Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014148.1 Kokia drynarioides strain JFW-HI SEQ_129181, 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: 216257
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Warning! 174 characters in sequence are not A, C, G, or T
Found at i:158 original size:4 final size:4
Alignment explanation
Indices: 136--210 Score: 71
Period size: 4 Copynumber: 18.2 Consensus size: 4
126 AACACATTAC
* * * * *
136 CTTT CTCT CCTT C-TT CTTT CTTT CCTCT CCTT CTTC CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
184 CTTT CCTTT CTTT CCTTT CTTT CTTT C
1 CTTT -CTTT CTTT -CTTT CTTT CTTT C
211 CCGTTTATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
3 3 0.05
4 44 0.76
5 11 0.19
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (4 bp):
CTTT
Found at i:170 original size:17 final size:17
Alignment explanation
Indices: 136--211 Score: 70
Period size: 17 Copynumber: 4.6 Consensus size: 17
126 AACACATTAC
*
136 CTTTCTCTCC-TT-CTT
1 CTTTCTTTCCTTTCCTT
*
151 CTTTCTTTCCTCTCCTT
1 CTTTCTTTCCTTTCCTT
* *
168 CTTCCTTT-CTTTCTTT
1 CTTTCTTTCCTTTCCTT
184 CTTTCCTTT-CTTTCCTTT
1 CTTT-CTTTCCTTTCC-TT
202 CTTTCTTTCC
1 CTTTCTTTCC
212 CGTTTATTTG
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
15 9 0.18
16 10 0.20
17 23 0.47
18 7 0.14
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (17 bp):
CTTTCTTTCCTTTCCTT
Found at i:194 original size:13 final size:13
Alignment explanation
Indices: 149--211 Score: 85
Period size: 13 Copynumber: 4.9 Consensus size: 13
139 TCTCTCCTTC
149 TTCTTTCTTTCCT
1 TTCTTTCTTTCCT
* *
162 CTCCTTC-TTCCT
1 TTCTTTCTTTCCT
174 TTCTTTCTTT-CT
1 TTCTTTCTTTCCT
186 TTCCTTTCTTTCCT
1 TT-CTTTCTTTCCT
200 TTCTTTCTTTCC
1 TTCTTTCTTTCC
212 CGTTTATTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
12 14 0.33
13 25 0.58
14 4 0.09
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (13 bp):
TTCTTTCTTTCCT
Found at i:204 original size:9 final size:9
Alignment explanation
Indices: 135--210 Score: 72
Period size: 9 Copynumber: 8.7 Consensus size: 9
125 AAACACATTA
*
135 CCTTTCTCT
1 CCTTTCTTT
144 CC-TTC-TT
1 CCTTTCTTT
151 -CTTTCTTT
1 CCTTTCTTT
*
159 CCTCTCCTTCTT
1 CCT-TTC-T-TT
171 CCTTTCTTT
1 CCTTTCTTT
180 -CTTTCTTT
1 CCTTTCTTT
188 CCTTTCTTT
1 CCTTTCTTT
197 CCTTTCTTT
1 CCTTTCTTT
206 -CTTTC
1 CCTTTC
211 CCGTTTATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
6 1 0.02
7 4 0.07
8 18 0.32
9 23 0.40
10 3 0.05
11 3 0.05
12 5 0.09
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (9 bp):
CCTTTCTTT
Found at i:1317 original size:17 final size:17
Alignment explanation
Indices: 1291--1324 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1281 AATATTTGAC
*
1291 ATATAAATATTATATAT
1 ATATAAATATAATATAT
*
1308 ATATATATATAATATAT
1 ATATAAATATAATATAT
1325 CAAAGAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATAAATATAATATAT
Found at i:10598 original size:21 final size:21
Alignment explanation
Indices: 10572--10613 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
10562 CCTAACGGCA
10572 ATCCTACGTGACATTTCAAAT
1 ATCCTACGTGACATTTCAAAT
10593 ATCCTACGTGACATTTCAAAT
1 ATCCTACGTGACATTTCAAAT
10614 GGGTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (21 bp):
ATCCTACGTGACATTTCAAAT
Found at i:11315 original size:23 final size:22
Alignment explanation
Indices: 11272--11321 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
11262 ATAGAATATA
* **
11272 ATTTAAAATTTAATTGGATAAT
1 ATTTAAAATTAAATTAAATAAT
11294 ATTTAAAATTAAAATTAAATAAT
1 ATTTAAAATT-AAATTAAATAAT
*
11317 TTTTA
1 ATTTA
11322 TAAGTTTATG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
ATTTAAAATTAAATTAAATAAT
Found at i:11569 original size:18 final size:18
Alignment explanation
Indices: 11524--11571 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
11514 ATAATATAAA
* *
11524 TTAAATAGTAAATTATTT
1 TTAAATATTAAAATATTT
**
11542 AGAAAT-TTAAAATATTT
1 TTAAATATTAAAATATTT
11559 TTAAATATTAAAA
1 TTAAATATTAAAA
11572 ATTCGATTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (18 bp):
TTAAATATTAAAATATTT
Found at i:13490 original size:21 final size:21
Alignment explanation
Indices: 13466--13518 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 21
13456 TTGCACTAGC
13466 TCTACCGATACAAGT-ATG-A
1 TCTACCGATACAAGTCATGCA
13485 TTTCTACCGATACAAGTCATGCA
1 --TCTACCGATACAAGTCATGCA
13508 TCTACCGATAC
1 TCTACCGATAC
13519 CAAAAATCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 26 0.87
22 3 0.10
23 1 0.03
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.28
Consensus pattern (21 bp):
TCTACCGATACAAGTCATGCA
Found at i:44153 original size:26 final size:25
Alignment explanation
Indices: 44091--44156 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 25
44081 TTATAGATTT
44091 GCCACAAAGGCGTACTGTAACAAAATA
1 GCCACAAAGGC-T-CTGTAACAAAATA
* *
44118 GCCACAAAGGCTCTTTAACAGAATCA
1 GCCACAAAGGCTCTGTAACAAAAT-A
44144 GCCACAAAGGCTC
1 GCCACAAAGGCTC
44157 CTTTCAAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
25 10 0.28
26 15 0.42
27 11 0.31
ACGTcount: A:0.39, C:0.27, G:0.18, T:0.15
Consensus pattern (25 bp):
GCCACAAAGGCTCTGTAACAAAATA
Found at i:46918 original size:6 final size:6
Alignment explanation
Indices: 46907--46947 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
46897 CAAAAAGTGA
46907 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAAT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAAT
46948 GAGCCGAGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:50742 original size:76 final size:76
Alignment explanation
Indices: 50613--50768 Score: 303
Period size: 76 Copynumber: 2.1 Consensus size: 76
50603 TGGCTTATTT
*
50613 CTTTGTATATAGAATGGCTAGTGATTACTTTAGACGGATGGATGATTCGTCATTATTTATATGAT
1 CTTTGTATATAGAATGGCTAGTGATTACTTTAGACGGATGGATGATTCATCATTATTTATATGAT
50678 AACCTTGTACC
66 AACCTTGTACC
50689 CTTTGTATATAGAATGGCTAGTGATTACTTTAGACGGATGGATGATTCATCATTATTTATATGAT
1 CTTTGTATATAGAATGGCTAGTGATTACTTTAGACGGATGGATGATTCATCATTATTTATATGAT
50754 AACCTTGTACC
66 AACCTTGTACC
50765 CTTT
1 CTTT
50769 TTTTTAATCT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 79 1.00
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (76 bp):
CTTTGTATATAGAATGGCTAGTGATTACTTTAGACGGATGGATGATTCATCATTATTTATATGAT
AACCTTGTACC
Found at i:60316 original size:21 final size:20
Alignment explanation
Indices: 60277--60316 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
60267 GATGGAGGCA
*
60277 AGGCACTACAAACATTTTCT
1 AGGCACTACAAAAATTTTCT
*
60297 AGGCACTATAGAAAATTTTC
1 AGGCACTACA-AAAATTTTC
60317 ACATTAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (20 bp):
AGGCACTACAAAAATTTTCT
Found at i:68808 original size:11 final size:11
Alignment explanation
Indices: 68792--68816 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
68782 AAATATGAAG
68792 GGAAAACAGGA
1 GGAAAACAGGA
68803 GGAAAACAGGA
1 GGAAAACAGGA
68814 GGA
1 GGA
68817 GTACGGAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.40, T:0.00
Consensus pattern (11 bp):
GGAAAACAGGA
Found at i:70939 original size:261 final size:261
Alignment explanation
Indices: 70470--70997 Score: 993
Period size: 261 Copynumber: 2.0 Consensus size: 261
70460 GAAAAACTCG
* *
70470 AAAATTAATTTAAATTTTAAATTAAATAGTTCAAATTATTTGAGTTAATCAAGTTATTCGGATAA
1 AAAAATAATTTAAATTTTAAATTAAATAGTTCAAATTATTTGAGTTAATCAAATTATTCGGATAA
70535 ACTTAAATAAAAAATTAAGTTTTTCGGTTTAATTCGAATATGAATTATACAATTTGAATTATTCG
66 ACTTAAATAAAAAATTAAGTTTTTCGGTTTAATTCGAATATGAATTATACAATTTGAATTATTCG
* *
70600 AAAATCTAAATAAGAAAAGGTAAAAATACGTCGTTTTGATATATGTTTACTTTTTTTAAAGTTAA
131 AAAATCTAAATAAGAAAAGGTAAAAATACGTCGTTTTGATAAATGTTTACCTTTTTTAAAGTTAA
* *
70665 AAGTCAAAACCATTAAATTAAAAGTCAAAATTACGTTGTTTTAATAAATGTTTACTCATTAAGTT
196 AAGTCAAAACCATTAAATTAAAAGTCAAAATTACGTCGTTTTAATAAATATTTACTCATTAAGTT
70730 A
261 A
70731 AAAAATAATTTAAATTTTAAATTAAATAGTTCAAATTATTTGAGTTAATCAAATTATTCGGATAA
1 AAAAATAATTTAAATTTTAAATTAAATAGTTCAAATTATTTGAGTTAATCAAATTATTCGGATAA
70796 ACTTAAATAAAAAATTAAGTTTTTCGGTTTAATTCGAATATGAATTATACAATTTGAATTATTCG
66 ACTTAAATAAAAAATTAAGTTTTTCGGTTTAATTCGAATATGAATTATACAATTTGAATTATTCG
70861 AAAATCTAAATAAGAAAAGGTAAAAATACGTCGTTTTGATAAATGTTTACCTTTTTTAAAGTTAA
131 AAAATCTAAATAAGAAAAGGTAAAAATACGTCGTTTTGATAAATGTTTACCTTTTTTAAAGTTAA
*
70926 AAGTCAAAACCATTAAATTAAAAGTCAAAATTACGTCGTTTTAATAAATATTTACTCGTTAAGTT
196 AAGTCAAAACCATTAAATTAAAAGTCAAAATTACGTCGTTTTAATAAATATTTACTCATTAAGTT
70991 A
261 A
70992 AAAAAT
1 AAAAAT
70998 GAAACTATTA
Statistics
Matches: 260, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
261 260 1.00
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (261 bp):
AAAAATAATTTAAATTTTAAATTAAATAGTTCAAATTATTTGAGTTAATCAAATTATTCGGATAA
ACTTAAATAAAAAATTAAGTTTTTCGGTTTAATTCGAATATGAATTATACAATTTGAATTATTCG
AAAATCTAAATAAGAAAAGGTAAAAATACGTCGTTTTGATAAATGTTTACCTTTTTTAAAGTTAA
AAGTCAAAACCATTAAATTAAAAGTCAAAATTACGTCGTTTTAATAAATATTTACTCATTAAGTT
A
Found at i:75057 original size:23 final size:25
Alignment explanation
Indices: 75005--75058 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
74995 TTTATTATAA
* *
75005 TAAT-ATTATTAAAATATTATATTT
1 TAATAATTATTAAAATAATATACTT
75029 TAAATAATTATT-AAATAATA-ACTT
1 T-AATAATTATTAAAATAATATACTT
75053 TAATAA
1 TAATAA
75059 AAAAAATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 5 0.19
24 5 0.19
25 10 0.38
26 6 0.23
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TAATAATTATTAAAATAATATACTT
Found at i:78692 original size:81 final size:81
Alignment explanation
Indices: 78554--78725 Score: 292
Period size: 81 Copynumber: 2.1 Consensus size: 81
78544 GACTGGAAAT
*
78554 ATTTTACCCTGAATCTCAATAGGGCACCACCTACATACTTGATTTACTATCCGTGAATGTCCCAT
1 ATTTTAACCTGAATCTCAATAGGGCACCACCTACATACTTGATTTACTATCCGTGAATGTCCCAT
*
78619 TGGATTTGAAACATTA
66 TAGATTTGAAACATTA
*
78635 ATTTTAACCTGAATCTCAATAGGGCACCGCCTACATACTTGATTTACTATCAC-TGAATGTCCCA
1 ATTTTAACCTGAATCTCAATAGGGCACCACCTACATACTTGATTTACTATC-CGTGAATGTCCCA
78699 TTAGATTTGAAACATTA
65 TTAGATTTGAAACATTA
*
78716 ATTCTAACCT
1 ATTTTAACCT
78726 CAGACATCTT
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
81 85 0.99
82 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (81 bp):
ATTTTAACCTGAATCTCAATAGGGCACCACCTACATACTTGATTTACTATCCGTGAATGTCCCAT
TAGATTTGAAACATTA
Found at i:78981 original size:18 final size:18
Alignment explanation
Indices: 78954--78997 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
78944 TCCCTTGATT
* **
78954 ACCTCTAGTACTGGCACC
1 ACCTCGAGTACTACCACC
*
78972 ACCTCGAGTACTACCACG
1 ACCTCGAGTACTACCACC
78990 ACCTCGAG
1 ACCTCGAG
78998 CTACAGAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.39, G:0.18, T:0.18
Consensus pattern (18 bp):
ACCTCGAGTACTACCACC
Found at i:82356 original size:23 final size:25
Alignment explanation
Indices: 82304--82357 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
82294 TATATAATAA
* *
82304 TAAT-ATTATTAAAATATTATATTT
1 TAATAATTATTAAAATAATATACTT
82328 TAAATAATTATT-AAATAATA-ACTT
1 T-AATAATTATTAAAATAATATACTT
82352 TAATAA
1 TAATAA
82358 AAAAAATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 5 0.19
24 5 0.19
25 10 0.38
26 6 0.23
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TAATAATTATTAAAATAATATACTT
Found at i:91684 original size:15 final size:15
Alignment explanation
Indices: 91651--91719 Score: 52
Period size: 15 Copynumber: 4.7 Consensus size: 15
91641 CACAAGTTGT
* *
91651 TTCTCAATTTTTTTG
1 TTCTCAATTTTATTA
*
91666 TTCTCGATTTTATTA
1 TTCTCAATTTTATTA
*
91681 TTCTCAATTGTCA--A
1 TTCTCAATT-TTATTA
* *
91695 TTCTCATTTTTTTTA
1 TTCTCAATTTTATTA
*
91710 TTCTAAATTT
1 TTCTCAATTT
91720 CCAATTCCAA
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
13 1 0.02
14 9 0.22
15 29 0.71
16 2 0.05
ACGTcount: A:0.20, C:0.14, G:0.04, T:0.61
Consensus pattern (15 bp):
TTCTCAATTTTATTA
Found at i:91776 original size:22 final size:22
Alignment explanation
Indices: 91750--91811 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 22
91740 TTAAATTTCG
91750 ATTTTATTAATTCTTCGATTTT
1 ATTTTATTAATTCTTCGATTTT
* * * *
91772 TTTTTA-AAATCCTTTGATTTT
1 ATTTTATTAATTCTTCGATTTT
*
91793 ATTTTATTAATTCGTCGAT
1 ATTTTATTAATTCTTCGAT
91812 GGCATATCAA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.60
Consensus pattern (22 bp):
ATTTTATTAATTCTTCGATTTT
Found at i:92463 original size:3 final size:3
Alignment explanation
Indices: 92455--92531 Score: 147
Period size: 3 Copynumber: 26.0 Consensus size: 3
92445 TTCTAGGTCA
92455 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
92503 AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
92532 CTAAACTAAT
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 71 0.97
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:103351 original size:20 final size:22
Alignment explanation
Indices: 103313--103355 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
103303 AATCAAATAG
103313 TATTTTATATTTGTTTTGTAAA
1 TATTTTATATTTGTTTTGTAAA
103335 TATTTTA-ATTT-TTTTGTAAA
1 TATTTTATATTTGTTTTGTAAA
103355 T
1 T
103356 TACAAGAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.48
21 4 0.19
22 7 0.33
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (22 bp):
TATTTTATATTTGTTTTGTAAA
Found at i:113266 original size:26 final size:26
Alignment explanation
Indices: 113237--113286 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
113227 TCTTTCTCTT
*
113237 ATATTTTTATAATATTA-AATAATAAA
1 ATATTATTAT-ATATTATAATAATAAA
*
113263 ATATTATTATTTATTATAATAATA
1 ATATTATTATATATTATAATAATA
113287 TTATTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATATTATTATATATTATAATAATAAA
Found at i:113283 original size:18 final size:18
Alignment explanation
Indices: 113262--113302 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
113252 TAAATAATAA
*
113262 AATATTATTATTTATTAT
1 AATATTATTATTAATTAT
*
113280 AATAATATTATTAATTAT
1 AATATTATTATTAATTAT
*
113298 TATAT
1 AATAT
113303 CTTTTGATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATATTATTATTAATTAT
Found at i:113286 original size:21 final size:20
Alignment explanation
Indices: 113258--113301 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
113248 ATATTAAATA
*
113258 ATAAAATATTATTATTTATT
1 ATAAAATATTATTAATTATT
113278 ATAATAATATTATTAATTATT
1 ATAA-AATATTATTAATTATT
113299 ATA
1 ATA
113302 TCTTTTGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAAAATATTATTAATTATT
Found at i:114818 original size:13 final size:13
Alignment explanation
Indices: 114800--114826 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
114790 TGCATAGCAT
114800 AAGGACTATTATG
1 AAGGACTATTATG
114813 AAGGACTATTATG
1 AAGGACTATTATG
114826 A
1 A
114827 GCCTCTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (13 bp):
AAGGACTATTATG
Found at i:120424 original size:18 final size:18
Alignment explanation
Indices: 120384--120418 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
120374 TAAATAATAA
*
120384 AATATTATTATTTATTAT
1 AATATTATTATTAATTAT
120402 AATATTATTATTAATTA
1 AATATTATTATTAATTA
120419 ATATATCTTT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATATTATTATTAATTAT
Found at i:121493 original size:15 final size:15
Alignment explanation
Indices: 121473--121501 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
121463 ATTTTCTTCT
121473 TATATAACACAACCA
1 TATATAACACAACCA
121488 TATATAACACAACC
1 TATATAACACAACC
121502 TCACAAGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.21
Consensus pattern (15 bp):
TATATAACACAACCA
Found at i:121995 original size:28 final size:26
Alignment explanation
Indices: 121966--122140 Score: 127
Period size: 28 Copynumber: 6.4 Consensus size: 26
121956 GATAACGTCT
*
121966 TTTTCAAATATCCTTTCGGATATAACC
1 TTTTCAAATATCCTTTCGGATAT-TCC
* * *
121993 TTTTCAATGATATCCCTTCGAATATCCC
1 TTTTCAA--ATATCCTTTCGGATATTCC
* * *
122021 TTTTCATAGTATCCTTACAGATATTCC
1 TTTTCA-AATATCCTTTCGGATATTCC
* * *
122048 TTTTCATTGATATCCTTGCGGATATCCC
1 TTTTCA--AATATCCTTTCGGATATTCC
* *
122076 TTTTCAATAATATCCTTACGGATATTTC
1 TTTTC-A-AATATCCTTTCGGATATTCC
* *
122104 TTTTCAAATAT-CTATTTGGATATAACC
1 TTTTCAAATATCCT-TTCGGATAT-TCC
122131 TTTTCAAATA
1 TTTTCAAATA
122141 ATTTTAGAGC
Statistics
Matches: 119, Mismatches: 22, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
25 2 0.02
26 12 0.10
27 38 0.32
28 51 0.43
29 16 0.13
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.43
Consensus pattern (26 bp):
TTTTCAAATATCCTTTCGGATATTCC
Found at i:122034 original size:56 final size:55
Alignment explanation
Indices: 121966--122110 Score: 177
Period size: 56 Copynumber: 2.6 Consensus size: 55
121956 GATAACGTCT
*
121966 TTTTCA-AATATCCTTTCGGATATAACCTTTTCAATGATATCCCTT-CGAATATCCC
1 TTTTCATAATATCCTTACGGATAT-ACCTTTTCAATGATAT-CCTTGCGAATATCCC
* * * * *
122021 TTTTCATAGTATCCTTACAGATATTCCTTTTCATTGATATCCTTGCGGATATCCC
1 TTTTCATAATATCCTTACGGATATACCTTTTCAATGATATCCTTGCGAATATCCC
**
122076 TTTTCAATAATATCCTTACGGATATTTCTTTTCAA
1 TTTTC-ATAATATCCTTACGGATATACCTTTTCAA
122111 ATATCTATTT
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
54 4 0.05
55 34 0.44
56 39 0.51
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.43
Consensus pattern (55 bp):
TTTTCATAATATCCTTACGGATATACCTTTTCAATGATATCCTTGCGAATATCCC
Found at i:125755 original size:28 final size:28
Alignment explanation
Indices: 125723--125782 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
125713 GGCTTAGGTT
*
125723 TTAAACCTTAAACCCTAAACACATAACC
1 TTAAACCATAAACCCTAAACACATAACC
* * *
125751 TTAAACCATGAATCCTAAACATATAACC
1 TTAAACCATAAACCCTAAACACATAACC
125779 TTAA
1 TTAA
125783 CCCTAAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.47, C:0.27, G:0.02, T:0.25
Consensus pattern (28 bp):
TTAAACCATAAACCCTAAACACATAACC
Found at i:126235 original size:6 final size:6
Alignment explanation
Indices: 126198--126244 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
126188 CTACCTCTTC
* * * *
126198 CTCTAG CTTTTG CTCTTG -TCTAG CTCTGG CTCTAG CTCTAG CTCTAG
1 CTCTAG CTCTAG CTCTAG CTCTAG CTCTAG CTCTAG CTCTAG CTCTAG
126245 TGTAGGAGGC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
5 4 0.12
6 30 0.88
ACGTcount: A:0.11, C:0.30, G:0.19, T:0.40
Consensus pattern (6 bp):
CTCTAG
Found at i:129712 original size:80 final size:80
Alignment explanation
Indices: 129584--129791 Score: 312
Period size: 80 Copynumber: 2.6 Consensus size: 80
129574 TCAGTTAACT
* * * *
129584 AACTAAAGCTGGGCT-TACTTTTGCAGTTTATCCGCTAGACACTGGGTGCCAGGATTTGACGGAT
1 AACTAGAGCTGGGCTCT-CTTTTGCTGTTTATCCGCTAGGCACTGGGTGCCAAGATTTGACGGAT
129648 ATTTGTTGGTTAATCC
65 ATTTGTTGGTTAATCC
* * *
129664 AACTAGAGTTGGGCTCTCTTTTGCTGTTTATCCACTAGGCACTAGGTGCCAAGATTTGACGGATA
1 AACTAGAGCTGGGCTCTCTTTTGCTGTTTATCCGCTAGGCACTGGGTGCCAAGATTTGACGGATA
129729 TTTGTTGGTTAATCC
66 TTTGTTGGTTAATCC
*
129744 AACTAGAGCTGGGCTCACTTTTG-TGGTTTATCCGCTAGGCACTGGGTG
1 AACTAGAGCTGGGCTCTCTTTTGCT-GTTTATCCGCTAGGCACTGGGTG
129792 TCATGACCGT
Statistics
Matches: 115, Mismatches: 11, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
79 1 0.01
80 113 0.98
81 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (80 bp):
AACTAGAGCTGGGCTCTCTTTTGCTGTTTATCCGCTAGGCACTGGGTGCCAAGATTTGACGGATA
TTTGTTGGTTAATCC
Found at i:138108 original size:5 final size:5
Alignment explanation
Indices: 138098--138125 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
138088 TTTTCTAACA
138098 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
138126 AACAACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:138662 original size:147 final size:145
Alignment explanation
Indices: 138092--138679 Score: 409
Period size: 144 Copynumber: 4.0 Consensus size: 145
138082 AACTTATTTT
* * * *
138092 CTAACAAAATTAAATTAAATTAAATTAAATTA-AA-AACAACAAAACTTAC----A-TTTCTTTC
1 CTAACAAAATTAAATTAAATTAAATTAAA-AACAACAACAACAAACCTTTCTTTTAGTTTTTTTC
** *
138150 TCTCCCTTTAATCTACTCTACTAAAT----AAA--ATAACAAATCGCATAAAAATTAAAAAATTA
65 TCT-CC-TTAATCTACT-TACTAAATAAAAAAATTATAACAAATAACATAAAAATTAAATAA--A
*
138209 AACAAATAATTTATAATAATTA
125 AA-AAATATTTTATAATAATTA
* * * ** * *
138231 CTAAAAAATAACTTTAAATTAAATTAAACTAAACAAATAATTTATAATAATCACCTTTCTTTTAG
1 CT-AACAA-AA--TTAAATTAAATTAAA-TTAA-AAACAA-CAACAACAA--ACCTTTCTTTTAG
* * * * *
138296 CTTTTTTC-GTCCTCTAATCTACCTACTGAAA-AAAAACAATTATAACAAATCACATAAACATTA
57 TTTTTTTCTCTCCT-TAATCTACTTACT-AAATAAAAA-AATTATAACAAATAACATAAAAATTA
138359 AACT-AAAAAAATATTTTATAATAATTA
119 AA-TAAAAAAAATATTTTATAATAATTA
* * *
138386 CTAACAAAATTAAATTAAATTAAATTAAAAACAACAACAACAAAACTTAC----A-TTTCTTTCT
1 CTAACAAAATTAAATTAAATTAAATTAAAAACAACAACAACAAACCTTTCTTTTAGTTTTTTTCT
* * * *
138446 CTCCTTTCAGTCTACTCTACTAAATAACAAAATTAATAACAAATTACATAAAAATTAAATAAAAC
66 CTCC-TT-AATCTACT-TACTAAATAAAAAAATT-ATAACAAATAACATAAAAATTAAATAAAAA
* *
138511 AAATAATTTATAATAATTT
127 AAATATTTTATAATAATTA
* * *
138530 CT-A-AAAA-TAACTTTAAATTAAATTAAAAA-AACAA-AATATTTACCTTTCTTTTAGTTTTTT
1 CTAACAAAATTAA-ATTAAATTAAATTAAAAACAACAACAACA--AACCTTTCTTTTAGTTTTTT
* *
138590 TCTTTCCTTAATCTACTTACTAAATAAATAAAATTATAACAAATAACATTAAATATTAAAATTAA
63 TCTCTCCTTAATCTACTTACTAAATAAA-AAAATTATAACAAATAACA-TAAAAATT-AAA-TAA
138655 AAAAAATATTTTATAATAATTA
124 AAAAAATATTTTATAATAATTA
138677 CTA
1 CTA
138680 CTACTAACAA
Statistics
Matches: 353, Mismatches: 50, Indels: 83
0.73 0.10 0.17
Matches are distributed among these distances:
139 2 0.01
140 7 0.02
141 16 0.05
142 31 0.09
143 31 0.09
144 78 0.22
145 23 0.07
146 11 0.03
147 40 0.11
148 5 0.01
149 10 0.03
150 3 0.01
151 20 0.06
152 13 0.04
153 4 0.01
154 10 0.03
155 21 0.06
156 5 0.01
158 23 0.07
ACGTcount: A:0.51, C:0.14, G:0.01, T:0.35
Consensus pattern (145 bp):
CTAACAAAATTAAATTAAATTAAATTAAAAACAACAACAACAAACCTTTCTTTTAGTTTTTTTCT
CTCCTTAATCTACTTACTAAATAAAAAAATTATAACAAATAACATAAAAATTAAATAAAAAAAAT
ATTTTATAATAATTA
Found at i:143860 original size:20 final size:19
Alignment explanation
Indices: 143830--143874 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
143820 CCAAACAACC
143830 AAAACAATAGCAA-AAATAAT
1 AAAA-AATAGCAATAAA-AAT
143850 AGAAAAATAGCAATAAAAAT
1 A-AAAAATAGCAATAAAAAT
143870 AAAAA
1 AAAAA
143875 TAAAAGCAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 4 0.17
20 13 0.57
21 6 0.26
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.13
Consensus pattern (19 bp):
AAAAAATAGCAATAAAAAT
Found at i:143891 original size:23 final size:23
Alignment explanation
Indices: 143865--143987 Score: 66
Period size: 23 Copynumber: 5.6 Consensus size: 23
143855 AATAGCAATA
143865 AAAATA-AAAATAAAAGCAGC-ACC
1 AAAATAGAAAA-AAAA-CAGCAACC
*
143888 AAAATAGTAAAAAAACAGCAACC
1 AAAATAGAAAAAAAACAGCAACC
* *
143911 AAAACAG-TAAAAAA-AGC-ACC
1 AAAATAGAAAAAAAACAGCAACC
* *
143931 AAAATA-ATAAAAACACAAC-ACC
1 AAAATAGA-AAAAAAACAGCAACC
* * *
143953 GAAATAG--CAAAAATAGCAACC
1 AAAATAGAAAAAAAACAGCAACC
* *
143974 AAAACAGCAAAAAA
1 AAAATAGAAAAAAA
143988 TAGCACCAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 18
0.70 0.14 0.17
Matches are distributed among these distances:
20 14 0.18
21 16 0.21
22 20 0.26
23 23 0.30
24 3 0.04
ACGTcount: A:0.66, C:0.19, G:0.08, T:0.07
Consensus pattern (23 bp):
AAAATAGAAAAAAAACAGCAACC
Found at i:143906 original size:22 final size:21
Alignment explanation
Indices: 143876--143998 Score: 106
Period size: 22 Copynumber: 5.8 Consensus size: 21
143866 AAATAAAAAT
*
143876 AAAAGCAGCACCAAAATAGTAA
1 AAAAACAGCACCAAAATAGT-A
*
143898 AAAAACAGCAACCAAAACAGTA
1 AAAAACAGC-ACCAAAATAGTA
*
143920 AAAAA-AGCACCAAAATAATA
1 AAAAACAGCACCAAAATAGTA
* * *
143940 AAAACACAACACCGAAATAG-C
1 AAAA-ACAGCACCAAAATAGTA
* * *
143961 AAAAATAGCAACCAAAACAGCA
1 AAAAACAGC-ACCAAAATAGTA
*
143983 AAAAATAGCACCAAAA
1 AAAAACAGCACCAAAA
143999 CAACAATATA
Statistics
Matches: 83, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
20 17 0.20
21 23 0.28
22 33 0.40
23 10 0.12
ACGTcount: A:0.63, C:0.21, G:0.09, T:0.07
Consensus pattern (21 bp):
AAAAACAGCACCAAAATAGTA
Found at i:143929 original size:43 final size:42
Alignment explanation
Indices: 143882--144000 Score: 123
Period size: 42 Copynumber: 2.8 Consensus size: 42
143872 AAATAAAAGC
*
143882 AGCACCAAAATAGTAAAAAAACAGCAACCAAAACAGTAAAAAA
1 AGCACCAAAATAGTAAAAAAACAGC-ACCAAAACAGCAAAAAA
* * * * * *
143925 AGCACCAAAATAATAAAAACACAACACCGAAATAGCAAAAAT
1 AGCACCAAAATAGTAAAAAAACAGCACCAAAACAGCAAAAAA
* * *
143967 AGCAACCAAAACAG-CAAAAAATAGCACCAAAACA
1 AGC-ACCAAAATAGTAAAAAAACAGCACCAAAACA
144001 ACAATATAAT
Statistics
Matches: 60, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
42 30 0.50
43 30 0.50
ACGTcount: A:0.63, C:0.22, G:0.08, T:0.07
Consensus pattern (42 bp):
AGCACCAAAATAGTAAAAAAACAGCACCAAAACAGCAAAAAA
Found at i:145612 original size:25 final size:25
Alignment explanation
Indices: 145531--145612 Score: 60
Period size: 25 Copynumber: 3.2 Consensus size: 25
145521 AAAAAAACTC
* *
145531 AAAATAAAAAATTCATTTGCTTGAT
1 AAAATCAAAAACTCATTTGCTTGAT
** *
145556 -AAA-CAAATTTTCTCATTTGATTTGAAT
1 AAAATCAAA--AACTCATTTG-CTTG-AT
145583 CAAAATCAAAAACTCATTTGCTTGAT
1 -AAAATCAAAAACTCATTTGCTTGAT
145609 AAAA
1 AAAA
145613 CCCAAACTGG
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
23 3 0.07
24 3 0.07
25 11 0.26
26 5 0.12
27 5 0.12
28 8 0.19
29 3 0.07
30 4 0.10
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.35
Consensus pattern (25 bp):
AAAATCAAAAACTCATTTGCTTGAT
Found at i:145749 original size:11 final size:10
Alignment explanation
Indices: 145735--145803 Score: 58
Period size: 9 Copynumber: 6.9 Consensus size: 10
145725 GATGATGATT
145735 ATAATTTTAAA
1 ATAATTTT-AA
145746 ATAATTTT-A
1 ATAATTTTAA
145755 ATAATTTT--
1 ATAATTTTAA
145763 AT-ATTTTAAAAA
1 ATAATTTT---AA
145775 ATAATTTTAA
1 ATAATTTTAA
145785 ATTAATTTT-A
1 A-TAATTTTAA
145795 ATAATTTTA
1 ATAATTTTA
145804 TATTAAAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 17
0.75 0.00 0.25
Matches are distributed among these distances:
7 5 0.10
8 2 0.04
9 16 0.32
10 5 0.10
11 15 0.30
12 2 0.04
13 5 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
ATAATTTTAA
Found at i:145779 original size:40 final size:40
Alignment explanation
Indices: 145735--145832 Score: 151
Period size: 40 Copynumber: 2.5 Consensus size: 40
145725 GATGATGATT
**
145735 ATAATTTTAAAATAATTTTAATAATTTTATATTTTAAAAA
1 ATAATTTTAAAATAATTTTAATAATTTTATATTAAAAAAA
*
145775 ATAATTTTAAATTAATTTTAATAATTTTATATTAAAAAAA
1 ATAATTTTAAAATAATTTTAATAATTTTATATTAAAAAAA
* *
145815 ACAATTTTAAAATCATTT
1 ATAATTTTAAAATAATTT
145833 GCTGATATGG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (40 bp):
ATAATTTTAAAATAATTTTAATAATTTTATATTAAAAAAA
Found at i:145808 original size:20 final size:20
Alignment explanation
Indices: 145735--145809 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
145725 GATGATGATT
*
145735 ATAATTTTAAAATAATTTTA
1 ATAATTTTAAATTAATTTTA
* **
145755 ATAATTTTATATT--TTAAAAA
1 ATAATTTTAAATTAATT--TTA
145775 ATAATTTTAAATTAATTTTA
1 ATAATTTTAAATTAATTTTA
*
145795 ATAATTTTATATTAA
1 ATAATTTTAAATTAA
145810 AAAAAACAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
18 2 0.05
20 39 0.91
22 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAATTTTAAATTAATTTTA
Found at i:157598 original size:25 final size:25
Alignment explanation
Indices: 157570--157618 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
157560 TGAGCAATTT
*
157570 AATTTTTTTCCTTTTATGTTCTTTA
1 AATTTTCTTCCTTTTATGTTCTTTA
* * *
157595 AATTTTCTTCTTTTTTTTTTCTTT
1 AATTTTCTTCCTTTTATGTTCTTT
157619 TTTTTCTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.73
Consensus pattern (25 bp):
AATTTTCTTCCTTTTATGTTCTTTA
Found at i:171408 original size:33 final size:33
Alignment explanation
Indices: 171370--171439 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
171360 ATAATAAATT
* * *
171370 ATATTTAAATAATTTAATATAATGATACATGAA
1 ATATTTAAATAATTTAAAATAATGATAAATAAA
*
171403 ATATTTAAATAATTTAAAATAATTATAAATAAA
1 ATATTTAAATAATTTAAAATAATGATAAATAAA
171436 ATAT
1 ATAT
171440 AAATTAATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (33 bp):
ATATTTAAATAATTTAAAATAATGATAAATAAA
Found at i:172301 original size:32 final size:31
Alignment explanation
Indices: 172264--172344 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
172254 GGATGTCAAA
*
172264 AAGTTTAAGTATCAACTTAAAAAAAAACTGTC
1 AAGTTTAAGTATCAAATT-AAAAAAAACTGTC
* * * *
172296 AAGTTTAGGTACCAAATTAAGAAAAAGTGTC
1 AAGTTTAAGTATCAAATTAAAAAAAACTGTC
*
172327 AAGTTTGAGTATCAAATT
1 AAGTTTAAGTATCAAATT
172345 GGATTAAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 26 0.63
32 15 0.37
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.30
Consensus pattern (31 bp):
AAGTTTAAGTATCAAATTAAAAAAAACTGTC
Found at i:172327 original size:31 final size:30
Alignment explanation
Indices: 172286--172401 Score: 98
Period size: 31 Copynumber: 3.9 Consensus size: 30
172276 CAACTTAAAA
*
172286 AAAAACTGTCAAGTTTAGGTACCAAATTAAG
1 AAAAAGTGTCAAGTTTAGGTACCAAATT-AG
* *
172317 AAAAAGTGTCAAGTTT-GAGTATCAAATTGG
1 AAAAAGTGTCAAGTTTAG-GTACCAAATTAG
*
172347 ATTAAAA----AAAGTTTAGGTACCAAATTAG
1 A--AAAAGTGTCAAGTTTAGGTACCAAATTAG
* * *
172375 AAACAGTGTCAAATTCAGGTACCAAAT
1 AAAAAGTGTCAAGTTTAGGTACCAAAT
172402 GTTATATTAA
Statistics
Matches: 67, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
26 3 0.04
28 17 0.25
29 1 0.01
30 18 0.27
31 24 0.36
32 4 0.06
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.27
Consensus pattern (30 bp):
AAAAAGTGTCAAGTTTAGGTACCAAATTAG
Found at i:176307 original size:4 final size:4
Alignment explanation
Indices: 176251--176290 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
176241 AGGCAGTCTG
*
176251 CATA CATA CATA TATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
176291 TATATATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.28
Consensus pattern (4 bp):
CATA
Found at i:185056 original size:31 final size:30
Alignment explanation
Indices: 184994--185056 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
184984 CAAATTGGGT
** * *
184994 ACCCAATTTTTAGGTATTTTCGTTTTGATC
1 ACCCAATTTTTAGACATTTTCATTTTAATC
185024 ACCCAATTTTTAAGACATTTTCATTTTAATC
1 ACCCAATTTTT-AGACATTTTCATTTTAATC
185055 AC
1 AC
185057 TCTAGCGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 11 0.39
31 17 0.61
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.46
Consensus pattern (30 bp):
ACCCAATTTTTAGACATTTTCATTTTAATC
Found at i:186236 original size:18 final size:18
Alignment explanation
Indices: 186200--186237 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
186190 TGAATTTTCG
*
186200 AATTCAAATAACTCGAAT
1 AATTCAAATAACTCAAAT
186218 AATTCAAATAAAC-CAAAT
1 AATTCAAAT-AACTCAAAT
186236 AA
1 AA
186238 AACTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.58, C:0.16, G:0.03, T:0.24
Consensus pattern (18 bp):
AATTCAAATAACTCAAAT
Found at i:186447 original size:34 final size:34
Alignment explanation
Indices: 186377--186449 Score: 112
Period size: 34 Copynumber: 2.1 Consensus size: 34
186367 AAACTAAATT
* *
186377 CAAATATTTTTAATTTTTTACTTTTTATCTTTTC
1 CAAATATTTTTAATTTTTTACCTTTTATCTTATC
186411 CAAATATTTTTAATTTTTTACCTTTTA-CATTATC
1 CAAATATTTTTAATTTTTTACCTTTTATC-TTATC
186445 CAAAT
1 CAAAT
186450 GTTGTTTACT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 1 0.03
34 35 0.97
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.58
Consensus pattern (34 bp):
CAAATATTTTTAATTTTTTACCTTTTATCTTATC
Found at i:194765 original size:14 final size:13
Alignment explanation
Indices: 194739--194763 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
194729 AGGAATTATG
194739 ATTTAAATTTTTA
1 ATTTAAATTTTTA
194752 ATTTAAATTTTT
1 ATTTAAATTTTT
194764 TATAATTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTAAATTTTTA
Found at i:199601 original size:30 final size:29
Alignment explanation
Indices: 199567--199824 Score: 157
Period size: 30 Copynumber: 8.6 Consensus size: 29
199557 ACCCTCGAGC
199567 TTTCTAAAAATTCATTTTTGACCCCTAAAT
1 TTTCTAAAAATTCA-TTTTGACCCCTAAAT
* * *
199597 TTTCT-AAAATATCATTTTCGACCCTTGAAC
1 TTTCTAAAAAT-TCATTTT-GACCCCTAAAT
* * *
199627 TTTCTAAAATTTTAATTTTGACCCTTAAAT
1 TTTCTAAAA-ATTCATTTTGACCCCTAAAT
* * * * *
199657 TTTCTATAATTTCATTTTCAACCCTTAAAC
1 TTTCTAAAAATTCATTTT-GACCCCTAAAT
* * * * *
199687 TTTCTAAAATTTTATTTT-AGCCCAAAAC
1 TTTCTAAAAATTCATTTTGACCCCTAAAT
* * * *
199715 TTTATGGAAATTTCATTTTGACCCTTAAACT
1 TTTCT-AAAAATTCATTTTGACCCCTAAA-T
*
199746 TTT-TAAAAATTTCATTTTAACCCCTAAACT
1 TTTCTAAAAA-TTCATTTTGACCCCTAAA-T
* *
199776 TTT-TTAAAATTGCATTTTGACCCTCAAAAT
1 TTTCTAAAAATT-CATTTTGACCC-CTAAAT
199806 TTT-TGAAAAATTACATTTT
1 TTTCT-AAAAATT-CATTTT
199825 AGCCTCTAAA
Statistics
Matches: 184, Mismatches: 32, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
28 11 0.06
29 33 0.18
30 111 0.60
31 28 0.15
32 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.45
Consensus pattern (29 bp):
TTTCTAAAAATTCATTTTGACCCCTAAAT
Found at i:199633 original size:60 final size:58
Alignment explanation
Indices: 199566--199824 Score: 241
Period size: 60 Copynumber: 4.3 Consensus size: 58
199556 TACCCTCGAG
* *
199566 CTTTCTAAAAATTCATTTTTGACCCCTAAATTTTCTAAAATATCATTTTCGACCCTTGAA
1 CTTTCTAAAAATTCA-TTTTGACCCCTAAATTTTCTAAAATTTCATTTT-GACCCTTAAA
* * * * *
199626 CTTTCTAAAATTTTAATTTTGACCCTTAAATTTTCTATAATTTCATTTTCAACCCTTAAA
1 CTTTCTAAAA-ATTCATTTTGACCCCTAAATTTTCTAAAATTTCATTTT-GACCCTTAAA
* * * * * * *
199686 CTTTCTAAAATTTTATTTT-AGCCCAAAACTTTATGGAAATTTCATTTTGACCCTTAAA
1 CTTTCTAAAAATTCATTTTGACCCCTAAATTTTCT-AAAATTTCATTTTGACCCTTAAA
* * * * *
199744 CTTTTTAAAAATTTCATTTTAACCCCTAAACTTTTTTAAAATTGCATTTTGACCCTCAAA
1 CTTTCTAAAAA-TTCATTTTGACCCCTAAA-TTTTCTAAAATTTCATTTTGACCCTTAAA
* *
199804 ATTTTTGAAAAATTACATTTT
1 CTTTCT-AAAAATT-CATTTT
199825 AGCCTCTAAA
Statistics
Matches: 165, Mismatches: 27, Indels: 13
0.80 0.13 0.06
Matches are distributed among these distances:
58 28 0.17
59 26 0.16
60 93 0.56
61 18 0.11
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.45
Consensus pattern (58 bp):
CTTTCTAAAAATTCATTTTGACCCCTAAATTTTCTAAAATTTCATTTTGACCCTTAAA
Found at i:206805 original size:18 final size:18
Alignment explanation
Indices: 206778--206819 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
206768 ATGATCCCTA
*
206778 ATGCAAATTAACCTAAGT
1 ATGCAGATTAACCTAAGT
206796 ATGCAGATTAACCTAAGT
1 ATGCAGATTAACCTAAGT
206814 ATGCAG
1 ATGCAG
206820 GGTATATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (18 bp):
ATGCAGATTAACCTAAGT
Found at i:207820 original size:23 final size:22
Alignment explanation
Indices: 207789--207832 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
207779 AAAGAAATAA
*
207789 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
207811 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
207833 GAAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:208846 original size:15 final size:15
Alignment explanation
Indices: 208826--208855 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
208816 CTCTCGATAG
208826 TACTCTTGACAAAAT
1 TACTCTTGACAAAAT
208841 TACTCTTGACAAAAT
1 TACTCTTGACAAAAT
208856 GGACTGTAGA
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:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (15 bp):
TACTCTTGACAAAAT
Found at i:215017 original size:38 final size:38
Alignment explanation
Indices: 214893--215305 Score: 283
Period size: 39 Copynumber: 10.7 Consensus size: 38
214883 ATTTTATAAG
* * ** *
214893 TCTCTTACCCTGATCATGGGGCAAATCAAAGCATTCAAA
1 TCTCTTACCCCGATCATGGGGCAGATTGAAGCA-TCCAA
** ** * * * **
214932 TCTCTTACCCTAATCAAAGGGAAAATTAAAGACCGCCAA
1 TCTCTTACCCCGATCATGGGGCAGATTGAAG-CATCCAA
214971 TCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAA
1 TCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAA
* *** * *
215009 TCTTTTACCTTAATCA-GAAGGCAAATTGAAGACA-CAACAA
1 TCTCTTACCCCGATCATG-GGGCAGATTGAAG-CATC--CAA
* * *
215049 TCTCTTACCCCGATCATGGGACAAATTGAAGCATCTAA
1 TCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAA
* *** ** * *
215087 TCTTTTACCTTAATCA-GAATGCCGATTGAAGACATCAAA
1 TCTCTTACCCCGATCATG-GGGCAGATTGAAG-CATCCAA
* *
215126 TCTCTTACCCCGATCATGGGGCAAATTGAAGCATCCAG
1 TCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAA
*** *** **
215164 TCTCTTACCTTAATCAAAAGGCAGATTGAAGACATGTAA
1 TCTCTTACCCCGATCATGGGGCAGATTGAAG-CATCCAA
* **
215203 TCTCTTACCCTGATCATGGAACAGATTGAAGCATCCAA
1 TCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAA
** *
215241 TCTCTTACCCCGATCATGGGGCAGATTGAAAAAACTCAA
1 TCTCTTACCCCGATCATGGGGCAGATTGAAGCATC-CAA
*
215280 TCTCTTACCCCAATCATGGGGCAGAT
1 TCTCTTACCCCGATCATGGGGCAGAT
215306 AGAAAACACA
Statistics
Matches: 286, Mismatches: 76, Indels: 24
0.74 0.20 0.06
Matches are distributed among these distances:
37 2 0.01
38 114 0.40
39 140 0.49
40 29 0.10
41 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (38 bp):
TCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAA
Found at i:215137 original size:155 final size:154
Alignment explanation
Indices: 214969--215249 Score: 436
Period size: 155 Copynumber: 1.8 Consensus size: 154
214959 AAAGACCGCC
* * *
214969 AATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAAGGCAAA
1 AATCTCTTACCCCGATCATGGGGCAAATTGAAGCATCCAATCTCTTACCTTAATCAAAAGGCAAA
* * *
215034 TTGAAGACACAACAATCTCTTACCCCGATCATGGGACAAATTGAAGCATCTAATCTTTTACCTTA
66 TTGAAGACA-AACAATCTCTTACCCCGATCATGGAACAAATTGAAGCATCCAATCTCTTACCTTA
215099 ATCAGAATGCCGATTGAAGACATCA
130 ATCAGAATGCCGATTGAAGACATCA
* *
215124 AATCTCTTACCCCGATCATGGGGCAAATTGAAGCATCCAGTCTCTTACCTTAATCAAAAGGCAGA
1 AATCTCTTACCCCGATCATGGGGCAAATTGAAGCATCCAATCTCTTACCTTAATCAAAAGGCAAA
*** * *
215189 TTGAAGACATGTAATCTCTTACCCTGATCATGGAACAGATTGAAGCATCCAATCTCTTACC
66 TTGAAGACAAACAATCTCTTACCCCGATCATGGAACAAATTGAAGCATCCAATCTCTTACC
215250 CCGATCATGG
Statistics
Matches: 113, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
154 44 0.39
155 69 0.61
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.27
Consensus pattern (154 bp):
AATCTCTTACCCCGATCATGGGGCAAATTGAAGCATCCAATCTCTTACCTTAATCAAAAGGCAAA
TTGAAGACAAACAATCTCTTACCCCGATCATGGAACAAATTGAAGCATCCAATCTCTTACCTTAA
TCAGAATGCCGATTGAAGACATCA
Found at i:215305 original size:77 final size:76
Alignment explanation
Indices: 214893--215305 Score: 425
Period size: 77 Copynumber: 5.3 Consensus size: 76
214883 ATTTTATAAG
* * ** * * * *
214893 TCTCTTACCCTGATCATGGGGCAAATCAAAGCATTCAAATCTCTTACCCTAATCA-AAGGGAAAA
1 TCTCTTACCCCGATCATGGGGCAGATTGAAGCA-TCCAATCTCTTACCTTAATCAGAA-GGCAGA
* **
214957 TTAAAGACCGCCAA
64 TTGAAGA-CATCAA
* *
214971 TCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAAGGCAAATT
1 TCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATT
*
215036 GAAGACACAACAA
66 GAAG--ACATCAA
* * * * * *
215049 TCTCTTACCCCGATCATGGGACAAATTGAAGCATCTAATCTTTTACCTTAATCAGAATGCCGATT
1 TCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATT
215114 GAAGACATCAAA
66 GAAGACATC-AA
* * *
215126 TCTCTTACCCCGATCATGGGGCAAATTGAAGCATCCAGTCTCTTACCTTAATCAAAAGGCAGATT
1 TCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATT
*
215191 GAAGACATGTAA
66 GAAGACAT-CAA
* ** *** *
215203 TCTCTTACCCTGATCATGGAACAGATTGAAGCATCCAATCTCTTACCCCGATCATG-GGGCAGAT
1 TCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTCTTACCTTAATCA-GAAGGCAGAT
* *
215267 TGAAAAAACTCAA
65 TGAAGACA-TCAA
*
215280 TCTCTTACCCCAATCATGGGGCAGAT
1 TCTCTTACCCCGATCATGGGGCAGAT
215306 AGAAAACACA
Statistics
Matches: 285, Mismatches: 43, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
76 4 0.01
77 181 0.64
78 99 0.35
79 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (76 bp):
TCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATT
GAAGACATCAA
Found at i:215311 original size:39 final size:40
Alignment explanation
Indices: 215238--215330 Score: 143
Period size: 39 Copynumber: 2.4 Consensus size: 40
215228 TTGAAGCATC
* *
215238 CAATCTCTTACCCCGATCATGGGGCAGATTGAAAAAAC-T
1 CAATCTCTTACCCCAATCATGGGGCAGATAGAAAAAACAT
*
215277 CAATCTCTTACCCCAATCATGGGGCAGATAGAAAACACAT
1 CAATCTCTTACCCCAATCATGGGGCAGATAGAAAAAACAT
*
215317 CAATTTCTTACCCC
1 CAATCTCTTACCCC
215331 GAACGTAGGG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 35 0.71
40 14 0.29
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (40 bp):
CAATCTCTTACCCCAATCATGGGGCAGATAGAAAAAACAT
Found at i:215342 original size:40 final size:39
Alignment explanation
Indices: 215238--215344 Score: 135
Period size: 39 Copynumber: 2.7 Consensus size: 39
215228 TTGAAGCATC
* *
215238 CAATCTCTTACCCCGATCATGGGGCAGATTGAAAAAACT
1 CAATCTCTTACCCCGAACATGGGGCAGATAGAAAAAACT
*
215277 CAATCTCTTACCCC-AATCATGGGGCAGATAGAAAACACAT
1 CAATCTCTTACCCCGAA-CATGGGGCAGATAGAAAAAAC-T
* * *
215317 CAATTTCTTACCCCGAACGTAGGGCAGA
1 CAATCTCTTACCCCGAACATGGGGCAGA
215345 CTGAGGGTGA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
38 1 0.02
39 33 0.56
40 23 0.39
41 2 0.03
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (39 bp):
CAATCTCTTACCCCGAACATGGGGCAGATAGAAAAAACT
Done.