Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007929.1 Hibiscus syriacus cultivar Beakdansim tig00110336_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: 398994
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:373651 original size:15 final size:15
Alignment explanation
Indices: 373631--373663 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
373621 CGTAGGACCC
*
373631 CTACATCCCGAAGGA
1 CTACATCACGAAGGA
373646 CTACATCACGAAGGA
1 CTACATCACGAAGGA
373661 CTA
1 CTA
373664 TTATACCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.30, G:0.18, T:0.15
Consensus pattern (15 bp):
CTACATCACGAAGGA
Found at i:373812 original size:23 final size:26
Alignment explanation
Indices: 373775--373843 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
373765 TTCTCTTGTG
373775 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
373799 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
373824 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
373844 AAAATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:373825 original size:12 final size:12
Alignment explanation
Indices: 373808--373843 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
373798 TATCATGTTC
373808 TCATATCACATG
1 TCATATCACATG
*
373820 TCATATCACATA
1 TCATATCACATG
373832 TCATATCACATG
1 TCATATCACATG
373844 AAAATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:374348 original size:64 final size:64
Alignment explanation
Indices: 374151--374376 Score: 206
Period size: 64 Copynumber: 3.5 Consensus size: 64
374141 TAATGAAGGT
* * * ** ** * ** *
374151 ATGCATCGATGCACTACTGATGCATCGGTGGATAAAAGGTATTCGATGTATT-ATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
* * * *
374215 ATACATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
* ** *
374279 ATGCATCGATGTACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATG-TTTCATTATTAAAGAG
** *
374342 AGTGCATCGATGCACTACCAATGCATCGATACACC
1 A-TGCATCGATGCACTACTTATGCATCGATGCACC
374377 GTTAAACAAT
Statistics
Matches: 134, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
63 4 0.03
64 124 0.93
65 6 0.04
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:380570 original size:15 final size:15
Alignment explanation
Indices: 380550--380582 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
380540 CGTAGGACCC
*
380550 CTACATCCCGAAGGA
1 CTACATCACGAAGGA
380565 CTACATCACGAAGGA
1 CTACATCACGAAGGA
380580 CTA
1 CTA
380583 TTATACCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.30, G:0.18, T:0.15
Consensus pattern (15 bp):
CTACATCACGAAGGA
Found at i:380731 original size:23 final size:26
Alignment explanation
Indices: 380694--380762 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
380684 TTCTCTTGTG
380694 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
380718 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
380743 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
380763 AAGATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:380744 original size:12 final size:12
Alignment explanation
Indices: 380727--380762 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
380717 TATCATGTTC
380727 TCATATCACATG
1 TCATATCACATG
*
380739 TCATATCACATA
1 TCATATCACATG
380751 TCATATCACATG
1 TCATATCACATG
380763 AAGATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:381202 original size:64 final size:63
Alignment explanation
Indices: 381134--381276 Score: 164
Period size: 64 Copynumber: 2.2 Consensus size: 63
381124 TATTGCTGGG
* *
381134 ATGCATCGATGCACCAATTGCATTCGATG-TTTCATTATT-AATGGGATGCATCGATGCACTACT
1 ATGCATCGATGCACCAATTGCATTCGATGTTTTCATT-TTAAAAGAG-TGCATCGATGCACTAC-
*
381197 T
63 C
** * *
381198 ATGCATCGATGCATGAATTGCATTTGATGTTTTTATTTTAAAAGAGTGCATCGATGCACTACC
1 ATGCATCGATGCACCAATTGCATTCGATGTTTTCATTTTAAAAGAGTGCATCGATGCACTACC
*
381261 ACTGCATCGATACACC
1 A-TGCATCGATGCACC
381277 TTCAAACAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
63 1 0.02
64 55 0.83
65 10 0.15
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACCAATTGCATTCGATGTTTTCATTTTAAAAGAGTGCATCGATGCACTACC
Found at i:382808 original size:31 final size:31
Alignment explanation
Indices: 382773--382831 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
382763 AAAAAAAGAA
382773 AAAAGTAAA-AACAAAAGAAAAGAAAAAGCTG
1 AAAAGTAAAGAA-AAAAGAAAAGAAAAAGCTG
*
382804 AAAAGTAAAGGAAAAAGAAAAGAAAAAG
1 AAAAGTAAAGAAAAAAGAAAAGAAAAAG
382832 AAAAGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.73, C:0.03, G:0.19, T:0.05
Consensus pattern (31 bp):
AAAAGTAAAGAAAAAAGAAAAGAAAAAGCTG
Found at i:382841 original size:6 final size:6
Alignment explanation
Indices: 382761--382841 Score: 55
Period size: 5 Copynumber: 13.7 Consensus size: 6
382751 CATCTATTAG
* * *
382761 AAAA-A AAAAGAA AAAAGTA AAAA-C AAAAG- AAAAGA AAAAGCTG AAAAGT
1 AAAAGA AAAAG-A AAAAG-A AAAAGA AAAAGA AAAAGA AAAAG--A AAAAGA
*
382810 AAAGGA AAAAG- AAAAGA AAAAG- AAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA
382842 AAGAAGGAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 15
0.73 0.08 0.18
Matches are distributed among these distances:
5 23 0.38
6 22 0.36
7 11 0.18
8 5 0.08
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAAGA
Found at i:382855 original size:12 final size:11
Alignment explanation
Indices: 382759--382841 Score: 68
Period size: 11 Copynumber: 7.6 Consensus size: 11
382749 CTCATCTATT
382759 AGAAAAA-AAA
1 AGAAAAAGAAA
382769 AGAAAAAAGTAAA
1 AG-AAAAAG-AAA
382782 A-ACAAAAGAAA
1 AGA-AAAAGAAA
*
382793 AGAAAAAG--C
1 AGAAAAAGAAA
*
382802 TG-AAAAGTAAA
1 AGAAAAAG-AAA
*
382813 GGAAAAAGAAA
1 AGAAAAAGAAA
382824 AGAAAAAGAAA
1 AGAAAAAGAAA
382835 AGAAAAA
1 AGAAAAA
382842 AAGAAGGAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
8 5 0.08
9 1 0.02
10 2 0.03
11 36 0.61
12 11 0.19
13 4 0.07
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:386056 original size:123 final size:123
Alignment explanation
Indices: 385713--386823 Score: 1070
Period size: 123 Copynumber: 8.8 Consensus size: 123
385703 CACTCGAGGG
* *
385713 ATCAACATTTTCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* *
385778 ATCTGAAGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAAT
66 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* * * *
385836 ATTAATATTTCCAGAAGGAGTTCATAATAAG-A-AACTCATCTGAAGAGGAAGAAGATGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * *
385899 ATCTGAAGAACTTATTCAACTTTTTTCTCGACTCTATCGCATAAGGAGATAGAGCAAC
66 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
*
385957 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * *
386022 ATCTGAAGAACTTATTCAACCTTTTGCTCAACTCTATCGCAAAAGGAGATAGAGTAGC
66 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* *
386080 ATCAACATTTCCAGAAGGAGTTCGTAATAAGGATAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * *
386145 ATCTAAAGAACTTATTCAACTTTTTGATCGACTCTATCGCAGAAGGAGATAGAGCATC
66 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* * *
386203 ATCAACATTTTCAGAAGGAGGTT-GTAATAAGAAGAACTCATTTGAAGAGGAATAAGAAGTTCAT
1 ATCAACATTTCCAGAAGGA-GTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
* * * * * * * * ** *
386267 AATTTGAAGAAGTTTATAATTTGAAGAACTTAT--TCAACCTTTTGCTCGACTCAATCGCAGA-A
65 AATCTGAAGAA--CT-T-A-TT-CA-ACCTTTTGCTCGA-C-TCT-ATCG-CAGAA--GGAGATA
*
386329 GGAGATAGAGC
117 -GAG-CA-A-C
* * * * * * ** ** * * *
386340 AGCATCAACATTTC--CAGAAG-GAGTTCGTAATAAGAAGAACTCATATTAAGAGGAAGAAGAAG
1 ATCAAC-A-TTTCCAGAAGGAGTTCG-TAATAA-GA-A-GAACTCATCTGAAGAGGAAGAAGAAG
* * * *
386402 TTTATAATCTGAAGAACTTATTCAACTTTTTGCTCGACTCTATCGTAGAAGGATATAGAGCAAC
60 TTCATAATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* * *
386466 ATCAACATTTCCAAAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAATAAATTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * *
386531 ATCTGAAGAACTTATTCAACCTTTTGGTCGACTCTATTGCAGAATGAGATAGAGCAGC
66 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
*
386589 ATCAACATTTCCAGAAGGAGCTCGTATAATAAGAAGAACTCATCTGAAGATGAAGAAGAAGTTCA
1 ATCAACATTTCCAGAAGGAGTTCG--TAATAAGAAGAACTCATCTG-A-A-G-AG--GAAG----
* * * * *
386654 TAATAAGAAGTTCATAATATGAAGAACTTATTCAACCATTTGCTCGACTCTATTGCATAAGGATA
54 ----AAGAAGTTCATAATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGA
**
386719 TAGAGCAGT
115 TAGAGCAAC
* * * *
386728 ATCAAGATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCCAATGAAGAGGAAGAAGAAGTTC
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCAT-C--TGAAGAGGAAGAAGAAGTTC
** * * *
386793 ATAATGAGAATAGCTTGTTCAACCTTTTGCT
63 ATAATCTGAAGAACTTATTCAACCTTTTGCT
386824 ACATTCCATC
Statistics
Matches: 811, Mismatches: 125, Indels: 101
0.78 0.12 0.10
Matches are distributed among these distances:
121 110 0.14
122 2 0.00
123 385 0.47
124 7 0.01
125 23 0.03
126 49 0.06
127 4 0.00
128 7 0.01
129 10 0.01
130 7 0.01
131 9 0.01
132 6 0.01
133 7 0.01
134 13 0.02
135 6 0.01
136 5 0.01
137 30 0.04
138 5 0.01
139 87 0.11
140 39 0.05
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (123 bp):
ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
Found at i:386278 original size:17 final size:17
Alignment explanation
Indices: 386256--386294 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
386246 GAAGAGGAAT
386256 AAGAAGTTCATAATTTG
1 AAGAAGTTCATAATTTG
*
386273 AAGAAGTTTATAATTTG
1 AAGAAGTTCATAATTTG
386290 AAGAA
1 AAGAA
386295 CTTATTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.03, G:0.18, T:0.33
Consensus pattern (17 bp):
AAGAAGTTCATAATTTG
Found at i:386346 original size:140 final size:140
Alignment explanation
Indices: 386132--386417 Score: 441
Period size: 140 Copynumber: 2.0 Consensus size: 140
386122 TGAAGAGGAA
* *
386132 GAAGAAGTTCATAATCTAAAGAACTTATTCAACTTTTTGATCGACTCTATCGCAGAAGGAGATAG
1 GAAGAAGTTCATAATCTAAAGAACTTATTCAACCTTTTGATCGACTCAATCGCAGAAGGAGATAG
* * *
386197 AGCATCATCAACATTTTCAGAAGGAGGTT-GTAATAAGAAGAACTCAT-TTGAAGAGGAATAAGA
66 AGCAGCATCAACATTTCCAGAAGGA-GTTCGTAATAAGAAGAACTCATATT-AAGAGGAAGAAGA
*
386260 AGTTCATAATTT
129 AGTTCATAATCT
* * * *
386272 GAAGAAGTTTATAATTTGAAGAACTTATTCAACCTTTTGCTCGACTCAATCGCAGAAGGAGATAG
1 GAAGAAGTTCATAATCTAAAGAACTTATTCAACCTTTTGATCGACTCAATCGCAGAAGGAGATAG
386337 AGCAGCATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATATTAAGAGGAAGAAGAAG
66 AGCAGCATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATATTAAGAGGAAGAAGAAG
*
386402 TTTATAATCT
131 TTCATAATCT
386412 GAAGAA
1 GAAGAA
386418 CTTATTCAAC
Statistics
Matches: 133, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
139 3 0.02
140 128 0.96
141 2 0.02
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (140 bp):
GAAGAAGTTCATAATCTAAAGAACTTATTCAACCTTTTGATCGACTCAATCGCAGAAGGAGATAG
AGCAGCATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATATTAAGAGGAAGAAGAAG
TTCATAATCT
Found at i:386495 original size:263 final size:260
Alignment explanation
Indices: 386009--386797 Score: 926
Period size: 263 Copynumber: 3.0 Consensus size: 260
385999 TGAAGAGGAA
* *
386009 GAAGAAATTCATAATCTGAAGAACTTATTCAACCTTTTGCTCAACTCTATCGCAAAAGGAGATAG
1 GAAG-AATTCATAATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAG
* * *
386074 AGTAGCATCAACATTTCCAGAAGGAGTTCGTAATAAGGATAACTCATCTGAAGAGGAAGAAGAAG
65 AGCAGCATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAG
* * * * *
386139 TTCATAATCTAAAGAACTTATTCAACTTTTTGATCGACTCTATCGCAGAAGGAGATAGAGCATCA
130 TTTATAATCTGAAGAACTTATTCAACTTTTTGCTCGACTCTATCGCAGAAGGATATAGAGCAACA
* * *
386204 TCAACATTTTCAGAAGGAGGTT-GTAATAAGAAGAACTCATTTGAAGAGGAATAAGAAGTTCATA
195 TCAACATTTCCAAAAGGA-GTTCGTAATAAGAAGAACTCATATGAAGAGGAA-AAGAAGTTCATA
386268 ATTT
258 A-TT
* * *
386272 GAAGAAGTTTATAATTTGAAGAACTTATTCAACCTTTTGCTCGACTCAATCGCAGAAGGAGATAG
1 GAAGAA-TTCATAATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAG
* *
386337 AGCAGCATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATATTAAGAGGAAGAAGAAG
65 AGCAGCATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAG
*
386402 TTTATAATCTGAAGAACTTATTCAACTTTTTGCTCGACTCTATCGTAGAAGGATATAGAGCAACA
130 TTTATAATCTGAAGAACTTATTCAACTTTTTGCTCGACTCTATCGCAGAAGGATATAGAGCAACA
*
386467 TCAACATTTCCAAAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGA-G----GAAG-----AA-
195 TCAACATTTCCAAAAGGAGTTCGTAATAAGAAGAACTCATATGAAGAGGAAAAGAAGTTCATAAT
386521 T
260 T
* * *
386522 --A-AATTCATAATCTGAAGAACTTATTCAACCTTTTGGTCGACTCTATTGCAGAATGAGATAGA
1 GAAGAATTCATAATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGA
* *
386584 GCAGCATCAACATTTCCAGAAGGAGCTCGTATAATAAGAAGAACTCATCTGAAGATGAAGAAGAA
66 GCAGCATCAACATTTCCAGAAGGAGTTCG--TAATAAGAAGAACTCATCTGAAGAGGAAGAAGAA
** * *
386649 GTTCATAATAAGAAGTTCATAATATGAAGAACTTATTCAACCATTTGCTCGACTCTATTGCATAA
129 GTT--T-AT---AA--TC------TGAAGAACTTATTCAACTTTTTGCTCGACTCTATCGCAGAA
** * * *
386714 GGATATAGAGCAGTATCAAGATTTCCAGAAA-GAGTTCATAATGAGAAGAACTCATCCAATGAAG
180 GGATATAGAGCAACATCAACATTTCCA-AAAGGAGTTCGTAATAAGAAGAACTCAT---ATGAAG
386778 AGGAAGAAGAAGTTCATAAT
241 AGGAA-AAGAAGTTCATAAT
386798 GAGAATAGCT
Statistics
Matches: 452, Mismatches: 40, Indels: 54
0.83 0.07 0.10
Matches are distributed among these distances:
246 81 0.18
247 2 0.00
248 35 0.08
250 2 0.00
251 2 0.00
252 2 0.00
254 2 0.00
256 2 0.00
257 4 0.01
262 88 0.19
263 219 0.48
265 6 0.01
266 1 0.00
271 4 0.01
276 2 0.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (260 bp):
GAAGAATTCATAATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGA
GCAGCATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGT
TTATAATCTGAAGAACTTATTCAACTTTTTGCTCGACTCTATCGCAGAAGGATATAGAGCAACAT
CAACATTTCCAAAAGGAGTTCGTAATAAGAAGAACTCATATGAAGAGGAAAAGAAGTTCATAATT
Found at i:386663 original size:14 final size:14
Alignment explanation
Indices: 386644--386677 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
386634 GAAGATGAAG
386644 AAGAAGTTCATAAT
1 AAGAAGTTCATAAT
386658 AAGAAGTTCATAAT
1 AAGAAGTTCATAAT
*
386672 ATGAAG
1 AAGAAG
386678 AACTTATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (14 bp):
AAGAAGTTCATAAT
Found at i:386663 original size:17 final size:16
Alignment explanation
Indices: 386642--386679 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 16
386632 CTGAAGATGA
386642 AGAAGAAGTTCATAAT
1 AGAAGAAGTTCATAAT
386658 --AAGAAGTTCATAAT
1 AGAAGAAGTTCATAAT
386672 ATGAAGAA
1 A-GAAGAA
386680 CTTATTCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
14 14 0.74
17 5 0.26
ACGTcount: A:0.53, C:0.05, G:0.18, T:0.24
Consensus pattern (16 bp):
AGAAGAAGTTCATAAT
Found at i:388189 original size:14 final size:14
Alignment explanation
Indices: 388153--388229 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
388143 TACTTTATAT
*
388153 TTTAATTT-ATGTCA
1 TTTAATTTCAT-TAA
*
388167 TTTATATTTTATTAA
1 TTTA-ATTTCATTAA
* **
388182 TTTAATTTCAGTCT
1 TTTAATTTCATTAA
388196 TTTAATTTCATT--
1 TTTAATTTCATTAA
*
388208 TTTAATTTCATTAC
1 TTTAATTTCATTAA
388222 TTTAATTT
1 TTTAATTT
388230 TCTATTTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
12 12 0.23
14 29 0.55
15 10 0.19
16 2 0.04
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (14 bp):
TTTAATTTCATTAA
Found at i:388199 original size:29 final size:27
Alignment explanation
Indices: 388138--388243 Score: 78
Period size: 26 Copynumber: 3.9 Consensus size: 27
388128 TTTATTTTAA
*
388138 TCATTTACTTT-ATATTTTAATTT-ATG
1 TCATTTAATTTCAT-TTTTAATTTCATG
*
388164 TCATTTATATTTTATTAATTTAATTTCA-G
1 TCATTTA-ATTTCATT--TTTAATTTCATG
*
388193 TCTTTTAATTTCATTTTTAATTTCAT-
1 TCATTTAATTTCATTTTTAATTTCATG
*
388219 T-ACTTTAATTTTCTATTTTTTATTT
1 TCA-TTTAA-TTTC-ATTTTTAATTT
388244 TTTCTTTACA
Statistics
Matches: 66, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
26 23 0.35
27 8 0.12
28 19 0.29
29 15 0.23
30 1 0.02
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.64
Consensus pattern (27 bp):
TCATTTAATTTCATTTTTAATTTCATG
Found at i:388250 original size:26 final size:26
Alignment explanation
Indices: 388196--388257 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 26
388186 ATTTCAGTCT
388196 TTTAA-TTTCATTTTTAATTTCATTAC
1 TTTAATTTTCATTTTTAATTT-ATTAC
* *
388222 TTTAATTTTCTATTTTTTATTT-TTTC
1 TTTAATTTTC-ATTTTTAATTTATTAC
388248 TTTACATTTT
1 TTTA-ATTTT
388258 TCAATACTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 12 0.39
27 9 0.29
28 10 0.32
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (26 bp):
TTTAATTTTCATTTTTAATTTATTAC
Found at i:391565 original size:35 final size:34
Alignment explanation
Indices: 391480--391591 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 34
391470 ATCCCATTAT
* * *
391480 CATTTTCAACAAAAATCTACCAAACTTTGAAAAAC
1 CATTTTCAAGAAACATTTACCAAACTTTG-AAAAC
* *
391515 TATTTTTCAAAGAAACATTTACCAAATTTTGAAAAC
1 CA-TTTTC-AAGAAACATTTACCAAACTTTGAAAAC
*
391551 CATTTTCAAGGAAACATTTACCAAACTTTAAAAAC
1 CATTTTCAA-GAAACATTTACCAAACTTTGAAAAC
391586 CATTTT
1 CATTTT
391592 TTCAAAGTTG
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
34 2 0.03
35 35 0.53
36 11 0.17
37 18 0.27
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (34 bp):
CATTTTCAAGAAACATTTACCAAACTTTGAAAAC
Found at i:396130 original size:37 final size:36
Alignment explanation
Indices: 396068--396186 Score: 161
Period size: 35 Copynumber: 3.3 Consensus size: 36
396058 TCCCATTATC
* *
396068 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACT
* *
396104 ATTTTTCAAAGAAATATTTACCAAACTTTGAAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
*
396140 A-TTTTCAAGGAAACATTTACCAAACTTTGAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
396175 ATTTTTTCAAAG
1 A-TTTTTCAAAG
396187 TTGGTTACCA
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
35 32 0.44
36 13 0.18
37 27 0.38
ACGTcount: A:0.43, C:0.18, G:0.06, T:0.34
Consensus pattern (36 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
Found at i:396184 original size:72 final size:68
Alignment explanation
Indices: 396070--396217 Score: 192
Period size: 72 Copynumber: 2.1 Consensus size: 68
396060 CCATTATCAT
*
396070 TTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAGAAATATTTACCAAACTTTGA
1 TTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAG--ATAGTTACCAAAC-TTGA
396135 AAACCA
63 AAACCA
* * * *
396141 TTTTCAAGGAAACATTTACCAAACTTTG-AAAACTATTTTTTCAAAGTTGGTTACCAAACTTGAA
1 TTTTCAA-CAAACATCTACCAAACTTTGAAAAACTA-TTTTTCAAAGATAGTTACCAAACTTGAA
396205 AACCA
64 AACCA
396210 TTTT-AACA
1 TTTTCAACA
396218 TGTAGGACGT
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
67 1 0.01
68 2 0.03
69 14 0.20
70 10 0.14
71 14 0.20
72 28 0.41
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (68 bp):
TTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAGATAGTTACCAAACTTGAAAA
CCA
Done.