Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005415.1 Hibiscus syriacus cultivar Beakdansim tig00012420_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: 147792
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:213 original size:62 final size:62
Alignment explanation
Indices: 107--246 Score: 201
Period size: 62 Copynumber: 2.2 Consensus size: 62
97 CACAAGTTCA
*
107 AACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCCAATTTCAGAGCCAATTTC
1 AACTTCAC-ACGAAGGGACCGCTGGTTGTCAACAAACAATTTTCCAATTTCAGAGCCAATTTC
* * * *
170 AACTTCACATGAAGGGACCGCTGGTTTGTCAATAAACCA-TTTCCCATTTCAGAGCCAATTTC
1 AACTTCACACGAAGGGACCGCTGG-TTGTCAACAAACAATTTTCCAATTTCAGAGCCAATTTC
232 AACTTCACAGCGAAG
1 AACTTCACA-CGAAG
247 ATATTGGACT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
62 45 0.65
63 24 0.35
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (62 bp):
AACTTCACACGAAGGGACCGCTGGTTGTCAACAAACAATTTTCCAATTTCAGAGCCAATTTC
Found at i:302 original size:165 final size:165
Alignment explanation
Indices: 15--342 Score: 493
Period size: 165 Copynumber: 2.0 Consensus size: 165
5 TCACGACGAA
*
15 AAGGGACCGCTGGTTGTCAAAACAACTTCCCAATTTTAGAGCCAATTTCAACTCACAGCGAAGGA
1 AAGGGACCGCTGGTTGTCAAAACAACTTCCCAATTTCAGAGCCAATTTCAACTCACAGCGAAGGA
80 TATTGGACTCGAGACAACACAAGTTCAAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACA
66 TATTGGACTC-AGACAACACAAGTTCAAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACA
* * * *
145 ATTTTCCAATTTCAGAGCCAATTTCAACTTCACATG
130 AATTCCCAATTCCAGAACCAATTTCAACTTCACATG
* *
181 AAGGGACCGCTGGTTTGTCAATAAACCATTTCCC-ATTTCAGAGCCAATTTCAACTTCACAGCGA
1 AAGGGACCGCTGG-TTGTC-A-AAACAACTTCCCAATTTCAGAGCCAATTTCAAC-TCACAGCGA
* *
245 A-GATATTGGACTC-GACAACATAAGTTC-AACTTCACAACGAAGGGATGGCTGGTTGTCAACAA
62 AGGATATTGGACTCAGACAACACAAGTTCAAACTTCACAACGAAGGGACGGCTGGTTGTCAACAA
*
307 ACAAATTCCCAGTTCCAGAACCAATTTCAACTTCAC
127 ACAAATTCCCAATTCCAGAACCAATTTCAACTTCAC
343 GGCGGGGATA
Statistics
Matches: 148, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
165 65 0.44
166 26 0.18
167 5 0.03
168 32 0.22
169 20 0.14
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (165 bp):
AAGGGACCGCTGGTTGTCAAAACAACTTCCCAATTTCAGAGCCAATTTCAACTCACAGCGAAGGA
TATTGGACTCAGACAACACAAGTTCAAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA
ATTCCCAATTCCAGAACCAATTTCAACTTCACATG
Found at i:353 original size:103 final size:102
Alignment explanation
Indices: 167--359 Score: 262
Period size: 103 Copynumber: 1.9 Consensus size: 102
157 CAGAGCCAAT
* * * * * *
167 TTCAACTTCACATGAAGGGACCGCTGGTTTGTCAATAAACCATTTCCCATTTCAGAGCCAATTTC
1 TTCAACTTCACACGAAGGGACCGCTGGTTTGTCAACAAACAAATTCCCATTCCAGAACCAATTTC
232 AACTTCACAGCGAAGATATTGGACTCGACAACATAAG
66 AACTTCACAGCGAAGATATTGGACTCGACAACATAAG
**
269 TTCAACTTCACAACGAAGGGATGGCTGG-TTGTCAACAAACAAATTCCCAGTTCCAGAACCAATT
1 TTCAACTTCAC-ACGAAGGGACCGCTGGTTTGTCAACAAACAAATTCCCA-TTCCAGAACCAATT
* **
333 TCAACTTCACGGCGGGGATATTGGACT
64 TCAACTTCACAGCGAAGATATTGGACT
360 TGGAACAGTA
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
102 29 0.37
103 49 0.63
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (102 bp):
TTCAACTTCACACGAAGGGACCGCTGGTTTGTCAACAAACAAATTCCCATTCCAGAACCAATTTC
AACTTCACAGCGAAGATATTGGACTCGACAACATAAG
Found at i:856 original size:82 final size:81
Alignment explanation
Indices: 545--899 Score: 271
Period size: 82 Copynumber: 4.4 Consensus size: 81
535 AAAGTAGGAG
* * * *
545 TATCTGTCAAC-AAGAGCTTCGAGTTCGATTACACTCAGCTCCAAGGCGCATCATTTAC-G-ATA
1 TATCTGTCATCAAAGACCTTCGAGTTCGATTACACTCAACT-CAAGGCACATCATTTACAGCATA
607 GCTCAAGGCT--AAGGGC
65 -CTCAAGGCTAGAAGGGC
* * * ** * **
623 TATCTGTCAGCAAAGACCTTCGAGTTTGACTACACTCCGCTTCAAGGCACATCATTTGCAATATA
1 TATCTGTCATCAAAGACCTTCGAGTTCGATTACACTCAAC-TCAAGGCACATCATTTACAGCATA
*
688 CTCAAGGCAAGAAGGGC
65 CTCAAGGCTAGAAGGGC
* ** * * * * * * * *
705 TAT-TTTCCAAAAAAGACCTTCGAGTTTGACTACGCTTAACTCCGAGGCATATTATTTGCAGCAT
1 TATCTGT-CATCAAAGACCTTCGAGTTCGATTACACTCAACT-CAAGGCACATCATTTACAGCAT
769 AACTCAAGGCTAGAAGGG-
64 -ACTCAAGGCTAGAAGGGC
* *
787 TGATC-GTCATCAAAGACCTTCGAGTTCGATTACATTCAACTCAGAGGCAAATCAATTTACAGCA
1 T-ATCTGTCATCAAAGACCTTCGAGTTCGATTACACTCAACTCA-AGGCACATC-ATTTACAGCA
* * *
851 TACTCAAGACGAGAAGGGT
63 TACTCAAGGCTAGAAGGGC
* *
870 TATCTGCCATCAAA-A-TTGTCGAGTTCGATT
1 TATCTGTCATCAAAGACCT-TCGAGTTCGATT
900 CTATTTAGCT
Statistics
Matches: 223, Mismatches: 38, Indels: 28
0.77 0.13 0.10
Matches are distributed among these distances:
78 10 0.04
79 39 0.17
80 9 0.04
81 8 0.04
82 119 0.53
83 38 0.17
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (81 bp):
TATCTGTCATCAAAGACCTTCGAGTTCGATTACACTCAACTCAAGGCACATCATTTACAGCATAC
TCAAGGCTAGAAGGGC
Found at i:6469 original size:2 final size:2
Alignment explanation
Indices: 6462--6494 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6452 GTTAAACTAT
6462 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6495 CATTTTCGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7157 original size:2 final size:2
Alignment explanation
Indices: 7150--7196 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
7140 AAATCCCTCA
*
7150 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7192 AT AT A
1 AT AT A
7197 CAAAAATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8608 original size:64 final size:63
Alignment explanation
Indices: 8507--8635 Score: 240
Period size: 64 Copynumber: 2.0 Consensus size: 63
8497 TCGGCAGTAA
*
8507 TTAGTTCATTGTCTCAGGAATAGATATAGCTAATAAAAACAGCAAGTGCAAGGTTGATCACAAT
1 TTAGTTCATTGTCTCAGGAATAGATATAGCTAATAAAAACAAC-AGTGCAAGGTTGATCACAAT
8571 TTAGTTCATTGTCTCAGGAATAGATATAGCTAATAAAAACAACAGTGCAAGGTTGATCACAAT
1 TTAGTTCATTGTCTCAGGAATAGATATAGCTAATAAAAACAACAGTGCAAGGTTGATCACAAT
8634 TT
1 TT
8636 CTTTTGAAAG
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
63 22 0.34
64 42 0.66
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (63 bp):
TTAGTTCATTGTCTCAGGAATAGATATAGCTAATAAAAACAACAGTGCAAGGTTGATCACAAT
Found at i:11936 original size:37 final size:37
Alignment explanation
Indices: 11895--11965 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
11885 TCTAATCCGC
11895 GTTAATATCTAAAGTAGCTCTTTATATAGTCTTATGT
1 GTTAATATCTAAAGTAGCTCTTTATATAGTCTTATGT
11932 GTTAATATCTAAAGTAGCTCTTTATATAGTCTTA
1 GTTAATATCTAAAGTAGCTCTTTATATAGTCTTA
11966 GGAAGTGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (37 bp):
GTTAATATCTAAAGTAGCTCTTTATATAGTCTTATGT
Found at i:14990 original size:31 final size:31
Alignment explanation
Indices: 14952--15065 Score: 142
Period size: 31 Copynumber: 3.7 Consensus size: 31
14942 CTAATATTTA
*
14952 TTTTTGTTTCATTTTAGTACTCATC-GTTAAC
1 TTTTTATTTCATTTTAGTAC-CATCTGTTAAC
* * * * *
14983 ATTTTGTTTCATTTTAGTACCCTCTATTAAT
1 TTTTTATTTCATTTTAGTACCATCTGTTAAC
15014 TTTTTATTTCATTTTAGTA-CATACTGTTAAC
1 TTTTTATTTCATTTTAGTACCAT-CTGTTAAC
15045 TTTTTATTTCATTTTAGTACC
1 TTTTTATTTCATTTTAGTACC
15066 TAAATTTTTA
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
30 5 0.07
31 65 0.92
32 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.56
Consensus pattern (31 bp):
TTTTTATTTCATTTTAGTACCATCTGTTAAC
Found at i:21319 original size:3 final size:3
Alignment explanation
Indices: 21311--21345 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
21301 GGTTCTACAT
*
21311 TTA TTA TTA TTA TTA TTA CTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21346 ACAAAATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:23068 original size:15 final size:15
Alignment explanation
Indices: 23050--23088 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
23040 ACGTCTTTTA
23050 AAAAACAATTTTAAG
1 AAAAACAATTTTAAG
* *
23065 AAAAATGATTTTTAAG
1 AAAAA-CAATTTTAAG
23081 AAAAACAA
1 AAAAACAA
23089 AGCTAGTCCG
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.26
Consensus pattern (15 bp):
AAAAACAATTTTAAG
Found at i:23922 original size:152 final size:154
Alignment explanation
Indices: 23695--24000 Score: 499
Period size: 152 Copynumber: 2.0 Consensus size: 154
23685 TTACGCTACG
* *
23695 AACATTAGTGTAAAGATTGAAACACACCTTAAAAAAATATGTATAATATCACGCATGCATGTAAT
1 AACATTAGTATAAAGATTGAAACACACCTT-AAAAAATATATATAATATCACGCATGCATGTAAT
*
23760 GAGAAAAGCAAAGTATAAAATATATTTAACATTATATAATTAATTAAAAACATTATATATATGCT
65 GAGAAAAGCAAAGTATAAAATATATTTAACATTATATAATTAATTAAAAACATTATACATATGCT
*
23825 TAGAAATATAACTTGGACTAAAACA
130 TAGAAATATAACATGGACTAAAACA
* * *
23850 AACATTAGTATAAAGATTGAAACACACC-T-AAACATATATATAATATCATGCATGTATGTAATG
1 AACATTAGTATAAAGATTGAAACACACCTTAAAAAATATATATAATATCACGCATGCATGTAATG
* * *
23913 AGAAGAGCAAAGTATAAAATATATTTAGCATTATATAATTAATTAGAAACATTATACATATGCTT
66 AGAAAAGCAAAGTATAAAATATATTTAACATTATATAATTAATTAAAAACATTATACATATGCTT
23978 AGAAATATAACATGGACTAAAAC
131 AGAAATATAACATGGACTAAAAC
24001 GAATAATAAA
Statistics
Matches: 141, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
152 113 0.80
154 1 0.01
155 27 0.19
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (154 bp):
AACATTAGTATAAAGATTGAAACACACCTTAAAAAATATATATAATATCACGCATGCATGTAATG
AGAAAAGCAAAGTATAAAATATATTTAACATTATATAATTAATTAAAAACATTATACATATGCTT
AGAAATATAACATGGACTAAAACA
Found at i:25506 original size:128 final size:128
Alignment explanation
Indices: 25201--26023 Score: 759
Period size: 128 Copynumber: 6.4 Consensus size: 128
25191 CGTCTAAGGG
* * * * *
25201 TGACAAAACTCCTATATAATGAGGAAATCTAGTCAGGGGATGACACTG-CTCATACGCGATGAAG
1 TGACACAACTCCTACATAATGAGGAAATCTGGTCAGGTGATGACAC-GACTCATACGTGATGAAG
* * * ** * * * * *
25265 AGTTCTTGGCCATCTTTAGGAAATGTGATAACACGACTCATACTTGATGAAGA-GTTCTAGTTAT
65 AGATC-AGGCCATC--T---AAAGGTGATAACACGGTTCCTACGTGATGAGGATG-GCTGGTTAT
* *
25329 CAAGGAT
123 C-TGGGT
* * * * *
25336 TGACACGACTCCTACATAATGATGAGATCAGGTC-GGATGATGACACGACTCATATGTGATGAAG
1 TGACACAACTCCTACATAATGAGGAAATCTGGTCAGG-TGATGACACGACTCATACGTGATGAAG
* *
25400 AGATCTGGCCATCTAAAGGTGATAACATGGTTCCTACGTGATGAGGATGGCTGGTTATCTGGGT
65 AGATCAGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGATGGCTGGTTATCTGGGT
* ** * *
25464 TGACACAACTCATACATAATGAGGAAATCTGGTCAGGTGATGACACGGTTCCTACGTG-TTAAG-
1 TGACACAACTCCTACATAATGAGGAAATCTGGTCAGGTGATGACACGACTCATACGTGATGAAGA
* * ** * * *
25527 GACGGCAGGCCATCTAAGGGTGATAACACAATTCCTACGTGATGAGGATAGTTGGTTATATGGGT
66 GA--TCAGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGATGGCTGGTTATCTGGGT
* * * * * * *
25592 TGACACAGCTCTTACATAACGAGGAAATCTGGTCAGGTGATGACAC-AGTTCCTACGTAATGAGG
1 TGACACAACTCCTACATAATGAGGAAATCTGGTCAGGTGATGACACGA-CTCATACGTGATGAAG
* * * * * *
25656 ACGA-CAGTCCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGAACGACTGGTTATCTGAGT
65 A-GATCAGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGATGGCTGGTTATCTGGGT
* ** *
25720 TAACACAACTCCTACATAATGA-GAAGATCTGGTCAATTTATGACACGACTCATACGTGATGAAG
1 TGACACAACTCCTACATAATGAGGAA-ATCTGGTCAGGTGATGACACGACTCATACGTGATGAAG
* * * * * * * *
25784 AGTTCTGGCCATCTTAAGGTGATAACACGGTTCCTACTTGATGGGGACGGTTGATTATCTGGGGT
65 AGATCAGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGATGGCTGGTTATCT-GGGT
* * * * * *
25849 TGACACAGCTCCTACATAATGAGGAAATCTGGTCAAGTGATGACAC-AGTTCCTACGCGATGAGG
1 TGACACAACTCCTACATAATGAGGAAATCTGGTCAGGTGATGACACGA-CTCATACGTGATGAAG
* * *
25913 ACGA-CAGACCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGATAGCTGGTTATCTGGGG
65 A-GATCAGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGATGGCTGGTTATCT-GGG
25977 T
128 T
*
25978 TGACACAGCTCCTACATAATGAGGAAATCTGGTC-GGTGATGACACG
1 TGACACAACTCCTACATAATGAGGAAATCTGGTCAGGTGATGACACG
26024 GTTCCTACGC
Statistics
Matches: 569, Mismatches: 101, Indels: 42
0.80 0.14 0.06
Matches are distributed among these distances:
126 2 0.00
127 8 0.01
128 308 0.54
129 179 0.31
130 5 0.01
131 2 0.00
132 1 0.00
134 11 0.02
135 53 0.09
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (128 bp):
TGACACAACTCCTACATAATGAGGAAATCTGGTCAGGTGATGACACGACTCATACGTGATGAAGA
GATCAGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGATGGCTGGTTATCTGGGT
Found at i:26018 original size:385 final size:384
Alignment explanation
Indices: 25338--26059 Score: 1099
Period size: 385 Copynumber: 1.9 Consensus size: 384
25328 TCAAGGATTG
* * *
25338 ACACGACTCCTACATAATGATGAGATCAGGTCGGATGATGACACGACTCATATGTGATGAAGAGA
1 ACACAACTCCTACATAATGATGAGATCAGGTCGAATGATGACACGACTCATACGTGATGAAGAGA
* * *
25403 TCTGGCCATCTAAAGGTGATAACATGGTTCCTACGTGATGAGGATGGCTGGTTATCTGGGTTGAC
66 TCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGATTATCTGGGTTGAC
* * * * *
25468 ACAACTCATACATAATGAGGAAATCTGGTCAGGTGATGACACGGTTCCTACGTGTTAAGGACGGC
131 ACAACTCATACATAATGAGGAAATCTGGTCAAGTGATGACACAGTTCCTACGCGATAAGGACGAC
* *
25533 AGGCCATCTAAGGGTGATAACACAATTCCTACGTGATGAGGATAGTTGGTTATATGGGTTGACAC
196 AGACCATCTAAGGGTGATAACACAATTCCTACGTGATGAGGATAGCTGGTTATATGGGTTGACAC
* *
25598 AGCTCTTACATAACGAGGAAATCTGGTCAGGTGATGACACAGTTCCTACGTAATGAGGACGACAG
261 AGCTCCTACATAACGAGGAAATCTGGTCAGGTGATGACACAGTTCCTACGCAATGAGGACGACAG
*
25663 TCCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGAACGACTGGTTATCTGAGTTA
326 ACCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGAACGACTGGTTATCTGAGTTA
* *
25722 ACACAACTCCTACATAATGA-GAAGATCTGGTC-AATTTATGACACGACTCATACGTGATGAAGA
1 ACACAACTCCTACATAATGATG-AGATCAGGTCGAA-TGATGACACGACTCATACGTGATGAAGA
* * * * *
25785 GTTCTGGCCATCTTAAGGTGATAACACGGTTCCTACTTGATGGGGACGGTTGATTATCTGGGGTT
64 GATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGATTATCT-GGGTT
* * *
25850 GACACAGCTCCTACATAATGAGGAAATCTGGTCAAGTGATGACACAGTTCCTACGCGATGAGGAC
128 GACACAACTCATACATAATGAGGAAATCTGGTCAAGTGATGACACAGTTCCTACGCGATAAGGAC
** *
25915 GACAGACCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGATAGCTGGTTATCTGGGGTTG
193 GACAGACCATCTAAGGGTGATAACACAATTCCTACGTGATGAGGATAGCTGGTTATAT-GGGTTG
* * *
25980 ACACAGCTCCTACATAATGAGGAAATCTGGTC-GGTGATGACACGGTTCCTACGCGATGAGGACG
257 ACACAGCTCCTACATAACGAGGAAATCTGGTCAGGTGATGACACAGTTCCTACGCAATGAGGACG
26044 ACAGACCATCTAAGGG
322 ACAGACCATCTAAGGG
26060 AATTTGGTTT
Statistics
Matches: 302, Mismatches: 32, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
383 2 0.01
384 105 0.35
385 159 0.53
386 36 0.12
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (384 bp):
ACACAACTCCTACATAATGATGAGATCAGGTCGAATGATGACACGACTCATACGTGATGAAGAGA
TCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGATTATCTGGGTTGAC
ACAACTCATACATAATGAGGAAATCTGGTCAAGTGATGACACAGTTCCTACGCGATAAGGACGAC
AGACCATCTAAGGGTGATAACACAATTCCTACGTGATGAGGATAGCTGGTTATATGGGTTGACAC
AGCTCCTACATAACGAGGAAATCTGGTCAGGTGATGACACAGTTCCTACGCAATGAGGACGACAG
ACCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGAACGACTGGTTATCTGAGTTA
Found at i:26208 original size:67 final size:65
Alignment explanation
Indices: 26099--26235 Score: 202
Period size: 67 Copynumber: 2.1 Consensus size: 65
26089 GATAATGTTT
* * * * *
26099 CAAAAGAAGTTGTCTCAAAAGAAACAATTTTGTTTCTAAAGAAACAAACTCAAAGATTTTTTTTC
1 CAAAAGAAATTGCCTCAAAAGAAAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTTC
26164 CAAAAGAAATTGCCTCAAAAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCT
1 CAAAAGAAATTGCCTCAAAAGA-A-AAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCT
26229 TC
64 TC
*
26231 AAAAA
1 CAAAA
26236 CTGTCTTGAG
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 20 0.31
66 1 0.02
67 43 0.67
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.28
Consensus pattern (65 bp):
CAAAAGAAATTGCCTCAAAAGAAAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTTC
Found at i:29834 original size:2 final size:2
Alignment explanation
Indices: 29827--29898 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
29817 ACAACAAGGG
29827 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
*
29869 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29899 TGATAAATGA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30882 original size:27 final size:27
Alignment explanation
Indices: 30851--30919 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
30841 CTTAAAAATG
*
30851 AAATGCAGATGCAAAAT-ACAAAGATAC
1 AAATGAAGATGCAAAATGA-AAAGATAC
* *
30878 AAATGTAGATGCAAAATGAAAAGATGC
1 AAATGAAGATGCAAAATGAAAAGATAC
30905 AAATGAAGATGCAAA
1 AAATGAAGATGCAAA
30920 TGCAGATGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 37 0.97
28 1 0.03
ACGTcount: A:0.55, C:0.10, G:0.19, T:0.16
Consensus pattern (27 bp):
AAATGAAGATGCAAAATGAAAAGATAC
Found at i:30892 original size:12 final size:12
Alignment explanation
Indices: 30871--30931 Score: 68
Period size: 12 Copynumber: 4.8 Consensus size: 12
30861 GCAAAATACA
*
30871 AAGATACAAATG
1 AAGATGCAAATG
*
30883 TAGATGCAAAATG
1 AAGATGC-AAATG
30896 AAAAGATGCAAATG
1 --AAGATGCAAATG
30910 AAGATGCAAATG
1 AAGATGCAAATG
*
30922 CAGATGCAAA
1 AAGATGCAAA
30932 AATATTGATC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
12 26 0.62
13 5 0.12
14 5 0.12
15 6 0.14
ACGTcount: A:0.52, C:0.10, G:0.21, T:0.16
Consensus pattern (12 bp):
AAGATGCAAATG
Found at i:30904 original size:15 final size:13
Alignment explanation
Indices: 30851--30932 Score: 62
Period size: 12 Copynumber: 6.2 Consensus size: 13
30841 CTTAAAAATG
*
30851 AAATGCAGATGCA
1 AAATGAAGATGCA
* *
30864 AAATACAAAGATAC-
1 AAAT--GAAGATGCA
*
30878 AAATGTAGATGCA
1 AAATGAAGATGCA
30891 AAATGAAAAGATGC-
1 AAATG--AAGATGCA
30905 AAATGAAGATGC-
1 AAATGAAGATGCA
*
30917 AAATGCAGATGCA
1 AAATGAAGATGCA
30930 AAA
1 AAA
30933 ATATTGATCC
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
12 23 0.42
13 12 0.22
14 9 0.16
15 11 0.20
ACGTcount: A:0.54, C:0.11, G:0.20, T:0.16
Consensus pattern (13 bp):
AAATGAAGATGCA
Found at i:33349 original size:152 final size:154
Alignment explanation
Indices: 33136--33440 Score: 524
Period size: 152 Copynumber: 2.0 Consensus size: 154
33126 TTACGCTACG
* *
33136 AACATTAGTGTAAAGATTGAAACACACCTTAAAAAATATGTATAATATCACGCATGCATGTAATG
1 AACATTAGTATAAAGATTGAAACACACCTTAAAAAATATATATAATATCACGCATGCATGTAATG
*
33201 AGAAGAGCAAAGTATAAAATATATTTAACATTATATAATTAATTAAAAACATTATATATATGCTT
66 AGAAGAGCAAAGTATAAAATATATTTAACATTATATAATTAATTAAAAACATTATACATATGCTT
*
33266 AGAAATATAACTTGGACTAAAACA
131 AGAAATATAACATGGACTAAAACA
* *
33290 AACATTAGTATAAAGATTGAAACACACC-T-AAAAATATATATAATATCATGCATGTATGTAATG
1 AACATTAGTATAAAGATTGAAACACACCTTAAAAAATATATATAATATCACGCATGCATGTAATG
* *
33353 AGAAGAGCAAAGTATAAAATATATTTAGCATTATATAATTAATTAGAAACATTATACATATGCTT
66 AGAAGAGCAAAGTATAAAATATATTTAACATTATATAATTAATTAAAAACATTATACATATGCTT
33418 AGAAATATAACATGGACTAAAAC
131 AGAAATATAACATGGACTAAAAC
33441 GAATAATAAA
Statistics
Matches: 143, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
152 115 0.80
153 1 0.01
154 27 0.19
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (154 bp):
AACATTAGTATAAAGATTGAAACACACCTTAAAAAATATATATAATATCACGCATGCATGTAATG
AGAAGAGCAAAGTATAAAATATATTTAACATTATATAATTAATTAAAAACATTATACATATGCTT
AGAAATATAACATGGACTAAAACA
Found at i:34301 original size:186 final size:186
Alignment explanation
Indices: 33974--34365 Score: 644
Period size: 186 Copynumber: 2.1 Consensus size: 186
33964 TTTTCTAATT
* * **
33974 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAACAATTTCTAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAACAATTTAAAATTAATTTAAATAATATATA
34038 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
*
34103 TTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGAGTTGAGCCCATATGTTA
131 TTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGAGTTGAGCCCATATATTA
* * *
34159 TATATAATATATTTAATATTTTTTAATTATAAAAAAATAGTTTAAAATTAATTTAAATAATATAT
1 TATATAATATATTTAATATTTTTTAATT-CAAAAAAACAATTTAAAATTAATTTAAATAATATAT
* *
34224 AATTATAAAATAAAAA-TTTATATAAATTTTTTAATTAATTAATTTTGATTTAGGTTTAAAATTT
65 AATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
* * *
34288 ATTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGTTGAGCCTATATATTA
130 ATTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGAGTTGAGCCCATATATTA
34345 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
34366 AAAATTTAAT
Statistics
Matches: 192, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
185 7 0.04
186 138 0.72
187 47 0.24
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.47
Consensus pattern (186 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAACAATTTAAAATTAATTTAAATAATATATA
ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
TTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGAGTTGAGCCCATATATTA
Found at i:34992 original size:13 final size:13
Alignment explanation
Indices: 34974--34998 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34964 CATTGATCGG
34974 CGATGGCTCGGCT
1 CGATGGCTCGGCT
34987 CGATGGCTCGGC
1 CGATGGCTCGGC
34999 GTTGGTGGCG
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:0.08, C:0.32, G:0.40, T:0.20
Consensus pattern (13 bp):
CGATGGCTCGGCT
Found at i:39887 original size:735 final size:733
Alignment explanation
Indices: 37971--40165 Score: 4291
Period size: 733 Copynumber: 3.0 Consensus size: 733
37961 GAACCGAAAG
37971 CAAAAGGAAAGAAACCCATCATCAAGCACTATAAAAAAAAGCCTGCAAAACAAAGAAGGAAGTTT
1 CAAAAGGAAAGAAACCCATCATCAAGCACTATAAAAAAAAGCCTGCAAAACAAAGAAGGAAGTTT
*
38036 TTCAGACAGAGTTTTCGGTGATATTCTGAAACAAAAATACTAAAAAATCAGAGAAAATAGAGAAG
66 TTCAGACGGAGTTTTCGGTGATATTCTGAAACAAAAATACTAAAAAATCAGAGAAAATAGAGAAG
*
38101 GATTTTTGAGAGACTTAACTTGCTCATGTTTTCCTAGGAGGAAGCGAAAGATCATTTAGAATTTC
131 GATTTTTGAGAGACTTAACTTGCTCATGTTGTCCTAGGAGGAAGCGAAAGATCATTTAGAATTTC
38166 AATGGCCGCCGCGGAGAAGGTAAAAAAATGACACCTTCAATCGTAGGTTTAGGCTTAATGGGGTA
196 AATGGCCGCCGCGGAGAAGGTAAAAAAATGACACCTTCAATCGTAGGTTTAGGCTTAATGGGGTA
38231 TTGTTTGAGCATTTGAAGGTTAGATTTGAGTTTTGGTCGAAGATGGGTTTCGAATGGTATAGTTT
261 TTGTTTGAGCATTTGAAGGTTAGATTTGAGTTTTGGTCGAAGATGGGTTTCGAATGGTATAGTTT
38296 TTAGGTTTTTAGCCACTTTGAGCGGTGGCTGGCGCGATGGTCGGGGCTAGATTTCCGGTGGGAAG
326 TTAGGTTTTTAGCCACTTTGAGCGGTGGCTGGCGCGATGGTCGGGGCTAGATTTCCGGTGGGAAG
38361 CCACCGAAATCTAGGTAAGACTCACCGAACGAAGGGTTTTGGTTGAGAGAGTAGAGAGCATTTTT
391 CCACCGAAATCTAGGTAAGACTCACCGAACGAAGGGTTTTGGTTGAGAGAGTAGAGAGCATTTTT
38426 GCTCTAAGATTTTAGGAGAGAGTAGAGAGTGGGACAAAATCAAGTCTGGGGGTATTTATAGTGGA
456 GCTCTAAGATTTTAGGAGAGAGTAGAGAGTGGGACAAAATCAAGTCTGGGGGTATTTATAGTGGA
38491 ACATTTCATGTGAACCGATTCGGTCCAAAAAGAGATTGAACCGCGTAATTTTACTTGTTTTAGAG
521 ACATTTCATGTGAACCGATTCGGTCCAAAAAGAGATTGAACCGCGTAATTTTACTTGTTTTAGAG
38556 CTATTCCTTTATGTAGTCCTCCTTAATTTTAGAAAATTACATTTTTGTCCTTAAACCTTCAAATT
586 CTATTCCTTTATGTAGTCCTCCTTAATTTTAGAAAATTACATTTTTGTCCTTAAACCTTCAAATT
38621 AGGCCTTTTTACCCTGATTTTTAATTTAGATACAATTGGGTTCCTATTCCCTTATGATTTGTTTA
651 AGGCCTTTTTACCCTGATTTTTAATTTAGATACAATTGGGTTCCTATTCCCTTATGATTTGTTTA
38686 ATTTCCTATTAAAACCTT
716 ATTTCCTATTAAAACCTT
38704 CAAAAGGAAAGAAACCCATCATCAAGCACTATAAAAAAAAGCCTGCAAAACAAAGAAGGAAGTTT
1 CAAAAGGAAAGAAACCCATCATCAAGCACTATAAAAAAAAGCCTGCAAAACAAAGAAGGAAGTTT
38769 TTCAGACGGAGTTTTCGGTGATATTCTGAAACAAAAATACTAAAAAATCAGAGAAAATAGAGAAG
66 TTCAGACGGAGTTTTCGGTGATATTCTGAAACAAAAATACTAAAAAATCAGAGAAAATAGAGAAG
38834 GATTTTTGAGAGACTTAACTTGCTCATGTTGTCCTAGGAGGAAGCGAAAGATCATTTAGAATTTC
131 GATTTTTGAGAGACTTAACTTGCTCATGTTGTCCTAGGAGGAAGCGAAAGATCATTTAGAATTTC
*
38899 AATGGCCGCCGCGGAGAAGGTAAAAATATGACACCTTCAATCGTAGGTTTAGGCTTAATGGGGTA
196 AATGGCCGCCGCGGAGAAGGTAAAAAAATGACACCTTCAATCGTAGGTTTAGGCTTAATGGGGTA
38964 TTGTTTGAGCATTTGAAGGTTAGATTTGAGTTTTGGTCGAAGATGGGTTTCGAATGGTATAGTTT
261 TTGTTTGAGCATTTGAAGGTTAGATTTGAGTTTTGGTCGAAGATGGGTTTCGAATGGTATAGTTT
* *
39029 TTAGGTTTTTAGTCACTTTGAGCGGTGGCTGGTGCGATGGTCGGGGCTAGATTTCCGGTGGGAAG
326 TTAGGTTTTTAGCCACTTTGAGCGGTGGCTGGCGCGATGGTCGGGGCTAGATTTCCGGTGGGAAG
39094 CCACCGAAATCTAGGTAAGACTCACCGAACGAAGGGTTTTGGTTGAGAGAGTAGAGAGCATTTTT
391 CCACCGAAATCTAGGTAAGACTCACCGAACGAAGGGTTTTGGTTGAGAGAGTAGAGAGCATTTTT
39159 GCTCTAAGATTTTAGGAGAGAGTAGAGAGTGGGACAAAATCAAGTCTGGGGGTATTTATAGTGGA
456 GCTCTAAGATTTTAGGAGAGAGTAGAGAGTGGGACAAAATCAAGTCTGGGGGTATTTATAGTGGA
39224 ACATTTCATGTGAACCGATTCGGTCCAAAAAGAGATTGAACCGCGTAATTTTACTTGTTTTAGAG
521 ACATTTCATGTGAACCGATTCGGTCCAAAAAGAGATTGAACCGCGTAATTTTACTTGTTTTAGAG
*
39289 CTATTCCATTATGTAGTCCTCCTTAATTTTAGAAAATTACATTTTTGTCCTTAAACCTTCAAATT
586 CTATTCCTTTATGTAGTCCTCCTTAATTTTAGAAAATTACATTTTTGTCCTTAAACCTTCAAATT
39354 AGGCCTTTTTACCCTGATTTTTAATTTAGATACAATTGGGTTCCTATTCCCTTATGATTTGTTTA
651 AGGCCTTTTTACCCTGATTTTTAATTTAGATACAATTGGGTTCCTATTCCCTTATGATTTGTTTA
39419 ATTTCCTATTAAAACCTT
716 ATTTCCTATTAAAACCTT
*
39437 CAAAAGGAAAGAAACCCATCATCAAGCACTACAAAAAAAAAAGCCTGCAAAACAAAGAAGGAAGT
1 CAAAAGGAAAGAAACCCATCATCAAGCACT--ATAAAAAAAAGCCTGCAAAACAAAGAAGGAAGT
39502 TTTTCAGACGGAGTTTTCGGTGATATTCTGAAACAAAAATACTAAAAAATCAGAGAAAATAGAGA
64 TTTTCAGACGGAGTTTTCGGTGATATTCTGAAACAAAAATACTAAAAAATCAGAGAAAATAGAGA
39567 AGGATTTTTGAGAGACTTAACTTGCTCATGTTGTCCTAGGAGGAAGCGAAAGATCATTTAGAATT
129 AGGATTTTTGAGAGACTTAACTTGCTCATGTTGTCCTAGGAGGAAGCGAAAGATCATTTAGAATT
39632 TCAATGGCCGCCGCGGAGAAGGTAAAAAAATGACACCTTCAATCGTAGGTTTAGGCTTAATGGGG
194 TCAATGGCCGCCGCGGAGAAGGTAAAAAAATGACACCTTCAATCGTAGGTTTAGGCTTAATGGGG
39697 TATTGTTTGAGCATTTGAAGGTTAGATTTGAGTTTTGGTCGAAGATGGGTTTCGAATGGTATAGT
259 TATTGTTTGAGCATTTGAAGGTTAGATTTGAGTTTTGGTCGAAGATGGGTTTCGAATGGTATAGT
*
39762 TTTTAGGTTTTTAGCCACTTTGAGCGGTGGCTGGCGCGATGGTCGGGGCTAGATTTCCGGTGAGA
324 TTTTAGGTTTTTAGCCACTTTGAGCGGTGGCTGGCGCGATGGTCGGGGCTAGATTTCCGGTGGGA
39827 AGCCACCGAAATCTAGGTAAGACTCACCGAACGAAGGGTTTTGGTTGAGAGAGTAGAGAGCATTT
389 AGCCACCGAAATCTAGGTAAGACTCACCGAACGAAGGGTTTTGGTTGAGAGAGTAGAGAGCATTT
*
39892 TTGCTCTAAGATTTTAGGAGAGAGTAGAGAGTGGAACAAAATCAAGTCTGGGGGTATTTATAGTG
454 TTGCTCTAAGATTTTAGGAGAGAGTAGAGAGTGGGACAAAATCAAGTCTGGGGGTATTTATAGTG
39957 GAACATTTCATGTGAACCGATTCGGTCCAAAAAGAGATTGAACCGCGTAATTTTACTTGTTTTAG
519 GAACATTTCATGTGAACCGATTCGGTCCAAAAAGAGATTGAACCGCGTAATTTTACTTGTTTTAG
40022 AGCTATTCCTTTATGTAGTCCTCCTTAATTTTAGAAAATTACATTTTTGTCCTTAAACCTTCAAA
584 AGCTATTCCTTTATGTAGTCCTCCTTAATTTTAGAAAATTACATTTTTGTCCTTAAACCTTCAAA
40087 TTAGGCCTTTTTACCCTGATTTTTAATTTAGATACAATTGGGTTCCTATTCCCTTATGATTTGTT
649 TTAGGCCTTTTTACCCTGATTTTTAATTTAGATACAATTGGGTTCCTATTCCCTTATGATTTGTT
40152 TAATTTCCTATTAA
714 TAATTTCCTATTAA
40166 TTGTTTAATT
Statistics
Matches: 1447, Mismatches: 13, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
733 757 0.52
735 690 0.48
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (733 bp):
CAAAAGGAAAGAAACCCATCATCAAGCACTATAAAAAAAAGCCTGCAAAACAAAGAAGGAAGTTT
TTCAGACGGAGTTTTCGGTGATATTCTGAAACAAAAATACTAAAAAATCAGAGAAAATAGAGAAG
GATTTTTGAGAGACTTAACTTGCTCATGTTGTCCTAGGAGGAAGCGAAAGATCATTTAGAATTTC
AATGGCCGCCGCGGAGAAGGTAAAAAAATGACACCTTCAATCGTAGGTTTAGGCTTAATGGGGTA
TTGTTTGAGCATTTGAAGGTTAGATTTGAGTTTTGGTCGAAGATGGGTTTCGAATGGTATAGTTT
TTAGGTTTTTAGCCACTTTGAGCGGTGGCTGGCGCGATGGTCGGGGCTAGATTTCCGGTGGGAAG
CCACCGAAATCTAGGTAAGACTCACCGAACGAAGGGTTTTGGTTGAGAGAGTAGAGAGCATTTTT
GCTCTAAGATTTTAGGAGAGAGTAGAGAGTGGGACAAAATCAAGTCTGGGGGTATTTATAGTGGA
ACATTTCATGTGAACCGATTCGGTCCAAAAAGAGATTGAACCGCGTAATTTTACTTGTTTTAGAG
CTATTCCTTTATGTAGTCCTCCTTAATTTTAGAAAATTACATTTTTGTCCTTAAACCTTCAAATT
AGGCCTTTTTACCCTGATTTTTAATTTAGATACAATTGGGTTCCTATTCCCTTATGATTTGTTTA
ATTTCCTATTAAAACCTT
Found at i:47878 original size:16 final size:16
Alignment explanation
Indices: 47854--47887 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
47844 TATCACCGAT
*
47854 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
47870 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
47886 CG
1 CG
47888 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:48356 original size:15 final size:15
Alignment explanation
Indices: 48336--48365 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
48326 AAACTTTGAA
*
48336 AAACATTTTTCAAAG
1 AAACATTTTCCAAAG
48351 AAACATTTTCCAAAG
1 AAACATTTTCCAAAG
48366 TTGGTTGCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.30
Consensus pattern (15 bp):
AAACATTTTCCAAAG
Found at i:59135 original size:20 final size:20
Alignment explanation
Indices: 59092--59136 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
59082 ATATTTATAT
*
59092 AAAAAGTATAATAAGATAAT
1 AAAAAGTATAATAAGATAAA
59112 AAAAAGTATAATAA-ATACAA
1 AAAAAGTATAATAAGATA-AA
59132 AAAAA
1 AAAAA
59137 ATGAAAGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (20 bp):
AAAAAGTATAATAAGATAAA
Found at i:59443 original size:19 final size:19
Alignment explanation
Indices: 59419--59455 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
59409 AAAAACACGT
59419 GGGTCTGAGGGAACACGCG
1 GGGTCTGAGGGAACACGCG
59438 GGGTCTGAGGGAACACGC
1 GGGTCTGAGGGAACACGC
59456 AGGTCGGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.46, T:0.11
Consensus pattern (19 bp):
GGGTCTGAGGGAACACGCG
Found at i:61003 original size:106 final size:106
Alignment explanation
Indices: 60816--61174 Score: 470
Period size: 106 Copynumber: 3.5 Consensus size: 106
60806 ATTGCTCCAA
* * * * *
60816 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGGAACTAGGAAATTGTTTGTTGACAGTC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTATGAAATTAGGGAATTGTTTGTTGACAGTC
* *
60881 AGCCGCCCCTTTGCCGTGAAGTTGAGCTTGTGCTATCTTTG
66 AGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTTTG
60922 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATT-TGAAATTAGGGAATTGTTTGTTGACAGT
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGG-TTATGAAATTAGGGAATTGTTTGTTGACAGT
60986 CAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTC-TTG
65 CAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTTTG
* * * * *
61027 AGTTCAATATCCTTCGTTGTGAAGTTGAAATTGACTT-TG-AA--A--G--TTGTTTGTTGATAA
1 -GTCCAATATCCTTCGCTGTGAAGTTGAAATTG-GTTATGAAATTAGGGAATTGTTTGTTGACAG
* * *
61084 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGG
64 TCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTTTG
*
61127 GTCCAATATCCTTCACTGTGAAGTTGAAATTGGTTATGAAATT-GGGAA
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTATGAAATTAGGGAA
61175 ACCCCTTCAC
Statistics
Matches: 223, Mismatches: 18, Indels: 25
0.84 0.07 0.09
Matches are distributed among these distances:
98 2 0.01
99 80 0.36
100 4 0.02
101 1 0.00
103 2 0.01
105 5 0.02
106 127 0.57
107 2 0.01
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.36
Consensus pattern (106 bp):
GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTATGAAATTAGGGAATTGTTTGTTGACAGTC
AGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTTTG
Found at i:61134 original size:99 final size:98
Alignment explanation
Indices: 60971--61167 Score: 295
Period size: 99 Copynumber: 2.0 Consensus size: 98
60961 AATTAGGGAA
* *
60971 TTGTTTGTTGACAGTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTTGAGTTCAATA
1 TTGTTTGTTGACAGTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATA
*
61036 TCCTTCGTTGTGAAGTTGAAATTGACTTTGAAAG
66 TCCTTCGCTGTGAAGTTGAAATTGA-TTTGAAAG
* * * *
61070 TTGTTTGTTGATAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATA
1 TTGTTTGTTGACAGTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATA
* *
61135 TCCTTCACTGTGAAGTTGAAATTGGTTATGAAA
66 TCCTTCGCTGTGAAGTTGAAATTGATT-TGAAA
61168 TTGGGAAACC
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
98 2 0.02
99 86 0.98
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (98 bp):
TTGTTTGTTGACAGTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATA
TCCTTCGCTGTGAAGTTGAAATTGATTTGAAAG
Found at i:62313 original size:7 final size:7
Alignment explanation
Indices: 62303--62346 Score: 70
Period size: 7 Copynumber: 6.0 Consensus size: 7
62293 CTTCATTCCT
62303 TTTTTTC
1 TTTTTTC
62310 TTTTTTC
1 TTTTTTC
62317 TTTTGTTC
1 TTTT-TTC
62325 TTTTGTTC
1 TTTT-TTC
62333 TTTTTTC
1 TTTTTTC
62340 TTTTTTC
1 TTTTTTC
62347 AATTTAGGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 21 0.58
8 15 0.42
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:62314 original size:8 final size:8
Alignment explanation
Indices: 62301--62345 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
62291 CTCTTCATTC
62301 CTTTTTTT
1 CTTTTTTT
62309 C-TTTTTT
1 CTTTTTTT
*
62316 CTTTTGTT
1 CTTTTTTT
*
62324 CTTTTGTT
1 CTTTTTTT
62332 C-TTTTTT
1 CTTTTTTT
62339 CTTTTTT
1 CTTTTTT
62346 CAATTTAGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 13 0.39
8 20 0.61
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.82
Consensus pattern (8 bp):
CTTTTTTT
Found at i:62402 original size:16 final size:16
Alignment explanation
Indices: 62383--62418 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
62373 ACCCTAAACA
62383 TTTTTC-TTTTTCTTGT
1 TTTTTCTTTTTTCTT-T
62399 TTTTTCTTTTTTCTTT
1 TTTTTCTTTTTTCTTT
62415 TTTT
1 TTTT
62419 CCTAACTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (16 bp):
TTTTTCTTTTTTCTTT
Found at i:62454 original size:75 final size:72
Alignment explanation
Indices: 62311--62454 Score: 191
Period size: 75 Copynumber: 2.0 Consensus size: 72
62301 CTTTTTTTCT
* * *
62311 TTTTTCTTTTGTTCTTTTGTTCTTTTTTCTTTTTTCAATTTAGGGCGCCCTTTCGAGTTTTCACC
1 TTTTTCTTTTCTTCTTTTGTTCTTTTTTCTTTTTTCAACTTAGGACGCCCTTTCGAGTTTTCACC
62376 CTAAACA
66 CTAAACA
* *
62383 TTTTTCTTTTTCTTGTTTT-TTCTTTTTTCTTTTTTTCCTAACTTAGGACGCCCTTTCGGGTTTT
1 TTTTTC-TTTTCTTCTTTTGTTCTTTTTTC-TTTTTT-C-AACTTAGGACGCCCTTTCGAGTTTT
*
62447 CATCCTAA
62 CACCCTAA
62455 GCGAAGTATT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
72 16 0.26
73 16 0.26
74 1 0.02
75 29 0.47
ACGTcount: A:0.11, C:0.21, G:0.10, T:0.58
Consensus pattern (72 bp):
TTTTTCTTTTCTTCTTTTGTTCTTTTTTCTTTTTTCAACTTAGGACGCCCTTTCGAGTTTTCACC
CTAAACA
Found at i:73544 original size:21 final size:21
Alignment explanation
Indices: 73518--73557 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
73508 CCCCCTTTGA
*
73518 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
73539 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
73558 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:82701 original size:3 final size:3
Alignment explanation
Indices: 82684--82717 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
82674 ATATACACGT
*
82684 TAA TGA TAA TAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
82718 ACAGTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:82777 original size:20 final size:20
Alignment explanation
Indices: 82733--82777 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
82723 ATATTTATAT
82733 AAAAAAGTATAATAAGATAC
1 AAAAAAGTATAATAAGATAC
*
82753 TAAAAAGTATAATAA-ATAC
1 AAAAAAGTATAATAAGATAC
82772 AAAAAA
1 AAAAAA
82778 CGGAAAGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.69, C:0.04, G:0.07, T:0.20
Consensus pattern (20 bp):
AAAAAAGTATAATAAGATAC
Found at i:85683 original size:2 final size:2
Alignment explanation
Indices: 85676--85738 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
85666 GAGGCATGAA
85676 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
85718 AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG A
85739 TCCTGCCAAG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:86542 original size:2 final size:2
Alignment explanation
Indices: 86535--86561 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
86525 TTATACTTGT
86535 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
86562 CCCAGTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:88507 original size:24 final size:25
Alignment explanation
Indices: 88479--88542 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
88469 GGAATGGAAG
88479 AATGAGTATAATATTTAA-TAAAAA
1 AATGAGTATAATATTTAATTAAAAA
88503 AATGAGTATAATATTTAATTAAAAA
1 AATGAGTATAATATTTAATTAAAAA
88528 AATGAGTATAATATT
1 AATGAGTATAATATT
88543 AGGTATATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
24 18 0.46
25 21 0.54
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (25 bp):
AATGAGTATAATATTTAATTAAAAA
Found at i:93684 original size:28 final size:28
Alignment explanation
Indices: 93653--93756 Score: 174
Period size: 28 Copynumber: 3.7 Consensus size: 28
93643 CCTTTTTATA
93653 AATTATACTAATTACTGTTTACGGACTC
1 AATTATACTAATTACTGTTTACGGACTC
*
93681 AATTATGCTAATTACTGTTTACGGACTC
1 AATTATACTAATTACTGTTTACGGACTC
93709 AATTATGA-TAATTACTGTTTACGGACTC
1 AATTAT-ACTAATTACTGTTTACGGACTC
*
93737 AATTATGCTAATTACTGTTT
1 AATTATACTAATTACTGTTT
93757 TCCTAGATTG
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
28 71 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (28 bp):
AATTATACTAATTACTGTTTACGGACTC
Found at i:94935 original size:24 final size:22
Alignment explanation
Indices: 94893--94977 Score: 81
Period size: 24 Copynumber: 4.0 Consensus size: 22
94883 GAATGCAATT
94893 AATGCATCGATGCA---TAAGG
1 AATGCATCGATGCACTTTAAGG
94912 AATGCATCGATGCACATGTTAAGG
1 AATGCATCGATGCAC-T-TTAAGG
* * *
94936 GATGCATCGATACACTTT-A-T
1 AATGCATCGATGCACTTTAAGG
*
94956 AATGCATCGATGCACTTCAAGG
1 AATGCATCGATGCACTTTAAGG
94978 GGAAATTGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
19 14 0.27
20 15 0.29
21 2 0.04
22 2 0.04
23 1 0.02
24 18 0.35
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (22 bp):
AATGCATCGATGCACTTTAAGG
Found at i:96483 original size:57 final size:57
Alignment explanation
Indices: 96395--96515 Score: 233
Period size: 57 Copynumber: 2.1 Consensus size: 57
96385 CTTCGGGATA
*
96395 TATATGTATTCCTTGGAACATGTGTGATGTCTTTTGAGACACATACTTGATCCTTTG
1 TATATGTATTCCTTGGAACATGTGTGATGTCTTTTGAGACACATACTTGATCATTTG
96452 TATATGTATTCCTTGGAACATGTGTGATGTCTTTTGAGACACATACTTGATCATTTG
1 TATATGTATTCCTTGGAACATGTGTGATGTCTTTTGAGACACATACTTGATCATTTG
96509 TATATGT
1 TATATGT
96516 CTATGATTCT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 63 1.00
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (57 bp):
TATATGTATTCCTTGGAACATGTGTGATGTCTTTTGAGACACATACTTGATCATTTG
Found at i:99510 original size:30 final size:30
Alignment explanation
Indices: 99475--99534 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
99465 GAATTTTTGC
*
99475 AAAAATGACCGGAAACATTATTAGGCGCTA
1 AAAAATGACCGAAAACATTATTAGGCGCTA
99505 AAAAATGACCGAAAACATTATTAGGCGCTA
1 AAAAATGACCGAAAACATTATTAGGCGCTA
99535 TCAGTTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.17, G:0.18, T:0.20
Consensus pattern (30 bp):
AAAAATGACCGAAAACATTATTAGGCGCTA
Found at i:114132 original size:2 final size:2
Alignment explanation
Indices: 114125--114155 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
114115 CAAAATTCTT
114125 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
114156 TTCATACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:114359 original size:3 final size:3
Alignment explanation
Indices: 114353--114420 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
114343 CATCATCGTC
114353 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
114401 ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
114421 TGCATCTGCA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:120051 original size:15 final size:15
Alignment explanation
Indices: 120031--120062 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
120021 AAAATATTTC
*
120031 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
120046 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
120061 TT
1 TT
120063 AGATCTGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:122383 original size:19 final size:19
Alignment explanation
Indices: 122347--122384 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
122337 TCAAAATAAG
*
122347 AAATATTTCAAATTACAAT
1 AAATATTTCAAATCACAAT
122366 AAATATTT-ACAATCACAAT
1 AAATATTTCA-AATCACAAT
122385 CGTAAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATATTTCAAATCACAAT
Found at i:123233 original size:43 final size:42
Alignment explanation
Indices: 123094--123324 Score: 134
Period size: 43 Copynumber: 5.3 Consensus size: 42
123084 GCGACGATTG
* *
123094 TTCAACAAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTATC
1 TTCAA-AAACGCCGCAATA-GTATTGATGTTTAGCGGCGTTT-TC
* * * *
123139 ATT--AAAACGCCGCAATAGGTTTTGATATTTAACGGC-ATTT-
1 -TTCAAAAACGCCGCAATA-GTATTGATGTTTAGCGGCGTTTTC
** *
123179 GGCAGACAAACGCCGCAATAGTCGTTGATGTTTAGCGGCGTTTTC
1 TTCA-A-AAACGCCGCAATAGT-ATTGATGTTTAGCGGCGTTTTC
* * * * * *
123224 TTCAAAAACGCCGCAGTAAATTTTTATTTTTACCGGCGTTTTC
1 TTCAAAAACGCCGCAAT-AGTATTGATGTTTAGCGGCGTTTTC
* *
123267 CT-AAAAACGCCGCAGAATATGTATTGA-GATTTTGCGGCGTTTT-
1 TTCAAAAACGCCGC--AATA-GTATTGATG-TTTAGCGGCGTTTTC
123310 TATCAAAAACGCCGC
1 T-TCAAAAACGCCGC
123325 TAAATGTATG
Statistics
Matches: 144, Mismatches: 27, Indels: 29
0.72 0.14 0.14
Matches are distributed among these distances:
41 1 0.01
42 16 0.11
43 86 0.60
44 26 0.18
45 13 0.09
46 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (42 bp):
TTCAAAAACGCCGCAATAGTATTGATGTTTAGCGGCGTTTTC
Found at i:123725 original size:21 final size:21
Alignment explanation
Indices: 123661--123790 Score: 109
Period size: 21 Copynumber: 6.2 Consensus size: 21
123651 TGATATATTA
* * *
123661 CTTCTCTCTGTTCTGCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* * * *
123682 CCTCTCTGTGTGCTGCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
123703 CTTCTCTCTCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* **
123724 CTGCTCTAGCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* **
123745 CTGCTCTAGCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* *
123766 CTGCTCTCTCTGTTTCC-CTTG
1 CTTCTCTCTCTGCTTCCGC-TG
123787 CTTC
1 CTTC
123791 ATTTTCCGCT
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 1 0.01
21 93 0.99
ACGTcount: A:0.02, C:0.39, G:0.20, T:0.39
Consensus pattern (21 bp):
CTTCTCTCTCTGCTTCCGCTG
Found at i:132884 original size:41 final size:41
Alignment explanation
Indices: 132818--132978 Score: 213
Period size: 41 Copynumber: 4.0 Consensus size: 41
132808 CGTTTATACA
132818 AAAAAACGCCACTATTGATTA-CACTATT-CTGGCGTTTGTT
1 AAAAAACGCCACTATTGATTATCACTATTGC-GGCGTTTGTT
132858 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTT-TT
1 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGTT
* * * **
132898 CTAAAAACGCCATTATTGATTAACACTATTATGGCGTTTGTCT
1 -AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGT-T
*
132941 -AAAAACACCACTATTGATTATCACTATTGCGGCGTTTG
1 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTG
132979 AGGAATAAAC
Statistics
Matches: 106, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
40 23 0.22
41 80 0.75
42 2 0.02
43 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (41 bp):
AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGTT
Found at i:132936 original size:82 final size:81
Alignment explanation
Indices: 132819--132977 Score: 266
Period size: 82 Copynumber: 2.0 Consensus size: 81
132809 GTTTATACAA
* *
132819 AAAAACGCCACTATTGATTACACTATTCTGGCGTTTGT-TAAAAAACGCCACTATTGATTATCAC
1 AAAAACGCCACTATTGATTACACTATTATGGCGTTTGTCT-AAAAACACCACTATTGATTATCAC
132883 TATTGCGGCGTTTTTCT
65 TATTGCGGCGTTTTTCT
*
132900 AAAAACGCCATTATTGATTAACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCAC
1 AAAAACGCCACTATTGATT-ACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCAC
132965 TATTGCGGCGTTT
65 TATTGCGGCGTTT
132978 GAGGAATAAA
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
81 18 0.25
82 54 0.74
83 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.35
Consensus pattern (81 bp):
AAAAACGCCACTATTGATTACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCACT
ATTGCGGCGTTTTTCT
Found at i:133053 original size:42 final size:42
Alignment explanation
Indices: 132964--133188 Score: 167
Period size: 42 Copynumber: 5.4 Consensus size: 42
132954 TTGATTATCA
* * *
132964 CTATTGCGGCGTTTGAGGAATAAACGACACTATATGTGTA--A-T
1 CTATTGCGGCGTTTGTGGTATAAACGCCACTA-AT-T-TACCACT
* *
133006 ATATTGCGGCGTTTGTGGTATAAACGCCACGAATTTACCACT
1 CTATTGCGGCGTTTGTGGTATAAACGCCACTAATTTACCACT
* * * * *
133048 CTATTGCGGCGTTT-TGGCT-CAATCGCCGCAAAATTTA-TACT
1 CTATTGCGGCGTTTGTGG-TATAAACGCCAC-TAATTTACCACT
* * *
133089 CTATTGTGGCGTTTGTGGTATAAACGCCGCTAATTTACCACC
1 CTATTGCGGCGTTTGTGGTATAAACGCCACTAATTTACCACT
* * * * * *
133131 CTATTGCGGCATTTTTTGTAAAAACGCCACTATATGT-CAACT
1 CTATTGCGGCGTTTGTGGTATAAACGCCACTA-ATTTACCACT
*
133173 CTATTGCAGCGTTTGT
1 CTATTGCGGCGTTTGT
133189 ACTAAAAACG
Statistics
Matches: 145, Mismatches: 29, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
39 2 0.01
40 1 0.01
41 36 0.25
42 103 0.71
43 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (42 bp):
CTATTGCGGCGTTTGTGGTATAAACGCCACTAATTTACCACT
Found at i:141932 original size:178 final size:180
Alignment explanation
Indices: 141635--142016 Score: 594
Period size: 178 Copynumber: 2.1 Consensus size: 180
141625 TTTTCTAATT
* * * *
141635 TATATAAAA-ATTAAATGTTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAAAATATTTAAT-ATTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
141699 TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT
65 TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT
141764 GGATCTTAAATTATTAATTGGGTTTTAAATAGTTT-G-G-G-CATATGTTA
130 GGATCTTAAATTATTAATTGGGTTTTAAATAGTTTGGCGAGCCATATGTTA
141811 TATATAAAATATTTAATATTTTTAATTAAAAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAAAATATTTAATATTTTTAATT-AAAAAAA-AGTTTACAATTAATTTAAATAATATATAA
* * *
141876 TTATAAAATAAAAATTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
64 TTATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
*
141941 TGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
129 TGGATCTTAAATTATTAATTGGGTTTTAAATAGTTT-GGC-GAG-CCATATGTTA
*
141996 TATATAATATATTTAATATTT
1 TATATAAAATATTTAATATTT
142017 AAAATTTAAT
Statistics
Matches: 187, Mismatches: 9, Indels: 11
0.90 0.04 0.05
Matches are distributed among these distances:
176 18 0.10
177 12 0.06
178 125 0.67
180 1 0.01
182 1 0.01
183 1 0.01
185 29 0.16
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (180 bp):
TATATAAAATATTTAATATTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATT
ATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTG
GATCTTAAATTATTAATTGGGTTTTAAATAGTTTGGCGAGCCATATGTTA
Found at i:142063 original size:11 final size:11
Alignment explanation
Indices: 142047--142077 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
142037 TCGGTTAATT
142047 AACCGAATTCG
1 AACCGAATTCG
142058 AACCGAATTCG
1 AACCGAATTCG
142069 AACCGAATT
1 AACCGAATT
142078 AACCGTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (11 bp):
AACCGAATTCG
Found at i:143744 original size:13 final size:13
Alignment explanation
Indices: 143726--143751 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
143716 CATTGCGACC
143726 GCTACCAAACATA
1 GCTACCAAACATA
143739 GCTACCAAACATA
1 GCTACCAAACATA
143752 AGGAAACAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.31, G:0.08, T:0.15
Consensus pattern (13 bp):
GCTACCAAACATA
Found at i:146435 original size:2 final size:2
Alignment explanation
Indices: 146428--146452 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
146418 TTGGATTCCT
146428 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
146453 TTCTTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.