Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2735
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: 74816
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Found at i:216 original size:29 final size:29
Alignment explanation
Indices: 184--241 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
174 TCAAATACAT
184 AATAATAATAATTT-ATTAAATTATTTTAA
1 AATAATAATAATTTGA-TAAATTATTTTAA
* * *
213 AATAATATTATTTTGATAATTTATTTTAA
1 AATAATAATAATTTGATAAATTATTTTAA
242 GTATAGTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
AATAATAATAATTTGATAAATTATTTTAA
Found at i:542 original size:18 final size:18
Alignment explanation
Indices: 519--563 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
509 CACGAGTTAC
519 TTATTTAAATTAAAAAAA
1 TTATTTAAATTAAAAAAA
* *
537 TTATTTGATATTTAAAAAA
1 TTATTT-AAATTAAAAAAA
556 TT-TTTAAA
1 TTATTTAAA
564 AAATAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 2 0.09
18 9 0.39
19 12 0.52
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTATTTAAATTAAAAAAA
Found at i:713 original size:20 final size:20
Alignment explanation
Indices: 662--713 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
652 CCTAATATGG
662 TTATATA-ATATGTATTATAT
1 TTATATATAT-TGTATTATAT
*
682 TTATTATATATTGTATTATTT
1 TTA-TATATATTGTATTATAT
703 TTATATATATT
1 TTATATATATT
714 AATAATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 11 0.38
21 16 0.55
22 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
TTATATATATTGTATTATAT
Found at i:1208 original size:21 final size:22
Alignment explanation
Indices: 1153--1210 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
1143 ATTCAAATTG
*
1153 ATTTAAT-TTAATTTATTATTT
1 ATTTAATATTAATATATTATTT
** **
1174 AAATAATAAAAATATATT-TTT
1 ATTTAATATTAATATATTATTT
1195 ATTTAATATTAATATA
1 ATTTAATATTAATATA
1211 AAATAAAAAT
Statistics
Matches: 27, Mismatches: 9, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTAATATTAATATATTATTT
Found at i:1213 original size:28 final size:27
Alignment explanation
Indices: 1162--1233 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 27
1152 GATTTAATTT
1162 AATTTATTATTTAA-A-TAATAAAAATA
1 AATTT-TTATTTAATATTAATAAAAATA
*
1188 TATTTTTATTTAATATTAATATAAAATA
1 AATTTTTATTTAATATTAATA-AAAATA
**
1216 AAAATTTATTTTAATATT
1 AATTTTTA-TTTAATATT
1234 TTAATAGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
25 8 0.21
26 5 0.13
27 5 0.13
28 11 0.29
29 9 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
AATTTTTATTTAATATTAATAAAAATA
Found at i:4184 original size:16 final size:16
Alignment explanation
Indices: 4165--4219 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
4155 AAAGCCTAAT
4165 AATTTAAAAGTATCTA
1 AATTTAAAAGTATCTA
* *
4181 AATTTAAAACTA-AT-
1 AATTTAAAAGTATCTA
4195 AATTTAAAAGTATCTA
1 AATTTAAAAGTATCTA
4211 AATTTAAAA
1 AATTTAAAA
4220 CTTAAGCTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 11 0.33
15 2 0.06
16 20 0.61
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (16 bp):
AATTTAAAAGTATCTA
Found at i:4196 original size:30 final size:30
Alignment explanation
Indices: 4160--4221 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
4150 CTCTCAAAGC
4160 CTAATAATTTAAAAGTATCTAAATTTAAAA
1 CTAATAATTTAAAAGTATCTAAATTTAAAA
4190 CTAATAATTTAAAAGTATCTAAATTTAAAA
1 CTAATAATTTAAAAGTATCTAAATTTAAAA
4220 CT
1 CT
4222 TAAGCTATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.37
Consensus pattern (30 bp):
CTAATAATTTAAAAGTATCTAAATTTAAAA
Found at i:5629 original size:3 final size:3
Alignment explanation
Indices: 5621--5650 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5611 GACTTTGAGC
5621 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5651 CATGATCATC
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:6461 original size:16 final size:15
Alignment explanation
Indices: 6425--6457 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
6415 TATATTATAA
6425 TTATATTAAAAAATT
1 TTATATTAAAAAATT
*
6440 TTATATTATAAAATT
1 TTATATTAAAAAATT
6455 TTA
1 TTA
6458 ATATATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATATTAAAAAATT
Found at i:6502 original size:10 final size:9
Alignment explanation
Indices: 6399--6542 Score: 56
Period size: 8 Copynumber: 16.0 Consensus size: 9
6389 TCCTAGTAAT
6399 ATATTTA-A
1 ATATTTATA
*
6407 ATATTTATT
1 ATATTTATA
6416 ATA-TTATA
1 ATATTTATA
*
6424 ATTATATTAAA
1 A-TAT-TTATA
*
6435 AAATTT-T-
1 ATATTTATA
6442 ATA-TTATA
1 ATATTTATA
*
6450 AAATTT-TA
1 ATATTTATA
6458 ATATATTATTA
1 ATAT-TTA-TA
*
6469 ATATGCCTATA
1 ATAT--TTATA
*
6480 AT-TTAATA
1 ATATTTATA
6488 ATATTTATA
1 ATATTTATA
*
6497 ATTATTTATT
1 A-TATTTATA
6507 ATA-TTATA
1 ATATTTATA
*
6515 ATTATATTAAAA
1 A-TAT-TT-ATA
6527 ATATTT-T-
1 ATATTTATA
6534 ATATTTATA
1 ATATTTATA
6543 TAAATTTTGA
Statistics
Matches: 100, Mismatches: 17, Indels: 37
0.65 0.11 0.24
Matches are distributed among these distances:
6 2 0.02
7 9 0.09
8 30 0.30
9 21 0.21
10 13 0.13
11 20 0.20
12 5 0.05
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (9 bp):
ATATTTATA
Found at i:6658 original size:5 final size:5
Alignment explanation
Indices: 6648--6694 Score: 66
Period size: 5 Copynumber: 10.2 Consensus size: 5
6638 AATTTTATTA
6648 TATAT TATAT TAT-T TATAT TATAT TATAT T-TAT T-T-T TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
6694 T
1 T
6695 TAACATGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
3 2 0.05
4 10 0.26
5 27 0.69
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (5 bp):
TATAT
Found at i:6688 original size:17 final size:20
Alignment explanation
Indices: 6648--6696 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
6638 AATTTTATTA
6648 TATATTATA-TTATTTATAT
1 TATATTATATTTATTTATAT
6667 TATATTATATTTA-TT-T-T
1 TATATTATATTTATTTATAT
6684 TATATTATATTTA
1 TATATTATATTTA
6697 ACATGATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.48
18 1 0.03
19 11 0.38
20 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TATATTATATTTATTTATAT
Found at i:7058 original size:16 final size:17
Alignment explanation
Indices: 7001--7060 Score: 61
Period size: 16 Copynumber: 3.5 Consensus size: 17
6991 AATTAAAAAA
*
7001 ATAATAAAT-AAATTAT
1 ATAATTAATAAAATTAT
**
7017 ATAATTTTTAAATATTAT
1 ATAATTAATAAA-ATTAT
7035 ATTAATTAATAAAATTAT
1 A-TAATTAATAAAATTAT
7053 AT-ATTAAT
1 ATAATTAAT
7061 TAATATTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
16 12 0.33
17 3 0.08
18 12 0.33
19 9 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAATTAATAAAATTAT
Found at i:8373 original size:22 final size:22
Alignment explanation
Indices: 8345--8406 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
8335 AAATTTTGTA
8345 AATAATTTTTTATTAAATAAAT
1 AATAATTTTTTATTAAATAAAT
** *
8367 AATAA-TTTAAATTAAATTAAT
1 AATAATTTTTTATTAAATAAAT
8388 AA-AATATTTTTATTTAAAT
1 AATAAT-TTTTTA-TTAAAT
8407 TTAATTTTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.06
21 15 0.47
22 9 0.28
23 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTTTATTAAATAAAT
Found at i:13217 original size:22 final size:21
Alignment explanation
Indices: 13174--13213 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
13164 ATATTTTATT
13174 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
13195 TAAATATTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
13214 ATATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:13832 original size:30 final size:28
Alignment explanation
Indices: 13797--13868 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 28
13787 AAATATTTTA
* *
13797 AAAAAATTAATTTAATTATTATTTAATAAT
1 AAAAAATTAATTTAAAT-TTAATTAA-AAT
*
13827 AAAAAATTTTATTTAAATTTAATTAAAAT
1 AAAAAA-TTAATTTAAATTTAATTAAAAT
13856 ATAAAATATTAAT
1 A-AAAA-ATTAAT
13869 ATTTTTTTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
29 4 0.11
30 21 0.60
31 10 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AAAAAATTAATTTAAATTTAATTAAAAT
Found at i:15234 original size:2 final size:2
Alignment explanation
Indices: 15227--15255 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
15217 TTCATTGGCA
15227 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15256 TACAAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21832 original size:18 final size:20
Alignment explanation
Indices: 21792--21830 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21782 TTGAATGGTG
*
21792 TTTTTATTTTTATGTATATA
1 TTTTTATTTTTATATATATA
*
21812 TTTTTATTTTAATATATAT
1 TTTTTATTTTTATATATAT
21831 TTATAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTTTATTTTTATATATATA
Found at i:22929 original size:12 final size:12
Alignment explanation
Indices: 22908--22969 Score: 58
Period size: 12 Copynumber: 5.4 Consensus size: 12
22898 TTATGTTGTA
* *
22908 TTTATATTATTT
1 TTTATTTTATAT
22920 TTTATTTTATAT
1 TTTATTTTATAT
*
22932 TTTATTTTGTAT
1 TTTATTTTATAT
**
22944 CGTATTTTA-A-
1 TTTATTTTATAT
22954 TTT-TTTTATAT
1 TTTATTTTATAT
22965 TTTAT
1 TTTAT
22970 AATAATATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
9 5 0.13
10 2 0.05
11 4 0.10
12 28 0.72
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.73
Consensus pattern (12 bp):
TTTATTTTATAT
Found at i:24213 original size:15 final size:17
Alignment explanation
Indices: 24184--24217 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
24174 CTAAATTCAT
24184 TATTTTATAATTAAAAA
1 TATTTTATAATTAAAAA
24201 TATTTTA-AA-TAAAAA
1 TATTTTATAATTAAAAA
24216 TA
1 TA
24218 ATAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 2 0.12
17 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTTTATAATTAAAAA
Found at i:24638 original size:19 final size:17
Alignment explanation
Indices: 24596--24641 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 17
24586 TTTATTTAAT
24596 TTTAATTATAAAAATATA
1 TTTAA-TATAAAAATATA
24614 TATTAATATAAAAATAATAA
1 T-TTAATATAAAAAT-AT-A
24634 TTTAATAT
1 TTTAATAT
24642 TTTAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.40
19 13 0.52
20 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAATATAAAAATATA
Found at i:25238 original size:30 final size:31
Alignment explanation
Indices: 25204--25279 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 31
25194 ATTCGATAAT
*
25204 ATTAAATATGATATAAAAATAAT-TAAAATA
1 ATTAAATATAATATAAAAATAATATAAAATA
*
25234 ATTAAATATAATATAAAAATAATATAAATTTA
1 ATTAAATATAATATAAAAATAATATAAA-ATA
25266 ATATAAATA-AATAT
1 AT-TAAATATAATAT
25280 TTTAAAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 22 0.54
31 4 0.10
32 9 0.22
33 6 0.15
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (31 bp):
ATTAAATATAATATAAAAATAATATAAAATA
Found at i:25273 original size:11 final size:11
Alignment explanation
Indices: 25199--25279 Score: 89
Period size: 11 Copynumber: 7.6 Consensus size: 11
25189 AACCGATTCG
25199 ATAATATTAAAT
1 ATAATA-TAAAT
* *
25211 ATGATATAAAA
1 ATAATATAAAT
25222 ATAAT-TAAA-
1 ATAATATAAAT
25231 ATAAT-TAAAT
1 ATAATATAAAT
*
25241 ATAATATAAAA
1 ATAATATAAAT
25252 ATAATATAAAT
1 ATAATATAAAT
*
25263 TTAATATAAAT
1 ATAATATAAAT
25274 A-AATAT
1 ATAATAT
25280 TTTAAAATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
9 9 0.15
10 14 0.23
11 32 0.53
12 5 0.08
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:25277 original size:24 final size:23
Alignment explanation
Indices: 25229--25307 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 23
25219 AAAATAATTA
*
25229 AAATAATTAAATATAATAT-AA-
1 AAATAATTAAATTTAATATAAAT
25250 AAATAATATAAATTTAATATAAAT
1 AAATAAT-TAAATTTAATATAAAT
*
25274 AAATATTTTAAAATTT-ATATAATAT
1 AAATA-ATT-AAATTTAATATAA-AT
*
25299 AAATTATTA
1 AAATAATTA
25308 TTATATTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
21 7 0.15
22 11 0.23
23 3 0.06
24 14 0.29
25 13 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATAATTAAATTTAATATAAAT
Found at i:25281 original size:17 final size:17
Alignment explanation
Indices: 25261--25354 Score: 53
Period size: 17 Copynumber: 5.9 Consensus size: 17
25251 AATAATATAA
25261 ATTTAATATAAATAAAT
1 ATTTAATATAAATAAAT
*
25278 ATTT--TA-AAAT--TT
1 ATTTAATATAAATAAAT
* * *
25290 ATATAATATAAATTATT
1 ATTTAATATAAATAAAT
* *
25307 ATTATATTA-AAATATAT
1 ATT-TAATATAAATAAAT
25324 A-TTAATATAAATAAA-
1 ATTTAATATAAATAAAT
25339 ATTATAATAT-AATAAA
1 ATT-TAATATAAATAAA
25355 ATACACAAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 19
0.68 0.10 0.22
Matches are distributed among these distances:
12 4 0.07
14 6 0.10
15 11 0.19
16 14 0.24
17 20 0.34
18 4 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTAATATAAATAAAT
Found at i:25311 original size:20 final size:20
Alignment explanation
Indices: 25288--25343 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
25278 ATTTTAAAAT
25288 TTATATAATATAAATTATTA
1 TTATATAATATAAATTATTA
* *
25308 TTATATTAAAATATA-TATTA
1 TTATA-TAATATAAATTATTA
*
25328 ATATA-AATA-AAATTAT
1 TTATATAATATAAATTAT
25344 AATATAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
17 2 0.07
18 6 0.21
20 14 0.48
21 7 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTATATAATATAAATTATTA
Found at i:26874 original size:16 final size:13
Alignment explanation
Indices: 26868--26901 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
26858 TTCAATAAAT
26868 ATAATTTTAAAAA
1 ATAATTTTAAAAA
26881 ATAATTATT-AAAA
1 ATAATT-TTAAAAA
26894 ATAATTTT
1 ATAATTTT
26902 TTATTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 2 0.10
13 16 0.80
14 2 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAATTTTAAAAA
Found at i:26886 original size:13 final size:12
Alignment explanation
Indices: 26863--26901 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
26853 TTATTTTCAA
*
26863 TAAATATAATTT
1 TAAAAATAATTT
26875 TAAAAAATAATTAT
1 T-AAAAATAATT-T
26889 TAAAAATAATTT
1 TAAAAATAATTT
26901 T
1 T
26902 TTATTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 3 0.12
13 19 0.79
14 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAATAATTT
Found at i:27751 original size:30 final size:28
Alignment explanation
Indices: 27668--27754 Score: 79
Period size: 30 Copynumber: 3.0 Consensus size: 28
27658 ATTTTTATTA
27668 TATTCAAACATAA-TTTTAAT-TTAATTTG
1 TATTCAAA-A-AATTTTTAATCTTAATTTG
* * *
27696 CATCCAAAAAAGTTATTAACTCTTAATTTG
1 TATTCAAAAAA-TTTTTAA-TCTTAATTTG
27726 TATTCAAATAAATTTTTAATACTTAATTT
1 TATTCAAA-AAATTTTTAAT-CTTAATTT
27755 ATATATAACT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
26 2 0.04
27 1 0.02
28 11 0.23
29 2 0.04
30 28 0.60
31 3 0.06
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.46
Consensus pattern (28 bp):
TATTCAAAAAATTTTTAATCTTAATTTG
Found at i:28074 original size:21 final size:22
Alignment explanation
Indices: 28050--28127 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 22
28040 AACTCAAAAA
28050 AAATTATAAAAATTAA-TATTT
1 AAATTATAAAAATTAATTATTT
*
28071 AAA-TATAATAAATTAATTAAATT
1 AAATTATAA-AAATTAATT-ATTT
* *
28094 AAATT-TTAAATTTAATTATTT
1 AAATTATAAAAATTAATTATTT
*
28115 AATATTAAAAAAA
1 AA-ATTATAAAAA
28128 ATAAAAGTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
20 5 0.11
21 15 0.34
22 12 0.27
23 11 0.25
24 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATTATAAAAATTAATTATTT
Found at i:28429 original size:17 final size:17
Alignment explanation
Indices: 28407--28455 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
28397 ATATAAATTT
28407 TTTATATTTTTTAATAA
1 TTTATATTTTTTAATAA
28424 TTTATATTTTTTAATAA
1 TTTATATTTTTTAATAA
*
28441 TTTATATTTTATAAT
1 TTTATATTTTTTAAT
28456 TTTTAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTATATTTTTTAATAA
Found at i:35396 original size:23 final size:23
Alignment explanation
Indices: 35363--35416 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
35353 ATTAAACTCA
*
35363 ATAATATTAAAAAAATAA-AATTAT
1 ATAATA-T-AAAAAATAATAATAAT
*
35387 ATAATATAAAAAATAATTATAAT
1 ATAATATAAAAAATAATAATAAT
35410 ATAATAT
1 ATAATAT
35417 TAAATATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 9 0.33
23 12 0.44
24 6 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
ATAATATAAAAAATAATAATAAT
Found at i:35422 original size:12 final size:12
Alignment explanation
Indices: 35385--35482 Score: 50
Period size: 11 Copynumber: 8.2 Consensus size: 12
35375 AAATAAAATT
35385 ATATAATA-TAA
1 ATATAATATTAA
35396 A-A-AATAATTATA
1 ATATAAT-ATTA-A
35408 ATATAATATTAAA
1 ATATAATATT-AA
*
35421 TATTATACGATATAAA
1 -A-TATA--ATATTAA
35437 ATATAAT-TTAA
1 ATATAATATTAA
*
35448 ATAT-ATATTTA
1 ATATAATATTAA
35459 A-AT-ATATTAA
1 ATATAATATTAA
35469 TATATAAT-TTAA
1 -ATATAATATTAA
35481 AT
1 AT
35483 TATTAATATA
Statistics
Matches: 69, Mismatches: 4, Indels: 28
0.68 0.04 0.28
Matches are distributed among these distances:
9 3 0.04
10 12 0.17
11 17 0.25
12 10 0.14
13 7 0.10
14 9 0.13
15 5 0.07
16 2 0.03
17 4 0.06
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (12 bp):
ATATAATATTAA
Found at i:35470 original size:20 final size:20
Alignment explanation
Indices: 35447--35493 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
35437 ATATAATTTA
35447 AATATAT-ATTTAAATATATT
1 AATATATAATTTAAAT-TATT
35467 AATATATAATTTAAATTATT
1 AATATATAATTTAAATTATT
35487 AATATAT
1 AATATAT
35494 TAAAATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATATAATTTAAATTATT
Found at i:35472 original size:38 final size:38
Alignment explanation
Indices: 35384--35529 Score: 99
Period size: 40 Copynumber: 3.8 Consensus size: 38
35374 AAAATAAAAT
*
35384 TATA-TAATATAAAAAATAA-TTATAATATA-ATATTAAA
1 TATATTAATATAAAATATAATTTA-AATATATAT-TTAAA
35421 TAT-TATACGATATAAAATATAATTTAAATATATATTTAAA
1 TATAT-TA--ATATAAAATATAATTTAAATATATATTTAAA
* * * * *
35461 TATATTAATATATAATTTAAATT-ATTAATATATTAAAA
1 TATATTAATATAAAATATAATTTAAAT-ATATATTTAAA
* *
35499 TTTATATAAAAATAAAATAT--TTTAAATATAT
1 --TATATTAATATAAAATATAATTTAAATATAT
35530 TTATAGTACG
Statistics
Matches: 86, Mismatches: 12, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
37 5 0.06
38 31 0.36
39 2 0.02
40 42 0.49
41 6 0.07
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (38 bp):
TATATTAATATAAAATATAATTTAAATATATATTTAAA
Found at i:35527 original size:9 final size:10
Alignment explanation
Indices: 35435--35532 Score: 59
Period size: 10 Copynumber: 10.1 Consensus size: 10
35425 ATACGATATA
35435 AAATATAATTT
1 AAATAT-ATTT
35446 AAATATATATTT
1 -AA-ATATATTT
35458 AAATATA-TT
1 AAATATATTT
35467 AATATATAATTT
1 AA-ATAT-ATTT
35479 AAAT-TA-TT
1 AAATATATTT
*
35487 -AATATATTA
1 AAATATATTT
* *
35496 AAATTTATAT
1 AAATATATTT
*
35506 AAA-A-A-TA
1 AAATATATTT
35513 AAATAT-TTT
1 AAATATATTT
35522 AAATATATTT
1 AAATATATTT
35532 A
1 A
35533 TAGTACGGTA
Statistics
Matches: 67, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
7 6 0.09
8 6 0.09
9 13 0.19
10 23 0.34
11 5 0.07
12 10 0.15
13 4 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
AAATATATTT
Found at i:35942 original size:15 final size:16
Alignment explanation
Indices: 35909--35943 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
35899 ACATTATTTT
* *
35909 AAAATGAAATTAATAA
1 AAAATAAAAATAATAA
35925 AAAATAAAAATAATAA
1 AAAATAAAAATAATAA
35941 AAA
1 AAA
35944 GTATTAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (16 bp):
AAAATAAAAATAATAA
Found at i:36704 original size:42 final size:43
Alignment explanation
Indices: 36586--36705 Score: 109
Period size: 48 Copynumber: 2.7 Consensus size: 43
36576 AATAAATTTG
* *
36586 AATATTTA-ATAAATAATATTATTTAATTCAAATTTAAATTTAAAT
1 AATATTTATATAAAT-ATA-AATTTAAAT-AAATTTAAATTTAAAT
* * *
36631 AATTATATATATATTTAATATAAATAATAAATAAATTTAAATTTTAA-
1 AA-TAT-T-TATA-TAAATATAAAT-TTAAATAAATTTAAATTTAAAT
36678 AATATTTATATAAATATAAATTTAAATA
1 AATATTTATATAAATATAAATTTAAATA
36706 TTATAAAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
42 6 0.10
43 10 0.16
44 4 0.06
45 3 0.05
46 6 0.10
47 3 0.05
48 18 0.29
49 8 0.13
50 4 0.06
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (43 bp):
AATATTTATATAAATATAAATTTAAATAAATTTAAATTTAAAT
Found at i:37468 original size:9 final size:9
Alignment explanation
Indices: 37450--37545 Score: 53
Period size: 9 Copynumber: 11.0 Consensus size: 9
37440 TAAATTAAGC
37450 AATTTATAT
1 AATTTATAT
*
37459 AATTTGTAT
1 AATTTATAT
*
37468 -ATTAATATT
1 AATTTATA-T
37477 ATATTTATAT
1 A-ATTTATAT
37487 --TTTATAT
1 AATTTATAT
*
37494 AATTTTTAT
1 AATTTATAT
37503 -ATTTA-A-
1 AATTTATAT
37509 AATATTA-AT
1 AAT-TTATAT
*
37518 TATTTATAT
1 AATTTATAT
* *
37527 ATTTTTTAAT
1 AATTTAT-AT
37537 AATTTATAT
1 AATTTATAT
37546 TATATAAATT
Statistics
Matches: 65, Mismatches: 12, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
7 10 0.15
8 16 0.25
9 25 0.38
10 8 0.12
11 6 0.09
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (9 bp):
AATTTATAT
Found at i:37546 original size:25 final size:26
Alignment explanation
Indices: 37504--37570 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 26
37494 AATTTTTATA
* * **
37504 TTTAAAATATTAATTATTTATATATTT
1 TTTAATATATTTA-TATTTATATAAAT
37531 TTTAATA-ATTTATA-TTATATAAAT
1 TTTAATATATTTATATTTATATAAAT
37555 TTTAATATATTTATAT
1 TTTAATATATTTATAT
37571 ATCTGAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
24 15 0.44
25 9 0.26
26 4 0.12
27 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTAATATATTTATATTTATATAAAT
Found at i:37548 original size:24 final size:25
Alignment explanation
Indices: 37517--37570 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
37507 AAAATATTAA
**
37517 TTAT-TTATATATTTTTTAATA-AT
1 TTATATTATATAAATTTTAATATAT
37540 TTATATTATATAAATTTTAATATAT
1 TTATATTATATAAATTTTAATATAT
37565 TTATAT
1 TTATAT
37571 ATCTGAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 4 0.15
24 15 0.56
25 8 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TTATATTATATAAATTTTAATATAT
Found at i:37568 original size:44 final size:42
Alignment explanation
Indices: 37476--37572 Score: 119
Period size: 40 Copynumber: 2.3 Consensus size: 42
37466 ATATTAATAT
*
37476 TATATTTATAT-TTTATATAATTTTTATATTTAAAATATTAA
1 TATATTTATATATTTATATAATATTTATATTTAAAATATTAA
* *
37517 T-TATTTATATATTT-TTTAATAATTTATATTATATAAATTTTAA
1 TATATTTATATATTTATATAAT-ATTTATATT-TA-AAATATTAA
37560 TATATTTATATAT
1 TATATTTATATAT
37573 CTGAATATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
40 14 0.29
41 12 0.25
42 2 0.04
43 9 0.19
44 11 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (42 bp):
TATATTTATATATTTATATAATATTTATATTTAAAATATTAA
Found at i:39579 original size:29 final size:29
Alignment explanation
Indices: 39516--39580 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
39506 CATACATATA
* *
39516 TATATATATATATATATTAAAAAATTATT
1 TATATTTATATATAAATTAAAAAATTATT
* *
39545 TATATTTATATA-AAATTAAATTAATTTTT
1 TATATTTATATATAAATTAAA-AAATTATT
39574 TATATTT
1 TATATTT
39581 TTTTAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 7 0.23
29 24 0.77
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TATATTTATATATAAATTAAAAAATTATT
Found at i:40018 original size:2 final size:2
Alignment explanation
Indices: 40013--40051 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
40003 GATATATGTG
40013 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40052 CACAAGCATG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40300 original size:13 final size:13
Alignment explanation
Indices: 40244--40301 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
40234 TCTTAAAATT
40244 TTTATATATTTTA
1 TTTATATATTTTA
* *
40257 --TATTTATTTAA
1 TTTATATATTTTA
*
40268 TTT-TATTATTGTA
1 TTTATA-TATTTTA
40281 TTT-TATATTTTA
1 TTTATATATTTTA
40293 TTTATATAT
1 TTTATATAT
40302 ATCATGCATA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
11 9 0.26
12 10 0.29
13 16 0.46
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (13 bp):
TTTATATATTTTA
Found at i:40646 original size:2 final size:2
Alignment explanation
Indices: 40641--40665 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40631 CTTCATATTG
40641 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 T
40666 TTAAATCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42279 original size:17 final size:19
Alignment explanation
Indices: 42257--42293 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
42247 TTGGTGTGTA
42257 AATTCTAATA-A-ATATAT
1 AATTCTAATATACATATAT
42274 AATTCTAATATACATATAT
1 AATTCTAATATACATATAT
42293 A
1 A
42294 TATATATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 1 0.06
19 7 0.39
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTCTAATATACATATAT
Found at i:43243 original size:15 final size:15
Alignment explanation
Indices: 43205--43255 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
43195 TAATATTTAC
*
43205 TATAATTAATATAAT
1 TATAATTATTATAAT
* * *
43220 AATATTTATTATATT
1 TATAATTATTATAAT
*
43235 TATAATTATTATAAA
1 TATAATTATTATAAT
43250 TATAAT
1 TATAAT
43256 ATAATTAAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATAATTATTATAAT
Found at i:43397 original size:18 final size:18
Alignment explanation
Indices: 43370--43429 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 18
43360 CATTTAAAGT
*
43370 AATTTTATATTTATATAA
1 AATTTAATATTTATATAA
43388 AATTTAATA--TAT-TAA
1 AATTTAATATTTATATAA
43403 TAATTT-ATATTT-TATAA
1 -AATTTAATATTTATATAA
*
43420 ATTTTAATAT
1 AATTTAATAT
43430 ATTTATTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
15 6 0.17
16 13 0.37
17 8 0.23
18 8 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AATTTAATATTTATATAA
Found at i:43422 original size:15 final size:15
Alignment explanation
Indices: 43373--43423 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
43363 TTAAAGTAAT
43373 TTTATATTTATATAAAA
1 TTTATATTT-TAT-AAA
*
43390 TTTAATATATTA-ATAA
1 TTT-ATATTTTATA-AA
43406 TTTATATTTTATAAA
1 TTTATATTTTATAAA
43421 TTT
1 TTT
43424 TAATATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 13 0.45
16 6 0.21
17 5 0.17
18 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTATATTTTATAAA
Found at i:44699 original size:30 final size:30
Alignment explanation
Indices: 44647--44704 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
44637 TAATAATTAT
*
44647 TTTTAAAATATAAAAAATTATTTTTTATAA
1 TTTTAAAATATAAAAAATTATTTATTATAA
44677 TTTTAAAGATA-AAAAACA-TATTTATTAT
1 TTTTAAA-ATATAAAAA-ATTATTTATTAT
44705 TTATCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (30 bp):
TTTTAAAATATAAAAAATTATTTATTATAA
Found at i:44753 original size:36 final size:36
Alignment explanation
Indices: 44686--44786 Score: 104
Period size: 33 Copynumber: 2.9 Consensus size: 36
44676 ATTTTAAAGA
* *
44686 TAAAAA-ACATATTTATTATTT-ATCTTTTTAAAAAAT
1 TAAAAATA-ATATTTATT-TTTAATATTATTAAAAAAT
* *
44722 TTAAAATGATATTTATTTTTAATATTATT---AAAT
1 TAAAAATAATATTTATTTTTAATATTATTAAAAAAT
*
44755 TAAAAATAATATTTATTTTTATTATTATTAAA
1 TAAAAATAATATTTATTTTTAATATTATTAAA
44787 TTTAAAATAA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
33 30 0.57
35 3 0.06
36 20 0.38
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (36 bp):
TAAAAATAATATTTATTTTTAATATTATTAAAAAAT
Found at i:44755 original size:33 final size:33
Alignment explanation
Indices: 44718--44797 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
44708 TCTTTTTAAA
*
44718 AAATTTAAAATGATATTTATTTTTAATATTATT
1 AAATTTAAAATAATATTTATTTTTAATATTATT
* *
44751 AAATTAAAAATAATATTTATTTTTATTATTATT
1 AAATTTAAAATAATATTTATTTTTAATATTATT
44784 AAATTTAAAATAAT
1 AAATTTAAAATAAT
44798 TTTTTTATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (33 bp):
AAATTTAAAATAATATTTATTTTTAATATTATT
Found at i:44865 original size:32 final size:33
Alignment explanation
Indices: 44823--44908 Score: 90
Period size: 31 Copynumber: 2.7 Consensus size: 33
44813 ATCTTATTTC
44823 TAATAAAATTTTTATTTTATAATATTTGATATAT
1 TAAT-AAATTTTTATTTTATAATATTTGATATAT
* *
44857 TAAT-AA--TTTATTTTATATAAATTTTATATAT
1 TAATAAATTTTTATTTTATA-ATATTTGATATAT
* *
44888 TTATAAATTTATATTTT-TAAT
1 TAATAAATTTTTATTTTATAAT
44909 GTTTTGGGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
30 11 0.26
31 14 0.33
32 5 0.12
33 2 0.05
34 11 0.26
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (33 bp):
TAATAAATTTTTATTTTATAATATTTGATATAT
Found at i:46477 original size:18 final size:19
Alignment explanation
Indices: 46454--46491 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
46444 TAAGGTTTCG
* *
46454 TTTTTTGAAT-TTTTTATT
1 TTTTTTAAATATTTATATT
46472 TTTTTTAAATATTTATATT
1 TTTTTTAAATATTTATATT
46491 T
1 T
46492 AAAATATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (19 bp):
TTTTTTAAATATTTATATT
Found at i:46527 original size:20 final size:18
Alignment explanation
Indices: 46483--46530 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 18
46473 TTTTTAAATA
*
46483 TTTATATTTAAAATATAT
1 TTTATATATAAAATATAT
46501 TTATATATATAAAAGTATAAT
1 TT-TATATATAAAA-TAT-AT
46522 TTTATATAT
1 TTTATATAT
46531 TTTTCGTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 2 0.08
19 10 0.38
20 10 0.38
21 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TTTATATATAAAATATAT
Found at i:48427 original size:20 final size:20
Alignment explanation
Indices: 48386--48424 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
48376 TTAATTTTTT
*
48386 TATTTTTATATTAAAATTAA
1 TATTTTTATAGTAAAATTAA
*
48406 TATTTTTA-AGTAAATTTAA
1 TATTTTTATAGTAAAATTAA
48425 ATAAAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
TATTTTTATAGTAAAATTAA
Found at i:50793 original size:6 final size:6
Alignment explanation
Indices: 50782--50818 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
50772 TTCTAGTACC
*
50782 AAAAA- AAAAAA AAAAAG AAAAAG AAAAAG -AAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
50819 GAGTGGCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:50808 original size:17 final size:17
Alignment explanation
Indices: 50782--50818 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
50772 TTCTAGTACC
50782 AAAAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAAG
* *
50799 AAAAAGAAAAAGAAAAG
1 AAAAAAAAAAAAAAAAG
50816 AAA
1 AAA
50819 GAGTGGCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAAAG
Found at i:52068 original size:23 final size:24
Alignment explanation
Indices: 52042--52094 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
52032 AATTTTTTTT
*
52042 TAAAAT-TTAATTATAAA-AATTTA
1 TAAAATATTAA-TAAAAATAATTTA
*
52065 T-AAATATTAATAAAAATAATTTT
1 TAAAATATTAATAAAAATAATTTA
52088 TAAAATA
1 TAAAATA
52095 ATTTTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 9 0.36
23 11 0.44
24 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAAATATTAATAAAAATAATTTA
Found at i:52253 original size:23 final size:23
Alignment explanation
Indices: 52226--52271 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
52216 TCTTAATACA
52226 AAAAAACAATATT-TTAAATATATG
1 AAAAAA-AAT-TTATTAAATATATG
52250 AAAAAAAATTTATTAAATATAT
1 AAAAAAAATTTATTAAATATAT
52272 ATTTATTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 2 0.10
23 13 0.62
24 6 0.29
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
AAAAAAAATTTATTAAATATATG
Found at i:58736 original size:6 final size:6
Alignment explanation
Indices: 58719--58753 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
58709 TATTTAAATG
58719 AATATCA AATATA AATATA AATAT- AATATA AATAT
1 AATAT-A AATATA AATATA AATATA AATATA AATAT
58754 TTTTAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 17 0.63
7 5 0.19
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (6 bp):
AATATA
Found at i:58746 original size:11 final size:12
Alignment explanation
Indices: 58719--58753 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
58709 TATTTAAATG
58719 AATATCAAATATA
1 AATAT-AAATATA
58732 AATATAAATAT-
1 AATATAAATATA
58743 AATATAAATAT
1 AATATAAATAT
58754 TTTTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 6 0.27
13 5 0.23
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (12 bp):
AATATAAATATA
Found at i:58817 original size:13 final size:13
Alignment explanation
Indices: 58807--58837 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
58797 TTTTATATTT
58807 ATATTAAATATAA
1 ATATTAAATATAA
58820 ATATTAAATATAA
1 ATATTAAATATAA
58833 ATATT
1 ATATT
58838 TTACGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATTAAATATAA
Found at i:60575 original size:21 final size:20
Alignment explanation
Indices: 60542--60601 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
60532 TTAAAAAAAT
*
60542 AAAAAT-AATAATTATTATTA
1 AAAAATAAAAAATTATT-TTA
60562 AAAAATAAAAAATTATTTTA
1 AAAAATAAAAAATTATTTTA
*
60582 AAAATTAAAAAAATTATTTT
1 AAAAAT-AAAAAATTATTTT
60602 TTAAAAACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 14 0.39
21 22 0.61
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATAAAAAATTATTTTA
Found at i:61931 original size:20 final size:20
Alignment explanation
Indices: 61897--61934 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
61887 AAAAATGTTA
**
61897 ATTATTATATTTAATATAAT
1 ATTATTATAAATAATATAAT
61917 ATTATTATAAATAATATA
1 ATTATTATAAATAATATA
61935 TTAACTAAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTATTATAAATAATATAAT
Found at i:62914 original size:3 final size:3
Alignment explanation
Indices: 62906--62943 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
62896 AACACGATAC
62906 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
62944 GGATTTATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:63542 original size:16 final size:16
Alignment explanation
Indices: 63521--63558 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
63511 AGATTCAATG
*
63521 AACTTTTCGAATATTA
1 AACTTTTCGAATACTA
63537 AAC-TTTCGAATACTA
1 AACTTTTCGAATACTA
*
63552 AAGTTTT
1 AACTTTT
63559 AATAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (16 bp):
AACTTTTCGAATACTA
Found at i:63743 original size:16 final size:15
Alignment explanation
Indices: 63717--63759 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
63707 ATTTGTTCGA
63717 TTAAATAAATTCTAT
1 TTAAATAAATTCTAT
*
63732 TTAAATTAAATTGTAT
1 TTAAA-TAAATTCTAT
63748 TTAAAATAAATT
1 TT-AAATAAATT
63760 TTTAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 5 0.20
16 17 0.68
17 3 0.12
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
TTAAATAAATTCTAT
Found at i:63798 original size:56 final size:55
Alignment explanation
Indices: 63718--63825 Score: 139
Period size: 56 Copynumber: 1.9 Consensus size: 55
63708 TTTGTTCGAT
* * *
63718 TAAATAAATTCTATTTAAATTAAAT-TGT-ATTTAAAATAAATTTTTAATATTTAAA
1 TAAATAAATTCGATTCAAATTAAATAT-TAATAT-AAATAAATTTTTAATATTTAAA
*
63773 TAAATTAAATTCGATTCAAATTAAATATTAATATAAATTAATTTTTAATATTT
1 TAAA-TAAATTCGATTCAAATTAAATATTAATATAAATAAATTTTTAATATTT
63826 TTATATATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
55 4 0.09
56 38 0.83
57 4 0.09
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (55 bp):
TAAATAAATTCGATTCAAATTAAATATTAATATAAATAAATTTTTAATATTTAAA
Found at i:63812 original size:17 final size:17
Alignment explanation
Indices: 63790--63823 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
63780 AATTCGATTC
63790 AAATTAAATATTAATAT
1 AAATTAAATATTAATAT
* *
63807 AAATTAATTTTTAATAT
1 AAATTAAATATTAATAT
63824 TTTTATATAT
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):
AAATTAAATATTAATAT
Found at i:64340 original size:3 final size:3
Alignment explanation
Indices: 64332--64384 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
64322 TCATTGTAGC
64332 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
64380 TTA TT
1 TTA TT
64385 TCTCTCTTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:65005 original size:13 final size:15
Alignment explanation
Indices: 64976--65008 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
64966 TTCAAGTAAC
64976 AATTTTATTTATATA
1 AATTTTATTTATATA
64991 AATTTT-TTT-TATA
1 AATTTTATTTATATA
65004 AATTT
1 AATTT
65009 AATAATTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 3 0.17
15 6 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
AATTTTATTTATATA
Found at i:65732 original size:13 final size:13
Alignment explanation
Indices: 65694--65761 Score: 59
Period size: 13 Copynumber: 5.0 Consensus size: 13
65684 AATTATAATA
65694 TAATATTATAATTAT
1 TAATATT-T-ATTAT
65709 TAATTTATTTATTAT
1 TAA--TATTTATTAT
*
65724 TAATATTTATGA-
1 TAATATTTATTAT
*
65736 TAATTATTTA-TAA
1 TAA-TATTTATTAT
65749 TAATATTTATTAT
1 TAATATTTATTAT
65762 ATTTGAATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
12 10 0.22
13 19 0.42
15 11 0.24
16 1 0.02
17 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (13 bp):
TAATATTTATTAT
Found at i:66619 original size:3 final size:3
Alignment explanation
Indices: 66611--66637 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
66601 TGCACCTCCG
66611 CCA CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA
66638 ACGCAGCTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:67080 original size:2 final size:2
Alignment explanation
Indices: 67075--67105 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
67065 ATATATGTTT
*
67075 TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
67106 TGACTGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:71335 original size:33 final size:35
Alignment explanation
Indices: 71278--71345 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
71268 TATGAAATAG
*
71278 TTCATATAATTATATATTAAATTAAT-TTATTTATT
1 TTCATATAATTATATATT-AATTAATATTAATTATT
71313 TTCATAT-ATATATATATT-ATTAATATTAATTAT
1 TTCATATAAT-TATATATTAATTAATATTAATTAT
71346 ATGTTTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 6 0.20
34 9 0.30
35 15 0.50
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (35 bp):
TTCATATAATTATATATTAATTAATATTAATTATT
Found at i:71366 original size:39 final size:37
Alignment explanation
Indices: 71281--71372 Score: 91
Period size: 39 Copynumber: 2.5 Consensus size: 37
71271 GAAATAGTTC
* *
71281 ATATA-AT-TATATATTAAATTAATTTATTTATTTTC
1 ATATATATATATATATTAAATTAATTTATGTATTTTA
71316 ATATATATATATATTATTAATATTAATTATATGT-TTTTA
1 ATATATATATATA-TATTAA-ATTAATT-TATGTATTTTA
* *
71355 ATATTTCTATATTATATT
1 ATATATATATA-TATATT
71373 CTTTAAAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
35 5 0.11
36 2 0.04
37 4 0.09
38 6 0.13
39 24 0.51
40 6 0.13
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (37 bp):
ATATATATATATATATTAAATTAATTTATGTATTTTA
Done.