Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010491.1 Kokia drynarioides strain JFW-HI SEQ_125399, 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: 121634
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Warning! 60 characters in sequence are not A, C, G, or T
Found at i:2040 original size:31 final size:31
Alignment explanation
Indices: 2002--2062 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
1992 AACATTAGCT
2002 TTTCCGGGATAGTAGTCTATAACACAGTCAA
1 TTTCCGGGATAGTAGTCTATAACACAGTCAA
2033 TTTCCGGGATAGTAGTCTATAACACAGTCA
1 TTTCCGGGATAGTAGTCTATAACACAGTCA
2063 TATGGTAGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (31 bp):
TTTCCGGGATAGTAGTCTATAACACAGTCAA
Found at i:2074 original size:23 final size:23
Alignment explanation
Indices: 2044--2087 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2034 TTCCGGGATA
*
2044 GTAGTCTATAACACAGTCATATG
1 GTAGTCTATAACACAATCATATG
2067 GTAGTCTATAACACAATCATA
1 GTAGTCTATAACACAATCATA
2088 ATCTTTTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (23 bp):
GTAGTCTATAACACAATCATATG
Found at i:17704 original size:27 final size:27
Alignment explanation
Indices: 17666--17721 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
17656 CGCTAGAACT
17666 AGCACAAGTACCAGTAGAAATCTGCAC
1 AGCACAAGTACCAGTAGAAATCTGCAC
*
17693 AGCACAAGTACCGGTAGAAATCTGCAC
1 AGCACAAGTACCAGTAGAAATCTGCAC
17720 AG
1 AG
17722 TTTTTGAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.14
Consensus pattern (27 bp):
AGCACAAGTACCAGTAGAAATCTGCAC
Found at i:23258 original size:23 final size:24
Alignment explanation
Indices: 23202--23270 Score: 95
Period size: 23 Copynumber: 2.9 Consensus size: 24
23192 TCATTAACAT
*
23202 TGTTCGTGAACATTTTCAATTATA
1 TGTTCGTGAACATGTTCAATTATA
* *
23226 TGTTCATGAACATGTTCATTTA-A
1 TGTTCGTGAACATGTTCAATTATA
*
23249 TGTTCGTGAACATGTTCGATTA
1 TGTTCGTGAACATGTTCAATTA
23271 AGTTAAATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (24 bp):
TGTTCGTGAACATGTTCAATTATA
Found at i:23271 original size:23 final size:23
Alignment explanation
Indices: 23202--23289 Score: 90
Period size: 23 Copynumber: 3.8 Consensus size: 23
23192 TCATTAACAT
* * *
23202 TGTTCGTGAACATTTTCAATTATA
1 TGTTCATGAACATGTTCGATTA-A
23226 TGTTCATGAACATGTTC-ATTTAA
1 TGTTCATGAACATGTTCGA-TTAA
*
23249 TGTTCGTGAACATGTTCGATTAA
1 TGTTCATGAACATGTTCGATTAA
*
23272 -GTTAAATGAACATGTTCG
1 TGTT-CATGAACATGTTCG
23290 TGAACATTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
22 3 0.05
23 34 0.61
24 19 0.34
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (23 bp):
TGTTCATGAACATGTTCGATTAA
Found at i:23299 original size:23 final size:23
Alignment explanation
Indices: 23255--23301 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
23245 TTAATGTTCG
* *
23255 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
23278 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
23301 T
1 T
23302 AAACGAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:25412 original size:2 final size:2
Alignment explanation
Indices: 25407--25434 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25397 ATTAAAAAAC
25407 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25435 TACTCTACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32352 original size:22 final size:22
Alignment explanation
Indices: 32324--32376 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
32314 CATTAATTTG
32324 TTTGCTCGTTAGTAAAGTCTCA
1 TTTGCTCGTTAGTAAAGTCTCA
32346 TTTGCTCGTTAGTAAAGTCTCA
1 TTTGCTCGTTAGTAAAGTCTCA
*
32368 ATTGCTCGT
1 TTTGCTCGT
32377 GATTTTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (22 bp):
TTTGCTCGTTAGTAAAGTCTCA
Found at i:35768 original size:19 final size:20
Alignment explanation
Indices: 35693--35767 Score: 57
Period size: 20 Copynumber: 3.7 Consensus size: 20
35683 CGAAATCATA
* *
35693 CAAACAATTATGATAGTATAC
1 CAAA-AATTAAGAGAGTATAC
35714 CGAAAAATCTAAGAGAGTA-A-
1 C-AAAAAT-TAAGAGAGTATAC
*
35734 CAAAAAATAAGA-AGATATAC
1 CAAAAATTAAGAGAG-TATAC
*
35754 CAAAAATTATGAGA
1 CAAAAATTAAGAGA
35768 TGATAGAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
17 2 0.05
18 7 0.16
19 6 0.14
20 11 0.26
21 6 0.14
22 11 0.26
ACGTcount: A:0.56, C:0.11, G:0.13, T:0.20
Consensus pattern (20 bp):
CAAAAATTAAGAGAGTATAC
Found at i:36631 original size:20 final size:20
Alignment explanation
Indices: 36577--36633 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
36567 GAGATTACTA
*
36577 AAAAATGTGAG-GAAATATCG
1 AAAAATGTGAGAG-AATAACG
* ** *
36597 GAAAACATGATAGAATAACG
1 AAAAATGTGAGAGAATAACG
36617 AAAAATGTGAGAGAATA
1 AAAAATGTGAGAGAATA
36634 CCAAAAGAAT
Statistics
Matches: 27, Mismatches: 9, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.54, C:0.05, G:0.23, T:0.18
Consensus pattern (20 bp):
AAAAATGTGAGAGAATAACG
Found at i:36666 original size:20 final size:20
Alignment explanation
Indices: 36617--36680 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
36607 TAGAATAACG
* *
36617 AAAAATGTGAGAGAATACCA
1 AAAAATGTAAGGGAATACCA
* *
36637 AAAGAA--TAAGGGCATACTA
1 AAA-AATGTAAGGGAATACCA
36656 AAAAATGTAAGGGAATACCA
1 AAAAATGTAAGGGAATACCA
36676 AAAAA
1 AAAAA
36681 CCATTAGAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 2 0.06
19 12 0.34
20 19 0.54
21 2 0.06
ACGTcount: A:0.58, C:0.09, G:0.19, T:0.14
Consensus pattern (20 bp):
AAAAATGTAAGGGAATACCA
Found at i:36681 original size:79 final size:79
Alignment explanation
Indices: 36572--36718 Score: 179
Period size: 79 Copynumber: 1.9 Consensus size: 79
36562 AATGAGAGAT
* * ** *
36572 TACTAAAAAATGTGAGGAAATATCGGAAAA-CATGATAGAATAACGAAAAATGTGAGAGAATACC
1 TACTAAAAAATGTAAGGAAATACCAAAAAACCATGAGAGAAT-ACGAAAAATGTGAGAGAATACC
36636 AAAAGAATAAGGGCA
65 AAAAGAATAAGGGCA
* * ** * *
36651 TACTAAAAAATGTAAGGGAATACCAAAAAACCATTAGAGAATATTAAAAATGTGAGGGATTACCA
1 TACTAAAAAATGTAAGGAAATACCAAAAAACCATGAGAGAATACGAAAAATGTGAGAGAATACCA
36716 AAA
66 AAA
36719 AAACATGAGG
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 47 0.84
80 9 0.16
ACGTcount: A:0.53, C:0.10, G:0.19, T:0.18
Consensus pattern (79 bp):
TACTAAAAAATGTAAGGAAATACCAAAAAACCATGAGAGAATACGAAAAATGTGAGAGAATACCA
AAAGAATAAGGGCA
Found at i:36709 original size:40 final size:39
Alignment explanation
Indices: 36557--36721 Score: 127
Period size: 40 Copynumber: 4.2 Consensus size: 39
36547 AAAAAATATA
* * * *
36557 AAAAAAATGAGAGATTACTAAAAAATGTGAGGAAATATCG
1 AAAAAAATAAGAGAATACTAAAAAATGTGAGGGAATA-CC
* * * * * *
36597 GAAAACATGATAGAATAAC-GAAAAATGTGAGAGAATACC
1 AAAAAAATAAGAGAAT-ACTAAAAAATGTGAGGGAATACC
* * * *
36636 AAAAGAATAAGGGCATACTAAAAAATGTAAGGGAATACC
1 AAAAAAATAAGAGAATACTAAAAAATGTGAGGGAATACC
* * *
36675 AAAAAACCATTAGAGAATA-TTAAAAATGTGAGGGATTACC
1 AAAAAA--ATAAGAGAATACTAAAAAATGTGAGGGAATACC
36715 AAAAAAA
1 AAAAAAA
36722 CATGAGGATG
Statistics
Matches: 96, Mismatches: 25, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
38 3 0.03
39 32 0.33
40 51 0.53
41 10 0.10
ACGTcount: A:0.55, C:0.08, G:0.19, T:0.18
Consensus pattern (39 bp):
AAAAAAATAAGAGAATACTAAAAAATGTGAGGGAATACC
Found at i:42733 original size:18 final size:19
Alignment explanation
Indices: 42712--42750 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
42702 AAATTGAATT
*
42712 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAA
42730 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTATTTTGAA
42749 TT
1 TT
42751 ATTTTGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:42733 original size:19 final size:20
Alignment explanation
Indices: 42705--42750 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
42695 TTAAAAAAAA
*
42705 TTGAATTTTTTATAAA-TATT
1 TTGAA-TTTTTAAAAATTATT
42725 TTGAA-TTTTAAAAATTATT
1 TTGAATTTTTAAAAATTATT
42744 TTGAATT
1 TTGAATT
42751 ATTTTGTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 8 0.35
19 9 0.39
20 6 0.26
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (20 bp):
TTGAATTTTTAAAAATTATT
Found at i:58489 original size:2 final size:2
Alignment explanation
Indices: 58482--58515 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
58472 CTTAATAAGA
58482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58516 GTATCAACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59156 original size:19 final size:18
Alignment explanation
Indices: 59114--59159 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
59104 ATAATAATAT
* *
59114 TATTAATTTTTTTTTATA
1 TATTAATTTTTTTTAACA
59132 TATTAATTTTTTTTAAACA
1 TATTAATTTTTTTT-AACA
*
59151 TTTTAATTT
1 TATTAATTT
59160 CGCAATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTAATTTTTTTTAACA
Found at i:59853 original size:22 final size:24
Alignment explanation
Indices: 59828--59874 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
59818 AAAATAATAA
*
59828 AAATCTAAATTTTTA-AT-TAAAT
1 AAATATAAATTTTTATATATAAAT
*
59850 AAATATAATTTTTTATATATAAAT
1 AAATATAAATTTTTATATATAAAT
59874 A
1 A
59875 TGATTTTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.62
23 2 0.10
24 6 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATATAAATTTTTATATATAAAT
Found at i:61433 original size:132 final size:132
Alignment explanation
Indices: 61195--61451 Score: 478
Period size: 132 Copynumber: 1.9 Consensus size: 132
61185 AATGAGAGAA
*
61195 AATAAGAATGAATGAAAATATACCTCTAAATGGTAGATGATCAACAATTAAGCACCCTCACACAA
1 AATAAGAATGAATGAAAATATACCTCTAAATGATAGATGATCAACAATTAAGCACCCTCACACAA
*
61260 AGTTACAATAATTGAAAGAATGATAGAAAACTTAACCCACAAGTGTGTATAAGAAATATTAAGAA
66 AGTTACAACAATTGAAAGAATGATAGAAAACTTAACCCACAAGTGTGTATAAGAAATATTAAGAA
61325 AT
131 AT
61327 AATAAGAATGAATGAAAATATACCTCTAAATGATAGATGATCAACAATTAAGCACCCTCACACAA
1 AATAAGAATGAATGAAAATATACCTCTAAATGATAGATGATCAACAATTAAGCACCCTCACACAA
* *
61392 AGTTACAACACTTGAAAGAATGATAGAAAACTTAACTCACAAGTGTGTATAAGAAATATT
66 AGTTACAACAATTGAAAGAATGATAGAAAACTTAACCCACAAGTGTGTATAAGAAATATT
61452 TAGTAAAATA
Statistics
Matches: 121, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 121 1.00
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.24
Consensus pattern (132 bp):
AATAAGAATGAATGAAAATATACCTCTAAATGATAGATGATCAACAATTAAGCACCCTCACACAA
AGTTACAACAATTGAAAGAATGATAGAAAACTTAACCCACAAGTGTGTATAAGAAATATTAAGAA
AT
Found at i:64491 original size:25 final size:25
Alignment explanation
Indices: 64395--64496 Score: 98
Period size: 25 Copynumber: 4.0 Consensus size: 25
64385 ACAGAGTTTA
64395 GCTCTTACGAGCCTAGACAGAATATC
1 GCTCTTACGAGCC-AGACAGAATATC
** * * * *
64421 GCTCTTATAAGCTAGTCATAATATT
1 GCTCTTACGAGCCAGACAGAATATC
* *
64446 GCTCTTACGA-CTTAGATAGAATATC
1 GCTCTTACGAGC-CAGACAGAATATC
*
64471 GGTCTTACGAGCCAGACAGAATATC
1 GCTCTTACGAGCCAGACAGAATATC
64496 G
1 G
64497 TCCTTGTAAC
Statistics
Matches: 59, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
24 1 0.02
25 47 0.80
26 11 0.19
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (25 bp):
GCTCTTACGAGCCAGACAGAATATC
Found at i:64494 original size:50 final size:52
Alignment explanation
Indices: 64382--64494 Score: 124
Period size: 50 Copynumber: 2.2 Consensus size: 52
64372 CATATGAGTG
* *
64382 CAGACAGAGT-TTAGCTCTTACGAGCCTAGACAGAATATCGCTCTTATAAGC
1 CAGACAGAATATTAGCTCTTACGAGCCTAGACAGAATATCGCTCTTACAAGC
* * * * * * *
64433 TAGTCATAATATT-GCTCTTACGA-CTTAGATAGAATATCGGTCTTACGAGC
1 CAGACAGAATATTAGCTCTTACGAGCCTAGACAGAATATCGCTCTTACAAGC
64483 CAGACAGAATAT
1 CAGACAGAATAT
64495 CGTCCTTGTA
Statistics
Matches: 49, Mismatches: 12, Indels: 3
0.77 0.19 0.05
Matches are distributed among these distances:
50 31 0.63
51 16 0.33
52 2 0.04
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (52 bp):
CAGACAGAATATTAGCTCTTACGAGCCTAGACAGAATATCGCTCTTACAAGC
Found at i:67712 original size:27 final size:27
Alignment explanation
Indices: 67652--67767 Score: 114
Period size: 27 Copynumber: 4.4 Consensus size: 27
67642 TCACTTTTAT
*
67652 GAGCCAG-A-CAGAATATCGCTCTTAT-
1 GAGCCAGAATCAGAATAACGCTCTT-TC
* * *
67677 GAACCAGAATCAAAATAACACTCTTTC
1 GAGCCAGAATCAGAATAACGCTCTTTC
* * * *
67704 GA-CATAGAATTAGAATATCGCTCATTC
1 GAGC-CAGAATCAGAATAACGCTCTTTC
67731 GAGCCAGAATCAGAATAACGCTCTTTC
1 GAGCCAGAATCAGAATAACGCTCTTTC
67758 GAGCCAGAAT
1 GAGCCAGAAT
67768 TAGATTACTC
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
25 6 0.08
26 3 0.04
27 62 0.86
28 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.23
Consensus pattern (27 bp):
GAGCCAGAATCAGAATAACGCTCTTTC
Found at i:67767 original size:54 final size:54
Alignment explanation
Indices: 67661--67771 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
67651 TGAGCCAGAC
* *
67661 AGAATATCGCTCTTATGAACCAGAATCAAAATAACACTCTTTCGACATAGAATT
1 AGAATATCGCTCTTACGAACCAGAATCAAAATAACACTCTTTCGACACAGAATT
* * *
67715 AGAATATCGCTCATT-CGAGCCAGAATCAGAATAACGCTCTTTCGAGC-CAGAATT
1 AGAATATCGCTC-TTACGAACCAGAATCAAAATAACACTCTTTCGA-CACAGAATT
67769 AGA
1 AGA
67772 TTACTCCTCA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
54 47 0.94
55 3 0.06
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (54 bp):
AGAATATCGCTCTTACGAACCAGAATCAAAATAACACTCTTTCGACACAGAATT
Found at i:71390 original size:15 final size:15
Alignment explanation
Indices: 71370--71399 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
71360 TTCCTATCGG
71370 TAGAAGTCAAGTCAA
1 TAGAAGTCAAGTCAA
71385 TAGAAGTCAAGTCAA
1 TAGAAGTCAAGTCAA
71400 GTCAACAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGAAGTCAAGTCAA
Found at i:72277 original size:25 final size:25
Alignment explanation
Indices: 72249--72300 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
72239 CAGATTAATG
*
72249 CTCTTATGAGCCAGACAGAATATCA
1 CTCTTACGAGCCAGACAGAATATCA
*
72274 CTCTTACGAGTCAGACAGAATATCA
1 CTCTTACGAGCCAGACAGAATATCA
72299 CT
1 CT
72301 TTTCTCGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (25 bp):
CTCTTACGAGCCAGACAGAATATCA
Found at i:75892 original size:25 final size:25
Alignment explanation
Indices: 75864--75920 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
75854 CAAATTAATG
*
75864 CTCTTACAAGTTAGACAAAATATCA
1 CTCTTACAAGCTAGACAAAATATCA
* * *
75889 CTCTTACAAGCTAGATAGAATATCC
1 CTCTTACAAGCTAGACAAAATATCA
75914 CTCTTAC
1 CTCTTAC
75921 GAGCCAAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.37, C:0.25, G:0.09, T:0.30
Consensus pattern (25 bp):
CTCTTACAAGCTAGACAAAATATCA
Found at i:78092 original size:25 final size:25
Alignment explanation
Indices: 78023--78126 Score: 118
Period size: 25 Copynumber: 4.1 Consensus size: 25
78013 TCATATAAGC
* * *
78023 CCAGACAGAGTTTAGCTCTTACGAG
1 CCAGACAGAATATCGCTCTTACGAG
** *
78048 CCTAGACAGAATATTTCTCTTATGAG
1 CC-AGACAGAATATCGCTCTTACGAG
*
78074 CCAGTCAGAATATCGCTCTTACGAG
1 CCAGACAGAATATCGCTCTTACGAG
* *
78099 CCAAACAGAATATCGCTCTTACAAG
1 CCAGACAGAATATCGCTCTTACGAG
78124 CCA
1 CCA
78127 AAATCAGAAT
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
25 46 0.70
26 20 0.30
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (25 bp):
CCAGACAGAATATCGCTCTTACGAG
Found at i:78127 original size:25 final size:27
Alignment explanation
Indices: 78037--78218 Score: 135
Period size: 27 Copynumber: 6.9 Consensus size: 27
78027 ACAGAGTTTA
* * *
78037 GCTCTTACGAGCCTAGA-CAGAATATT
1 GCTCTTACGAGCCAAAATCAGAATATC
* * *
78063 TCTCTTATGAGCC--AGTCAGAATATC
1 GCTCTTACGAGCCAAAATCAGAATATC
78088 GCTCTTACGAGCC-AAA-CAGAATATC
1 GCTCTTACGAGCCAAAATCAGAATATC
* *
78113 GCTCTTACAAGCCAAAATCAGAATAATG
1 GCTCTTACGAGCCAAAATCAGAAT-ATC
* * * *
78141 GTTTTTTA--ATCCAGAATCAGAATATC
1 G-CTCTTACGAGCCAAAATCAGAATATC
*
78167 GCTCTTTCGAGCCAAAATCAGAATATC
1 GCTCTTACGAGCCAAAATCAGAATATC
* ** * *
78194 ACTCTTTTGAGCCAGAATCAAAATA
1 GCTCTTACGAGCCAAAATCAGAATA
78219 ACTCTCTTTC
Statistics
Matches: 124, Mismatches: 24, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
25 43 0.35
26 18 0.15
27 56 0.45
28 3 0.02
29 4 0.03
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (27 bp):
GCTCTTACGAGCCAAAATCAGAATATC
Found at i:78185 original size:27 final size:27
Alignment explanation
Indices: 78078--78231 Score: 143
Period size: 27 Copynumber: 5.8 Consensus size: 27
78068 TATGAGCCAG
*
78078 TCAGAATATCGCTCTTACGAGCC-AAA
1 TCAGAATATCGCTCTTTCGAGCCAAAA
* *
78104 -CAGAATATCGCTCTTACAAGCCAAAA
1 TCAGAATATCGCTCTTTCGAGCCAAAA
* * ** * *
78130 TCAGAATAAT-GGTTTTTTAATCCAGAA
1 TCAGAAT-ATCGCTCTTTCGAGCCAAAA
78157 TCAGAATATCGCTCTTTCGAGCCAAAA
1 TCAGAATATCGCTCTTTCGAGCCAAAA
* * *
78184 TCAGAATATCACTCTTTTGAGCCAGAA
1 TCAGAATATCGCTCTTTCGAGCCAAAA
* * *
78211 TCAAAATAACTCTCTTTCGAG
1 TCAGAATATCGCTCTTTCGAG
78232 TCAGAATTAG
Statistics
Matches: 104, Mismatches: 20, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
25 21 0.20
26 5 0.05
27 76 0.73
28 2 0.02
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.28
Consensus pattern (27 bp):
TCAGAATATCGCTCTTTCGAGCCAAAA
Found at i:78209 original size:54 final size:54
Alignment explanation
Indices: 78078--78231 Score: 170
Period size: 54 Copynumber: 2.9 Consensus size: 54
78068 TATGAGCCAG
** * *
78078 TCAGAATATCGCTCTTACGAGCCA-AA-CAGAATATCGCTCTTACAAGCCAAAA
1 TCAGAATATCGCTCTTTTGAGCCAGAATCAGAATATCGCTCTTTCGAGCCAAAA
* * * *
78130 TCAGAATAAT-GGTTTTTTAATCCAGAATCAGAATATCGCTCTTTCGAGCCAAAA
1 TCAGAAT-ATCGCTCTTTTGAGCCAGAATCAGAATATCGCTCTTTCGAGCCAAAA
* * * *
78184 TCAGAATATCACTCTTTTGAGCCAGAATCAAAATAACTCTCTTTCGAG
1 TCAGAATATCGCTCTTTTGAGCCAGAATCAGAATATCGCTCTTTCGAG
78232 TCAGAATTAG
Statistics
Matches: 82, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
52 15 0.18
53 6 0.07
54 61 0.74
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.28
Consensus pattern (54 bp):
TCAGAATATCGCTCTTTTGAGCCAGAATCAGAATATCGCTCTTTCGAGCCAAAA
Found at i:79976 original size:27 final size:27
Alignment explanation
Indices: 79933--80001 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
79923 ACTGTATGAT
* *
79933 CTCGTTTTTATTATCCT-AGCGGACTAC
1 CTCGTGTTTAATATCCTGA-CGGACTAC
* *
79960 CTTGTGTTTACTATCCTGACGGACTAC
1 CTCGTGTTTAATATCCTGACGGACTAC
79987 CTCGTGTTTAATATC
1 CTCGTGTTTAATATC
80002 TTGGTGAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
27 35 0.97
28 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.41
Consensus pattern (27 bp):
CTCGTGTTTAATATCCTGACGGACTAC
Found at i:82910 original size:21 final size:20
Alignment explanation
Indices: 82859--82910 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
82849 TAAAAATTTC
*
82859 CTATTATTTTTCCATTTTTTG
1 CTATT-TTTTTCCACTTTTTG
* * *
82880 TTGTTATTTTCTCACTTTTTG
1 CTATTTTTTTC-CACTTTTTG
82901 CTATTTTTTT
1 CTATTTTTTT
82911 ACTACCATTT
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.12, C:0.13, G:0.06, T:0.69
Consensus pattern (20 bp):
CTATTTTTTTCCACTTTTTG
Found at i:90539 original size:30 final size:31
Alignment explanation
Indices: 90480--90563 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 31
90470 CTTTTTTGGG
90480 GTCTAATTTGGTACCTGAACTTGACTTTTTT
1 GTCTAATTTGGTACCTGAACTTGACTTTTTT
***
90511 -TCTAATTTGGTACCT-AATCTTTTTTTTTTT
1 GTCTAATTTGGTACCTGAA-CTTGACTTTTTT
* * *
90541 GTTTAGTTTGGTACTTGAACTTG
1 GTCTAATTTGGTACCTGAACTTG
90564 TCAAACGTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
29 2 0.05
30 24 0.56
31 15 0.35
32 2 0.05
ACGTcount: A:0.18, C:0.13, G:0.15, T:0.54
Consensus pattern (31 bp):
GTCTAATTTGGTACCTGAACTTGACTTTTTT
Found at i:91893 original size:18 final size:18
Alignment explanation
Indices: 91867--91901 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
91857 GGTTTATGAG
*
91867 ATAATTTAAAATATAAAT
1 ATAAATTAAAATATAAAT
*
91885 ATAAATTAAAATTTAAA
1 ATAAATTAAAATATAAA
91902 AAAAAAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAAATTAAAATATAAAT
Found at i:92451 original size:62 final size:62
Alignment explanation
Indices: 92375--92498 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
92365 TCTCGATTGA
92375 GATAATACCTTTCGTTGATAGTTTGAGACCCAACTCTCCTCAACAAAAACAATAATTTATTT
1 GATAATACCTTTCGTTGATAGTTTGAGACCCAACTCTCCTCAACAAAAACAATAATTTATTT
92437 GATAATACCTTTCGTTGATAGTTTGAGACCCAACTCTCCTCAACAAAAACAATAATTTATTT
1 GATAATACCTTTCGTTGATAGTTTGAGACCCAACTCTCCTCAACAAAAACAATAATTTATTT
92499 TTACTTTTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (62 bp):
GATAATACCTTTCGTTGATAGTTTGAGACCCAACTCTCCTCAACAAAAACAATAATTTATTT
Found at i:96680 original size:4 final size:4
Alignment explanation
Indices: 96671--96699 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
96661 TTAAAATTAC
96671 AGTG AGTG AGTG AGTG AGTG AGTG AGTG A
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG A
96700 TACTTACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.48, T:0.24
Consensus pattern (4 bp):
AGTG
Found at i:97305 original size:40 final size:40
Alignment explanation
Indices: 97260--97388 Score: 116
Period size: 40 Copynumber: 3.2 Consensus size: 40
97250 ATTAATCATG
97260 TGACATTATTTTTCTTTAAATCATATGGAAATGATTAATT
1 TGACATTATTTTTCTTTAAATCATATGGAAATGATTAATT
***** * * * * * * *
97300 TGACATT-TTATTAAGGGAAATTATTAAGGACACTTAATCATG
1 TGACATTATT-TTTCTTTAAATCA-TATGGA-AATGATTAATT
97342 TGACATTATTTTTCTTTAAATCATATGGAAATGATTAATT
1 TGACATTATTTTTCTTTAAATCATATGGAAATGATTAATT
97382 TGACATT
1 TGACATT
97389 TTATTAAGGG
Statistics
Matches: 61, Mismatches: 24, Indels: 8
0.66 0.26 0.09
Matches are distributed among these distances:
39 2 0.03
40 27 0.44
41 10 0.16
42 20 0.33
43 2 0.03
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (40 bp):
TGACATTATTTTTCTTTAAATCATATGGAAATGATTAATT
Found at i:97346 original size:82 final size:82
Alignment explanation
Indices: 97251--97417 Score: 325
Period size: 82 Copynumber: 2.0 Consensus size: 82
97241 ATAAATATTA
97251 TTAATCATGTGACATTATTTTTCTTTAAATCATATGGAAATGATTAATTTGACATTTTATTAAGG
1 TTAATCATGTGACATTATTTTTCTTTAAATCATATGGAAATGATTAATTTGACATTTTATTAAGG
97316 GAAATTATTAAGGACAC
66 GAAATTATTAAGGACAC
97333 TTAATCATGTGACATTATTTTTCTTTAAATCATATGGAAATGATTAATTTGACATTTTATTAAGG
1 TTAATCATGTGACATTATTTTTCTTTAAATCATATGGAAATGATTAATTTGACATTTTATTAAGG
*
97398 GAAATTATTAATGACAC
66 GAAATTATTAAGGACAC
97415 TTA
1 TTA
97418 GAAGTATTCA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 84 1.00
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.43
Consensus pattern (82 bp):
TTAATCATGTGACATTATTTTTCTTTAAATCATATGGAAATGATTAATTTGACATTTTATTAAGG
GAAATTATTAAGGACAC
Found at i:102359 original size:129 final size:128
Alignment explanation
Indices: 102130--102370 Score: 295
Period size: 129 Copynumber: 1.9 Consensus size: 128
102120 GCTGTTGTTT
* **
102130 GGTTGAGGATCCACAACCACTCGCAGATAAAGCTGTTAGAGGGATTGCGGACACCCCGTACATAA
1 GGTTGAGGATCCACAACCACTCGCAGATAAAGCTGTCAGAGGGATCACGGACACCCCGTACATAA
*** * *
102195 AGTTGTAGTTGGAATCTACTAAGGTTGTCAATACACAACGAACATTCGATTTTGCAGTATAAA
66 AGTCACAGTTGGAATATACTAAGATTGTCAATACACAACGAACATTCGATTTTGCAGTATAAA
* ** * * *
102258 GGTTGGGGATCCACAACTGCTCGCAGGTAAAAGCTGTCAGAGGGATCATGGACACCCTGTACATA
1 GGTTGAGGATCCACAACCACTCGCAGAT-AAAGCTGTCAGAGGGATCACGGACACCCCGTACATA
* * **
102323 AAGTCACAGTTGGAATATGCTAA-ATCTGTGAATACACAGGGAACATTC
65 AAGTCACAGTTGGAATATACTAAGAT-TGTCAATACACAACGAACATTC
102371 ATCTATACAG
Statistics
Matches: 93, Mismatches: 18, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
128 25 0.27
129 68 0.73
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (128 bp):
GGTTGAGGATCCACAACCACTCGCAGATAAAGCTGTCAGAGGGATCACGGACACCCCGTACATAA
AGTCACAGTTGGAATATACTAAGATTGTCAATACACAACGAACATTCGATTTTGCAGTATAAA
Found at i:106147 original size:103 final size:102
Alignment explanation
Indices: 105862--106135 Score: 403
Period size: 103 Copynumber: 2.7 Consensus size: 102
105852 TTAAGAATAT
* * *
105862 ATTAGTCCTTTTGACGTGAAATTAAATGACAA-CCAAACACTCCATCCCGGTTACTCAGCCCAAT
1 ATTAGCCCTTTTGACGTGAAATGAAATGACAACCCAAACACTCCATCCCGGTTACTCAGTCCAAT
* *
105926 ATACTCCCAATCA--ATTTTCTCTTTTTTTAGAATGT
66 ATACTCCCAATCATTTTTTTCTCTTTTTTTAGAATGC
* * *
105961 ATTAGCCCTTTTGACGTGAAGTGAAATGACAACCCAAACACTCCATCCTGGTTACTCAGTCCAAC
1 ATTAGCCCTTTTGACGTGAAATGAAATGACAACCCAAACACTCCATCCCGGTTACTCAGTCCAAT
106026 ATACTCCCAATCATTTTTTTTCTCTTTTTTTAGAATGC
66 ATACTCCCAATCA-TTTTTTTCTCTTTTTTTAGAATGC
**
106064 ATTAGCCCTTTTGACACGAAATGAAATGACAACCCAAACACTCCATCCCGGTTACTC-GATCCAA
1 ATTAGCCCTTTTGACGTGAAATGAAATGACAACCCAAACACTCCATCCCGGTTACTCAG-TCCAA
*
106128 TACACTCC
65 TATACTCC
106136 TAATTTATTT
Statistics
Matches: 156, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
99 29 0.19
100 42 0.27
102 1 0.01
103 84 0.54
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.31
Consensus pattern (102 bp):
ATTAGCCCTTTTGACGTGAAATGAAATGACAACCCAAACACTCCATCCCGGTTACTCAGTCCAAT
ATACTCCCAATCATTTTTTTCTCTTTTTTTAGAATGC
Found at i:106953 original size:10 final size:10
Alignment explanation
Indices: 106938--106969 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
106928 TAAAACTAAA
106938 AAATAAAAAT
1 AAATAAAAAT
106948 AAAT-AAAAT
1 AAATAAAAAT
106957 AAATAAAAAT
1 AAATAAAAAT
106967 AAA
1 AAA
106970 ATTAGATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:106955 original size:15 final size:15
Alignment explanation
Indices: 106937--106971 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
106927 CTAAAACTAA
106937 AAAATAAA-AATAAAT
1 AAAATAAATAA-AAAT
106952 AAAATAAATAAAAAT
1 AAAATAAATAAAAAT
106967 AAAAT
1 AAAAT
106972 TAGATTATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.89
16 2 0.11
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAATAAATAAAAAT
Found at i:112081 original size:6 final size:6
Alignment explanation
Indices: 112067--112133 Score: 98
Period size: 6 Copynumber: 10.7 Consensus size: 6
112057 AGTGCAAGAA
*
112067 AAAAAT AAAACT AAAAAAT AAAAAT AAAAAT AAAAAAT AAAAAAT AAAAAT
1 AAAAAT AAAAAT -AAAAAT AAAAAT AAAAAT -AAAAAT -AAAAAT AAAAAT
112118 AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAA
112134 TTGGGTTGCC
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
6 39 0.68
7 18 0.32
ACGTcount: A:0.84, C:0.01, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:112084 original size:13 final size:13
Alignment explanation
Indices: 112066--112133 Score: 104
Period size: 13 Copynumber: 5.3 Consensus size: 13
112056 AAGTGCAAGA
*
112066 AAAAAATAAAACT
1 AAAAAATAAAAAT
112079 AAAAAATAAAAAT
1 AAAAAATAAAAAT
112092 -AAAAATAAAAAAT
1 AAAAAAT-AAAAAT
112105 AAAAAATAAAAAT
1 AAAAAATAAAAAT
112118 -AAAAATAAAAAT
1 AAAAAATAAAAAT
112130 AAAA
1 AAAA
112134 TTGGGTTGCC
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
12 18 0.35
13 27 0.53
14 6 0.12
ACGTcount: A:0.84, C:0.01, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:112102 original size:32 final size:32
Alignment explanation
Indices: 112066--112133 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
112056 AAGTGCAAGA
*
112066 AAAAAAT-AAAACTAAAAAATAAAAATAAAAAT
1 AAAAAATAAAAAAT-AAAAATAAAAATAAAAAT
112098 AAAAAATAAAAAATAAAAATAAAAATAAAAAT
1 AAAAAATAAAAAATAAAAATAAAAATAAAAAT
112130 AAAA
1 AAAA
112134 TTGGGTTGCC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 29 0.85
33 5 0.15
ACGTcount: A:0.84, C:0.01, G:0.00, T:0.15
Consensus pattern (32 bp):
AAAAAATAAAAAATAAAAATAAAAATAAAAAT
Found at i:116230 original size:12 final size:12
Alignment explanation
Indices: 116213--116261 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
116203 CAGGTTCTAT
116213 TTCTTCTTTCTC
1 TTCTTCTTTCTC
116225 TTCTTCCTTTC-C
1 TTCTT-CTTTCTC
*
116237 TTCTTCTTTTTC
1 TTCTTCTTTCTC
* *
116249 TTCATCCTTCTC
1 TTCTTCTTTCTC
116261 T
1 T
116262 CGATTACCTC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 4 0.13
12 22 0.71
13 5 0.16
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (12 bp):
TTCTTCTTTCTC
Found at i:119154 original size:6 final size:6
Alignment explanation
Indices: 119145--119216 Score: 60
Period size: 6 Copynumber: 12.3 Consensus size: 6
119135 ATTGATTTTG
** **
119145 AATTTA AATTT- CTTTTA AATTTA AATTT- GTTTTAA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA
* *
119191 AATTTA AATTTA GATTTA TATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AA
119217 ACTTATTATA
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
5 11 0.22
6 37 0.73
7 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (6 bp):
AATTTA
Found at i:119184 original size:35 final size:35
Alignment explanation
Indices: 119112--119217 Score: 110
Period size: 35 Copynumber: 3.0 Consensus size: 35
119102 TTAAACCCAT
*
119112 TTTAAGATTTATTTTAAGA-TTAAA-TTGATTTT-GAA
1 TTTAA-ATTTATTTTAA-ATTTAAATTTG-TTTTAAAA
*
119147 TTTAAATTTCTTTTAAATTTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAATTTAAATTTGTTTTAAAA
* * *
119182 TTTAAATTTAATTTAAATTTAGATTTATATTTAAAA
1 TTTAAATTTATTTTAAATTTAAATTTGT-TTTAAAA
119218 CTTATTATAA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
33 1 0.02
34 19 0.31
35 34 0.56
36 7 0.11
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.54
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTTGTTTTAAAA
Found at i:119207 original size:17 final size:17
Alignment explanation
Indices: 119112--119216 Score: 86
Period size: 17 Copynumber: 6.0 Consensus size: 17
119102 TTAAACCCAT
*
119112 TTTAAGATTTATTTTAAGA
1 TTTAA-ATTTAATTTAA-A
* * *
119131 -TTAAATTGATTTTGAA
1 TTTAAATTTAATTTAAA
**
119147 TTTAAATTTCTTTTAAA
1 TTTAAATTTAATTTAAA
**
119164 TTTAAATTTGTTTTAAAA
1 TTTAAATTTAATTT-AAA
119182 TTTAAATTTAATTTAAA
1 TTTAAATTTAATTTAAA
*
119199 TTTAGATTTATATTTAAA
1 TTTAAATTTA-ATTTAAA
119217 ACTTATTATA
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
16 1 0.01
17 47 0.64
18 26 0.35
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAATTTAAA
Found at i:119213 original size:12 final size:11
Alignment explanation
Indices: 119180--119215 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
119170 TTTGTTTTAA
119180 AATTTAAATTT
1 AATTTAAATTT
119191 AATTTAAATTT
1 AATTTAAATTT
*
119202 AGATTTATATTT
1 A-ATTTAAATTT
119214 AA
1 AA
119216 AACTTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:119886 original size:3 final size:3
Alignment explanation
Indices: 119878--119902 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
119868 TAATAAAGAG
119878 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
119903 TATTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:119907 original size:3 final size:3
Alignment explanation
Indices: 119901--119939 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
119891 AATAATAATA
119901 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
119940 TTAATAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:120355 original size:65 final size:65
Alignment explanation
Indices: 120237--120366 Score: 172
Period size: 65 Copynumber: 2.0 Consensus size: 65
120227 TGTACCAACA
* * * * * *
120237 GGTGACGAACGTCGAAGCATGGTGGTCACGCTCGTCGATCGATGATGCGCGTGCAGCGGAGCCAC
1 GGTGACGAACGTCGAAGCATGGTGGTCACGCGCGCCGATCGACGAGGCACGTGCAGCAGAGCCAC
* *
120302 GGTGACGGACGTCGAAGCATGGTGGTCACGCGCGCCGAAT-GACGAGGTACGTGCAGCAGAGCCA
1 GGTGACGAACGTCGAAGCATGGTGGTCACGCGCGCCG-ATCGACGAGGCACGTGCAGCAGAGCCA
120366 C
65 C
120367 AGTGGCCGGA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 54 0.96
66 2 0.04
ACGTcount: A:0.22, C:0.26, G:0.38, T:0.15
Consensus pattern (65 bp):
GGTGACGAACGTCGAAGCATGGTGGTCACGCGCGCCGATCGACGAGGCACGTGCAGCAGAGCCAC
Found at i:121009 original size:29 final size:30
Alignment explanation
Indices: 120979--121259 Score: 247
Period size: 30 Copynumber: 9.5 Consensus size: 30
120969 TAAATTGTCT
* * * *
120979 AAAAATTACATTTTT-ACCCTCGAGCTTCT
1 AAAAATTCCATTTTTAACCCTCAAACTTCC
* *
121008 AAAAATTCCATTTTTGACCC-CAAAACTTCA
1 AAAAATTCCATTTTTAACCCTC-AAACTTCC
* * **
121038 AAAAAATCCA-CTTTAACCCTTGAACTTCC
1 AAAAATTCCATTTTTAACCCTCAAACTTCC
* *
121067 AAAAGTTCCATTTTTGA-CCTCGAAACTTCC
1 AAAAATTCCATTTTTAACCCTC-AAACTTCC
*
121097 AAAAATTCCA-TTTTAACCCCCAAACTTCC
1 AAAAATTCCATTTTTAACCCTCAAACTTCC
* *
121126 AAAAATTCCATTTTTAACCCTAAAACTTTC
1 AAAAATTCCATTTTTAACCCTCAAACTTCC
121156 AAAAATTCCATTTTTAACCC-CAAAACTTCC
1 AAAAATTCCATTTTTAACCCTC-AAACTTCC
* * *
121186 AAAATTTCCATTTTT-ACCCTCGAACCT-C
1 AAAAATTCCATTTTTAACCCTCAAACTTCC
* * * *
121214 TAAAATATCCAATTTTT-ACCTTAAAACTTTC
1 AAAAAT-TCC-ATTTTTAACCCTCAAACTTCC
121245 AAAAATTACCATTTT
1 AAAAATT-CCATTTT
121260 GCCCTCGAAT
Statistics
Matches: 205, Mismatches: 34, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
28 5 0.02
29 73 0.36
30 119 0.58
31 8 0.04
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.34
Consensus pattern (30 bp):
AAAAATTCCATTTTTAACCCTCAAACTTCC
Found at i:121076 original size:59 final size:58
Alignment explanation
Indices: 120979--121204 Score: 247
Period size: 59 Copynumber: 3.8 Consensus size: 58
120969 TAAATTGTCT
* * * * * *
120979 AAAAATTACATTTTTACCCTCGAGCTTCTAAAAATTCCATTTTTGACCCCAAAACTTC
1 AAAAATTCCATTTTAACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
* * *** * * *
121037 AAAAAAATCCACTTTAACCCTTGAACTTCCAAAAGTTCCATTTTTGACCTCGAAACTTCC
1 -AAAAATTCCATTTTAACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTT-C
* *
121097 AAAAATTCCATTTTAACCCCCAAACTTCCAAAAATTCCATTTTTAACCCTAAAACTTTC
1 AAAAATTCCATTTTAACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAAAAC-TTC
* *
121156 AAAAATTCCATTTTTAACCCCAAAACTTCCAAAATTTCCATTTTT-ACCC
1 AAAAATTCCA-TTTTAACCCCCAAACTTCCAAAAATTCCATTTTTGACCC
121205 TCGAACCTCT
Statistics
Matches: 142, Mismatches: 22, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
59 107 0.75
60 35 0.25
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (58 bp):
AAAAATTCCATTTTAACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTC
Found at i:121094 original size:30 final size:30
Alignment explanation
Indices: 120979--121300 Score: 234
Period size: 30 Copynumber: 10.9 Consensus size: 30
120969 TAAATTGTCT
* * * *
120979 AAAAATTACATTTTTACCCTCG-AGCTTCT
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
* * * *
121008 AAAAATTCCATTTTTGACCCCAAAACTTCA
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
* * *
121038 AAAAAATCCA-CTTTAACCCTTG-AACTTCC
1 AAAAATTCCATTTTTAA-CCTCGAAACTTCC
* *
121067 AAAAGTTCCATTTTTGACCTCGAAACTTCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
* *
121097 AAAAATTCCA-TTTTAACCCCCAAACTTCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
* *
121126 AAAAATTCCATTTTTAACC-CTAAAACTTTC
1 AAAAATTCCATTTTTAACCTC-GAAACTTCC
* *
121156 AAAAATTCCATTTTTAACCCCAAAACTTCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
* * *
121186 AAAATTTCCATTTTTACCCTCG-AACCT-C
1 AAAAATTCCATTTTTAACCTCGAAACTTCC
* ** *
121214 TAAAATATCCAATTTTT-ACCTTAAAACTTTC
1 AAAAAT-TCC-ATTTTTAACCTCGAAACTTCC
**
121245 AAAAATTACCA-TTTTGCCCTCG-AA-TGTCC
1 AAAAATT-CCATTTTTAACCTCGAAACT-TCC
* **
121274 AAAAACTCCATTTTCGACCTCGAAACT
1 AAAAATTCCATTTTTAACCTCGAAACT
121301 CTCGAAATTA
Statistics
Matches: 231, Mismatches: 45, Indels: 32
0.75 0.15 0.10
Matches are distributed among these distances:
28 9 0.04
29 99 0.43
30 113 0.49
31 10 0.04
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.33
Consensus pattern (30 bp):
AAAAATTCCATTTTTAACCTCGAAACTTCC
Found at i:121142 original size:89 final size:87
Alignment explanation
Indices: 120979--121287 Score: 266
Period size: 89 Copynumber: 3.5 Consensus size: 87
120969 TAAATTGTCT
* * * *
120979 AAAAATTACATTTTTACCCTCG-AGCTTCTAAAAATTCCATTTTTGACCCCAAAACTTCAAAAAA
1 AAAAATTCCATTTTTA-CCTCGAAACTTCCAAAAATTCCA-TTTTAACCCCAAAACTTCAAAAAA
**
121043 ATCCACTTTAACCCTTGAACTTCC
64 ATCCACTTTAACCCTAAAACTTCC
* * * *
121067 AAAAGTTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTAACCCCCAAACTTCCAAAAAT
1 AAAAATTCCATTTTT-ACCTCGAAACTTCCAAAAATTCCATTTTAACCCCAAAACTTCAAAAAAA
* *
121132 TCCATTTTTAACCCTAAAACTTTC
65 TCCA-CTTTAACCCTAAAACTTCC
* * * * * * * *
121156 AAAAATTCCATTTTTAACCCCAAAACTTCCAAAATTTCCATTTTTACCCTC-GAACCTCTAAAAT
1 AAAAATTCCATTTTT-ACCTCGAAACTTCCAAAAATTCCATTTTAACCC-CAAAACTTCAAAAAA
* * * *
121220 ATCCAATTTTTACCTTAAAACTTTC
64 ATCC-ACTTTAACCCTAAAACTTCC
** *
121245 AAAAATTACCATTTTGCCCTCG-AA-TGTCCAAAAACTCCATTTT
1 AAAAATT-CCATTTTTACCTCGAAACT-TCCAAAAATTCCATTTT
121288 CGACCTCGAA
Statistics
Matches: 183, Mismatches: 31, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
87 1 0.01
88 60 0.33
89 113 0.62
90 9 0.05
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (87 bp):
AAAAATTCCATTTTTACCTCGAAACTTCCAAAAATTCCATTTTAACCCCAAAACTTCAAAAAAAT
CCACTTTAACCCTAAAACTTCC
Found at i:121205 original size:59 final size:59
Alignment explanation
Indices: 121003--121259 Score: 243
Period size: 59 Copynumber: 4.3 Consensus size: 59
120993 TACCCTCGAG
* * * * ***
121003 CTTCTAAAAATTCCATTTTTGACCCCAAAAC-TTCAAAAAAATCCACTTTAACCCTTGAA
1 CTTCCAAAAATTCCATTTTTGACCCTAAAACTTTC-AAAAATTCCATTTTAACCCCAAAA
* * * *
121062 CTTCCAAAAGTTCCATTTTTGA-CCTCGAAACTTCCAAAAATTCCATTTTAACCCCCAAA
1 CTTCCAAAAATTCCATTTTTGACCCT-AAAACTTTCAAAAATTCCATTTTAACCCCAAAA
*
121121 CTTCCAAAAATTCCATTTTTAACCCTAAAACTTTCAAAAATTCCATTTTTAACCCCAAAA
1 CTTCCAAAAATTCCATTTTTGACCCTAAAACTTTCAAAAATTCCA-TTTTAACCCCAAAA
* ** * * * **
121181 CTTCCAAAATTTCCATTTTT-ACCCTCGAAC-CTCTAAAATATCCAATTTTTACCTTAAAA
1 CTTCCAAAAATTCCATTTTTGACCCTAAAACTTTCAAAAAT-TCC-ATTTTAACCCCAAAA
*
121240 CTTTCAAAAATTACCATTTT
1 CTTCCAAAAATT-CCATTTT
121260 GCCCTCGAAT
Statistics
Matches: 166, Mismatches: 25, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
58 9 0.05
59 112 0.67
60 45 0.27
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (59 bp):
CTTCCAAAAATTCCATTTTTGACCCTAAAACTTTCAAAAATTCCATTTTAACCCCAAAA
Found at i:121276 original size:29 final size:29
Alignment explanation
Indices: 121244--121335 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 29
121234 TTAAAACTTT
121244 CAAAAATTACCATTTTGCCCTCGAATGTC
1 CAAAAATTACCATTTTGCCCTCGAATGTC
* * **
121273 CAAAAACT-CCATTTTCGACCTCGAAACTC
1 CAAAAATTACCATTTT-GCCCTCGAATGTC
* * *
121302 TC-GAAATTACCCTTTTACCCTCGAATGTC
1 -CAAAAATTACCATTTTGCCCTCGAATGTC
*
121331 TAAAA
1 CAAAA
121336 TTTTTTTTTT
Statistics
Matches: 46, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
28 7 0.15
29 32 0.70
30 7 0.15
ACGTcount: A:0.33, C:0.29, G:0.09, T:0.29
Consensus pattern (29 bp):
CAAAAATTACCATTTTGCCCTCGAATGTC
Done.