Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007511.1 Hibiscus syriacus cultivar Beakdansim tig00020894_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: 143478
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:3078 original size:16 final size:16
Alignment explanation
Indices: 3057--3089 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3047 TGAAATAGTG
3057 GGAGCTATCCGTAATA
1 GGAGCTATCCGTAATA
3073 GGAGCTATCCGTAATA
1 GGAGCTATCCGTAATA
3089 G
1 G
3090 AAGATATGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.24
Consensus pattern (16 bp):
GGAGCTATCCGTAATA
Found at i:21391 original size:5 final size:5
Alignment explanation
Indices: 21381--21406 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
21371 AGTCATATAT
21381 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
21407 GAAACATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:35498 original size:255 final size:255
Alignment explanation
Indices: 34851--35613 Score: 1125
Period size: 247 Copynumber: 3.0 Consensus size: 255
34841 CTTTTGTGTT
* *
34851 ATGATGTTCCTCGATGGTCTTCTGTAATGACGTTCTTGTTAATG-C-CTCATCCGACATGCAACA
1 ATGATGTTCCTCGATGCTCTTCTGTAATGACCTTCTTGTTAATGTCTCTCATCCGACATGCAACA
* * *
34914 C-AGAAAACAGTTCATTTTGGTCTTCCTTGCAAAGCAAGACATCCCAAATTCTTGAAGAAAATGT
66 CGA-AAAACAGTTCATTTTGGTCTTCCTTGCAAAGGAAGACATCCCAAATTCATGAACAAAATGT
* * * * * *
34978 TTGATATGTATGCTCAAGAATTAATGAAAACCAACAGCTGATCAATGGGAAACAAGAAACCTACC
130 CTGATATATATGCTCAAGAATGAAGGAAAATCAACAGCTGATCAATGGGAAACAGGAAACCTACC
*
35043 TCCTCCCGGAGGCAACCGAATCGTATTCGGTCCCTCAAGAGGGCACAAGGAACAATGTCTC
195 TCCTCCCGGAGGCAACCGAATCGTATTCGGTCCCTCAGGAGGGCACAAGGAACAATGTCTC
* *
35104 ---A--TT-CTTGATGCTCTTCTGTAATGACCTTCTTGTT-A-GTGTCTCATCCGACATGCAACA
1 ATGATGTTCCTCGATGCTCTTCTGTAATGACCTTCTTGTTAATGTCTCTCATCCGACATGCAACA
* *
35161 CGAAAAACAGTTCATTTTGGTTTTCCTTGCAAAGGAAGACATCCCAAATTCATGAACAAAATGAC
66 CGAAAAACAGTTCATTTTGGTCTTCCTTGCAAAGGAAGACATCCCAAATTCATGAACAAAATGTC
* * * *
35226 TGATATATATGCTCAAGAATGAAGGAAAATCAACAGCTGACCTATGGGAAACAGGACACCTACAT
131 TGATATATATGCTCAAGAATGAAGGAAAATCAACAGCTGATCAATGGGAAACAGGAAACCTACCT
*
35291 CCTCCCGGAGGCAACCGAATCATATTCGGTCCCTCAGGAGGGCACAAGGAACAATGTCTC
196 CCTCCCGGAGGCAACCGAATCGTATTCGGTCCCTCAGGAGGGCACAAGGAACAATGTCTC
* * *
35351 ATGATGTTCCTCGATGCTCTTTTGTAATGACCTTCTTATTAATGTCTCTCATCCGACATACAACA
1 ATGATGTTCCTCGATGCTCTTCTGTAATGACCTTCTTGTTAATGTCTCTCATCCGACATGCAACA
* * *
35416 CGAAAAACAATTCATTTCGGTCTTCCTTGAAAAGGAAGACATCCCAAATTCATGAACAAAATGTC
66 CGAAAAACAGTTCATTTTGGTCTTCCTTGCAAAGGAAGACATCCCAAATTCATGAACAAAATGTC
* *
35481 TGATATATATCCTCAAGAATGAAGGAAAATCAACAGCTGATCAATGGGAAACGGGAAACCTACCT
131 TGATATATATGCTCAAGAATGAAGGAAAATCAACAGCTGATCAATGGGAAACAGGAAACCTACCT
* * * * *
35546 CCTCCCGGAGGCAACCGAATCGTATTCAGCCCCTTAGGAGGGTACAAGGAACAATGTTTC
196 CCTCCCGGAGGCAACCGAATCGTATTCGGTCCCTCAGGAGGGCACAAGGAACAATGTCTC
*
35606 ATTATGTT
1 ATGATGTT
35614 TTTTTTTTCT
Statistics
Matches: 455, Mismatches: 44, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
245 1 0.00
246 1 0.00
247 217 0.48
248 3 0.01
250 2 0.00
252 2 0.00
253 28 0.06
254 1 0.00
255 200 0.44
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (255 bp):
ATGATGTTCCTCGATGCTCTTCTGTAATGACCTTCTTGTTAATGTCTCTCATCCGACATGCAACA
CGAAAAACAGTTCATTTTGGTCTTCCTTGCAAAGGAAGACATCCCAAATTCATGAACAAAATGTC
TGATATATATGCTCAAGAATGAAGGAAAATCAACAGCTGATCAATGGGAAACAGGAAACCTACCT
CCTCCCGGAGGCAACCGAATCGTATTCGGTCCCTCAGGAGGGCACAAGGAACAATGTCTC
Found at i:39044 original size:11 final size:11
Alignment explanation
Indices: 39021--39052 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
39011 TGTAATTAAT
39021 TATTTATATATA
1 TATTTA-ATATA
39033 TATTTAATATA
1 TATTTAATATA
39044 TATTTAATA
1 TATTTAATA
39053 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:39056 original size:3 final size:3
Alignment explanation
Indices: 39048--39094 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
39038 AATATATATT
*
39048 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
39095 TGGATAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:39545 original size:114 final size:114
Alignment explanation
Indices: 39411--39972 Score: 747
Period size: 114 Copynumber: 4.9 Consensus size: 114
39401 TAGAATTATG
* * * *
39411 CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** *
39476 TTATGAACTCTTC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
66 TTATGAACT-TTCTCTGGAAAAATTAATCCATCAAATGATGAATTCAAAC
* *
39525 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
39590 TTATGAACTTTCTCTGGAAAAATTAATTCATCCAGTGATGAATTCAGA-
66 TTATGAACTTTCTCTGGAAAAATTAATCCATCAAATGATGAATTCAAAC
*
39638 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
* ** *
39703 TCATTATGAACTCTTC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
63 TCATTATGAACT-TTCTCTGGAAAAATTAATCCATCAAATGATGAATTCAAAC
* *
39755 CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * **
39820 TTATGAACTTTCTCTGAAAAAAATAATCCATCAATTTGATGAATTC-AGG
66 TTATGAACTTTCTCTGGAAAAATTAATCCATCAA-ATGATGAATTCAAAC
*
39869 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** *
39934 TTATAAACCTTT-TCTGGAAAAGCTAATCTATCAAATGAT
66 TTATGAA-CTTTCTCTGGAAAAATTAATCCATCAAATGAT
39973 AGATTTGAAT
Statistics
Matches: 397, Mismatches: 42, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
113 60 0.15
114 222 0.56
115 14 0.04
116 48 0.12
117 53 0.13
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (114 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAATTAATCCATCAAATGATGAATTCAAAC
Found at i:39748 original size:230 final size:228
Alignment explanation
Indices: 39412--39937 Score: 892
Period size: 230 Copynumber: 2.3 Consensus size: 228
39402 AGAATTATGC
* * * *
39412 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
39477 TATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAACCAAAAAGTTGAACAAGT
66 TATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAACCAAAAAGTTGAACAAAT
*
39542 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGA
* * *
39607 AAAAATTAATTCATCCA-GTGATGAATTCAGAT
196 AAAAAATAATCCATCAATGTGATGAATTCAGAT
39639 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCT
*
39704 CATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAACCAAAAGGTTGAACA
63 CATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAACCAAAAAGTTGAACA
* *
39769 AATTCTTCTTATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
128 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* *
39834 TGAAAAAAATAATCCATCAATTTGATGAATTCAGGT
193 TGAAAAAAATAATCCATCAATGTGATGAATTCAGAT
39870 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
39935 TAT
66 TAT
39938 AAACCTTTTC
Statistics
Matches: 281, Mismatches: 14, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
227 48 0.17
228 16 0.06
230 152 0.54
231 65 0.23
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (228 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAACCAAAAAGTTGAACAAAT
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGA
AAAAAATAATCCATCAATGTGATGAATTCAGAT
Found at i:40583 original size:84 final size:84
Alignment explanation
Indices: 40313--41040 Score: 1252
Period size: 84 Copynumber: 8.7 Consensus size: 84
40303 GTAATTCCTA
*
40313 CCAACCCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCA-TCTTCC
1 CCAA-CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATT-ATTCTTCC
*
40376 ACATTCAATGATTGGTTCTG-
64 AAATTCAATGATTGGTTCTGT
*
40396 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA-CAAATTCA-TCTTCC
1 CC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATT-ATTCTTCC
*
40459 AAACTCAATGATTGGTTCTGT
64 AAATTCAATGATTGGTTCTGT
*
40480 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACACATTATTCTTCCAA
1 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
40545 ATTCAATGATTGGTTCTGT
66 ATTCAATGATTGGTTCTGT
* *
40564 CCAACCAGATCAGATAACTCAAAGAACACTTTCAGAAGATGCTATTGAACACATTATTCTTCCAA
1 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
40629 ATTCAATGATTGGTTCTGT
66 ATTCAATGATTGGTTCTGT
* * *
40648 CCAACCAGATCAGATAACTCAAAGAACACTTCTAAAAGATGCTATTGAGTACATTCA-TCTTCCA
1 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATT-ATTCTTCCA
40712 AATTCAATGATTGGTTCTGT
65 AATTCAATGATTGGTTCTGT
*
40732 CTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
1 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
*
40797 ATTCAATGATTAGTTCTGT
66 ATTCAATGATTGGTTCTGT
*
40816 CTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
1 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
40881 ATTCAATGATTGGTTCTGT
66 ATTCAATGATTGGTTCTGT
40900 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
1 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
40965 ATTCAATGATTGGTTCTGT
66 ATTCAATGATTGGTTCTGT
40984 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTAT
1 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTAT
41041 ATTTGTTCCA
Statistics
Matches: 621, Mismatches: 17, Indels: 13
0.95 0.03 0.02
Matches are distributed among these distances:
83 125 0.20
84 495 0.80
85 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.28
Consensus pattern (84 bp):
CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAA
ATTCAATGATTGGTTCTGT
Found at i:42203 original size:10 final size:10
Alignment explanation
Indices: 42188--42246 Score: 82
Period size: 10 Copynumber: 5.7 Consensus size: 10
42178 TTGACCCCCC
42188 CTTTTTTTTT
1 CTTTTTTTTT
*
42198 CTTTTTTTCT
1 CTTTTTTTTT
42208 CTTTTTTTTTT
1 C-TTTTTTTTT
*
42219 TTTTTTTTTT
1 CTTTTTTTTT
42229 CTTTTTTTTT
1 CTTTTTTTTT
42239 CATTTTTT
1 C-TTTTTT
42247 CTTCAAGCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
10 29 0.67
11 14 0.33
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:42213 original size:21 final size:20
Alignment explanation
Indices: 42188--42248 Score: 86
Period size: 21 Copynumber: 3.0 Consensus size: 20
42178 TTGACCCCCC
42188 CTTTTTTTTTCTTTTTTTCT
1 CTTTTTTTTTCTTTTTTTCT
* *
42208 CTTTTTTTTTTTTTTTTTTTT
1 C-TTTTTTTTTCTTTTTTTCT
*
42229 CTTTTTTTTTCATTTTTTCT
1 CTTTTTTTTTCTTTTTTTCT
42249 TCAAGCATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 17 0.49
21 18 0.51
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.87
Consensus pattern (20 bp):
CTTTTTTTTTCTTTTTTTCT
Found at i:42246 original size:1 final size:1
Alignment explanation
Indices: 42189--42238 Score: 64
Period size: 1 Copynumber: 50.0 Consensus size: 1
42179 TGACCCCCCC
* * * *
42189 TTTTTTTTTCTTTTTTTCTCTTTTTTTTTTTTTTTTTTTTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
42239 CATTTTTTCT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:52932 original size:32 final size:34
Alignment explanation
Indices: 52877--52939 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 34
52867 TGCAAATAAA
*
52877 ATGAAATATTAATAAGAAAATATATATAAATACT
1 ATGAAATATTAATAAGAAAATATATAAAAATACT
* *
52911 ATGAAA-A-TAATAAGTATATATATAAAAAT
1 ATGAAATATTAATAAGAAAATATATAAAAAT
52940 TTTGAAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 19 0.73
33 1 0.04
34 6 0.23
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (34 bp):
ATGAAATATTAATAAGAAAATATATAAAAATACT
Found at i:55068 original size:11 final size:11
Alignment explanation
Indices: 55045--55076 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
55035 TGTAATTAAT
55045 TATTTATATATA
1 TATTTA-ATATA
55057 TATTTAATATA
1 TATTTAATATA
55068 TATTTAATA
1 TATTTAATA
55077 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:55080 original size:3 final size:3
Alignment explanation
Indices: 55072--55124 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
55062 AATATATATT
*
55072 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55120 TAA TA
1 TAA TA
55125 TGGATAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:63599 original size:13 final size:13
Alignment explanation
Indices: 63581--63606 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
63571 ACCAACGCAT
63581 AATCAAATCAATA
1 AATCAAATCAATA
63594 AATCAAATCAATA
1 AATCAAATCAATA
63607 TTTCATAACA
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:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (13 bp):
AATCAAATCAATA
Found at i:63656 original size:25 final size:26
Alignment explanation
Indices: 63585--63658 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 26
63575 ACGCATAATC
*
63585 AAATCAATAAATCAAATCAATATTTCATA
1 AAATTAATAAAT-AAAT--ATATTTCATA
* *
63614 ACATTAATTAATAAATATATTTCA-A
1 AAATTAATAAATAAATATATTTCATA
63639 AAATTAA-AAAT-AATATATTT
1 AAATTAATAAATAAATATATTT
63659 GAATCAATCA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
23 9 0.22
24 3 0.08
25 7 0.17
26 8 0.20
28 4 0.10
29 9 0.22
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.36
Consensus pattern (26 bp):
AAATTAATAAATAAATATATTTCATA
Found at i:64063 original size:29 final size:29
Alignment explanation
Indices: 64020--64076 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
64010 TTGCTTTATG
64020 TTGATAAACAGCTTACTGCTGCAGATACT
1 TTGATAAACAGCTTACTGCTGCAGATACT
* * *
64049 TTGATAAACATCTTAGTGCTGCTGATAC
1 TTGATAAACAGCTTACTGCTGCAGATAC
64077 ATTATTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (29 bp):
TTGATAAACAGCTTACTGCTGCAGATACT
Found at i:64836 original size:28 final size:26
Alignment explanation
Indices: 64797--64850 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
64787 TATCTTGAGA
64797 ATATTCTAAAATAAT-ATAAAAATAAT
1 ATATTCTAAAATAATCAT-AAAATAAT
*
64823 ATATATCTAAAAATATTCATAAAATAAT
1 ATAT-TCT-AAAATAATCATAAAATAAT
64851 CTAGATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.17
27 3 0.12
28 15 0.62
29 2 0.08
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (26 bp):
ATATTCTAAAATAATCATAAAATAAT
Found at i:81566 original size:15 final size:15
Alignment explanation
Indices: 81548--81577 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
81538 CTACAGTGCT
*
81548 ATTAGAACTTGTCAC
1 ATTAGAACTCGTCAC
81563 ATTAGAACTCGTCAC
1 ATTAGAACTCGTCAC
81578 GCCGATGTGA
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:0.33, C:0.23, G:0.13, T:0.30
Consensus pattern (15 bp):
ATTAGAACTCGTCAC
Found at i:82718 original size:14 final size:13
Alignment explanation
Indices: 82691--82715 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
82681 TATAATTCTC
82691 TAAATATTTTTTA
1 TAAATATTTTTTA
82704 TAAATATTTTTT
1 TAAATATTTTTT
82716 TATTTTCACC
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TAAATATTTTTTA
Found at i:86712 original size:24 final size:25
Alignment explanation
Indices: 86663--86712 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
86653 TAAACAATAA
86663 TAATAAACATAATCTAATAATGCAACT
1 TAATAAACATAATC--ATAATGCAACT
86690 TAATAAACATAATC-TAATGCAAC
1 TAATAAACATAATCATAATGCAAC
86713 CTAGAGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.39
27 14 0.61
ACGTcount: A:0.52, C:0.16, G:0.04, T:0.28
Consensus pattern (25 bp):
TAATAAACATAATCATAATGCAACT
Found at i:86924 original size:12 final size:12
Alignment explanation
Indices: 86907--86937 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
86897 ACAACAGTAA
86907 CAGTGCCCGAGC
1 CAGTGCCCGAGC
86919 CAGTGCCCGAGC
1 CAGTGCCCGAGC
86931 CAGTGCC
1 CAGTGCC
86938 AGTTTGCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.42, G:0.32, T:0.10
Consensus pattern (12 bp):
CAGTGCCCGAGC
Found at i:91270 original size:2 final size:2
Alignment explanation
Indices: 91228--91262 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
91218 AAAAAAGGAT
*
91228 TA TA AA 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 TA T
91263 TGATATATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:94327 original size:75 final size:72
Alignment explanation
Indices: 94235--94386 Score: 241
Period size: 75 Copynumber: 2.1 Consensus size: 72
94225 AGTGAAAGTT
*
94235 CTTCAATTTCACCTGAATTTTCTTTCCTATGAGCAGTTTGTACTTCCTCATAGATCTGGTCTTCA
1 CTTCAATTTCACCTGAATTTTCTTTCATATGAGCAGTTTGTACTTCCTCATAGATCTGG---TCA
94300 CCTACATGAG
63 CCTACATGAG
* *
94310 CTTCAATTTCACTTGAATTTTCTTTCATATGAGCAGTTTGTACTTCCTCATTGATCTGGTCACCT
1 CTTCAATTTCACCTGAATTTTCTTTCATATGAGCAGTTTGTACTTCCTCATAGATCTGGTCACCT
*
94375 TCATGAG
66 ACATGAG
94382 CTTCA
1 CTTCA
94387 TCATGATTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
72 17 0.23
75 56 0.77
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.41
Consensus pattern (72 bp):
CTTCAATTTCACCTGAATTTTCTTTCATATGAGCAGTTTGTACTTCCTCATAGATCTGGTCACCT
ACATGAG
Found at i:98156 original size:21 final size:21
Alignment explanation
Indices: 98130--98169 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
98120 AAAAAAAGTC
98130 AGAAGGAAGATAAACTTTACT
1 AGAAGGAAGATAAACTTTACT
98151 AGAAGGAAGATAAACTTTA
1 AGAAGGAAGATAAACTTTA
98170 TTATAGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (21 bp):
AGAAGGAAGATAAACTTTACT
Found at i:104345 original size:7 final size:8
Alignment explanation
Indices: 104324--104350 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
104314 ATAATTTAAT
104324 TTAAAAAA
1 TTAAAAAA
104332 TTAAAAAA
1 TTAAAAAA
104340 TTAAAAAA
1 TTAAAAAA
104348 TTA
1 TTA
104351 TTTTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
TTAAAAAA
Found at i:113779 original size:9 final size:9
Alignment explanation
Indices: 113767--113800 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
113757 GAATTCGGTT
113767 AATTAACCG
1 AATTAACCG
113776 AATTAACCG
1 AATTAACCG
113785 AATTAACCG
1 AATTAACCG
113794 AAATTAA
1 -AATTAA
113801 ATATTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.75
10 6 0.25
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:114326 original size:15 final size:15
Alignment explanation
Indices: 114306--114334 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
114296 AAAAAAAGTT
114306 TGGTTAATTCGGTTA
1 TGGTTAATTCGGTTA
114321 TGGTTAATTCGGTT
1 TGGTTAATTCGGTT
114335 CGGTCGGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (15 bp):
TGGTTAATTCGGTTA
Found at i:115972 original size:150 final size:153
Alignment explanation
Indices: 115698--115975 Score: 411
Period size: 150 Copynumber: 1.8 Consensus size: 153
115688 CCTGATCCTG
* * *
115698 CTGAAGCCGAAGCTAAGGATTTGTGTACCGGATCACTCGTCGCAGAGGAAGAAAACACCACCCTG
1 CTGAAGCCGAAGCTAAGGATTTGAGTACCGGACCACTCGTCGAAGAGGAAGAAAACACCACCCTG
* * * *
115763 GATGGAGGAGTAACACAAGCACATGAAGCTCCTTCTTCCGTTCAAACAGAGGAATCTAAGCAACA
66 GATGGAGGAGTAACACAAACAAAGGAAGCTCCGTCTTCCGTTCAAACAGAGGAATCTAAGCAACA
115828 ACTAATAAAAGAACCCGATCATC
131 ACTAATAAAAGAACCCGATCATC
* * * *
115851 CTGAAGCCTAAGCTAAGGATTTGAGTACCGGACCGCTTGTC-AAGGAGGAAG-AAA-A-CACCTT
1 CTGAAGCCGAAGCTAAGGATTTGAGTACCGGACCACTCGTCGAA-GAGGAAGAAAACACCACCCT
*
115912 GGATGGAGGAGTAACACAAACAAAGGAAGCTCCGTCTTCTGTTCAAACAGAGGAATCTAAGCAA
65 GGATGGAGGAGTAACACAAACAAAGGAAGCTCCGTCTTCCGTTCAAACAGAGGAATCTAAGCAA
115976 TAGCTTACAA
Statistics
Matches: 112, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
150 64 0.57
151 1 0.01
152 4 0.04
153 43 0.38
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (153 bp):
CTGAAGCCGAAGCTAAGGATTTGAGTACCGGACCACTCGTCGAAGAGGAAGAAAACACCACCCTG
GATGGAGGAGTAACACAAACAAAGGAAGCTCCGTCTTCCGTTCAAACAGAGGAATCTAAGCAACA
ACTAATAAAAGAACCCGATCATC
Found at i:117076 original size:39 final size:39
Alignment explanation
Indices: 117022--117101 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
117012 AGTAGATGTC
117022 TGATTCACGCAGCTATTGATGTTAGTGTTCTCTGTCACT
1 TGATTCACGCAGCTATTGATGTTAGTGTTCTCTGTCACT
*
117061 TGATTCACGGAGCTATTGATGTTAGTGTTCTCTGTCACT
1 TGATTCACGCAGCTATTGATGTTAGTGTTCTCTGTCACT
117100 TG
1 TG
117102 TGAGTTGATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (39 bp):
TGATTCACGCAGCTATTGATGTTAGTGTTCTCTGTCACT
Found at i:120045 original size:13 final size:13
Alignment explanation
Indices: 120015--120082 Score: 54
Period size: 11 Copynumber: 5.4 Consensus size: 13
120005 TTTGAAAATA
120015 TTTAAAATATAA-
1 TTTAAAATATAAT
120027 -TTAAAATATAAT
1 TTTAAAATATAAT
120039 TTTAAAATA-AAT
1 TTTAAAATATAAT
* * *
120051 TAT-ATATTTAAT
1 TTTAAAATATAAT
*
120063 ATTTAAATTATCAAT
1 -TTTAAAATAT-AAT
120078 TTTAA
1 TTTAA
120083 TTTATTTTAG
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
11 14 0.33
12 8 0.19
13 10 0.23
14 8 0.19
15 3 0.07
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (13 bp):
TTTAAAATATAAT
Found at i:120054 original size:18 final size:20
Alignment explanation
Indices: 120028--120083 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 20
120018 AAAATATAAT
*
120028 TAAAATATAATTTTAA-A-A
1 TAAATTATAATTTTAATATA
*
120046 TAAATTAT-ATATTTAATATT
1 TAAATTATAAT-TTTAATATA
120066 TAAATTATCAATTTTAAT
1 TAAATTAT-AATTTTAAT
120084 TTATTTTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 2 0.06
18 12 0.39
19 1 0.03
20 8 0.26
21 6 0.19
22 2 0.06
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TAAATTATAATTTTAATATA
Found at i:120062 original size:24 final size:25
Alignment explanation
Indices: 120011--120078 Score: 77
Period size: 24 Copynumber: 2.7 Consensus size: 25
120001 TTATTTTGAA
120011 AATATTTAAAATATAATTAAAATAT
1 AATATTTAAAATATAATTAAAATAT
* *
120036 AAT-TTTAAAATA-AATTATATATTT
1 AATATTTAAAATATAATTA-AAATAT
*
120060 AATATTTAAATTATCAATT
1 AATATTTAAAATAT-AATT
120079 TTAATTTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 5 0.14
24 16 0.44
25 11 0.31
27 4 0.11
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (25 bp):
AATATTTAAAATATAATTAAAATAT
Found at i:122538 original size:20 final size:22
Alignment explanation
Indices: 122500--122554 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
122490 TTATTATTTT
*
122500 TTAATATTTTTT-TGATAAAAAA
1 TTAATATTTTTTAT-TTAAAAAA
*
122522 TT-AT-TTTTTTATTTAAAATA
1 TTAATATTTTTTATTTAAAAAA
122542 TTAATATTTTTTA
1 TTAATATTTTTTA
122555 ATATTTTCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 14 0.50
21 5 0.18
22 9 0.32
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTAATATTTTTTATTTAAAAAA
Found at i:122539 original size:19 final size:19
Alignment explanation
Indices: 122504--122554 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 19
122494 TATTTTTTAA
122504 TATTTTTTTGATAAAAA-AT
1 TATTTTTTT-ATAAAAATAT
*
122523 TATTTTTTTATTTAAAATAT
1 TATTTTTTTA-TAAAAATAT
122543 TAATATTTTTTA
1 T-AT-TTTTTTA
122555 ATATTTTCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 1 0.04
19 14 0.52
20 3 0.11
21 2 0.07
22 7 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TATTTTTTTATAAAAATAT
Found at i:122678 original size:21 final size:21
Alignment explanation
Indices: 122652--122691 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
122642 TAAAGCGCCC
*
122652 AATAATAATGTTTTCGGTAGA
1 AATAATAATGTTTTAGGTAGA
122673 AATAATAATGTTTTAGGTA
1 AATAATAATGTTTTAGGTA
122692 ATTTTTTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (21 bp):
AATAATAATGTTTTAGGTAGA
Found at i:123166 original size:17 final size:17
Alignment explanation
Indices: 123130--123169 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
123120 AAATATTTAA
123130 TAAAAATATAAAAGTATT
1 TAAAAATATAAAAG-ATT
123148 TAAAATATATAAAAG-TT
1 TAAAA-ATATAAAAGATT
123165 TAAAA
1 TAAAA
123170 CTTTTAAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.33
18 5 0.24
19 9 0.43
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
TAAAAATATAAAAGATT
Found at i:129093 original size:60 final size:60
Alignment explanation
Indices: 128961--129094 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
128951 ATTAGGCACT
* * * *
128961 GGATTTGTCACTGGTGTGCTCAATGGGACTCCTCCAGCCGGGGCAGGATACGTAGTTACA
1 GGATTCGTCACCGGTGTGCTCAACGGGACTCCTCCAGCCGGCGCAGGATACGTAGTTACA
* * * * * * *
129021 GGATTCGCCACCGGTGTGCTCACCGGGACTCCTCCAGTCGGCGCGGGGTACGTCGTTACC
1 GGATTCGTCACCGGTGTGCTCAACGGGACTCCTCCAGCCGGCGCAGGATACGTAGTTACA
*
129081 GGATTCTTCACCGG
1 GGATTCGTCACCGG
129095 CTGCTGCGCC
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.16, C:0.29, G:0.32, T:0.23
Consensus pattern (60 bp):
GGATTCGTCACCGGTGTGCTCAACGGGACTCCTCCAGCCGGCGCAGGATACGTAGTTACA
Found at i:129737 original size:2 final size:2
Alignment explanation
Indices: 129730--129764 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
129720 ATCGTAGTGA
129730 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
129765 AAGAAAAGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:130248 original size:2 final size:2
Alignment explanation
Indices: 130243--130293 Score: 56
Period size: 2 Copynumber: 27.5 Consensus size: 2
130233 TTTTATTTTT
* *
130243 TA TA TA TT TA TA T- TT TA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
130283 TA T- TA T- TA TA T
1 TA TA TA TA TA TA T
130294 TTTTTATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
1 4 0.10
2 38 0.90
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (2 bp):
TA
Found at i:130306 original size:9 final size:10
Alignment explanation
Indices: 130291--130319 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
130281 TATATTATTA
130291 TATTTTTTAT
1 TATTTTTTAT
130301 TATTTTTTAT
1 TATTTTTTAT
130311 T-TTTTTTAT
1 TATTTTTTAT
130320 AGGCACCCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (10 bp):
TATTTTTTAT
Found at i:133407 original size:14 final size:14
Alignment explanation
Indices: 133388--133441 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
133378 CACAATTCAC
133388 AATCTTAAACCATA
1 AATCTTAAACCATA
133402 AATCTTAAACTCA-A
1 AATCTTAAAC-CATA
*
133416 AATTTTAAACC-TCA
1 AATCTTAAACCAT-A
*
133430 AATCATAAACCA
1 AATCTTAAACCA
133442 CACACACACT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 1 0.03
14 30 0.91
15 2 0.06
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (14 bp):
AATCTTAAACCATA
Found at i:133474 original size:21 final size:20
Alignment explanation
Indices: 133450--133496 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
133440 CACACACACA
* *
133450 CTAAAACTTAAATTTTAAACT
1 CTAAAACCTAAATTTT-AACC
*
133471 CTAAACCCTAAATTTTAACC
1 CTAAAACCTAAATTTTAACC
133491 CTAAAA
1 CTAAAA
133497 ATATTATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (20 bp):
CTAAAACCTAAATTTTAACC
Found at i:135725 original size:4 final size:4
Alignment explanation
Indices: 135716--135746 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
135706 ATATGCATGT
*
135716 ATAA ATAA ATAA ATGA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
135747 GTTGAACAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:137456 original size:14 final size:15
Alignment explanation
Indices: 137423--137460 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
137413 TATAACTTTT
*
137423 TTTAAATTATTAATA
1 TTTAATTTATTAATA
*
137438 TTTAATTTATTCATA
1 TTTAATTTATTAATA
137453 -TTAATTTA
1 TTTAATTTA
137461 AATTAAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAATTTATTAATA
Found at i:142351 original size:6 final size:6
Alignment explanation
Indices: 142337--143096 Score: 1004
Period size: 6 Copynumber: 132.0 Consensus size: 6
142327 TATGAATCAC
* * * *
142337 CATATA CATACA CATACA CATACA CATACA CATATA CATATA CATATA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
* * * * * * *
142385 CATATA CAT--A CATATA CATATA CATATA CATATA CATATA CATATA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
* * * * * *
142431 CATATA CATATA CATATA CATATA CATATA CATATA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
142479 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
142527 CATACA C--A-A CATACA CATACA CATACA C-TACA CATACA CATTACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CA-TACA
142572 C--ACA CATACATA CATACA C-TA-A CATACA C--AC- CATACA CATACA
1 CATACA CATAC--A CATACA CATACA CATACA CATACA CATACA CATACA
*
142615 CATACA CATACA CA-AAA CAT--A CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
142660 CATACA CATACA CATACA CATACA C-TACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
142707 CATACA CATACA CA-ACA CATACCA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATA-CA CATACA CATACA CATACA CATACA
142755 C-TACA CAT--A CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
142800 C-TACA CATACA CATACA CATACA CATACA CATACA CATA-A CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
142846 -A-AC- CATACA CATACACA CATACA CATACA -ATACA CATACA CATACA
1 CATACA CATACA CAT--ACA CATACA CATACA CATACA CATACA CATACA
142892 CATACA CCA-A-A CATACA CATACA CATACA CATACA CATACA CA-ACA
1 CATACA -CATACA CATACA CATACA CATACA CATACA CATACA CATACA
142938 CATACA CATACA -ATACA CATACA CATACA CATACA CATACA C-TACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
142984 CATACA CATACA CAT--A CATACA CATACA CATACA C-TACA CATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
143029 C-TACA CATACA CATACA CATACA CAT--A CATACA CATACA CATAC-
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
* *
143073 CATACA CATACA TACACA CATACA
1 CATACA CATACA CATACA CATACA
143097 ACACCATATA
Statistics
Matches: 700, Mismatches: 8, Indels: 92
0.88 0.01 0.12
Matches are distributed among these distances:
3 3 0.00
4 34 0.05
5 81 0.12
6 557 0.80
7 13 0.02
8 12 0.02
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (6 bp):
CATACA
Done.