Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006795.1 Hibiscus syriacus cultivar Beakdansim tig00017241_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: 64997
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1017 original size:84 final size:85
Alignment explanation
Indices: 857--1177 Score: 260
Period size: 84 Copynumber: 3.8 Consensus size: 85
847 AAATATAATT
* * **
857 TTATCTAATTTGAATGGAAATTATTTCAGTTTATCTAAGTTGATGTGATATGTCAATGAAAAGCA
1 TTATCTAATTTGAATGGAAATTATTTCAGTTTATCTAAGCTGATGTGAAATCACAATGAAAAGCA
* *
922 AATGACGTGAATAGTGTAGA
66 AAGGACATGAATAGTGTAGA
* *
942 TTATCTGATTTGAATGGAAATTATTTCAG-TTATC-AGAGCTGATGTTAAATCACAATGAAAAGC
1 TTATCTAATTTGAATGGAAATTATTTCAGTTTATCTA-AGCTGATGTGAAATCACAATGAAAAGC
* *
1005 AAAGGATATGAATAGTGTAGT
65 AAAGGACATGAATAGTGTAGA
* * * * * * * * *** * *
1026 TTCTCTAATTCT--CT--AAAATATTTTAGTTTATCCATGTTGATGTGATATGTTAATAAAAAGT
1 TTATCTAATT-TGAATGGAAATTATTTCAGTTTATCTAAGCTGATGTGAAATCACAATGAAAAGC
* * *
1087 AAA-TACTTGAATAGTGTAAA
65 AAAGGACATGAATAGTGTAGA
* * * * ** * **
1107 TTCTATGATTTGAATGGAAATTATTTCAGTTTATCTGATTTGGTGTGAAATGTCAATGAAAAGCA
1 TTATCTAATTTGAATGGAAATTATTTCAGTTTATCTAAGCTGATGTGAAATCACAATGAAAAGCA
1172 AAGGAC
66 AAGGAC
1178 CTTAATTATG
Statistics
Matches: 183, Mismatches: 44, Indels: 18
0.75 0.18 0.07
Matches are distributed among these distances:
80 1 0.01
81 30 0.16
82 27 0.15
83 3 0.02
84 91 0.50
85 31 0.17
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.37
Consensus pattern (85 bp):
TTATCTAATTTGAATGGAAATTATTTCAGTTTATCTAAGCTGATGTGAAATCACAATGAAAAGCA
AAGGACATGAATAGTGTAGA
Found at i:1173 original size:166 final size:166
Alignment explanation
Indices: 878--1176 Score: 429
Period size: 166 Copynumber: 1.8 Consensus size: 166
868 GAATGGAAAT
* * *
878 TATTTCAGTTTATCTAAGTTGATGTGATATGTCAATGAAAAGCAAATGACGTGAATAGTGTAGAT
1 TATTTCAGTTTATCCAAGTTGATGTGATATGTCAATAAAAAGCAAATGACGTGAATAGTGTAAAT
* *
943 TATCTGATTTGAATGGAAATTATTTCAGTTATCAGAGCTGATGTTAAATCACAATGAAAAGCAAA
66 TATATGATTTGAATGGAAATTATTTCAGTTATCAGAGCTGATGTGAAATCACAATGAAAAGCAAA
1008 GGATATGAATAGTGTAGTTTCTCTAATTCTCTAAAA
131 GGATATGAATAGTGTAGTTTCTCTAATTCTCTAAAA
* * * * *
1044 TATTTTAGTTTATCCATGTTGATGTGATATGTTAATAAAAAGTAAAT-ACTTGAATAGTGTAAAT
1 TATTTCAGTTTATCCAAGTTGATGTGATATGTCAATAAAAAGCAAATGACGTGAATAGTGTAAAT
* * ** * **
1108 TCTATGATTTGAATGGAAATTATTTCAGTTTATCTGATTTGGTGTGAAATGTCAATGAAAAGCAA
66 TATATGATTTGAATGGAAATTATTTCAG-TTATCAGAGCTGATGTGAAATCACAATGAAAAGCAA
1173 AGGA
130 AGGA
1177 CCTTAATTAT
Statistics
Matches: 115, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
165 41 0.36
166 74 0.64
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (166 bp):
TATTTCAGTTTATCCAAGTTGATGTGATATGTCAATAAAAAGCAAATGACGTGAATAGTGTAAAT
TATATGATTTGAATGGAAATTATTTCAGTTATCAGAGCTGATGTGAAATCACAATGAAAAGCAAA
GGATATGAATAGTGTAGTTTCTCTAATTCTCTAAAA
Found at i:10800 original size:111 final size:114
Alignment explanation
Indices: 10512--10802 Score: 285
Period size: 111 Copynumber: 2.6 Consensus size: 114
10502 GAGAAAACGA
* * * *
10512 TTGAACAAGTTCTTTTCATTATGAACTTTTTCTCACTCTTTAAACGAGTTATTCTCATTATGAGC
1 TTGAACAAGTTATTTTCATTATGAAC-TTTTCTCACTCATTAGACGAGTTATTCTCATTATGAAC
* *
10577 TCCTTAGTGGAAATGCTAATCAACCTCCTCTGTGATGGTCTTGAGCGAAAGG
65 TCCTTAGTGGAAATGCTAATC-ACAT-CTCTGTGATGGTCTTGAGCCAAAGG
* * * * ** * *
10629 TTTAATAAGTTATTCTCATTATGAAC--TTCTCCCTCATCGGACGGGTTCTTCTCATTATGAACT
1 TTGAACAAGTTATTTTCATTATGAACTTTTCTCACTCATTAGACGAGTTATTCTCATTATGAACT
**
10692 -CTCTA-TTTAAATGC-AATGC-CAT-TCTGTGATGGAT-TTGAGCCAAAGG
66 CCT-TAGTGGAAATGCTAAT-CACATCTCTGTGATGG-TCTTGAGCCAAAGG
* * *
10738 TTGAACAA-TTTTTTTCATTATGAACTTATTCTCTCTCATTAGACGAGTTTTTCTCATTATGAAC
1 TTGAACAAGTTATTTTCATTATGAACTT-TTCTCACTCATTAGACGAGTTATTCTCATTATGAAC
10802 T
65 T
10803 ACTTCAAATT
Statistics
Matches: 143, Mismatches: 25, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
108 15 0.10
109 27 0.19
110 1 0.01
111 34 0.24
112 3 0.02
113 10 0.07
114 31 0.22
117 22 0.15
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (114 bp):
TTGAACAAGTTATTTTCATTATGAACTTTTCTCACTCATTAGACGAGTTATTCTCATTATGAACT
CCTTAGTGGAAATGCTAATCACATCTCTGTGATGGTCTTGAGCCAAAGG
Found at i:11556 original size:69 final size:67
Alignment explanation
Indices: 11418--11707 Score: 297
Period size: 67 Copynumber: 4.4 Consensus size: 67
11408 AATTCATATA
* * * * *
11418 TCAAGAGAAAATATCCCTAGTGAGATAAAAACTTTATTTCGAGTGAAACAATTTCAAAATTTGTG
1 TCAAGAGAAAATATCTCAAGTGAGATAAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTGTA
11483 TT
66 TT
* * * *
11485 TCAAGGGAAATTATCTCAAGTGAGATAAAAATTTCTTGTTTTGAGTGAAACAATTTTAAAAATTT
1 TCAAGAGAAAATATCTCAAGTGAGATAAAAA-TT-TTGTTTCGAGTGAAACAA-TTTCAAAATTT
11550 -TATT
63 GTATT
* * * * ** *
11554 TCAAGAGAAAGTGTCTCAAGTGGGATAAAAA-----TTT-GAATGAAATGATTTCAAAATTCGTA
1 TCAAGAGAAAATATCTCAAGTGAGATAAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTGTA
11613 TT
66 TT
* * * *
11615 TCAAGAGAAAATACCTCAAGTGAGATATAAATTTTGTTTCGAGTGAAACATTTTCAAAATTTGTT
1 TCAAGAGAAAATATCTCAAGTGAGATAAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTGTA
11680 TT
66 TT
* * *
11682 TCAAGGGAAACTGTCTCAAGTGAGAT
1 TCAAGAGAAAATATCTCAAGTGAGAT
11708 GAAATTTGTT
Statistics
Matches: 180, Mismatches: 33, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
60 9 0.05
61 38 0.21
62 3 0.02
66 3 0.02
67 70 0.39
68 1 0.01
69 46 0.26
70 10 0.06
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (67 bp):
TCAAGAGAAAATATCTCAAGTGAGATAAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTGTA
TT
Found at i:11637 original size:130 final size:128
Alignment explanation
Indices: 11468--11703 Score: 339
Period size: 130 Copynumber: 1.8 Consensus size: 128
11458 GAGTGAAACA
* * * * * *
11468 ATTTCAAAATTTGTGTTTCAAGGGAAATTATCTCAAGTGAGATAAAAATTTCTTGTTTTGAGTGA
1 ATTTCAAAATTCGTATTTCAAGAGAAAATACCTCAAGTGAGATAAAAA-TT-TTGTTTCGAGTGA
*
11533 AACAATTTTAAAAATTT-TATTTCAAGAGAAAGTGTCTCAAGTGGGATAAAAATTTGAATGAAAT
64 AAC-ATTTTAAAAATTTGTATTTCAAGAGAAACTGTCTCAAGTGGGATAAAAATTTGAATGAAAT
11597 G
128 G
*
11598 ATTTCAAAATTCGTATTTCAAGAGAAAATACCTCAAGTGAGATATAAATTTTGTTTCGAGTGAAA
1 ATTTCAAAATTCGTATTTCAAGAGAAAATACCTCAAGTGAGATAAAAATTTTGTTTCGAGTGAAA
* * *
11663 CATTTTCAAAATTTGTTTTTCAAGGGAAACTGTCTCAAGTG
66 CATTTTAAAAATTTGTATTTCAAGAGAAACTGTCTCAAGTG
11704 AGATGAAATT
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
127 12 0.13
128 38 0.40
129 2 0.02
130 42 0.45
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (128 bp):
ATTTCAAAATTCGTATTTCAAGAGAAAATACCTCAAGTGAGATAAAAATTTTGTTTCGAGTGAAA
CATTTTAAAAATTTGTATTTCAAGAGAAACTGTCTCAAGTGGGATAAAAATTTGAATGAAATG
Found at i:11672 original size:197 final size:197
Alignment explanation
Indices: 11276--11707 Score: 595
Period size: 197 Copynumber: 2.2 Consensus size: 197
11266 AAGTAATATG
* * * *
11276 AAATTT-TGTTTCAAAGGAAATAACCTCAAGTGAGATAAAAAAAAATTCTTGTTTCGAGTGAAAT
1 AAATTTGTGTTTCAAGGGAAATTATCTCAAGTGAGAT--AAAAAAATTCTTGTTTCGAGTGAAAC
* *
11340 GATTTTAAAATTTGTATTTCAAGAGAAAATGTTTCAAGTGGGATAAAAATTTTGAATGATGATTT
64 AATTTTAAAATTTGTATTTCAAGAGAAAATGTCTCAAGTGGGATAAAAATTTTGAATGATGATTT
* *
11405 GAAAATTCATATATCAAGAGAAAATATCCCTAGTGAGATAAAAACTTTATTTCGAGTGAAACAAT
129 CAAAATTCATATATCAAGAGAAAATATCCCAAGTGAGATAAAAACTTTATTTCGAGTGAAACAAT
11470 TTCA
194 TTCA
* *
11474 AAATTTGTGTTTCAAGGGAAATTATCTCAAGTGAGAT-AAAAATTTCTTGTTTTGAGTGAAACAA
1 AAATTTGTGTTTCAAGGGAAATTATCTCAAGTGAGATAAAAAAATTCTTGTTTCGAGTGAAACAA
*
11538 TTTTAAAAATTT-TATTTCAAGAGAAAGTGTCTCAAGTGGGATAAAAA-TTTGAATGAAATGATT
66 TTTT-AAAATTTGTATTTCAAGAGAAAATGTCTCAAGTGGGATAAAAATTTTGAATG--ATGATT
* * * * *
11601 TCAAAATTCGTATTTCAAGAGAAAATA-CCTCAAGTGAGATATAAATTTTGTTTCGAGTGAAACA
128 TCAAAATTCATATATCAAGAGAAAATATCC-CAAGTGAGATAAAAACTTTATTTCGAGTGAAACA
*
11665 TTTTCA
192 ATTTCA
* * *
11671 AAATTTGTTTTTCAAGGGAAACTGTCTCAAGTGAGAT
1 AAATTTGTGTTTCAAGGGAAATTATCTCAAGTGAGAT
11708 GAAATTTGTT
Statistics
Matches: 209, Mismatches: 20, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
195 8 0.04
196 62 0.30
197 106 0.51
198 6 0.03
199 27 0.13
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (197 bp):
AAATTTGTGTTTCAAGGGAAATTATCTCAAGTGAGATAAAAAAATTCTTGTTTCGAGTGAAACAA
TTTTAAAATTTGTATTTCAAGAGAAAATGTCTCAAGTGGGATAAAAATTTTGAATGATGATTTCA
AAATTCATATATCAAGAGAAAATATCCCAAGTGAGATAAAAACTTTATTTCGAGTGAAACAATTT
CA
Found at i:15140 original size:19 final size:18
Alignment explanation
Indices: 15118--15163 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
15108 CAAAGATGTG
* *
15118 AATGCAATTGCAAACTCAA
1 AATGCAAATGCAAACGC-A
15137 AATGCAAAATGCAAACGCA
1 AATGC-AAATGCAAACGCA
15156 AATGCAAA
1 AATGCAAA
15164 AAAGGTATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 3 0.12
19 11 0.46
20 10 0.42
ACGTcount: A:0.52, C:0.20, G:0.13, T:0.15
Consensus pattern (18 bp):
AATGCAAATGCAAACGCA
Found at i:15163 original size:26 final size:26
Alignment explanation
Indices: 15073--15164 Score: 73
Period size: 26 Copynumber: 3.5 Consensus size: 26
15063 ATGTAGAGAT
15073 GCAAATGCACAAATGCAAAGATG-AGAAC
1 GCAAATGCA-AAATGCAAA-ATGCA-AAC
* ** **
15101 GCCAATGCAAAGATG-TGAATGCAATT
1 GCAAATGCAAA-ATGCAAAATGCAAAC
15127 GCAAACT-CAAAATGCAAAATGCAAAC
1 GCAAA-TGCAAAATGCAAAATGCAAAC
15153 GCAAATGCAAAA
1 GCAAATGCAAAA
15165 AAGGTATTGA
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
25 4 0.08
26 29 0.59
27 5 0.10
28 11 0.22
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.14
Consensus pattern (26 bp):
GCAAATGCAAAATGCAAAATGCAAAC
Found at i:15165 original size:20 final size:20
Alignment explanation
Indices: 15126--15164 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
15116 TGAATGCAAT
*
15126 TGCAAACTCAAAATGCAAAA
1 TGCAAACGCAAAATGCAAAA
15146 TGCAAACGC-AAATGCAAAA
1 TGCAAACGCAAAATGCAAAA
15165 AAGGTATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.54, C:0.21, G:0.13, T:0.13
Consensus pattern (20 bp):
TGCAAACGCAAAATGCAAAA
Found at i:16870 original size:21 final size:21
Alignment explanation
Indices: 16830--16870 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16820 AACCATTCAA
*
16830 GGGGAATCGGTACCCCCTTGG
1 GGGGAATCGATACCCCCTTGG
* *
16851 GGGGAATCGATTCCCTCTTG
1 GGGGAATCGATACCCCCTTG
16871 ACAAACTGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.27, G:0.34, T:0.24
Consensus pattern (21 bp):
GGGGAATCGATACCCCCTTGG
Found at i:16930 original size:11 final size:11
Alignment explanation
Indices: 16914--16938 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16904 AAATACTTTG
16914 TAAAATTGTTT
1 TAAAATTGTTT
16925 TAAAATTGTTT
1 TAAAATTGTTT
16936 TAA
1 TAA
16939 TATTAAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (11 bp):
TAAAATTGTTT
Found at i:19536 original size:22 final size:19
Alignment explanation
Indices: 19482--19542 Score: 77
Period size: 19 Copynumber: 3.1 Consensus size: 19
19472 AAACCAGAAT
19482 CCTAGGGGGTATCGATTCC
1 CCTAGGGGGTATCGATTCC
* *
19501 CCTAGGGGGAATCGGTTCC
1 CCTAGGGGGTATCGATTCC
19520 CCTTCAAGGGGGTATCGATTCC
1 CC-T--AGGGGGTATCGATTCC
19542 C
1 C
19543 TCTGCCCTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 19 0.54
20 1 0.03
22 15 0.43
ACGTcount: A:0.16, C:0.28, G:0.31, T:0.25
Consensus pattern (19 bp):
CCTAGGGGGTATCGATTCC
Found at i:27170 original size:19 final size:19
Alignment explanation
Indices: 27148--27186 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
27138 GGGTTCAATC
*
27148 TAAAAACTAAGATAACTAA
1 TAAAAACTAAGAAAACTAA
* *
27167 TAAAAATTTAGAAAACTAA
1 TAAAAACTAAGAAAACTAA
27186 T
1 T
27187 TATAATAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.26
Consensus pattern (19 bp):
TAAAAACTAAGAAAACTAA
Found at i:27640 original size:22 final size:22
Alignment explanation
Indices: 27598--27658 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 22
27588 ATAAAGTTAC
27598 AAGGATAAAAAAAAAACAAGA-A
1 AAGGA-AAAAAAAAAACAAGAGA
27620 AAGGAAAAAGAAAAAGA-AAGAGA
1 AAGGAAAAA-AAAAA-ACAAGAGA
27643 AA-GAAAACTAAAAAAA
1 AAGGAAAA--AAAAAAA
27659 GTATGAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
21 4 0.12
22 20 0.59
23 9 0.26
24 1 0.03
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.03
Consensus pattern (22 bp):
AAGGAAAAAAAAAAACAAGAGA
Found at i:31152 original size:18 final size:20
Alignment explanation
Indices: 31111--31155 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
31101 TCCCTAGACC
31111 CAAAACCCAAACCAGAACAT
1 CAAAACCCAAACCAGAACAT
*
31131 -AAAACCC-AACCAGCAC-T
1 CAAAACCCAAACCAGAACAT
31148 CAAAACCC
1 CAAAACCC
31156 GACCCGGGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 1 0.04
18 15 0.65
19 7 0.30
ACGTcount: A:0.51, C:0.40, G:0.04, T:0.04
Consensus pattern (20 bp):
CAAAACCCAAACCAGAACAT
Found at i:37755 original size:9 final size:9
Alignment explanation
Indices: 37743--37776 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
37733 TTTTTACTAT
37743 TTTTAATTA
1 TTTTAATTA
37752 TTTT--TTA
1 TTTTAATTA
37759 TTTTAATTA
1 TTTTAATTA
37768 TTTTAATTA
1 TTTTAATTA
37777 AGTTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.30
9 16 0.70
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTAATTA
Found at i:41478 original size:7 final size:7
Alignment explanation
Indices: 41468--41553 Score: 57
Period size: 7 Copynumber: 11.3 Consensus size: 7
41458 AAAATAATAG
41468 AAAAGAAA
1 AAAAG-AA
41476 AAAAGAAAA
1 AAAAG--AA
41485 AAATAGATA
1 AAA-AGA-A
*
41494 AAAGGAA
1 AAAAGAA
41501 AAAAGAA
1 AAAAGAA
*
41508 AAAATAA
1 AAAAGAA
41515 AAAA-ATA
1 AAAAGA-A
*
41522 AAAAAAA
1 AAAAGAA
41529 TAAAAGAA
1 -AAAAGAA
41537 AGAAAGAA
1 A-AAAGAA
*
41545 GAAAGAA
1 AAAAGAA
41552 AA
1 AA
41554 CATATCAAAC
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
6 1 0.02
7 31 0.48
8 21 0.32
9 10 0.15
10 2 0.03
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (7 bp):
AAAAGAA
Found at i:41479 original size:8 final size:8
Alignment explanation
Indices: 41468--41553 Score: 63
Period size: 8 Copynumber: 11.1 Consensus size: 8
41458 AAAATAATAG
41468 AAAAGAAA
1 AAAAGAAA
41476 AAAAGAAA
1 AAAAGAAA
* *
41484 AAAATAGAT
1 AAAAGA-AA
*
41493 AAAAGGAA
1 AAAAGAAA
41501 AAAAG-AA
1 AAAAGAAA
*
41508 AAAATAAA
1 AAAAGAAA
*
41516 AAAA-TAA
1 AAAAGAAA
*
41523 AAAA-AAT
1 AAAAGAAA
41530 AAAAGAAA
1 AAAAGAAA
*
41538 GAAAG-AA
1 AAAAGAAA
*
41545 GAAAGAAA
1 AAAAGAAA
41553 A
1 A
41554 CATATCAAAC
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
7 24 0.39
8 33 0.53
9 5 0.08
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (8 bp):
AAAAGAAA
Found at i:41484 original size:23 final size:23
Alignment explanation
Indices: 41449--41541 Score: 79
Period size: 23 Copynumber: 4.2 Consensus size: 23
41439 AAGATATAGT
**
41449 GAAAAAATTAAAATAATAGAAAA
1 GAAAAAAAGAAAATAATAGAAAA
*
41472 GAAAAAAAGAAAAAAATAGATAAAA
1 GAAAAAAAGAAAATAATAG--AAAA
*
41497 GGAAAAAAGAAAA-AATA-AAAA
1 GAAAAAAAGAAAATAATAGAAAA
* *
41518 -AATAAAA-AAAATAAAAG-AAA
1 GAAAAAAAGAAAATAATAGAAAA
41538 GAAA
1 GAAA
41542 GAAGAAAGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
19 4 0.07
20 11 0.19
21 6 0.11
23 16 0.28
24 4 0.07
25 16 0.28
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.10
Consensus pattern (23 bp):
GAAAAAAAGAAAATAATAGAAAA
Found at i:41505 original size:33 final size:30
Alignment explanation
Indices: 41449--41544 Score: 88
Period size: 32 Copynumber: 3.1 Consensus size: 30
41439 AAGATATAGT
* * *
41449 GAAAAAATTAAAATAATAGAAAAGAAAAAAA
1 GAAAAAAATAAAA-AAAATAAAAGAAAAAAA
41480 GAAAAAAATAGATAAAAGGAA-AAAAG-AAAAAA
1 GAAAAAAATA-A-AAAA--AATAAAAGAAAAAAA
* *
41512 TAAAAAAATAAAAAAAATAAAAGAAAGAAA
1 GAAAAAAATAAAAAAAATAAAAGAAAAAAA
41542 GAA
1 GAA
41545 GAAAGAAAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
28 2 0.04
29 5 0.09
30 11 0.20
31 10 0.19
32 18 0.33
33 7 0.13
34 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.09
Consensus pattern (30 bp):
GAAAAAAATAAAAAAAATAAAAGAAAAAAA
Found at i:41547 original size:40 final size:40
Alignment explanation
Indices: 41468--41548 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 40
41458 AAAATAATAG
* *
41468 AAAAGAAAAAAAGAAAAAAATAGATAAAAGGAAAAAAGAA
1 AAAAGAAAAAAAAAAAAAAATAGATAAAAAGAAAAAAGAA
* *
41508 AAAATAAAAAAATAAAAAAAATA-A-AAGAAAGAAAGAAGAA
1 AAAAGAAAAAAA-AAAAAAAATAGATAA-AAAGAAAAAAGAA
41548 A
1 A
41549 GAAAACATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
39 2 0.06
40 24 0.69
41 9 0.26
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.06
Consensus pattern (40 bp):
AAAAGAAAAAAAAAAAAAAATAGATAAAAAGAAAAAAGAA
Found at i:43783 original size:109 final size:108
Alignment explanation
Indices: 43542--43862 Score: 385
Period size: 109 Copynumber: 2.9 Consensus size: 108
43532 TCAAACAAAC
* * * * * * * *
43542 TTTTAAAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGTTTTCAAATGCGTTTTTTTAGAA
1 TTTTTAAAGAAGCTAAGCCTAATTTT-TAGGGTTTCTTGATGTTTTAAAATGAG--ATTTTAGAA
*
43607 ACTAAGCTTGATTTT-TAGGGTTTCTTGATGATTATTTCCAATGAA
63 ACTAAGCTTGATTTTCAAGGGTTTCTTGATGATTATTTCCAATGAA
* * *
43652 TTTTTAAAAGAAGCTAACCCTAATTTTTAGGGATTTCTTGATGTTTTTAAATGAGCTTTTAGAAA
1 TTTTT-AAAGAAGCTAAGCCTAATTTTTAGGG-TTTCTTGATGTTTTAAAATGAGATTTTAGAAA
*
43717 CTAAGCCTGATTTTCAAGGGTTTCTTGATGATTATTTCCAAAT-AA
64 CTAAGCTTGATTTTCAAGGGTTTCTTGATGATTATTTCC-AATGAA
*
43762 TTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATAATTGAAAATGAAAGATTTTA
1 TTTTTAAAGAAGCTAAGCCTAATTTTTA-GGGTTTCTTGATG-T--TTTAAAATG--AGATTTT-
43827 AGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGA
59 AGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGA
43863 GTAAGTCATT
Statistics
Matches: 184, Mismatches: 16, Indels: 17
0.85 0.07 0.08
Matches are distributed among these distances:
109 54 0.29
110 42 0.23
111 40 0.22
112 7 0.04
114 6 0.03
115 35 0.19
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (108 bp):
TTTTTAAAGAAGCTAAGCCTAATTTTTAGGGTTTCTTGATGTTTTAAAATGAGATTTTAGAAACT
AAGCTTGATTTTCAAGGGTTTCTTGATGATTATTTCCAATGAA
Found at i:43787 original size:57 final size:57
Alignment explanation
Indices: 43471--43862 Score: 308
Period size: 57 Copynumber: 6.9 Consensus size: 57
43461 GACATGATGT
* * * * * *
43471 TTTCAAAAGAATTTTTAAAGAAACCAGGTCTGATTTTC-AGAGGCTCCTTGACATGATGT-
1 TTTCAAATGAATTTTTAAAGAAACTAAGCCTGATTTTCAAG-GGTTTCTTG--ATGAT-TA
** * *
43530 TTTCAAACAAACTTTTAAAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATG--T-
1 TTTCAAATGAA-TTTTTAAAGAAACTAAGCCTGATTTTCAAGGGTTTCTTGATGATTA
** ** * *
43585 TTTCAAATGCGTTTTTTTAGAAACTAAGCTTGATTTT-TAGGGTTTCTTGATGATTA
1 TTTCAAATGAATTTTTAAAGAAACTAAGCCTGATTTTCAAGGGTTTCTTGATGATTA
* * * * *
43641 TTTCCAATGAATTTTTAAAAGAAGCTAACCCTAATTTT-TAGGGATTTCTTGATG-TT-
1 TTTCAAATGAATTTTT-AAAGAAACTAAGCCTGATTTTCAAGGG-TTTCTTGATGATTA
**
43697 TTT-AAATGAGCTTTT--AGAAACTAAGCCTGATTTTCAAGGGTTTCTTGATGATTA
1 TTTCAAATGAATTTTTAAAGAAACTAAGCCTGATTTTCAAGGGTTTCTTGATGATTA
* * * * *
43751 TTTCCAAAT-AATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATAA
1 TTT-CAAATGAATTTTTAAAGAAACTAAGCCTGATTTTCAAGGGTTTCTTGATGATTA
** * *
43808 TTGAAAATGAAAGATTTT-AAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGA
1 TTTCAAATG-AA-TTTTTAAAGAAACTAAGCCTGATTTTCAAGGGTTTCTTGATGA
43863 GTAAGTCATT
Statistics
Matches: 268, Mismatches: 48, Indels: 35
0.76 0.14 0.10
Matches are distributed among these distances:
52 26 0.10
53 20 0.07
54 26 0.10
55 23 0.09
56 24 0.09
57 58 0.22
58 47 0.18
59 13 0.05
60 29 0.11
61 2 0.01
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (57 bp):
TTTCAAATGAATTTTTAAAGAAACTAAGCCTGATTTTCAAGGGTTTCTTGATGATTA
Found at i:44108 original size:39 final size:39
Alignment explanation
Indices: 44054--44221 Score: 250
Period size: 39 Copynumber: 4.3 Consensus size: 39
44044 AGGGGTCAAC
* *
44054 ATCTCGCTTGAGATAGTTTCACAAGAAACATAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTAGAAACAGAAGATTTT
*
44093 ATCTCGCTTGAGATAGTTTCACTCA-AAACAGAATATTTT
1 ATCTCGCTTGAGATAGTTTCACT-AGAAACAGAAGATTTT
* * *
44132 ATCTCGCTTGAGATAGTTTTACTCGAAACAAAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTAGAAACAGAAGATTTT
*
44171 ATCTCGCTTGAGATAGTTTCACTTGAAACAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTAGAAACAGAAGATTTT
44209 ATCTCGCTTGAGA
1 ATCTCGCTTGAGA
44222 ATGAAAGATG
Statistics
Matches: 117, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
38 16 0.14
39 100 0.85
40 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Consensus pattern (39 bp):
ATCTCGCTTGAGATAGTTTCACTAGAAACAGAAGATTTT
Found at i:45788 original size:4 final size:4
Alignment explanation
Indices: 45744--45809 Score: 57
Period size: 4 Copynumber: 16.8 Consensus size: 4
45734 TATATTTAGG
* * *
45744 TTTA TTTTA TTT- TTCA TTTA TGTTG TTT- TTTA CTT- TTTA TTTA TTTA
1 TTTA -TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
*
45791 TTTA TTTA TTTA ATTA TTT
1 TTTA TTTA TTTA TTTA TTT
45810 TAATTATTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
3 7 0.14
4 36 0.72
5 7 0.14
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:45813 original size:9 final size:9
Alignment explanation
Indices: 45799--45824 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
45789 TATTTATTTA
45799 TTTAATTAT
1 TTTAATTAT
45808 TTTAATTAT
1 TTTAATTAT
45817 TTTAATTA
1 TTTAATTA
45825 AGTTTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTAATTAT
Found at i:55709 original size:9 final size:8
Alignment explanation
Indices: 55691--55728 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
55681 AAGAGAAAAG
55691 AAAAAGAA
1 AAAAAGAA
55699 AAAATAGAA
1 AAAA-AGAA
55708 AAAAA-AA
1 AAAAAGAA
*
55715 GAAAAGAA
1 AAAAAGAA
55723 AAAAAG
1 AAAAAG
55729 GTTAAAGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 6 0.23
8 12 0.46
9 8 0.31
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (8 bp):
AAAAAGAA
Found at i:55709 original size:15 final size:15
Alignment explanation
Indices: 55672--55727 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
55662 TATTACGCCT
*
55672 AAGAAAGAAAAGAGAA
1 AAGAAA-AAAAAAGAA
55688 AAGAAAAAGAAAA-AA
1 AAGAAAAA-AAAAGAA
*
55703 TAGAAAAAAAAAGAA
1 AAGAAAAAAAAAGAA
55718 AAGAAAAAAA
1 AAGAAAAAAA
55728 GGTTAAAGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 4 0.11
15 22 0.63
16 9 0.26
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (15 bp):
AAGAAAAAAAAAGAA
Found at i:55713 original size:19 final size:20
Alignment explanation
Indices: 55679--55719 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
55669 CCTAAGAAAG
55679 AAAAGAGAAAAGAAAAAGAA
1 AAAAGAGAAAAGAAAAAGAA
*
55699 AAAATAGAAAA-AAAAAGAA
1 AAAAGAGAAAAGAAAAAGAA
55718 AA
1 AA
55720 GAAAAAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (20 bp):
AAAAGAGAAAAGAAAAAGAA
Found at i:55725 original size:12 final size:12
Alignment explanation
Indices: 55675--55726 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
55665 TACGCCTAAG
*
55675 AAAGAAAAGAGA
1 AAAGAAAAGAAA
55687 AAAGAAAAAGAAA
1 AAAG-AAAAGAAA
*
55700 AAATAGAAA-AAA
1 AAAGA-AAAGAAA
55712 AAAGAAAAGAAA
1 AAAGAAAAGAAA
55724 AAA
1 AAA
55727 AGGTTAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.09
12 18 0.53
13 13 0.38
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:56966 original size:136 final size:136
Alignment explanation
Indices: 56722--57576 Score: 1000
Period size: 136 Copynumber: 6.3 Consensus size: 136
56712 AAGATAAACC
* * * * *
56722 GATCAATATTTCCAATGGAGAGTTCATAATGAAAAGAACTCATATGACA-ACAGGAGAAGAAGTT
1 GATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCTGACAGA-GGGAGAAGAAATT
* ** * *
56786 CATAATGAGAAGAACTTGTTCAACCTATTGCTCGATTCTTGACATTTCAAATCAGCAATGCCTTG
65 CATAATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTCAAATCAGCAACGCCTCG
56851 CTTGAGG
130 CTTGAGG
* *
56858 GATCAACATTTCCAATAGAGAGTTCATAACGAGAAGAACTCATCTGACAGAGGGAGAAGAAATTC
1 GATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAATTC
* * * * * *
56923 ATAATAAGAAGAACTTGTTTGACCTATTGCTCGATTCACGACATTTCGAATTAGCAAAGCCTGGC
66 ATAATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTCAAATCAGCAACGCCTCGC
* *
56988 CTGATG
131 TTGAGG
*
56994 GATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATATGACAGAGGGAGAAGAAATTC
1 GATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAATTC
* * * * * *
57059 GTAATAAGAAGAACTTGTTTGACCTATTGCTCGATTCACGACATTTAAAATCAGCAAAGCCTGGC
66 ATAATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTCAAATCAGCAACGCCTCGC
* * *
57124 CTCATG
131 TTGAGG
* * *
57130 GATCAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCAT-TCGACAGAGGGAAAAGAAGTT
1 GATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCT-GACAGAGGGAGAAGAAATT
** * * *
57194 CATAATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTTGAATCAGTAACACCTCA
65 CATAATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTCAAATCAGCAACGCCTCG
57259 CTTGAGG
130 CTTGAGG
* ** * * * *
57266 GATTAACATTTCCTGTGGATAGATT-ATAATGAGAAGAATTCATCCGACAGAGGGAGAAGAAGTT
1 GATCAACATTTCCAATGGAGAG-TTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAATT
* * * * *
57330 CATAATGAGAAGAACTTATTCGACCTATTGCTCGATTCACGACATTTCAAATTAGTAACACATCG
65 CATAATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTCAAATCAGCAACGCCTCG
*
57395 CTTGAGA
130 CTTGAGG
* * * *
57402 GATTAACATTTCTAATGGAGAGTTCATAATGAGAAGAACTAATCCGACAGAGGGAGAA-AAAGTT
1 GATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAA-TT
* * * * * * ** * * *
57466 AATAATGACAAGAACTTATTTGACCTATTCCTCGATTCATGGGATTTCAAATTAGTAACGCCTCA
65 CATAATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTCAAATCAGCAACGCCTCG
*
57531 CTTAAGG
130 CTTGAGG
* * *
57538 GATAAACATTTCCAATAGGA-AGATCATGATGAGAAGAAC
1 GATCAACATTTCCAAT-GGAGAGTTCATAATGAGAAGAAC
57577 CCGTAACTTG
Statistics
Matches: 632, Mismatches: 80, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
135 5 0.01
136 621 0.98
137 6 0.01
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (136 bp):
GATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAATTC
ATAATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTCAAATCAGCAACGCCTCGC
TTGAGG
Found at i:57798 original size:18 final size:18
Alignment explanation
Indices: 57774--57824 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
57764 GCCCCAGACC
57774 CAAAACCCAACCAAAACA
1 CAAAACCCAACCAAAACA
* * *
57792 TAAAACCCAACCAGAACC
1 CAAAACCCAACCAAAACA
57810 CAAAACCCAATCCAA
1 CAAAACCCAA-CCAA
57825 GGCCCAAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 24 0.89
19 3 0.11
ACGTcount: A:0.55, C:0.39, G:0.02, T:0.04
Consensus pattern (18 bp):
CAAAACCCAACCAAAACA
Found at i:62306 original size:16 final size:16
Alignment explanation
Indices: 62285--62317 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
62275 CCCATTTATC
62285 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
62301 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
62317 A
1 A
62318 AAACCACTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTTTAAAACACACTT
Found at i:64595 original size:22 final size:22
Alignment explanation
Indices: 64567--64629 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 22
64557 TTCCCTGTGG
64567 GGGGAATCGGTTCCCCTTCAAA
1 GGGGAATCGGTTCCCCTTCAAA
*
64589 GGGGAATCGGTT-CCC-TCAAG
1 GGGGAATCGGTTCCCCTTCAAA
* *
64609 GGGGGATCGATTCCCTCTTCA
1 GGGGAATCGGTTCCC-CTTCA
64630 CCAAAATGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 14 0.40
21 5 0.14
22 13 0.37
23 3 0.09
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.24
Consensus pattern (22 bp):
GGGGAATCGGTTCCCCTTCAAA
Done.