Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1022
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: 59728
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.36
Found at i:1287 original size:19 final size:20
Alignment explanation
Indices: 1245--1284 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1235 TAAGTTGTGT
*
1245 ATTTTCTATTATTTAATTAA
1 ATTTTCTATTATATAATTAA
1265 ATTTT-TATTATAATAATTAA
1 ATTTTCTATTAT-ATAATTAA
1285 TTTAAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTCTATTATATAATTAA
Found at i:7091 original size:5 final size:6
Alignment explanation
Indices: 7073--7097 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
7063 TTCTTCACTG
7073 TTATTT TTATTT TTATTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT T
7098 CTTTAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:7310 original size:17 final size:17
Alignment explanation
Indices: 7271--7315 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
7261 GATATTATTA
7271 TTATTATTTTA-TAATTC
1 TTATT-TTTTATTAATTC
* *
7288 TAATTTTTTATTAATTT
1 TTATTTTTTATTAATTC
7305 TTATTTTTTAT
1 TTATTTTTTAT
7316 ATTTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTTTTTATTAATTC
Found at i:8391 original size:3 final size:3
Alignment explanation
Indices: 8383--8425 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
8373 AAGCTAAATC
8383 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
8426 TATTTAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9195 original size:45 final size:45
Alignment explanation
Indices: 9144--9234 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
9134 GTTCCTTATA
* *
9144 TGTTATTGATGCATCGGACCTATCA-ATTCTAAATTAAATTGATGT
1 TGTTATTGATCCATCAGACCTAT-ATATTCTAAATTAAATTGATGT
* **
9189 TGTTATTGTTCCATCAGACCTATATATTCTCGATTAAATTGATGT
1 TGTTATTGATCCATCAGACCTATATATTCTAAATTAAATTGATGT
9234 T
1 T
9235 ATTAATCCGC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 1 0.03
45 39 0.98
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (45 bp):
TGTTATTGATCCATCAGACCTATATATTCTAAATTAAATTGATGT
Found at i:13599 original size:39 final size:37
Alignment explanation
Indices: 13529--13603 Score: 87
Period size: 39 Copynumber: 2.0 Consensus size: 37
13519 TATAATAATA
*
13529 ATTTTTATTATTTAAATTAAAAATATTTATATTATATT
1 ATTTTTATTATTTAAATTAAAAATATATATA-TATATT
** * *
13567 ATTTTTAATTATTTTTATTATATATATATATATATAT
1 ATTTTT-ATTATTTAAATTAAAAATATATATATATAT
13604 GATATTATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 11 0.35
39 20 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (37 bp):
ATTTTTATTATTTAAATTAAAAATATATATATATATT
Found at i:16963 original size:3 final size:3
Alignment explanation
Indices: 16955--16993 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
16945 CAAAAGTCCA
*
16955 AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16994 GTAAAAGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17484 original size:18 final size:19
Alignment explanation
Indices: 17450--17486 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
17440 GATTTGACTT
17450 AAATTATTATATATTTAAA
1 AAATTATTATATATTTAAA
*
17469 AAATTATT-TTTATTTAAA
1 AAATTATTATATATTTAAA
17487 TTTAATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATTATTATATATTTAAA
Found at i:17953 original size:12 final size:12
Alignment explanation
Indices: 17938--17998 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
17928 ATATTTTTTA
17938 TAATTTAATAAT
1 TAATTTAATAAT
17950 TAATTTAAT--T
1 TAATTTAATAAT
*
17960 TAATTTAA-ATT
1 TAATTTAATAAT
17971 TAAATTTAA-AATT
1 T-AATTTAATAA-T
17984 TAATTTAGATAAT
1 TAATTTA-ATAAT
17997 TA
1 TA
17999 CGAGTTTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
10 9 0.21
11 2 0.05
12 23 0.55
13 6 0.14
14 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
TAATTTAATAAT
Found at i:17957 original size:5 final size:5
Alignment explanation
Indices: 17938--17990 Score: 52
Period size: 5 Copynumber: 9.4 Consensus size: 5
17928 ATATTTTTTA
17938 TAATT TAATAAT TAATT TAATT TAATT TAAATT TAAATT TAAAATT TAATT
1 TAATT TAAT--T TAATT TAATT TAATT T-AATT T-AATT T--AATT TAATT
17989 TA
1 TA
17991 GATAATTACG
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
5 22 0.50
6 11 0.25
7 11 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (5 bp):
TAATT
Found at i:17966 original size:29 final size:28
Alignment explanation
Indices: 17934--17990 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
17924 AAACATATTT
17934 TTTATAATTTAATAATT-AATTTAATTTAA
1 TTTA-AATTTAA-AATTAAATTTAATTTAA
*
17963 TTTAAATTTAAATTTAAAATTTAATTTA
1 TTTAAATTTAAAATT-AAATTTAATTTA
17991 GATAATTACG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 3 0.12
28 7 0.28
29 15 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTAAATTTAAAATTAAATTTAATTTAA
Found at i:19288 original size:17 final size:18
Alignment explanation
Indices: 19262--19300 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
19252 CATGTAATAG
19262 TATTAAA-TTTAATATTA
1 TATTAAATTTTAATATTA
*
19279 TATTATATTTTTAATATTA
1 TATTA-AATTTTAATATTA
19298 TAT
1 TAT
19301 ATTTAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 1 0.05
19 13 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTAAATTTTAATATTA
Found at i:20747 original size:22 final size:22
Alignment explanation
Indices: 20721--20764 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
20711 AAATTGATGA
20721 AATTAGTCAAATT-AAATTAATT
1 AATTA-TCAAATTAAAATTAATT
20743 AATTATCAAATTAAAATTAATT
1 AATTATCAAATTAAAATTAATT
20765 TAAGTTGTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (22 bp):
AATTATCAAATTAAAATTAATT
Found at i:21566 original size:38 final size:39
Alignment explanation
Indices: 21524--21598 Score: 107
Period size: 38 Copynumber: 1.9 Consensus size: 39
21514 AAATGTTAAA
* *
21524 TTTATTAAAATAAAATAAAGTTATAATAA-AATAATTAT
1 TTTATTAAAATAAAATAAAATAATAATAATAATAATTAT
* *
21562 TTTATTAGAATAAAATAAAATAATTATAATAATAATT
1 TTTATTAAAATAAAATAAAATAATAATAATAATAATT
21599 TGATTCAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 25 0.78
39 7 0.22
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (39 bp):
TTTATTAAAATAAAATAAAATAATAATAATAATAATTAT
Found at i:21588 original size:22 final size:22
Alignment explanation
Indices: 21529--21588 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
21519 TTAAATTTAT
*
21529 TAAAATAAAATAA--AGTTATAA
1 TAAAATAAAATAATTA-TTAGAA
* *
21550 TAAAAT-AATTATTTTATTAGAA
1 TAAAATAAAATA-ATTATTAGAA
21572 TAAAATAAAATAATTAT
1 TAAAATAAAATAATTAT
21589 AATAATAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 15 0.50
23 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (22 bp):
TAAAATAAAATAATTATTAGAA
Found at i:22251 original size:6 final size:6
Alignment explanation
Indices: 22230--22298 Score: 50
Period size: 6 Copynumber: 10.8 Consensus size: 6
22220 ATATATTTAA
* * * *
22230 TATACT TATATAT TATATT TATATA TAAATT AAAATATT TAATAATT TATA-T
1 TATATT TATAT-T TATATT TATATT TATATT --TATATT T-AT-ATT TATATT
22282 TATATT TATATT TATAT
1 TATATT TATATT TATAT
22299 AATTAACATA
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
5 5 0.10
6 27 0.54
7 10 0.20
8 8 0.16
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (6 bp):
TATATT
Found at i:22256 original size:17 final size:17
Alignment explanation
Indices: 22236--22298 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
22226 TTAATATACT
22236 TATATATTATATTTATA
1 TATATATTATATTTATA
*
22253 TATAAATTAAAATATTTAATAA
1 TATATATT---ATATTT-AT-A
*
22275 TTTATATTATATTTATA
1 TATATATTATATTTATA
*
22292 TTTATAT
1 TATATAT
22299 AATTAACATA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
17 15 0.39
18 2 0.05
19 6 0.16
20 6 0.16
21 2 0.05
22 7 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATATTATATTTATA
Found at i:23137 original size:15 final size:16
Alignment explanation
Indices: 23119--23148 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
23109 AATATTATTA
23119 TTTAAAA-TTTAAAAT
1 TTTAAAATTTTAAAAT
23134 TTTAAAATTTTAAAA
1 TTTAAAATTTTAAAA
23149 ATATTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAAATTTTAAAAT
Found at i:23139 original size:8 final size:8
Alignment explanation
Indices: 23119--23148 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
23109 AATATTATTA
23119 TTTAAAA-
1 TTTAAAAT
23126 TTTAAAAT
1 TTTAAAAT
23134 TTTAAAAT
1 TTTAAAAT
23142 TTTAAAA
1 TTTAAAA
23149 ATATTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TTTAAAAT
Found at i:23192 original size:23 final size:21
Alignment explanation
Indices: 23157--23198 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
23147 AAATATTTTT
*
23157 ATATTTTTATAATTAATATAA
1 ATATTTTTATAATAAATATAA
23178 ATATTTTTAATTAATAAATAT
1 ATATTTTT-A-TAATAAATAT
23199 TAATTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 1 0.06
23 9 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATATTTTTATAATAAATATAA
Found at i:23355 original size:14 final size:14
Alignment explanation
Indices: 23336--23379 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
23326 TTGATATAAA
23336 ATTTTAATTATTTT
1 ATTTTAATTATTTT
* *
23350 ATTTTATTTATTTG
1 ATTTTAATTATTTT
23364 ATTTTTAATCTATTTT
1 A-TTTTAAT-TATTTT
23380 TAGTTTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 13 0.54
15 6 0.25
16 5 0.21
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (14 bp):
ATTTTAATTATTTT
Found at i:23530 original size:30 final size:30
Alignment explanation
Indices: 23489--23549 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
23479 TTTTTAAAAT
* * *
23489 ATTTTTTTATATTTATT-TATTTAATATTTA
1 ATTTTTGTATATTAATTATATATAAT-TTTA
23519 ATTTTTGTATATTAATTATATATAATTTTA
1 ATTTTTGTATATTAATTATATATAATTTTA
23549 A
1 A
23550 AATTTATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (30 bp):
ATTTTTGTATATTAATTATATATAATTTTA
Found at i:28563 original size:18 final size:19
Alignment explanation
Indices: 28513--28568 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
28503 AATTATAACA
*
28513 AATAAAAAATTAACGATATT
1 AATAAAATATTAAC-ATATT
28533 AA-AAAATATTTAA-ATATT
1 AATAAAATA-TTAACATATT
*
28551 AATAAAATATTAATATAT
1 AATAAAATATTAACATAT
28569 CATGTGACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 11 0.34
19 15 0.47
20 6 0.19
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (19 bp):
AATAAAATATTAACATATT
Found at i:28813 original size:31 final size:31
Alignment explanation
Indices: 28733--28813 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 31
28723 ATTTATTATA
28733 ATTTTAA-A-AATAAAAAAGACTAAAATATTT
1 ATTTTAATATAATAAAAAA-ACTAAAATATTT
** *
28763 ATTTTAATATAATGTAAAAATTAAAATAATTT
1 ATTTTAATATAATAAAAAAACTAAAAT-ATTT
*
28795 -TTTTATTATAATAAAAAAA
1 ATTTTAATATAATAAAAAAA
28814 ACTTTTAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
30 7 0.17
31 24 0.57
32 11 0.26
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (31 bp):
ATTTTAATATAATAAAAAAACTAAAATATTT
Found at i:29757 original size:15 final size:15
Alignment explanation
Indices: 29737--29772 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
29727 CTTCCGCCCC
29737 TATTTTT-TCTTGAAA
1 TATTTTTGTC-TGAAA
29752 TATTTTTGTCTGAAA
1 TATTTTTGTCTGAAA
29767 TATTTT
1 TATTTT
29773 CGGACGTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 18 0.90
16 2 0.10
ACGTcount: A:0.25, C:0.06, G:0.08, T:0.61
Consensus pattern (15 bp):
TATTTTTGTCTGAAA
Found at i:37209 original size:12 final size:12
Alignment explanation
Indices: 37192--37217 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
37182 AATGAGACCC
37192 GTAAATCGACGA
1 GTAAATCGACGA
37204 GTAAATCGACGA
1 GTAAATCGACGA
37216 GT
1 GT
37218 CGGTTGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.19
Consensus pattern (12 bp):
GTAAATCGACGA
Found at i:38863 original size:16 final size:16
Alignment explanation
Indices: 38820--38864 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
38810 GATAAATAAA
*
38820 ATTTAAAATTT-AATT
1 ATTTTAAATTTAAATT
*
38835 A-ATTAAATTTAAATT
1 ATTTTAAATTTAAATT
38850 ATTTTAAATTTAAAT
1 ATTTTAAATTTAAAT
38865 CATTCTCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 7 0.28
15 6 0.24
16 12 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTTAAATTTAAATT
Found at i:39158 original size:16 final size:17
Alignment explanation
Indices: 39137--39173 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
39127 TTATAATTAT
*
39137 TATTTA-AAATATTTTA
1 TATTTATAAAAATTTTA
39153 TATTTATAAAAATTTTA
1 TATTTATAAAAATTTTA
39170 -ATTT
1 TATTT
39174 GTATTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTTATAAAAATTTTA
Found at i:39928 original size:12 final size:12
Alignment explanation
Indices: 39892--39985 Score: 56
Period size: 12 Copynumber: 7.9 Consensus size: 12
39882 AATTAAAAAA
39892 TTAT-TTATATT
1 TTATATTATATT
*
39903 ATTAT-GTATA-T
1 -TTATATTATATT
39914 TTATATTATATT
1 TTATATTATATT
*
39926 TTA-ATAAAGTATT
1 TTATAT-TA-TATT
*
39939 TTATATAATATT
1 TTATATTATATT
39951 TTAT-TTAT-TT
1 TTATATTATATT
* *
39961 TTTTATTTATGATG
1 TTATA-TTAT-ATT
39975 TTATATTATAT
1 TTATATTATAT
39986 ACTGTATCAA
Statistics
Matches: 66, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
10 9 0.14
11 10 0.15
12 27 0.41
13 13 0.20
14 7 0.11
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (12 bp):
TTATATTATATT
Found at i:46511 original size:4 final size:4
Alignment explanation
Indices: 46504--46528 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
46494 TAATATAATT
46504 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
46529 ATTCCTCCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:46680 original size:32 final size:32
Alignment explanation
Indices: 46644--46739 Score: 85
Period size: 32 Copynumber: 3.0 Consensus size: 32
46634 AAATAGATTT
46644 AATTTAATTTAAATTATTATTTAAATAATAAA
1 AATTTAATTTAAATTATTATTTAAATAATAAA
* * *
46676 AATTTTATTTAAATT-TAATTATAAATATTAATA
1 AATTTAATTTAAATTATTATT-TAAATAATAA-A
*
46709 TAA--AAATTT-AA-TATTATTTTAAATAATAAA
1 -AATTTAATTTAAATTATTA-TTTAAATAATAAA
46739 A
1 A
46740 TAAATTTATA
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
29 1 0.02
30 2 0.04
31 17 0.33
32 29 0.56
33 1 0.02
34 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
AATTTAATTTAAATTATTATTTAAATAATAAA
Found at i:46712 original size:37 final size:36
Alignment explanation
Indices: 46640--46768 Score: 111
Period size: 37 Copynumber: 3.5 Consensus size: 36
46630 ATTTAAATAG
* **
46640 ATTTAATTT-AATTTAAATTATTATTTAAATAATAAAA
1 ATTTAATTTAAATTT-AATTATAAAATAAAT-ATAAAA
* *
46677 ATTTTATTTAAATTTAATTATAAATATTAATATAAAA
1 ATTTAATTTAAATTTAATTATAAA-ATAAATATAAAA
* * * *
46714 ATTTAATATT-ATTTTAAATAATAAAATAAATTTATAA
1 ATTTAAT-TTAAATTT-AATTATAAAATAAATATAAAA
46751 A-TTAATTTAAATTTAATT
1 ATTTAATTTAAATTTAATT
46769 TAACTCATAT
Statistics
Matches: 74, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
35 5 0.07
36 9 0.12
37 41 0.55
38 19 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (36 bp):
ATTTAATTTAAATTTAATTATAAAATAAATATAAAA
Found at i:48518 original size:4 final size:4
Alignment explanation
Indices: 48511--48535 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
48501 TAATATAATT
48511 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
48536 ATTCCTCCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:48723 original size:31 final size:31
Alignment explanation
Indices: 48688--48748 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
48678 TAAAAATTTT
* *
48688 ATTTAAT-TTAATTATAAATATTAATATAAAA
1 ATTTAATATT-ATTATAAATAATAAAATAAAA
*
48719 ATTTAATATTATTTTAAATAATAAAATAAA
1 ATTTAATATTATTATAAATAATAAAATAAA
48749 TTTATAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
ATTTAATATTATTATAAATAATAAAATAAAA
Found at i:52702 original size:14 final size:14
Alignment explanation
Indices: 52683--52727 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
52673 TAATTATAAA
52683 AATATATAAATATT
1 AATATATAAATATT
52697 AATATA-AAA-A-T
1 AATATATAAATATT
* *
52708 AATATTTTAATATT
1 AATATATAAATATT
52722 AATATA
1 AATATA
52728 AATTATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
11 6 0.24
12 3 0.12
13 4 0.16
14 12 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATATATAAATATT
Found at i:52719 original size:25 final size:25
Alignment explanation
Indices: 52645--52729 Score: 86
Period size: 25 Copynumber: 3.4 Consensus size: 25
52635 ATGTTTTATC
* * *
52645 TTAATAATAAAAATATTTTATTTAACA
1 TTAAT-ATAAAAATAATAT-TTTAATA
*
52672 TTAATTATAAAAAT-ATA--TAAATA
1 TTAA-TATAAAAATAATATTTTAATA
52695 TTAATATAAAAATAATATTTTAATA
1 TTAATATAAAAATAATATTTTAATA
52720 TTAATATAAA
1 TTAATATAAA
52730 TTATAAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
22 9 0.18
23 11 0.22
25 15 0.31
26 1 0.02
27 12 0.24
28 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (25 bp):
TTAATATAAAAATAATATTTTAATA
Found at i:53021 original size:2 final size:2
Alignment explanation
Indices: 53014--53046 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
53004 TACATTAATA
53014 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53047 AATAAAGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53687 original size:13 final size:13
Alignment explanation
Indices: 53669--53693 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53659 ATATTAAGTC
53669 AAATTTAAGTATA
1 AAATTTAAGTATA
53682 AAATTTAAGTAT
1 AAATTTAAGTAT
53694 TCAGATTAAG
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:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (13 bp):
AAATTTAAGTATA
Found at i:54286 original size:8 final size:8
Alignment explanation
Indices: 54268--54327 Score: 59
Period size: 8 Copynumber: 7.6 Consensus size: 8
54258 ATAAAATGAA
*
54268 TTTATTAT
1 TTTAATAT
*
54276 TTTTATAT
1 TTTAATAT
*
54284 TTTAAAAT
1 TTTAATAT
54292 TTTAATAT
1 TTTAATAT
*
54300 TTTAATAA
1 TTTAATAT
* *
54308 ATTATTA-
1 TTTAATAT
54315 TTTAATAT
1 TTTAATAT
54323 TTTAA
1 TTTAA
54328 CTTTTTATGT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 5 0.12
8 36 0.88
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TTTAATAT
Found at i:55952 original size:23 final size:23
Alignment explanation
Indices: 55909--55952 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
55899 TAGATTTTTT
* *
55909 TTAATATTTTTATTTTTTTTATG
1 TTAATATTTTAATTTTATTTATG
55932 TTAA-ATTTTAATTTTAATTTA
1 TTAATATTTTAATTTT-ATTTA
55953 ATTTGATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
TTAATATTTTAATTTTATTTATG
Found at i:55981 original size:25 final size:24
Alignment explanation
Indices: 55937--55986 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
55927 TTATGTTAAA
55937 TTTTAATTTTAATTTAATTTGATTT
1 TTTTAATTTTAATTTAATTT-ATTT
*
55962 TTTTAATTATTTATTT-ATTTATTT
1 TTTTAATT-TTAATTTAATTTATTT
55986 T
1 T
55987 AAAATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 5 0.22
25 12 0.52
26 6 0.26
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (24 bp):
TTTTAATTTTAATTTAATTTATTT
Found at i:55994 original size:22 final size:22
Alignment explanation
Indices: 55948--56000 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
55938 TTTAATTTTA
*
55948 ATTTAATTTGATTTTTTTAATT
1 ATTTAATTTGATTTTTTTAAAT
55970 ATTT-ATTT-ATTTATTTTAAAAT
1 ATTTAATTTGATTT-TTTT-AAAT
*
55992 ATTAAATTT
1 ATTTAATTT
56001 TTTTACTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.15
21 8 0.31
22 10 0.38
23 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTTAATTTGATTTTTTTAAAT
Found at i:56000 original size:23 final size:22
Alignment explanation
Indices: 55974--56026 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
55964 TTAATTATTT
*
55974 ATTTATTTA-TTTTAAAATATTAA
1 ATTTATTTACTATT-AAAT-TTAA
*
55997 ATTTTTTTACTATTAAATTTAA
1 ATTTATTTACTATTAAATTTAA
*
56019 ATTAATTT
1 ATTTATTT
56027 TTATATAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 10 0.40
23 12 0.48
24 3 0.12
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTATTTACTATTAAATTTAA
Done.