Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001944.1 Hibiscus syriacus cultivar Beakdansim tig00003938_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: 71172
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2437 original size:13 final size:13
Alignment explanation
Indices: 2421--2457 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2411 TATAAATTAG
2421 TGATATAAGAATA
1 TGATATAAGAATA
2434 TGATATAAG-ATA
1 TGATATAAGAATA
2446 TGCA-ATAAGAAT
1 TG-ATATAAGAAT
2458 CGACGTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.51, C:0.03, G:0.16, T:0.30
Consensus pattern (13 bp):
TGATATAAGAATA
Found at i:8705 original size:15 final size:15
Alignment explanation
Indices: 8685--8720 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
8675 GTTTATTTTC
8685 TGTTTAGTCATTATA
1 TGTTTAGTCATTATA
8700 TGTTTAGTCATTATA
1 TGTTTAGTCATTATA
8715 TGTTTA
1 TGTTTA
8721 TTGTGTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.25, C:0.06, G:0.14, T:0.56
Consensus pattern (15 bp):
TGTTTAGTCATTATA
Found at i:13442 original size:11 final size:11
Alignment explanation
Indices: 13426--13459 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
13416 CAACACTATG
13426 CATTGCATTTA
1 CATTGCATTTA
**
13437 CATTGCATCCA
1 CATTGCATTTA
13448 CATTGCATTTA
1 CATTGCATTTA
13459 C
1 C
13460 CTTTTTTTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.38
Consensus pattern (11 bp):
CATTGCATTTA
Found at i:17837 original size:42 final size:42
Alignment explanation
Indices: 17764--17865 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 42
17754 TCCAAAATTG
* *
17764 GTAAGTCCTTCGGGCCATCAGTAAGGTTTTCGAGCATGATGA
1 GTAAATCCTTCGGGCCATCAGTAAGGTTTTCGAGCAAGATGA
* * *
17806 GTAAATCCTTTGGGTCATCTGTAA-GTCTTTCGAGCAAGATGA
1 GTAAATCCTTCGGGCCATCAGTAAGGT-TTTCGAGCAAGATGA
* *
17848 -TAAGTCCATCGGGCCATC
1 GTAAATCCTTCGGGCCATC
17866 CATAAGACCT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (42 bp):
GTAAATCCTTCGGGCCATCAGTAAGGTTTTCGAGCAAGATGA
Found at i:18080 original size:233 final size:232
Alignment explanation
Indices: 17696--18584 Score: 1094
Period size: 233 Copynumber: 3.9 Consensus size: 232
17686 ATTCTAATTC
* * *
17696 AAATATGAAAATGGAAATTGTTGAAAAATAAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAA
1 AAATATGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAA
17761 TTGGTAAGTCCTTCGGGCCATCAGTAAGGT-TTTCGAGCATGATGAGTAAATCCTTTGGGTCATC
66 TTGGTAAGTCCTTCGGGCCATCAGTAA-GTCTTTCGAGCATGATG-GTAAATCCTTTGGGTCATC
* * * *
17825 TGTAAGTCTTTCGAGCAAGATGATAAGTCCATCGGGCCATCCATAAGACCTTTGGGTAGGATGTT
129 TATAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTT
* *
17890 TTCACATGTCTCTCAAAAAATGATAAAGGTTTGTCATTT
194 TTCACATGTCTCTCAAAAAATGAGAAAGGTTTATCATTT
* *
17929 AAATATGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGTAAACAATTTCCAAAG
1 AAATATGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAA
* * * *
17994 TTGGTAAGTCCTTCGGGCCATTAGTAAGTCTTTTGAGCTTGATGCTTAAATCCTTTGGGTCATCT
66 TTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG-GTAAATCCTTTGGGTCATCT
* * * * * * *
18059 GTAAGTCTTTCGAGTAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTTGGGTATGATGGTT
130 ATAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTT
* ** *
18124 TCACATGTCTCTCAAAAAATGAGAAAGATTCCTCGTTT
195 TCACATGTCTCTCAAAAAATGAGAAAGGTTTATCATTT
* * *
18162 AAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAAATTTCTTACCTAGTAAACTATTTCCAAAA
1 AAATATGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAA
* * * *
18227 GTAGTAAGTTCTTCGGGCCATCAGTAAGGCTTTCGAGC---AT-G---A-----T--GTCATCTA
66 TTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGGTAAATCCTTTGGGTCATCTA
* * ** *
18278 TAAGCCTTTCGAGCAAGATGGTAAGTCCTTCGGGACATCCATAAGACCTTCGGACAGTATGTTTT
131 TAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTT
* * *
18343 CACCAAT-T-TCT-GAAAAATGAGAAAAGTTTATAATTT
196 CA-C-ATGTCTCTCAAAAAATGAGAAAGGTTTATCATTT
* * * *
18379 AAATCTGAAAATTGAAATTTTTTGAAAAGTAGGGAAAGTTTCTTACCTAGTAAATTATTTCCAAA
1 AAATATGAAAATTGAAA-TTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAA
* * *
18444 ATTTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGGGTAAATCCTTTGGTTCATT
65 ATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT-GGTAAATCCTTTGGGTCATC
* * * * * *
18509 TATAAGCCTTTCGAGCACGAGGATAAGTCTTTCGGGTCATCCATAAGACCTTCGGGAAGGGTGTT
129 TATAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTT
*
18574 TTTACATGTCT
194 TTCACATGTCT
18585 TTTTGAAAAA
Statistics
Matches: 563, Mismatches: 72, Indels: 42
0.83 0.11 0.06
Matches are distributed among these distances:
217 34 0.06
218 144 0.26
219 2 0.00
220 3 0.01
221 2 0.00
223 1 0.00
225 1 0.00
226 1 0.00
230 2 0.00
231 3 0.01
232 4 0.01
233 366 0.65
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (232 bp):
AAATATGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAA
TTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGGTAAATCCTTTGGGTCATCTA
TAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTT
CACATGTCTCTCAAAAAATGAGAAAGGTTTATCATTT
Found at i:18430 original size:218 final size:218
Alignment explanation
Indices: 18052--18488 Score: 578
Period size: 218 Copynumber: 2.0 Consensus size: 218
18042 AATCCTTTGG
* * * * * **
18052 GTCATCTGTAAGTCTTTCGAGTAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTTGGGTAT
1 GTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCTTCGAGACATCCATAAGACCTTCGGACAT
* **
18117 GATGGTTTCACATGTCTCTCAAAAAATGAGAAAGATTCCTCGTTTAAATCTAAAAATTGAAATTT
66 GATGGTTTCACATGTCTCTCAAAAAATGAGAAAGATTCATAATTTAAATCTAAAAATTGAAATTT
*
18182 TTGAAAAGTAAGAAAAATTTCTTACCTAGTAAACTATTTCCAAAAGTAGTAAGTTCTTCGGGCCA
131 TTGAAAAGTAAGAAAAATTTCTTACCTAGTAAACTATTTCCAAAAGTAGTAAGTCCTTCGGGCCA
18247 TCAGTAAGGCTTTCGAGCATGAT
196 TCAGTAAGGCTTTCGAGCATGAT
* *
18270 GTCATCTATAAGCCTTTCGAGCAAGATGGTAAGTCCTTCGGGACATCCATAAGACCTTCGGACA-
1 GTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCTTCGAGACATCCATAAGACCTTCGGACAT
* * * *
18334 GTATGTTTTCACCAAT-T-TCT-GAAAAATGAGAAA-AGTTTATAATTTAAATCTGAAAATTGAA
66 G-ATGGTTTCA-C-ATGTCTCTCAAAAAATGAGAAAGA-TTCATAATTTAAATCTAAAAATTGAA
* * * * * *
18395 ATTTTTTGAAAAGTAGGGAAAGTTTCTTACCTAGTAAATTATTTCCAAAATTTGTAAGTCCTTCG
127 A-TTTTTGAAAAGTAAGAAAAATTTCTTACCTAGTAAACTATTTCCAAAAGTAGTAAGTCCTTCG
*
18460 GGCCATCAGTAAGTCTTTCGAGCATGAT
191 GGCCATCAGTAAGGCTTTCGAGCATGAT
18488 G
1 G
18489 GGTAAATCCT
Statistics
Matches: 190, Mismatches: 24, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
216 1 0.01
217 35 0.18
218 150 0.79
219 2 0.01
220 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (218 bp):
GTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCTTCGAGACATCCATAAGACCTTCGGACAT
GATGGTTTCACATGTCTCTCAAAAAATGAGAAAGATTCATAATTTAAATCTAAAAATTGAAATTT
TTGAAAAGTAAGAAAAATTTCTTACCTAGTAAACTATTTCCAAAAGTAGTAAGTCCTTCGGGCCA
TCAGTAAGGCTTTCGAGCATGAT
Found at i:18583 original size:451 final size:457
Alignment explanation
Indices: 17672--18619 Score: 1151
Period size: 451 Copynumber: 2.1 Consensus size: 457
17662 TTTATAAGTT
* ** * * * *
17672 AAAAATGAGAAAAAATTCTAATTCAAATATGAAAATGGAAATTGTTGAAAAATAAGAAAAGTTTC
1 AAAAATGAGAAAAATTTCCCATTTAAATCTAAAAATGGAAATTGTTGAAAAATAAGAAAAATTTC
* * *
17737 TTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGGTTTTCGAGCATG
66 TTACCTAGTAAACTATTTCCAAAAGTAGTAAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCA--
* * *
17802 ATGAGTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCATCGGGCCATCC
129 AT-AG--AA----TT-GGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCATCGGGACATCC
* ** * * * *
17867 ATAAGACCTTTGGGTAGGATGTTTTCACATGTCTCTCAAAAAATGATAAAGGTTTGTCATTTAAA
186 ATAAGACCTTCGGACAGGATGTTTTCACATGTCTCTCAAAAAATGAGAAAAGTTTATAATTTAAA
*
17932 TATGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGTAAACAATTTCCAAAGTTG
251 TATGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGTAAACAATTTCCAAAATTG
* * * * *
17997 GTAAGTCCTTCGGGCCATTAGTAAGTCTTTTGAGCTTGATGCTTAAATCCTTTGGGTCATCTGTA
316 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCGTAAATCCTTTGGGTCATCTATA
* * * * * *
18062 AGTCTTTCGAGTAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTTGGGTATGATGGTTTCA
381 AGCCTTTCGAGCAAGAGGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGAAGGATGGTTTCA
18127 CATGTC-TCTCA
446 CATGTCTTCTCA
* * * * *
18138 AAAAATGAGAAAGA-TTCCTCGTTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAAATTT
1 AAAAATGAGAAAAATTTCC-CATTTAAATCTAAAAATGGAAATTGTTGAAAAATAAGAAAAATTT
*
18202 CTTACCTAGTAAACTATTTCCAAAAGTAGTAAGTTCTTCGGGCCATCAGTAAGGCTTTCGAGC-A
65 CTTACCTAGTAAACTATTTCCAAAAGTAGTAAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCAA
* *
18266 T-G-A-T-GTCATCTATAAGCCTTTCGAGCAAGATGGTAAGTCCTTCGGGACATCCATAAGACCT
130 TAGAATTGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCATCGGGACATCCATAAGACCT
* * *
18327 TCGGACAGTATGTTTTCACCAAT-T-TCT-GAAAAATGAGAAAAGTTTATAATTTAAATCTGAAA
195 TCGGACAGGATGTTTTCA-C-ATGTCTCTCAAAAAATGAGAAAAGTTTATAATTTAAATATGAAA
* * ** *
18389 ATTGAAATTTTTTGAAAAGTAGGGAAAGTTTCTTACCTAGTAAATTATTTCCAAAATTTGTAAGT
258 ATTGAAA-TTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGTAAACAATTTCCAAAATTGGTAAGT
* * *
18454 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGGGTAAATCCTTTGGTTCATTTATAAGCCTT
322 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCGTAAATCCTTTGGGTCATCTATAAGCCTT
* * * * * * *
18519 TCGAGCACGAGGATAAGTCTTTCGGGTCATCCATAAGACCTTCGGGAAGGGTGTTTTTACATGTC
387 TCGAGCAAGAGGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGAAGGATGGTTTCACATGTC
* **
18584 TTTTTG
452 TTCTCA
18590 AAAAATGAGAAAAATTTCCCATTTAAATCT
1 AAAAATGAGAAAAATTTCCCATTTAAATCT
18620 TTTTTGAAAA
Statistics
Matches: 414, Mismatches: 62, Indels: 26
0.82 0.12 0.05
Matches are distributed among these distances:
450 36 0.09
451 229 0.55
452 27 0.07
453 7 0.02
458 1 0.00
461 1 0.00
463 2 0.00
465 3 0.01
466 108 0.26
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (457 bp):
AAAAATGAGAAAAATTTCCCATTTAAATCTAAAAATGGAAATTGTTGAAAAATAAGAAAAATTTC
TTACCTAGTAAACTATTTCCAAAAGTAGTAAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCAAT
AGAATTGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCATCGGGACATCCATAAGACCTT
CGGACAGGATGTTTTCACATGTCTCTCAAAAAATGAGAAAAGTTTATAATTTAAATATGAAAATT
GAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGTAAACAATTTCCAAAATTGGTAAGTCCTT
CGGGCCATCAGTAAGTCTTTCGAGCATGATGCGTAAATCCTTTGGGTCATCTATAAGCCTTTCGA
GCAAGAGGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGAAGGATGGTTTCACATGTCTTCT
CA
Found at i:19115 original size:133 final size:134
Alignment explanation
Indices: 18866--19294 Score: 546
Period size: 133 Copynumber: 3.2 Consensus size: 134
18856 AATCGAACTT
* * *
18866 GATTCAATCTTCCCTGAAG-AACAGTGGAATAAATCAATGTCCTTAGATCTGATTTTCCCTTAAG
1 GATTCAATCTTCCCTGAAGTAACAGTGGAATGAATCAACGTCCCTAGATCTGATTTTCCCTTAAG
* * * * *
18930 AAGAAGCGGAACATATCCTTTTTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTT
66 AAGAAGTGGAACAAATCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTATT
18995 CCTC
131 CCTC
* * *
18999 GATTCAATCTTCCCT-AAGTGACAGTGGAATGAATCAACGTCCCTAGATATGATTTTCCCTCAAG
1 GATTCAATCTTCCCTGAAGTAACAGTGGAATGAATCAACGTCCCTAGATCTGATTTTCCCTTAAG
* * * *
19063 AAGAAGTGGAACAAATCCTCTCTTTCAAGATTTGATATTCTCTGAATGACAGTAGAACAAGTATG
66 AAGAAGTGGAACAAATCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTAT-
19128 T-CTC
130 TCCTC
* * * * *
19132 AATTCAATCTTCCCT-AAGTAATAGTGGAATGAATCAACATTCCC-AGATCTTATTTTCCCTTAG
1 GATTCAATCTTCCCTGAAGTAACAGTGGAATGAATCAAC-GTCCCTAGATCTGATTTTCCCTTAA
* * *
19195 GAAGAAGTGGAATAGATCTCTCTCTTTCAAGATTTGATATTCCCAGAGTAACAGTGGAACAAGTA
65 GAAGAAGTGGAACAAATC-CTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTA
*
19260 TGCCTC
129 TTCCTC
* *
19266 GA-TCTAATCTACCCTGAAGAAACAGTGGA
1 GATTC-AATCTTCCCTGAAGTAACAGTGGA
19295 GTAAATCCCT
Statistics
Matches: 254, Mismatches: 35, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
132 3 0.01
133 180 0.71
134 60 0.24
135 11 0.04
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (134 bp):
GATTCAATCTTCCCTGAAGTAACAGTGGAATGAATCAACGTCCCTAGATCTGATTTTCCCTTAAG
AAGAAGTGGAACAAATCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTATT
CCTC
Found at i:19452 original size:3 final size:3
Alignment explanation
Indices: 19446--19470 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19436 TTATTATTAT
19446 TAC TAC TAC TAC TAC TAC TAC TAC T
1 TAC TAC TAC TAC TAC TAC TAC TAC T
19471 TTTTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TAC
Found at i:20345 original size:20 final size:20
Alignment explanation
Indices: 20320--20358 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20310 TCTCTATTTT
*
20320 AAAAAAAAGAGAGAAAAAGG
1 AAAAAAAAAAGAGAAAAAGG
20340 AAAAAAAAAAGAGAAAAAG
1 AAAAAAAAAAGAGAAAAAG
20359 TTGGTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAGAGAAAAAGG
Found at i:22523 original size:48 final size:47
Alignment explanation
Indices: 22452--22546 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 47
22442 ACCAACTGCG
** *
22452 TTGAACATTGGTACACAAATGTACCAAAGCTGAACTGATAATTGATAA
1 TTGAACATTAATACACAAATGTACCAAAGCTGAACTGA-AACTGATAA
*
22500 TTGAACATTAATACACGAATGTACCAAAGCTGAACTGAAACTGATAA
1 TTGAACATTAATACACAAATGTACCAAAGCTGAACTGAAACTGATAA
22547 CTACTCACTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
47 8 0.19
48 35 0.81
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (47 bp):
TTGAACATTAATACACAAATGTACCAAAGCTGAACTGAAACTGATAA
Found at i:22728 original size:18 final size:18
Alignment explanation
Indices: 22645--22720 Score: 75
Period size: 18 Copynumber: 4.3 Consensus size: 18
22635 AATATGTATA
22645 TGATAACTGTAAAATATC
1 TGATAACTGTAAAATATC
** **
22663 TGATATTTGT-ATTTATC
1 TGATAACTGTAAAATATC
*
22680 AGATAACTGT-AAATCATC
1 TGATAACTGTAAAAT-ATC
22698 TGATAACTGTAAAATATC
1 TGATAACTGTAAAATATC
*
22716 CGATA
1 TGATA
22721 TTTGTAAACA
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
17 14 0.31
18 27 0.60
19 4 0.09
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (18 bp):
TGATAACTGTAAAATATC
Found at i:33085 original size:20 final size:21
Alignment explanation
Indices: 33051--33107 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
33041 TGATCAAAAT
*
33051 AAAAGAAAT-TAAAATTA-TA
1 AAAATAAATATAAAATTATTA
*
33070 AAACTAAATATAAAA-TATTA
1 AAAATAAATATAAAATTATTA
*
33090 AAAATAAAGATAATAATT
1 AAAATAAATATAA-AATT
33108 CAAAATATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 9 0.30
20 18 0.60
21 2 0.07
22 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (21 bp):
AAAATAAATATAAAATTATTA
Found at i:34331 original size:3 final size:3
Alignment explanation
Indices: 34323--34382 Score: 102
Period size: 3 Copynumber: 20.0 Consensus size: 3
34313 TTGTAATATT
**
34323 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34371 TAA TAA TAA TAA
1 TAA TAA TAA TAA
34383 ATTTAAATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:34670 original size:76 final size:76
Alignment explanation
Indices: 34516--35157 Score: 1160
Period size: 76 Copynumber: 8.4 Consensus size: 76
34506 GATGGAAATG
* * * *
34516 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
34580 CCCGAATGCTTT
66 CCCGAAGGC-TT
34592 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
34657 CCCGAAGGCTT
66 CCCGAAGGCTT
34668 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
34733 CCCGAAGGCTT
66 CCCGAAGGCTT
34744 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
34809 CCCGAAGGCTT
66 CCCGAAGGCTT
* * * *
34820 TTTGGAAACATCATGCACTGCAGAACTTATAAATGACCCTAAGGCTTTGAAAACATCAAAAATCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
34885 CCCGAAGGCTT
66 CCCGAAGGCTT
*
34896 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAATCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
34961 CCCGAAGGCTT
66 CCCGAAGGCTT
34972 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
35037 CCCGAAGGCTT
66 CCCGAAGGCTT
35048 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
35113 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
35124 TTTGGAAACATCATGCACTGTAGGATTTACAGAT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGAT
35158 ATGGGAAATA
Statistics
Matches: 550, Mismatches: 15, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
76 522 0.95
77 28 0.05
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:36028 original size:22 final size:22
Alignment explanation
Indices: 36003--36079 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
35993 CATAAAGCTT
*
36003 TCATCTTTGAAAAGAGAATATA
1 TCATCTTTGAAAAGAGAATTTA
*
36025 TCATCTTTAAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATTTA
36047 TCATCTTTGAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATTTA
36069 TCATCTTTGAA
1 TCATCTTTGAA
36080 GAATGTAGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATTTA
Found at i:37369 original size:75 final size:74
Alignment explanation
Indices: 37242--37486 Score: 269
Period size: 75 Copynumber: 3.3 Consensus size: 74
37232 CATGATGATG
* * * * *
37242 TGGGCCTTCAGCATGCCCCAA-AATGGGCTAATACAAGCGTGCAGAATGCATCAACATTCTTGAT
1 TGGGCTTTCAGCATGCCCCAACAAT-TGCTGATACAA-CGTTCAGAATACATCAACATTCTTGAT
37306 TCTGATTAAAA
64 TCTGATTAAAA
* * *
37317 TGGGCTTTCAGCATGCCCCAACAATTGCTGATACGAACGTTCAAAATACATCAACATTATTCATT
1 TGGGCTTTCAGCATGCCCCAACAATTGCTGATAC-AACGTTCAGAATACATCAACATTCTTGATT
*
37382 CTGATTGAAA
65 CTGATTAAAA
* * * * * * *
37392 GGGGCTTTCAGCATGCCCCATCATTTTGCTGATATAAACATTCAGGATACATCAACATTCCTGAT
1 TGGGCTTTCAGCATGCCCCAACA-ATTGCTGATA-CAACGTTCAGAATACATCAACATTCTTGAT
37457 TCTGATTGAAAA
64 TCTGATT-AAAA
*
37469 -GGGTTTTCAGCATGCCCC
1 TGGGCTTTCAGCATGCCCC
37487 CACTTTTCTT
Statistics
Matches: 144, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
75 80 0.56
76 61 0.42
77 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (74 bp):
TGGGCTTTCAGCATGCCCCAACAATTGCTGATACAACGTTCAGAATACATCAACATTCTTGATTC
TGATTAAAA
Found at i:38706 original size:114 final size:114
Alignment explanation
Indices: 38499--38707 Score: 328
Period size: 114 Copynumber: 1.8 Consensus size: 114
38489 ATGCAGTTCG
* * * *
38499 TCTTTCAATTCTAATGATTGGTTCTGGGGTTCATAGCAAATCAGATCAGATAACTCAAAGAACAC
1 TCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
* *
38564 TTCCAGAAGATGCTATGGGGTTTTCTTATTTCTAGTATGAGCAAATTCA
66 TTCCAGAAGATGCTATGGGGTCTCCTTATTTCTAGTATGAGCAAATTCA
* *
38613 TCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAT
1 TCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
* *
38678 TTTCAGAAGATGCTATTGGGTCTCCTTATT
66 TTCCAGAAGATGCTATGGGGTCTCCTTATT
38708 CCTACTACGA
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 85 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (114 bp):
TCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATGGGGTCTCCTTATTTCTAGTATGAGCAAATTCA
Found at i:43893 original size:7 final size:7
Alignment explanation
Indices: 43878--43936 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
43868 TAAAAGTATG
*
43878 AATGCAA
1 AATGAAA
43885 AATGAAA
1 AATGAAA
43892 AATGCAAA
1 AATG-AAA
* *
43900 GATGCAA
1 AATGAAA
43907 AATGAAA
1 AATGAAA
43914 AATGCAAA
1 AATG-AAA
* *
43922 GATGCAA
1 AATGAAA
43929 AATGAAA
1 AATGAAA
43936 A
1 A
43937 TGCATATATG
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
7 29 0.71
8 12 0.29
ACGTcount: A:0.61, C:0.08, G:0.17, T:0.14
Consensus pattern (7 bp):
AATGAAA
Found at i:43895 original size:14 final size:14
Alignment explanation
Indices: 43878--43950 Score: 76
Period size: 15 Copynumber: 5.1 Consensus size: 14
43868 TAAAAGTATG
43878 AATGCAAAATGAAA
1 AATGCAAAATGAAA
*
43892 AATGCAAAGATGCAA
1 AATGCAAA-ATGAAA
*
43907 AATGAAAAATGCAAA
1 AATGCAAAATG-AAA
*
43922 GATGCAAAATG-AA
1 AATGCAAAATGAAA
*
43935 AATGCATATATGAAA
1 AATGCA-AAATGAAA
43950 A
1 A
43951 GATGTGAGTG
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
13 7 0.15
14 15 0.31
15 26 0.54
ACGTcount: A:0.59, C:0.08, G:0.16, T:0.16
Consensus pattern (14 bp):
AATGCAAAATGAAA
Found at i:43905 original size:22 final size:22
Alignment explanation
Indices: 43879--43940 Score: 117
Period size: 22 Copynumber: 2.9 Consensus size: 22
43869 AAAAGTATGA
43879 ATGCAAAATGAAAAATGCAAAG
1 ATGCAAAATGAAAAATGCAAAG
43901 ATGCAAAATGAAAAATGCAAAG
1 ATGCAAAATGAAAAATGCAAAG
43923 ATGCAAAATG-AAAATGCA
1 ATGCAAAATGAAAAATGCA
43941 TATATGAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 8 0.20
22 32 0.80
ACGTcount: A:0.58, C:0.10, G:0.18, T:0.15
Consensus pattern (22 bp):
ATGCAAAATGAAAAATGCAAAG
Found at i:43954 original size:29 final size:30
Alignment explanation
Indices: 43878--43954 Score: 97
Period size: 29 Copynumber: 2.6 Consensus size: 30
43868 TAAAAGTATG
43878 AATGCAAAATGAAAA-ATGCAAAGATGCAA
1 AATGCAAAATGAAAAGATGCAAAGATGCAA
* *
43907 AATGAAAAATGCAAAGATGCAAA-ATG-AA
1 AATGCAAAATGAAAAGATGCAAAGATGCAA
*
43935 AATGCATATATGAAAAGATG
1 AATGCA-AAATGAAAAGATG
43955 TGAGTGATCA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 7 0.17
29 27 0.66
30 7 0.17
ACGTcount: A:0.57, C:0.08, G:0.18, T:0.17
Consensus pattern (30 bp):
AATGCAAAATGAAAAGATGCAAAGATGCAA
Found at i:44165 original size:13 final size:13
Alignment explanation
Indices: 44133--44166 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
44123 TCTCGTGAAG
*
44133 CCAGCTAAGTCCA
1 CCAGCTTAGTCCA
44146 CCAGCTTAGTCCA
1 CCAGCTTAGTCCA
44159 CCAGCTTA
1 CCAGCTTA
44167 TAAGCCACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.26, C:0.38, G:0.15, T:0.21
Consensus pattern (13 bp):
CCAGCTTAGTCCA
Found at i:46307 original size:17 final size:17
Alignment explanation
Indices: 46287--46337 Score: 50
Period size: 20 Copynumber: 2.8 Consensus size: 17
46277 GAATAAAATA
*
46287 AATAAATAAAAAATATT
1 AATAAATAAAAAATAGT
46304 AATAAAATAATAAAAATAGT
1 AAT-AAAT-A-AAAAATAGT
46324 AAGT-AATAAAAAAT
1 AA-TAAATAAAAAAT
46338 TTGAAAGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 9 0.31
18 5 0.17
19 4 0.14
20 10 0.34
21 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (17 bp):
AATAAATAAAAAATAGT
Found at i:47149 original size:20 final size:21
Alignment explanation
Indices: 47115--47171 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
47105 TGATCAAAAT
*
47115 AAAAGAAAT-TAAAATTA-TA
1 AAAATAAATATAAAATTATTA
*
47134 AAACTAAATATAAAA-TATTA
1 AAAATAAATATAAAATTATTA
47154 AAAATAAATATAATAATT
1 AAAATAAATATAA-AATT
47172 CAAAATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 9 0.29
20 19 0.61
21 2 0.06
22 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAATAAATATAAAATTATTA
Found at i:48424 original size:3 final size:3
Alignment explanation
Indices: 48398--48462 Score: 78
Period size: 3 Copynumber: 21.0 Consensus size: 3
48388 TTGTAATATT
*
48398 TAA TAA GTAA TAAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA -TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
48445 T-T TGAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA
48463 ATTTAAAATG
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 1 0.02
3 46 0.85
4 7 0.13
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:56087 original size:22 final size:23
Alignment explanation
Indices: 56061--56114 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
56051 CCTCGTAGAT
*
56061 CTCGTAG-TGCACTTGAAAATGC
1 CTCGTAGTTGCACTCGAAAATGC
*
56083 CTCGTAGTATTGCACTCGAAAGTGC
1 CTCGTAG--TTGCACTCGAAAATGC
56108 CTCGTAG
1 CTCGTAG
56115 GATTGCACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 7 0.26
25 20 0.74
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (23 bp):
CTCGTAGTTGCACTCGAAAATGC
Found at i:56103 original size:25 final size:25
Alignment explanation
Indices: 56068--56122 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
56058 GATCTCGTAG
* *
56068 TGCACTTGAAAATGCCTCGTAGTAT
1 TGCACTCGAAAATGCCTCGTAGGAT
*
56093 TGCACTCGAAAGTGCCTCGTAGGAT
1 TGCACTCGAAAATGCCTCGTAGGAT
56118 TGCAC
1 TGCAC
56123 CATAGGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (25 bp):
TGCACTCGAAAATGCCTCGTAGGAT
Found at i:56224 original size:13 final size:13
Alignment explanation
Indices: 56206--56230 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56196 CATTAGTCCA
56206 CATAATCAATATT
1 CATAATCAATATT
56219 CATAATCAATAT
1 CATAATCAATAT
56231 GCAATAGGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
CATAATCAATATT
Found at i:56337 original size:14 final size:16
Alignment explanation
Indices: 56304--56340 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
56294 TTCAATAAAG
56304 TTCAAAATAAAAATCA
1 TTCAAAATAAAAATCA
*
56320 TTCAAAAT-CAAA-CA
1 TTCAAAATAAAAATCA
56334 TTCAAAA
1 TTCAAAA
56341 CACAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 9 0.45
15 3 0.15
16 8 0.40
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.24
Consensus pattern (16 bp):
TTCAAAATAAAAATCA
Found at i:58899 original size:22 final size:19
Alignment explanation
Indices: 58853--58929 Score: 77
Period size: 18 Copynumber: 3.8 Consensus size: 19
58843 AGAATGCTCG
58853 GATGGTACCGATACCCCCA
1 GATGGTACCGATACCCCCA
*
58872 GA-GGTATCGATACCCCCA
1 GATGGTACCGATACCCCCA
58890 TGCAATGGTACCGATACCCCCTCA
1 -G--ATGGTACCGATA-CCCC-CA
58914 GGA-GGTACCGATACCC
1 -GATGGTACCGATACCC
58930 TCAGGCATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
18 15 0.31
19 3 0.06
20 3 0.06
21 11 0.22
22 10 0.20
23 4 0.08
24 3 0.06
ACGTcount: A:0.26, C:0.35, G:0.22, T:0.17
Consensus pattern (19 bp):
GATGGTACCGATACCCCCA
Found at i:58920 original size:21 final size:20
Alignment explanation
Indices: 58856--58929 Score: 82
Period size: 22 Copynumber: 3.6 Consensus size: 20
58846 ATGCTCGGAT
58856 GGTACCGATA-CCCC-CAGA
1 GGTACCGATACCCCCTCAGA
*
58874 GGTATCGATACCCCCATGCA-A
1 GGTACCGATACCCCC-T-CAGA
58895 TGGTACCGATACCCCCTCAGGA
1 -GGTACCGATACCCCCTCA-GA
58917 GGTACCGATACCC
1 GGTACCGATACCC
58930 TCAGGCATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
18 9 0.19
19 4 0.09
20 2 0.04
21 15 0.32
22 17 0.36
ACGTcount: A:0.26, C:0.36, G:0.22, T:0.16
Consensus pattern (20 bp):
GGTACCGATACCCCCTCAGA
Found at i:63824 original size:39 final size:39
Alignment explanation
Indices: 63770--63870 Score: 159
Period size: 39 Copynumber: 2.6 Consensus size: 39
63760 GGGTCGAACA
* *
63770 AGTTCTTCTCATTATGAACT-TATTCTCCCTTGTCGGATG
1 AGTTCTTCTCATTATGAACTCT-CTCCCCCTTGTCGGATG
*
63809 AGTTCTTCTCATTATGAACTCTCTCCCCCTTGTTGGATG
1 AGTTCTTCTCATTATGAACTCTCTCCCCCTTGTCGGATG
63848 AGTTCTTCTCATTATGAACTCTC
1 AGTTCTTCTCATTATGAACTCTC
63871 CAGTGGAAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 57 0.98
40 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.14, T:0.43
Consensus pattern (39 bp):
AGTTCTTCTCATTATGAACTCTCTCCCCCTTGTCGGATG
Found at i:63909 original size:91 final size:92
Alignment explanation
Indices: 63809--64013 Score: 317
Period size: 91 Copynumber: 2.2 Consensus size: 92
63799 TTGTCGGATG
*
63809 AGTTCTTCTCATTATGAACTCTC-TCCCCCTTGTTGGATGAGTTCTTCTCATTATGAACTCTCCA
1 AGTTCTTCTCATTATGAACTCTCTTCCCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCA
* *
63873 GTGGAAATGCTAG-GCCAAGGTTGAACA
66 CTGGAAAT-CTAGAACCAAGGTTGAACA
* *
63900 AGTTCTTCTCATTATGAACT-TCTTCTCCCTCGTTGGATGAGTTCTTCTCGTTATGAACTCTCCA
1 AGTTCTTCTCATTATGAACTCTCTTCCCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCA
* *
63964 CTGGAAATCTTGAACCAAGGTTGAATA
66 CTGGAAATCTAGAACCAAGGTTGAACA
63991 AGTTCTTCTCATTATGAACTCTC
1 AGTTCTTCTCATTATGAACTCTC
64014 CACTGGAAAT
Statistics
Matches: 104, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
90 5 0.05
91 97 0.93
92 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.37
Consensus pattern (92 bp):
AGTTCTTCTCATTATGAACTCTCTTCCCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCA
CTGGAAATCTAGAACCAAGGTTGAACA
Found at i:63912 original size:130 final size:129
Alignment explanation
Indices: 63679--64104 Score: 462
Period size: 130 Copynumber: 3.2 Consensus size: 129
63669 AAGTTGAACA
* * *** * *
63679 AGTTCTTCTCATTATGAACTTTTTGTTCCTTGTTGTATGAGTTATTCTCATTATGAACTCTCCAC
1 AGTTCTTCTCATTATGAACTCTCTCCCCCTTGTTGAATGAGTTCTTCTCATTATGAACTCTCCAC
* * * * *
63744 TGGTAACATCAAGG--AAGGGTCGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTTGTCGGA
66 TGG-AA-ATCTAGGCCAA-GGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGA
63807 TG
128 TG
* *
63809 AGTTCTTCTCATTATGAACTCTCTCCCCCTTGTTGGATGAGTTCTTCTCATTATGAACTCTCCAG
1 AGTTCTTCTCATTATGAACTCTCTCCCCCTTGTTGAATGAGTTCTTCTCATTATGAACTCTCCAC
63874 TGGAAATGCTAGGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATG
66 TGGAAAT-CTAGGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATG
* ** *
63939 AGTTCTTCTCGTTATGAACTCTC-CACTGGAAATCTTGAACCAAGGTTGAATAAGTTCTTCTCAT
1 AGTTCTTCTCATTATGAACTCTCTC-C-------C-----CC-TTGTTGAATGAGTTCTTCTCAT
* * * *
64003 TATGAACTCTCCACTGGAAATTTTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTGC
52 TATGAACTCTCCACTGGAAATCTAG-GCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
64068 TCCCTCGTTGGATG
116 TCCCTCGTTGGATG
64082 AGTTCTTCTCATTATGAACTCTC
1 AGTTCTTCTCATTATGAACTCTC
64105 CATTGGAAAT
Statistics
Matches: 254, Mismatches: 24, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
128 2 0.01
129 7 0.03
130 127 0.50
131 2 0.01
137 1 0.00
142 4 0.02
143 111 0.44
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (129 bp):
AGTTCTTCTCATTATGAACTCTCTCCCCCTTGTTGAATGAGTTCTTCTCATTATGAACTCTCCAC
TGGAAATCTAGGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATG
Found at i:64017 original size:52 final size:52
Alignment explanation
Indices: 63939--64062 Score: 221
Period size: 52 Copynumber: 2.4 Consensus size: 52
63929 TCGTTGGATG
* *
63939 AGTTCTTCTCGTTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAATA
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACA
*
63991 AGTTCTTCTCATTATGAACTCTCCACTGGAAATTTTGAACCAAGGTTGAACA
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACA
64043 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
64063 TCTGCTCCCT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (52 bp):
AGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACA
Found at i:64089 original size:91 final size:91
Alignment explanation
Indices: 63991--64210 Score: 386
Period size: 91 Copynumber: 2.4 Consensus size: 91
63981 AGGTTGAATA
*
63991 AGTTCTTCTCATTATGAACTCTCCACTGGAAATTTTGAACCAAGGTTGAACAAGTTCTTCTCATT
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAACCAAGGTTGAACAAGTTCTTCTCATT
64056 ATGAACTTCTGCTCCCTCGTTGGATG
66 ATGAACTTCTGCTCCCTCGTTGGATG
* *
64082 AGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTGAGCCAAGGTTGAACAAGTTCTTCTCATT
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAACCAAGGTTGAACAAGTTCTTCTCATT
* *
64147 ATGAACTTCTTCTCTCTCGTTGGATG
66 ATGAACTTCTGCTCCCTCGTTGGATG
*
64173 AGTTCTTCTCATTATGAACTCTCCACTGGCAATGTTGA
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGA
64211 TCGGTTTATC
Statistics
Matches: 122, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 122 1.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (91 bp):
AGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAACCAAGGTTGAACAAGTTCTTCTCATT
ATGAACTTCTGCTCCCTCGTTGGATG
Found at i:64106 original size:143 final size:143
Alignment explanation
Indices: 63848--64153 Score: 506
Period size: 143 Copynumber: 2.1 Consensus size: 143
63838 TTGTTGGATG
* *
63848 AGTTCTTCTCATTATGAACTCTCCAGTGGAAATGCTAGGCCAAGGTTGAACAAGTTCTTCTCATT
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAATGCTAGACCAAGGTTGAACAAGTTCTTCTCATT
* *
63913 ATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCGTTATGAACTCTCCACTGGAAATCTTGAA
66 ATGAACTTCTGCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAA
*
63978 CCAAGGTTGAATA
131 CCAAGGTTGAACA
* *
63991 AGTTCTTCTCATTATGAACTCTCCACTGGAAAT-TTTGAACCAAGGTTGAACAAGTTCTTCTCAT
1 AGTTCTTCTCATTATGAACTCTCCACTGGAAATGCTAG-ACCAAGGTTGAACAAGTTCTTCTCAT
* *
64055 TATGAACTTCTGCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTGA
65 TATGAACTTCTGCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGA
*
64120 GCCAAGGTTGAACA
130 ACCAAGGTTGAACA
64134 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
64154 TCTTCTCTCT
Statistics
Matches: 152, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
142 2 0.01
143 150 0.99
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.35
Consensus pattern (143 bp):
AGTTCTTCTCATTATGAACTCTCCACTGGAAATGCTAGACCAAGGTTGAACAAGTTCTTCTCATT
ATGAACTTCTGCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAA
CCAAGGTTGAACA
Found at i:64672 original size:67 final size:68
Alignment explanation
Indices: 64600--64794 Score: 206
Period size: 67 Copynumber: 2.9 Consensus size: 68
64590 GAAAACACAA
* * * * * *
64600 TCAAAG-TTGTTGAGCTTCAAGAGAAACTGTCTCTAGGGAGATAAAATTCAG-TTCAAGGGAAAC
1 TCAAAGATTGTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT-AGTTTCAAGAGAAAC
64663 GAT-C
65 -ATAC
* * *
64667 TCAAAGATCG--GTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACA
1 TCAAAGATTGTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAGAGAAACA
*
64730 TAT
66 TAC
* *
64733 TCAAAGATT-TTGTGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT-GTTTCAAGGGAAA
1 TCAAAGATTGTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGTTTCAAGAGAAA
64795 TTTTTTCAAG
Statistics
Matches: 108, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
65 3 0.03
66 50 0.46
67 51 0.47
68 4 0.04
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.26
Consensus pattern (68 bp):
TCAAAGATTGTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAGAGAAACA
TAC
Found at i:64686 original size:66 final size:67
Alignment explanation
Indices: 64615--64794 Score: 206
Period size: 66 Copynumber: 2.7 Consensus size: 67
64605 GTTGTTGAGC
* * * *
64615 TTCAAGAGAAACTGTCTCTAGGGAGATAAAATTCAG-TTCAAGGGAAACGAT-CTCAAAGA-TCG
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATT-AGTTTCAAGAGAAAC-ATACTCAAAGATTCG
64677 GTGT
64 GTGT
* * * **
64681 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACATATTCAAAGATTTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAGAGAAACATACTCAAAGATTCGGT
64746 GT
66 GT
* *
64748 TTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT-GTTTCAAGGGAAA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGTTTCAAGAGAAA
64795 TTTTTTCAAG
Statistics
Matches: 98, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
65 3 0.03
66 47 0.48
67 46 0.47
68 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (67 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAGAGAAACATACTCAAAGATTCGGT
GT
Found at i:64728 original size:36 final size:36
Alignment explanation
Indices: 64678--65192 Score: 416
Period size: 36 Copynumber: 14.0 Consensus size: 36
64668 CAAAGATCGG
*
64678 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
* **
64714 TGTTTCAAGAGAAACATAT-TC-A-A-AG---ATTTT
1 TGTTTCAAGGGAAAC-TATCTCAAGAGAGACAAAATT
* * * *
64744 GTGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACT
1 -TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
* * *
64781 TGTTTCAAGGGAAATTTTTTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
* *
64817 TGGTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
* * **
64853 TGTTCCAATGGAAACCGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
* * *
64889 TATTTCAAGGGAAACTGTCTCAAGAGCGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
* *
64925 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA--TT
* * * * *
64963 CTGTTTCGAGGAAAACTATCTCAAGCGATACAAATCTTT
1 -TGTTTCAAGGGAAACTATCTCAAGAGAGACAAA--ATT
* * *
65002 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA---TT
* * *
65041 TGTTTCAAGGGAAACTATCTCAAGCGATATAAAATCTCT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA--T-T
* *
65080 TGTTTCAAGGGAAACTACCTCAA-ACGAGATAAAATCTT
1 TGTTTCAAGGGAAACTATCTCAAGA-GAGACAAAA--TT
* * *
65118 CTGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATCTT
1 -TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA--TT
* * * *
65157 CTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAAT
1 -TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
65193 ATTCTTTAAA
Statistics
Matches: 405, Mismatches: 53, Indels: 41
0.81 0.11 0.08
Matches are distributed among these distances:
30 5 0.01
31 17 0.04
32 1 0.00
33 2 0.00
34 3 0.01
35 1 0.00
36 170 0.42
37 5 0.01
38 34 0.08
39 167 0.41
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
Found at i:64803 original size:67 final size:65
Alignment explanation
Indices: 64615--64939 Score: 204
Period size: 72 Copynumber: 4.7 Consensus size: 65
64605 GTTGTTGAGC
* * * *
64615 TTCAAGAGAAACTGTCTCTAGGGAGATAAAATTCAG-TTCAAGGGAAACGA-TCTCAAAGATCGG
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATT--GTTTCAAGGGAAAC-ATTTTCAAAGATCGG
64678 TGT
63 TGT
* * * **
64681 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACATATTCAAAGATTTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTGTTTCAAGGGAAACATTTTCAAAGA-TCGGT
64746 GT
64 GT
* ** *
64748 TTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTGTTTCAAGGGAAATTTTTTCAAGAGAGACAA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTGTTTCAAGGGAAACATTTTCAA-AGA-TC--
** *
64813 AATTTGG
61 --GGTGT
* * * ** * *
64820 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTCCAATGGAAACCGTCTCAAGAGAGACAA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTGTTTCAAGGGAAACATTTTCAA-AGA-TC--
** *
64885 AATTTAT
61 --GGTGT
* *
64892 TTCAAGGGAAACTGTCTCAAGAGCGACAAAATTTGTTTCAAGGGAAAC
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTGTTTCAAGGGAAAC
64940 TATCTCAAGC
Statistics
Matches: 215, Mismatches: 35, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
65 2 0.01
66 45 0.21
67 56 0.26
68 3 0.01
72 109 0.51
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (65 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTGTTTCAAGGGAAACATTTTCAAAGATCGGTGT
Found at i:64979 original size:39 final size:39
Alignment explanation
Indices: 64745--65197 Score: 447
Period size: 39 Copynumber: 12.0 Consensus size: 39
64735 AAAGATTTTG
* * *
64745 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAA-C-T-
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * * * *
64781 TGTTTCAAGGGAAATTTTTTCAAGAGAGACAAAA--TT-
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * * *
64817 TGGTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--TT-
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * ** * *
64853 TGTTCCAATGGAAACCGTCTCAAGAGAGACAAAA--TT-
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * * * *
64889 TATTTCAAGGGAAACTGTCTCAAGAGCGACAAAA--TT-
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
64925 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * *
64964 TGTTTCGAGGAAAACTATCTCAAGC--GATACAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATA-AAATCTTC
* *
65002 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
*
65041 TGTTTCAAGGGAAACTATCTCAAGCGATATAAAATC-TC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* *
65079 TTGTTTCAAGGGAAACTACCTCAAACGAGATAAAATCTTC
1 -TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
*
65119 TGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * *
65158 TGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATATTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
65197 T
1 T
65198 TTAAAAAGAA
Statistics
Matches: 370, Mismatches: 38, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
36 154 0.42
37 4 0.01
38 34 0.09
39 172 0.46
40 6 0.02
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (39 bp):
TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
Done.