Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 4 of 349
Found at i:1180234 original size:27 final size:28
Alignment explanation
Indices: 1180182--1180237 Score: 105
Period size: 27 Copynumber: 2.0 Consensus size: 28
1180172 GGACTAAAAG
1180182 TTAGATTAATATTTTTTTTACTAACTAT
1 TTAGATTAATATTTTTTTTACTAACTAT
1180210 TTAGATTAATA-TTTTTTTACTAACTAT
1 TTAGATTAATATTTTTTTTACTAACTAT
1180237 T
1 T
1180238 CCACCCTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (28 bp):
TTAGATTAATATTTTTTTTACTAACTAT
Found at i:1185998 original size:11 final size:11
Alignment explanation
Indices: 1185984--1186014 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1185974 TATCATTTAA
1185984 TTATTATTTTG
1 TTATTATTTTG
1185995 TTATTATTTTG
1 TTATTATTTTG
*
1186006 TTGTTATTT
1 TTATTATTT
1186015 CTTGGATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.10, T:0.74
Consensus pattern (11 bp):
TTATTATTTTG
Found at i:1189081 original size:18 final size:18
Alignment explanation
Indices: 1189023--1189086 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
1189013 GTATTGTTAT
* *
1189023 TTTTTAATAAAATTATAAA
1 TTTTTAA-ATAATTTTAAA
* *
1189042 TTTTT-TATAACTTTTATGA
1 TTTTTAAATAA-TTTTA-AA
1189061 TTTTTAAATAATTTTAAA
1 TTTTTAAATAATTTTAAA
1189079 TTTTTAAA
1 TTTTTAAA
1189087 AAGGCTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
17 3 0.08
18 13 0.36
19 16 0.44
20 4 0.11
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTTTAAATAATTTTAAA
Found at i:1191262 original size:19 final size:19
Alignment explanation
Indices: 1191226--1191262 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1191216 ATAATCAAAT
*
1191226 ATATATTATTGTTAAATAA
1 ATATATTATTGTCAAATAA
*
1191245 ATATATTATTGTCGAATA
1 ATATATTATTGTCAAATA
1191263 TTATATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (19 bp):
ATATATTATTGTCAAATAA
Found at i:1193091 original size:13 final size:13
Alignment explanation
Indices: 1193073--1193108 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1193063 TTTTTACCCA
1193073 TAATAATAATTAT
1 TAATAATAATTAT
1193086 TAATAATTAA-TAT
1 TAATAA-TAATTAT
1193099 TAATAATAAT
1 TAATAATAAT
1193109 AACTCTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.14
13 15 0.71
14 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATAATAATTAT
Found at i:1193100 original size:16 final size:17
Alignment explanation
Indices: 1193072--1193108 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1193062 ATTTTTACCC
*
1193072 ATAA-TAATAATTATTA
1 ATAATTAATAATTAATA
1193088 ATAATTAAT-ATTAATA
1 ATAATTAATAATTAATA
1193104 ATAAT
1 ATAAT
1193109 AACTCTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATTAATAATTAATA
Found at i:1193102 original size:10 final size:10
Alignment explanation
Indices: 1193073--1193110 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1193063 TTTTTACCCA
1193073 TAATAATAAT
1 TAATAATAAT
*
1193083 TATTAATAAT
1 TAATAATAAT
*
1193093 TAATATTAA-
1 TAATAATAAT
1193102 TAATAATAA
1 TAATAATAA
1193111 CTCTAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TAATAATAAT
Found at i:1194305 original size:14 final size:14
Alignment explanation
Indices: 1194286--1194316 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1194276 AGCACAATAT
*
1194286 TTTTATAGTTAGAG
1 TTTTATACTTAGAG
1194300 TTTTATACTTAGAG
1 TTTTATACTTAGAG
1194314 TTT
1 TTT
1194317 AAGAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.16, T:0.55
Consensus pattern (14 bp):
TTTTATACTTAGAG
Found at i:1194590 original size:14 final size:14
Alignment explanation
Indices: 1194568--1194600 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1194558 ATCATTTAAC
*
1194568 TATTATATTGTTAT
1 TATTTTATTGTTAT
1194582 TATTTTATTGTTAT
1 TATTTTATTGTTAT
1194596 T-TTTT
1 TATTTT
1194601 GGATATTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (14 bp):
TATTTTATTGTTAT
Found at i:1196859 original size:15 final size:16
Alignment explanation
Indices: 1196829--1196867 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 16
1196819 TAATAAAAAT
1196829 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
1196846 ATAATTTA-TATTTTA
1 ATAATTTATTATTTTA
1196861 ATAATTT
1 ATAATTT
1196868 TAAAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 14 0.64
16 4 0.18
17 4 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:1198231 original size:27 final size:28
Alignment explanation
Indices: 1198201--1198256 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
1198191 TAAGCACTCG
1198201 TAAATATAGTCAAAT-ATATATTATTGT
1 TAAATATAGTCAAATAATATATTATTGT
*
1198228 TAAATATAGTTAAATAAATATATTATTGT
1 TAAATATAGTCAAAT-AATATATTATTGT
1198257 CGATTATCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 14 0.54
29 12 0.46
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (28 bp):
TAAATATAGTCAAATAATATATTATTGT
Found at i:1200119 original size:13 final size:13
Alignment explanation
Indices: 1200101--1200136 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1200091 ATTTTACCCA
1200101 TAATAATAATTAT
1 TAATAATAATTAT
1200114 TAATAATTAA-TAT
1 TAATAA-TAATTAT
1200127 TAATAATAAT
1 TAATAATAAT
1200137 AACTCTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.14
13 15 0.71
14 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATAATAATTAT
Found at i:1200128 original size:16 final size:17
Alignment explanation
Indices: 1200100--1200136 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1200090 AATTTTACCC
*
1200100 ATAA-TAATAATTATTA
1 ATAATTAATAATTAATA
1200116 ATAATTAAT-ATTAATA
1 ATAATTAATAATTAATA
1200132 ATAAT
1 ATAAT
1200137 AACTCTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATTAATAATTAATA
Found at i:1200130 original size:10 final size:10
Alignment explanation
Indices: 1200101--1200138 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1200091 ATTTTACCCA
1200101 TAATAATAAT
1 TAATAATAAT
*
1200111 TATTAATAAT
1 TAATAATAAT
*
1200121 TAATATTAA-
1 TAATAATAAT
1200130 TAATAATAA
1 TAATAATAA
1200139 CTCTAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TAATAATAAT
Found at i:1203416 original size:13 final size:13
Alignment explanation
Indices: 1203398--1203425 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1203388 AGCAATTAAT
1203398 AAGTTTTGCAAAC
1 AAGTTTTGCAAAC
1203411 AAGTTTTGCAAAC
1 AAGTTTTGCAAAC
1203424 AA
1 AA
1203426 TTCAATTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (13 bp):
AAGTTTTGCAAAC
Found at i:1205862 original size:30 final size:29
Alignment explanation
Indices: 1205789--1205863 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
1205779 TTGACCCTTC
* *
1205789 AACTTTTTCATATTTATACTTTAACCACT
1 AACTTTTTCATATTTACACTTAAACCACT
* * **
1205818 TACATGTTAAATATTTACACTTAAACCACAT
1 AAC-TTTTTCATATTTACACTTAAACCAC-T
1205849 AACTTTTTCATATTT
1 AACTTTTTCATATTT
1205864 TTTTATGATT
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
29 2 0.06
30 29 0.85
31 3 0.09
ACGTcount: A:0.35, C:0.19, G:0.01, T:0.45
Consensus pattern (29 bp):
AACTTTTTCATATTTACACTTAAACCACT
Found at i:1206770 original size:30 final size:31
Alignment explanation
Indices: 1206736--1206806 Score: 72
Period size: 36 Copynumber: 2.2 Consensus size: 31
1206726 GTTGGCTATT
*
1206736 ATAATTG-TTAACATTAATGGAAGACAATTA
1 ATAATTGCTTAACATTAATGGAAGACAATCA
*
1206766 ATAATGGTTGCCATTAACATTAATGGGAGACAATCA
1 ATAA---TTG-C-TTAACATTAATGGAAGACAATCA
1206802 ATAAT
1 ATAAT
1206807 GACAACCACC
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
30 4 0.12
33 4 0.12
36 25 0.76
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (31 bp):
ATAATTGCTTAACATTAATGGAAGACAATCA
Found at i:1209606 original size:21 final size:21
Alignment explanation
Indices: 1209580--1209620 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1209570 AGACGAGCAA
* *
1209580 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1209601 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1209621 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1213362 original size:30 final size:29
Alignment explanation
Indices: 1213293--1213379 Score: 104
Period size: 30 Copynumber: 3.0 Consensus size: 29
1213283 ATTGCATTTT
* * *
1213293 GACCTCTAAACTTT-TCCTAAATTTCATTT
1 GACCCCTAAACTTTCT-TTAAATTTCATTA
*
1213322 GACCCTTAAACTTTCTTTAAATTTCACTTA
1 GACCCCTAAACTTTCTTTAAATTTCA-TTA
*
1213352 GACCCCTAAACTTTCATTAAATTTCATT
1 GACCCCTAAACTTTCTTTAAATTTCATT
1213380 TTAATCCTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.46
30 27 0.54
ACGTcount: A:0.30, C:0.24, G:0.03, T:0.43
Consensus pattern (29 bp):
GACCCCTAAACTTTCTTTAAATTTCATTA
Found at i:1213403 original size:59 final size:59
Alignment explanation
Indices: 1213278--1213403 Score: 130
Period size: 59 Copynumber: 2.1 Consensus size: 59
1213268 AATTAAAAAA
* * * *
1213278 TAAAAATTGCATTTTGACCTCTAAACTTTTCCTAAATTTCATTTGACCCTTAAACTTTC
1 TAAAAATTGCACTTAGACCCCTAAACTTTTCCTAAATTTCATTTAACCCTTAAACTTTC
** * * * *
1213337 TTTAAATTTCACTTAGACCCCTAAAC-TTTCATTAAATTTCATTTTAATCC-TAAATTTTC
1 TAAAAATTGCACTTAGACCCCTAAACTTTTC-CTAAATTTCA-TTTAACCCTTAAACTTTC
1213396 TAAAAATT
1 TAAAAATT
1213404 ACATTTAGCC
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
58 4 0.08
59 43 0.81
60 6 0.11
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.44
Consensus pattern (59 bp):
TAAAAATTGCACTTAGACCCCTAAACTTTTCCTAAATTTCATTTAACCCTTAAACTTTC
Found at i:1213756 original size:3 final size:3
Alignment explanation
Indices: 1213750--1213774 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1213740 GTGTAGGAGG
1213750 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
1213775 AGAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1213984 original size:16 final size:16
Alignment explanation
Indices: 1213943--1213982 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
1213933 AAACTAAAGC
1213943 AAAAAAAAGCAGCCCAA
1 AAAAAAAAG-AGCCCAA
*
1213960 AAAGAAAAG-GCCCAA
1 AAAAAAAAGAGCCCAA
1213975 AAAAAAAA
1 AAAAAAAA
1213983 AGAAAAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
17 8 0.38
ACGTcount: A:0.70, C:0.17, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAGCCCAA
Found at i:1214130 original size:10 final size:9
Alignment explanation
Indices: 1214110--1214188 Score: 81
Period size: 9 Copynumber: 8.6 Consensus size: 9
1214100 AAAAAGAGAG
1214110 AAAGAAAAA
1 AAAGAAAAA
1214119 GAAA-AAAGAA
1 -AAAGAAA-AA
*
1214129 GAAGAAAAA
1 AAAGAAAAA
1214138 GAAAGAGAAAA
1 -AAAGA-AAAA
*
1214149 AAAGGAAAA
1 AAAGAAAAA
*
1214158 AAAGGAAAA
1 AAAGAAAAA
1214167 AAAGAAAAA
1 AAAGAAAAA
1214176 AAA-AAAAA
1 AAAGAAAAA
1214184 AAAGA
1 AAAGA
1214189 GTTTCAATTC
Statistics
Matches: 60, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
8 8 0.13
9 32 0.53
10 16 0.27
11 4 0.07
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:1214133 original size:19 final size:18
Alignment explanation
Indices: 1214098--1214188 Score: 77
Period size: 17 Copynumber: 5.1 Consensus size: 18
1214088 AGCAGGCCAG
1214098 GAAAAAAGAGAGAAAGAAAAA
1 GAAAAAAGA-AG-AA-AAAAA
1214119 GAAAAAAGAAGAAGAAAAA
1 GAAAAAAGAAGAA-AAAAA
1214138 G---AAAG-AGAAAAAAA
1 GAAAAAAGAAGAAAAAAA
*
1214152 GGAAAAAA-AGGAAAAAAA
1 -GAAAAAAGAAGAAAAAAA
*
1214170 GAAAAAA-AAAAAAAAAA
1 GAAAAAAGAAGAAAAAAA
1214187 GA
1 GA
1214189 GTTTCAATTC
Statistics
Matches: 62, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
14 5 0.08
15 5 0.08
16 4 0.06
17 17 0.27
18 11 0.18
19 9 0.15
20 2 0.03
21 9 0.15
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
GAAAAAAGAAGAAAAAAA
Found at i:1214773 original size:20 final size:22
Alignment explanation
Indices: 1214733--1214774 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1214723 AATTTTGTGT
*
1214733 AAAAAATCCAGTGTTTTCAAAA
1 AAAAAATCCAGTGTTTCCAAAA
1214755 AAAAAATCCA-T-TTTCCAAAA
1 AAAAAATCCAGTGTTTCCAAAA
1214775 TTTTTAGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
22 10 0.53
ACGTcount: A:0.52, C:0.17, G:0.05, T:0.26
Consensus pattern (22 bp):
AAAAAATCCAGTGTTTCCAAAA
Found at i:1214932 original size:18 final size:17
Alignment explanation
Indices: 1214770--1214931 Score: 166
Period size: 17 Copynumber: 9.4 Consensus size: 17
1214760 ATCCATTTTC
* *
1214770 CAAAATTTTTAGTGTCTT
1 CAAAAATTTTCGTGT-TT
*
1214788 CTAAAAATTTTTGTGTTT
1 C-AAAAATTTTCGTGTTT
1214806 CAAAAATTTTCGT-TTT
1 CAAAAATTTTCGTGTTT
*
1214822 CAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTT
1214839 CAAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
* *
1214857 CAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTT
** *
1214874 CAAAAATCCTCTTGTTTT
1 CAAAAATTTTCGTG-TTT
1214892 CAAAAA-TTTCGGTGTTT
1 CAAAAATTTTC-GTGTTT
**
1214909 TGAAAATTTTCGTGTTT
1 CAAAAATTTTCGTGTTT
1214926 CAAAAA
1 CAAAAA
1214932 AAAAAAATCT
Statistics
Matches: 119, Mismatches: 19, Indels: 13
0.79 0.13 0.09
Matches are distributed among these distances:
16 15 0.13
17 58 0.49
18 34 0.29
19 12 0.10
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (17 bp):
CAAAAATTTTCGTGTTT
Found at i:1214932 original size:35 final size:33
Alignment explanation
Indices: 1214770--1214931 Score: 155
Period size: 35 Copynumber: 4.7 Consensus size: 33
1214760 ATCCATTTTC
* * *
1214770 CAAAATTTTTAGTGTCTTCTAAAAATTTTTGTGTTT
1 CAAAAATTTTCGTGT-TTC-AAAAA-TTTCGTGTTT
1214806 CAAAAATTTTCGT-TTTCAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTTCAAAAATTT-CGTGTTT
* *
1214839 CAAAAATTTTCGTGTTTTCAAAATTTTTCGTATTT
1 CAAAAATTTTCGTG-TTTCAAAA-ATTTCGTGTTT
** *
1214874 CAAAAATCCTCTTGTTTTCAAAAATTTCGGTGTTT
1 CAAAAATTTTCGTG-TTTCAAAAATTTC-GTGTTT
**
1214909 TGAAAATTTTCGTGTTTCAAAAA
1 CAAAAATTTTCGTGTTTCAAAAA
1214932 AAAAAAATCT
Statistics
Matches: 106, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
32 3 0.03
33 24 0.23
34 16 0.15
35 49 0.46
36 14 0.13
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (33 bp):
CAAAAATTTTCGTGTTTCAAAAATTTCGTGTTT
Found at i:1222912 original size:12 final size:12
Alignment explanation
Indices: 1222891--1222922 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1222881 GTTTCTTTCT
1222891 TTTA-TTTTTTA
1 TTTATTTTTTTA
1222902 TTTATTTTTTTA
1 TTTATTTTTTTA
1222914 TTT-TTTTTT
1 TTTATTTTTT
1222923 GGGACCTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTATTTTTTTA
Found at i:1225394 original size:191 final size:192
Alignment explanation
Indices: 1225068--1225459 Score: 777
Period size: 191 Copynumber: 2.0 Consensus size: 192
1225058 TGGTGTTATT
1225068 ACCCCGTTTAATTAAGATAAGGCGAGAGATAATCAGGTTGTGAACCGCGTGAAGGAGTTTATTTT
1 ACCCCGTTTAATTAAGATAAGGCGAGAGATAATCAGGTTGTGAACCGCGTGAAGGAGTTTATTTT
1225133 ATTTTTATCGTGATAAAATCTCGTTTGGACATTAGCAATGATAAAAACCACTTTTTAAAAAATAA
66 ATTTTTATCGTGATAAAATCTCGTTTGGACATTAGCAATGATAAAAACCACTTTTTAAAAAATAA
1225198 AAAATAAAAACCGCTATCCGGTTTTATAAAACCACTTTTCCTTTAGTCTTCTATAAATAAAG
131 AAAATAAAAACCGCTATCCGGTTTTATAAAACCACTTTTCCTTTAGTCTTCTATAAATAAAG
1225260 A-CCCGTTTAATTAAGATAAGGCGAGAGATAATCAGGTTGTGAACCGCGTGAAGGAGTTTATTTT
1 ACCCCGTTTAATTAAGATAAGGCGAGAGATAATCAGGTTGTGAACCGCGTGAAGGAGTTTATTTT
1225324 ATTTTTATCGTGATAAAATCTCGTTTGGACATTAGCAATGATAAAAACCACTTTTTAAAAAATAA
66 ATTTTTATCGTGATAAAATCTCGTTTGGACATTAGCAATGATAAAAACCACTTTTTAAAAAATAA
1225389 AAAATAAAAACCGCTATCCGGTTTTATAAAACCACTTTTCCTTTAGTCTTCTATAAATAAAG
131 AAAATAAAAACCGCTATCCGGTTTTATAAAACCACTTTTCCTTTAGTCTTCTATAAATAAAG
1225451 ACCCCGTTT
1 ACCCCGTTT
1225460 CATAGCTGCC
Statistics
Matches: 199, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
191 191 0.96
192 8 0.04
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (192 bp):
ACCCCGTTTAATTAAGATAAGGCGAGAGATAATCAGGTTGTGAACCGCGTGAAGGAGTTTATTTT
ATTTTTATCGTGATAAAATCTCGTTTGGACATTAGCAATGATAAAAACCACTTTTTAAAAAATAA
AAAATAAAAACCGCTATCCGGTTTTATAAAACCACTTTTCCTTTAGTCTTCTATAAATAAAG
Found at i:1237625 original size:141 final size:141
Alignment explanation
Indices: 1237371--1237650 Score: 420
Period size: 141 Copynumber: 2.0 Consensus size: 141
1237361 ATTTGATACC
* *** *
1237371 TTAAGCTAAGTTCATTAGAACTAGCCTAGAATTTCAAATTTTAGGCACGGCATAACCAGCAAATC
1 TTAAGCTAAGTTCATTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAACCAGCAAATC
* * *
1237436 AGTTCTTAACCTCTCATTCGCCATGACTCAATTTGATACCTTAAGCTAAGTTCAATCAGTTCAAG
66 AGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTCAAGCTAAGTTCAATCAGTTCAAC
1237501 TTCAATTAACT
131 TTCAATTAACT
* * *
1237512 TTAAGCTAA-TTCAGTTAAAACTAGCCTAGAGTTTCAAAAAATAGGCACTACATAGCCAAG-AAA
1 TTAAGCTAAGTTCA-TTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAACC-AGCAAA
*
1237575 TCAGTTCTTAACCTCTCATCCGCCATGATTCAATTTGATACCTCAAGCTAAGTTCAATCAGTTCA
64 TCAGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTCAAGCTAAGTTCAATCAGTTCA
1237640 ACTTCAATTAA
129 ACTTCAATTAA
1237651 AACTAGCTTA
Statistics
Matches: 125, Mismatches: 12, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
140 4 0.03
141 119 0.95
142 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (141 bp):
TTAAGCTAAGTTCATTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAACCAGCAAATC
AGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTCAAGCTAAGTTCAATCAGTTCAAC
TTCAATTAACT
Found at i:1238450 original size:23 final size:22
Alignment explanation
Indices: 1238424--1238466 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1238414 TTATCATAAT
1238424 ATTTTTTAATATTTATAAATTTA
1 ATTTTTTAATA-TTATAAATTTA
**
1238447 ATTTTTTTGTATTATAAATT
1 ATTTTTTAATATTATAAATT
1238467 AAATAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
ATTTTTTAATATTATAAATTTA
Found at i:1241120 original size:6 final size:6
Alignment explanation
Indices: 1241109--1241162 Score: 108
Period size: 6 Copynumber: 9.0 Consensus size: 6
1241099 GCTCTAAACA
1241109 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1241157 ATACAT
1 ATACAT
1241163 GAAGGTATAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:1242759 original size:28 final size:28
Alignment explanation
Indices: 1242712--1242769 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
1242702 TTTGGACTTA
** *
1242712 TTTTTTAATTTGGTACTTGAGCTTCTTC
1 TTTTTTAATTTGAAAATTGAGCTTCTTC
* *
1242740 TTTTTTAATTTGAAAATTGAGTTTTTTC
1 TTTTTTAATTTGAAAATTGAGCTTCTTC
1242768 TT
1 TT
1242770 ATCCCAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.19, C:0.09, G:0.12, T:0.60
Consensus pattern (28 bp):
TTTTTTAATTTGAAAATTGAGCTTCTTC
Found at i:1245989 original size:24 final size:24
Alignment explanation
Indices: 1245945--1245993 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1245935 ATTATGAAAA
1245945 TAATAAAGGTTAAAATACAAACAC
1 TAATAAAGGTTAAAATACAAACAC
*
1245969 TAATAAAAGGTTGAAAT-CAAACAC
1 TAAT-AAAGGTTAAAATACAAACAC
1245993 T
1 T
1245994 TGACAGTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.22
Consensus pattern (24 bp):
TAATAAAGGTTAAAATACAAACAC
Found at i:1249713 original size:13 final size:13
Alignment explanation
Indices: 1249690--1249727 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
1249680 TTAATAAAAA
1249690 TAAAAATTATATAT-
1 TAAAAA-TATA-ATC
1249704 TAAAAATATAATC
1 TAAAAATATAATC
1249717 TAAAAATATAA
1 TAAAAATATAA
1249728 ATACATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.09
13 15 0.65
14 6 0.26
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (13 bp):
TAAAAATATAATC
Found at i:1253071 original size:20 final size:20
Alignment explanation
Indices: 1253046--1253095 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1253036 TGGCTTAAAA
1253046 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1253066 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1253083 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1253096 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1257710 original size:20 final size:20
Alignment explanation
Indices: 1257685--1257734 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1257675 TGGCTTAAAA
1257685 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1257705 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1257722 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1257735 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1261149 original size:16 final size:18
Alignment explanation
Indices: 1261128--1261162 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1261118 TTAATATTTT
1261128 TTTTAATT-GTAC-ATAA
1 TTTTAATTGGTACAATAA
1261144 TTTTAATTGGTACAATAA
1 TTTTAATTGGTACAATAA
1261162 T
1 T
1261163 AAATTCAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 4 0.24
18 5 0.29
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (18 bp):
TTTTAATTGGTACAATAA
Found at i:1271910 original size:14 final size:15
Alignment explanation
Indices: 1271891--1271919 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1271881 TATATATGCA
1271891 TTTTTTATT-TTTAT
1 TTTTTTATTGTTTAT
1271905 TTTTTTATTGTTTAT
1 TTTTTTATTGTTTAT
1271920 AACTAGCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTTTATTGTTTAT
Found at i:1272737 original size:28 final size:28
Alignment explanation
Indices: 1272697--1272757 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
1272687 ATGGTCCCCT
1272697 TCTAAATTCCTAGGTGTACCCCAAAGAA
1 TCTAAATTCCTAGGTGTACCCCAAAGAA
1272725 TCTAAATTCCTAGGTGTACCCCAAAGAA
1 TCTAAATTCCTAGGTGTACCCCAAAGAA
1272753 TCTAA
1 TCTAA
1272758 TCTCTCTCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (28 bp):
TCTAAATTCCTAGGTGTACCCCAAAGAA
Found at i:1273540 original size:6 final size:6
Alignment explanation
Indices: 1273531--1273561 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1273521 GCTGAAGCTA
1273531 GCAATG GCAATG GCAATG GCAATG GCAATG G
1 GCAATG GCAATG GCAATG GCAATG GCAATG G
1273562 TTGCTCCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.16
Consensus pattern (6 bp):
GCAATG
Found at i:1273965 original size:25 final size:25
Alignment explanation
Indices: 1273931--1273982 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1273921 TTAAAGTGTA
1273931 TTGTAAAGGTACCTCTATCTCTTTT
1 TTGTAAAGGTACCTCTATCTCTTTT
1273956 TTGTAAAGGTACCTCTATCTCTTTT
1 TTGTAAAGGTACCTCTATCTCTTTT
1273981 TT
1 TT
1273983 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (25 bp):
TTGTAAAGGTACCTCTATCTCTTTT
Found at i:1285363 original size:18 final size:17
Alignment explanation
Indices: 1285330--1285368 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
1285320 TTGTATAAAT
1285330 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
1285348 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
1285365 TGTG
1 TGTG
1285369 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:1285620 original size:23 final size:23
Alignment explanation
Indices: 1285594--1285667 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
1285584 GTGTTATTGA
1285594 TCAGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
*
1285617 TCAGTGGTAGCTTTGGCTACA-T
1 TCAGTGGTAGCTTCGGCTACATT
* *
1285639 CCAGTGGTAGCTTCGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
1285662 TCAGTG
1 TCAGTG
1285668 TGGCACTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
22 20 0.44
23 25 0.56
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.32
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:1285646 original size:22 final size:22
Alignment explanation
Indices: 1285595--1285660 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
1285585 TGTTATTGAT
*
1285595 CAGTGGTAGCTTCGGCTACATTT
1 CAGTGGTAGCTTCGGCTACA-TC
*
1285618 CAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATC
1285640 CAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACAT
1285661 ATCAGTGTGG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 21 0.52
23 19 0.47
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (22 bp):
CAGTGGTAGCTTCGGCTACATC
Found at i:1289897 original size:28 final size:28
Alignment explanation
Indices: 1289855--1289946 Score: 98
Period size: 27 Copynumber: 3.2 Consensus size: 28
1289845 CAATATGATC
* * *
1289855 TTTGGTATCTGAATTTGAATTTTTTTAA
1 TTTGGTATATAAATTTGATTTTTTTTAA
1289883 TTTGGTATATAAATTT--TTTTTATTTAA
1 TTTGGTATATAAATTTGATTTTT-TTTAA
* *
1289910 TTTGATATTTAAATTTGACTTTTTTCTTAA
1 TTTGGTATATAAATTTGA-TTTTTT-TTAA
1289940 TTTGGTA
1 TTTGGTA
1289947 CCTAAAATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
26 4 0.08
27 19 0.36
28 14 0.26
29 1 0.02
30 15 0.28
ACGTcount: A:0.26, C:0.03, G:0.11, T:0.60
Consensus pattern (28 bp):
TTTGGTATATAAATTTGATTTTTTTTAA
Found at i:1290488 original size:31 final size:31
Alignment explanation
Indices: 1290420--1290493 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
1290410 AAAAAAGATT
1290420 AGGTACTAAATTAAGAAAAAGAGTCAAGTTC
1 AGGTACTAAATTAAGAAAAAGAGTCAAGTTC
* * * * * *
1290451 AAGTACTAGATTAGGAAAACGTGTCAAGTTT
1 AGGTACTAAATTAAGAAAAAGAGTCAAGTTC
*
1290482 GGGTACTAAATT
1 AGGTACTAAATT
1290494 GGACCCAAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (31 bp):
AGGTACTAAATTAAGAAAAAGAGTCAAGTTC
Found at i:1293011 original size:30 final size:32
Alignment explanation
Indices: 1292970--1293060 Score: 95
Period size: 31 Copynumber: 3.0 Consensus size: 32
1292960 CTATACGCAT
*
1292970 AATAC-AAGACTAAAATTTTA-AAA-TTAAAA
1 AATACAAAGACTAAAATTTAACAAATTTAAAA
* *
1292999 AGTATAAAGACTAAAA-TTAACAAATTTAAAA
1 AATACAAAGACTAAAATTTAACAAATTTAAAA
*
1293030 AATACAAAAACTAAAA-TTAATCAAA-TTAAAA
1 AATACAAAGACTAAAATTTAA-CAAATTTAAAA
1293061 TATAAAAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
29 6 0.12
30 13 0.25
31 29 0.56
32 4 0.08
ACGTcount: A:0.64, C:0.08, G:0.03, T:0.25
Consensus pattern (32 bp):
AATACAAAGACTAAAATTTAACAAATTTAAAA
Found at i:1293043 original size:31 final size:30
Alignment explanation
Indices: 1292990--1293068 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
1292980 TAAAATTTTA
* *
1292990 AAATTAAAAAGTATAAAGACTAAAATTAA-C
1 AAATTAAAAAATA-AAAAACTAAAATTAATC
1293020 AAATTTAAAAAATACAAAAACTAAAATTAATC
1 AAA-TTAAAAAATA-AAAAACTAAAATTAATC
*
1293052 AAATTAAAATATAAAAA
1 AAATTAAAAAATAAAAA
1293069 TTAACCCACC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 7 0.16
31 32 0.74
32 4 0.09
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.24
Consensus pattern (30 bp):
AAATTAAAAAATAAAAAACTAAAATTAATC
Found at i:1322899 original size:15 final size:15
Alignment explanation
Indices: 1322879--1322911 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1322869 CCAAAAAGTC
1322879 AAAAAACT-AAACTCT
1 AAAAAACTCAAAC-CT
1322894 AAAAAACTCAAACCT
1 AAAAAACTCAAACCT
1322909 AAA
1 AAA
1322912 CAAGTTCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAAAACTCAAACCT
Found at i:1324676 original size:5 final size:5
Alignment explanation
Indices: 1324666--1324705 Score: 53
Period size: 5 Copynumber: 7.4 Consensus size: 5
1324656 TAGGGTATAG
1324666 TAAAA TAAAA TAAAA TAAAA TAAAA TGAATATA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA T-AA-A-A TAAAA TA
1324706 TGGGACACGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 24 0.75
6 3 0.09
7 3 0.09
8 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (5 bp):
TAAAA
Found at i:1324686 original size:15 final size:18
Alignment explanation
Indices: 1324661--1324705 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 18
1324651 GTATATAGGG
1324661 TATAGTAAAATAAAAT-AA
1 TATA-TAAAATAAAATGAA
1324679 -A-ATAAAATAAAATGAA
1 TATATAAAATAAAATGAA
1324695 TATATAAAATA
1 TATATAAAATA
1324706 TGGGACACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 11 0.46
16 3 0.12
17 2 0.08
18 8 0.33
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (18 bp):
TATATAAAATAAAATGAA
Found at i:1329055 original size:134 final size:136
Alignment explanation
Indices: 1328814--1329211 Score: 464
Period size: 144 Copynumber: 2.9 Consensus size: 136
1328804 AAACAATAAT
* * * * * *
1328814 CGAAGATTAGCAGAGAAGAGAGAACAACTTCGAAAGCTGGTAACCACTTCAAAGTTATCGAAATT
1 CGAAGATTAGCAGAGAAGAGAGAACAATTTCG-ACGCTCGTAATCACTACAAAGCTATCGAAATT
* *
1328879 CGATCAAACGAAC-TTCATAATTC-AGCTATAAAACAACCATCCATCACCAAAAAAA-AAA-AAA
65 CTATCAAACGAACTTTCATAATTCGA-CTATAAAACAACGATCCATCACCAAAAAAAGAAAGAAA
1328940 TTCAAAAG
129 TTCAAAAG
* * * *
1328948 CGAAGGTTAGCAGAGAAGAGAGAACGATTTCGACGCTCGTAATCACTCCAAAGCTATCGAAGTTC
1 CGAAGATTAGCAGAGAAGAGAGAACAATTTCGACGCTCGTAATCACTACAAAGCTATCGAAATTC
*
1329013 TATCAAACGAACTTTCATAATTCGACTATAAAACAACGATCCATCACAAAAAAAAAAAAGAAAGA
66 TATCAAACGAACTTTCATAATTCGACTATAAAACAACGATCCATCAC-------CAAAA-AAAGA
1329078 AAGAAATTCAAAAG
123 AAGAAATTCAAAAG
* * * * *
1329092 CGAAGATTAGCAGAGCAGATAGAACAATTTCGACGCTCGTAATCACTACAAATCTTTCTAAATT-
1 CGAAGATTAGCAGAGAAGAGAGAACAATTTCGACGCTCGTAATCACTACAAAGCTATCGAAATTC
* ** *
1329156 TGATCAAACGAACTTGCATAACCCGACTATTAAACAACGATCCATCACCAAAAAAA
66 T-ATCAAACGAACTTTCATAATTCGACTATAAAACAACGATCCATCACCAAAAAAA
1329212 TTCAAAAAAC
Statistics
Matches: 225, Mismatches: 26, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
133 38 0.17
134 60 0.27
135 1 0.00
136 3 0.01
137 4 0.02
141 4 0.02
142 3 0.01
143 4 0.02
144 108 0.48
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.20
Consensus pattern (136 bp):
CGAAGATTAGCAGAGAAGAGAGAACAATTTCGACGCTCGTAATCACTACAAAGCTATCGAAATTC
TATCAAACGAACTTTCATAATTCGACTATAAAACAACGATCCATCACCAAAAAAAGAAAGAAATT
CAAAAG
Found at i:1344431 original size:16 final size:17
Alignment explanation
Indices: 1344388--1344436 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
1344378 TAGACATGAA
*
1344388 ATAAATTATTAATTAAT
1 ATAAATTATTAAATAAT
*
1344405 ATAAATT-TTAAATATT
1 ATAAATTATTAAATAAT
*
1344421 A-AAATTATTAATTAAT
1 ATAAATTATTAAATAAT
1344437 CCAATAACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 5 0.19
16 15 0.56
17 7 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAATTATTAAATAAT
Found at i:1345636 original size:17 final size:17
Alignment explanation
Indices: 1345614--1345647 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1345604 ATCCACTAAT
*
1345614 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1345631 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1345648 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1350274 original size:17 final size:17
Alignment explanation
Indices: 1350252--1350285 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1350242 ATCCACTAAT
*
1350252 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1350269 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1350286 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1354351 original size:21 final size:21
Alignment explanation
Indices: 1354307--1354367 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 21
1354297 TAATTCTTCT
1354307 ATTTTTTTATTTTGAAGTAAATAAA
1 ATTTTTTTA-TTTG--G-AAATAAA
*
1354332 ATTTTTTTATTTGGAAATAAG
1 ATTTTTTTATTTGGAAATAAA
1354353 ATTTTTTTATTTGGA
1 ATTTTTTTATTTGGA
1354368 CTTAAAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
21 21 0.60
22 1 0.03
24 4 0.11
25 9 0.26
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (21 bp):
ATTTTTTTATTTGGAAATAAA
Found at i:1355080 original size:43 final size:43
Alignment explanation
Indices: 1355019--1355107 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
1355009 TCAATCAATT
*
1355019 TAGTGAATTTCATTTTTGGCCTTTTTCTGTTATGGGTTGGGCC
1 TAGTGAATTTCATTTTTGGCCTTTTTCTGTTATGGGTTAGGCC
1355062 TAGTGAATTTCATTTTTGGCCTTTTTCTGTTATGGGTTAGGCC
1 TAGTGAATTTCATTTTTGGCCTTTTTCTGTTATGGGTTAGGCC
1355105 TAG
1 TAG
1355108 AGGGTTATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.13, C:0.13, G:0.25, T:0.48
Consensus pattern (43 bp):
TAGTGAATTTCATTTTTGGCCTTTTTCTGTTATGGGTTAGGCC
Found at i:1355971 original size:21 final size:21
Alignment explanation
Indices: 1355947--1356002 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
1355937 ATCGAAATAA
1355947 TAAAATCAAATTATATTAAAT
1 TAAAATCAAATTATATTAAAT
1355968 T-AAA--AAA-TATA-TAAAT
1 TAAAATCAAATTATATTAAAT
1355984 TAAATATCAAATT-TATTAA
1 TAAA-ATCAAATTATATTAA
1356003 TTTCATTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
16 6 0.21
17 6 0.21
18 4 0.14
20 8 0.28
21 5 0.17
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAATCAAATTATATTAAAT
Found at i:1359046 original size:31 final size:31
Alignment explanation
Indices: 1359011--1359070 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1359001 CTTTTAACCC
*
1359011 CTAAATCTGA-TAATTAGATTCATTTTGGTAT
1 CTAAAT-TGAGTAATTAGATTCAATTTGGTAT
*
1359042 CTAAATTTAGTAATTAGATTCAATTTGGT
1 CTAAATTGAGTAATTAGATTCAATTTGGT
1359071 CATTGATCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.45
Consensus pattern (31 bp):
CTAAATTGAGTAATTAGATTCAATTTGGTAT
Found at i:1372710 original size:13 final size:13
Alignment explanation
Indices: 1372692--1372720 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1372682 ATAATTCTAC
1372692 AATGAACAAATAA
1 AATGAACAAATAA
1372705 AATGAACAAATAA
1 AATGAACAAATAA
1372718 AAT
1 AAT
1372721 ACTCTCAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (13 bp):
AATGAACAAATAA
Found at i:1377175 original size:2 final size:2
Alignment explanation
Indices: 1377168--1377194 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1377158 TATTTATTAT
1377168 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1377195 TATGGCTTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1378374 original size:18 final size:18
Alignment explanation
Indices: 1378351--1378455 Score: 129
Period size: 18 Copynumber: 5.8 Consensus size: 18
1378341 TGTTTATGGT
1378351 ACTATTCACGTATACGGC
1 ACTATTCACGTATACGGC
* **
1378369 ACTATTTACGTATACGAT
1 ACTATTCACGTATACGGC
* * *
1378387 ACTATTCATGTATATGTC
1 ACTATTCACGTATACGGC
*
1378405 ACTATTCACATATACGGC
1 ACTATTCACGTATACGGC
*
1378423 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGGC
*
1378441 ACTGTTCACGTATAC
1 ACTATTCACGTATAC
1378456 AGTAGTTGGG
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 72 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (18 bp):
ACTATTCACGTATACGGC
Found at i:1378434 original size:54 final size:54
Alignment explanation
Indices: 1378351--1378454 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 54
1378341 TGTTTATGGT
* * *
1378351 ACTATTCACGTATACGGCACTATTTACGTATACGATACTATTCATGTATATGTC
1 ACTATTCACATATACGGCACTATTCACGTATACGATACTATTCACGTATATGTC
* *
1378405 ACTATTCACATATACGGCACTATTCACGTATACGGTACTGTTCACGTATA
1 ACTATTCACATATACGGCACTATTCACGTATACGATACTATTCACGTATA
1378455 CAGTAGTTGG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (54 bp):
ACTATTCACATATACGGCACTATTCACGTATACGATACTATTCACGTATATGTC
Found at i:1384282 original size:3 final size:3
Alignment explanation
Indices: 1384274--1384353 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
1384264 ATCACATGTT
1384274 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
1384322 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1384354 TGGATGTAAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1384471 original size:72 final size:72
Alignment explanation
Indices: 1384354--1384613 Score: 504
Period size: 72 Copynumber: 3.6 Consensus size: 72
1384344 TATTATTATT
1384354 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1384419 TTTTAAG
66 TTTTAAG
1384426 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1384491 TTTTAAG
66 TTTTAAG
1384498 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1384563 TTTTAAG
66 TTTTAAG
*
1384570 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAG-TTGTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTA
1384614 AGTTGTAAGC
Statistics
Matches: 187, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
71 6 0.03
72 181 0.97
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.42
Consensus pattern (72 bp):
TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
TTTTAAG
Found at i:1388833 original size:3 final size:3
Alignment explanation
Indices: 1388825--1388880 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
1388815 ATCACATGTT
1388825 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
1388873 TTA TTA TT
1 TTA TTA TT
1388881 TGGATGTAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1388962 original size:72 final size:72
Alignment explanation
Indices: 1388881--1389140 Score: 504
Period size: 72 Copynumber: 3.6 Consensus size: 72
1388871 TATTATTATT
1388881 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1388946 TTTTAAG
66 TTTTAAG
1388953 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1389018 TTTTAAG
66 TTTTAAG
1389025 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1389090 TTTTAAG
66 TTTTAAG
*
1389097 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAG-TTGTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTA
1389141 AGTTGTAAGC
Statistics
Matches: 187, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
71 6 0.03
72 181 0.97
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.42
Consensus pattern (72 bp):
TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
TTTTAAG
Found at i:1407706 original size:15 final size:15
Alignment explanation
Indices: 1407686--1407715 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1407676 TTTAATTCTT
*
1407686 TATAAATTATAAAAA
1 TATAAACTATAAAAA
1407701 TATAAACTATAAAAA
1 TATAAACTATAAAAA
1407716 ATTAAAATTT
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:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TATAAACTATAAAAA
Found at i:1415458 original size:18 final size:18
Alignment explanation
Indices: 1415435--1415477 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1415425 TCCAATAGTA
**
1415435 AAAAAAATTTTGAAAAAG
1 AAAAAAATACTGAAAAAG
*
1415453 AAAAAAATACTGAAAATG
1 AAAAAAATACTGAAAAAG
1415471 AAAAAAA
1 AAAAAAA
1415478 AAATTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.16
Consensus pattern (18 bp):
AAAAAAATACTGAAAAAG
Found at i:1415756 original size:152 final size:148
Alignment explanation
Indices: 1415565--1415858 Score: 405
Period size: 147 Copynumber: 2.0 Consensus size: 148
1415555 TTTATATTAA
* * *
1415565 TTTAATAAATAACCTTGATTTTGACACTTTCTTCGTATTTTTTTATTTTCGTATTTTATTTTTTA
1 TTTAATAAATAACCTTGATTTTGACACTTTATTC--A--TATTT-TTTTCGTATATTATTTTTTA
* * *
1415630 AAATATATTATATTCGTATTTTATTTCTTCATATTATTTTAGTACATAATGTTTCAAATGTATTA
61 AAATATATTATATTCGTATTTTATTTCTTCATATTATTTTAGCAAAAAATGTTTCAAATGTATTA
*
1415695 TTTAAGTGTTT-TTTTATGTTTT
126 TGTAAGTGTTTCTTTTATGTTTT
1415717 TTTAATAAATAACCCTT-ATTTT-AGCACTTTATTCATATTTTTTTCGTATATTATTTTTTAAAA
1 TTTAATAAATAA-CCTTGATTTTGA-CACTTTATTCATATTTTTTTCGTATATTATTTTTTAAAA
* * * *
1415780 TATATTATTTTCGTATTTTATTTTTTTATATTGTTTTAGCAAAAAATGTTTCAAATGTATTATGT
64 TATATTATATTCGTATTTTATTTCTTCATATTATTTTAGCAAAAAATGTTTCAAATGTATTATGT
1415845 AAGTGTTTCTTTTA
129 AAGTGTTTCTTTTA
1415859 CATTAATTTA
Statistics
Matches: 128, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
147 87 0.68
148 9 0.07
150 1 0.01
151 1 0.01
152 26 0.20
153 4 0.03
ACGTcount: A:0.28, C:0.08, G:0.07, T:0.57
Consensus pattern (148 bp):
TTTAATAAATAACCTTGATTTTGACACTTTATTCATATTTTTTTCGTATATTATTTTTTAAAATA
TATTATATTCGTATTTTATTTCTTCATATTATTTTAGCAAAAAATGTTTCAAATGTATTATGTAA
GTGTTTCTTTTATGTTTT
Found at i:1416189 original size:148 final size:149
Alignment explanation
Indices: 1415934--1416288 Score: 473
Period size: 148 Copynumber: 2.4 Consensus size: 149
1415924 GTATTTTATT
* *
1415934 TACGAAGAAAGTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAGAAACACTTAAATAATA
1 TACGAATAAAGTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAA-AAAAACTTAAATAATA
* *
1415999 CATTTGAAACATTTTTCGCTAAAACTATATAAAAAAATAAAATAAGAAAATAATATATTTTAAAA
65 CATTTGAAACATTTGTCACTAAAACTATATAAAAAAATAAAATAAGAAAATAATATATTTTAAAA
*
1416064 AATAATATACG-AAAAAAAA
130 AATAAGATACGAAAAAAAAA
* * ** *
1416083 TATGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAAAACTTAAATAATAT
1 TACGAATAAAGTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAAAACTTAAATAATAC
* * ** *
1416148 ATTTGAAACATTATGT-ACTAAAA-TAATATGAAGAAATAAAATACTAATATAATATATTTTAAA
66 ATTTGAAACATT-TGTCACTAAAACT-ATATAAAAAAATAAAATAAGAAAATAATATATTTTAAA
1416211 AAATAAGATACGAAAATAAAAAAAA
129 AAATAAGATACG---A-AAAAAAAA
* *
1416236 TACGAATAAAGTGCCAAAATCAAGATTATTTATTAAATTAATATAAAAAAAAA
1 TACGAATAAAGTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAAAA
1416289 ATACACTAGT
Statistics
Matches: 178, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
147 1 0.01
148 77 0.43
149 45 0.25
153 55 0.31
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.29
Consensus pattern (149 bp):
TACGAATAAAGTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAAAACTTAAATAATAC
ATTTGAAACATTTGTCACTAAAACTATATAAAAAAATAAAATAAGAAAATAATATATTTTAAAAA
ATAAGATACGAAAAAAAAA
Found at i:1416347 original size:19 final size:20
Alignment explanation
Indices: 1416323--1416378 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
1416313 CAACATGACC
*
1416323 CATTTTTTA-TTTTTTTTTT
1 CATTTTTCAGTTTTTTTTTT
*
1416342 CA-TTTTCAGTATTTTTTTT
1 CATTTTTCAGTTTTTTTTTT
1416361 C-TTTTTCAGTTTTTTTTT
1 CATTTTTCAGTTTTTTTTT
1416379 ATTGTTGGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 5 0.16
19 27 0.84
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.77
Consensus pattern (20 bp):
CATTTTTCAGTTTTTTTTTT
Found at i:1416356 original size:18 final size:18
Alignment explanation
Indices: 1416333--1416378 Score: 74
Period size: 19 Copynumber: 2.5 Consensus size: 18
1416323 CATTTTTTAT
1416333 TTTTTTTTTCATTTTCAG
1 TTTTTTTTTCATTTTCAG
*
1416351 TATTTTTTTTCTTTTTCAG
1 T-TTTTTTTTCATTTTCAG
1416370 TTTTTTTTT
1 TTTTTTTTT
1416379 ATTGTTGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.09, C:0.09, G:0.04, T:0.78
Consensus pattern (18 bp):
TTTTTTTTTCATTTTCAG
Found at i:1421329 original size:17 final size:17
Alignment explanation
Indices: 1421291--1421329 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1421281 TGAATTCCTG
1421291 ATCATTCTATTAAAATA
1 ATCATTCTATTAAAATA
*
1421308 TTCATTCTATTAATAA-A
1 ATCATTCTATTAA-AATA
1421325 ATCAT
1 ATCAT
1421330 AAAAACTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.44
Consensus pattern (17 bp):
ATCATTCTATTAAAATA
Found at i:1425033 original size:66 final size:66
Alignment explanation
Indices: 1424927--1425059 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
1424917 AGCAGCTTAA
1424927 GCGGCTAAACCAAGTTGAGGGTTGGCTTTCGAGGGCTGAAACTCTGATAAACGATGCTGATCAAT
1 GCGGCTAAACCAAGTTGAGGGTTGGCTTTCGAGGGCTGAAACTCTGATAAACGATGCTGATCAAT
1424992 T
66 T
1424993 GCGGCTAAACCAAGTTGAGGGTTGGCTTTCGAGGGCTGAAACTCTGATAAACGATGCTGATCAAT
1 GCGGCTAAACCAAGTTGAGGGTTGGCTTTCGAGGGCTGAAACTCTGATAAACGATGCTGATCAAT
1425058 T
66 T
1425059 G
1 G
1425060 ATTGTCCAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (66 bp):
GCGGCTAAACCAAGTTGAGGGTTGGCTTTCGAGGGCTGAAACTCTGATAAACGATGCTGATCAAT
T
Found at i:1427468 original size:75 final size:75
Alignment explanation
Indices: 1427345--1427487 Score: 259
Period size: 75 Copynumber: 1.9 Consensus size: 75
1427335 GAGAGGAGGG
*
1427345 ATGGTGGAAAGATGTAGAATGGGAGGATGAATCCACTCGAGTTGCTTTTCTCCCTTCTTTCAAAC
1 ATGGTGGAAAGATGTAGAATGGGAGGATGAATCCACTCGAATTGCTTTTCTCCCTTCTTTCAAAC
1427410 CTGAGGTGGA
66 CTGAGGTGGA
* *
1427420 ATGGTGGAAAGATGTAGAATGGGAGGATGAATCCAGTCGAATTGCTTTTCTCTCTTCTTTCAAAC
1 ATGGTGGAAAGATGTAGAATGGGAGGATGAATCCACTCGAATTGCTTTTCTCCCTTCTTTCAAAC
1427485 CTG
66 CTG
1427488 GTCTATTCTA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (75 bp):
ATGGTGGAAAGATGTAGAATGGGAGGATGAATCCACTCGAATTGCTTTTCTCCCTTCTTTCAAAC
CTGAGGTGGA
Found at i:1428251 original size:15 final size:14
Alignment explanation
Indices: 1428228--1428268 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
1428218 TTTAATAATA
1428228 AAAAAATTATTATT
1 AAAAAATTATTATT
*
1428242 ATACAAATTATTATT
1 A-AAAAATTATTATT
1428257 AAAAAATTATTA
1 AAAAAATTATTA
1428269 AAAACCAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAAAATTATTATT
Found at i:1437986 original size:130 final size:130
Alignment explanation
Indices: 1437751--1438123 Score: 399
Period size: 130 Copynumber: 2.9 Consensus size: 130
1437741 AAAATTCTTC
* * * * *
1437751 AAAATGAAGGCGAAATTTGATGTTCGGCGATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
1 AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * * * * *
1437816 TTTCGTATTTGCTCAGAATAATCGAATTTCCCTTCGAAATTTCATTCATACT-TTTTAAAATCCC
66 TTTCGCATTTGTTCAAAATAATCGAATATCCCTTCAAAATTTCACTCAT-CTCTCTTAAAATCCC
1437880 T
130 T
* * * * *
1437881 TAAATGAATATGAGATTTGATGTTTGGCAATTCGCGGAATTGTGCCCTAACGTGTTGGGTTGCAA
1 AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
** * ** * * *
1437946 TTTCGCATTTGTTCAAAATAATCGAATATCATTTTAAAATTTTGCTCGTGTCTCTTAAAATCTCT
66 TTTCGCATTTGTTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATCTCTCTTAAAATCCCT
* * * * *
1438011 AAAACGAAGGCGATATGTGATATTTGGCAATTCGC-GAGATCGTGCCCTAACGTGTTGGGTAGCA
1 AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGA-ATCGTGCCCTAACGTGTTGGGTTGCA
* * * *
1438075 ATTTCCCGATTTTTTTAAAATAATCAAATATCCCTTCAAAATTTCACTC
65 ATTTCGC-ATTTGTTCAAAATAATCGAATATCCCTTCAAAATTTCACTC
1438124 GGCTTTTCTA
Statistics
Matches: 198, Mismatches: 42, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
129 3 0.02
130 162 0.82
131 33 0.17
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (130 bp):
AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
TTTCGCATTTGTTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATCTCTCTTAAAATCCCT
Found at i:1440291 original size:16 final size:16
Alignment explanation
Indices: 1440267--1440298 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1440257 ATCCGGACAA
*
1440267 CTTATGTGCATGAATT
1 CTTACGTGCATGAATT
1440283 CTTACGTGCATGAATT
1 CTTACGTGCATGAATT
1440299 TGCATGAGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (16 bp):
CTTACGTGCATGAATT
Found at i:1459471 original size:18 final size:17
Alignment explanation
Indices: 1459422--1459460 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1459412 TAAAATTTTA
*
1459422 AAAAAATGAAATATATT
1 AAAAAATTAAATATATT
1459439 AAAAAATTAAATATATT
1 AAAAAATTAAATATATT
1459456 AAAAA
1 AAAAA
1459461 GGTTAAGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (17 bp):
AAAAAATTAAATATATT
Found at i:1459512 original size:61 final size:62
Alignment explanation
Indices: 1459437--1459555 Score: 213
Period size: 62 Copynumber: 1.9 Consensus size: 62
1459427 ATGAAATATA
*
1459437 TTAAAAAATTAAATATATT-AAAAAGGTTAAGTATAACCAATTTTAAAATTTTAATATATTT
1 TTAAAAAATTAAATATATTAAAAAAGGTTAAGTATAACCAATTTTAAAATTTCAATATATTT
*
1459498 TTAAAAAATTAAATATATTAAAAAATGTTAAGTATAACCAATTTTAAAATTTCAATAT
1 TTAAAAAATTAAATATATTAAAAAAGGTTAAGTATAACCAATTTTAAAATTTCAATAT
1459556 GTTCAATATA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
61 19 0.35
62 36 0.65
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (62 bp):
TTAAAAAATTAAATATATTAAAAAAGGTTAAGTATAACCAATTTTAAAATTTCAATATATTT
Found at i:1459687 original size:17 final size:18
Alignment explanation
Indices: 1459629--1459695 Score: 68
Period size: 17 Copynumber: 3.8 Consensus size: 18
1459619 AAAGAGAAAA
*
1459629 AAAATTTT-AATATATTT
1 AAAATTTTAAATATACTT
* *
1459646 AAATTTTTAAA-AAACTT
1 AAAATTTTAAATATACTT
1459663 AAAAAATTTTAAATATA-TT
1 --AAAATTTTAAATATACTT
1459682 AAAATTTTAAATAT
1 AAAATTTTAAATAT
1459696 GTTAAAGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
17 25 0.61
18 2 0.05
19 12 0.29
20 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAATTTTAAATATACTT
Found at i:1459779 original size:17 final size:16
Alignment explanation
Indices: 1459757--1459803 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 16
1459747 ATGTCAAAAT
1459757 ATATTAAAATTTTGAA
1 ATATTAAAATTTTGAA
1459773 CATATTAAAAAATTTTGAA
1 -ATATT--AAAATTTTGAA
*
1459792 GTATTAAAATTT
1 ATATTAAAATTT
1459804 CAAAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 7 0.26
17 5 0.19
18 4 0.15
19 11 0.41
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (16 bp):
ATATTAAAATTTTGAA
Found at i:1459796 original size:18 final size:19
Alignment explanation
Indices: 1459762--1459800 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1459752 AAAATATATT
1459762 AAAATTTTGAACATATTAA
1 AAAATTTTGAACATATTAA
*
1459781 AAAATTTTGAA-GTATTAA
1 AAAATTTTGAACATATTAA
1459799 AA
1 AA
1459801 TTTCAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (19 bp):
AAAATTTTGAACATATTAA
Found at i:1461095 original size:21 final size:21
Alignment explanation
Indices: 1461071--1461115 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1461061 AATTTTTTAA
1461071 TTAAATAAAATATAAAACCAC
1 TTAAATAAAATATAAAACCAC
1461092 TTAAATAAAATATAAAACCAC
1 TTAAATAAAATATAAAACCAC
1461113 TTA
1 TTA
1461116 CAATTTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (21 bp):
TTAAATAAAATATAAAACCAC
Found at i:1461221 original size:34 final size:35
Alignment explanation
Indices: 1461173--1461238 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
1461163 AGATTTTCTT
* *
1461173 AATATATTTAAAATTTTTAAAATTTTAAAAAAATG
1 AATATATTTAAAATTTTAAAAATATTAAAAAAATG
1461208 AATATA-TTAAAATTTTAAAAATATTAAAAAA
1 AATATATTTAAAATTTTAAAAATATTAAAAAA
1461239 TGTTAAGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 23 0.79
35 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (35 bp):
AATATATTTAAAATTTTAAAAATATTAAAAAAATG
Found at i:1461408 original size:18 final size:19
Alignment explanation
Indices: 1461354--1461410 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 19
1461344 GATTTTTTAG
1461354 TATATTTAAAATTTTAAAA
1 TATATTTAAAATTTTAAAA
* **
1461373 -AAATTTAAAAAATT-AAA
1 TATATTTAAAATTTTAAAA
1461390 TATA-TTAAAATTTTAAAA
1 TATATTTAAAATTTTAAAA
1461408 TAT
1 TAT
1461411 TTTTTAATAG
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
17 11 0.37
18 19 0.63
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATATTTAAAATTTTAAAA
Found at i:1475102 original size:19 final size:19
Alignment explanation
Indices: 1475037--1475109 Score: 87
Period size: 18 Copynumber: 3.9 Consensus size: 19
1475027 AATTGATTGG
* *
1475037 TTATCCAGTAACAGTC-AA
1 TTATTCAGTAACAATCAAA
*
1475055 TTATTCAGTAAAAATCAAA
1 TTATTCAGTAACAATCAAA
* *
1475074 -TATACAGTAACAATTAAA
1 TTATTCAGTAACAATCAAA
1475092 TTATTCAGTAACAATCAA
1 TTATTCAGTAACAATCAA
1475110 TCTTTCCAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
18 28 0.62
19 17 0.38
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (19 bp):
TTATTCAGTAACAATCAAA
Found at i:1475343 original size:12 final size:12
Alignment explanation
Indices: 1475326--1475350 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1475316 AGTGCCGAAT
1475326 CGGTAACAGTAA
1 CGGTAACAGTAA
1475338 CGGTAACAGTAA
1 CGGTAACAGTAA
1475350 C
1 C
1475351 AGTAGTCGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:1476157 original size:17 final size:17
Alignment explanation
Indices: 1476125--1476166 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1476115 AACCTTGAAT
* *
1476125 TTTCCTTTTTTTTCTTTC
1 TTTCC-TTTCTTTCTTCC
1476143 TTTCCTTTCTTTCTTCC
1 TTTCCTTTCTTTCTTCC
1476160 TTTCCTT
1 TTTCCTT
1476167 CCCCTGCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTCCTTTCTTTCTTCC
Found at i:1478617 original size:13 final size:13
Alignment explanation
Indices: 1478599--1478623 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1478589 TGTATATATA
1478599 AAAAAGGAAAAAT
1 AAAAAGGAAAAAT
1478612 AAAAAGGAAAAA
1 AAAAAGGAAAAA
1478624 AGAAATAAAG
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:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (13 bp):
AAAAAGGAAAAAT
Found at i:1478727 original size:21 final size:21
Alignment explanation
Indices: 1478677--1478720 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
1478667 AAAGCAGGGG
1478677 AAAGAAAGAAAGAAAAAGAGA
1 AAAGAAAGAAAGAAAAAGAGA
*
1478698 AAAGAAAGAAA-AAAAAGGGA
1 AAAGAAAGAAAGAAAAAGAGA
1478718 AAA
1 AAA
1478721 TCGAAGATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (21 bp):
AAAGAAAGAAAGAAAAAGAGA
Found at i:1480702 original size:46 final size:46
Alignment explanation
Indices: 1480650--1480783 Score: 259
Period size: 46 Copynumber: 2.9 Consensus size: 46
1480640 AGTGTGCTCT
1480650 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
1480696 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1480742 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGG
1480784 TTGAAAGATA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:1480782 original size:16 final size:16
Alignment explanation
Indices: 1480761--1480799 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
1480751 AATGTGTAAG
1480761 ACCATGGTTGAAAGAT
1 ACCATGGTTGAAAGAT
1480777 ACCATGGTTGAAAGAT
1 ACCATGGTTGAAAGAT
1480793 ACCATGG
1 ACCATGG
1480800 CAACATTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (16 bp):
ACCATGGTTGAAAGAT
Found at i:1486456 original size:341 final size:341
Alignment explanation
Indices: 1485833--1486473 Score: 874
Period size: 341 Copynumber: 1.9 Consensus size: 341
1485823 TGGAATGCAA
* *
1485833 AGGTTTAAAAGAAATCATCAGTGAAGAAAAACCTGGTGAAGTCGCTGAGCTAAAAGAAAATTCAG
1 AGGTTTAAAAGAAATCATCAGTGAAGAAAAACCTAGTGAAGTCGCTGAGCTAAAAGAAAATTCAA
* * ** * * **
1485898 ACTTGTTTTCTAAGCCCGAGATTTTGCGTCTACGTCATCTGCCCAAACTAAAGACTGTATACCAT
66 ACTTGTTTTCTAAGCCAGAGATTTTGCATCTAAATAATCTGCCCAAAATAAAGACAATATACCAT
* * ** *
1485963 CATGCTCTGCCTTTCCCACAGCTGAAGAAAATATACATTACAGGATGCCCAATGTTAAAGAAGCT
131 CATGCTCTACCTTTCCCACAGCTGAAGAAAATACACATTACAAAATGCCCAATGCTAAAGAAGCT
*
1486028 CCCACTAAACTCCAATAGTGCAAAAAGACAGAGGATGGTCATTGAAGGAGATGTGGGATGGTGGA
196 CCCACTAAACTCCAATAGTGCAAAAAGACAGAGGATGGTCATTGAAGGAGATGAGGGATGGTGGA
* *
1486093 AAGATGTCGAATGGGAGGATGAATCCACTAAAATTGCTTTTCTCCCCACTTTCAAACCTCGTATA
261 AAGATGTAGAATGGAAGGATGAATCCACTAAAATTGCTTTTCTCCCCACTTTCAAACCTCGTATA
1486158 TGTTGGTTATTAATTG
326 TGTTGGTTATTAATTG
* * * * * *
1486174 AGGTTTAGAAGAAATGATCAGTGAGGAAAAACTTAGTGAAGTCGCTGAGCTAAAGGGAAATTCAA
1 AGGTTTAAAAGAAATCATCAGTGAAGAAAAACCTAGTGAAGTCGCTGAGCTAAAAGAAAATTCAA
* * *
1486239 ACTTGTTTTCTAAGCTAGAGTTTTTGCATCTAAATAATCTGCCCAAAATGAAGACAATATACCCA
66 ACTTGTTTTCTAAGCCAGAGATTTTGCATCTAAATAATCTGCCCAAAATAAAGACAATATA-CCA
* * * * ** *
1486304 -CATGCTCTACTTTTTCCGCAGCTGAAGAGAAT-CACAATTTTAAAATGCCCAATGCTGAAGAAG
130 TCATGCTCTACCTTTCCCACAGCTGAAGAAAATACAC-ATTACAAAATGCCCAATGCTAAAGAAG
* * * *
1486367 TTCCCACTAAACTCCAATAGTGCAAAAGGAC-GAAGGCTTGTCATTGAAGGAGATGAGGGATGGT
194 CTCCCACTAAACTCCAATAGTGCAAAAAGACAG-AGGATGGTCATTGAAGGAGATGAGGGATGGT
* *
1486431 GGAAAGATGTAGGATGGAAGGATGAATCCACTCAAATTGCTTT
258 GGAAAGATGTAGAATGGAAGGATGAATCCACTAAAATTGCTTT
1486474 ACTCTCTTCT
Statistics
Matches: 257, Mismatches: 40, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
340 3 0.01
341 251 0.98
342 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (341 bp):
AGGTTTAAAAGAAATCATCAGTGAAGAAAAACCTAGTGAAGTCGCTGAGCTAAAAGAAAATTCAA
ACTTGTTTTCTAAGCCAGAGATTTTGCATCTAAATAATCTGCCCAAAATAAAGACAATATACCAT
CATGCTCTACCTTTCCCACAGCTGAAGAAAATACACATTACAAAATGCCCAATGCTAAAGAAGCT
CCCACTAAACTCCAATAGTGCAAAAAGACAGAGGATGGTCATTGAAGGAGATGAGGGATGGTGGA
AAGATGTAGAATGGAAGGATGAATCCACTAAAATTGCTTTTCTCCCCACTTTCAAACCTCGTATA
TGTTGGTTATTAATTG
Found at i:1488750 original size:30 final size:30
Alignment explanation
Indices: 1488716--1488778 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
1488706 ATTTATTTTA
* *
1488716 TTGTTTATTTTTTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
1488746 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1488776 TTG
1 TTG
1488779 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.22, C:0.03, G:0.14, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:1488882 original size:18 final size:18
Alignment explanation
Indices: 1488861--1488900 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1488851 GAAATATTTA
*
1488861 TTTTGATGT-TTCTAGTAT
1 TTTTGATGTATTATA-TAT
1488879 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
1488897 TTTT
1 TTTT
1488901 AAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.03, G:0.12, T:0.65
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:1496374 original size:30 final size:30
Alignment explanation
Indices: 1496340--1496402 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
1496330 ACTTATTTTA
*
1496340 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTATAAAGGCAT
*
1496370 TTGTTAATTTTGTTATTATTATAGAGGCAT
1 TTGTTAATTTTGTTATTATTATAAAGGCAT
1496400 TTG
1 TTG
1496403 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.16, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTATAAAGGCAT
Found at i:1497024 original size:9 final size:9
Alignment explanation
Indices: 1496997--1497040 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
1496987 AGTATTTTAA
1496997 TTATAATTT
1 TTATAATTT
1497006 TTAATAATTT
1 TT-ATAATTT
1497016 TTGAT-ATTT
1 TT-ATAATTT
1497025 TTATAATTT
1 TTATAATTT
1497034 TT-TAATT
1 TTATAATT
1497041 AACAAATTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
8 7 0.22
9 14 0.44
10 11 0.34
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (9 bp):
TTATAATTT
Found at i:1502031 original size:21 final size:22
Alignment explanation
Indices: 1501985--1502027 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
1501975 TGTAAAAGTG
*
1501985 ATTTCTCTATCAATAACCTTTC
1 ATTTCTCTATCAATAAACTTTC
1502007 ATTT-TCTATC-ATAAACTTTC
1 ATTTCTCTATCAATAAACTTTC
1502027 A
1 A
1502028 ATTTACAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 6 0.30
22 4 0.20
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTCTCTATCAATAAACTTTC
Found at i:1506899 original size:24 final size:24
Alignment explanation
Indices: 1506872--1506921 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1506862 AAACTATGAG
1506872 TAAG-TTTAAAATTATAATGGTAAT
1 TAAGTTTTAAAA-TATAATGGTAAT
1506896 TAAGTTTTAAAATATAATGGTAAT
1 TAAGTTTTAAAATATAATGGTAAT
1506920 TA
1 TA
1506922 TGTAATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (24 bp):
TAAGTTTTAAAATATAATGGTAAT
Found at i:1507398 original size:21 final size:21
Alignment explanation
Indices: 1507365--1507423 Score: 50
Period size: 21 Copynumber: 2.8 Consensus size: 21
1507355 ATTTTAAGAA
**
1507365 TTGTTTTGGTATTATTTTTAT
1 TTGTTTTAATATTATTTTTAT
*
1507386 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATA-TTATTTTTAT
*
1507408 AT-TTTTAA-ATATATTT
1 TTGTTTTAATAT-TATTT
1507424 GATTTATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.03
20 5 0.16
21 15 0.48
22 10 0.32
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (21 bp):
TTGTTTTAATATTATTTTTAT
Found at i:1507421 original size:24 final size:26
Alignment explanation
Indices: 1507394--1507443 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1507384 ATTTGTTTTA
1507394 ATATTTG-TTT-TTATATTTTTAAAT
1 ATATTTGATTTATTATATTTTTAAAT
1507418 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTGATTTATTATATTTTTAAAT
1507444 TTTTTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 7 0.29
25 3 0.12
26 14 0.58
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (26 bp):
ATATTTGATTTATTATATTTTTAAAT
Found at i:1522318 original size:20 final size:20
Alignment explanation
Indices: 1522262--1522320 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
1522252 TACCCCACTC
*
1522262 TTAA-TTTTAATCCAATTAA
1 TTAAGTTTTAATACAATTAA
* * *
1522281 -AAAGTTTTCATTATAATTAA
1 TTAAGTTTT-AATACAATTAA
1522301 TTAAGTTTTAATACAATTAA
1 TTAAGTTTTAATACAATTAA
1522321 CACCTGACAA
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
18 2 0.07
19 4 0.13
20 17 0.57
21 7 0.23
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (20 bp):
TTAAGTTTTAATACAATTAA
Found at i:1525124 original size:17 final size:17
Alignment explanation
Indices: 1525102--1525136 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1525092 GCCCAATTTA
*
1525102 ACTAATGTCTAATGAAT
1 ACTAATGTCTAAGGAAT
*
1525119 ACTAATGTTTAAGGAAT
1 ACTAATGTCTAAGGAAT
1525136 A
1 A
1525137 AACAACACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (17 bp):
ACTAATGTCTAAGGAAT
Found at i:1526384 original size:19 final size:18
Alignment explanation
Indices: 1526328--1526385 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
1526318 TCACATCAAC
*
1526328 AAATAATTTTAAAATTAA
1 AAATAAATTTAAAATTAA
* * *
1526346 AAA-ATATTCAAAAAATAA
1 AAATAAATT-TAAAATTAA
1526364 AAATAAATTTAAAATTCAA
1 AAATAAATTTAAAATT-AA
1526383 AAA
1 AAA
1526386 AATAGCATGA
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
17 3 0.10
18 18 0.60
19 9 0.30
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAAATTTAAAATTAA
Found at i:1528636 original size:80 final size:80
Alignment explanation
Indices: 1528532--1528755 Score: 278
Period size: 79 Copynumber: 2.8 Consensus size: 80
1528522 GCTCCTCGTT
* *
1528532 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
1528597 ATTTAGTAACTCGCA
66 AATTAGTAACTCGCA
* * *
1528612 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCG
*
1528675 GAATTAGTATCTCGCA
65 GAATTAGTAACTCGCA
* * * * *
1528691 CAAATGCCTTC-GGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCC
1528753 GGA
64 GGA
1528756 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
78 13 0.10
79 55 0.44
80 54 0.44
81 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
AATTAGTAACTCGCA
Found at i:1528693 original size:39 final size:40
Alignment explanation
Indices: 1528532--1528755 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
1528522 GCTCCTCGTT
* * *
1528532 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1528572 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1528612 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
1528652 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * *
1528691 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGAT-TTAGTAAC-TCGCA
*
1528732 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
1528756 CAGCATTCAA
Statistics
Matches: 164, Mismatches: 14, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
38 2 0.01
39 48 0.29
40 105 0.64
41 9 0.05
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:1530428 original size:14 final size:14
Alignment explanation
Indices: 1530406--1530435 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1530396 TGAAAAATGG
*
1530406 ATTAGAAAATATTT
1 ATTAAAAAATATTT
1530420 ATTAAAAAATATTT
1 ATTAAAAAATATTT
1530434 AT
1 AT
1530436 GAAATTAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (14 bp):
ATTAAAAAATATTT
Found at i:1531586 original size:15 final size:14
Alignment explanation
Indices: 1531566--1531607 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
1531556 CGATGAATTT
1531566 ATTGAATTTATATTG
1 ATTGAA-TTATATTG
*
1531581 ATTGAAATTATTTTG
1 ATTG-AATTATATTG
1531596 ATTGAATTATAT
1 ATTGAATTATAT
1531608 AATATATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.29
15 15 0.62
16 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (14 bp):
ATTGAATTATATTG
Found at i:1532050 original size:21 final size:21
Alignment explanation
Indices: 1532007--1532066 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
1531997 TGTATTTCAA
1532007 GCACCTCGTGTGTCGTATCAG
1 GCACCTCGTGTGTCGTATCAG
* *
1532028 GCACCTCGTGTGTCGTTTTAG
1 GCACCTCGTGTGTCGTATCAG
* **
1532049 GCACTTTATGTGTCGTAT
1 GCACCTCGTGTGTCGTAT
1532067 ACTGATCAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.13, C:0.23, G:0.27, T:0.37
Consensus pattern (21 bp):
GCACCTCGTGTGTCGTATCAG
Found at i:1535401 original size:24 final size:24
Alignment explanation
Indices: 1535374--1535421 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1535364 TATACCCACT
1535374 TGTCAAATCTAAAAATTATAATTA
1 TGTCAAATCTAAAAATTATAATTA
1535398 TGTCAAATCTAAAAATTATAATTA
1 TGTCAAATCTAAAAATTATAATTA
1535422 AAATGTGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
TGTCAAATCTAAAAATTATAATTA
Found at i:1535632 original size:21 final size:21
Alignment explanation
Indices: 1535595--1535634 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1535585 AATGGGACCG
*
1535595 CTGATGTGGCAAGTTAACTAA
1 CTGATGTGCCAAGTTAACTAA
1535616 CTGATGTGACCAA-TTAACT
1 CTGATGTG-CCAAGTTAACT
1535635 TACCACGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (21 bp):
CTGATGTGCCAAGTTAACTAA
Found at i:1537062 original size:30 final size:30
Alignment explanation
Indices: 1537026--1537088 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
1537016 ACTTATTTTA
1537026 TTGTTAATTTTATTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
* *
1537056 TTGTTAATTTTGTTATTATTTTACAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
1537086 TTG
1 TTG
1537089 CTTGTTATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:1537237 original size:12 final size:12
Alignment explanation
Indices: 1537207--1537239 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1537197 TATATTTTTT
1537207 AAAATT-ATATA
1 AAAATTAATATA
1537218 AAAA-TAATATA
1 AAAATTAATATA
1537229 AAAATTAATAT
1 AAAATTAATAT
1537240 GGGCAGGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:1538844 original size:3 final size:3
Alignment explanation
Indices: 1538836--1538866 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1538826 GACAGTGAAC
*
1538836 GGT GGT GGT GAT GGT GGT GGT GGT GGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT G
1538867 AGTAGCGGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.03, C:0.00, G:0.65, T:0.32
Consensus pattern (3 bp):
GGT
Found at i:1541092 original size:23 final size:23
Alignment explanation
Indices: 1541057--1541102 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1541047 TAGTTGATCC
1541057 TGTTAAAAATTATTA-ATTTAATT
1 TGTTAAAAATTATTATA-TTAATT
* *
1541080 TGTTGAAATTTATTATATTAATT
1 TGTTAAAAATTATTATATTAATT
1541103 CTTTTAACCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (23 bp):
TGTTAAAAATTATTATATTAATT
Found at i:1541744 original size:18 final size:18
Alignment explanation
Indices: 1541721--1541757 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1541711 CTACTTTCAT
1541721 TGTTCTTCACTACTGAAA
1 TGTTCTTCACTACTGAAA
1541739 TGTTCTTCACTACTGAAA
1 TGTTCTTCACTACTGAAA
1541757 T
1 T
1541758 TTTAAGTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (18 bp):
TGTTCTTCACTACTGAAA
Found at i:1541878 original size:32 final size:32
Alignment explanation
Indices: 1541837--1541900 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1541827 GGATCATGAG
1541837 TTGATTTCACAAGGGGTTCAAAAGTTCTTGAA
1 TTGATTTCACAAGGGGTTCAAAAGTTCTTGAA
1541869 TTGATTTCACAAGGGGTTCAAAAGTTCTTGAA
1 TTGATTTCACAAGGGGTTCAAAAGTTCTTGAA
1541901 CAATCCCCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.34
Consensus pattern (32 bp):
TTGATTTCACAAGGGGTTCAAAAGTTCTTGAA
Done.