Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004309.1 Hibiscus syriacus cultivar Beakdansim tig00009447_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: 426183
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:394102 original size:36 final size:36
Alignment explanation
Indices: 394053--394162 Score: 134
Period size: 36 Copynumber: 3.1 Consensus size: 36
394043 AAAGATTGAA
*
394053 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* *
394089 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAA--A
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * * * *
394123 CTTCCAAAAGAAACTGTCTCAAGGGAGACAAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
394159 GTTT
1 GTTT
394163 AACGTAAAAC
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
34 27 0.45
36 33 0.55
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (36 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:394135 original size:34 final size:35
Alignment explanation
Indices: 394062--394153 Score: 114
Period size: 34 Copynumber: 2.6 Consensus size: 35
394052 AGTTTCAAGG
** * *
394062 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAA-TACTTCCAAAA
*
394098 GAAACTATCTCAAGAGAGACAAAA-ACTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
*
394132 GAAACTGTCTCAAGGGAGACAA
1 GAAACTGTCTCAAGAGAGACAA
394154 GATTTGTTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
34 26 0.53
36 23 0.47
ACGTcount: A:0.46, C:0.17, G:0.18, T:0.18
Consensus pattern (35 bp):
GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
Found at i:394224 original size:30 final size:30
Alignment explanation
Indices: 394176--394232 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
394166 GTAAAACATA
*
394176 TTCAAAGATTTTGTTTCAA-AGGAAACTGTT
1 TTCAAAGATTTTGCTTCAAGA-GAAACTGTT
394206 TTCAAAG-TTTATGCTTCAAGAGAAACT
1 TTCAAAGATTT-TGCTTCAAGAGAAACT
394233 ATCTCAAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 3 0.12
30 20 0.83
31 1 0.04
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (30 bp):
TTCAAAGATTTTGCTTCAAGAGAAACTGTT
Found at i:394267 original size:36 final size:36
Alignment explanation
Indices: 394220--394302 Score: 112
Period size: 36 Copynumber: 2.3 Consensus size: 36
394210 AAGTTTATGC
* * **
394220 TTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGT
1 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT
* *
394256 TTCAAGGGAAACTATCTCATGAGTGACAAAATTCAT
1 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT
394292 TTCAAGGGAAA
1 TTCAAGGGAAA
394303 TGTTTTTTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.25
Consensus pattern (36 bp):
TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT
Found at i:394339 original size:101 final size:102
Alignment explanation
Indices: 394189--394571 Score: 414
Period size: 102 Copynumber: 3.8 Consensus size: 102
394179 AAAGATTTTG
* * *
394189 TTTCAAAGGAAACTGTTTTCAAAGTTTATGCTTCAAGAGAAACTATCTCAAGGGAGACAAAA-TT
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
* * * *
394253 TGTTTCAAGGGAAACTATCTCATGAGTGACAAAATTCA
65 TCTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAA
** **
394291 TTTCAAGGGAAATGTTTTTTATGTTTATGTTTCAAGAGAAACCGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
*
394356 CTTTCAAGGGAACCTATCTCAAGAGAGACAAAATTAA
66 CTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAA
* * * * *
394393 TCTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGATAAAACTTA
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
* * ** * * * * **
394458 GTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTG
66 CTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAA
** * * * *
394495 TTTCAAGGGAAACATATTCAAAGATTT-TGTTTCAAGAGAAACTATCTCAAGAGCGACAAAA--T
1 TTTCAAGGGAAATGTTTTCAATG-TTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
394557 TCATTTCAAGGGAAA
65 TC-TTTCAAGGGAAA
394572 TGTTTTCAAT
Statistics
Matches: 234, Mismatches: 44, Indels: 7
0.82 0.15 0.02
Matches are distributed among these distances:
100 1 0.00
101 52 0.22
102 178 0.76
103 3 0.01
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
CTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAA
Found at i:394530 original size:167 final size:167
Alignment explanation
Indices: 394347--394871 Score: 818
Period size: 167 Copynumber: 3.1 Consensus size: 167
394337 TCAAGGGAGA
* * * * *
394347 CAAA-ATTTTCTTTCAAGGGAACCTATCTCAAGAGAGACAAAATTAATCTCAAGGGAAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
*
394411 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGATAAAACTTAGTTCCAAAAGAAAATGTC
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
*
394476 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACATATT
131 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATT
*
394513 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGCGACAAAATTCATTTCAAGGGAAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
* * *
394578 CAATGTTTATGTTTCTAGAGAAACTATCACAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGAC
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
* *
394643 TCAAGGGAGACGAAATATGTTTCAAGAGAAACAGATT
131 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATT
*
394680 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAATGGAAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
* * * *
394745 AAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAAGAAAATGTC
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
* * * *
394810 TCAAGGGAGACGAAATTAGTTTAAATGAAAACAGATT
131 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATT
* * *
394847 TAAATATTTTGTTTCAAGGGAAACT
1 CAAAGATTTTGTTTCAAGAGAAACT
394872 TGGAAACTGT
Statistics
Matches: 327, Mismatches: 31, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
166 4 0.01
167 323 0.99
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (167 bp):
CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
TCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATT
Found at i:394555 original size:204 final size:203
Alignment explanation
Indices: 394191--394570 Score: 460
Period size: 204 Copynumber: 1.9 Consensus size: 203
394181 AGATTTTGTT
* *
394191 TCAAAGGAAACTGTTTTCAAAGTTTATGCTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGT
1 TCAAAGGAAACTGTTTTCAAAGTTTATGCTTCAAGAGAAACTATCTCAAGAGAGACAAAATTAGT
* ** * * * ** * ** *
394256 TTCAAGGGAAACTATCTCATGAGTGACAAAATTCATTTCAAGGGAAATGTTTTTTATGTTTATGT
66 TCCAAAAGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAGTTTATGT
* *
394321 TTCAAGAGAAACCGTCTCAAGGGAGACAAAATTTTC-TTTCAAGGGAACCTATCTCAAGAGAGAC
131 TTCAAGAGAAACCATCTCAAGAGAGACAAAA--TTCATTTCAAGGGAACCTATCTCAAGAGAGAC
394385 AAAATTAATC
194 AAAATTAATC
* * * *
394395 TCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGATAAAACTTAG
1 TCAAAGGAAACTGTTTTCAAAGTTTATGCTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TTAG
* * * **
394459 TTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACATATTCAAAGATTT-T
65 TTCCAAAAGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAG-TTTAT
* *
394523 GTTTCAAGAGAAACTATCTCAAGAGCGACAAAATTCATTTCAAGGGAA
129 GTTTCAAGAGAAACCATCTCAAGAGAGACAAAATTCATTTCAAGGGAA
394571 ATGTTTTCAA
Statistics
Matches: 146, Mismatches: 27, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
202 3 0.02
203 56 0.38
204 84 0.58
205 3 0.02
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (203 bp):
TCAAAGGAAACTGTTTTCAAAGTTTATGCTTCAAGAGAAACTATCTCAAGAGAGACAAAATTAGT
TCCAAAAGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAGTTTATGT
TTCAAGAGAAACCATCTCAAGAGAGACAAAATTCATTTCAAGGGAACCTATCTCAAGAGAGACAA
AATTAATC
Found at i:394570 original size:65 final size:65
Alignment explanation
Indices: 394477--394620 Score: 173
Period size: 65 Copynumber: 2.2 Consensus size: 65
394467 GAAAATGTCT
* * **
394477 CAAGGGAGACGAAATTTGTTTCAAGGGAAACATATTCAAAGATTT-TGTTTCAAGAGAAACTATC
1 CAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAG-TTTATGTTTCAAGAGAAACTATC
*
394541 T
65 A
* ** * * *
394542 CAAGAGCGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCTAGAGAAACTATCA
1 CAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAGTTTATGTTTCAAGAGAAACTATCA
394607 CAAGAGAGACAAAA
1 CAAGAGAGACAAAA
394621 CTTAGTTCCA
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
64 3 0.05
65 63 0.95
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (65 bp):
CAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAGTTTATGTTTCAAGAGAAACTATCA
Found at i:395211 original size:106 final size:106
Alignment explanation
Indices: 395020--395341 Score: 439
Period size: 106 Copynumber: 3.0 Consensus size: 106
395010 GTATTGTTCT
* * * * ** *
395020 GAGTCCAATATCCTCCGTCT-TGAAGTTAAAATTGACTCTGGAACTAAGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGT-TGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
* * * * * * *
395084 ACCAACCGCCCCTTTGCTGTGAAGTTGAGCTTGTGCTCTCTC
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* *
395126 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCCGAAATTGGGAAATTTTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
*
395191 CCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
*
395232 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
* * *
395297 TCAGCCGTCCCTTCGTTATGCAGTTGAACTTGTGTTGTCTC
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
395338 GAGT
1 GAGT
395342 GGCACGATAT
Statistics
Matches: 192, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
105 1 0.01
106 191 0.99
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
Found at i:395973 original size:32 final size:32
Alignment explanation
Indices: 395937--396006 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
395927 ATTCCCAAAG
*
395937 ATGCCCCAATATTCGATGTTGAATCTTAAAAA
1 ATGCCCCAACATTCGATGTTGAATCTTAAAAA
* * *
395969 ATGCCCCAACATTTGATGTTGAATCTTCAAAG
1 ATGCCCCAACATTCGATGTTGAATCTTAAAAA
396001 ATGCCC
1 ATGCCC
396007 TCATTGGTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (32 bp):
ATGCCCCAACATTCGATGTTGAATCTTAAAAA
Found at i:397034 original size:69 final size:69
Alignment explanation
Indices: 396918--397055 Score: 240
Period size: 69 Copynumber: 2.0 Consensus size: 69
396908 TGTCTCTCTC
* *
396918 TTGATGCTCTATGATCTTCGAGTGAAGTGATTGAGTGATCCGGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATCCGAAAATGATTGTGCTTGATCAATC
396983 TCAT
66 TCAT
* *
396987 TTGATGCTTTATGATCTTCGAGTGAAGTGATTCAGTGATTCGAAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATCCGAAAATGATTGTGCTTGATCAATC
397052 TCAT
66 TCAT
397056 AGTTTGAATC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATCCGAAAATGATTGTGCTTGATCAATC
TCAT
Found at i:397143 original size:24 final size:24
Alignment explanation
Indices: 397116--397172 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
397106 TATTGTCTTC
397116 TTTTTTCTTCAATTTTC-CTTTGTT
1 TTTTTTCTT-AATTTTCTCTTTGTT
*
397140 TTTTCTT-TTTATTTTCTCTTTGTT
1 TTTT-TTCTTAATTTTCTCTTTGTT
*
397164 TTTTCTCTT
1 TTTTTTCTT
397173 TTTTTTATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 7 0.25
24 19 0.68
25 2 0.07
ACGTcount: A:0.05, C:0.16, G:0.04, T:0.75
Consensus pattern (24 bp):
TTTTTTCTTAATTTTCTCTTTGTT
Found at i:397159 original size:13 final size:12
Alignment explanation
Indices: 397128--397178 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
397118 TTTTCTTCAA
397128 TTTTC-CTTTGTT
1 TTTTCTCTTT-TT
*
397140 TTTTCT-TTTTA
1 TTTTCTCTTTTT
397151 TTTTCTCTTTGTT
1 TTTTCTCTTT-TT
397164 TTTTCTCTTTTT
1 TTTTCTCTTTTT
397176 TTT
1 TTT
397179 ATTCTGATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 7 0.21
12 16 0.47
13 11 0.32
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.80
Consensus pattern (12 bp):
TTTTCTCTTTTT
Found at i:397178 original size:24 final size:23
Alignment explanation
Indices: 397127--397178 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 23
397117 TTTTTCTTCA
397127 ATTTTCCTTTGTTTTTTCTTTTT
1 ATTTTCCTTTGTTTTTTCTTTTT
397150 ATTTTCTCTTTGTTTTTTCTCTTTT
1 ATTTTC-CTTTGTTTTTTCT-TTTT
397175 -TTTT
1 ATTTT
397179 ATTCTGATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 6 0.22
24 17 0.63
25 4 0.15
ACGTcount: A:0.04, C:0.13, G:0.04, T:0.79
Consensus pattern (23 bp):
ATTTTCCTTTGTTTTTTCTTTTT
Found at i:400581 original size:25 final size:25
Alignment explanation
Indices: 400553--400601 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
400543 TATAAACAAT
* *
400553 GTATAAAAAATAATAGTAATAATAA
1 GTATAAAAAACAATAATAATAATAA
*
400578 GTATTAAAAACAATAATAATAATA
1 GTATAAAAAACAATAATAATAATA
400602 GTAATGAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (25 bp):
GTATAAAAAACAATAATAATAATAA
Found at i:400613 original size:28 final size:27
Alignment explanation
Indices: 400557--400626 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 27
400547 AACAATGTAT
* *
400557 AAAAAATAATAGTAATAATAAGTATTA
1 AAAAAATAATAATAATAATAAGTAATA
*
400584 AAAACAATAATAATAATAGTAA-TGAATA
1 AAAA-AATAATAATAATAATAAGT-AATA
* *
400612 AAAAAACAAAAATAA
1 AAAAAATAATAATAA
400627 AAGAAATTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 14 0.39
28 22 0.61
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.23
Consensus pattern (27 bp):
AAAAAATAATAATAATAATAAGTAATA
Found at i:400665 original size:2 final size:2
Alignment explanation
Indices: 400658--400714 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
400648 AATCAAAGTA
400658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
400700 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
400715 AAAAAAAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:400732 original size:22 final size:22
Alignment explanation
Indices: 400707--400748 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
400697 TATATATATA
*
400707 TATATATAAAAAAAAAATAAAG
1 TATAAATAAAAAAAAAATAAAG
* *
400729 TATAAATGAAATAAAAATAA
1 TATAAATAAAAAAAAAATAA
400749 TAATAATGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (22 bp):
TATAAATAAAAAAAAAATAAAG
Found at i:406406 original size:65 final size:64
Alignment explanation
Indices: 406327--406452 Score: 155
Period size: 65 Copynumber: 2.0 Consensus size: 64
406317 TACACTAGGG
* * *** * *
406327 TGTGCATCGGTGCACAAATTTGCTTCGATATTTCAAAAATAGT-CGGGGTGCATCGATGCATGAC
1 TGTGCATAGGTGCACAAAATCAATTCGATATTT-AAAAA-AATCCGGAGTGCATCGATGCATGAC
406391 T
64 T
*
406392 TGTGCATAGGTGCACAAAATCAATTCGATATTTAAAAAAATCCTGAGTGCATCGATGCATG
1 TGTGCATAGGTGCACAAAATCAATTCGATATTTAAAAAAATCCGGAGTGCATCGATGCATG
406453 GTTTGCATAA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
63 2 0.04
64 22 0.42
65 28 0.54
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29
Consensus pattern (64 bp):
TGTGCATAGGTGCACAAAATCAATTCGATATTTAAAAAAATCCGGAGTGCATCGATGCATGACT
Found at i:406886 original size:20 final size:23
Alignment explanation
Indices: 406832--406888 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
406822 CAATTTTGAA
406832 ATTACTCCCCCTTACTATAATACTT
1 ATTAC-CCCCCTTACTATAATAC-T
*
406857 ATTACTCCCCTTACTATAATA-T
1 ATTACCCCCCTTACTATAATACT
406879 -TT-CCCCCCTT
1 ATTACCCCCCTT
406889 TTTGTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 7 0.23
21 2 0.07
22 1 0.03
24 15 0.50
25 5 0.17
ACGTcount: A:0.25, C:0.35, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTACCCCCCTTACTATAATACT
Found at i:409212 original size:23 final size:23
Alignment explanation
Indices: 409139--409214 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 23
409129 ACAGAGTGTT
*
409139 TCGATGCACATTCAAGGCATGCA
1 TCGATGCACATTCAAGGGATGCA
* * * *
409162 ACGGTGCACCTTC-ATGG-TG-A
1 TCGATGCACATTCAAGGGATGCA
409182 TTCGATGCACATTCAAGGGATGCA
1 -TCGATGCACATTCAAGGGATGCA
409206 TCGATGCAC
1 TCGATGCAC
409215 TAACTAGTGT
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
20 1 0.03
21 12 0.30
22 5 0.12
23 21 0.52
24 1 0.03
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (23 bp):
TCGATGCACATTCAAGGGATGCA
Found at i:413086 original size:22 final size:21
Alignment explanation
Indices: 413045--413087 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
413035 AAGACTATTT
*
413045 TCATTTTTCAATTTTTAAATA
1 TCATTTTTCAATTTTAAAATA
413066 TCATTTTT-ATATTTTGAAAATA
1 TCATTTTTCA-ATTTT-AAAATA
413088 AAGTCTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.05
21 13 0.68
22 5 0.26
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:415044 original size:65 final size:64
Alignment explanation
Indices: 414964--415120 Score: 176
Period size: 65 Copynumber: 2.4 Consensus size: 64
414954 TACACTAGGG
* * *** *
414964 TGTGCATCGGGGCACAAATTTGCTTCGATGTTTCAA-AAATAGT-CGGGGTGCATCGATGCATGA
1 TGTGCATCGGTGCACAAAATCAATTCGATGTTTCAATAAA-A-TCCGGAGTGCATCGATGCATG-
415027 CT
63 CT
* *
415029 TGTGCATCGGTGCACAAAATCAATTCGATGTTTCAATAAAATCCTGAGTGCATCGATGCATGGT
1 TGTGCATCGGTGCACAAAATCAATTCGATGTTTCAATAAAATCCGGAGTGCATCGATGCATGCT
*
415093 TGTGCATCGGTGCATAAAATGC-ATTCGA
1 TGTGCATCGGTGCACAAAAT-CAATTCGA
415121 AGTGGGTGTG
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
64 27 0.34
65 50 0.62
66 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (64 bp):
TGTGCATCGGTGCACAAAATCAATTCGATGTTTCAATAAAATCCGGAGTGCATCGATGCATGCT
Found at i:417327 original size:71 final size:72
Alignment explanation
Indices: 417151--417449 Score: 345
Period size: 72 Copynumber: 4.2 Consensus size: 72
417141 AGACTCCAAC
* ** *
417151 TTAAATGAGGAATTAGTAGCTGATGAGAGC-AGTGATGTTGCTACTTCCCAAGATGCATAAAAAA
1 TTAAATGAGAAATCGGTAGCTGATGAGA-CTAGTGATGTTGCTACTTCCCAAGATGCATACAAAA
417215 TCAAGAAG
65 TCAAGAAG
* * * *
417223 TTAATTGAGAAATCGGTAGTTGATGAGACTAGTGATGTTACTATTTCCCAAGATGCATACAAAAT
1 TTAAATGAGAAATCGGTAGCTGATGAGACTAGTGATGTTGCTACTTCCCAAGATGCATACAAAAT
*
417288 -AATAAG
66 CAAGAAG
** * * ***
417294 TTAAATGAGAAATTTGTAGCTGATGAGACTAGTGATGTTGCTATTTCCCAAGATGAATTTGAAAT
1 TTAAATGAGAAATCGGTAGCTGATGAGACTAGTGATGTTGCTACTTCCCAAGATGCATACAAAAT
* *
417359 CGAGAAC
66 CAAGAAG
* * *
417366 TGAAATGAGAAATCGGTAGCTGATTAGACCAGTGATGTT-CTTACTTCCCAAGATGCATAC-AAA
1 TTAAATGAGAAATCGGTAGCTGATGAGACTAGTGATGTTGC-TACTTCCCAAGATGCATACAAAA
*
417429 TCGAGAAG
65 TCAAGAAG
*
417437 TTAAATAAGAAAT
1 TTAAATGAGAAAT
417450 GTTGATTGAT
Statistics
Matches: 191, Mismatches: 33, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
71 84 0.44
72 107 0.56
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.28
Consensus pattern (72 bp):
TTAAATGAGAAATCGGTAGCTGATGAGACTAGTGATGTTGCTACTTCCCAAGATGCATACAAAAT
CAAGAAG
Found at i:417414 original size:143 final size:143
Alignment explanation
Indices: 417151--417428 Score: 389
Period size: 143 Copynumber: 1.9 Consensus size: 143
417141 AGACTCCAAC
* *
417151 TTAAATGAGGAATTAGTAGCTGATGAGAGCAGTGATGTTGCTACTTCCCAAGATGCATAAAAAAT
1 TTAAATGAGAAATTAGTAGCTGATGAGAGCAGTGATGTTGCTACTTCCCAAGATGAATAAAAAAT
* * * * * *
417216 CAAGAAGTTAATTGAGAAATCGGTAGTTGATGAGACTAGTGATGTTACTATTTCCCAAGATGCAT
66 CAAGAACTGAAATGAGAAATCGGTAGCTGATGAGACCAGTGATGTTACTACTTCCCAAGATGCAT
417281 ACAAAATAATAAG
131 ACAAAATAATAAG
* * ***
417294 TTAAATGAGAAATTTGTAGCTGATGAGA-CTAGTGATGTTGCTATTTCCCAAGATGAATTTGAAA
1 TTAAATGAGAAATTAGTAGCTGATGAGAGC-AGTGATGTTGCTACTTCCCAAGATGAATAAAAAA
* *
417358 TCGAGAACTGAAATGAGAAATCGGTAGCTGATTAGACCAGTGATGTT-CTTACTTCCCAAGATGC
65 TCAAGAACTGAAATGAGAAATCGGTAGCTGATGAGACCAGTGATGTTAC-TACTTCCCAAGATGC
417422 ATACAAA
129 ATACAAA
417429 TCGAGAAGTT
Statistics
Matches: 118, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
142 2 0.02
143 116 0.98
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.29
Consensus pattern (143 bp):
TTAAATGAGAAATTAGTAGCTGATGAGAGCAGTGATGTTGCTACTTCCCAAGATGAATAAAAAAT
CAAGAACTGAAATGAGAAATCGGTAGCTGATGAGACCAGTGATGTTACTACTTCCCAAGATGCAT
ACAAAATAATAAG
Found at i:420675 original size:20 final size:20
Alignment explanation
Indices: 420636--420674 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
420626 ATGTGCAATA
*
420636 ATTTATGGCTTTGACAAAAG
1 ATTTATGGCTTAGACAAAAG
420656 ATTTCATGGCTTAGACAAA
1 ATTT-ATGGCTTAGACAAA
420675 GGCCTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (20 bp):
ATTTATGGCTTAGACAAAAG
Found at i:425160 original size:14 final size:14
Alignment explanation
Indices: 425141--425170 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
425131 TGATGGAATG
425141 CTCAAAGAAATGTT
1 CTCAAAGAAATGTT
425155 CTCAAAGAAATGTT
1 CTCAAAGAAATGTT
425169 CT
1 CT
425171 TTGGTTGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (14 bp):
CTCAAAGAAATGTT
Done.