Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014921.1 Kokia drynarioides strain JFW-HI SEQ_129964, 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: 122905
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 86 characters in sequence are not A, C, G, or T
Found at i:957 original size:24 final size:23
Alignment explanation
Indices: 908--957 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
898 TAAAGTAGAT
* *
908 TATATATTATTTTTCTAATATTA
1 TATATATAATTTTTCTAATATCA
931 TATATTATAATTTTTACTAAT-TCA
1 TATA-TATAATTTTT-CTAATATCA
955 TAT
1 TAT
958 TTTAATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (23 bp):
TATATATAATTTTTCTAATATCA
Found at i:1084 original size:25 final size:25
Alignment explanation
Indices: 1055--1106 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
1045 TATTTATTAT
1055 TCTTATT-AAATTATAA-ATATAATAA
1 TCTTATTAAAATT-TAATA-ATAATAA
1080 TCTTATTAAAATTTAATAATAATAA
1 TCTTATTAAAATTTAATAATAATAA
1105 TC
1 TC
1107 ATCTAACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (25 bp):
TCTTATTAAAATTTAATAATAATAA
Found at i:1091 original size:57 final size:57
Alignment explanation
Indices: 960--1096 Score: 158
Period size: 57 Copynumber: 2.5 Consensus size: 57
950 ATTCATATTT
* **
960 TAAT-ATAATTATATTAAAA-AT-ATTAAATTATATATTATTTCATTAAATTGTATT
1 TAATAATAATTATATTAAAATATAATTAAATTATATATTATTTCATTAAATTATAAA
* * *
1014 TAATAATAATTATGTTAAAATATAATTAAATTATTTATTATTCTTATTAAATTATAAA
1 TAATAATAATTATATTAAAATATAATTAAATTATATATTATT-TCATTAAATTATAAA
*
1072 T-ATAATAATCT-TATTAAAATTTAAT
1 TAATAATAAT-TATATTAAAATATAAT
1097 AATAATAATC
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
54 4 0.06
55 14 0.20
56 2 0.03
57 37 0.53
58 13 0.19
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (57 bp):
TAATAATAATTATATTAAAATATAATTAAATTATATATTATTTCATTAAATTATAAA
Found at i:1098 original size:28 final size:27
Alignment explanation
Indices: 1055--1121 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 27
1045 TATTTATTAT
1055 TCTTATT-AAA-TTATAA-ATATAATAA
1 TCTTATTAAAATTTATAATA-ATAATAA
*
1080 TCTTATTAAAATTTAATAATAATAATCA
1 TCTTATTAAAATTT-ATAATAATAATAA
* *
1108 TCTAACTAAAATTT
1 TCTTATTAAAATTT
1122 TTTTGTTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 7 0.20
26 3 0.09
27 2 0.06
28 22 0.63
29 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.43
Consensus pattern (27 bp):
TCTTATTAAAATTTATAATAATAATAA
Found at i:1232 original size:16 final size:16
Alignment explanation
Indices: 1211--1265 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
1201 CGAATTACTG
*
1211 ATTACAGTTCTATTCT
1 ATTACAGTTTTATTCT
1227 ATTACAGTTTTATT-T
1 ATTACAGTTTTATTCT
* *
1242 CATTACAATTTTATTCC
1 -ATTACAGTTTTATTCT
1259 ATTACAG
1 ATTACAG
1266 CGAACCAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 32 0.97
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.49
Consensus pattern (16 bp):
ATTACAGTTTTATTCT
Found at i:6996 original size:2 final size:2
Alignment explanation
Indices: 6989--7018 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6979 AGACTTTTAA
6989 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
7019 TAGGTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16142 original size:21 final size:20
Alignment explanation
Indices: 16114--16152 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
16104 GGTTTCTATG
*
16114 TTTAAATTTGAGATTTAATC
1 TTTAAATTTAAGATTTAATC
*
16134 TTTATAATTTAAGTTTTAA
1 TTTA-AATTTAAGATTTAA
16153 CATAATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.54
Consensus pattern (20 bp):
TTTAAATTTAAGATTTAATC
Found at i:18642 original size:12 final size:12
Alignment explanation
Indices: 18613--18660 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
18603 TTTTTATTCC
18613 TTCTCTCTC-AA
1 TTCTCTCTCAAA
*
18624 TTTTCTCTCAAA
1 TTCTCTCTCAAA
*
18636 TTCTCTCCCAAA
1 TTCTCTCTCAAA
18648 TTCTCTCT-AAA
1 TTCTCTCTCAAA
18659 TT
1 TT
18661 TTTCTCTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 13 0.41
12 19 0.59
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (12 bp):
TTCTCTCTCAAA
Found at i:18846 original size:27 final size:27
Alignment explanation
Indices: 18816--18891 Score: 93
Period size: 27 Copynumber: 2.7 Consensus size: 27
18806 TGTATATTAT
18816 TTATTTATTTTATTTTTTATAATTTAA
1 TTATTTATTTTATTTTTTATAATTTAA
*
18843 TTATTTTATATTA-TTTTTATAATTTAA
1 TTA-TTTATTTTATTTTTTATAATTTAA
18870 TTAATTT-TTTAATATTTTTTAT
1 TT-ATTTATTT--TATTTTTTAT
18892 GTGAATAGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
26 2 0.05
27 22 0.52
28 11 0.26
29 7 0.17
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (27 bp):
TTATTTATTTTATTTTTTATAATTTAA
Found at i:18858 original size:18 final size:18
Alignment explanation
Indices: 18811--18858 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 18
18801 AATTTTGTAT
*
18811 ATTA-TTTAT-TTATTTT
1 ATTATTTTATATTATTTA
18827 ATT-TTTTATA--ATTTA
1 ATTATTTTATATTATTTA
18842 ATTATTTTATATTATTT
1 ATTATTTTATATTATTT
18859 TTATAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
15 7 0.27
16 15 0.58
18 4 0.15
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTATTTTATATTATTTA
Found at i:18859 original size:28 final size:29
Alignment explanation
Indices: 18819--18891 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 29
18809 ATATTATTTA
*
18819 TTTATTTTATTTTTTATAATTTAATT-AT
1 TTTATATTATTTTTTATAATTTAATTAAT
18847 TTTATATTA-TTTTTATAATTTAATTAAT
1 TTTATATTATTTTTTATAATTTAATTAAT
* *
18875 TTTTTAATATTTTTTAT
1 TTTATATTATTTTTTAT
18892 GTGAATAGTC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 16 0.40
28 17 0.43
29 7 0.17
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (29 bp):
TTTATATTATTTTTTATAATTTAATTAAT
Found at i:20897 original size:59 final size:59
Alignment explanation
Indices: 20800--20944 Score: 209
Period size: 59 Copynumber: 2.5 Consensus size: 59
20790 AATACATGCA
* * * *
20800 TTGATTATTTTTGTAAACATTATTTTTATATTGTTTCATTTAACAAAAGCGAAGTTCAT
1 TTGAATATTTTTGTACACATTATTTTTATATTGTTTCATTTAACAAAAACAAAGTTCAT
* * *
20859 TTGAATATTTTTGTACACATTATTTTTATATTGTTTCATTTAATAAAAATAAATTTCAT
1 TTGAATATTTTTGTACACATTATTTTTATATTGTTTCATTTAACAAAAACAAAGTTCAT
* *
20918 TTGAATATTTTTATACACATTAATTTT
1 TTGAATATTTTTGTACACATTATTTTT
20945 GAGTAAAGTT
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 77 1.00
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.52
Consensus pattern (59 bp):
TTGAATATTTTTGTACACATTATTTTTATATTGTTTCATTTAACAAAAACAAAGTTCAT
Found at i:21265 original size:19 final size:22
Alignment explanation
Indices: 21232--21288 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
21222 TTATGATTTC
*
21232 TTTAAAAATAAATAA-TAAAT-A
1 TTTAATAA-AAATAATTAAATAA
21253 TTT-ATAAAAATAATTAAATAA
1 TTTAATAAAAATAATTAAATAA
21274 TTTGAATAAAAATAA
1 TTT-AATAAAAATAA
21289 AACAGAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 6 0.19
20 8 0.26
21 7 0.23
23 10 0.32
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
TTTAATAAAAATAATTAAATAA
Found at i:28605 original size:94 final size:94
Alignment explanation
Indices: 28441--28618 Score: 227
Period size: 94 Copynumber: 1.9 Consensus size: 94
28431 CATAAAGTCT
* * * * *
28441 CTTAAGTAACAAAGTACCTTATTATGTATTAACCATCCAAACGACAAAAGTAACCAAGTATATAT
1 CTTAAGCAACAAAGTACCTTAATAAGCATTAACCATCCAAAAGACAAAAGTAACCAAGTATATAT
*
28506 CTTGATATGAGCAGCCAATCACAAATTCC
66 CTTGATATAAGCAGCCAATCACAAATTCC
* *
28535 CTTAAGCAACTAAA-TACCTTAATAAGCATTAACCAT-CAACAAGACATAAGTGACCAAGTACT-
1 CTTAAGCAAC-AAAGTACCTTAATAAGCATTAACCATCCAA-AAGACAAAAGTAACCAAGTA-TA
*
28597 TATTTTGATATAAGCAGCCAAT
63 TATCTTGATATAAGCAGCCAAT
28619 TACCCCCAGA
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
93 3 0.04
94 65 0.90
95 4 0.06
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (94 bp):
CTTAAGCAACAAAGTACCTTAATAAGCATTAACCATCCAAAAGACAAAAGTAACCAAGTATATAT
CTTGATATAAGCAGCCAATCACAAATTCC
Found at i:36766 original size:2 final size:2
Alignment explanation
Indices: 36759--36795 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
36749 ATACATAAAT
36759 TA TA TA TA 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 TA T
36796 TCATAAATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:37367 original size:20 final size:22
Alignment explanation
Indices: 37344--37384 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
37334 AATTTTTTTA
37344 TAAAA-TTAAT-AAAACATATT
1 TAAAATTTAATAAAAACATATT
*
37364 TAAAATTTTATAAAAACATAT
1 TAAAATTTAATAAAAACATAT
37385 ACAAATTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 4 0.22
22 9 0.50
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAAATTTAATAAAAACATATT
Found at i:47147 original size:23 final size:24
Alignment explanation
Indices: 47104--47148 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
47094 AATTTAATTT
*
47104 ATTAAATTTAATAATTATCATTAG
1 ATTAAAATTAATAATTATCATTAG
*
47128 ATTAAAATTAA-AATTTTCATT
1 ATTAAAATTAATAATTATCATT
47149 TCAAATTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (24 bp):
ATTAAAATTAATAATTATCATTAG
Found at i:53209 original size:24 final size:23
Alignment explanation
Indices: 53166--53213 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
53156 GATTTTGTTA
*
53166 TTTTATTATTTATTTATTTCAAT
1 TTTTATTATTTATTCATTTCAAT
53189 TTTTATTATTT-TATCAGTTTCAAT
1 TTTTATTATTTAT-TCA-TTTCAAT
53213 T
1 T
53214 AGTTGGCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 13 0.59
24 8 0.36
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTATTATTTATTCATTTCAAT
Found at i:56691 original size:21 final size:21
Alignment explanation
Indices: 56640--56692 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
56630 TTTGTATTTA
* * *
56640 TTATCTTTAAAATTATATAATT
1 TTAT-TTTTAAATTAAATAAAT
*
56662 TTA-TATTAAATTAAATAAAT
1 TTATTTTTAAATTAAATAAAT
56682 TTATTTTTAAA
1 TTATTTTTAAA
56693 CATTAAATGA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 16 0.64
21 6 0.24
22 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TTATTTTTAAATTAAATAAAT
Found at i:59151 original size:21 final size:21
Alignment explanation
Indices: 59100--59152 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
59090 TTTGTATTTA
* * *
59100 TTATCTTTAAAATTATATAATT
1 TTAT-TTTTAAATTAAATAAAT
*
59122 TTA-TATTAAATTAAATAAAT
1 TTATTTTTAAATTAAATAAAT
59142 TTATTTTTAAA
1 TTATTTTTAAA
59153 CATTAAATGA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 16 0.64
21 6 0.24
22 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TTATTTTTAAATTAAATAAAT
Found at i:60129 original size:24 final size:25
Alignment explanation
Indices: 60100--60147 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
60090 TATTAAATAT
60100 AATTTAATAA-AAATAATAATATAG
1 AATTTAATAACAAATAATAATATAG
* *
60124 AATTTAATAACAATTATTAATATA
1 AATTTAATAACAAATAATAATATA
60148 ATTATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (25 bp):
AATTTAATAACAAATAATAATATAG
Found at i:60877 original size:15 final size:15
Alignment explanation
Indices: 60857--60910 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
60847 ATACTACAAA
60857 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
60872 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
60889 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
60906 ATATT
1 ATATT
60911 AATACCCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:60967 original size:15 final size:16
Alignment explanation
Indices: 60947--60976 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
60937 GAATAATATT
60947 TTTTAAAA-TTATTAA
1 TTTTAAAACTTATTAA
60962 TTTTAAAACTTATTA
1 TTTTAAAACTTATTA
60977 TTAAAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAAAACTTATTAA
Found at i:61172 original size:18 final size:19
Alignment explanation
Indices: 61128--61174 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
61118 TCACCCCAAG
61128 TATATTAAAAAAAAAAACCT
1 TATATTAAAAAAAAAAA-CT
* *
61148 TATTATTAAAATAATAAA-T
1 TA-TATTAAAAAAAAAAACT
61167 TATATTAA
1 TATATTAA
61175 TTATATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 6 0.25
19 3 0.12
20 2 0.08
21 13 0.54
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
TATATTAAAAAAAAAAACT
Found at i:61198 original size:12 final size:13
Alignment explanation
Indices: 61165--61206 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
61155 AAAATAATAA
61165 ATTATATTAATTAT
1 ATTATA-TAATTAT
61179 ATTA-ATAATT-T
1 ATTATATAATTAT
*
61190 ATTATATAATTAG
1 ATTATATAATTAT
61203 ATTA
1 ATTA
61207 AATATGTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 5 0.20
12 11 0.44
13 5 0.20
14 4 0.16
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (13 bp):
ATTATATAATTAT
Found at i:61210 original size:25 final size:26
Alignment explanation
Indices: 61156--61210 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
61146 CTTATTATTA
*
61156 AAATAATAAATTATATTAATTATATT
1 AAATAATAAATTATATTAATTAGATT
**
61182 -AATAATTTATTATA-TAATTAGATT
1 AAATAATAAATTATATTAATTAGATT
61206 AAATA
1 AAATA
61211 TGTATGTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
AAATAATAAATTATATTAATTAGATT
Found at i:62425 original size:17 final size:17
Alignment explanation
Indices: 62400--62441 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
62390 CCCAATCAAC
*
62400 TTAAATTTATTTTAAAA
1 TTAAATTTATTCTAAAA
* *
62417 TTAAGTTTATTCTAAAT
1 TTAAATTTATTCTAAAA
62434 TTAAATTT
1 TTAAATTT
62442 GGTTGAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TTAAATTTATTCTAAAA
Found at i:64256 original size:29 final size:28
Alignment explanation
Indices: 64188--64418 Score: 182
Period size: 29 Copynumber: 7.9 Consensus size: 28
64178 GAAGGTCCCT
* *
64188 AAACTATCCAAAAATTACCATTTGACCTCT
1 AAACT-TCCAAAAATTACCATTTTACC-CC
*
64218 AAACGGTCC-AAAATATACCATTTTACCGCC
1 AAAC-TTCCAAAAAT-TACCATTTTACC-CC
* *
64248 AAACTTCCAAAAA-TCCCATTTTAACCCTG
1 AAACTTCCAAAAATTACCATTTT-ACCC-C
*
64277 AAACTTCCAAAAATTACTATTTTACCCAC
1 AAACTTCCAAAAATTACCATTTTACCC-C
*
64306 AAAACTTTCAAAAATTACCATTTTACCCCC
1 -AAACTTCCAAAAATTACCATTTTA-CCCC
* ** *
64336 GAACTTCTTAAAATTACCATTTAACCCCC
1 AAACTTCCAAAAATTACCATTTTA-CCCC
* *
64365 GAACTTCCAAAAA-T-CTCATTTTTGACCCG
1 AAACTTCCAAAAATTAC-CA-TTTT-ACCCC
*
64394 ACACTTCCAAAAATTACCATTTTAC
1 AAACTTCCAAAAATTACCATTTTAC
64419 TCCCGGATGT
Statistics
Matches: 164, Mismatches: 24, Indels: 28
0.76 0.11 0.13
Matches are distributed among these distances:
27 1 0.01
28 14 0.09
29 84 0.51
30 61 0.37
31 4 0.02
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (28 bp):
AAACTTCCAAAAATTACCATTTTACCCC
Found at i:64349 original size:88 final size:88
Alignment explanation
Indices: 64184--64423 Score: 210
Period size: 88 Copynumber: 2.7 Consensus size: 88
64174 CCCCGAAGGT
* * * ** * *
64184 CCCT-AAACTATCCAAAAATTACCATTTGACCTC-TAAACGGTCCAAAATATACCATTTTACCGC
1 CCCTGAAACT-TCCAAAAATTACTATTTTACC-CACAAACTTTCAAAAAT-TACCATTTTACCCC
* *
64247 CAAACTTCCAAAAA-TCCCATTTTAA-
63 CGAACTTCCAAAAATTACCA-TTTAAC
64272 CCCTGAAACTTCCAAAAATTACTATTTTACCCACAAAACTTTCAAAAATTACCATTTTACCCCCG
1 CCCTGAAACTTCCAAAAATTACTATTTTACCCAC-AAACTTTCAAAAATTACCATTTTACCCCCG
**
64337 AACTTCTTAAAATTACCATTTAAC
65 AACTTCCAAAAATTACCATTTAAC
* * *
64361 CCCCG-AACTTCCAAAAA-T-CTCATTTTTGACCCGAC--ACTTCCAAAAATTACCATTTTACTC
1 CCCTGAAACTTCCAAAAATTACT-A-TTTT-ACCC-ACAAACTTTCAAAAATTACCATTTTACCC
64421 CCG
62 CCG
64424 GATGTCCGAA
Statistics
Matches: 129, Mismatches: 14, Indels: 19
0.80 0.09 0.12
Matches are distributed among these distances:
86 2 0.02
87 29 0.22
88 68 0.53
89 28 0.22
90 2 0.02
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.29
Consensus pattern (88 bp):
CCCTGAAACTTCCAAAAATTACTATTTTACCCACAAACTTTCAAAAATTACCATTTTACCCCCGA
ACTTCCAAAAATTACCATTTAAC
Found at i:66190 original size:30 final size:30
Alignment explanation
Indices: 66155--66261 Score: 137
Period size: 30 Copynumber: 3.6 Consensus size: 30
66145 ATTTGAGGGT
*
66155 AAAAATATAATTTTTGGAAGTTTCGAGTTC
1 AAAAATATAATTTTTGGAAGTTTCGAGGTC
* *
66185 GAAAATAGAATTTTTGGAAG-TTCGAGGGT-
1 AAAAATATAATTTTTGGAAGTTTCGA-GGTC
* *
66214 AAAAATATAATTTTTGGAAATTTTGAGGTC
1 AAAAATATAATTTTTGGAAGTTTCGAGGTC
*
66244 AAAAATGTAATTTTTGGA
1 AAAAATATAATTTTTGGA
66262 CTGTTTAGGG
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
29 25 0.38
30 41 0.62
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.37
Consensus pattern (30 bp):
AAAAATATAATTTTTGGAAGTTTCGAGGTC
Found at i:66220 original size:59 final size:59
Alignment explanation
Indices: 66149--66261 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 59
66139 AATATTATTT
* * *
66149 GAGGGTAAAAATATAATTTTTGGAAGTTTCGAGTTCGAAAATAG-AATTTTTGGAAGTTC
1 GAGGGTAAAAATATAATTTTTGGAAATTTCGAGGTCAAAAAT-GTAATTTTTGGAAGTTC
*
66208 GAGGGTAAAAATATAATTTTTGGAAATTTTGAGGTCAAAAATGTAATTTTTGGA
1 GAGGGTAAAAATATAATTTTTGGAAATTTCGAGGTCAAAAATGTAATTTTTGGA
66262 CTGTTTAGGG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 1 0.02
59 48 0.98
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (59 bp):
GAGGGTAAAAATATAATTTTTGGAAATTTCGAGGTCAAAAATGTAATTTTTGGAAGTTC
Found at i:68389 original size:180 final size:180
Alignment explanation
Indices: 68071--68433 Score: 462
Period size: 180 Copynumber: 2.0 Consensus size: 180
68061 TTTCATTGAC
* **
68071 TTGGCCTTCTTCTTAGTATCTTATCAGAAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTG
1 TTGGCCTTCTTCTTAGTATCTCATCAGAAAGATGACCGCATCACTTGTTTCAATCCACTTCTCTG
* * * * * * **
68136 TGTTTCATTAGGAAGACGAATTATGTTCACTTTTCCGTATCTCATAAGGAATCTAACCACTTTAT
66 TATCTCATCAGGAAGACGAATTATGTCCACTTCTCAGTATCTCATAAGGAAGATAACCACTTTAT
* * * *
68201 TGCTTCGACCTGTTTCTCAGTATCTCATCAAGAAGTTGAGGTTCGAAGAT
131 TACTTCGACCTGGTTCTCAGTATCTAATCAAGAAGCTGAGGTTCGAAGAT
* ** *
68251 TTGGTCTTCTT-TTCAGTATCTCATCA-AGAAGATGACCGCATCGTTTGTTTCAATCCACTTCTT
1 TTGGCCTTCTTCTT-AGTATCTCATCAGA-AAGATGACCGCATCACTTGTTTCAATCCACTTCTC
* *
68314 TGTATCTCATCAGGAAGACGAATT-TGGTCCACTTCTCAGTATCTCATTAGGAAGATAACCATTT
64 TGTATCTCATCAGGAAGACGAATTAT-GTCCACTTCTCAGTATCTCATAAGGAAGATAACCACTT
* * *
68378 TATTACTTCGACCTGGTTCTTAGTATCTAATCAGGAAGCTGGGGTTCGAAGAT
128 TATTACTTCGACCTGGTTCTCAGTATCTAATCAAGAAGCTGAGGTTCGAAGAT
68431 TTG
1 TTG
68434 TTCATATCGA
Statistics
Matches: 156, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
179 4 0.03
180 152 0.97
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.37
Consensus pattern (180 bp):
TTGGCCTTCTTCTTAGTATCTCATCAGAAAGATGACCGCATCACTTGTTTCAATCCACTTCTCTG
TATCTCATCAGGAAGACGAATTATGTCCACTTCTCAGTATCTCATAAGGAAGATAACCACTTTAT
TACTTCGACCTGGTTCTCAGTATCTAATCAAGAAGCTGAGGTTCGAAGAT
Found at i:68606 original size:206 final size:206
Alignment explanation
Indices: 68248--68845 Score: 991
Period size: 206 Copynumber: 2.9 Consensus size: 206
68238 GAGGTTCGAA
68248 GATTTGGTCTTCTTTTCAGTATCTCATCAAGAAGATGACCGCATCGTTTGTTTCAATCCACTTCT
1 GATTTGGTCTTCTTTTCAGTATCTCATCAAGAAGATGACCGCATCGTTTGTTTCAATCCACTTCT
* *
68313 TTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATTAGGAAGATAACCATTT
66 CTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGATAACCATTT
* *
68378 TATTACTTCGACCTGGTTCTTAGTATCTAATCAGGAAGCTGGGGTTCGAAGATTTGTTCATATCG
131 TATTACTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCATATCG
*
68443 AGCGTGGGTTT
196 AGCGTGAGTTT
* *
68454 GATTTGGTCTTCTTTTCAGTATCTCATCAAGAAGATGACCGCATCGTTTATTTCAATCCGCTTCT
1 GATTTGGTCTTCTTTTCAGTATCTCATCAAGAAGATGACCGCATCGTTTGTTTCAATCCACTTCT
* * *
68519 CTGTATCTCATCAGGAAGACGAATTTGGTCTACTTCTCAGTATCTTATCAGGAAGGTAACCATTT
66 CTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGATAACCATTT
68584 TATTACTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCATATCG
131 TATTACTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCATATCG
68649 AGCGTGAGTTT
196 AGCGTGAGTTT
* * * *
68660 GATTTGGTCCTCTTCTCAGTATCTCATCAGGAAGATAACCGCATCGTTTGTTTCAATCCACTTCT
1 GATTTGGTCTTCTTTTCAGTATCTCATCAAGAAGATGACCGCATCGTTTGTTTCAATCCACTTCT
* * *
68725 CTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCGGTATCTCATCAAGAAGCTAACCATTT
66 CTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGATAACCATTT
* * * *
68790 TATTGCTTCGACCTACTTCTTAATATCTCATCAGGAAG-TCGAGGTTCGAAGATTTG
131 TATTACTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCT-GGGGTTCGAAGATTTG
68846 CTTGCTTTGA
Statistics
Matches: 366, Mismatches: 25, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
205 1 0.00
206 365 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (206 bp):
GATTTGGTCTTCTTTTCAGTATCTCATCAAGAAGATGACCGCATCGTTTGTTTCAATCCACTTCT
CTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGATAACCATTT
TATTACTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCATATCG
AGCGTGAGTTT
Found at i:69219 original size:101 final size:101
Alignment explanation
Indices: 69066--69267 Score: 260
Period size: 101 Copynumber: 2.0 Consensus size: 101
69056 GCTGCTGTAG
* * * ** *
69066 TTTTATTCCAACTTCGCTGCAACTTCAAGAAGATAGGATTTGTTGTTGAAGCTTCATCTTGATCT
1 TTTTAATCCAACTTCACTGCAACTTCAAGAAGATAGGAATTGACGTTAAAGCTTCATCTTGATCT
*
69131 TACTACAACTTCAAAGAGATAAAGACTTGCTATTGT
66 TACTACAACTTCAAAGAGATAAAGACTTGCCATTGT
* * * * * *
69167 TTTTAATCCAACTTTACTGTAACTTCAAGAGGATAGGAATTGACGTTAAAGCTTCGTTTTGCTCT
1 TTTTAATCCAACTTCACTGCAACTTCAAGAAGATAGGAATTGACGTTAAAGCTTCATCTTGATCT
* * *
69232 TACTGCAACTTCAGAGAGATGAAGACTTGCCATTGT
66 TACTACAACTTCAAAGAGATAAAGACTTGCCATTGT
69268 AGTTTTCATC
Statistics
Matches: 85, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
101 85 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (101 bp):
TTTTAATCCAACTTCACTGCAACTTCAAGAAGATAGGAATTGACGTTAAAGCTTCATCTTGATCT
TACTACAACTTCAAAGAGATAAAGACTTGCCATTGT
Found at i:69566 original size:150 final size:150
Alignment explanation
Indices: 69380--69655 Score: 385
Period size: 150 Copynumber: 1.8 Consensus size: 150
69370 TAAACTTTTC
* *
69380 CCCTTCAAATCTTCGTGGTAGTAGATTCGTCGTTGCGACTTAAATCTTT-CGCTTATTCTCTTCT
1 CCCTTCAAATCTTCGTGGTACTAGATTCGTCGTTGCGACTTAAATCTTTGC-CTTAGTCTCTTCT
*
69444 AAGGTACAAGGTC-CGCCGTCGCGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGATCT
65 AAGGTACAAGGTCTCG-CGTCACGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGATCT
69508 GTCGTTGCGGTCTTAGATCTTT
129 GTCGTTGCGGTCTTAGATCTTT
** * * * *
69530 CCCTTCATGTCTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTGCCTTCGTGTCTTCTG
1 CCCTTCAAATCTTCGTGGTACTAGATTCGTCGTTGCGACTTAAATCTTTGCCTTAGTCTCTTCTA
* * * * * *
69595 AGGTACACGGTCTTGCGTTACGACTTAGACCTTTCCCTTTTTTATTTTTGTGGTACTGGAT
66 AGGTACAAGGTCTCGCGTCACGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGAT
69656 TCACCGTTGC
Statistics
Matches: 109, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
150 107 0.98
151 2 0.02
ACGTcount: A:0.15, C:0.24, G:0.21, T:0.41
Consensus pattern (150 bp):
CCCTTCAAATCTTCGTGGTACTAGATTCGTCGTTGCGACTTAAATCTTTGCCTTAGTCTCTTCTA
AGGTACAAGGTCTCGCGTCACGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGATCTGT
CGTTGCGGTCTTAGATCTTT
Found at i:69600 original size:100 final size:99
Alignment explanation
Indices: 69506--69850 Score: 399
Period size: 101 Copynumber: 3.4 Consensus size: 99
69496 GGTACTGGAT
* * * *
69506 CTGTCGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTCGTGGTACTAGATTCGTCGTTGCGGCTT
1 CTGTCGTTGC-GACTTAGACCTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTT
69571 AAATCTTTGCCTTCGTGTCTTCTGAGGTACACGGTC
65 AAATCTTT-CCTTCGTGTCTTCTGAGGTACACGGTC
* * ** * * * * *
69607 TTG-CGTTACGACTTAGACCTTTCCCTTTTTTATTTTTGTGGTACTGGATTCACCGTTGCGTCTT
1 CTGTCGTTGCGACTTAGACCTTTCCC-TTCATGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTT
* *
69671 AAATCTTTCTTTTCGTGTCTTTTGAGGTACACGGTC
65 AAATCTTTC-CTTCGTGTCTTCTGAGGTACACGGTC
* * * * *
69707 CTGCCGTTGCGACTTAGACCTTTCCCTT-TTGTATCTTTGTGGTACTGGATCCGCCGTTGCGGTT
1 CTGTCGTTGCGACTTAGACCTTTCCCTTCATG--TCTTCGTGGTACTGGATTCGCCGTTGCGGCT
*
69771 TGAATCTTTTCCTTCGTGTCTTCTGAGGTACACGGTC
64 TAAATC-TTTCCTTCGTGTCTTCTGAGGTACACGGTC
*
69808 CTG-CTGTTGCGACTTAGACCTTTCCCTTCATGTCTTCATGGTA
1 CTGTC-GTTGCGACTTAGACCTTTCCCTTCATGTCTTCGTGGTA
69851 TTGAGACTTG
Statistics
Matches: 207, Mismatches: 29, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
99 17 0.08
100 80 0.39
101 104 0.50
102 6 0.03
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.41
Consensus pattern (99 bp):
CTGTCGTTGCGACTTAGACCTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTA
AATCTTTCCTTCGTGTCTTCTGAGGTACACGGTC
Found at i:69765 original size:101 final size:101
Alignment explanation
Indices: 69539--69835 Score: 413
Period size: 101 Copynumber: 3.0 Consensus size: 101
69529 TCCCTTCATG
* * * *
69539 TCTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTGC-CTTCGTGTCTTCTGAGGTACAC
1 TCTTTGTGGTACTGGATTCGCCGTTGCGTCTTAAATCTTT-CTCTTCGTGTCTTCTGAGGTACAC
* * *
69603 GGTCTTG-CGTTACGACTTAGACCTTTCCCTTTTTTA
65 GGTCCTGCCGTTGCGACTTAGACCTTTCCCTTTTGTA
* * * *
69639 TTTTTGTGGTACTGGATTCACCGTTGCGTCTTAAATCTTTCTTTTCGTGTCTTTTGAGGTACACG
1 TCTTTGTGGTACTGGATTCGCCGTTGCGTCTTAAATCTTTCTCTTCGTGTCTTCTGAGGTACACG
69704 GTCCTGCCGTTGCGACTTAGACCTTTCCCTTTTGTA
66 GTCCTGCCGTTGCGACTTAGACCTTTCCCTTTTGTA
* *
69740 TCTTTGTGGTACTGGATCCGCCGTTGCGGT-TTGAATCTTT-TCCTTCGTGTCTTCTGAGGTACA
1 TCTTTGTGGTACTGGATTCGCCGTTGC-GTCTTAAATCTTTCT-CTTCGTGTCTTCTGAGGTACA
*
69803 CGGTCCTGCTGTTGCGACTTAGACCTTTCCCTT
64 CGGTCCTGCCGTTGCGACTTAGACCTTTCCCTT
69836 CATGTCTTCA
Statistics
Matches: 175, Mismatches: 18, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
99 1 0.01
100 61 0.35
101 111 0.63
102 2 0.01
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.41
Consensus pattern (101 bp):
TCTTTGTGGTACTGGATTCGCCGTTGCGTCTTAAATCTTTCTCTTCGTGTCTTCTGAGGTACACG
GTCCTGCCGTTGCGACTTAGACCTTTCCCTTTTGTA
Found at i:69836 original size:51 final size:51
Alignment explanation
Indices: 69410--69844 Score: 216
Period size: 50 Copynumber: 8.6 Consensus size: 51
69400 GTAGATTCGT
* * * ** * * *
69410 CGTTGCGACTTAAATCTTTCGCTTATTCTCTTCTAAGGTACAAGGTCC-GC
1 CGTTGCGACTTAGACCTTTCCCTTCGTGTCTTCTGAGGTACACGGTCCTGC
* * * * * * *
69460 CGTCGCGACTTAAACCTTTCCCTTTTGTATCTT-TGTGGTAC-TGGAT-CTGT
1 CGTTGCGACTTAGACCTTTCCC-TTCGTGTCTTCTGAGGTACACGG-TCCTGC
* * * * * * *
69510 CGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTC-GTGGTACTA-GATTC-GT
1 CGTTGC-GACTTAGACCTTTCCCTTCGTGTCTTCTGAGGTAC-ACGGTCCTGC
* * * * *
69560 CGTTGCGGCTTAAATCTTTGCCTTCGTGTCTTCTGAGGTACACGGTCTTG-
1 CGTTGCGACTTAGACCTTTCCCTTCGTGTCTTCTGAGGTACACGGTCCTGC
* * * * * * * * *
69610 CGTTACGACTTAGACCTTTCCCTT-TTTTATTTTTGTGGTAC-TGGATTC-AC
1 CGTTGCGACTTAGACCTTTCCCTTCGTGT-CTTCTGAGGTACACGG-TCCTGC
* * * ** *
69660 CGTTGCGTCTTAAATCTTTCTTTTCGTGTCTTTTGAGGTACACGGTCCTGC
1 CGTTGCGACTTAGACCTTTCCCTTCGTGTCTTCTGAGGTACACGGTCCTGC
* * * *
69711 CGTTGCGACTTAGACCTTTCCCTTTTGTATCTT-TGTGGTAC-TGGATCC-GC
1 CGTTGCGACTTAGACCTTTCCC-TTCGTGTCTTCTGAGGTACACGG-TCCTGC
* * * *
69761 CGTTGCG-GTTTGAATCTTTTCCTTCGTGTCTTCTGAGGTACACGGTCCTGC
1 CGTTGCGACTTAG-ACCTTTCCCTTCGTGTCTTCTGAGGTACACGGTCCTGC
* *
69812 TGTTGCGACTTAGACCTTTCCCTTCATGTCTTC
1 CGTTGCGACTTAGACCTTTCCCTTCGTGTCTTC
69845 ATGGTATTGA
Statistics
Matches: 285, Mismatches: 76, Indels: 47
0.70 0.19 0.12
Matches are distributed among these distances:
49 42 0.15
50 150 0.53
51 82 0.29
52 11 0.04
ACGTcount: A:0.13, C:0.25, G:0.21, T:0.41
Consensus pattern (51 bp):
CGTTGCGACTTAGACCTTTCCCTTCGTGTCTTCTGAGGTACACGGTCCTGC
Found at i:70940 original size:18 final size:18
Alignment explanation
Indices: 70894--70932 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
70884 TTGCTTTCCC
70894 TTTTTCTTC-T-TTCTTT
1 TTTTTCTTCATCTTCTTT
70910 TTTTTCTTCATCTTCTTT
1 TTTTTCTTCATCTTCTTT
70928 TTTTT
1 TTTTT
70933 TTGTATCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.43
17 1 0.05
18 11 0.52
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTCTTCATCTTCTTT
Found at i:76653 original size:58 final size:59
Alignment explanation
Indices: 76546--77007 Score: 353
Period size: 58 Copynumber: 7.9 Consensus size: 59
76536 TGGATACCGA
* * * * *
76546 GGGGCAAAATGGTAATTTTGGGAAAATTTAG-GGTTAAAAATGGAATTTTTAGACATTCG
1 GGGGTAAAATGGTAATTTT-TGAAAGTTTCGAGGTTAAAAATGGAATTTTTGGACATTCG
* * * * *
76605 GGGGTAAAAGGGTAA-TTTT-AAGAGTTTTGAGGTTAAAAATGGAGTTTTTAGACATTCAA
1 GGGGTAAAATGGTAATTTTTGAA-AGTTTCGAGGTTAAAAATGGAATTTTTGGACATTC-G
* *
76664 GGGGCAAAATGGTAATTTTTGAAAGTTTCG-GG-TCAAAATGGAATTTTTGGACATTC-
1 GGGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTTAAAAATGGAATTTTTGGACATTCG
* * * ** *
76720 GGGGTGAAATAGTAATTTTTGAAAGTTTCGAGG-TCAAAATGGAATTTTTGGAGGTTTG
1 GGGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTTAAAAATGGAATTTTTGGACATTCG
** * * *
76778 GGGACAAAAAT-GTAATTTTTGGAAGTTTTGAGGTTAAAAATGGATTTTTTGGA-AGTTCG
1 GGG-GTAAAATGGTAATTTTTGAAAGTTTCGAGGTTAAAAATGGAATTTTTGGACA-TTCG
* * * *
76837 AGGGTAAAAAT-ATAATTTTTGGAAGTTTCGAGG-TCAAAATGGAATTTTTGGA-AGTTCG
1 GGGGT-AAAATGGTAATTTTTGAAAGTTTCGAGGTTAAAAATGGAATTTTTGGACA-TTCG
* * * * * ** *
76895 GGAGTAAAAT-ATATTTTTTGGAAGTTTCGGGGCCAAAAATGGAATTTTTGGA-AGTTTG
1 GGGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTTAAAAATGGAATTTTTGGACA-TTCG
* * * * **
76953 AGGGTAAAAAT-ATAATTTTTGGAAA-TTTCAAGGTCAAAAATATAATTTTTGGACA
1 GGGGT-AAAATGGTAATTTTT-GAAAGTTTCGAGGTTAAAAATGGAATTTTTGGACA
77008 GTTTAGGGGC
Statistics
Matches: 337, Mismatches: 51, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
56 29 0.09
57 53 0.16
58 124 0.37
59 115 0.34
60 14 0.04
61 2 0.01
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTTAAAAATGGAATTTTTGGACATTCG
Found at i:76819 original size:30 final size:30
Alignment explanation
Indices: 76669--77011 Score: 279
Period size: 29 Copynumber: 11.7 Consensus size: 30
76659 TTCAAGGGGC
* *
76669 AAAATGGTAATTTTTGAAAGTTTC--GGGTC
1 AAAAT-GTAATTTTTGGAAGTTTCGAGGGTA
*
76698 AAAATGGAATTTTTGGACA--TTCG-GGGT-
1 AAAATGTAATTTTTGGA-AGTTTCGAGGGTA
* * *
76725 GAAATAGTAATTTTTGAAAGTTTCGA-GGTC
1 AAAAT-GTAATTTTTGGAAGTTTCGAGGGTA
* * *
76755 AAAATGGAATTTTTGGAGGTTT-G-GGGACA
1 AAAATGTAATTTTTGGAAGTTTCGAGGG-TA
* *
76784 AAAATGTAATTTTTGGAAGTTTTGAGGTTA
1 AAAATGTAATTTTTGGAAGTTTCGAGGGTA
* *
76814 AAAATGGATTTTTTGGAAG-TTCGAGGGTA
1 AAAATGTAATTTTTGGAAGTTTCGAGGGTA
* *
76843 AAAATATAATTTTTGGAAGTTTCGA-GGTC
1 AAAATGTAATTTTTGGAAGTTTCGAGGGTA
*
76872 AAAATGGAATTTTTGGAAG-TTCG-GGAGT-
1 AAAATGTAATTTTTGGAAGTTTCGAGG-GTA
* * *
76900 AAAATATATTTTTTGGAAGTTTCG-GGGCCA
1 AAAATGTAATTTTTGGAAGTTTCGAGGG-TA
*
76930 AAAATGGAATTTTTGGAAGTTT-GAGGGTA
1 AAAATGTAATTTTTGGAAGTTTCGAGGGTA
* * *
76959 AAAATATAATTTTTGGAAATTTC-AAGGTCA
1 AAAATGTAATTTTTGGAAGTTTCGAGGGT-A
*
76989 AAAATATAATTTTTGGACAGTTT
1 AAAATGTAATTTTTGGA-AGTTT
77012 AGGGGCCTTT
Statistics
Matches: 255, Mismatches: 38, Indels: 40
0.77 0.11 0.12
Matches are distributed among these distances:
27 8 0.03
28 49 0.19
29 124 0.49
30 68 0.27
31 6 0.02
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAGTTTCGAGGGTA
Found at i:76957 original size:116 final size:116
Alignment explanation
Indices: 76676--77010 Score: 419
Period size: 116 Copynumber: 2.9 Consensus size: 116
76666 GGCAAAATGG
* *
76676 TAATTTTTGAAAGTTTC-GGGTC-AAAATGGAATTTTTGGACA-TTCG-GGGT-GAAATAGTAAT
1 TAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAATA-TAAT
* * * *
76736 TTTTGAAAGTTTCGAGGTCAAAATGGAATTTTTGGAGGTTTGGGGACAAAAATG
64 TTTTGGAAGTTTCGAGGTCAAAATGGAATTTTTGGAAG-TTCGGGACAAAAATA
* * * *
76790 TAATTTTTGGAAGTTTTGAGGTTAAAAATGGATTTTTTGGAAGTTCGAGGGTAAAAATATAATTT
1 TAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTT
**
76855 TTGGAAGTTTCGAGGTCAAAATGGAATTTTTGGAAGTTCGGGAGTAAAATA
66 TTGGAAGTTTCGAGGTCAAAATGGAATTTTTGGAAGTTCGGGACAAAAATA
* * *
76906 TATTTTTTGGAAGTTTCGGGGCCAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATATAATTT
1 TAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTT
* * **
76971 TTGGAAATTTCAAGGTCAAAAATATAATTTTTGGACAGTT
66 TTGGAAGTTTCGAGGTC-AAAATGGAATTTTTGGA-AGTT
77011 TAGGGGCCTT
Statistics
Matches: 191, Mismatches: 23, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
114 15 0.08
115 4 0.02
116 104 0.54
117 59 0.31
118 9 0.05
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (116 bp):
TAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTT
TTGGAAGTTTCGAGGTCAAAATGGAATTTTTGGAAGTTCGGGACAAAAATA
Found at i:76992 original size:59 final size:57
Alignment explanation
Indices: 76676--77010 Score: 358
Period size: 59 Copynumber: 5.8 Consensus size: 57
76666 GGCAAAATGG
*
76676 TAATTTTT-GAAAGTTTCG-GGTCAAAATGGAATTTTTGGACA-TTCGGGGT-GAAATA
1 TAATTTTTGGAAA-TTTCGAGGTCAAAATGGAATTTTTGGA-AGTTCGGGGTAAAAATA
* * * *
76731 GTAATTTTT-GAAAGTTTCGAGGTCAAAATGGAATTTTTGGAGGTTTGGGGACAAAAATG
1 -TAATTTTTGGAAA-TTTCGAGGTCAAAATGGAATTTTTGGAAGTTCGGGG-TAAAAATA
* * * *
76790 TAATTTTTGGAAGTTTTGAGGTTAAAAATGGATTTTTTGGAAGTTCGAGGGTAAAAATA
1 TAATTTTTGGAAATTTCGAGG-TCAAAATGGAATTTTTGGAAGTTCG-GGGTAAAAATA
*
76849 TAATTTTTGGAAGTTTCGAGGTCAAAATGGAATTTTTGGAAGTTCGGGAGT-AAAATA
1 TAATTTTTGGAAATTTCGAGGTCAAAATGGAATTTTTGGAAGTTCGGG-GTAAAAATA
* * * * *
76906 TATTTTTTGGAAGTTTCGGGGCCAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATA
1 TAATTTTTGGAAATTTCGAGGTC-AAAATGGAATTTTTGGAAGTTCG-GGGTAAAAATA
* **
76965 TAATTTTTGGAAATTTCAAGGTCAAAAATATAATTTTTGGACAGTT
1 TAATTTTTGGAAATTTCGAGGTC-AAAATGGAATTTTTGGA-AGTT
77011 TAGGGGCCTT
Statistics
Matches: 240, Mismatches: 27, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
56 18 0.08
57 55 0.23
58 64 0.27
59 96 0.40
60 7 0.03
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (57 bp):
TAATTTTTGGAAATTTCGAGGTCAAAATGGAATTTTTGGAAGTTCGGGGTAAAAATA
Found at i:78656 original size:27 final size:29
Alignment explanation
Indices: 78606--78662 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
78596 CACATAATTA
*
78606 TCATATTTATAATTAAATATATCATTTAC
1 TCATATTTATAATTAAATATATCATATAC
* *
78635 TCATTTTTATAA-TAATTA-ATCATATAC
1 TCATATTTATAATTAAATATATCATATAC
78662 T
1 T
78663 AAAACCATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.36
28 5 0.20
29 11 0.44
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (29 bp):
TCATATTTATAATTAAATATATCATATAC
Found at i:79148 original size:18 final size:16
Alignment explanation
Indices: 79117--79160 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
79107 GATTTAGGGT
*
79117 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
79134 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
79148 TTAAAAATTTATT
1 TTAAAAATTTATT
79161 CTCATTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:96322 original size:3 final size:3
Alignment explanation
Indices: 96314--96338 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
96304 TCTGTCTTAG
96314 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
96339 GGATGTTTAA
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:104202 original size:18 final size:18
Alignment explanation
Indices: 104175--104209 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
104165 GCGCTCTCGT
104175 TCTCTCTCCTTCTCCCGC
1 TCTCTCTCCTTCTCCCGC
*
104193 TCTCTTTCCTTCTCCCG
1 TCTCTCTCCTTCTCCCG
104210 TCGCTCCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.51, G:0.06, T:0.43
Consensus pattern (18 bp):
TCTCTCTCCTTCTCCCGC
Found at i:104250 original size:12 final size:12
Alignment explanation
Indices: 104229--104271 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
104219 GATGCGCAAA
*
104229 CGTTCACGTTCT
1 CGTTCCCGTTCT
104241 CGTTCCCGTTCT
1 CGTTCCCGTTCT
* *
104253 CGTACTCGTTCT
1 CGTTCCCGTTCT
*
104265 CGCTCCC
1 CGTTCCC
104272 TCTCCCTCTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.05, C:0.42, G:0.16, T:0.37
Consensus pattern (12 bp):
CGTTCCCGTTCT
Found at i:104260 original size:18 final size:18
Alignment explanation
Indices: 104229--104263 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
104219 GATGCGCAAA
*
104229 CGTTCACGTTCTCGTTCC
1 CGTTCACGTACTCGTTCC
*
104247 CGTTCTCGTACTCGTTC
1 CGTTCACGTACTCGTTC
104264 TCGCTCCCTC
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:0.06, C:0.37, G:0.17, T:0.40
Consensus pattern (18 bp):
CGTTCACGTACTCGTTCC
Found at i:107535 original size:169 final size:169
Alignment explanation
Indices: 107238--107575 Score: 489
Period size: 169 Copynumber: 2.0 Consensus size: 169
107228 TTGTATGGTC
** * * *
107238 TTCTTCGCTCGCACTGTTTTTATCAATTGAAAACTCTCATCCTCTTATTTTCTACAGTTCAATTT
1 TTCTTCGCTCGCACTGCCTGTATCAATCGAAAACTCTCATCCCCTTATTTTCTACAGTTCAATTT
* ** ** * * *
107303 TTTCATGAAACAGATTTAAATGTTAGGAATTTGTGAACCAAAATTTAAACAATTTTCTTCTCCAA
66 TTTAATGAAACAGATTTAAATGTTAAAAAGCTGTGAACCAAAATTCAAACAACTTTATTCTCCAA
* *
107368 TCACCGATATTGATTATCAAATTGATTTGGATCTAAGAT
131 TCACCGATATTGATCATCAAATTAATTTGGATCTAAGAT
* * * *
107407 TTCTTCGCTCGCACTGCCTGTATCAATCGAAAGCTCTCATCCCCTTCTTTTCTACGGTTTAATTT
1 TTCTTCGCTCGCACTGCCTGTATCAATCGAAAACTCTCATCCCCTTATTTTCTACAGTTCAATTT
107472 TTTAATGAAACA-ACTTTAAATGTTAAAAAGCTGTGAACCAAAATTCAAACAACTTTATTCTCCA
66 TTTAATGAAACAGA-TTTAAATGTTAAAAAGCTGTGAACCAAAATTCAAACAACTTTATTCTCCA
107536 ATCACCGATATTGATCATCAAATTAATTTGGATCTAAGAT
130 ATCACCGATATTGATCATCAAATTAATTTGGATCTAAGAT
107576 ATGTTATTCT
Statistics
Matches: 149, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
168 1 0.01
169 148 0.99
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (169 bp):
TTCTTCGCTCGCACTGCCTGTATCAATCGAAAACTCTCATCCCCTTATTTTCTACAGTTCAATTT
TTTAATGAAACAGATTTAAATGTTAAAAAGCTGTGAACCAAAATTCAAACAACTTTATTCTCCAA
TCACCGATATTGATCATCAAATTAATTTGGATCTAAGAT
Found at i:115146 original size:24 final size:21
Alignment explanation
Indices: 115119--115181 Score: 54
Period size: 24 Copynumber: 2.6 Consensus size: 21
115109 TGTTTAGTAC
115119 TTGAATTAAATTTTAATGTTTAAT
1 TTGAATTAAATTTT--T-TTTAAT
115143 TTGATATTTGAAATTTTTTTTAAT
1 TTGA-A-TT-AAATTTTTTTTAAT
115167 TTGATAATTAAATTT
1 TTG--AATTAAATTT
115182 GATTTCAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
23 6 0.18
24 15 0.44
25 3 0.09
26 3 0.09
27 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (21 bp):
TTGAATTAAATTTTTTTTAAT
Found at i:116326 original size:96 final size:96
Alignment explanation
Indices: 116145--116329 Score: 264
Period size: 96 Copynumber: 1.9 Consensus size: 96
116135 GAAAAGGATG
** * *
116145 TTCGATTATCTCGATTTGAAGAAAGGTTGCACCAAGTAAGTTAAGGCTCAAATTTTCAGAATCGA
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCAAGTAAGTTAAGGCGCAAATTTTCAAAATCGA
**
116210 AGATAAGGAAACATTACCTCGATTAAGGGTA
66 AGATAAAAAAACATTACCTCGATTAAGGGTA
* *
116241 TTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCGAAAATCG
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCAAGTAAGTTAAGGCGCAAATTTTC-AAAATCG
* *
116306 AA-ATAAAAAAATATTGCCTCGATT
65 AAGATAAAAAAACATTACCTCGATT
116330 TTAAAGTCTT
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
96 70 0.90
97 8 0.10
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTGCACCAAGTAAGTTAAGGCGCAAATTTTCAAAATCGA
AGATAAAAAAACATTACCTCGATTAAGGGTA
Found at i:118717 original size:6 final size:6
Alignment explanation
Indices: 118706--118768 Score: 60
Period size: 6 Copynumber: 11.0 Consensus size: 6
118696 TTATAATAAT
* * *
118706 TTTAAA TTTAAA -ATAAA TTTAAA CTTAAA -TTAAA TTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
118752 -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
118769 ACAAATTTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
5 13 0.28
6 33 0.72
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (6 bp):
TTTAAA
Found at i:118720 original size:17 final size:17
Alignment explanation
Indices: 118700--118796 Score: 124
Period size: 17 Copynumber: 5.7 Consensus size: 17
118690 TTACAATTAT
*
118700 AATAATTTTAAATTTAA
1 AATAAATTTAAATTTAA
*
118717 AATAAATTTAAACTTAA
1 AATAAATTTAAATTTAA
* *
118734 ATTAAATTCAAATTTAA
1 AATAAATTTAAATTTAA
*
118751 AATAAATCTAAATTTAA
1 AATAAATTTAAATTTAA
*
118768 AACAAATTT-AATCTTAA
1 AATAAATTTAAAT-TTAA
118785 AATAAATTTAAA
1 AATAAATTTAAA
118797 AGGGGTCCGA
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
16 3 0.04
17 62 0.93
18 2 0.03
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAAATTTAAATTTAA
Found at i:118724 original size:11 final size:11
Alignment explanation
Indices: 118708--118762 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
118698 ATAATAATTT
118708 TAAATTTAAAA
1 TAAATTTAAAA
*
118719 TAAATTTAAACT
1 TAAATTTAAA-A
*
118731 TAAA-TTAAAT
1 TAAATTTAAAA
118741 TCAAATTTAAAA
1 T-AAATTTAAAA
*
118753 TAAATCTAAA
1 TAAATTTAAA
118763 TTTAAAACAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
10 2 0.05
11 26 0.68
12 10 0.26
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.36
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:118762 original size:23 final size:23
Alignment explanation
Indices: 118720--118764 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
118710 AATTTAAAAT
*
118720 AAATTTAAACTTAAATTAAATTC
1 AAATTTAAACATAAATTAAATTC
118743 AAATTTAAA-ATAAATCTAAATT
1 AAATTTAAACATAAAT-TAAATT
118765 TAAAACAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATTTAAACATAAATTAAATTC
Done.