Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2587
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: 46680
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.39
Found at i:468 original size:2 final size:2
Alignment explanation
Indices: 461--487 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
451 GAAAGAAGAA
461 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
488 AAAAGTAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:773 original size:28 final size:28
Alignment explanation
Indices: 719--774 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
709 AATTTTAAAT
* *
719 TATTTATATTTATTTAATTTAATTTTTA
1 TATTTATATTTATTTAATTAAAATTTTA
*
747 TATTTTTA-TTATTTAATATAAAATTTTA
1 TATTTATATTTATTTAAT-TAAAATTTTA
775 ATTATTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TATTTATATTTATTTAATTAAAATTTTA
Found at i:778 original size:21 final size:21
Alignment explanation
Indices: 748--787 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
738 TAATTTTTAT
* *
748 ATTTTTATTATTTAATATAAA
1 ATTTTAATTATTAAATATAAA
769 ATTTTAATTATTAAATATA
1 ATTTTAATTATTAAATATA
788 TTAAAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTTAATTATTAAATATAAA
Found at i:873 original size:21 final size:21
Alignment explanation
Indices: 849--907 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
839 TTTATGTGTA
*
849 TAAAAAATATAATTATATTAT
1 TAAAATATATAATTATATTAT
*
870 T-AAATTTAATAATTA-ATTTAT
1 TAAAATAT-ATAATTATA-TTAT
891 TAAAATAT-TAATTATAT
1 TAAAATATATAATTATAT
908 AAAAAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
20 12 0.39
21 14 0.45
22 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAAATATATAATTATATTAT
Found at i:947 original size:20 final size:20
Alignment explanation
Indices: 901--947 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
891 TAAAATATTA
901 ATTATATAAAAAATTATAAT
1 ATTATATAAAAAATTATAAT
* *
921 ATAATATGAAATAATT-TAAT
1 ATTATAT-AAAAAATTATAAT
*
941 TTTATAT
1 ATTATAT
948 TAATATAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATTATATAAAAAATTATAAT
Found at i:976 original size:26 final size:26
Alignment explanation
Indices: 922--971 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 26
912 AATTATAATA
*
922 TAATATGAAATAATTTAATTTTATAT
1 TAATATGAAATAATATAATTTTATAT
948 TAATAT-AAAT-ATAT-ATATTTATAT
1 TAATATGAAATAATATAAT-TTTATAT
972 GTTAACAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 2 0.09
24 10 0.45
25 4 0.18
26 6 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
TAATATGAAATAATATAATTTTATAT
Found at i:1108 original size:11 final size:11
Alignment explanation
Indices: 1090--1292 Score: 67
Period size: 11 Copynumber: 18.5 Consensus size: 11
1080 ATAAAATAAT
1090 TTATATTTATA
1 TTATATTTATA
*
1101 TCATATTTATA
1 TTATATTTATA
*
1112 TTATTTTTTATA
1 TTA-TATTTATA
*
1124 TTATAATTATA
1 TTATATTTATA
**
1135 TT-TA-AAATA
1 TTATATTTATA
1144 TTATATATT-TA
1 TTATAT-TTATA
*
1155 TATAAATTTAATAAA
1 T-TATATTT-AT--A
*
1170 TTAAAATTTATA
1 TT-ATATTTATA
*
1182 TTATA--TAAA
1 TTATATTTATA
* *
1191 TTTTA-ATATA
1 TTATATTTATA
1201 TTA-ATTTTATA
1 TTATA-TTTATA
1212 TT-TATTTATA
1 TTATATTTATA
*
1222 TAATATTT-TAA
1 TTATATTTAT-A
1233 TT-T-TTTAT-
1 TTATATTTATA
1241 TTATATTTATAAA
1 TTATATTTAT--A
*
1254 TTTTTATTTAATA
1 -TTATATTT-ATA
1267 TTATATTT-TAA
1 TTATATTTAT-A
1278 TT-T-TTTATA
1 TTATATTTATA
1287 TTATAT
1 TTATAT
1293 AATTATATCA
Statistics
Matches: 144, Mismatches: 20, Indels: 56
0.65 0.09 0.25
Matches are distributed among these distances:
8 2 0.01
9 23 0.16
10 28 0.19
11 45 0.31
12 24 0.17
13 2 0.01
14 10 0.07
15 10 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTATATTTATA
Found at i:1145 original size:29 final size:29
Alignment explanation
Indices: 1089--1165 Score: 72
Period size: 29 Copynumber: 2.8 Consensus size: 29
1079 AATAAAATAA
* *
1089 TTTATATTTATATCATATTTATATTATTT
1 TTTATATTTATATCATATTTAAAATATTT
*
1118 TTTATA-TTATAATTATATTTAAAATA--T
1 TTTATATTTAT-ATCATATTTAAAATATTT
* *
1145 TATATATTTATAT-AAATTTAA
1 TTTATATTTATATCATATTTAA
1166 TAAATTAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
26 7 0.17
27 8 0.20
28 8 0.20
29 18 0.44
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTATATTTATATCATATTTAAAATATTT
Found at i:1160 original size:20 final size:20
Alignment explanation
Indices: 1121--1160 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1111 ATTATTTTTT
*
1121 ATATTATAATTATATTTAAA
1 ATATTATAATTATATATAAA
1141 ATATTATATATT-TATATAAA
1 ATATTATA-ATTATATATAAA
1161 TTTAATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATAATTATATATAAA
Found at i:1172 original size:26 final size:25
Alignment explanation
Indices: 1134--1182 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
1124 TTATAATTAT
*
1134 ATTTAAAATATTATATATTTATATAA
1 ATTTAAAATATTA-AAATTTATATAA
1160 ATTTAATAA-ATTAAAATTTATAT
1 ATTTAA-AATATTAAAATTTATAT
1183 TATATAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 9 0.43
26 10 0.48
27 2 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATTTAAAATATTAAAATTTATATAA
Found at i:1186 original size:30 final size:30
Alignment explanation
Indices: 1147--1213 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
1137 TAAAATATTA
1147 TATATTTATATAAA-TTTAATAAATTAAAATT
1 TATA-TTATATAAATTTTAATAAATT-AAATT
* *
1178 TATATTATATAAATTTTAATATATTAATTT
1 TATATTATATAAATTTTAATAAATTAAATT
1208 TATATT
1 TATATT
1214 TATTTATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 19 0.58
31 14 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
TATATTATATAAATTTTAATAAATTAAATT
Found at i:1239 original size:20 final size:21
Alignment explanation
Indices: 1197--1292 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 21
1187 TAAATTTTAA
1197 TATATTA-ATTTTATATTTATT
1 TATATTATATTTTA-ATTTATT
*
1218 TATATAATATTTTAATTT-TT
1 TATATTATATTTTAATTTATT
1238 TAT-TTATATTTATAAATTTTTATT
1 TATATTATATTT-T-AA--TTTATT
1262 TAATATTATATTTTAATTT-TT
1 T-ATATTATATTTTAATTTATT
1283 TATATTATAT
1 TATATTATAT
1293 AATTATATCA
Statistics
Matches: 65, Mismatches: 2, Indels: 17
0.77 0.02 0.20
Matches are distributed among these distances:
19 7 0.11
20 15 0.23
21 15 0.23
22 9 0.14
23 3 0.05
24 5 0.08
25 3 0.05
26 8 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TATATTATATTTTAATTTATT
Found at i:1239 original size:30 final size:28
Alignment explanation
Indices: 1201--1284 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
1191 TTTTAATATA
*
1201 TTAATTTTATA-TT-TATTTATATAATATT
1 TTAATTTTTTATTTATATTTATA-AAT-TT
1229 TTAATTTTTTATTTATATTTATAAATTT
1 TTAATTTTTTATTTATATTTATAAATTT
** *
1257 TT-ATTTAATA-TTATATTT-TAATTTT
1 TTAATTTTTTATTTATATTTATAAATTT
1282 TTA
1 TTA
1285 TATTATATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
25 8 0.16
26 8 0.16
27 6 0.12
28 14 0.29
29 5 0.10
30 8 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (28 bp):
TTAATTTTTTATTTATATTTATAAATTT
Found at i:1246 original size:45 final size:47
Alignment explanation
Indices: 1197--1297 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 47
1187 TAAATTTTAA
**
1197 TATATTAATTTTATATTTATTT-ATATAATATTTTAATTTTTTAT-T
1 TATATTAATTAAATATTTATTTAATATAATATTTTAATTTTTTATAT
* * *
1242 TATATTTA-TAAATTTTTATTTAATATTATATTTTAATTTTTTATAT
1 TATATTAATTAAATATTTATTTAATATAATATTTTAATTTTTTATAT
1288 TATA-TAATTA
1 TATATTAATTA
1298 TATCAAATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
44 10 0.21
45 30 0.64
46 7 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (47 bp):
TATATTAATTAAATATTTATTTAATATAATATTTTAATTTTTTATAT
Found at i:1623 original size:35 final size:35
Alignment explanation
Indices: 1563--1632 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
1553 TATATTTAGC
* *
1563 TATTATATATTCATATTTTTTATATTAAATTTATA
1 TATTATATATTCATATTTTTAATATTAAATATATA
1598 TATTATA-ATT-ATATTTTTAAAATATTAAATATATA
1 TATTATATATTCATATTTTT--AATATTAAATATATA
1633 AATCTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 8 0.26
34 3 0.10
35 20 0.65
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (35 bp):
TATTATATATTCATATTTTTAATATTAAATATATA
Found at i:1846 original size:15 final size:15
Alignment explanation
Indices: 1800--1873 Score: 53
Period size: 15 Copynumber: 4.9 Consensus size: 15
1790 CTCATTTAAG
* *
1800 TTTTAATACATTAAT
1 TTTTAATATATTTAT
* *
1815 ATTTAATAT-TATAAT
1 TTTTAATATAT-TTAT
1830 TTTTAATATATTTAT
1 TTTTAATATATTTAT
* *
1845 TTTTTATATAATATTAA
1 TTTTAATAT-AT-TTAT
1862 TTTTAAT-TATTT
1 TTTTAATATATTT
1874 TTCATATCAT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
14 3 0.06
15 32 0.67
16 4 0.08
17 9 0.19
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTAATATATTTAT
Found at i:1858 original size:18 final size:17
Alignment explanation
Indices: 1818--1865 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
1808 CATTAATATT
*
1818 TAATATTATAATTTTTAA
1 TAATATT-TATTTTTTAA
1836 T-ATATTTATTTTTTATA
1 TAATATTTATTTTTTA-A
*
1853 TAATATTAATTTT
1 TAATATTTATTTT
1866 AATTATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 8 0.31
17 7 0.27
18 11 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TAATATTTATTTTTTAA
Found at i:1900 original size:27 final size:27
Alignment explanation
Indices: 1843--1900 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
1833 TAATATATTT
* * *
1843 ATTTTTTATATAATATTAATTTTAATT
1 ATTTTTCATATAATATTAATTGTAATA
*
1870 ATTTTTCATATCATATTATATTGT-ATA
1 ATTTTTCATATAATATTA-ATTGTAATA
1897 ATTT
1 ATTT
1901 AATTGTATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (27 bp):
ATTTTTCATATAATATTAATTGTAATA
Found at i:2351 original size:11 final size:11
Alignment explanation
Indices: 2331--2437 Score: 62
Period size: 11 Copynumber: 9.6 Consensus size: 11
2321 AAAATAATTA
2331 AAATATAATAT
1 AAATATAATAT
2342 -AATATAAATAT
1 AAATAT-AATAT
* *
2353 ATAAT-TATTTT
1 A-AATATAATAT
*
2364 AAA-ATTTATAT
1 AAATA-TAATAT
*
2375 AAATATAAAAT
1 AAATATAATAT
* *
2386 -ATTTTAAATAT
1 AAATAT-AATAT
*
2397 AATTATAATAT
1 AAATATAATAT
2408 -AATAATATATAT
1 AAAT-ATA-ATAT
2420 AAATATAATAT
1 AAATATAATAT
2431 AAATATA
1 AAATATA
2438 TCAATTTTTA
Statistics
Matches: 73, Mismatches: 12, Indels: 22
0.68 0.11 0.21
Matches are distributed among these distances:
10 12 0.16
11 42 0.58
12 13 0.18
13 6 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATATAATAT
Found at i:2382 original size:6 final size:6
Alignment explanation
Indices: 2371--2437 Score: 54
Period size: 6 Copynumber: 11.8 Consensus size: 6
2361 TTTAAAATTT
* * * *
2371 ATATAA ATATAA A-AT-A TTTTAA ATATAA TTAT-A ATAT-A ATAATAT
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA AT-ATAA
2416 ATATAA ATAT-A ATATAA ATATA
1 ATATAA ATATAA ATATAA ATATA
2438 TCAATTTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
4 1 0.02
5 15 0.31
6 30 0.62
7 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (6 bp):
ATATAA
Found at i:2904 original size:34 final size:33
Alignment explanation
Indices: 2866--2961 Score: 87
Period size: 31 Copynumber: 3.0 Consensus size: 33
2856 AATTCGTATG
2866 TATATTATATTTTTATATTTTATTATATTATAAT
1 TATATTATATTTTTATATTTTATTATATTA-AAT
*
2900 TATATTTAAATTTTT-TA-TTT-TTATA-TAAAT
1 TATA-TTATATTTTTATATTTTATTATATTAAAT
* * **
2930 TTTAATATATTAATA-ATTTTATTATA-TAAAT
1 TATATTATATTTTTATATTTTATTATATTAAAT
2961 T
1 T
2962 TTTAAAATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
29 7 0.13
30 9 0.17
31 13 0.25
32 5 0.10
33 3 0.06
34 6 0.12
35 9 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (33 bp):
TATATTATATTTTTATATTTTATTATATTAAAT
Found at i:2923 original size:21 final size:21
Alignment explanation
Indices: 2873--2932 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
2863 ATGTATATTA
* *
2873 TATTTTTATATTT-TATTATAT
1 TATTTTTATATTTAAATT-TTT
**
2894 TATAATTATATTTAAATTTTT
1 TATTTTTATATTTAAATTTTT
2915 TATTTTTATA--TAAATTTT
1 TATTTTTATATTTAAATTTT
2933 AATATATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
19 8 0.25
21 21 0.66
22 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTTTTATATTTAAATTTTT
Found at i:2958 original size:31 final size:32
Alignment explanation
Indices: 2920--2986 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
2910 TTTTTTATTT
*
2920 TTATATAAA-TTTTAATATATTAATAATTTTA
1 TTATATAAATTTTTAAAATATTAATAATTTTA
* * *
2951 TTATATAAATTTTTAAAATATTTATACTTTTT
1 TTATATAAATTTTTAAAATATTAATAATTTTA
2983 TTAT
1 TTAT
2987 TATTTTTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 9 0.29
32 22 0.71
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (32 bp):
TTATATAAATTTTTAAAATATTAATAATTTTA
Found at i:2963 original size:14 final size:14
Alignment explanation
Indices: 2920--2963 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 14
2910 TTTTTTATTT
2920 TTATATAAATTTTA
1 TTATATAAATTTTA
*
2934 ATATATTAATAATTTTA
1 TTATA-T-A-AATTTTA
2951 TTATATAAATTTT
1 TTATATAAATTTT
2964 TAAAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 10 0.40
15 2 0.08
16 2 0.08
17 11 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATATAAATTTTA
Found at i:3301 original size:21 final size:21
Alignment explanation
Indices: 3264--3319 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
3254 AATTTTATTT
*
3264 TATTATTTATAATATT-ATTAAA
1 TATTATTT-TTATATTAATT-AA
*
3286 TATTATTTTTATATTAATTTA
1 TATTATTTTTATATTAATTAA
3307 TATTATTTTTATA
1 TATTATTTTTATA
3320 AATAAATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTATTTTTATATTAATTAA
Found at i:3505 original size:18 final size:20
Alignment explanation
Indices: 3473--3509 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
3463 GTTTTCACCA
3473 TAAATAAAATATTAAATAAG
1 TAAATAAAATATTAAATAAG
3493 TAAA-AAAAT-TTAAATAA
1 TAAATAAAATATTAAATAA
3510 AAAAGGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (20 bp):
TAAATAAAATATTAAATAAG
Found at i:3591 original size:16 final size:15
Alignment explanation
Indices: 3572--3622 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 15
3562 ATTTGTATTA
3572 ATTTATATTTTTAAAT
1 ATTTAT-TTTTTAAAT
*
3588 ATTTATTATTTTAAAC
1 ATTTATT-TTTTAAAT
*
3604 ATATATTTTTTAAAT
1 ATTTATTTTTTAAAT
3619 ATTT
1 ATTT
3623 TAATTTTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTATTTTTTAAAT
Found at i:3629 original size:16 final size:15
Alignment explanation
Indices: 3572--3630 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
3562 ATTTGTATTA
3572 ATTTATATTTTTAAAT
1 ATTTA-ATTTTTAAAT
* *
3588 ATTTATTATTTTAAAC
1 ATTTAAT-TTTTAAAT
* *
3604 ATATATTTTTTAAAT
1 ATTTAATTTTTAAAT
3619 ATTTTAATTTTT
1 A-TTTAATTTTT
3631 CATAATTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 9 0.26
16 26 0.74
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTAATTTTTAAAT
Found at i:4559 original size:37 final size:37
Alignment explanation
Indices: 4499--4575 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
4489 TTTATTTTAA
*
4499 AAAATTTATTTTATTATTTATATTAATATTAAAAATT
1 AAAATTTATTTTATTATTGATATTAATATTAAAAATT
* * *
4536 AAAATTTATTATTA-TATTGATATTGATATTGATAATT
1 AAAATTTATT-TTATTATTGATATTAATATTAAAAATT
4573 AAA
1 AAA
4576 TTAAATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 32 0.91
38 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (37 bp):
AAAATTTATTTTATTATTGATATTAATATTAAAAATT
Found at i:4761 original size:20 final size:20
Alignment explanation
Indices: 4728--4785 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
4718 TTTTTTAATT
*
4728 TTTAAAA-AATTATTTTATAA
1 TTTAAAATAATTATTATA-AA
4748 TTTAAAATAA-TATTATAAA
1 TTTAAAATAATTATTATAAA
* *
4767 ATTAAAATTTATTATTATA
1 TTTAAAA-TAATTATTATA
4786 TTAATATTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 8 0.25
20 15 0.47
21 9 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTAAAATAATTATTATAAA
Found at i:7371 original size:22 final size:22
Alignment explanation
Indices: 7319--7371 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
7309 TATAAAATTA
*
7319 TTAAATTAATTTTATATTAATAT
1 TTAAA-TATTTTTATATTAATAT
**
7342 TTTTATATTTTTATAATTAA-AT
1 TTAAATATTTTTAT-ATTAATAT
7364 TTAAATAT
1 TTAAATAT
7372 AAATATTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTAAATATTTTTATATTAATAT
Found at i:7391 original size:35 final size:34
Alignment explanation
Indices: 7315--7391 Score: 95
Period size: 35 Copynumber: 2.3 Consensus size: 34
7305 TATTTATAAA
* *
7315 ATTATTA-AATTAATTTTATATTAATATTTTTAT
1 ATTATTATAATTAATTTAATATAAATATTTTTAT
*
7348 ATTTTTATAATTAAATTTAAATATAAATATTTTT-T
1 ATTATTATAATT-AATTT-AATATAAATATTTTTAT
7383 ATTATTATA
1 ATTATTATA
7392 TAATAATTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 6 0.16
34 4 0.11
35 14 0.38
36 13 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
ATTATTATAATTAATTTAATATAAATATTTTTAT
Found at i:8837 original size:15 final size:15
Alignment explanation
Indices: 8814--8849 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
8804 GTAAAAATTT
* *
8814 TATAGATAATATAAA
1 TATAAATAATACAAA
8829 TATAAATAATACAAA
1 TATAAATAATACAAA
8844 TATAAA
1 TATAAA
8850 GTAGATGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
TATAAATAATACAAA
Found at i:8901 original size:14 final size:15
Alignment explanation
Indices: 8873--8905 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
8863 TAAAAAAATT
8873 AATTATAAATATTAA
1 AATTATAAATATTAA
*
8888 AATTA-AAATTTTAA
1 AATTATAAATATTAA
8902 AATT
1 AATT
8906 TATTAGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTATAAATATTAA
Found at i:10020 original size:14 final size:13
Alignment explanation
Indices: 9990--10044 Score: 51
Period size: 12 Copynumber: 4.3 Consensus size: 13
9980 ATTTAAATAA
*
9990 ATATATATATTTT
1 ATATAAATATTTT
*
10003 ATATTAATATTATT
1 ATATAAATATT-TT
*
10017 ATATAAATA-TTG
1 ATATAAATATTTT
*
10029 ATAT-AATATTTA
1 ATATAAATATTTT
10041 ATAT
1 ATAT
10045 CGAATAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
11 4 0.11
12 11 0.31
13 10 0.29
14 10 0.29
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (13 bp):
ATATAAATATTTT
Found at i:11331 original size:5 final size:5
Alignment explanation
Indices: 11323--11368 Score: 65
Period size: 5 Copynumber: 8.6 Consensus size: 5
11313 AATCTAAACT
11323 AATTA AATTA AATTA AATTA AATTA AATTTA AATTTA AATTTA AAT
1 AATTA AATTA AATTA AATTA AATTA AA-TTA AA-TTA AA-TTA AAT
11369 AAAAAATTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 23 0.57
6 17 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
AATTA
Found at i:12467 original size:12 final size:12
Alignment explanation
Indices: 12450--12485 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
12440 TTATTCTAAT
12450 TTTAAATATATA
1 TTTAAATATATA
12462 TTTAAATATATA
1 TTTAAATATATA
*
12474 TATAAATATATA
1 TTTAAATATATA
12486 ATCTATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTTAAATATATA
Found at i:12638 original size:17 final size:17
Alignment explanation
Indices: 12616--12648 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12606 TATTATGGGT
*
12616 TCCTTTATTTGTTTTGC
1 TCCTTTACTTGTTTTGC
12633 TCCTTTACTTGTTTTG
1 TCCTTTACTTGTTTTG
12649 TATCCATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.18, G:0.12, T:0.64
Consensus pattern (17 bp):
TCCTTTACTTGTTTTGC
Found at i:13641 original size:43 final size:43
Alignment explanation
Indices: 13594--13679 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
13584 GGTACAAATA
13594 TAGTTTTGACGTAATAGAATATGTTTAAGATAGGTACGGACAT
1 TAGTTTTGACGTAATAGAATATGTTTAAGATAGGTACGGACAT
13637 TAGTTTTGACGTAATAGAATATGTTTAAGATAGGTACGGACAT
1 TAGTTTTGACGTAATAGAATATGTTTAAGATAGGTACGGACAT
13680 GTAAGAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (43 bp):
TAGTTTTGACGTAATAGAATATGTTTAAGATAGGTACGGACAT
Found at i:14296 original size:2 final size:2
Alignment explanation
Indices: 14289--14322 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
14279 ATGGATTCAA
14289 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14323 TTAATACATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14459 original size:25 final size:25
Alignment explanation
Indices: 14431--14504 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 25
14421 TTAAAAAGTA
*
14431 TTAAAATATTATTTTTATATTAAAT
1 TTAAAATATTATTTTTAAATTAAAT
* * *
14456 TTAACAT-TTATATTTCACATTAAA-
1 TTAAAATATTAT-TTTTAAATTAAAT
* * *
14480 TTCAAATAATAATTTTAAATTAAAT
1 TTAAAATATTATTTTTAAATTAAAT
14505 AAATAATAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
24 19 0.51
25 18 0.49
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (25 bp):
TTAAAATATTATTTTTAAATTAAAT
Found at i:14506 original size:18 final size:20
Alignment explanation
Indices: 14475--14511 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
14465 ATATTTCACA
14475 TTAAATTCAAAT-AATAATT
1 TTAAATTCAAATAAATAATT
14494 TTAAATT-AAATAAATAAT
1 TTAAATTCAAATAAATAAT
14512 AATTTAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAAATTCAAATAAATAATT
Found at i:14682 original size:15 final size:14
Alignment explanation
Indices: 14664--14715 Score: 61
Period size: 13 Copynumber: 3.6 Consensus size: 14
14654 TTATAATTTT
*
14664 ATATTTATACATAAA
1 ATATTTAAACAT-AA
14679 ATATATTAAACATAA
1 ATAT-TTAAACATAA
*
14694 ATA-TTAAATATAA
1 ATATTTAAACATAA
14707 ATATTTAAA
1 ATATTTAAA
14716 AAAGATACTG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 12 0.36
14 5 0.15
15 9 0.27
16 7 0.21
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATTTAAACATAA
Found at i:15305 original size:13 final size:13
Alignment explanation
Indices: 15287--15311 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15277 CTTCTTCTTC
15287 CCCCCCCCCCCCG
1 CCCCCCCCCCCCG
15300 CCCCCCCCCCCC
1 CCCCCCCCCCCC
15312 CCCAGTTTTA
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:0.00, C:0.96, G:0.04, T:0.00
Consensus pattern (13 bp):
CCCCCCCCCCCCG
Found at i:15305 original size:14 final size:14
Alignment explanation
Indices: 15286--15312 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
15276 TCTTCTTCTT
15286 CCCCCCCCCCCCCG
1 CCCCCCCCCCCCCG
15300 CCCCCCCCCCCCC
1 CCCCCCCCCCCCC
15313 CCAGTTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.96, G:0.04, T:0.00
Consensus pattern (14 bp):
CCCCCCCCCCCCCG
Found at i:16408 original size:25 final size:25
Alignment explanation
Indices: 16380--16435 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
16370 ATCGAACTTA
*
16380 TGAATTCTTTAATTATATATAATTT
1 TGAATTCTTTAATTATATATAATTG
16405 TGAATTCTTTAATTATATATAATTG
1 TGAATTCTTTAATTATATATAATTG
16430 TGAATT
1 TGAATT
16436 ATGGAGGATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
TGAATTCTTTAATTATATATAATTG
Found at i:17770 original size:2 final size:2
Alignment explanation
Indices: 17763--17789 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17753 TCCTTTCTTA
17763 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
17790 CACATTGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18629 original size:14 final size:15
Alignment explanation
Indices: 18601--18641 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
18591 AAAAAAAATG
18601 ATATTTAATAATTTTA
1 ATATTTAA-AATTTTA
*
18617 A-ATTTTAAATTTTA
1 ATATTTAAAATTTTA
18631 ATATTTAAAAT
1 ATATTTAAAAT
18642 ATTTTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 8 0.36
15 13 0.59
16 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATATTTAAAATTTTA
Found at i:20237 original size:21 final size:21
Alignment explanation
Indices: 20211--20250 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
20201 ATTATATTTT
20211 AAATA-TTATAATTATAAAATA
1 AAATATTTA-AATTATAAAATA
20232 AAATATTTAAATTATAAAA
1 AAATATTTAAATTATAAAA
20251 ATTTTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATATTTAAATTATAAAATA
Found at i:20556 original size:15 final size:15
Alignment explanation
Indices: 20536--20565 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20526 TCAGATAAAA
20536 AATGAAAAATTATTT
1 AATGAAAAATTATTT
*
20551 AATGAAAAGTTATTT
1 AATGAAAAATTATTT
20566 TTTCAGACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
AATGAAAAATTATTT
Found at i:20999 original size:5 final size:5
Alignment explanation
Indices: 20980--21015 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
20970 ATAAAAATAC
20980 TTATA -TATAA TTATA TTATA TTATA TTATA TTATA T
1 TTATA TTAT-A TTATA TTATA TTATA TTATA TTATA T
21016 ATTTTTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 3 0.10
5 23 0.79
6 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:21557 original size:18 final size:20
Alignment explanation
Indices: 21536--21574 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
21526 AAATTGATTT
21536 ATTTATTTAA-A-TTTAAAA
1 ATTTATTTAATATTTTAAAA
21554 ATTTATTTAATATTTTAAAA
1 ATTTATTTAATATTTTAAAA
21574 A
1 A
21575 ATATAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 1 0.05
20 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTATTTAATATTTTAAAA
Found at i:21712 original size:13 final size:14
Alignment explanation
Indices: 21694--21729 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
21684 TCATCTGATC
21694 TATTTTATA-ATTA
1 TATTTTATATATTA
21707 TATTTTATATATTA
1 TATTTTATATATTA
21721 -ATTTTATAT
1 TATTTTATAT
21730 TTTTATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTTTATATATTA
Found at i:21735 original size:21 final size:20
Alignment explanation
Indices: 21704--21742 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
21694 TATTTTATAA
21704 TTATATTTTATATATTAATT
1 TTATATTTTATATATTAATT
21724 TTATATTTTTATATATTAA
1 TTATA-TTTTATATATTAA
21743 ATAATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATATTTTATATATTAATT
Found at i:21751 original size:18 final size:18
Alignment explanation
Indices: 21709--21765 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 18
21699 TATAATTATA
*
21709 TTTTATATATTAATTTTATAT
1 TTTTATATATTAA--ATA-AT
21730 TTTTATATATTAAATAAT
1 TTTTATATATTAAATAAT
21748 TTTTAT-TATTTAAATAAT
1 TTTTATATA-TTAAATAAT
21766 ATATAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
17 2 0.06
18 17 0.50
19 2 0.06
21 13 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTATATATTAAATAAT
Found at i:21771 original size:25 final size:25
Alignment explanation
Indices: 21713--21778 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
21703 ATTATATTTT
*
21713 ATATATTAATTTTATATTTTTATATA
1 ATATA-TAATTTTATATTTTTAAATA
* *
21739 TTAAATAATTTT-TATTATTTAAATA
1 ATATATAATTTTATATT-TTTAAATA
*
21764 ATATATAATATTATA
1 ATATATAATTTTATA
21779 ATATAAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
24 4 0.12
25 23 0.72
26 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
ATATATAATTTTATATTTTTAAATA
Found at i:21781 original size:15 final size:14
Alignment explanation
Indices: 21761--21790 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
21751 TATTATTTAA
21761 ATAATATATAATATT
1 ATAATATA-AATATT
21776 ATAATATAAATATT
1 ATAATATAAATATT
21790 A
1 A
21791 AAAACATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATAATATAAATATT
Found at i:22084 original size:23 final size:21
Alignment explanation
Indices: 22058--22101 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
22048 TTTAATTTGA
22058 TAAAAAAGTTAATAACTCAAAAT
1 TAAAAAA-TTAA-AACTCAAAAT
* *
22081 TAAATAATTTAAACTCAAAAT
1 TAAAAAATTAAAACTCAAAAT
22102 AATTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 3 0.16
23 6 0.32
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (21 bp):
TAAAAAATTAAAACTCAAAAT
Found at i:22199 original size:37 final size:38
Alignment explanation
Indices: 22158--22236 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
22148 TTGATAAATT
* *
22158 TAAATACCAAACTTAATTAATCTAAATTAAAT-TAACA
1 TAAATACCAAACTTAATTAATATAAAATAAATATAACA
** * *
22195 TAAATATTAAATTTAATTAATATAAAATAAATATAATA
1 TAAATACCAAACTTAATTAATATAAAATAAATATAACA
22233 TAAA
1 TAAA
22237 ATTTTAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
37 27 0.77
38 8 0.23
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (38 bp):
TAAATACCAAACTTAATTAATATAAAATAAATATAACA
Found at i:22222 original size:16 final size:17
Alignment explanation
Indices: 22197--22240 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
22187 AATTAACATA
*
22197 AATATTAAATTTAAT-T
1 AATATAAAATTTAATAT
*
22213 AATATAAAA-TAAATAT
1 AATATAAAATTTAATAT
22229 AATATAAAATTT
1 AATATAAAATTT
22241 TAAAAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 4 0.17
16 18 0.78
17 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATAAAATTTAATAT
Found at i:22395 original size:5 final size:5
Alignment explanation
Indices: 22387--22414 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
22377 AACAAGTGCC
22387 TTTGG TTTGG TTTGG TTTGG TTTGG TTT
1 TTTGG TTTGG TTTGG TTTGG TTTGG TTT
22415 CTTTGTACCC
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:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (5 bp):
TTTGG
Found at i:28466 original size:31 final size:31
Alignment explanation
Indices: 28428--28486 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
28418 AAATCGTTAT
28428 TTTTTATATAAAAAAAGTTATAGCTCATTAC
1 TTTTTATATAAAAAAAGTTATAGCTCATTAC
28459 TTTTTATATAAAAAAAGTTATAGCTCAT
1 TTTTTATATAAAAAAAGTTATAGCTCAT
28487 GGATAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
TTTTTATATAAAAAAAGTTATAGCTCATTAC
Found at i:29263 original size:15 final size:16
Alignment explanation
Indices: 29232--29264 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
29222 CAAGGTTTCA
29232 TTTTTTTTTTGCCTTTT
1 TTTTTTTTTTG-CTTTT
29249 TTTTTTTTTTG-TTTT
1 TTTTTTTTTTGCTTTT
29264 T
1 T
29265 CATGGAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
17 11 0.69
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (16 bp):
TTTTTTTTTTGCTTTT
Found at i:29719 original size:44 final size:44
Alignment explanation
Indices: 29671--29756 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
29661 ATATATATAG
*
29671 ATTTTTGTATATTCGTACTCTGTCGTGATTTAATTATTTTTTTC
1 ATTTTTGTACATTCGTACTCTGTCGTGATTTAATTATTTTTTTC
* *
29715 ATTTTTGTACATTCGTATTGTGTCGTGATTTAATTATTTTTT
1 ATTTTTGTACATTCGTACTCTGTCGTGATTTAATTATTTTTT
29757 CCATGTCATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.19, C:0.09, G:0.13, T:0.59
Consensus pattern (44 bp):
ATTTTTGTACATTCGTACTCTGTCGTGATTTAATTATTTTTTTC
Found at i:34663 original size:28 final size:29
Alignment explanation
Indices: 34623--34678 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 29
34613 TATGATTTAA
34623 TTTTGACTTTTTTTATTAATAAATGAACT
1 TTTTGACTTTTTTTATTAATAAATGAACT
34652 TTTTGAC-TTTTTTATTAATAAATGAAC
1 TTTTGACTTTTTTTATTAATAAATGAAC
34679 ATAATTGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 20 0.74
29 7 0.26
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (29 bp):
TTTTGACTTTTTTTATTAATAAATGAACT
Found at i:34686 original size:29 final size:29
Alignment explanation
Indices: 34625--34686 Score: 90
Period size: 28 Copynumber: 2.1 Consensus size: 29
34615 TGATTTAATT
**
34625 TTGACTTTTTTTATTAATAAATGAACTTT
1 TTGACTTTTTTTATTAATAAATGAACTAA
34654 TTGAC-TTTTTTATTAATAAATGAACATAA
1 TTGACTTTTTTTATTAATAAATGAAC-TAA
34683 TTGA
1 TTGA
34687 GAAATAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 20 0.67
29 10 0.33
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.50
Consensus pattern (29 bp):
TTGACTTTTTTTATTAATAAATGAACTAA
Found at i:35137 original size:24 final size:25
Alignment explanation
Indices: 35101--35147 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
35091 TTTAAATATA
**
35101 ATTTTTTATTTTATTTTTAATTAAT
1 ATTTTTTATTTTAAATTTAATTAAT
35126 ATTTTTTA-TTTAAATTTAATTA
1 ATTTTTTATTTTAAATTTAATTA
35148 TAAAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
ATTTTTTATTTTAAATTTAATTAAT
Found at i:42924 original size:39 final size:41
Alignment explanation
Indices: 42845--42924 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
42835 ATAATGACTG
42845 CTATTTAAATCCTGCATGAAAGTTCTCTCGAGTCTGGATTA
1 CTATTTAAATCCTGCATGAAAGTTCTCTCGAGTCTGGATTA
42886 CTATTTAAATCCTGCATGAAAG-T-TCTCGAGTCTGGATTA
1 CTATTTAAATCCTGCATGAAAGTTCTCTCGAGTCTGGATTA
42925 TAACATCATC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 16 0.41
40 1 0.03
41 22 0.56
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (41 bp):
CTATTTAAATCCTGCATGAAAGTTCTCTCGAGTCTGGATTA
Found at i:43559 original size:16 final size:16
Alignment explanation
Indices: 43521--43551 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43511 TTAATTTAAT
43521 CTAAAATGACTCGAAA
1 CTAAAATGACTCGAAA
*
43537 CTAAAATGATTCGAA
1 CTAAAATGACTCGAA
43552 TTTAAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (16 bp):
CTAAAATGACTCGAAA
Found at i:44327 original size:19 final size:17
Alignment explanation
Indices: 44304--44378 Score: 60
Period size: 17 Copynumber: 4.2 Consensus size: 17
44294 TTGTATTATT
44304 ATTTAAAATATTTTTAA
1 ATTTAAAATATTTTTAA
** *
44321 ATTTTTAATTTATATTTAA
1 A--TTTAAAATATTTTTAA
** *
44340 ATTTAACTTGATTTATAA
1 ATTTAAAAT-ATTTTTAA
*
44358 ATTTAAAATATTTTTAT
1 ATTTAAAATATTTTTAA
44375 ATTT
1 ATTT
44379 TTACAATTAA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
17 18 0.40
18 13 0.29
19 14 0.31
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (17 bp):
ATTTAAAATATTTTTAA
Found at i:44844 original size:11 final size:12
Alignment explanation
Indices: 44828--44856 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
44818 ATAGGATACT
44828 AAATATAAT-TA
1 AAATATAATATA
44839 AAATATAATATA
1 AAATATAATATA
44851 AAATAT
1 AAATAT
44857 TACAAAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAATATAATATA
Found at i:44903 original size:31 final size:31
Alignment explanation
Indices: 44868--44932 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
44858 ACAAAACATA
* *
44868 AGAAAATGATACAAACGTAACACCAATAAAT
1 AGAAAATAATACAAACATAACACCAATAAAT
* * * *
44899 AGAAAATAATATAAATATAATATCAATAAAT
1 AGAAAATAATACAAACATAACACCAATAAAT
44930 AGA
1 AGA
44933 TATTTAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.62, C:0.09, G:0.08, T:0.22
Consensus pattern (31 bp):
AGAAAATAATACAAACATAACACCAATAAAT
Found at i:45835 original size:13 final size:14
Alignment explanation
Indices: 45817--45846 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
45807 TAATTTTTAT
45817 TAAAATT-ATATAA
1 TAAAATTAATATAA
45830 TAAAATTAATATAA
1 TAAAATTAATATAA
45844 TAA
1 TAA
45847 TATAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TAAAATTAATATAA
Found at i:45870 original size:17 final size:16
Alignment explanation
Indices: 45821--45900 Score: 67
Period size: 16 Copynumber: 5.0 Consensus size: 16
45811 TTTTATTAAA
*
45821 ATTATATAATAAAATTA
1 ATTA-ATAATAAAATTT
*
45838 ATATAATAATATAATTT
1 AT-TAATAATAAAATTT
*
45855 ATTAATAATAAAA-AT
1 ATTAATAATAAAATTT
*
45870 -TTAATGATAAAATTT
1 ATTAATAATAAAATTT
*
45885 AATAA-AATTAAAATTT
1 ATTAATAA-TAAAATTT
45901 TATACTTTGA
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
14 11 0.22
15 3 0.06
16 21 0.41
17 14 0.27
18 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (16 bp):
ATTAATAATAAAATTT
Found at i:45873 original size:14 final size:13
Alignment explanation
Indices: 45856--45889 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
45846 ATATAATTTA
45856 TTAATAATAAAAAT
1 TTAATAAT-AAAAT
*
45870 TTAATGATAAAAT
1 TTAATAATAAAAT
45883 TTAATAA
1 TTAATAA
45890 AATTAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (13 bp):
TTAATAATAAAAT
Found at i:45884 original size:30 final size:29
Alignment explanation
Indices: 45841--45900 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
45831 AAAATTAATA
* *
45841 TAATAATATAATTTATTAATAATAAAAATT
1 TAATAATAAAATTTAATAA-AATAAAAATT
* *
45871 TAATGATAAAATTTAATAAAATTAAAATT
1 TAATAATAAAATTTAATAAAATAAAAATT
45900 T
1 T
45901 TATACTTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (29 bp):
TAATAATAAAATTTAATAAAATAAAAATT
Found at i:46541 original size:16 final size:16
Alignment explanation
Indices: 46509--46541 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
46499 ATTCAGATAT
46509 TAAAAAAAAAATATAA
1 TAAAAAAAAAATATAA
46525 TAAACAAAAAAAT-TAA
1 TAAA-AAAAAAATATAA
46541 T
1 T
46542 TTTTATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (16 bp):
TAAAAAAAAAATATAA
Done.