Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011258.1 Kokia drynarioides strain JFW-HI SEQ_126237, 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: 131458
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 85 characters in sequence are not A, C, G, or T
Found at i:5271 original size:163 final size:163
Alignment explanation
Indices: 4990--5295 Score: 585
Period size: 163 Copynumber: 1.9 Consensus size: 163
4980 CAAATTCGGA
*
4990 TAGAGCTTATAAATGTTACCTCTTAGTCATGTTTGAACCTTCATATTTCTTCTTCATGGAATCTT
1 TAGAACTTATAAATGTTACCTCTTAGTCATGTTTGAACCTTCATATTTCTTCTTCATGGAATCTT
*
5055 ATATTTGTTTGGAAGTGTCTTTACAAAGAATAGTTTCCAAGATTCTACGATCAATTGCTTGGAAA
66 ATATTTGTTTAGAAGTGTCTTTACAAAGAATAGTTTCCAAGATTCTACGATCAATTGCTTGGAAA
5120 AGATAATTCTTTTCTTTGAGATCTTTCGGATTG
131 AGATAATTCTTTTCTTTGAGATCTTTCGGATTG
5153 TAGAACTTATAAATGTTACCTCTTAGTCATGTTTGAACCTTCATATTTCTTCTTCATGGAATCTT
1 TAGAACTTATAAATGTTACCTCTTAGTCATGTTTGAACCTTCATATTTCTTCTTCATGGAATCTT
*
5218 ATATTTGTTTAGAAGTGTCTTTACAAAGAATAGTTTCCAAGATTCTGCGATCAATTGCTTGGAAA
66 ATATTTGTTTAGAAGTGTCTTTACAAAGAATAGTTTCCAAGATTCTACGATCAATTGCTTGGAAA
5283 AGATAATTCTTTT
131 AGATAATTCTTTT
5296 TTTTTTTTTG
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
163 140 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (163 bp):
TAGAACTTATAAATGTTACCTCTTAGTCATGTTTGAACCTTCATATTTCTTCTTCATGGAATCTT
ATATTTGTTTAGAAGTGTCTTTACAAAGAATAGTTTCCAAGATTCTACGATCAATTGCTTGGAAA
AGATAATTCTTTTCTTTGAGATCTTTCGGATTG
Found at i:7984 original size:17 final size:17
Alignment explanation
Indices: 7964--8028 Score: 94
Period size: 17 Copynumber: 3.8 Consensus size: 17
7954 ATTAAATATA
7964 AAAATAAATTTAAATTT
1 AAAATAAATTTAAATTT
* * *
7981 AAAATGAGTTTAAATTC
1 AAAATAAATTTAAATTT
7998 AAAATAAATTTAAATTT
1 AAAATAAATTTAAATTT
*
8015 AAACTAAATTTAAA
1 AAAATAAATTTAAA
8029 AATAAATTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (17 bp):
AAAATAAATTTAAATTT
Found at i:8013 original size:6 final size:6
Alignment explanation
Indices: 7968--8046 Score: 56
Period size: 6 Copynumber: 13.7 Consensus size: 6
7958 AATATAAAAA
* * * * *
7968 TAAATT TAAATT TAAA-A TGAGTT TAAATT CAAA-A TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* ** *
8014 TAAA-C TAAATT TAAAAA TAAATT AAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
8047 AAAAGGGTAA
Statistics
Matches: 52, Mismatches: 18, Indels: 6
0.68 0.24 0.08
Matches are distributed among these distances:
5 9 0.17
6 43 0.83
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (6 bp):
TAAATT
Found at i:8027 original size:34 final size:35
Alignment explanation
Indices: 7955--8034 Score: 108
Period size: 34 Copynumber: 2.3 Consensus size: 35
7945 TAATTTTTAA
* *
7955 TTAAATATAAAAATAAATTTAAATTTAAAATGAGT
1 TTAAATATAAAAATAAATTTAAATTTAAAATAAAT
* *
7990 TTAAAT-TCAAAATAAATTTAAATTTAAACTAAAT
1 TTAAATATAAAAATAAATTTAAATTTAAAATAAAT
*
8024 TTAAAAATAAA
1 TTAAATATAAA
8035 TTAAAATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 29 0.76
35 9 0.24
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (35 bp):
TTAAATATAAAAATAAATTTAAATTTAAAATAAAT
Found at i:8034 original size:17 final size:17
Alignment explanation
Indices: 8002--8048 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
7992 AAATTCAAAA
**
8002 TAAATTTAAATTTAAAC
1 TAAATTTAAAAATAAAC
*
8019 TAAATTTAAAAATAAAT
1 TAAATTTAAAAATAAAC
8036 TAAAATTTAAAAA
1 T-AAATTTAAAAA
8049 AAGGGTAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAATTTAAAAATAAAC
Found at i:12249 original size:21 final size:22
Alignment explanation
Indices: 12223--12264 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
12213 ATTAGTGCAA
12223 TATTTTAA-TATATTTT-TTTTG
1 TATTTTAACTA-ATTTTATTTTG
12244 TATTTTAACTAATTTTATTTT
1 TATTTTAACTAATTTTATTTT
12265 TTTTATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TATTTTAACTAATTTTATTTTG
Found at i:19101 original size:20 final size:20
Alignment explanation
Indices: 19069--19121 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
19059 TCTCTCTCAA
19069 CAAAAATTACAAAATAATTT-T
1 CAAAAATT-CAAAAT-ATTTAT
19090 CAAAAATTCAAAATATTTAT
1 CAAAAATTCAAAATATTTAT
19110 -AAAAATTTCAAA
1 CAAAAA-TTCAAA
19122 TTTTATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.30
20 13 0.43
21 8 0.27
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.32
Consensus pattern (20 bp):
CAAAAATTCAAAATATTTAT
Found at i:19122 original size:26 final size:26
Alignment explanation
Indices: 19093--19143 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
19083 TAATTTTCAA
19093 AAATTCAAAATATTTATAAAAATTTC
1 AAATTCAAAATATTTATAAAAATTTC
** * *
19119 AAATTTTATATATTTTTAAAAATTT
1 AAATTCAAAATATTTATAAAAATTT
19144 ATAAAAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (26 bp):
AAATTCAAAATATTTATAAAAATTTC
Found at i:19152 original size:11 final size:10
Alignment explanation
Indices: 19135--19181 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
19125 TATATATTTT
*
19135 TAAAAATTTA
1 TAAAAAATTA
19145 TAAAAAATTA
1 TAAAAAATTA
* *
19155 -ATAAAATTC
1 TAAAAAATTA
19164 TAAAAAATATA
1 TAAAAAAT-TA
19175 TAAAAAA
1 TAAAAAA
19182 AAGTTGAGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
9 7 0.23
10 15 0.50
11 8 0.27
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:20420 original size:25 final size:23
Alignment explanation
Indices: 20375--20436 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 23
20365 ATAAAGGAAG
*
20375 AAAAATAATAATAATGGAAAA-AA
1 AAAAAGAA-AATAATGGAAAAGAA
*
20398 ATAAAGAGAGAAATAATGTAAAAGAA
1 A-AAA-AGA-AAATAATGGAAAAGAA
20424 AAAAAGAAAATAA
1 AAAAAGAAAATAA
20437 AAGAGTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
23 7 0.21
24 6 0.18
25 16 0.48
26 4 0.12
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.15
Consensus pattern (23 bp):
AAAAAGAAAATAATGGAAAAGAA
Found at i:21140 original size:19 final size:20
Alignment explanation
Indices: 21118--21160 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
21108 TTAGTACAGT
21118 AAAATAAAATTATAT-TTTAA
1 AAAATAAAA-TATATCTTTAA
21138 AAAATAAAATATATGCTTTAA
1 AAAATAAAATATAT-CTTTAA
21159 AA
1 AA
21161 TTAAAACACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 9 0.43
21 7 0.33
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAATAAAATATATCTTTAA
Found at i:29363 original size:135 final size:136
Alignment explanation
Indices: 29120--29406 Score: 540
Period size: 135 Copynumber: 2.1 Consensus size: 136
29110 GGTGATATTG
*
29120 GTTCGGTTTCATTATTATTATTATTTTTTATAATTTTTATATGTTTATCATAATTTGGTTTCATG
1 GTTCGGTTTCATTATTATTATTATTTTTTATAATTTTTATATGTTTATCATAATTTGGTTTCATA
*
29185 ATAAACATAATTCTGTTTGGCTTCCAGTAATCTCAGATTTTAAATTTACATTCTATAAATCAATT
66 ATAAACATAATTCTGTTTGGCTTCCAGTAATCTCAAATTTTAAATTTACATTCTATAAATCAATT
29250 TCTTCA
131 TCTTCA
29256 GTTCGGTTTCATTATTATTATT-TTTTTTATAATTTTTATATGTTTATCATAATTTGGTTTCATA
1 GTTCGGTTTCATTATTATTATTATTTTTTATAATTTTTATATGTTTATCATAATTTGGTTTCATA
*
29320 ATAAACATAATTCTGTTTGGCTTCCAGTAATCTCAAATTTTAAATTTACATTCTATAAGTCAATT
66 ATAAACATAATTCTGTTTGGCTTCCAGTAATCTCAAATTTTAAATTTACATTCTATAAATCAATT
29385 TCTTCA
131 TCTTCA
29391 GTTCGGTTTCATTATT
1 GTTCGGTTTCATTATT
29407 TTCGATTTAA
Statistics
Matches: 148, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
135 126 0.85
136 22 0.15
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.51
Consensus pattern (136 bp):
GTTCGGTTTCATTATTATTATTATTTTTTATAATTTTTATATGTTTATCATAATTTGGTTTCATA
ATAAACATAATTCTGTTTGGCTTCCAGTAATCTCAAATTTTAAATTTACATTCTATAAATCAATT
TCTTCA
Found at i:41924 original size:37 final size:38
Alignment explanation
Indices: 41874--41963 Score: 119
Period size: 39 Copynumber: 2.4 Consensus size: 38
41864 AGTAGGAATT
* ** *
41874 GATGTAATGAAATTAAAATTGT-GTACCCTAATGTTGG
1 GATGTAATGAAATTAAAATTATAAAACCCTAATGTTGA
41911 GATGTAATGAAATTAAAATTATAAAAACCCTAATGTTGA
1 GATGTAATGAAATTAAAATTAT-AAAACCCTAATGTTGA
*
41950 GATGTGATGAAATT
1 GATGTAATGAAATT
41964 GGAACACTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 21 0.46
39 25 0.54
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (38 bp):
GATGTAATGAAATTAAAATTATAAAACCCTAATGTTGA
Found at i:42107 original size:2 final size:2
Alignment explanation
Indices: 42100--42126 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42090 TAATAAAAGA
42100 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 A
42127 AATAAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45617 original size:3 final size:3
Alignment explanation
Indices: 45609--45633 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
45599 TCAAATCCAA
45609 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
45634 CATTCTTTTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:58242 original size:2 final size:2
Alignment explanation
Indices: 58235--58279 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
58225 AATCCTTAAA
58235 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58277 AT A
1 AT A
58280 CTCATCTTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:63182 original size:2 final size:2
Alignment explanation
Indices: 63175--63207 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
63165 TTTAGATTTA
*
63175 TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
63208 TTTGACATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:77334 original size:21 final size:22
Alignment explanation
Indices: 77294--77336 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
77284 CAGCAACTGA
*
77294 TTTTAAAATTATTAAAATTATT
1 TTTTAAAATTAATAAAATTATT
*
77316 TTTTAAAA-TAATAACATTATT
1 TTTTAAAATTAATAAAATTATT
77337 AAATAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAAAATTAATAAAATTATT
Found at i:78328 original size:31 final size:30
Alignment explanation
Indices: 78285--78358 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
78275 ATTAAAATTA
*
78285 TTTAATAATTTTATTATTTCAAAAAAATATT
1 TTTAATAATTTTA-TATTTCAAAAAAATAAT
* **
78316 TTTAATATTTTTATATTTTTAAAAAATAAT
1 TTTAATAATTTTATATTTCAAAAAAATAAT
78346 TTTAATAATTTTA
1 TTTAATAATTTTA
78359 AAATTATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 26 0.68
31 12 0.32
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (30 bp):
TTTAATAATTTTATATTTCAAAAAAATAAT
Found at i:79182 original size:21 final size:21
Alignment explanation
Indices: 79134--79183 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
79124 TCCGAAGTTC
* *
79134 AAGATATAGGGTTCATGATTA
1 AAGATTTAGGGTTCAAGATTA
* * *
79155 AAAATTTAGGGTTCAAGGTTT
1 AAGATTTAGGGTTCAAGATTA
79176 AAGATTTA
1 AAGATTTA
79184 AAATTTAAGG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (21 bp):
AAGATTTAGGGTTCAAGATTA
Found at i:79202 original size:28 final size:28
Alignment explanation
Indices: 79140--79205 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
79130 GTTCAAGATA
* *
79140 TAGGGTTCATGATTAAAAATTTAGGGTT
1 TAGGGTTCAAGATTAAAAATTTAAGGTT
* * * *
79168 CAAGGTTTAAGATTTAAAATTTAAGGTT
1 TAGGGTTCAAGATTAAAAATTTAAGGTT
79196 TAGGGTTCAA
1 TAGGGTTCAA
79206 AGATCAAGGT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.38
Consensus pattern (28 bp):
TAGGGTTCAAGATTAAAAATTTAAGGTT
Found at i:81641 original size:30 final size:30
Alignment explanation
Indices: 81599--81684 Score: 104
Period size: 30 Copynumber: 2.8 Consensus size: 30
81589 TATATAATTA
81599 AAATTAAAAAAAATTAATAAAGAA-AAAACT-
1 AAATTAAAAAAAA-TAATAAA-AATAAAACTG
* *
81629 AAAGTTAAAAAAACTAATAAAAATAAAATTG
1 AAA-TTAAAAAAAATAATAAAAATAAAACTG
*
81660 AAATTAAAAAAAATAATTAAAATAA
1 AAATTAAAAAAAATAATAAAAATAA
81685 GTCATCTATA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
29 2 0.04
30 35 0.71
31 12 0.24
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.22
Consensus pattern (30 bp):
AAATTAAAAAAAATAATAAAAATAAAACTG
Found at i:85356 original size:24 final size:24
Alignment explanation
Indices: 85329--85374 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
85319 GGTTAATGAA
* * *
85329 TAAAAAATGAAAATAATTATATTT
1 TAAAAAATAAAAAAAATAATATTT
85353 TAAAAAATAAAAAAAATAATAT
1 TAAAAAATAAAAAAAATAATAT
85375 GGACAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (24 bp):
TAAAAAATAAAAAAAATAATATTT
Found at i:86039 original size:7 final size:7
Alignment explanation
Indices: 86027--86052 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
86017 TTTTAAATAT
86027 ATTTTGA
1 ATTTTGA
86034 ATTTTGA
1 ATTTTGA
86041 ATTTTGA
1 ATTTTGA
86048 ATTTT
1 ATTTT
86053 TTTTGCTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.62
Consensus pattern (7 bp):
ATTTTGA
Found at i:91061 original size:32 final size:31
Alignment explanation
Indices: 91025--91112 Score: 117
Period size: 29 Copynumber: 2.8 Consensus size: 31
91015 TAATTCAATA
91025 TTTAATTAATTTTTTAAATTTTAAAAAATAAT
1 TTTAA-TAATTTTTTAAATTTTAAAAAATAAT
* *
91057 TTTAATGA-TTTTT-AATTTTTAAAAATAAT
1 TTTAATAATTTTTTAAATTTTAAAAAATAAT
91086 TTTAATATATTTTTTGAAATTTTAAAA
1 TTTAATA-ATTTTTT-AAATTTTAAAA
91113 TTTTAAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 21 0.44
30 6 0.12
31 7 0.15
32 5 0.10
33 9 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (31 bp):
TTTAATAATTTTTTAAATTTTAAAAAATAAT
Found at i:92671 original size:3 final size:3
Alignment explanation
Indices: 92663--92692 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
92653 AAACCTTCTG
92663 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
92693 CAAAAGATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:95427 original size:6 final size:6
Alignment explanation
Indices: 95418--95464 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
95408 CAAATTTATT
* * *
95418 TTTAAA TTTAAA TTT-AT TTTAAA TTTCAA TTT-AA TTAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
95464 T
1 T
95465 AGATTTAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
5 8 0.24
6 26 0.76
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:95439 original size:17 final size:17
Alignment explanation
Indices: 95409--95464 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
95399 AAATTGATTC
95409 AAATTTATTTTTAAATTT
1 AAATTTA-TTTTAAATTT
95427 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
* * *
95444 CAATTTAATTAAAATTT
1 AAATTTATTTTAAATTT
95461 AAAT
1 AAAT
95465 AGATTTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 27 0.79
18 7 0.21
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:95934 original size:28 final size:28
Alignment explanation
Indices: 95898--95953 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
95888 TTGATCATTC
*
95898 AAAACCAATACAAAAATAG-GGATTCAAA
1 AAAACCAATA-AAAAATAGCGCATTCAAA
* *
95926 AAAATCAATAACAAATAGCGCATTCAAA
1 AAAACCAATAAAAAATAGCGCATTCAAA
95954 GCAATACAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.59, C:0.16, G:0.09, T:0.16
Consensus pattern (28 bp):
AAAACCAATAAAAAATAGCGCATTCAAA
Found at i:96615 original size:30 final size:30
Alignment explanation
Indices: 96560--96656 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
96550 GGAAACAGTG
* *
96560 GCGCGTGCACCGGAGGATTGTGGGACGACA
1 GCGCGTGCACCGGAGGACTGCGGGACGACA
* **
96590 GCGCGTGCACCGGAGGACTACGGGAC-AGTG
1 GCGCGTGCACCGGAGGACTGCGGGACGA-CA
* * * *
96620 GTGCGTGCACCAGAGGGCTGCGGGATGACA
1 GCGCGTGCACCGGAGGACTGCGGGACGACA
96650 GCGCGTG
1 GCGCGTG
96657 GTGCACGTAG
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
29 1 0.02
30 50 0.96
31 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.44, T:0.12
Consensus pattern (30 bp):
GCGCGTGCACCGGAGGACTGCGGGACGACA
Found at i:97338 original size:29 final size:29
Alignment explanation
Indices: 97305--97693 Score: 267
Period size: 29 Copynumber: 13.3 Consensus size: 29
97295 CTAAACTGTC
*
97305 CAAAAACTT-CATTTTTACCCTAAAACTT
1 CAAAAAATTCCATTTTTACCCTAAAACTT
97333 CAAAAAATTCCATTTTTACCCTAAAACTTT
1 CAAAAAATTCCATTTTTACCCTAAAAC-TT
*
97363 C-AAAAATTCTATTTTTACCCCT-AAACTT
1 CAAAAAATTCCATTTTTA-CCCTAAAACTT
* * *
97391 CAACAAATTCCATTTTGA-CCTCGAAACTT
1 CAAAAAATTCCATTTTTACCCT-AAAACTT
* ** **
97420 CCAAAAATTCCATAATTACCCCCAAACTT
1 CAAAAAATTCCATTTTTACCCTAAAACTT
*
97449 CAACAAATTCCATTTTTGACCCTAAAACTT
1 CAAAAAATTCCATTTTT-ACCCTAAAACTT
* ** *
97479 CCAAAAATTCCATTTTTACCCCCAAATTT
1 CAAAAAATTCCATTTTTACCCTAAAACTT
* * * * *
97508 CTAAAAATCCCATTTTTAACCTCGAAATTT
1 CAAAAAATTCCATTTTTACCCT-AAAACTT
* * *
97538 C-CAGAATTCCATTTTTA-CCTACGAACTT
1 CAAAAAATTCCATTTTTACCCTA-AAACTT
* *
97566 CCAAAAA-TCCTATTTTTAATCCC-AAAACTC
1 CAAAAAATTCC-ATTTTT-A-CCCTAAAACTT
* * * **
97596 CCAAAAATTTCGTTTTTACCCTTGAACTTT
1 CAAAAAATTCCATTTTTACCCTAAAAC-TT
* *
97626 C-AAAAATCCCATTTTTAACCCCAAAACTCT
1 CAAAAAATTCCATTTTT-ACCCTAAAACT-T
* * *
97656 C-AAAAATTTCATTTTTAACCTCAAAACTC
1 CAAAAAATTCCATTTTTACCCT-AAAACTT
*
97685 CTAAAAATT
1 CAAAAAATT
97694 TTATGTTTTA
Statistics
Matches: 285, Mismatches: 54, Indels: 42
0.75 0.14 0.11
Matches are distributed among these distances:
27 3 0.01
28 25 0.09
29 157 0.55
30 95 0.33
31 3 0.01
32 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (29 bp):
CAAAAAATTCCATTTTTACCCTAAAACTT
Found at i:97498 original size:59 final size:57
Alignment explanation
Indices: 97293--97761 Score: 344
Period size: 58 Copynumber: 8.0 Consensus size: 57
97283 CCTTGAAGGT
**
97293 CCCT-AAACTGTCCAAAAACTT-CATTTTTACCCTAAAACTTCAAAAAATTCCATTTTTA
1 CCCTAAAACT-TCCAAAAA-TTCCATTTTTACCCCCAAACTTC-AAAAATTCCATTTTTA
* * * *
97351 CCCTAAAACTTTCAAAAATTCTATTTTTACCCCTAAACTTCAACAAATTCCATTTTGA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCAA-AAATTCCATTTTTA
* **
97409 -CCTCGAAACTTCCAAAAATTCCATAATTACCCCCAAACTTCAACAAATTCCATTTTTGA
1 CCCT-AAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCAA-AAATTCCATTTTT-A
* *
97468 CCCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAATTTCTAAAAATCCCATTTTTA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTC-AAAAATTCCATTTTTA
* * * * ** *
97526 ACCTCGAAATTTCC-AGAATTCCATTTTTACCTACGAACTTCCAAAAA-TCCTATTTTTAA
1 CCCT-AAAACTTCCAAAAATTCCATTTTTACCCCCAAACTT-CAAAAATTCC-ATTTTT-A
* * * *** *
97585 TCCC-AAAACTCCCAAAAATTTCGTTTTTACCCTTGAACTTTCAAAAATCCCATTTTTAA
1 -CCCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAAC-TTCAAAAATTCCATTTTT-A
* * * * * **
97644 CCCCAAAAC-TCTCAAAAATTTCATTTTTAACCTCAAAACTCCTAAAAATTTTATGTTTTA
1 CCCTAAAACTTC-CAAAAATTCCATTTTT-ACCCCCAAACTTC-AAAAATTCCAT-TTTTA
*** * *
97704 CCCCCGAACTTCCAAAAA-TCTGATTTTTACCCCCGAA-TGTCTAAAAATTCCATTTTTA
1 CCCTAAAACTTCCAAAAATTC-CATTTTTACCCCCAAACT-TC-AAAAATTCCATTTTTA
97762 ACACTGAATT
Statistics
Matches: 331, Mismatches: 57, Indels: 46
0.76 0.13 0.11
Matches are distributed among these distances:
57 9 0.03
58 139 0.42
59 132 0.40
60 45 0.14
61 6 0.02
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (57 bp):
CCCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCAAAAATTCCATTTTTA
Found at i:97521 original size:117 final size:113
Alignment explanation
Indices: 97319--97759 Score: 343
Period size: 117 Copynumber: 3.8 Consensus size: 113
97309 AACTTCATTT
* *
97319 TTACCCTA-AAACTTCAAAAAATTCCATTTTTACCCTAAAACTTTCAAAAATTCTATTTTTACCC
1 TTACCC-ACAAACTTC-AAAAATTCCATTTTTACCCTAAAACTTCCAAAAATTCCATTTTTACCC
* * * *
97383 CTAAACTTCAACAAATTCCATTTTGACCTCGAAACTTCCAAAAATTCCATAA
64 CCAAATTTCAA-AAATCCCATTTTAACCTCGAAACTTCC-AAAATTCCATAA
*
97435 TTACCCCCAAACTTCAACAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTCCATTTTTACCC
1 TTACCCACAAACTTCAA-AAATTCCATTTTT-ACCCTAAAACTTCCAAAAATTCCATTTTTACCC
* * **
97500 CCAAATTTCTAAAAATCCCATTTTTAACCTCGAAATTTCCAGAATTCCATTT
64 CCAAATTTC-AAAAATCCCA-TTTTAACCTCGAAACTTCCAAAATTCCATAA
* * * * *
97552 TTACCTACGAACTTCCAAAAA-TCCTATTTTTAATCCC-AAAACTCCCAAAAATTTCGTTTTTAC
1 TTACCCACAAACTT-CAAAAATTCC-ATTTTT-A-CCCTAAAACTTCCAAAAATTCCATTTTTAC
** * * * * * **
97615 CCTTGAACTTTCAAAAATCCCATTTTTAACCCCAAAACTCTCAAAAATTTCATTT
62 CC-CCAAATTTCAAAAATCCCA-TTTTAACCTCGAAACT-TCCAAAATTCCATAA
* ** *** *
97670 TTAACCTCA-AAACTCCTAAAAATTTTATGTTTTACCCCCGAACTTCCAAAAA-TCTGATTTTTA
1 TT-ACC-CACAAACTTC-AAAAATTCCAT-TTTTACCCTAAAACTTCCAAAAATTC-CATTTTTA
* * *
97733 CCCCCGAATGTCTAAAAATTCCATTTT
61 CCCCCAAATTTC-AAAAATCCCATTTT
97760 TAACACTGAA
Statistics
Matches: 263, Mismatches: 44, Indels: 34
0.77 0.13 0.10
Matches are distributed among these distances:
115 2 0.01
116 29 0.11
117 124 0.47
118 58 0.22
119 44 0.17
120 6 0.02
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (113 bp):
TTACCCACAAACTTCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAATTCCATTTTTACCCCC
AAATTTCAAAAATCCCATTTTAACCTCGAAACTTCCAAAATTCCATAA
Found at i:97731 original size:29 final size:29
Alignment explanation
Indices: 97298--97761 Score: 177
Period size: 29 Copynumber: 15.8 Consensus size: 29
97288 AAGGTCCCTA
***
97298 AACTGTCCAAAAA-CTTCATTTTTACCCTAA
1 AACT-TCCAAAAATC-TCATTTTTACCCCCG
* ***
97328 AACTTCAAAAAAT-TCCATTTTTACCCTAA
1 AACTTCCAAAAATCT-CATTTTTACCCCCG
* **
97357 AACTTTCAAAAAT-TCTATTTTTACCCCTA
1 AACTTCCAAAAATCTC-ATTTTTACCCCCG
* *
97386 AACTT-CAACAAAT-TCCATTTTGA-CCTCG
1 AACTTCCAA-AAATCT-CATTTTTACCCCCG
** *
97414 AAACTTCCAAAAAT-TCCATAATTACCCCCA
1 -AACTTCCAAAAATCT-CATTTTTACCCCCG
***
97444 AACTT-CAACAAAT-TCCATTTTTGACCCTAA
1 AACTTCCAA-AAATCT-CATTTTT-ACCCCCG
*
97474 AACTTCCAAAAAT-TCCATTTTTACCCCCA
1 AACTTCCAAAAATCT-CATTTTTACCCCCG
* * * * *
97503 AATTTCTAAAAATCCCATTTTTAACCTCG
1 AACTTCCAAAAATCTCATTTTTACCCCCG
* * * **
97532 AAATTTCCAGAATTC-CATTTTTACCTACG
1 -AACTTCCAAAAATCTCATTTTTACCCCCG
* **
97561 AACTTCCAAAAATC-CTATTTTTAATCCCAA
1 AACTTCCAAAAATCTC-ATTTTT-ACCCCCG
* * * **
97591 AACTCCCAAAAATTTCGTTTTTACCCTTG
1 AACTTCCAAAAATCTCATTTTTACCCCCG
* * **
97620 AACTTTCAAAAATCCCATTTTTAACCCCAA
1 AACTTCCAAAAATCTCATTTTT-ACCCCCG
* * **
97650 AAC-TCTCAAAAATTTCATTTTTAACCTCAA
1 AACTTC-CAAAAATCTCATTTTT-ACCCCCG
* *
97680 AAC-TCCTAAAAATTTTATGTTTTACCCCCG
1 AACTTCC-AAAAATCTCAT-TTTTACCCCCG
*
97710 AACTTCCAAAAATCTGATTTTTACCCCCG
1 AACTTCCAAAAATCTCATTTTTACCCCCG
*
97739 AA-TGTCTAAAAAT-TCCATTTTTA
1 AACT-TCCAAAAATCT-CATTTTTA
97762 ACACTGAATT
Statistics
Matches: 344, Mismatches: 67, Indels: 47
0.75 0.15 0.10
Matches are distributed among these distances:
28 24 0.07
29 186 0.54
30 123 0.36
31 11 0.03
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
AACTTCCAAAAATCTCATTTTTACCCCCG
Found at i:102076 original size:22 final size:21
Alignment explanation
Indices: 102035--102077 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
102025 CCCAGATAAA
*
102035 TAGAAGAAAAATACAGGCGAT
1 TAGAAGAAAAATACACGCGAT
102056 TAGAAGAGAAAAT-CAACGCGAT
1 TAGAAGA-AAAATAC-ACGCGAT
102078 GCAGGGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.51, C:0.12, G:0.23, T:0.14
Consensus pattern (21 bp):
TAGAAGAAAAATACACGCGAT
Found at i:109868 original size:205 final size:205
Alignment explanation
Indices: 109559--110036 Score: 812
Period size: 205 Copynumber: 2.3 Consensus size: 205
109549 TAGCTTTCTA
*
109559 ATGAGGTACAGAGAAGCGAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAG
1 ATGAGATACAGAGAAGCGAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAG
* *
109624 AAGACCAAATCAAACCCACGCTCGATGTGAGTAAATCTTCGAATCCCAGCTTCCTGATGAGATAC
66 AAGACCAAATCAAACCCACGCTCAATGTGAGTAAATCTTCGAATCCCAGCTTCCTGATAAGATAC
* * * *
109689 CGAGAAGCAAATCGAAGCAATAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTCGACTAAATT
131 CGAGAAGCAAATCGAAGCAATAAACGATTAGCTTCCTGATAAGATACTGAGAAGTCGACCAAATT
109754 CGTCTTCCTG
196 CGTCTTCCTG
*
109764 ATGAGATACAGAGAAGCGAATTGAAACAAAAGACGCGGTCATCTTCCTGATGAGATACCGAGAAG
1 ATGAGATACAGAGAAGCGAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAG
109829 AAGACCAAATCAAACCCACGCTCAATGTGAGTAAATCTTCGAATCCCAGCTTCCTGATAAGATAC
66 AAGACCAAATCAAACCCACGCTCAATGTGAGTAAATCTTCGAATCCCAGCTTCCTGATAAGATAC
* * *
109894 CGAGAAGCAGATCGAAGCAATAAACGATTAGCTTCCTGATAAGATATTGAGAAGTGGACCAAATT
131 CGAGAAGCAAATCGAAGCAATAAACGATTAGCTTCCTGATAAGATACTGAGAAGTCGACCAAATT
109959 CGTCTTCCTG
196 CGTCTTCCTG
* * * * *
109969 ATGAGATACAAAGAAGCGGATTGAAACAAACGACGCGATCATCTTCCTAATGAGATACTGAGAAG
1 ATGAGATACAGAGAAGCGAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAG
110034 AAG
66 AAG
110037 GTCAAGTAAA
Statistics
Matches: 256, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
205 256 1.00
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (205 bp):
ATGAGATACAGAGAAGCGAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAG
AAGACCAAATCAAACCCACGCTCAATGTGAGTAAATCTTCGAATCCCAGCTTCCTGATAAGATAC
CGAGAAGCAAATCGAAGCAATAAACGATTAGCTTCCTGATAAGATACTGAGAAGTCGACCAAATT
CGTCTTCCTG
Found at i:110413 original size:17 final size:17
Alignment explanation
Indices: 110391--110428 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
110381 AAATTGATTC
* *
110391 AAATTTATTTTAAATTT
1 AAATTTAATTAAAATTT
110408 AAATTTAATTAAAATTT
1 AAATTTAATTAAAATTT
110425 AAAT
1 AAAT
110429 GGATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTTAATTAAAATTT
Found at i:110968 original size:27 final size:28
Alignment explanation
Indices: 110925--110980 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
110915 TTGAGCATTC
*
110925 AAAATCAATACAAAAATAG-GGATTCAAA
1 AAAATCAATAC-AAAATAGCGCATTCAAA
110953 AAAATCAATAGC-AAATAGCGCATTCAAA
1 AAAATCAATA-CAAAATAGCGCATTCAAA
110981 GCAATACAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 6 0.24
28 18 0.72
29 1 0.04
ACGTcount: A:0.57, C:0.14, G:0.11, T:0.18
Consensus pattern (28 bp):
AAAATCAATACAAAATAGCGCATTCAAA
Found at i:111624 original size:30 final size:30
Alignment explanation
Indices: 111561--111655 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 30
111551 GAAATAGTGA
* **
111561 CGCGTGCACCGGAGGACTGTGGGACGGCAG
1 CGCGTGCACCGGAGGACTATGGGACAACAG
**
111591 CGCGTGCACCGGAGGACTATGGGACAATGG
1 CGCGTGCACCGGAGGACTATGGGACAACAG
** * * *
111621 CGCGTGCACTAGAGG-CTGTAGGACTACAG
1 CGCGTGCACCGGAGGACTATGGGACAACAG
111650 CGCGTG
1 CGCGTG
111656 GTGCGCGTGG
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 15 0.28
30 38 0.72
ACGTcount: A:0.20, C:0.25, G:0.41, T:0.14
Consensus pattern (30 bp):
CGCGTGCACCGGAGGACTATGGGACAACAG
Found at i:112343 original size:29 final size:29
Alignment explanation
Indices: 112292--112457 Score: 181
Period size: 30 Copynumber: 5.6 Consensus size: 29
112282 CCTTGGAGGT
* *
112292 CCCTAAACTATCCAAAAACTCCATTTTTAC
1 CCCTAAACT-TCAAAAAATTCCATTTTTAC
112322 CCCTAAACTTCAAAAAATTCCATTTTTGAC
1 CCCTAAACTTCAAAAAATTCCATTTTT-AC
* * *
112352 CCCAAAACTTCTAGAAATTCCATTTTTAC
1 CCCTAAACTTCAAAAAATTCCATTTTTAC
* *
112381 CCCCAAACTTCAAAAAATTCCAATTTTGAC
1 CCCTAAACTTCAAAAAATTCC-ATTTTTAC
* * *
112411 CCCAAAACTTC-CAAAATTCTATTTTTAC
1 CCCTAAACTTCAAAAAATTCCATTTTTAC
* *
112439 CCCTGAACTTTTAAAAAAT
1 CCCTAAAC-TTCAAAAAAT
112458 CTCATTTGTA
Statistics
Matches: 115, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
28 13 0.11
29 45 0.39
30 57 0.50
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.32
Consensus pattern (29 bp):
CCCTAAACTTCAAAAAATTCCATTTTTAC
Found at i:112398 original size:59 final size:58
Alignment explanation
Indices: 112296--112482 Score: 232
Period size: 59 Copynumber: 3.2 Consensus size: 58
112286 GGAGGTCCCT
*
112296 AAACTATCCAAAAACTCCATTTTTACCCCTAAACTTCAAAAAATTCCATTTTTGACCCCA
1 AAACT-TCC-AAAATTCCATTTTTACCCCTAAACTTCAAAAAATTCCATTTTTGACCCCA
* * *
112356 AAACTTCTAGAAATTCCATTTTTACCCCCAAACTTCAAAAAATTCCAATTTTGACCCCA
1 AAACTTCCA-AAATTCCATTTTTACCCCTAAACTTCAAAAAATTCCATTTTTGACCCCA
* * * * *
112415 AAACTTCCAAAATTCTATTTTTACCCCTGAACTTTTAAAAAA-TCTCATTTGTAACCCCA
1 AAACTTCCAAAATTCCATTTTTACCCCTAAAC-TTCAAAAAATTC-CATTTTTGACCCCA
*
112474 AAAATTCCA
1 AAACTTCCA
112483 TTTTTTACCC
Statistics
Matches: 111, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
58 23 0.21
59 83 0.75
60 5 0.05
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.32
Consensus pattern (58 bp):
AAACTTCCAAAATTCCATTTTTACCCCTAAACTTCAAAAAATTCCATTTTTGACCCCA
Found at i:112500 original size:80 final size:80
Alignment explanation
Indices: 112393--112556 Score: 183
Period size: 80 Copynumber: 2.0 Consensus size: 80
112383 CCAAACTTCA
* * * *
112393 AAAAATTCCAATTTTGACCCCAAAACTTC-CAAAATTCTATTTTTAC-CCCTGAACT-TTTAAAA
1 AAAAATTCCAATTTTGACCCCAAAACTTCAAAAAATCCCATTTTTACACCC-GAA-TGTCTAAAA
112455 AATCTCATTTGTAACCCC
64 AATC-CATTTGTAACCCC
* * *
112473 AAAAATTCCATTTTTTACCCTC-GAACTTCAAAAAATCCCATTTTTACACCCGAATGTCTAAAAA
1 AAAAATTCCAATTTTGACCC-CAAAACTTCAAAAAATCCCATTTTTACACCCGAATGTCTAAAAA
* *
112537 TTCCATTTTTAACCCC
65 ATCCATTTGTAACCCC
112553 AAAA
1 AAAA
112557 TTTTCCCAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
80 41 0.58
81 27 0.38
82 3 0.04
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (80 bp):
AAAAATTCCAATTTTGACCCCAAAACTTCAAAAAATCCCATTTTTACACCCGAATGTCTAAAAAA
TCCATTTGTAACCCC
Found at i:112516 original size:29 final size:29
Alignment explanation
Indices: 112473--112551 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 29
112463 TTGTAACCCC
112473 AAAAATTCCATTTTTTAC-CCTCGAACT-TCA
1 AAAAATTCCA-TTTTTACACC-CGAA-TGTCA
* *
112503 AAAAATCCCATTTTTACACCCGAATGTCT
1 AAAAATTCCATTTTTACACCCGAATGTCA
112532 AAAAATTCCATTTTTA-ACCC
1 AAAAATTCCATTTTTACACCC
112552 CAAAATTTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
28 5 0.11
29 28 0.64
30 11 0.25
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAAATTCCATTTTTACACCCGAATGTCA
Found at i:114433 original size:21 final size:21
Alignment explanation
Indices: 114408--114449 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
114398 AAACTTAATT
**
114408 TTTTTAAATTATAAAAAAATA
1 TTTTTAAAAAATAAAAAAATA
114429 TTTTTAAAAAATAAAAAAATA
1 TTTTTAAAAAATAAAAAAATA
114450 AATTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTTTAAAAAATAAAAAAATA
Found at i:114543 original size:29 final size:28
Alignment explanation
Indices: 114480--114535 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
114470 AAATATTATT
*
114480 AAAATTTAT-AAAAAAATAAATAAAATTC
1 AAAATTT-TCAAAAAAATAAATAAAAATC
114508 AAAATTTTCAAAAAAATAAAATAAAAAT
1 AAAATTTTCAAAAAAAT-AAATAAAAAT
114536 AACCATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 1 0.04
28 15 0.60
29 9 0.36
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.27
Consensus pattern (28 bp):
AAAATTTTCAAAAAAATAAATAAAAATC
Found at i:121232 original size:12 final size:12
Alignment explanation
Indices: 121215--121286 Score: 63
Period size: 12 Copynumber: 5.9 Consensus size: 12
121205 ATAACATCCA
*
121215 AACAACCAAAAT
1 AACAACAAAAAT
* *
121227 AACAACTAAAAC
1 AACAACAAAAAT
*
121239 AACAGCAAAAAT
1 AACAACAAAAAT
* *
121251 AATAGAAAAAAAT
1 AACA-ACAAAAAT
*
121264 AGCAACAAAAAT
1 AACAACAAAAAT
*
121276 AACAATAAAAA
1 AACAACAAAAA
121287 CAGCACCAAA
Statistics
Matches: 46, Mismatches: 13, Indels: 2
0.75 0.21 0.03
Matches are distributed among these distances:
12 38 0.83
13 8 0.17
ACGTcount: A:0.71, C:0.15, G:0.04, T:0.10
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:121273 original size:24 final size:23
Alignment explanation
Indices: 121246--121327 Score: 65
Period size: 24 Copynumber: 3.4 Consensus size: 23
121236 AACAACAGCA
* *
121246 AAAATAATAGAAAAAAATAGCAACA
1 AAAACAATA-AAAAAAATAGC-ACC
* * * *
121271 AAAATAACAATAAAAACAGCACC
1 AAAACAATAAAAAAAATAGCACC
* *
121294 AAAGCAGTAAAAAAAAATAGCACC
1 AAAACAAT-AAAAAAAATAGCACC
121318 AAAACAATAA
1 AAAACAATAA
121328 CCAAAGCATC
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
23 8 0.18
24 28 0.64
25 8 0.18
ACGTcount: A:0.68, C:0.15, G:0.07, T:0.10
Consensus pattern (23 bp):
AAAACAATAAAAAAAATAGCACC
Found at i:121806 original size:18 final size:20
Alignment explanation
Indices: 121783--121819 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
121773 TTCAAGTCTT
121783 ATTTTAA-C-AAATTTTTTA
1 ATTTTAACCTAAATTTTTTA
121801 ATTTTAACCTAAATTTTTT
1 ATTTTAACCTAAATTTTTT
121820 TTATAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 1 0.06
20 9 0.53
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTAACCTAAATTTTTTA
Found at i:122189 original size:21 final size:24
Alignment explanation
Indices: 122159--122211 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
122149 AATTTTATTG
*
122159 TTATTATTTTT-TA-TAA-TAAAA
1 TTATTTTTTTTCTATTAATTAAAA
*
122180 TTATTTTTTTTCTATTAATTATAA
1 TTATTTTTTTTCTATTAATTAAAA
122204 TTATTTTT
1 TTATTTTT
122212 CATAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 10 0.37
22 2 0.07
23 3 0.11
24 12 0.44
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
TTATTTTTTTTCTATTAATTAAAA
Found at i:123814 original size:23 final size:21
Alignment explanation
Indices: 123781--123838 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
123771 AATAACATTC
* *
123781 AAACAGTAAAAAAAGCACCAA
1 AAACAATAAAAAAAACACCAA
123802 AACAGCAA-AAAAAAAACACCAA
1 AA-A-CAATAAAAAAAACACCAA
123824 AAACAATAAAAAAAA
1 AAACAATAAAAAAAA
123839 TCAATATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 3 0.09
21 11 0.34
22 16 0.50
23 2 0.06
ACGTcount: A:0.74, C:0.17, G:0.05, T:0.03
Consensus pattern (21 bp):
AAACAATAAAAAAAACACCAA
Found at i:125067 original size:141 final size:141
Alignment explanation
Indices: 124819--125096 Score: 405
Period size: 141 Copynumber: 2.0 Consensus size: 141
124809 AGAACCAATC
* * * *
124819 TTTTTCCGATGAACCCAACTTTCCTTCATTCTCAATATCGACTTTCCTGGAATTTTTATTTTCGC
1 TTTTTCCAATGAAACCAACTTGCCTTCATTCTCAATATCGACTTTCCTGGAATTTTGATTTTCGC
* * *
124884 TTGCAATCCTCTGGTTGTACGGTGAAAAAAGCACTAACAACCCTACTGTGCCAAAACCAGAACCG
66 TTGCAATCCTCTGATTGTACAGTGAAAAAAGCACTAACAACCCAACTGTGCCAAAACCAGAACCG
*
124949 GAGAACAAGCT
131 GAAAACAAGCT
* * *
124960 TTTTTCCAATGAAACCAACTTGCCTTCATTTTCAATATTGACGTTT-CTTGAATTTTGATTTTCG
1 TTTTTCCAATGAAACCAACTTGCCTTCATTCTCAATATCGAC-TTTCCTGGAATTTTGATTTTCG
* * * *
125024 CTTGCAATTCTCTGATTGTACAGTGAAAAAAGCACTAAGAACCCAACTGTGCCAGAAGCAGAACC
65 CTTGCAATCCTCTGATTGTACAGTGAAAAAAGCACTAACAACCCAACTGTGCCAAAACCAGAACC
125089 GGAAAACA
130 GGAAAACA
125097 TGAAGTTCGG
Statistics
Matches: 121, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
141 118 0.98
142 3 0.02
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (141 bp):
TTTTTCCAATGAAACCAACTTGCCTTCATTCTCAATATCGACTTTCCTGGAATTTTGATTTTCGC
TTGCAATCCTCTGATTGTACAGTGAAAAAAGCACTAACAACCCAACTGTGCCAAAACCAGAACCG
GAAAACAAGCT
Found at i:129664 original size:17 final size:18
Alignment explanation
Indices: 129626--129666 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
129616 GAAACCCTTA
*
129626 TTTTATTTTTCTTATTAT
1 TTTTATTTATCTTATTAT
129644 TTTTATTTAT-TTATTAT
1 TTTTATTTATCTTATTAT
129661 TTTTAT
1 TTTTAT
129667 AAATATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTATTTATCTTATTAT
Found at i:129710 original size:4 final size:4
Alignment explanation
Indices: 129697--129733 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
129687 TAATATTAAT
129697 TTTA -TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
129734 ATTGTATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:129764 original size:78 final size:75
Alignment explanation
Indices: 129627--129800 Score: 217
Period size: 78 Copynumber: 2.3 Consensus size: 75
129617 AAACCCTTAT
* * *
129627 TTTATTTTTCTTATTATTTTTATTTATTTATTATTTTTATAAATATAAATAAATATAAAATAATA
1 TTTATTTAT-TTATT-TATTTATTTATTTATTATTTTAATAAATATAAATAAATATAAAATAATA
129692 TTAATTTTATTA
64 TTAATTTTATTA
*
129704 TTTATTTATTTATTTATTTATTTATTTATTATTGTATGAATATAA-ATAAATAAATGTAAAATAA
1 TTTATTTATTTATTTATTTATTTATTTATTATT-T-T-AATA-AATATAAATAAATATAAAATAA
* *
129768 TATTAATTTTGTTT
62 TATTAATTTTATTA
129782 TATTATTTATTTA-TTATTT
1 T-TTATTTATTTATTTATTT
129801 TATGAATATA
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
75 18 0.21
76 6 0.07
77 9 0.10
78 40 0.47
79 13 0.15
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (75 bp):
TTTATTTATTTATTTATTTATTTATTTATTATTTTAATAAATATAAATAAATATAAAATAATATT
AATTTTATTA
Found at i:129803 original size:75 final size:73
Alignment explanation
Indices: 129625--129803 Score: 208
Period size: 75 Copynumber: 2.4 Consensus size: 73
129615 CGAAACCCTT
* * *
129625 ATTTTATTTTTCTTA-TTATTT-TTA-TTTATTTATTATTTTTATAAATATAAATAAATATAAAA
1 ATTTTAGTTTTATTATTTATTTATTATTTTATTTATTATTTTAATAAATATAAATAAATATAAAA
129687 TAATATTA
66 TAATATTA
*
129695 ATTTTATTATTTATTTATTTATTTATT-TATTTATTTATTATTGTATGAATATAA-ATAAATAAA
1 ATTTTAGT-TTTA-TTATTTATTTATTAT-TTTATTTATTATT-T-T-AATA-AATATAAATAAA
*
129758 TGTAAAATAATATTA
59 TATAAAATAATATTA
129773 ATTTT-GTTTTATTATTTATTTATTATTTTAT
1 ATTTTAGTTTTATTATTTATTTATTATTTTAT
129804 GAATATAAAT
Statistics
Matches: 94, Mismatches: 4, Indels: 17
0.82 0.03 0.15
Matches are distributed among these distances:
70 8 0.09
71 3 0.03
72 3 0.03
73 6 0.06
74 2 0.02
75 31 0.33
76 6 0.06
77 2 0.02
78 31 0.33
79 2 0.02
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (73 bp):
ATTTTAGTTTTATTATTTATTTATTATTTTATTTATTATTTTAATAAATATAAATAAATATAAAA
TAATATTA
Done.