTATGAAAA-TATCA-TCATTTTCAAAAAAATTACAAAAATAACACCATTT
17483 TCAAAATAATTAC
64 TCAAAATAATTAC
17496 CACCACTAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
85 39 0.58
86 13 0.19
87 15 0.22
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.40
Consensus pattern (87 bp):
TTTTTTTAAAAAATTTATGAAAATATCATCATTTTCAAAAAAATTACAAAAATAACACCATTTTC
AAAATAATTACTAAAATATCAT
Found at i:25797 original size:11 final size:14
Alignment explanation
Indices: 25769--25799 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
25759 GCCACCTCGT
25769 AGAAAAACTAGAGA
1 AGAAAAACTAGAGA
*
25783 AGAAAAACTGGAGA
1 AGAAAAACTAGAGA
25797 AGA
1 AGA
25800 TGAGAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.26, T:0.06
Consensus pattern (14 bp):
AGAAAAACTAGAGA
Found at i:25839 original size:204 final size:206
Alignment explanation
Indices: 25522--25935 Score: 600
Period size: 204 Copynumber: 2.0 Consensus size: 206
25512 AAGATTCAGC
** *
25522 TGATACAGAAGAGAAAATGCCGAAGGTGTCACCACCTCGTAGAAAAGCAACAAGAGAAGAAACAC
1 TGATACAGAAGAGAAAATAACGAAGGTGTCACCACCTCGTAGAAAA-CAACAAGAGAAGAAAAAC
* * *
25587 CAGAGAAGATGAGGAATATGGCCAAGAAAGATGGTGGAACTTCTGATTTGTCCACTTCAAACTCT
65 CAGAGAAGATGAGAAATATGGCCAAGAAAGATGGAGGAACATCTGATTTGTCCACTTCAAACTCT
* * *
25652 AGGC-GAGCGAATGCTGTTAATAATTATGAAGCAAATAACTTTGGATATAGACAATATGATCCTG
130 AGGCAG-GCGAATGCTGTTAATAATTACGAAACAAATAACGTTGGATATAGACAATATGATCCTG
*
25716 AGCCTTCCACTGA
194 AGCCTCCCACTGA
* * * *
25729 TGATACAGAAGAGAAAGTAACGAAGGTGTCGCCACCTCGTAG-AAA-AACTAGAGAAGAAAAACT
1 TGATACAGAAGAGAAAATAACGAAGGTGTCACCACCTCGTAGAAAACAACAAGAGAAGAAAAACC
* ** **
25792 GGAGAAGATGAGAAATATGGCCAAGAAAGATGGAGGAGGATCTGATTTGTCTGCTTCAAACTCTA
66 AGAGAAGATGAGAAATATGGCCAAGAAAGATGGAGGAACATCTGATTTGTCCACTTCAAACTCTA
* *
25857 GGCAGGTGAATGCTGTTAATAATTACGAAACAAGTAACGTTGGATATAGACAATATGATCCTGAG
131 GGCAGGCGAATGCTGTTAATAATTACGAAACAAATAACGTTGGATATAGACAATATGATCCTGAG
25922 CCTCCCACTGA
196 CCTCCCACTGA
25933 TGA
1 TGA
25936 GAATATCAAT
Statistics
Matches: 185, Mismatches: 21, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
204 143 0.77
205 1 0.01
206 3 0.02
207 38 0.21
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (206 bp):
TGATACAGAAGAGAAAATAACGAAGGTGTCACCACCTCGTAGAAAACAACAAGAGAAGAAAAACC
AGAGAAGATGAGAAATATGGCCAAGAAAGATGGAGGAACATCTGATTTGTCCACTTCAAACTCTA
GGCAGGCGAATGCTGTTAATAATTACGAAACAAATAACGTTGGATATAGACAATATGATCCTGAG
CCTCCCACTGA
Found at i:29944 original size:24 final size:24
Alignment explanation
Indices: 29911--29973 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
29901 TAATTTATTA
*
29911 TGTTCGTTTACATTCATTCGTTTG
1 TGTTCGTTTACATTCATTCATTTG
* *
29935 TGTTCATTTACATTCGTTCATTTG
1 TGTTCGTTTACATTCATTCATTTG
*
29959 TATTCGTTTATCATT
1 TGTTCGTTTA-CATT
29974 TAAATGAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
24 29 0.88
25 4 0.12
ACGTcount: A:0.16, C:0.16, G:0.13, T:0.56
Consensus pattern (24 bp):
TGTTCGTTTACATTCATTCATTTG
Found at i:31303 original size:13 final size:13
Alignment explanation
Indices: 31266--31305 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
31256 TTGATATTGA
31266 AAAATAAATA-TT
1 AAAATAAATATTT
*
31278 AAAATAATTTATTT
1 AAAATAA-ATATTT
31292 AAAATAAATATTT
1 AAAATAAATATTT
31305 A
1 A
31306 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:32710 original size:3 final size:3
Alignment explanation
Indices: 32702--32791 Score: 153
Period size: 3 Copynumber: 29.7 Consensus size: 3
32692 TTAATATATT
*
32702 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
32750 TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TTAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TA
32792 TGGGTAAAAA
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
3 79 0.96
4 3 0.04
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:33356 original size:114 final size:114
Alignment explanation
Indices: 33106--33777 Score: 1141
Period size: 114 Copynumber: 5.9 Consensus size: 114
33096 GATAGAATTA
* * *
33106 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTTTCATTAT
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
* * * * * * * * *
33171 GAACTCTAC-CTGGCAATGTTGATCCATCAA-ATGATGAATTCAAGCAAAAGA
63 GAACT-TTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
*
33222 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
33287 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
* *
33336 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTGTGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
33401 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
*
33450 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
33515 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
33564 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
33629 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
33678 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
33743 CCTTCTCTGGAAAAGATAATCCATCAATTTGATGA
66 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGA
33778 TAGATTTCAA
Statistics
Matches: 537, Mismatches: 17, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
112 2 0.00
113 37 0.07
114 453 0.84
116 45 0.08
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (114 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
Found at i:34721 original size:83 final size:83
Alignment explanation
Indices: 34577--34830 Score: 438
Period size: 83 Copynumber: 3.1 Consensus size: 83
34567 CTTATTTCTA
* * * * *
34577 CTATGAGCAAATTCGTCTTTCAAATTTAATGATTGGTTCT-ACCAAACCAGATCAGATAACTCAA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAA
*
34641 AGAACACTTTCAGAAGATG
65 AGAACACTTCCAGAAGATG
34660 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
34725 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
34743 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
34808 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
34826 CTATT
1 CTATT
34831 GAGTCTCCTT
Statistics
Matches: 164, Mismatches: 6, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
83 162 0.99
84 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (83 bp):
CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:34859 original size:188 final size:188
Alignment explanation
Indices: 34660--35017 Score: 628
Period size: 188 Copynumber: 1.9 Consensus size: 188
34650 TCAGAAGATG
*
34660 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
*
34725 GAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-AA
66 GAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAA
34789 CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTA
130 CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTA
* * *
34848 CTATGAGCAAATTCGTCTTTCAAATTTAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
* * *
34913 GAATACTTCCAGAAGATGCTATGAGCACATTCATCTTCCCAATTCAATGATTGGTTCTGCCAAAC
66 GAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAAC
34978 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
131 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
35018 GAGCACATTC
Statistics
Matches: 161, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
187 2 0.01
188 159 0.99
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (188 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAAC
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTA
Found at i:34930 original size:105 final size:105
Alignment explanation
Indices: 34743--34934 Score: 339
Period size: 105 Copynumber: 1.8 Consensus size: 105
34733 CCAGAAGATG
*
34743 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
34808 GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTA
66 GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTA
* * *
34848 CTATGAGCAAATTCGTCTTTCAAATTTAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
*
34913 GAATACTTCCAGAAGATGCTAT
66 GAACACTTCCAGAAGATGCTAT
34935 GAGCACATTC
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 82 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (105 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTA
Found at i:34987 original size:83 final size:83
Alignment explanation
Indices: 34848--35117 Score: 445
Period size: 83 Copynumber: 3.3 Consensus size: 83
34838 CTTATTTCTA
* * * *
34848 CTATGAGCAAATTCGTCTTTCAAATTTAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAA
1 CTATGAGCAAATTCATCTTCCCAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAA
*
34912 AGAATACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
*
34931 CTATGAGCACATTCATCTTCCCAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCCAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
34996 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
35014 CTATGAGCACATTCATCTTCCCAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCCAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
35079 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
35097 CTATTG-GCAAATTCATCTTCC
1 CTA-TGAGCAAATTCATCTTCC
35118 AGTTAATGTT
Statistics
Matches: 178, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
82 2 0.01
83 174 0.98
84 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCCCAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:34999 original size:271 final size:271
Alignment explanation
Indices: 34513--35102 Score: 1051
Period size: 271 Copynumber: 2.2 Consensus size: 271
34503 GTAGTTCCTA
34513 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTAC
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTAC
34578 TATGAGCAAATTCGTCTTTCAAATTTAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAAG
66 TATGAGCAAATTCGTCTTTCAAATTTAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAAG
* *
34643 AACACTTTCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACC
131 AACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACC
*
34708 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAAT
196 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTCAAT
34773 GATTGGTTCTG
261 GATTGGTTCTG
34784 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTA
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTA
*
34848 CTATGAGCAAATTCGTCTTTCAAATTTAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAA
65 CTATGAGCAAATTCGTCTTTCAAATTTAATGATTGGTTCT-ACCAAACCAGATCAGATAACTCAA
* * *
34912 AGAATACTTCCAGAAGATGCTATGAGCACATTCATCTTCCCAATTCAATGATTGGTTCTG-CCAA
129 AGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-A
* *
34976 ACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCCAATTC
193 ACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTC
35041 AATGATTGGTTCTG
258 AATGATTGGTTCTG
35055 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
35103 GCAAATTCAT
Statistics
Matches: 306, Mismatches: 9, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
270 4 0.01
271 298 0.97
272 4 0.01
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (271 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTAC
TATGAGCAAATTCGTCTTTCAAATTTAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACC
AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTCAAT
GATTGGTTCTG
Found at i:36273 original size:14 final size:14
Alignment explanation
Indices: 36254--36316 Score: 87
Period size: 14 Copynumber: 4.6 Consensus size: 14
36244 GACCCCCCTT
36254 TTTTCTTTTTTTTC
1 TTTTCTTTTTTTTC
36268 TTTTCTTTTTTTTC
1 TTTTCTTTTTTTTC
36282 TTCTT-TTTTTTTTC
1 TT-TTCTTTTTTTTC
*
36296 TTTT-TTTTTTCT-
1 TTTTCTTTTTTTTC
36308 TTTTCTTTT
1 TTTTCTTTT
36317 CCTTTTTCTT
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
12 4 0.09
13 13 0.28
14 27 0.59
15 2 0.04
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTCTTTTTTTTC
Found at i:36282 original size:23 final size:23
Alignment explanation
Indices: 36252--36323 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
36242 TTGACCCCCC
36252 TTTTTTCTTTTTTTTCTTTTCTT
1 TTTTTTCTTTTTTTTCTTTTCTT
36275 TTTTTTCTTCTTTTTT-TTTTCTT
1 TTTTTTCTT-TTTTTTCTTTTCTT
* *
36298 TTTTTT-TTCTTTTTCTTTTCCT
1 TTTTTTCTTTTTTTTCTTTTCTT
36320 TTTT
1 TTTT
36324 CTTCAAGCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
21 5 0.11
22 12 0.27
23 22 0.49
24 6 0.13
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (23 bp):
TTTTTTCTTTTTTTTCTTTTCTT
Found at i:36291 original size:28 final size:28
Alignment explanation
Indices: 36259--36326 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
36249 CCCTTTTTTC
36259 TTTTTTTTCTTTTCTTTTTT-TTCTTCTT
1 TTTTTTTTCTTTT-TTTTTTCTTCTTCTT
*
36287 TTTTTTTTCTTTTTTTTTTCTTTTTCTT
1 TTTTTTTTCTTTTTTTTTTCTTCTTCTT
*
36315 TTCCTTTTTCTT
1 TT-TTTTTTCTT
36327 CAAGCATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 6 0.17
28 22 0.61
29 8 0.22
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (28 bp):
TTTTTTTTCTTTTTTTTTTCTTCTTCTT
Found at i:36323 original size:1 final size:1
Alignment explanation
Indices: 36252--36316 Score: 58
Period size: 1 Copynumber: 65.0 Consensus size: 1
36242 TTGACCCCCC
* * * * * * * *
36252 TTTTTTCTTTTTTTTCTTTTCTTTTTTTTCTTCTTTTTTTTTTCTTTTTTTTTTCTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
36317 CCTTTTTCTT
Statistics
Matches: 48, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:36326 original size:12 final size:11
Alignment explanation
Indices: 36251--36323 Score: 94
Period size: 11 Copynumber: 6.5 Consensus size: 11
36241 CTTGACCCCC
*
36251 CTTTTTTCTTT
1 CTTTTTTTTTT
*
36262 -TTTTTCTTTT
1 CTTTTTTTTTT
36272 CTTTTTTTTCTT
1 CTTTTTTTT-TT
36284 CTTTTTTTTTT
1 CTTTTTTTTTT
36295 CTTTTTTTTTT
1 CTTTTTTTTTT
*
36306 CTTTTTCTTTTC
1 CTTTTT-TTTTT
36318 CTTTTT
1 CTTTTT
36324 CTTCAAGCAT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
10 8 0.15
11 26 0.47
12 21 0.38
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:48439 original size:3 final size:3
Alignment explanation
Indices: 48431--48509 Score: 104
Period size: 3 Copynumber: 26.3 Consensus size: 3
48421 TTAATATATT
* * * * *
48431 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTA TTA TTA TTA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
48479 TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
48510 TAATTAATAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:49798 original size:23 final size:24
Alignment explanation
Indices: 49687--49798 Score: 117
Period size: 23 Copynumber: 4.9 Consensus size: 24
49677 AAAAAATGAA
* *
49687 AAACGTGCCACAAAT-ACAGAGAT
1 AAACGTGCAACACATGACAGAGAT
* * *
49710 AAACGTGCCACA-AAGATAGAGAT
1 AAACGTGCAACACATGACAGAGAT
*
49733 AAATGTGCAACACATG-CAGAGAT
1 AAACGTGCAACACATGACAGAGAT
*
49756 AAATGTGCAACACATG-CAGAGAT
1 AAACGTGCAACACATGACAGAGAT
*
49779 AAACATGCAACAC-TGACAGA
1 AAACGTGCAACACATGACAGA
49799 ATTATTCTTA
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
22 3 0.04
23 73 0.94
24 2 0.03
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.14
Consensus pattern (24 bp):
AAACGTGCAACACATGACAGAGAT
Found at i:50163 original size:18 final size:18
Alignment explanation
Indices: 50123--50166 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
50113 ATGATTAATC
*
50123 ATTAATAATTAATTATTT
1 ATTAATAATTAATAATTT
*
50141 TTTAATAATTAA-AATTT
1 ATTAATAATTAATAATTT
50158 GATTAATAA
1 -ATTAATAA
50167 AATTTAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
ATTAATAATTAATAATTT
Found at i:59032 original size:37 final size:37
Alignment explanation
Indices: 58991--59066 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
58981 GTTCAAAGAT
*
58991 GACGTCCTTGATATCCATTAATTGCTCGAATGGTAAA
1 GACGTCCTTGATATCCATTAATTGCTCGAATGATAAA
* *
59028 GACGTCTTTGATATCCATTAATTGGTCGAATGATAAA
1 GACGTCCTTGATATCCATTAATTGCTCGAATGATAAA
59065 GA
1 GA
59067 ATATTCATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (37 bp):
GACGTCCTTGATATCCATTAATTGCTCGAATGATAAA
Found at i:60590 original size:129 final size:130
Alignment explanation
Indices: 60359--60656 Score: 364
Period size: 129 Copynumber: 2.3 Consensus size: 130
60349 CCAATAAAAC
* * * * * *
60359 AGTCCTAAGATCGATGTAAATGGTTCCATCTCTTTTTTTCTGGAATTCTGATAAAATGAGATTGA
1 AGTCCTAAGATCGATGTAAATGATTCCATCTCGTTTGTTATGGAATTCTAATAAAATGAGATAGA
* ** * * * ** * *
60424 AGTCCTGAAATTGGTGTAAATGATCCCATCTCATTTGTTATGGAATTCTGATAAAATGAGATTGA
66 AGTCCTAAAATCAGTGTAAACGATCCCATCTCATTTGTTATAGAACTCCAATAAAATGACATAGA
60489 AGTCCTAAGATCGATGTAAATGATTCCATCTCGTTTGTTATGG-ATTCTAATAAAATGAGATAGA
1 AGTCCTAAGATCGATGTAAATGATTCCATCTCGTTTGTTATGGAATTCTAATAAAATGAGATAGA
* * * *
60553 AGTCCTAAAATCAGTGTAAACGATCCTATCTCGTTTGTTCTAGAACTCCAATAGAATGACATAGA
66 AGTCCTAAAATCAGTGTAAACGATCCCATCTCATTTGTTATAGAACTCCAATAAAATGACATAGA
* * * * *
60618 AGTCCTAAGTTCGGTGTAAATGCTCCCATCTTGTTTGTT
1 AGTCCTAAGATCGATGTAAATGATTCCATCTCGTTTGTT
60657 CTATAATAGA
Statistics
Matches: 143, Mismatches: 25, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
129 104 0.73
130 39 0.27
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.35
Consensus pattern (130 bp):
AGTCCTAAGATCGATGTAAATGATTCCATCTCGTTTGTTATGGAATTCTAATAAAATGAGATAGA
AGTCCTAAAATCAGTGTAAACGATCCCATCTCATTTGTTATAGAACTCCAATAAAATGACATAGA
Found at i:60657 original size:65 final size:65
Alignment explanation
Indices: 60359--60659 Score: 318
Period size: 65 Copynumber: 4.6 Consensus size: 65
60349 CCAATAAAAC
* * * * * * * *
60359 AGTCCTAAGATCGATGTAAATGGTTCCATCTCTTTTTTTCTGGAATTCTGATAAAATGAGATTGA
1 AGTCCTAAGATCGGTGTAAATGATCCCATCTCGTTTGTTCTAGAATTCTAATAAAATGAGATAGA
* * * * * *
60424 AGTCCTGAA-ATTGGTGTAAATGATCCCATCTCATTTGTTATGGAATTCTGATAAAATGAGATTG
1 AGTCCT-AAGATCGGTGTAAATGATCCCATCTCGTTTGTTCTAGAATTCTAATAAAATGAGATAG
60488 A
65 A
* * * *
60489 AGTCCTAAGATCGATGTAAATGATTCCATCTCGTTTGTTAT-GGATTCTAATAAAATGAGATAGA
1 AGTCCTAAGATCGGTGTAAATGATCCCATCTCGTTTGTTCTAGAATTCTAATAAAATGAGATAGA
* * * * * * * *
60553 AGTCCTAAAATCAGTGTAAACGATCCTATCTCGTTTGTTCTAGAACTCCAATAGAATGACATAGA
1 AGTCCTAAGATCGGTGTAAATGATCCCATCTCGTTTGTTCTAGAATTCTAATAAAATGAGATAGA
* * *
60618 AGTCCTAAGTTCGGTGTAAATGCTCCCATCTTGTTTGTTCTA
1 AGTCCTAAGATCGGTGTAAATGATCCCATCTCGTTTGTTCTA
60660 TAATAGACTA
Statistics
Matches: 200, Mismatches: 33, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
64 56 0.28
65 142 0.71
66 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (65 bp):
AGTCCTAAGATCGGTGTAAATGATCCCATCTCGTTTGTTCTAGAATTCTAATAAAATGAGATAGA
Found at i:74806 original size:19 final size:20
Alignment explanation
Indices: 74782--74829 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
74772 TGACTATTCA
*
74782 GTATCG-TACTCGACTGTTG
1 GTATCGATACCCGACTGTTG
**
74801 GTATCGATACCCTCCTGTTG
1 GTATCGATACCCGACTGTTG
74821 GTATCGATA
1 GTATCGATA
74830 TCCCCTGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (20 bp):
GTATCGATACCCGACTGTTG
Found at i:83678 original size:30 final size:30
Alignment explanation
Indices: 83565--83678 Score: 90
Period size: 30 Copynumber: 3.8 Consensus size: 30
83555 GACCACGCGG
83565 TGCTGCAGCTGAT-CT-TACTGGACCACT-CCC
1 TGCTGCAGCTGATCCTGT-C-GGACCA-TGCCC
* * * * * *
83595 TGTTGTAGCTGATCCTGCCGAACCACGCCT
1 TGCTGCAGCTGATCCTGTCGGACCATGCCC
* *
83625 TGCTGCAACTGATCCTATCGGACCATGCCC
1 TGCTGCAGCTGATCCTGTCGGACCATGCCC
* *
83655 TGCTGCAGCTGATTCTGTTGGACC
1 TGCTGCAGCTGATCCTGTCGGACC
83679 TCAACCTACT
Statistics
Matches: 63, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
30 60 0.95
31 3 0.05
ACGTcount: A:0.17, C:0.33, G:0.23, T:0.27
Consensus pattern (30 bp):
TGCTGCAGCTGATCCTGTCGGACCATGCCC
Found at i:84871 original size:23 final size:23
Alignment explanation
Indices: 84818--84871 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
84808 ACTACACTCA
*
84818 ATTTACTTTTGCCAAGACATTTCC
1 ATTTA-TTTTGCCAAGACATCTCC
* *
84842 ATCTATTTTGCCACA-ACATCTCT
1 ATTTATTTTGCCA-AGACATCTCC
84865 ATTTATT
1 ATTTATT
84872 GCCACATTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (23 bp):
ATTTATTTTGCCAAGACATCTCC
Found at i:86574 original size:2 final size:2
Alignment explanation
Indices: 86567--86592 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
86557 AATCACAAGA
86567 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
86593 TAAATACCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86934 original size:2 final size:2
Alignment explanation
Indices: 86927--86956 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
86917 AGTCTGACTT
*
86927 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
86957 AATTCCTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Done.