Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003399.1 Hibiscus syriacus cultivar Beakdansim tig00007152_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: 77027
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:6627 original size:21 final size:21
Alignment explanation
Indices: 6585--6628 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
6575 ACTCCGGGAG
* *
6585 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
6606 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
6627 CT
1 CT
6629 CTGGCTCCAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:13156 original size:116 final size:111
Alignment explanation
Indices: 12952--13194 Score: 278
Period size: 116 Copynumber: 2.1 Consensus size: 111
12942 TTTTTTAACA
* * * * * *
12952 ATTTATTTCATTTTATAAAATAGAATCTTTCAGATCATGAAATAAATTTGATGATTTATTTGCTT
1 ATTTATTTCCTTTTACAAAATAGAATCTATAAGATCATGAAATAAATTTAATGATTTATTTCCTT
13017 TCATAAATTAGAATCATATAAGATTCTC-ATGAATATAAATTCAAAC
66 TCATAAATTAGAATCATATAAGATTCTCAATGAA-ATAAATTCAAAC
13063 ATTTATTTCCTTTTACAAAATAGAATCATATAAGATTCCATAGAAAATAAATTTAATGATTTATT
1 ATTTATTTCCTTTTACAAAATAGAATC-TATAAGA-T-CAT-G-AAATAAATTTAATGATTTATT
* * **
13128 TCCTTTTACA-AAATT-GAATCAT-TCAAGATTCTCAATTAAATAAATTCGATG
61 TCC-TTT-CATAAATTAGAATCATAT-AAGATTCTCAATGAAATAAATTCAAAC
*
13179 ATTGATTTCCTTTTAC
1 ATTTATTTCCTTTTAC
13195 TGTAACCCCA
Statistics
Matches: 112, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
111 25 0.22
112 5 0.04
113 1 0.01
114 3 0.03
115 2 0.02
116 62 0.55
117 12 0.11
118 2 0.02
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.42
Consensus pattern (111 bp):
ATTTATTTCCTTTTACAAAATAGAATCTATAAGATCATGAAATAAATTTAATGATTTATTTCCTT
TCATAAATTAGAATCATATAAGATTCTCAATGAAATAAATTCAAAC
Found at i:13180 original size:58 final size:58
Alignment explanation
Indices: 12819--13194 Score: 222
Period size: 58 Copynumber: 6.5 Consensus size: 58
12809 AGATTTTACG
* * * * * * *
12819 AAAATAAATTGAAT-AGTTTATTTCATTTCATAAAATTAAATCAT-TCAAGATTTTCAAG
1 AAAATAAATTCAATGA-TTTATTTCCTTTTACAAAATTGAATCATAT-AAGATTCTCAAT
* * * * * * **
12877 AAAATGAATTCAAAGATATATTT-CTTTTACAAAATAGAGTCATGTAAGATTGC-CAGG
1 AAAATAAATTCAATGATTTATTTCCTTTTACAAAATTGAATCATATAAGATT-CTCAAT
* * ** * * * * *
12934 AAAATAATTTTTTTAACAATTTATTTCATTTTATAAAATAGAATC-TTTCAGA---TC-AT
1 AAAATAA---ATTCAATGATTTATTTCCTTTTACAAAATTGAATCATATAAGATTCTCAAT
* ** *
12990 GAAATAAATTTGATGATTTATTTGC-TTT-CATAAATTAGAATCATATAAGATTCTC-AT
1 AAAATAAATTCAATGATTTATTTCCTTTTACA-AAATT-GAATCATATAAGATTCTCAAT
* ** * *
13047 GAATATAAATTCAAACATTTATTTCCTTTTACAAAATAGAATCATATAAGATTC-CATAG
1 -AAAATAAATTCAATGATTTATTTCCTTTTACAAAATTGAATCATATAAGATTCTCA-AT
*
13106 AAAATAAATTTAATGATTTATTTCCTTTTACAAAATTGAATCAT-TCAAGATTCTCAAT
1 AAAATAAATTCAATGATTTATTTCCTTTTACAAAATTGAATCATAT-AAGATTCTCAAT
* * *
13164 TAAATAAATTCGATGATTGATTTCCTTTTAC
1 AAAATAAATTCAATGATTTATTTCCTTTTAC
13195 TGTAACCCCA
Statistics
Matches: 242, Mismatches: 55, Indels: 42
0.71 0.16 0.12
Matches are distributed among these distances:
51 1 0.00
52 7 0.03
53 17 0.07
54 5 0.02
56 6 0.02
57 36 0.15
58 126 0.52
59 11 0.05
60 18 0.07
61 15 0.06
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (58 bp):
AAAATAAATTCAATGATTTATTTCCTTTTACAAAATTGAATCATATAAGATTCTCAAT
Found at i:14223 original size:13 final size:13
Alignment explanation
Indices: 14192--14225 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
14182 TTGACTTTTT
*
14192 GGTCAAAGTCAAC
1 GGTCAAAGTCAAA
*
14205 GATCAAAGTCAAA
1 GGTCAAAGTCAAA
14218 GGTCAAAG
1 GGTCAAAG
14226 GTCGGACAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (13 bp):
GGTCAAAGTCAAA
Found at i:14240 original size:13 final size:13
Alignment explanation
Indices: 14224--14267 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
14214 CAAAGGTCAA
14224 AGGTCGGACAGTC
1 AGGTCGGACAGTC
* *
14237 AGGTCGGATAGTT
1 AGGTCGGACAGTC
*
14250 AGGTCGGGCAGTC
1 AGGTCGGACAGTC
*
14263 GGGTC
1 AGGTC
14268 AGACCAGGTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.18, C:0.18, G:0.43, T:0.20
Consensus pattern (13 bp):
AGGTCGGACAGTC
Found at i:15137 original size:57 final size:58
Alignment explanation
Indices: 15021--15140 Score: 138
Period size: 57 Copynumber: 2.1 Consensus size: 58
15011 GATTCTGAGA
* * * *
15021 AAAATAAATTCAATGGTTTATTTCCCTTTCCAAAGTAGAATCATTCAAGATTTTCAAG
1 AAAATAAATTCAATGGTTTATTTCCCTTTACAAAATAGAATCATTCAAAATCTTCAAG
* * *
15079 AAAATAAAATTC-A-GGTTTATTTCCTTTTATAAAATAGAATGATTCAAAATACTT-AAG
1 AAAAT-AAATTCAATGGTTTATTTCCCTTTACAAAATAGAATCATTCAAAAT-CTTCAAG
15136 AAAAT
1 AAAAT
15141 TCCTTTTTTC
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
57 39 0.74
58 8 0.15
59 6 0.11
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (58 bp):
AAAATAAATTCAATGGTTTATTTCCCTTTACAAAATAGAATCATTCAAAATCTTCAAG
Found at i:15527 original size:44 final size:45
Alignment explanation
Indices: 15446--15551 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 45
15436 TAATCATTTC
* *
15446 ATTTTAAATTTGACAACCCAACAATCAAAAAGAACTAATTCTTTA
1 ATTTTAATTTTGACAACCCAACAATCAAAAAGAACTAATACTTTA
* * * * *
15491 ATTTTAATTTTGGCAA-CCAATAATTAAAATGAACTAATACTTTG
1 ATTTTAATTTTGACAACCCAACAATCAAAAAGAACTAATACTTTA
* *
15535 ATTTTAGTTTTAACAAC
1 ATTTTAATTTTGACAAC
15552 TCAATTATCA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 36 0.72
45 14 0.28
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (45 bp):
ATTTTAATTTTGACAACCCAACAATCAAAAAGAACTAATACTTTA
Found at i:16184 original size:5 final size:6
Alignment explanation
Indices: 16169--16194 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
16159 TTGAGATGAT
16169 AAAAAG AAAAAG AAAAAG AAAAAG AA
1 AAAAAG AAAAAG AAAAAG AAAAAG AA
16195 TCATTGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:19616 original size:32 final size:32
Alignment explanation
Indices: 19578--19655 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
19568 ATGTACATAC
* *
19578 TCTAAATATAACACTAACACTGTTGTGCATTA
1 TCTAAATACAACACTAACACTGTTATGCATTA
* *
19610 TCTAAATGCAACACTAACTCTGTTATGCATTA
1 TCTAAATACAACACTAACACTGTTATGCATTA
*
19642 TCTAAATGCAACAC
1 TCTAAATACAACAC
19656 ACTGCTAGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (32 bp):
TCTAAATACAACACTAACACTGTTATGCATTA
Found at i:30603 original size:35 final size:36
Alignment explanation
Indices: 30551--30650 Score: 109
Period size: 36 Copynumber: 2.8 Consensus size: 36
30541 TATGTTAGAT
**
30551 AAAAAGAGAAAACAAAATGCTAATAAATAA-AA-AATG
1 AAAAA-AGAAAACAAAATAATAAT-AATAATAATAATG
*
30587 AAAAAAGAAAAGAAAATAATAATAATAATAATAATG
1 AAAAAAGAAAACAAAATAATAATAATAATAATAATG
30623 AAAGAAAGAATAA-AAAA-AATAATAATAA
1 AAA-AAAGAA-AACAAAATAATAATAATAA
30651 AAGGTTAAGT
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
34 5 0.09
35 17 0.30
36 23 0.40
37 10 0.18
38 2 0.04
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (36 bp):
AAAAAAGAAAACAAAATAATAATAATAATAATAATG
Found at i:30643 original size:27 final size:28
Alignment explanation
Indices: 30594--30653 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
30584 ATGAAAAAAG
* * *
30594 AAAAGAAAATAATAATAATAATAATAAT
1 AAAAGAAAAGAATAAAAAAAATAATAAT
*
30622 GAAAG-AAAGAATAAAAAAAATAATAAT
1 AAAAGAAAAGAATAAAAAAAATAATAAT
30649 AAAAG
1 AAAAG
30654 GTTAAGTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.18
Consensus pattern (28 bp):
AAAAGAAAAGAATAAAAAAAATAATAAT
Found at i:30652 original size:12 final size:12
Alignment explanation
Indices: 30599--30652 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
30589 AAAAGAAAAG
30599 AAAATAATAATA
1 AAAATAATAATA
*
30611 ATAATAATAATGAA
1 AAAATAATAAT--A
* *
30625 AGAAAGAATAAAA
1 A-AAATAATAATA
30638 AAAATAATAATA
1 AAAATAATAATA
30650 AAA
1 AAA
30653 GGTTAAGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
12 22 0.67
13 2 0.06
14 2 0.06
15 7 0.21
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:31891 original size:21 final size:21
Alignment explanation
Indices: 31871--31939 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
31861 AAAAGAAATA
31871 AATAAATAAGAA-AA-AATAAT
1 AATAAA-AAGAATAATAATAAT
*
31891 AATTAAAAGAATAATAATAAT
1 AATAAAAAGAATAATAATAAT
*
31912 AATAAAATATAATATATAATATAT
1 AATAAAA-AGAATA-ATAATA-AT
31936 AATA
1 AATA
31940 TATAAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
19 5 0.12
20 7 0.17
21 12 0.29
22 5 0.12
23 6 0.15
24 6 0.15
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (21 bp):
AATAAAAAGAATAATAATAAT
Found at i:31893 original size:3 final size:3
Alignment explanation
Indices: 31885--31949 Score: 55
Period size: 3 Copynumber: 21.3 Consensus size: 3
31875 AATAAGAAAA
*
31885 AAT AAT AATT AA- AAG AAT AAT AAT AAT AAT AA- AAT -AT AAT ATAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
*
31929 AAT ATAT AAT ATAT AAA AAT A
1 AAT A-AT AAT A-AT AAT AAT A
31950 TTTTCAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
2 6 0.12
3 34 0.65
4 12 0.23
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:31928 original size:7 final size:7
Alignment explanation
Indices: 31901--31944 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
31891 AATTAAAAGA
31901 ATAATA-
1 ATAATAT
31907 ATAATA-
1 ATAATAT
*
31913 ATAAAAT
1 ATAATAT
31920 ATAATAT
1 ATAATAT
31927 ATAATAT
1 ATAATAT
31934 ATAATAT
1 ATAATAT
31941 ATAA
1 ATAA
31945 AAATATTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
6 11 0.31
7 24 0.69
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
ATAATAT
Found at i:31976 original size:35 final size:36
Alignment explanation
Indices: 31922--32033 Score: 104
Period size: 39 Copynumber: 3.0 Consensus size: 36
31912 AATAAAATAT
31922 AATATATAATATATAATATATAAAAATATTTTCAAAAAA
1 AATATAT-ATA-AT-ATATATAAAAATATTTTCAAAAAA
31961 AAT-TATATAATATATATTTTTTAAAAATA-TTT-AAAAAA
1 AATATATATAATATATA-----TAAAAATATTTTCAAAAAA
* * *
31999 AATATATATTATATATTTAAAAATATTTTCCAAAA
1 AATATATATAATATATATAAAAATATTTTCAAAAA
32034 TTATATATTA
Statistics
Matches: 62, Mismatches: 3, Indels: 19
0.74 0.04 0.23
Matches are distributed among these distances:
34 8 0.13
35 8 0.13
36 6 0.10
37 3 0.05
38 12 0.19
39 17 0.27
40 8 0.13
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (36 bp):
AATATATATAATATATATAAAAATATTTTCAAAAAA
Found at i:32006 original size:37 final size:37
Alignment explanation
Indices: 31922--32068 Score: 140
Period size: 34 Copynumber: 4.0 Consensus size: 37
31912 AATAAAATAT
*
31922 AATATATAATATATAATATATAAAAATATTTTCAAAAAA
1 AATATATAATATATAATATTTAAAAATA-TTT-AAAAAA
* *
31961 AATTATATAATATATATTTTTTAAAAATATTTAAAAAA
1 AA-TATATAATATATAATATTTAAAAATATTTAAAAAA
***
31999 AATATAT-AT-TAT-ATATTTAAAAATATTTTCCAAA
1 AATATATAATATATAATATTTAAAAATATTTAAAAAA
* * * *
32033 ATTATATATTATATAAT-TTTCAAAAATGTTTTAAAA
1 AATATATAATATATAATATTT-AAAAATATTTAAAAA
32069 TTAATATTAC
Statistics
Matches: 90, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
34 23 0.26
35 4 0.04
36 8 0.09
37 19 0.21
38 8 0.09
39 5 0.06
40 23 0.26
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.43
Consensus pattern (37 bp):
AATATATAATATATAATATTTAAAAATATTTAAAAAA
Found at i:32023 original size:34 final size:36
Alignment explanation
Indices: 31922--32026 Score: 133
Period size: 40 Copynumber: 2.8 Consensus size: 36
31912 AATAAAATAT
*
31922 AATATATAATATATAATATATAAAAATATTTTCAAAAAA
1 AATATATAATATAT-ATATTTAAAAATA-TTT-AAAAAA
*
31961 AATTATATAATATATATTTTTTAAAAATATTTAAAAAA
1 AA-TATATAATATATA-TATTTAAAAATATTTAAAAAA
31999 AATATAT-AT-TATATATTTAAAAATATTT
1 AATATATAATATATATATTTAAAAATATTT
32027 TCCAAAATTA
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
34 14 0.23
35 4 0.07
36 2 0.03
37 5 0.08
38 8 0.13
39 6 0.10
40 22 0.36
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (36 bp):
AATATATAATATATATATTTAAAAATATTTAAAAAA
Found at i:32039 original size:34 final size:34
Alignment explanation
Indices: 31959--32297 Score: 151
Period size: 34 Copynumber: 9.5 Consensus size: 34
31949 ATTTTCAAAA
* ***
31959 AAAATTATATAATATATATTTTTTAAAAATATTTAAA
1 AAAATTATAT-AT-TATA-TATTTAAAAATATTTTCC
*
31996 AAAAATATATATTATATATTTAAAAATATTTTCC
1 AAAATTATATATTATATATTTAAAAATATTTTCC
*
32030 AAAATTATATATTATATAATTTTCAAAAATGTTTT--
1 AAAATTATATATTATAT-A-TTT-AAAAATATTTTCC
* * * **
32065 AAAATTA-ATATTACATGTTTTCAAAAATGTTTTTTT
1 AAAATTATATATTATAT-ATTT-AAAAAT-ATTTTCC
*
32101 TAAA-TATATA-T-TATATTTAAAAATGA-TTT-C
1 AAAATTATATATTATATATTTAAAAAT-ATTTTCC
* * * * *
32131 AAAACTATATAATATATATTTTTAAAATGTTTTCA
1 AAAATTATATATTATATA-TTTAAAAATATTTTCC
* *
32166 AAAATTATATATATATATATATATATATTAAAATGTTTTCA
1 AAAA-T-TATATAT-TATATAT-T-TA--AAAATATTTTCC
*
32207 AAAATCATATATTATATATGTTTCCAAAAA-AGTTTTCC
1 AAAATTATATATTATATA--TTT--AAAAATA-TTTTCC
* **
32245 AAAAATTATATAATATATATTTTCAAAAACCGTTTT-C
1 -AAAATTATATATTATATA-TTT-AAAAA-TATTTTCC
32282 AAAATTATATA-TATAT
1 AAAATTATATATTATAT
32298 TATATGTATT
Statistics
Matches: 244, Mismatches: 30, Indels: 58
0.73 0.09 0.17
Matches are distributed among these distances:
30 3 0.01
31 9 0.04
32 8 0.03
33 17 0.07
34 55 0.23
35 24 0.10
36 22 0.09
37 33 0.14
38 30 0.12
39 24 0.10
40 3 0.01
41 16 0.07
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (34 bp):
AAAATTATATATTATATATTTAAAAATATTTTCC
Found at i:32191 original size:42 final size:41
Alignment explanation
Indices: 32104--32225 Score: 147
Period size: 41 Copynumber: 3.2 Consensus size: 41
32094 TTTTTTTTAA
*
32104 ATATATAT-TATAT-TTAAAAATGATTTC-AAAA-C-TATAT
1 ATATATATATATATATT-AAAATGTTTTCAAAAATCATATAT
*
32141 A-ATATATAT-T-T-TTAAAATGTTTTCAAAAATTATATAT
1 ATATATATATATATATTAAAATGTTTTCAAAAATCATATAT
32178 ATATATATATATATATTAAAATGTTTTCAAAAATCATATAT
1 ATATATATATATATATTAAAATGTTTTCAAAAATCATATAT
32219 -TATATAT
1 ATATATAT
32226 GTTTCCAAAA
Statistics
Matches: 74, Mismatches: 3, Indels: 13
0.82 0.03 0.14
Matches are distributed among these distances:
34 10 0.14
35 7 0.09
36 7 0.09
37 8 0.11
38 8 0.11
39 1 0.01
40 8 0.11
41 25 0.34
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (41 bp):
ATATATATATATATATTAAAATGTTTTCAAAAATCATATAT
Found at i:32230 original size:25 final size:26
Alignment explanation
Indices: 32188--32236 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
32178 ATATATATAT
32188 ATATATTAAAATGTTTT-CAAAAATC
1 ATATATTAAAATGTTTTCCAAAAATC
*
32213 ATATATTATATATG-TTTCCAAAAA
1 ATATATTA-AAATGTTTTCCAAAAA
32237 AGTTTTCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (26 bp):
ATATATTAAAATGTTTTCCAAAAATC
Found at i:32234 original size:26 final size:25
Alignment explanation
Indices: 32188--32236 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
32178 ATATATATAT
*
32188 ATATATTAAAATGTTTTCAAAAATC
1 ATATATTAAAATGTTTCCAAAAATC
*
32213 ATATATTATATATGTTTCCAAAAA
1 ATATATTA-AAATGTTTCCAAAAA
32237 AGTTTTCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (25 bp):
ATATATTAAAATGTTTCCAAAAATC
Found at i:32242 original size:38 final size:37
Alignment explanation
Indices: 32195--32314 Score: 127
Period size: 38 Copynumber: 3.1 Consensus size: 37
32185 TATATATATT
* *
32195 AAAATGTTTTCAAAAATCATATATTATATATGTTTCCA
1 AAAAAGTTTTCAAAAATTATATATTATATATGTTT-CA
*
32233 AAAAAGTTTTCCAAAAATTATATAATATATAT-TTTCA
1 AAAAAGTTTT-CAAAAATTATATATTATATATGTTTCA
*
32270 AAAACCGTTTTC-AAAATTATATATATATTATATGTATTTCA
1 AAAA-AGTTTTCAAAAATTATATAT-TA-TATATG--TTTCA
32311 AAAA
1 AAAA
32315 CATTCGCAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
36 11 0.16
37 9 0.13
38 22 0.31
39 19 0.27
41 9 0.13
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (37 bp):
AAAAAGTTTTCAAAAATTATATATTATATATGTTTCA
Found at i:32255 original size:76 final size:74
Alignment explanation
Indices: 32104--32297 Score: 186
Period size: 75 Copynumber: 2.6 Consensus size: 74
32094 TTTTTTTTAA
* * *
32104 ATATATAT-TATATTTAAAAATGATTTCAAAACTATATAATATATATTTTTAAAATGTTTTCAAA
1 ATATATATATATATTTAAAAATGATTTCAAAAATATATAATATATATTTTAAAAAAGTTTTCAAA
32168 AATTATATAT
66 AA-TATATAT
* *
32178 ATATATATATATATATT-AAAATGTTTTCAAAAATCATATATTATATATGTTTCCAAAAAAGTTT
1 ATATATATATATAT-TTAAAAATGATTTCAAAAAT-ATATAATATATAT-TTT--AAAAAAGTTT
32242 TCCAAAAAT-TATAT
61 T-CAAAAATATATAT
* * * *
32256 A-ATATATAT-T-TTCAAAAACCGTTTTCAAAATTATAT-ATATAT
1 ATATATATATATATTTAAAAA-TGATTTCAAAAATATATAATATAT
32298 TATATGTATT
Statistics
Matches: 102, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
74 14 0.14
75 29 0.28
76 26 0.25
77 11 0.11
78 6 0.06
79 10 0.10
80 6 0.06
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (74 bp):
ATATATATATATATTTAAAAATGATTTCAAAAATATATAATATATATTTTAAAAAAGTTTTCAAA
AATATATAT
Found at i:32272 original size:37 final size:35
Alignment explanation
Indices: 32200--32297 Score: 99
Period size: 37 Copynumber: 2.6 Consensus size: 35
32190 ATATTAAAAT
*
32200 GTTTTCAAAAATCATATATTATATATGTTTCCAAAAA-A
1 GTTTTC-AAAAT--TATA-TATATATATTTCCAAAAACA
* *
32238 GTTTTCCAAAAATTATATAATATATATTTTCAAAAACC
1 GTTTT-C-AAAATTATAT-ATATATATTTCCAAAAACA
32276 GTTTTCAAAATTATATATATAT
1 GTTTTCAAAATTATATATATAT
32298 TATATGTATT
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
35 6 0.11
36 11 0.20
37 20 0.37
38 10 0.19
39 7 0.13
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (35 bp):
GTTTTCAAAATTATATATATATATTTCCAAAAACA
Found at i:33103 original size:84 final size:85
Alignment explanation
Indices: 32968--33690 Score: 721
Period size: 84 Copynumber: 8.7 Consensus size: 85
32958 AAGTTGAATA
* * *
32968 TAATCGAACTCAAAGGTC---T-TTAGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGA
1 TAATCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA
* *
33029 TGTG-CCTTGGAGCTGAGCG
66 TGTGCCCTCGAAGCTGAGCG
* * *
33048 TAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
1 TAATCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA
*
33113 TGTGCCCTCGAAGCTGAGTG
66 TGTGCCCTCGAAGCTGAGCG
*** * * * *
33133 TAATCGAACTCGGGGGTC---T-TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGA
1 TAATCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA
* *
33194 TGTG-CCTTGGAGCTGAGCG
66 TGTGCCCTCGAAGCTGAGCG
* * * ** * * *
33213 TAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGA
1 TAATCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA
* *
33278 TGTGCCGTTG-AGCTGAGCG
66 TGTGCCCTCGAAGCTGAGCG
* * *
33297 TAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
1 TAATCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA
*
33362 TGTGCCCTCGAAGCTGAGTG
66 TGTGCCCTCGAAGCTGAGCG
*** * ** * * *
33382 TAATCGAACTCGGGGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGA
1 TAATCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA
*
33447 TGTGCCCTCGAAGCTGAGTG
66 TGTGCCCTCGAAGCTGAGCG
** * * *
33467 TAATCGAACTCAGGGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
1 TAATCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA
* *
33528 TGTGCCGTTG-AGCTGAGCG
66 TGTGCCCTCGAAGCTGAGCG
* * ** * * * *
33547 TAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGA
1 TAATCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA
*
33612 TGTGCCCTCGAAGCTGAGTG
66 TGTGCCCTCGAAGCTGAGCG
*** * * * *
33632 TAATCGAACTCGGGGGTC---T-TTGGCAGATAGCCCTTTTTGACTTAAGCTATGCTGCAAAT
1 TAATCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAAT
33691 AGTTTGTTTG
Statistics
Matches: 529, Mismatches: 98, Indels: 31
0.80 0.15 0.05
Matches are distributed among these distances:
80 67 0.13
81 111 0.21
82 3 0.01
83 3 0.01
84 195 0.37
85 150 0.28
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (85 bp):
TAATCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA
TGTGCCCTCGAAGCTGAGCG
Found at i:33153 original size:165 final size:165
Alignment explanation
Indices: 32909--33690 Score: 1057
Period size: 165 Copynumber: 4.7 Consensus size: 165
32899 ATTTTATTGG
* * * * * * * * *
32909 CAGATAACCCTTCTTGCCTTGAGCTATTCTGTAAGCTTGATTTG-CCTCTAAGTTGAATATAATC
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAA--ATGATGTGCCCTCGAAGCTGAGTGTAATC
** *
32973 GAACTCAAAGGTCTTTAGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTG
64 GAACTCAGGGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTG
* **
33038 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGG
129 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCA
* * * * *
33075 CAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
* * *
33140 ACTCGGGGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGA
66 ACTCAGGGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGA
*
33205 GCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCA
131 GCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCA
* * * *
33240 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCGTTG-AGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
** * * *
33304 ACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCC
66 ACTCAGGGGTC---T-TTGGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG-CC
* * * * ***
33369 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTTGGTCA
126 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCA
33409 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
* *
33474 ACTCAGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-G
66 ACTCAGGGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCC-TTGG
33538 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCA
130 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCA
*
33574 CAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
* * *
33639 ACTCGGGGGTCTTTGGCAGATAGCCCTTTTTGACTTAAGCTATGCTGCAAAT
66 ACTCAGGGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAAT
33691 AGTTTGTTTG
Statistics
Matches: 542, Mismatches: 66, Indels: 17
0.87 0.11 0.03
Matches are distributed among these distances:
164 28 0.05
165 295 0.54
166 71 0.13
167 2 0.00
168 41 0.08
169 82 0.15
170 23 0.04
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (165 bp):
CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
ACTCAGGGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGA
GCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCA
Found at i:33436 original size:334 final size:330
Alignment explanation
Indices: 32909--33690 Score: 1039
Period size: 334 Copynumber: 2.4 Consensus size: 330
32899 ATTTTATTGG
* * * * * * * ***
32909 CAGATAACCCTTCTTGCCTTGAGCTATTCTGTAAGCTTGATTTG-CCTCTAAGTTGAATATAATC
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAA--ATGATGTGCCCTCGAAGCTGAGCGTAATC
* * *
32973 GAACTCAAAGGTCTTTAGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTG
64 GAACTCAAAGGTCTTTAGCAGACAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCG
* * * ** *
33038 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTCGACTTAAGTTATG
129 AAGCTGAGCGTAATCGAACTCAAAGGTCTTTTGGTCACAGACAACCCTTCTAGACTTAAGTTATG
*
33103 CTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAACCCTT
194 CTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAGGGGTCTTTGGCAGATAACCCTT
* * * *
33168 CTTGCCTTGAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
259 CTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCT
33232 TTTGGTCA
323 TTTGGTCA
* * *
33240 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCGTTG-AGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCGA
* *
33304 ACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCC
66 ACTCAAAGGTC---T-TTAGCAGACAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CC
* *** * * *
33369 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTT
126 TCGAAGCTGAGCGTAATCGAACTCAAAGGTCTTTTGGTCACAGACAACCCTTCTAGACTTAAGTT
* *
33434 ATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAGGGGTCTTTGGCAGATAGCC
191 ATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAGGGGTCTTTGGCAGATAACC
33499 CTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGT
256 CTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGT
33564 CTTTTGGTCA
321 CTTTTGGTCA
* *
33574 CAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCGA
*** * * * * *
33639 ACTCGGGGGTCTTTGGCAGATAGCCCTTTTTGACTTAAGCTATGCTGCAAAT
66 ACTCAAAGGTCTTTAGCAGACAACCCTTCTCGACTTAAGCTATGCTGCAAAT
33691 AGTTTGTTTG
Statistics
Matches: 392, Mismatches: 51, Indels: 16
0.85 0.11 0.03
Matches are distributed among these distances:
329 28 0.07
330 2 0.01
331 66 0.17
332 2 0.01
333 42 0.11
334 228 0.58
335 24 0.06
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (330 bp):
CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCGA
ACTCAAAGGTCTTTAGCAGACAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCGAA
GCTGAGCGTAATCGAACTCAAAGGTCTTTTGGTCACAGACAACCCTTCTAGACTTAAGTTATGCT
GCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAGGGGTCTTTGGCAGATAACCCTTCT
CGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTT
GGTCA
Found at i:37112 original size:18 final size:19
Alignment explanation
Indices: 37071--37115 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
37061 AGTTAATGTG
37071 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
37090 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
37108 AATGCAAA
1 AATGCAAA
37116 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:38859 original size:35 final size:36
Alignment explanation
Indices: 38807--38903 Score: 101
Period size: 36 Copynumber: 2.7 Consensus size: 36
38797 TATGTTAGAT
* **
38807 AAAAAGAGAAAACAAAATGCTAATAAATAA-AA-AAAG
1 AAAAA-AGAAAAAAAAATAATAAT-AATAATAAGAAAG
38843 AAAAAAGAAAAAAAAATAATAATAATAATAATGAAAG
1 AAAAAAGAAAAAAAAATAATAATAATAATAA-GAAAG
* *
38880 AAAGAA-TAAAAAAAATAATAATAA
1 AAAAAAGAAAAAAAAATAATAATAA
38904 AAGGTTAAGT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
34 5 0.09
35 17 0.32
36 22 0.42
37 9 0.17
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.14
Consensus pattern (36 bp):
AAAAAAGAAAAAAAAATAATAATAATAATAAGAAAG
Found at i:38881 original size:30 final size:30
Alignment explanation
Indices: 38846--38903 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
38836 AAAAAAGAAA
38846 AAAGAAA-AA-AAAATAATAATAATAATAATG
1 AAAGAAAGAATAAAA-AA-AATAATAATAATG
38876 AAAGAAAGAATAAAAAAAATAATAATAA
1 AAAGAAAGAATAAAAAAAATAATAATAA
38904 AAGGTTAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 18 0.69
31 4 0.15
32 4 0.15
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (30 bp):
AAAGAAAGAATAAAAAAAATAATAATAATG
Found at i:38905 original size:12 final size:12
Alignment explanation
Indices: 38854--38905 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
38844 AAAAAGAAAA
38854 AAAAATAATAAT
1 AAAAATAATAAT
*
38866 AATAATAATGAA-
1 AAAAATAAT-AAT
* * *
38878 AGAAAGAATAAA
1 AAAAATAATAAT
38890 AAAAATAATAAT
1 AAAAATAATAAT
38902 AAAA
1 AAAA
38906 GGTTAAGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
11 2 0.06
12 27 0.87
13 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:40130 original size:35 final size:35
Alignment explanation
Indices: 40050--40352 Score: 259
Period size: 34 Copynumber: 8.5 Consensus size: 35
40040 ATATTTAAAA
* *
40050 AAAACTATATATTATATA-TTT-AAAAATATTTTCC
1 AAAATTATATATTATATATTTTCAAAAATGTTTT-C
40084 AAAATTATATATTATATAATTTTCAAAAATGTTTT-
1 AAAATTATATATTATAT-ATTTTCAAAAATGTTTTC
* * *
40119 AAAATTATATATTACATGTTTTCAAAAATGTTTTTT
1 AAAATTATATATTATATATTTTCAAAAATG-TTTTC
* *
40155 TAAA-TATATA-T-TATA-TTT-AAAAATGATTTC
1 AAAATTATATATTATATATTTTCAAAAATGTTTTC
* *
40185 AAAACTATATAATATATATTTTC-AAAATGTTTTC
1 AAAATTATATATTATATATTTTCAAAAATGTTTTC
40219 AAAAATTATATAATATATATATATATAT-ATTAAAATGTTTTC
1 -AAAATTATAT-AT-TATATAT-T-T-TCA--AAAATGTTTTC
* *
40261 AAAAATCATATATTATATATGTTTCCAAAAAAGTTTTCC
1 -AAAATTATATATTATATAT-TTT-CAAAAATGTTTT-C
* *
40300 AAAAATTATATAATATATATTTTCAAAAACCGTTTTC
1 -AAAATTATATATTATATATTTTCAAAAA-TGTTTTC
40337 AAAATTATATA-TATAT
1 AAAATTATATATTATAT
40353 TATATGTATT
Statistics
Matches: 227, Mismatches: 19, Indels: 45
0.78 0.07 0.15
Matches are distributed among these distances:
30 6 0.03
31 13 0.06
32 4 0.02
33 6 0.03
34 42 0.19
35 41 0.18
36 18 0.08
37 24 0.11
38 19 0.08
39 21 0.09
40 10 0.04
41 2 0.01
42 21 0.09
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (35 bp):
AAAATTATATATTATATATTTTCAAAAATGTTTTC
Found at i:40215 original size:77 final size:81
Alignment explanation
Indices: 40134--40319 Score: 219
Period size: 77 Copynumber: 2.4 Consensus size: 81
40124 TATATATTAC
* * *
40134 ATGTTTTCAAAAATGTTTTTTTAA-ATATATAT-TATAT-TTAAAAATGATTTCAAAACT-ATAT
1 ATGTTTTCAAAAA--TTTATATAATATATATATATATATATT-AAAATGATTTCAAAAATCATAT
40195 AATATATAT-TTT-C-AAA
63 AATATATATGTTTCCAAAA
* *
40211 ATGTTTTCAAAAA-TTATATAATATATATATATATATATTAAAATGTTTTCAAAAATCATATATT
1 ATGTTTTCAAAAATTTATATAATATATATATATATATATTAAAATGATTTCAAAAATCATATAAT
40275 ATATATGTTTCCAAAA
66 ATATATGTTTCCAAAA
*
40291 AAGTTTTCCAAAAA-TTATATAATATATAT
1 ATGTTTT-CAAAAATTTATATAATATATAT
40320 TTTCAAAAAC
Statistics
Matches: 95, Mismatches: 6, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
74 6 0.06
75 8 0.08
76 20 0.21
77 27 0.28
78 3 0.03
79 1 0.01
80 9 0.09
81 21 0.22
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (81 bp):
ATGTTTTCAAAAATTTATATAATATATATATATATATATTAAAATGATTTCAAAAATCATATAAT
ATATATGTTTCCAAAA
Found at i:40271 original size:25 final size:26
Alignment explanation
Indices: 40243--40291 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
40233 ATATATATAT
*
40243 ATATATTA-AAATGTTTTCAAAAATC
1 ATATATTATAAATGTTTCCAAAAATC
*
40268 ATATATTATATATGTTTCCAAAAA
1 ATATATTATAAATGTTTCCAAAAA
40292 AGTTTTCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (26 bp):
ATATATTATAAATGTTTCCAAAAATC
Found at i:40279 original size:44 final size:42
Alignment explanation
Indices: 40190--40318 Score: 144
Period size: 42 Copynumber: 3.1 Consensus size: 42
40180 ATTTCAAAAC
*
40190 TATATAATATATATTTTCAAAATGTTTTCAAAAATTATATAA
1 TATATAATATATATATTCAAAATGTTTTCAAAAATTATATAA
*
40232 TATATATATATATATATT-AAAATGTTTTCAAAAATCATAT-A
1 TATATA-ATATATATATTCAAAATGTTTTCAAAAATTATATAA
* * *
40273 T-TAT-ATATGT-T-TCCAAAAAAGTTTTCCAAAAATTATATAA
1 TATATAATATATATATTC-AAAATGTTTT-CAAAAATTATATAA
40313 TATATA
1 TATATA
40319 TTTTCAAAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
36 1 0.01
37 1 0.01
38 14 0.19
39 11 0.15
40 5 0.07
41 5 0.07
42 27 0.36
43 10 0.14
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.43
Consensus pattern (42 bp):
TATATAATATATATATTCAAAATGTTTTCAAAAATTATATAA
Found at i:40297 original size:38 final size:37
Alignment explanation
Indices: 40250--40369 Score: 127
Period size: 38 Copynumber: 3.1 Consensus size: 37
40240 TATATATATT
* *
40250 AAAATGTTTTCAAAAATCATATATTATATATGTTTCCA
1 AAAAAGTTTTCAAAAATTATATATTATATATGTTT-CA
*
40288 AAAAAGTTTTCCAAAAATTATATAATATATAT-TTTCA
1 AAAAAGTTTT-CAAAAATTATATATTATATATGTTTCA
*
40325 AAAACCGTTTTC-AAAATTATATATATATTATATGTATTTCA
1 AAAA-AGTTTTCAAAAATTATATAT-TA-TATATG--TTTCA
40366 AAAA
1 AAAA
40370 CATTCGCAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
36 11 0.16
37 9 0.13
38 22 0.31
39 19 0.27
41 9 0.13
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (37 bp):
AAAAAGTTTTCAAAAATTATATATTATATATGTTTCA
Found at i:40316 original size:79 final size:74
Alignment explanation
Indices: 40155--40320 Score: 210
Period size: 76 Copynumber: 2.2 Consensus size: 74
40145 AATGTTTTTT
* *
40155 TAAATATATATTATATTTAAAAATGATTTCAAAACTATATAATATATATTTTCAAAATGTTTTCA
1 TAAATATATATTATATTTAAAAATGATTTCAAAAATATATAATATATATTTTCAAAAAGTTTTCA
40220 AAAATTATA
66 AAAATTATA
* *
40229 TAATATATATATATATATATT-AAAATGTTTTCAAAAATCATATATTATATATGTTTCCAAAAAA
1 TAA-ATATATAT-TATAT-TTAAAAATGATTTCAAAAAT-ATATAATATATAT-TTT-C-AAAAA
40293 GTTTTCCAAAAATTATA
59 GTTTT-CAAAAATTATA
40310 T-AATATATATT
1 TAAATATATATT
40321 TTCAAAAACC
Statistics
Matches: 80, Mismatches: 4, Indels: 12
0.83 0.04 0.12
Matches are distributed among these distances:
74 3 0.04
75 8 0.10
76 20 0.25
77 14 0.17
78 4 0.05
79 9 0.11
80 10 0.12
81 12 0.15
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (74 bp):
TAAATATATATTATATTTAAAAATGATTTCAAAAATATATAATATATATTTTCAAAAAGTTTTCA
AAAATTATA
Found at i:40319 original size:81 final size:75
Alignment explanation
Indices: 40158--40319 Score: 218
Period size: 81 Copynumber: 2.1 Consensus size: 75
40148 GTTTTTTTAA
* *
40158 ATATATATTATATTTAAAAATGATTTCAAAACTATATAATATATATTTTCAAAATGTTTTCAAAA
1 ATATATATTATATTTAAAAATGATTTCAAAAATATATAATATATATTTTCAAAAAGTTTTCAAAA
40223 ATTATATAAT
66 ATTATATAAT
* *
40233 ATATATATATATATATT-AAAATGTTTTCAAAAATCATATATTATATATGTTTCCAAAAAAGTTT
1 ATATATAT-TATAT-TTAAAAATGATTTCAAAAAT-ATATAATATATAT-TTT-C-AAAAAGTTT
40297 TCCAAAAATTATATAAT
60 T-CAAAAATTATATAAT
40314 ATATAT
1 ATATAT
40320 TTTCAAAAAC
Statistics
Matches: 76, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
75 8 0.11
76 20 0.26
77 14 0.18
78 3 0.04
79 1 0.01
80 9 0.12
81 21 0.28
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (75 bp):
ATATATATTATATTTAAAAATGATTTCAAAAATATATAATATATATTTTCAAAAAGTTTTCAAAA
ATTATATAAT
Found at i:40692 original size:15 final size:15
Alignment explanation
Indices: 40651--40693 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40641 ATAAAATAAT
* *
40651 AAAAAATACATAAAT
1 AAAAAATACAGAAAA
*
40666 ATAAAATA-AGAAAA
1 AAAAAATACAGAAAA
40680 AAAAAATACAGAAA
1 AAAAAATACAGAAA
40694 CAGATGCCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.14
Consensus pattern (15 bp):
AAAAAATACAGAAAA
Found at i:45673 original size:14 final size:15
Alignment explanation
Indices: 45643--45681 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
45633 CAACAGGTTC
45643 GAGTCAACTCAGTCT
1 GAGTCAACTCAGTCT
*
45658 GAGTCAAC-CCGTCT
1 GAGTCAACTCAGTCT
45672 GAGTCAACTC
1 GAGTCAACTC
45682 GTTGACTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.23
Consensus pattern (15 bp):
GAGTCAACTCAGTCT
Found at i:45698 original size:14 final size:14
Alignment explanation
Indices: 45681--45735 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
45671 TGAGTCAACT
45681 CGTTGACTTTGACC
1 CGTTGACTTTGACC
* *
45695 CGTTGATTTTGTCC
1 CGTTGACTTTGACC
*
45709 CGTTTACTTTGA-C
1 CGTTGACTTTGACC
* *
45722 TGTTGATTTTGACC
1 CGTTGACTTTGACC
45736 AAAAAGTCAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
13 10 0.31
14 22 0.69
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (14 bp):
CGTTGACTTTGACC
Found at i:63418 original size:3 final size:3
Alignment explanation
Indices: 63410--63456 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
63400 TTGCATCTTA
* *
63410 ATT ATT ATT ATT ATT ACT GTT ATT ATT ATT ATT ATT ATT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
63457 TTTCTTTCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:65481 original size:39 final size:39
Alignment explanation
Indices: 65437--65511 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
65427 TTTTATTTTA
65437 AAAATATTTAAA-AATTTATTATTTAAAATTTAAATTATG
1 AAAATA-TTAAATAATTTATTATTTAAAATTTAAATTATG
* * * *
65476 AAAATATTAAATTATTTGTTTTTTAAATTTTAAATT
1 AAAATATTAAATAATTTATTATTTAAAATTTAAATT
65512 TAAATAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 5 0.16
39 26 0.84
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (39 bp):
AAAATATTAAATAATTTATTATTTAAAATTTAAATTATG
Found at i:65485 original size:16 final size:15
Alignment explanation
Indices: 65461--65490 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
65451 TTTATTATTT
65461 AAAATTTAAATTATG
1 AAAATTTAAATTATG
65476 AAAATATTAAATTAT
1 AAAAT-TTAAATTAT
65491 TTGTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
AAAATTTAAATTATG
Found at i:65767 original size:21 final size:22
Alignment explanation
Indices: 65720--65797 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 22
65710 TTTGAAAATG
*
65720 ATAAAAATATTAAATTATTATT
1 ATAAAAATATTAAAATATTATT
*
65742 CTAAAAA-ATTAAAAT-TTATT
1 ATAAAAATATTAAAATATTATT
*
65762 A-ATAAAAT-CTAAAATA-TA-T
1 ATA-AAAATATTAAAATATTATT
*
65781 ATAAAAAT-CTAAAATAT
1 ATAAAAATATTAAAATAT
65798 AAAAAATACA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
19 16 0.34
20 18 0.38
21 7 0.15
22 6 0.13
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAAAAATATTAAAATATTATT
Found at i:71398 original size:18 final size:18
Alignment explanation
Indices: 71375--71417 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
71365 TTATTCCTCA
71375 TGTTTCTGTTCCTAGTAC
1 TGTTTCTGTTCCTAGTAC
71393 TGTTTCTGTTCCTAGTAC
1 TGTTTCTGTTCCTAGTAC
71411 TGTTTCT
1 TGTTTCT
71418 ACTAGGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.09, C:0.21, G:0.16, T:0.53
Consensus pattern (18 bp):
TGTTTCTGTTCCTAGTAC
Done.