Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 58 of 325
Found at i:21220018 original size:18 final size:18
Alignment explanation
Indices: 21219995--21220032 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
21219985 CTAATAACAT
*
21219995 TAAAATATATATAATATA
1 TAAAATACATATAATATA
21220013 TAAAATACATATAATATA
1 TAAAATACATATAATATA
21220031 TA
1 TA
21220033 TATTAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATACATATAATATA
Found at i:21220127 original size:19 final size:19
Alignment explanation
Indices: 21220103--21220139 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
21220093 TATAAATAGT
*
21220103 AATGATGTTAGAAATATAC
1 AATGATATTAGAAATATAC
21220122 AATGATATTAGAAATATA
1 AATGATATTAGAAATATA
21220140 TATAAAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.32
Consensus pattern (19 bp):
AATGATATTAGAAATATAC
Found at i:21220255 original size:29 final size:29
Alignment explanation
Indices: 21220223--21220296 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 29
21220213 TTGAAAACAT
*
21220223 ATATACATAATATATACAAAAATATATAG
1 ATATACATAATATATACAAAAATATATAC
** *
21220252 ATATACATAATATAATATTAAAATATTTAC
1 ATATACATAATAT-ATACAAAAATATATAC
21220282 ATAATACATAA-ATAT
1 AT-ATACATAATATAT
21220297 TAGGGATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 15 0.38
30 16 0.41
31 8 0.21
ACGTcount: A:0.57, C:0.07, G:0.01, T:0.35
Consensus pattern (29 bp):
ATATACATAATATATACAAAAATATATAC
Found at i:21220360 original size:23 final size:22
Alignment explanation
Indices: 21220334--21220376 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
21220324 CTACATAAGT
21220334 ATATACATAAATATATTAAAAAC
1 ATATACATAAATATA-TAAAAAC
*
21220357 ATATACATATATATATAAAA
1 ATATACATAAATATATAAAA
21220377 TAAAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
ATATACATAAATATATAAAAAC
Found at i:21220390 original size:28 final size:31
Alignment explanation
Indices: 21220333--21220401 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 31
21220323 GCTACATAAG
*
21220333 TATATACATAAATATATTAAAAACATATACA-
1 TATATATATAAATATA-TAAAAACATATACAC
*
21220364 TATATATATAAA-ATA-AAAAATATATACAC
1 TATATATATAAATATATAAAAACATATACAC
21220393 TA-ATATATA
1 TATATATATA
21220402 GTAATCATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 19 0.54
29 2 0.06
30 3 0.09
31 11 0.31
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (31 bp):
TATATATATAAATATATAAAAACATATACAC
Found at i:21230165 original size:7 final size:7
Alignment explanation
Indices: 21230153--21230185 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
21230143 GATGGATGTA
21230153 ATGGTGG
1 ATGGTGG
21230160 ATGGTGG
1 ATGGTGG
21230167 ATGGTGG
1 ATGGTGG
21230174 ATGGTGG
1 ATGGTGG
21230181 ATGGT
1 ATGGT
21230186 CATTATAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.00, G:0.55, T:0.30
Consensus pattern (7 bp):
ATGGTGG
Found at i:21250275 original size:13 final size:13
Alignment explanation
Indices: 21250257--21250317 Score: 88
Period size: 13 Copynumber: 4.7 Consensus size: 13
21250247 TTGATAATGT
21250257 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
21250270 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
*
21250283 -TGTGAAAAAGTGC
1 TTTTG-AAAAGTGC
*
21250296 TTTTGAGAAGTGC
1 TTTTGAAAAGTGC
21250309 TTTTGAAAA
1 TTTTGAAAA
21250318 ATTTGGTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
12 3 0.07
13 36 0.86
14 3 0.07
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.36
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:21252537 original size:22 final size:20
Alignment explanation
Indices: 21252508--21252553 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
21252498 AAACATTAAA
21252508 ATATAAAAAAGTAAATAA-AT
1 ATATAAAAAAGT-AATAATAT
21252528 ATATAAAAAAGTAATAATAT
1 ATATAAAAAAGTAATAATAT
21252548 ATATAA
1 ATATAA
21252554 TATGAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (20 bp):
ATATAAAAAAGTAATAATAT
Found at i:21255660 original size:20 final size:22
Alignment explanation
Indices: 21255635--21255679 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
21255625 TCATTAGAAA
21255635 ATAT-AAAAAT-AGAAATAAAT
1 ATATAAAAAATCAGAAATAAAT
*
21255655 ATATAAAAAATCAGAAATATAT
1 ATATAAAAAATCAGAAATAAAT
21255677 ATA
1 ATA
21255680 ATCTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 6 0.27
22 12 0.55
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (22 bp):
ATATAAAAAATCAGAAATAAAT
Found at i:21255680 original size:20 final size:20
Alignment explanation
Indices: 21255635--21255680 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
21255625 TCATTAGAAA
21255635 ATAT-AAAAATAGAAATAAAT
1 ATATAAAAAATAGAAAT-AAT
21255655 ATATAAAAAATCAGAAAT-AT
1 ATATAAAAAAT-AGAAATAAT
21255675 ATATAA
1 ATATAA
21255681 TCTAAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.50
21 6 0.25
22 6 0.25
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (20 bp):
ATATAAAAAATAGAAATAAT
Found at i:21255881 original size:17 final size:18
Alignment explanation
Indices: 21255859--21255902 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
21255849 TTTCAAGTTT
* *
21255859 TTTTTATACCTTTTTC-A
1 TTTTTATACATTTATCAA
21255876 TTTTTATAACATTTATCAA
1 TTTTTAT-ACATTTATCAA
21255895 TTTTTATA
1 TTTTTATA
21255903 TATTATTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 7 0.30
18 8 0.35
19 8 0.35
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTATACATTTATCAA
Found at i:21255934 original size:8 final size:8
Alignment explanation
Indices: 21255913--21255953 Score: 59
Period size: 8 Copynumber: 5.2 Consensus size: 8
21255903 TATTATTTTG
21255913 AATTTTA-
1 AATTTTAT
21255920 AATTTTTAT
1 AA-TTTTAT
21255929 AATTTTAT
1 AATTTTAT
21255937 -ATTTTAT
1 AATTTTAT
21255944 AATTTTAT
1 AATTTTAT
21255952 AA
1 AA
21255954 AAAATTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 9 0.29
8 20 0.65
9 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
AATTTTAT
Found at i:21255941 original size:15 final size:16
Alignment explanation
Indices: 21255913--21255952 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
21255903 TATTATTTTG
*
21255913 AATTTTAAATTTTTAT
1 AATTTTATATTTTTAT
21255929 AATTTTATA-TTTTAT
1 AATTTTATATTTTTAT
21255944 AATTTTATA
1 AATTTTATA
21255953 AAAAATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTTTATATTTTTAT
Found at i:21256375 original size:15 final size:15
Alignment explanation
Indices: 21256355--21256385 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21256345 TTTTTTTAGA
21256355 ATTTTAGAATTATAT
1 ATTTTAGAATTATAT
*
21256370 ATTTTAGAATTTTAT
1 ATTTTAGAATTATAT
21256385 A
1 A
21256386 AAAAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
ATTTTAGAATTATAT
Found at i:21257561 original size:39 final size:39
Alignment explanation
Indices: 21257475--21257587 Score: 163
Period size: 39 Copynumber: 2.8 Consensus size: 39
21257465 ACAATATCGG
* *
21257475 TGGCATGCTTTACATGCAATCAACATGTACGGTAATATTCAA
1 TGGCATGC-TTACATGCAATC-A-ATATACGATAATATTCAA
* *
21257517 TGGCATGCTTACATGCAATCAATATACGATAATATTTAT
1 TGGCATGCTTACATGCAATCAATATACGATAATATTCAA
21257556 TGGCATGCTTACATGCAATCAATATACGATAA
1 TGGCATGCTTACATGCAATCAATATACGATAA
21257588 CAATCAGCAC
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
39 46 0.69
40 1 0.01
41 12 0.18
42 8 0.12
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (39 bp):
TGGCATGCTTACATGCAATCAATATACGATAATATTCAA
Found at i:21258591 original size:20 final size:20
Alignment explanation
Indices: 21258566--21258605 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
21258556 AGGGATTCAA
21258566 ACTCAAGTTTTAAGGACAAT
1 ACTCAAGTTTTAAGGACAAT
21258586 ACTCAAGTTTTAAGGACAAT
1 ACTCAAGTTTTAAGGACAAT
21258606 TTCACTAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (20 bp):
ACTCAAGTTTTAAGGACAAT
Found at i:21260817 original size:26 final size:25
Alignment explanation
Indices: 21260788--21260869 Score: 69
Period size: 26 Copynumber: 3.1 Consensus size: 25
21260778 CAAACCCTAA
21260788 TTTCTCCTTTTTCTTTTCTTTTCTTC
1 TTTCT-CTTTTTCTTTTCTTTTCTTC
*
21260814 TTTCT-TTCTTTCTATTTCGTTTCTTC
1 TTTCTCTT-TTTCT-TTTCTTTTCTTC
* *
21260840 TTTGATTCTTTTTCTTGT-TTTTCTTTC
1 TTT--CTCTTTTTCTTTTCTTTTC-TTC
21260867 TTT
1 TTT
21260870 TTATTTATTC
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
24 2 0.04
25 5 0.11
26 23 0.50
27 8 0.17
28 6 0.13
29 2 0.04
ACGTcount: A:0.02, C:0.21, G:0.04, T:0.73
Consensus pattern (25 bp):
TTTCTCTTTTTCTTTTCTTTTCTTC
Found at i:21260855 original size:40 final size:39
Alignment explanation
Indices: 21260811--21260901 Score: 94
Period size: 40 Copynumber: 2.3 Consensus size: 39
21260801 TTTTCTTTTC
* * *
21260811 TTCTTTCTTTCTTTCTATTTCGTTTCTTCTTTGA-TTCTTT
1 TTCTTTCTTTCTTTCT-TTTCATTTATTCTTT-ATTTCATT
* *
21260851 TTCTTGTTTTTCTTTCTTTTTATTTATTCTTTATTTCATT
1 TTCTT-TCTTTCTTTCTTTTCATTTATTCTTTATTTCATT
*
21260891 TTATTTCTTTC
1 TTCTTTCTTTC
21260902 ATTTACTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
39 6 0.14
40 26 0.62
41 10 0.24
ACGTcount: A:0.08, C:0.16, G:0.03, T:0.73
Consensus pattern (39 bp):
TTCTTTCTTTCTTTCTTTTCATTTATTCTTTATTTCATT
Found at i:21264503 original size:27 final size:27
Alignment explanation
Indices: 21264446--21264497 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
21264436 AATATTTTTC
*
21264446 ATAT-TATAATTATATATTTATAACAA
1 ATATATATAATTATATAATTATAACAA
*
21264472 ATATATATAATTA-ATAATTATTACAA
1 ATATATATAATTATATAATTATAACAA
21264498 CCTATAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (27 bp):
ATATATATAATTATATAATTATAACAA
Found at i:21264686 original size:26 final size:25
Alignment explanation
Indices: 21264648--21264696 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
21264638 TTTAATTTCA
*
21264648 ATGATTTTGGAATTTAGGGTTTTTTT
1 ATGATTTTAGAATTTA-GGTTTTTTT
21264674 ATGATTTTAGAATTTAGGTTTTT
1 ATGATTTTAGAATTTAGGTTTTT
21264697 ACTTTTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.22, C:0.00, G:0.20, T:0.57
Consensus pattern (25 bp):
ATGATTTTAGAATTTAGGTTTTTTT
Found at i:21265245 original size:20 final size:19
Alignment explanation
Indices: 21265207--21265249 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
21265197 CACAATGTAA
*
21265207 TAATATATTTTAAAACTAT
1 TAATATATTATAAAACTAT
*
21265226 TAATATATGTATATAACTAT
1 TAATATAT-TATAAAACTAT
21265246 TAAT
1 TAAT
21265250 TAGTCCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (19 bp):
TAATATATTATAAAACTAT
Found at i:21269308 original size:8 final size:8
Alignment explanation
Indices: 21269291--21269329 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
21269281 AAAGTTGAAA
21269291 TATAATTT
1 TATAATTT
*
21269299 TATTATTT
1 TATAATTT
*
21269307 TAAAATTT
1 TATAATTT
21269315 TAT-ATTT
1 TATAATTT
21269322 TATAATTT
1 TATAATTT
21269330 AAAAAAAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATAATTT
Found at i:21269322 original size:15 final size:16
Alignment explanation
Indices: 21269294--21269329 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
21269284 GTTGAAATAT
21269294 AATTTTATTATTTTAA
1 AATTTTATTATTTTAA
*
21269310 AATTTTA-TATTTTAT
1 AATTTTATTATTTTAA
21269325 AATTT
1 AATTT
21269330 AAAAAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
AATTTTATTATTTTAA
Found at i:21270044 original size:29 final size:29
Alignment explanation
Indices: 21270012--21270067 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
21270002 TCTTTATAAT
* *
21270012 TTTTAAATAATTAAATTAAAATTTTATCA
1 TTTTAAAGAATTAAAATAAAATTTTATCA
* * *
21270041 TTTTGAAGGATTAAAATACAATTTTAT
1 TTTTAAAGAATTAAAATAAAATTTTAT
21270068 TTTTTATTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (29 bp):
TTTTAAAGAATTAAAATAAAATTTTATCA
Found at i:21273365 original size:35 final size:36
Alignment explanation
Indices: 21273236--21273363 Score: 118
Period size: 35 Copynumber: 3.5 Consensus size: 36
21273226 GCAAAGTGCG
* * *
21273236 AAATGTTGGTATGGTATTAT-CCATACTGAATTGTG
1 AAATGTAGGTATGGTATTATCCCATACTGAGTTGTA
*
21273271 AAATGTAGGTATGGTATTATCAAATCCATACTGAGTT-AA
1 AAATGTAGGTATGGTATTATC----CCATACTGAGTTGTA
** * *
21273310 GAAATGTAGGTATGACATT-TCCCAAACCGAGTTGTA
1 -AAATGTAGGTATGGTATTATCCCATACTGAGTTGTA
21273346 AAATGTAGGTATGGTATT
1 AAATGTAGGTATGGTATT
21273364 TCAATGAGGA
Statistics
Matches: 75, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
35 45 0.60
36 1 0.01
39 2 0.03
40 27 0.36
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (36 bp):
AAATGTAGGTATGGTATTATCCCATACTGAGTTGTA
Found at i:21274702 original size:13 final size:13
Alignment explanation
Indices: 21274686--21274719 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
21274676 TTTAATTAAA
21274686 TTAGTTAATTAGT
1 TTAGTTAATTAGT
*
21274699 TTAGATAATTAGT
1 TTAGTTAATTAGT
*
21274712 TTAATTAA
1 TTAGTTAA
21274720 AACAGACCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:21275119 original size:22 final size:22
Alignment explanation
Indices: 21275091--21275135 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
21275081 CCATTAGGAC
21275091 CATTACTTTTTGACGAAGAAAT
1 CATTACTTTTTGACGAAGAAAT
21275113 CATTACTTTTTGACGAAGAAAT
1 CATTACTTTTTGACGAAGAAAT
21275135 C
1 C
21275136 GATCGCACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (22 bp):
CATTACTTTTTGACGAAGAAAT
Found at i:21276235 original size:28 final size:28
Alignment explanation
Indices: 21276203--21276285 Score: 114
Period size: 28 Copynumber: 2.9 Consensus size: 28
21276193 ACCAATTTTG
21276203 GCCCACTCAACAATACCCAAAACCCCTA
1 GCCCACTCAACAATACCCAAAACCCCTA
* *
21276231 GCCCACTCAACAATATCCAAAACCCTTA
1 GCCCACTCAACAATACCCAAAACCCCTA
21276259 GCCCACTCAA-AATTAAACCCAAAACCC
1 GCCCACTCAACAA-T--ACCCAAAACCC
21276286 AATTATATCA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
27 2 0.04
28 37 0.76
30 10 0.20
ACGTcount: A:0.41, C:0.42, G:0.04, T:0.13
Consensus pattern (28 bp):
GCCCACTCAACAATACCCAAAACCCCTA
Found at i:21277368 original size:3 final size:3
Alignment explanation
Indices: 21277360--21277419 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
21277350 CTTTATTAAA
* * * *
21277360 TAT TAT TAT TAT TAT T-T CTAA TAT TAT TAA TAT TAT CAA TAT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
21277405 TAT TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT
21277420 ATATATTAGT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
2 1 0.02
3 44 0.98
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:21277382 original size:21 final size:20
Alignment explanation
Indices: 21277358--21277415 Score: 84
Period size: 18 Copynumber: 3.0 Consensus size: 20
21277348 TTCTTTATTA
21277358 AATATTATTATTATTATTTC
1 AATATTATTATTATTATTTC
*
21277378 TAATATTATTAATATTA--TC
1 -AATATTATTATTATTATTTC
21277397 AATATTATTATTATTATTT
1 AATATTATTATTATTATTT
21277416 TTATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 15 0.45
19 2 0.06
20 1 0.03
21 15 0.45
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
AATATTATTATTATTATTTC
Found at i:21277571 original size:20 final size:21
Alignment explanation
Indices: 21277517--21277625 Score: 67
Period size: 21 Copynumber: 5.4 Consensus size: 21
21277507 TTATTGTTAG
21277517 TATTATAATAT-TATAT-TTAT
1 TATTAT-ATATGTATATATTAT
21277537 TATTA-ATATTGGTATATATT-T
1 TATTATATA-T-GTATATATTAT
21277558 TATTATATATGTATATATATACT
1 TATTATATATGTATATAT-TA-T
* **
21277581 TTTTATATA-GTAT-TATCGT
1 TATTATATATGTATATATTAT
21277600 T-TCTAT-TAT-TATAT-TTAT
1 TAT-TATATATGTATATATTAT
21277618 TATTATAT
1 TATTATAT
21277626 TTATTATTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 27
0.69 0.05 0.26
Matches are distributed among these distances:
18 15 0.21
19 9 0.13
20 13 0.18
21 16 0.23
22 9 0.13
23 9 0.13
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.59
Consensus pattern (21 bp):
TATTATATATGTATATATTAT
Found at i:21277629 original size:21 final size:20
Alignment explanation
Indices: 21277603--21277656 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
21277593 TTATCGTTTC
*
21277603 TATTATTATATTTATTATTA-
1 TATTATTAT-TTTATAATTAT
21277623 TATTTATTATTTTCATAATTAT
1 TA-TTATTATTTT-ATAATTAT
21277645 TATTATTATTTT
1 TATTATTATTTT
21277657 TATCATTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 5 0.17
21 23 0.77
22 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTATTATTTTATAATTAT
Found at i:21277659 original size:12 final size:12
Alignment explanation
Indices: 21277525--21277633 Score: 65
Period size: 12 Copynumber: 9.3 Consensus size: 12
21277515 AGTATTATAA
21277525 TATTATATTTAT
1 TATTATATTTAT
21277537 TATTAATATTGGTA-
1 TATT-ATATT--TAT
21277551 TA-TAT-TTTAT
1 TATTATATTTAT
*
21277561 TA-TATATGTA-
1 TATTATATTTAT
21277571 TATATATACTTT-T
1 TAT-TATA-TTTAT
*
21277584 TA-TATA-GTAT
1 TATTATATTTAT
**
21277594 TATCGT-TTCTAT
1 TATTATATT-TAT
21277606 TATTATATTTAT
1 TATTATATTTAT
21277618 TATTATATTTAT
1 TATTATATTTAT
21277630 TATT
1 TATT
21277634 TTCATAATTA
Statistics
Matches: 75, Mismatches: 8, Indels: 28
0.68 0.07 0.25
Matches are distributed among these distances:
9 3 0.04
10 10 0.13
11 10 0.13
12 36 0.48
13 12 0.16
14 2 0.03
15 2 0.03
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (12 bp):
TATTATATTTAT
Found at i:21277777 original size:19 final size:18
Alignment explanation
Indices: 21277740--21277778 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
21277730 ATTATGTATA
21277740 TTATTTTTACTCAATTAT
1 TTATTTTTACTCAATTAT
* *
21277758 TTATTTATTTCTCTATTAT
1 TTATTT-TTACTCAATTAT
21277777 TT
1 TT
21277779 TAAATACTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTTTTACTCAATTAT
Found at i:21277898 original size:19 final size:19
Alignment explanation
Indices: 21277821--21277898 Score: 50
Period size: 24 Copynumber: 3.7 Consensus size: 19
21277811 TAAATAGTAA
*
21277821 ATTTTTATATATTATGTATAT
1 ATTTTAATATATTA--TATAT
*
21277842 ATTTTTATATCCTATTATTCATAT
1 A-TTTTA-AT-ATATTA-T-ATAT
*
21277866 ATTTTATTATATTATATAT
1 ATTTTAATATATTATATAT
21277885 ATTTTTAATA-ATTA
1 A-TTTTAATATATTA
21277899 CATTATGTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
19 9 0.20
20 8 0.17
21 6 0.13
22 5 0.11
23 8 0.17
24 10 0.22
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (19 bp):
ATTTTAATATATTATATAT
Found at i:21277903 original size:24 final size:25
Alignment explanation
Indices: 21277871--21277918 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
21277861 CATATATTTT
*
21277871 ATTATATTA-TATATATTTTTAATA
1 ATTACATTAGTATATATTTTTAATA
*
21277895 ATTACATTATGTATGTATTTTTAA
1 ATTACATTA-GTATATATTTTTAA
21277919 CTCTATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
26 12 0.60
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (25 bp):
ATTACATTAGTATATATTTTTAATA
Found at i:21278177 original size:23 final size:22
Alignment explanation
Indices: 21278151--21278198 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
21278141 TTATCTCATG
* *
21278151 TATATATTTTTTTATAACTATAT
1 TATATATATTTTAATAACT-TAT
*
21278174 TATATATATTTTAATACCTTAT
1 TATATATATTTTAATAACTTAT
21278196 TAT
1 TAT
21278199 GTACATGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (22 bp):
TATATATATTTTAATAACTTAT
Found at i:21283050 original size:20 final size:21
Alignment explanation
Indices: 21283025--21283076 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
21283015 AATCCTCCTA
21283025 TTTTTTATTT-ATTCTT-ATTT
1 TTTTTTATTTGATT-TTGATTT
21283045 TTTTTT-TTTGATTTTGATTT
1 TTTTTTATTTGATTTTGATTT
21283065 TTATTTTCATTT
1 TT-TTTT-ATTT
21283077 CAATTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 5 0.19
20 15 0.56
21 4 0.15
23 3 0.11
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.79
Consensus pattern (21 bp):
TTTTTTATTTGATTTTGATTT
Found at i:21285980 original size:13 final size:13
Alignment explanation
Indices: 21285964--21285996 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
21285954 TTTAATTAAA
*
21285964 TTAGTTAATTAGT
1 TTAGATAATTAGT
21285977 TTAGATAATTAGT
1 TTAGATAATTAGT
21285990 TTA-ATAA
1 TTAGATAA
21285997 ACAAATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:21292354 original size:18 final size:19
Alignment explanation
Indices: 21292307--21292354 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
21292297 CAATTAAATA
21292307 AAAAGGATTAAA-TTGTAAT
1 AAAAGGATTAAATTTGT-AT
*
21292326 AAAA--ATAAAATTTGT-T
1 AAAAGGATTAAATTTGTAT
21292342 AAAAGGATTAAAT
1 AAAAGGATTAAAT
21292355 AGCTCAAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
16 5 0.21
17 5 0.21
18 10 0.42
19 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.31
Consensus pattern (19 bp):
AAAAGGATTAAATTTGTAT
Found at i:21293397 original size:35 final size:35
Alignment explanation
Indices: 21293370--21293536 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
21293360 CATGGAAAAG
*
21293370 TGTGAAATGTAGGTATGGTATTATCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTATCCATACAGAGT
* *
21293405 TGTGAAATGTAGGTATGGTATTATCTATACTGAGT
1 TGTGAAATGTAGGTATGGTATTATCCATACAGAGT
*
21293440 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTA-T-T---ATCCATACAGAGT
** * *
21293480 TAAGAAATGTAGGTATGGCATT-TCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTAT-CCATACAGAGT
*
21293515 TGTAAAATGTAGGTATGGTATT
1 TGTGAAATGTAGGTATGGTATT
21293537 TCAATGAGGA
Statistics
Matches: 115, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
34 1 0.01
35 81 0.70
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 29 0.25
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.35
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATTATCCATACAGAGT
Found at i:21293489 original size:75 final size:74
Alignment explanation
Indices: 21293370--21293540 Score: 226
Period size: 75 Copynumber: 2.4 Consensus size: 74
21293360 CATGGAAAAG
** *
21293370 TGTGAAATGTAGGTATGGTA-TT---ATCCATACCGAGTTGTGAAATGTAGGTATGGTATTAT-C
1 TGTGAAATGTAGGTATGGTATTTCAAATCCATACCGAGTTAAGAAATGTAGGTATGGCATT-TCC
* *
21293430 TATACTGAGT
65 CATACCGAGT
*
21293440 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATT-TCAAATCCATACCGAGTTAAGAAATGTAGGTATGGCATTTCC
21293505 CATACCGAGT
65 CATACCGAGT
*
21293515 TGTAAAATGTAGGTATGGTATTTCAA
1 TGTGAAATGTAGGTATGGTATTTCAA
21293541 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 20 0.23
71 1 0.01
72 1 0.01
74 5 0.06
75 61 0.69
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (74 bp):
TGTGAAATGTAGGTATGGTATTTCAAATCCATACCGAGTTAAGAAATGTAGGTATGGCATTTCCC
ATACCGAGT
Found at i:21300898 original size:24 final size:25
Alignment explanation
Indices: 21300871--21300919 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
21300861 TTTTTTTTAT
*
21300871 TAAATAAAAAAC-TTTAAAATATAA
1 TAAATAAAAAACATTTAAAACATAA
* *
21300895 TAAATCAAATACATTTAAAACATAA
1 TAAATAAAAAACATTTAAAACATAA
21300920 AAACAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAATAAAAAACATTTAAAACATAA
Found at i:21300912 original size:25 final size:23
Alignment explanation
Indices: 21300883--21300947 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 23
21300873 AATAAAAAAC
*
21300883 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAA-CAAATACA
21300908 TTTAAAACATAAAAACAAAT--A
1 TTTAAAACATAAAAACAAATACA
21300929 -TTAAAACA-AAAAACAAATA
1 TTTAAAACATAAAAACAAATA
21300948 AAAAATAAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
19 10 0.26
20 8 0.21
21 1 0.03
23 5 0.13
24 3 0.08
25 11 0.29
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (23 bp):
TTTAAAACATAAAAACAAATACA
Found at i:21300942 original size:19 final size:20
Alignment explanation
Indices: 21300909--21300947 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
21300899 TCAAATACAT
21300909 TTAAAACATAAAAACAAATA
1 TTAAAACATAAAAACAAATA
21300929 TTAAAACA-AAAAACAAATA
1 TTAAAACATAAAAACAAATA
21300948 AAAAATAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (20 bp):
TTAAAACATAAAAACAAATA
Found at i:21302795 original size:21 final size:21
Alignment explanation
Indices: 21302766--21302824 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
21302756 ACATAAGTTA
*
21302766 CTGAGACGACACACGAGGTGC
1 CTGATACGACACACGAGGTGC
*
21302787 CTGATACGACACACGATGTGC
1 CTGATACGACACACGAGGTGC
21302808 CTGATACGACACACGAG
1 CTGATACGACACACGAG
21302825 ATGCTTGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.31, C:0.29, G:0.27, T:0.14
Consensus pattern (21 bp):
CTGATACGACACACGAGGTGC
Found at i:21302853 original size:44 final size:41
Alignment explanation
Indices: 21302749--21302866 Score: 110
Period size: 42 Copynumber: 2.7 Consensus size: 41
21302739 CCTAATCAGT
** * *
21302749 ATACGACACATAAGTTACTGAGACGACACACGAGGTGCCTG
1 ATACGACACATAAGTGCCTGATACGACACACGAGATGCCTG
* * *
21302790 ATACGACACACGATGTGCCTGATACGACACACGAGATGCTTG
1 ATACGACACA-TAAGTGCCTGATACGACACACGAGATGCCTG
*
21302832 AAATATGACACATAAAGTGCCTGATATACGACACA
1 --ATACGACACAT-AAGTGCCTG--ATACGACACA
21302867 TAAAGTGCCT
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
41 10 0.16
42 24 0.39
44 17 0.28
46 10 0.16
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTGATACGACACACGAGATGCCTG
Found at i:21302858 original size:21 final size:22
Alignment explanation
Indices: 21302834--21302879 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
21302824 GATGCTTGAA
21302834 ATAT-GACACATAAAGTGCCTG
1 ATATAGACACATAAAGTGCCTG
21302855 ATATACGACACATAAAGTGCCTG
1 ATATA-GACACATAAAGTGCCTG
21302878 AT
1 AT
21302880 TGGCAAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.17
23 19 0.83
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (22 bp):
ATATAGACACATAAAGTGCCTG
Found at i:21303020 original size:24 final size:24
Alignment explanation
Indices: 21302972--21303026 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
21302962 TATTCAATTT
21302972 TCATA-TTTCAATTCAATTACTTTC
1 TCATATTTTCAATTCAATTAC-TTC
*
21302996 TCATATTTTCCATTCAAATTA-TTC
1 TCATATTTTCAATTC-AATTACTTC
21303020 TCA-ATTT
1 TCATATTT
21303027 AAATCACAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 4 0.14
24 11 0.39
25 8 0.29
26 5 0.18
ACGTcount: A:0.29, C:0.20, G:0.00, T:0.51
Consensus pattern (24 bp):
TCATATTTTCAATTCAATTACTTC
Found at i:21304058 original size:13 final size:13
Alignment explanation
Indices: 21304040--21304066 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21304030 GCTCGATAGA
21304040 GACACGCCCGTGT
1 GACACGCCCGTGT
21304053 GACACGCCCGTGT
1 GACACGCCCGTGT
21304066 G
1 G
21304067 CGATTACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:21311109 original size:19 final size:18
Alignment explanation
Indices: 21311072--21311124 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
21311062 ATCTGTTAGA
*
21311072 AGAAAATAAATGAATAATT
1 AGAAAATAAAT-AAAAATT
21311091 AGAAAATAAAATAAAAATT
1 AGAAAAT-AAATAAAAATT
*
21311110 -GAAATTGAAATAAAA
1 AGAAAAT-AAATAAAA
21311125 GTAAAATGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 13 0.43
19 13 0.43
20 4 0.13
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.23
Consensus pattern (18 bp):
AGAAAATAAATAAAAATT
Found at i:21319463 original size:43 final size:43
Alignment explanation
Indices: 21319158--21319451 Score: 394
Period size: 43 Copynumber: 6.9 Consensus size: 43
21319148 GCATGAAACT
21319158 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
* *
21319201 CGGTGATGTGTATTCGTGCCTTCGTGCCTAACAGGCTTCGTGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
* * * * *
21319244 CGATGATGTGTATTAGGGCTTTCGTACCTAGCAGGCTTTGTGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
* * * *
21319287 TGATGATGTGTATTTGGGCCTTCGTGCCTAACAGGCTTCGTGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
* * * *
21319330 CAGTGATATGTATTC-GGCCTTCGTGCCTAG-ATGCTTCGTGT
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
* *
21319371 CGGTGATGTGTATTCAGGCTTTCGTGCCTAGCAGGCTTCGTGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
* * *
21319414 CGGTGATGTGTATTCGGGTCTTCGTGCTTAGCAAGCTT
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTT
21319452 AATACCGGTG
Statistics
Matches: 216, Mismatches: 33, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.10
42 28 0.13
43 166 0.77
ACGTcount: A:0.13, C:0.22, G:0.31, T:0.34
Consensus pattern (43 bp):
CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGC
Found at i:21319653 original size:29 final size:28
Alignment explanation
Indices: 21319620--21319776 Score: 111
Period size: 29 Copynumber: 5.5 Consensus size: 28
21319610 ATGATTAGAG
21319620 GCACTATGTGTGCAAATTCCTTTAACCGA
1 GCACTATGTGTGCAAATT-CTTTAACCGA
* ** **
21319649 GCACTATGTGTGCGAGA-TCAGTAATTGA
1 GCACTATGTGTGC-AAATTCTTTAACCGA
* *
21319677 GGCACTGTGTGTGCGAATTCCTTTAACCGA
1 -GCACTATGTGTGCAAATT-CTTTAACCGA
* ** **
21319707 GCACTATGTGTGCGAGA-TCGGTAATTGA
1 GCACTATGTGTGC-AAATTCTTTAACCGA
* * *
21319735 GGCACTGTGTGTGCAAGTTCTTCAACCGA
1 -GCACTATGTGTGCAAATTCTTTAACCGA
21319764 GCACTATGTGTGC
1 GCACTATGTGTGC
21319777 GAGATCGGTC
Statistics
Matches: 93, Mismatches: 28, Indels: 15
0.68 0.21 0.11
Matches are distributed among these distances:
28 26 0.28
29 58 0.62
30 9 0.10
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (28 bp):
GCACTATGTGTGCAAATTCTTTAACCGA
Found at i:21319688 original size:58 final size:58
Alignment explanation
Indices: 21319617--21319782 Score: 280
Period size: 58 Copynumber: 2.9 Consensus size: 58
21319607 CGAATGATTA
*
21319617 GAGGCACTATGTGTGCAAATTCCTTTAACCGAGCACTATGTGTGCGAGATCAGTAATT
1 GAGGCACTGTGTGTGCAAATTCCTTTAACCGAGCACTATGTGTGCGAGATCAGTAATT
* *
21319675 GAGGCACTGTGTGTGCGAATTCCTTTAACCGAGCACTATGTGTGCGAGATCGGTAATT
1 GAGGCACTGTGTGTGCAAATTCCTTTAACCGAGCACTATGTGTGCGAGATCAGTAATT
* *
21319733 GAGGCACTGTGTGTGCAAGTT-CTTCAACCGAGCACTATGTGTGCGAGATC
1 GAGGCACTGTGTGTGCAAATTCCTTTAACCGAGCACTATGTGTGCGAGATC
21319783 GGTCAGTGGG
Statistics
Matches: 102, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
57 28 0.27
58 74 0.73
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (58 bp):
GAGGCACTGTGTGTGCAAATTCCTTTAACCGAGCACTATGTGTGCGAGATCAGTAATT
Found at i:21319795 original size:28 final size:28
Alignment explanation
Indices: 21319649--21319803 Score: 80
Period size: 29 Copynumber: 5.4 Consensus size: 28
21319639 CTTTAACCGA
* * *
21319649 GCACTATGTGTGCGAGATCAGTAATTGAG
1 GCACTATGTGTGCGAGATCGGTCACTG-G
* ** * * *
21319678 GCACTGTGTGTGCGA-ATTCCTTTAACCGA
1 GCACTATGTGTGCGAGA-T-CGGTCACTGG
* *
21319707 GCACTATGTGTGCGAGATCGGTAATTGAG
1 GCACTATGTGTGCGAGATCGGTCACTG-G
* * * * * *
21319736 GCACTGTGTGTGCAAGTTC-TTCAACCGA
1 GCACTATGTGTGCGAGATCGGTC-ACTGG
*
21319764 GCACTATGTGTGCGAGATCGGTCAGTGG
1 GCACTATGTGTGCGAGATCGGTCACTGG
*
21319792 GCACTAAGTGTG
1 GCACTATGTGTG
21319804 TGAAATGAGA
Statistics
Matches: 92, Mismatches: 28, Indels: 13
0.69 0.21 0.10
Matches are distributed among these distances:
28 36 0.39
29 50 0.54
30 6 0.07
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.28
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGGTCACTGG
Found at i:21333440 original size:13 final size:13
Alignment explanation
Indices: 21333419--21333462 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
21333409 AATTTGAGAG
21333419 TTATTAATATTTA
1 TTATTAATATTTA
* * *
21333432 TTTTTAATAGTTG
1 TTATTAATATTTA
21333445 TTATTAATATTTAA
1 TTATTAATATTT-A
21333459 TTAT
1 TTAT
21333463 GTTTAAATAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (13 bp):
TTATTAATATTTA
Found at i:21333468 original size:30 final size:28
Alignment explanation
Indices: 21333418--21333487 Score: 74
Period size: 30 Copynumber: 2.5 Consensus size: 28
21333408 AAATTTGAGA
**
21333418 GTTATTAATATTT-ATTTTT-AATAGTT
1 GTTATTAATATTTAATTTTTAAATAAAT
21333444 GTTATTAATATTTAATTATGTTTAAATAAAT
1 GTTATTAATATTTAA-T-T-TTTAAATAAAT
21333475 -TTATTAATATTTA
1 GTTATTAATATTTA
21333488 TTTAATTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
26 13 0.35
27 1 0.03
28 1 0.03
29 1 0.03
30 16 0.43
31 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (28 bp):
GTTATTAATATTTAATTTTTAAATAAAT
Found at i:21341943 original size:57 final size:57
Alignment explanation
Indices: 21341855--21341988 Score: 268
Period size: 57 Copynumber: 2.4 Consensus size: 57
21341845 ATACAGCAGA
21341855 ATTACCAGTCCAGGCTAAATTTTGTTTGTATAGCATATACTCTAAGGGCTTTGTCGG
1 ATTACCAGTCCAGGCTAAATTTTGTTTGTATAGCATATACTCTAAGGGCTTTGTCGG
21341912 ATTACCAGTCCAGGCTAAATTTTGTTTGTATAGCATATACTCTAAGGGCTTTGTCGG
1 ATTACCAGTCCAGGCTAAATTTTGTTTGTATAGCATATACTCTAAGGGCTTTGTCGG
21341969 ATTACCAGTCCAGGCTAAAT
1 ATTACCAGTCCAGGCTAAAT
21341989 CCTTTATATG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 77 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (57 bp):
ATTACCAGTCCAGGCTAAATTTTGTTTGTATAGCATATACTCTAAGGGCTTTGTCGG
Found at i:21343631 original size:20 final size:22
Alignment explanation
Indices: 21343602--21343647 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
21343592 AAATCAAAAC
*
21343602 AAATACTATT-C-AAAATTATT
1 AAATACTATTACAAAAATTATA
*
21343622 AAATATTATTACAAAAATTATA
1 AAATACTATTACAAAAATTATA
21343644 AAAT
1 AAAT
21343648 CTTGTGGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 1 0.05
22 12 0.55
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATACTATTACAAAAATTATA
Found at i:21359403 original size:44 final size:44
Alignment explanation
Indices: 21359345--21359433 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
21359335 TTTTATCTGG
21359345 TTTAAAAAATACATTTAAATATGTTAACTTATCAACTTTTGGTT
1 TTTAAAAAATACATTTAAATATGTTAACTTATCAACTTTTGGTT
21359389 TTTAAAAAATACATTTAAATATGTTAACTTATCAACTTTTGGTT
1 TTTAAAAAATACATTTAAATATGTTAACTTATCAACTTTTGGTT
21359433 T
1 T
21359434 ATCTAATTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (44 bp):
TTTAAAAAATACATTTAAATATGTTAACTTATCAACTTTTGGTT
Found at i:21360839 original size:14 final size:15
Alignment explanation
Indices: 21360820--21360853 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
21360810 AATTTAGAAC
21360820 ATATTAAAATATAT-
1 ATATTAAAATATATA
21360834 ATATT-AAATATATA
1 ATATTAAAATATATA
21360848 ATATTA
1 ATATTA
21360854 CTCTAATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATATTAAAATATATA
Found at i:21364245 original size:21 final size:20
Alignment explanation
Indices: 21364219--21364264 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
21364209 TGGAAGTTTT
* *
21364219 ACATTTGTGTTGCATTTGAAG
1 ACATTTATGATGCATTTG-AG
*
21364240 ACATTTATGATGTATTTGAG
1 ACATTTATGATGCATTTGAG
21364260 ACATT
1 ACATT
21364265 GTTTGTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (20 bp):
ACATTTATGATGCATTTGAG
Found at i:21373967 original size:28 final size:26
Alignment explanation
Indices: 21373927--21373994 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 26
21373917 AATATAATAT
* *
21373927 TTAAGTTTTAAAAATATTTTTATCTATAA
1 TTAA-TTTTAAAAATA-ATTTATAT-TAA
21373956 TTAATTTTAAAAATAATTTATATTAA
1 TTAATTTTAAAAATAATTTATATTAA
*
21373982 TT-ATTTAAAAAAT
1 TTAATTTTAAAAAT
21373995 GTTTAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 10 0.28
26 5 0.14
27 6 0.17
28 11 0.31
29 4 0.11
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (26 bp):
TTAATTTTAAAAATAATTTATATTAA
Found at i:21374205 original size:13 final size:14
Alignment explanation
Indices: 21374181--21374209 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
21374171 CACTAATTAA
21374181 AAAAATATATTTTT
1 AAAAATATATTTTT
21374195 AAAAATA-ATTTTT
1 AAAAATATATTTTT
21374208 AA
1 AA
21374210 CCGCAATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AAAAATATATTTTT
Found at i:21375263 original size:25 final size:25
Alignment explanation
Indices: 21375227--21375319 Score: 89
Period size: 25 Copynumber: 3.6 Consensus size: 25
21375217 CTTTTTAAAA
*
21375227 TTTTAAATTAATAAATTATATATAT
1 TTTTAAAATAATAAATTATATATAT
21375252 TTTTAAAATAATAGAAATTATATATAT
1 TTTTAAAATAAT--AAATTATATATAT
* * * *
21375279 CATTTAAAATTTATAAA-GATATAAAT
1 -TTTTAAAA-TAATAAATTATATATAT
*
21375305 TATTAAAATAATAAA
1 TTTTAAAATAATAAA
21375320 ATTACATTTG
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
24 6 0.11
25 17 0.30
26 7 0.12
27 16 0.29
28 7 0.12
29 3 0.05
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (25 bp):
TTTTAAAATAATAAATTATATATAT
Found at i:21382892 original size:21 final size:21
Alignment explanation
Indices: 21382866--21382948 Score: 58
Period size: 21 Copynumber: 3.9 Consensus size: 21
21382856 TGATCAGTAT
*
21382866 ACGACACATAAAGTGCCTAAA
1 ACGACACACAAAGTGCCTAAA
* * * *
21382887 ACGACACACGAGGTGCCTGAT
1 ACGACACACAAAGTGCCTAAA
* *
21382908 ACGACACACGAGGTGCCTGAAA
1 ACGACACACAAAGTGCCT-AAA
** *
21382930 TACTTCACATAAAGTGCCT
1 -ACGACACACAAAGTGCCT
21382949 GATCAGTAAA
Statistics
Matches: 48, Mismatches: 12, Indels: 2
0.77 0.19 0.03
Matches are distributed among these distances:
21 34 0.71
22 1 0.02
23 13 0.27
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (21 bp):
ACGACACACAAAGTGCCTAAA
Found at i:21382938 original size:23 final size:21
Alignment explanation
Indices: 21382864--21382927 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
21382854 TTTGATCAGT
** * *
21382864 ATACGACACATAAAGTGCCTA
1 ATACGACACACGAGGTGCCTG
*
21382885 AAACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
21382906 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
21382927 A
1 A
21382928 AATACTTCAC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTG
Found at i:21396551 original size:24 final size:24
Alignment explanation
Indices: 21396457--21396540 Score: 105
Period size: 24 Copynumber: 3.5 Consensus size: 24
21396447 GATTCAACTC
* * * * *
21396457 CGCACACATAGTGCCAAATAATTC
1 CGCACACATAGTACCATACAAATA
* *
21396481 CGCACACATAGTGCCATACATATA
1 CGCACACATAGTACCATACAAATA
21396505 CGCACACATAGTACCATACAAATA
1 CGCACACATAGTACCATACAAATA
21396529 CGCACACATAGT
1 CGCACACATAGT
21396541 TCCACTCAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.39, C:0.30, G:0.12, T:0.19
Consensus pattern (24 bp):
CGCACACATAGTACCATACAAATA
Found at i:21399889 original size:43 final size:43
Alignment explanation
Indices: 21399814--21400078 Score: 347
Period size: 43 Copynumber: 6.4 Consensus size: 43
21399804 GATAAATCCC
* * *
21399814 GCAGGCCTAGTGCTGGT-AT-TATATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
21399855 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
21399898 GCAGGCTTAGTGCCGGTGATGTGTATTTGGG----C--G-CT-
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
21399933 --AGGCATAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
21399974 GCAGGCTTCGTACCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
21400017 GCAGGCTTCGTGCCGATGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
21400060 GCAGGCGTAATGCCGGTGA
1 GCAGGCTTAGTGCCGGTGA
21400079 AATGATATGT
Statistics
Matches: 197, Mismatches: 15, Indels: 22
0.84 0.06 0.09
Matches are distributed among these distances:
33 27 0.14
36 2 0.01
37 2 0.01
39 2 0.01
40 2 0.01
41 15 0.08
42 2 0.01
43 145 0.74
ACGTcount: A:0.13, C:0.23, G:0.34, T:0.29
Consensus pattern (43 bp):
GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
Found at i:21399947 original size:33 final size:33
Alignment explanation
Indices: 21399900--21399962 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
21399890 CGTGCCTAGC
* *
21399900 AGGCTTAGTGCCGGTGATGTGTATTTGGGCGCT
1 AGGCATAGTGCCGGTGATGTGTATTCGGGCGCT
21399933 AGGCATAGTGCCGGTGATGTGTATTCGGGC
1 AGGCATAGTGCCGGTGATGTGTATTCGGGC
21399963 CTTCGTGCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.14, C:0.16, G:0.40, T:0.30
Consensus pattern (33 bp):
AGGCATAGTGCCGGTGATGTGTATTCGGGCGCT
Found at i:21399990 original size:76 final size:80
Alignment explanation
Indices: 21399857--21400065 Score: 282
Period size: 76 Copynumber: 2.6 Consensus size: 80
21399847 CGTGCCTAGC
*
21399857 AGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATGTGT
1 AGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTAGTACCGGTGATGTGT
*
21399922 ATTTGGG-C-G-CT-
66 ATTCGGGCCGGCCTA
* *
21399933 AGGCATAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTACCGGTGATGTGT
1 AGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTAGTACCGGTGATGTGT
21399998 ATTCGGGCCTTCGTGCCTA
66 ATTCGGG-C--CG-GCCTA
* *
21400017 GCAGGCTTCGTGCCGATGATGTGTATTCGGGCCTTCGTGCCTAGCAGGC
1 --AGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGC
21400066 GTAATGCCGG
Statistics
Matches: 116, Mismatches: 7, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
76 68 0.59
80 1 0.01
82 1 0.01
83 2 0.02
86 44 0.38
ACGTcount: A:0.12, C:0.23, G:0.35, T:0.30
Consensus pattern (80 bp):
AGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTAGTACCGGTGATGTGT
ATTCGGGCCGGCCTA
Found at i:21402477 original size:15 final size:15
Alignment explanation
Indices: 21402457--21402517 Score: 63
Period size: 15 Copynumber: 4.0 Consensus size: 15
21402447 TCTCTCTCCT
21402457 TTCTTCTTTTATTCA
1 TTCTTCTTTTATTCA
21402472 TTCTTCTTTTATTCA
1 TTCTTCTTTTATTCA
* *
21402487 -TCTT-TTCCTATTAA
1 TTCTTCTT-TTATTCA
21402501 TTCATTTCTTTTATTCA
1 TTC--TTCTTTTATTCA
21402518 ATTTATTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 2 0.05
14 9 0.24
15 17 0.46
17 7 0.19
18 2 0.05
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (15 bp):
TTCTTCTTTTATTCA
Found at i:21403156 original size:104 final size:104
Alignment explanation
Indices: 21403012--21403273 Score: 301
Period size: 104 Copynumber: 2.5 Consensus size: 104
21403002 TATGGAAAAC
* * * * *
21403012 ACCATACCTACTTTTCAT-GCTCGGTATGGAAAATATCATACCTATATTTCATAACTTGGTATGG
1 ACCATACCTACGTTTCATAGCTCGGTATGG-AAATACCATACCTACATTTCACAACTCGGTATGG
* * *
21403076 ACGATACCATACCTACGTATCATAGCTCAATATGGACGAT
65 ACAATACCATACCTACGTATCACAACTCAATATGGACGAT
* * *
21403116 GCCATACCTACGTTTCATAGCTCGGTATGGAAATACCATACCTACGTTTCACAACTCGGTATGGT
1 ACCATACCTACGTTTCATAGCTCGGTATGGAAATACCATACCTACATTTCACAACTCGGTATGGA
* * * ** *
21403181 TAATACCATACCTATGTTTCACAACTCGGTATGGATGAT
66 CAATACCATACCTACGTATCACAACTCAATATGGACGAT
* * * * *
21403220 ACCATATCTACGTTTCACAACTCGGTATGGATGATACCATACCTACGTTTCACA
1 ACCATACCTACGTTTCATAGCTCGGTATGGA-AATACCATACCTACATTTCACA
21403274 CTTTGCCATG
Statistics
Matches: 134, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
104 102 0.76
105 32 0.24
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (104 bp):
ACCATACCTACGTTTCATAGCTCGGTATGGAAATACCATACCTACATTTCACAACTCGGTATGGA
CAATACCATACCTACGTATCACAACTCAATATGGACGAT
Found at i:21403231 original size:139 final size:139
Alignment explanation
Indices: 21403001--21403271 Score: 355
Period size: 139 Copynumber: 1.9 Consensus size: 139
21402991 TCACAACTCT
* ** * *
21403001 GTATGGAAAACACCATACCTACTTTTCATGCTCGGTATGGAAAATATCATACCTATATTTCATAA
1 GTATGGAAAACACCATACCTACGTTTCAAACTCGGTATGGAAAATACCATACCTATATTTCACAA
* * * *
21403066 CTTGGTATGGACGATACCATACCTACGTATCATAGCTCAATATGGACGATGCCATACCTACGTTT
66 CTCGGTATGGACGATACCATACCTACGTATCACAACTCAATATGGACGATACCATACCTACGTTT
21403131 CATAGCTCG
131 CATAGCTCG
* ** *
21403140 GTATGG-AAATACCATACCTACGTTTCACAACTCGGTATGGTTAATACCATACCTATGTTTCACA
1 GTATGGAAAACACCATACCTACGTTTCA-AACTCGGTATGGAAAATACCATACCTATATTTCACA
* * * ** *
21403204 ACTCGGTATGGATGATACCATATCTACGTTTCACAACTCGGTATGGATGATACCATACCTACGTT
65 ACTCGGTATGGACGATACCATACCTACGTATCACAACTCAATATGGACGATACCATACCTACGTT
21403269 TCA
130 TCA
21403272 CACTTTGCCA
Statistics
Matches: 112, Mismatches: 19, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
138 19 0.17
139 93 0.83
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (139 bp):
GTATGGAAAACACCATACCTACGTTTCAAACTCGGTATGGAAAATACCATACCTATATTTCACAA
CTCGGTATGGACGATACCATACCTACGTATCACAACTCAATATGGACGATACCATACCTACGTTT
CATAGCTCG
Found at i:21403285 original size:35 final size:35
Alignment explanation
Indices: 21402991--21403273 Score: 291
Period size: 35 Copynumber: 8.1 Consensus size: 35
21402981 ATACCATACC
* ** * *
21402991 TCACAACTCTGTATGGAAAACACCATACCTACTTT
1 TCACAACTCGGTATGGATGATACCATACCTACGTT
** ** * **
21403026 TCA-TGCTCGGTATGGAAAATATCATACCTATATT
1 TCACAACTCGGTATGGATGATACCATACCTACGTT
* * * *
21403060 TCATAACTTGGTATGGACGATACCATACCTACGTA
1 TCACAACTCGGTATGGATGATACCATACCTACGTT
* * ** * *
21403095 TCATAGCTCAATATGGACGATGCCATACCTACGTT
1 TCACAACTCGGTATGGATGATACCATACCTACGTT
* * *
21403130 TCATAGCTCGGTATGGA-AATACCATACCTACGTT
1 TCACAACTCGGTATGGATGATACCATACCTACGTT
* * *
21403164 TCACAACTCGGTATGGTTAATACCATACCTATGTT
1 TCACAACTCGGTATGGATGATACCATACCTACGTT
*
21403199 TCACAACTCGGTATGGATGATACCATATCTACGTT
1 TCACAACTCGGTATGGATGATACCATACCTACGTT
21403234 TCACAACTCGGTATGGATGATACCATACCTACGTT
1 TCACAACTCGGTATGGATGATACCATACCTACGTT
21403269 TCACA
1 TCACA
21403274 CTTTGCCATG
Statistics
Matches: 211, Mismatches: 35, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
34 56 0.27
35 155 0.73
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (35 bp):
TCACAACTCGGTATGGATGATACCATACCTACGTT
Found at i:21405561 original size:46 final size:45
Alignment explanation
Indices: 21405463--21405591 Score: 170
Period size: 46 Copynumber: 2.8 Consensus size: 45
21405453 TATTGTCTGT
* * *
21405463 CATGTGCATGATAGAAATGGA-TTTGTTTGTGTTAAAGTGTATGA
1 CATGTGCATGATAGAAATGGATTTTTTTTGTATTAAAATGTATGA
* *
21405507 CATGTGCATGATAGACATGGATTTTTTATTGTATTAAAATGTATGG
1 CATGTGCATGATAGAAATGGATTTTTT-TTGTATTAAAATGTATGA
*
21405553 CATGTGCATGATAGAAATTGATTTTTTTTTTGTATTAAA
1 CATGTGCATGATAGAAATGGA--TTTTTTTTGTATTAAA
21405592 GTATTTGGTT
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 20 0.27
45 4 0.05
46 34 0.46
47 10 0.14
48 6 0.08
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (45 bp):
CATGTGCATGATAGAAATGGATTTTTTTTGTATTAAAATGTATGA
Found at i:21409068 original size:7 final size:7
Alignment explanation
Indices: 21409056--21409081 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
21409046 ATTGAATTTC
21409056 ATTATTA
1 ATTATTA
21409063 ATTATTA
1 ATTATTA
21409070 ATTATTA
1 ATTATTA
21409077 ATTAT
1 ATTAT
21409082 ATTACATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTATTA
Found at i:21429005 original size:7 final size:7
Alignment explanation
Indices: 21428993--21429017 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
21428983 ATGCATTTTG
21428993 TTTTTAT
1 TTTTTAT
21429000 TTTTTAT
1 TTTTTAT
21429007 TTTTTAT
1 TTTTTAT
21429014 TTTT
1 TTTT
21429018 CTTTTGCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:21430031 original size:28 final size:29
Alignment explanation
Indices: 21429971--21430037 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
21429961 TTAAAATATA
* * * *
21429971 AAAAATTCAAAAAAGTATAAAATTTGTTTT
1 AAAAATT-AAAAAAATATAAAATGTATTAT
21430001 AAAAATTAAAAAAATATAAAA-GTATTAT
1 AAAAATTAAAAAAATATAAAATGTATTAT
21430029 AAAAATTAA
1 AAAAATTAA
21430038 TTAATTGCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 13 0.39
29 13 0.39
30 7 0.21
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (29 bp):
AAAAATTAAAAAAATATAAAATGTATTAT
Found at i:21434574 original size:11 final size:11
Alignment explanation
Indices: 21434558--21434597 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
21434548 ATATGGGAAA
21434558 TTTTATAA-TT
1 TTTTATAATTT
21434568 TTTT-T-ATTT
1 TTTTATAATTT
*
21434577 TTCTATAATTT
1 TTTTATAATTT
21434588 TTTTATAATT
1 TTTTATAATT
21434598 AAAGCAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
8 1 0.04
9 6 0.24
10 5 0.20
11 13 0.52
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:21437533 original size:6 final size:6
Alignment explanation
Indices: 21437522--21437546 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
21437512 AGTTTGTTAA
21437522 GGCTTG GGCTTG GGCTTG GGCTTG G
1 GGCTTG GGCTTG GGCTTG GGCTTG G
21437547 TAAGTAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGCTTG
Found at i:21443003 original size:19 final size:19
Alignment explanation
Indices: 21442979--21443015 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
21442969 TTTCTTGTTC
21442979 TTGTTTACACGAATTGAAA
1 TTGTTTACACGAATTGAAA
21442998 TTGTTTACACGAATTGAA
1 TTGTTTACACGAATTGAA
21443016 CTTATGATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (19 bp):
TTGTTTACACGAATTGAAA
Found at i:21455691 original size:13 final size:13
Alignment explanation
Indices: 21455673--21455697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21455663 TAAGATAAAT
21455673 TTGCTTGTGTTTG
1 TTGCTTGTGTTTG
21455686 TTGCTTGTGTTT
1 TTGCTTGTGTTT
21455698 TAGACCCTAG
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:0.08, G:0.28, T:0.64
Consensus pattern (13 bp):
TTGCTTGTGTTTG
Found at i:21460927 original size:19 final size:17
Alignment explanation
Indices: 21460897--21460938 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
21460887 GGCGCGACCC
21460897 ATTTTTTTAATAATATA
1 ATTTTTTTAATAATATA
*
21460914 ATTTTTTTAA-AATATT
1 ATTTTTTTAATAATATA
*
21460930 ATTATTTTA
1 ATTTTTTTA
21460939 TTATATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTTTTAATAATATA
Found at i:21463939 original size:12 final size:12
Alignment explanation
Indices: 21463917--21463984 Score: 57
Period size: 12 Copynumber: 5.7 Consensus size: 12
21463907 ATGCACCAAC
*
21463917 GCCGAAGCCAGA
1 GCCGGAGCCAGA
*
21463929 GCCAGAGCCAGA
1 GCCGGAGCCAGA
* *
21463941 GCCGGAGGCAGT
1 GCCGGAGCCAGA
*
21463953 GCCGGACCCAGA
1 GCCGGAGCCAGA
*
21463965 G-CGGCGGCCAGA
1 GCCGG-AGCCAGA
*
21463977 GTCGGAGC
1 GCCGGAGC
21463985 TATACTCAGG
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
11 3 0.07
12 37 0.86
13 3 0.07
ACGTcount: A:0.24, C:0.32, G:0.41, T:0.03
Consensus pattern (12 bp):
GCCGGAGCCAGA
Found at i:21468198 original size:16 final size:15
Alignment explanation
Indices: 21468161--21468199 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
21468151 TAAAATATAA
21468161 TAAAATAATAATATTT
1 TAAAA-AATAATATTT
*
21468177 TAAAAAATTATATTAT
1 TAAAAAATAATATT-T
21468193 TAAAAAA
1 TAAAAAA
21468200 ATGGGTCGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAAAATAATATTT
Found at i:21473274 original size:17 final size:17
Alignment explanation
Indices: 21473252--21473287 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
21473242 TAAACCGACC
21473252 ACTAACTTCATCACCCT
1 ACTAACTTCATCACCCT
21473269 ACTAACTTCATCACCCT
1 ACTAACTTCATCACCCT
21473286 AC
1 AC
21473288 CTTCCAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.42, G:0.00, T:0.28
Consensus pattern (17 bp):
ACTAACTTCATCACCCT
Found at i:21473801 original size:10 final size:10
Alignment explanation
Indices: 21473779--21473814 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
21473769 TTCTTTTGTA
21473779 TATTTTCATTC
1 TATTTT-ATTC
21473790 TATTTTATTC
1 TATTTTATTC
21473800 TATTTTATT-
1 TATTTTATTC
21473809 TATTTT
1 TATTTT
21473815 TTTTATGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 6 0.24
10 13 0.52
11 6 0.24
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.72
Consensus pattern (10 bp):
TATTTTATTC
Found at i:21473867 original size:22 final size:22
Alignment explanation
Indices: 21473825--21473867 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
21473815 TTTTATGAAC
*
21473825 ATTTTTAAAATATTGTATTATT
1 ATTTTTAAAATATTATATTATT
*
21473847 ATTTTTATATATATTAT-TTAT
1 ATTTTTA-AAATATTATATTAT
21473868 ATTAAGCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
ATTTTTAAAATATTATATTATT
Found at i:21474241 original size:25 final size:25
Alignment explanation
Indices: 21474213--21474262 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
21474203 AGATAGATCA
*
21474213 ATATTT-TGTATTTTATGCATTAATT
1 ATATTTATGTATTTTAT-AATTAATT
*
21474238 ATATTTATTTATTTTATAATTAATT
1 ATATTTATGTATTTTATAATTAATT
21474263 TTAAAGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (25 bp):
ATATTTATGTATTTTATAATTAATT
Found at i:21476305 original size:19 final size:19
Alignment explanation
Indices: 21476281--21476325 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
21476271 CTTACTTTCT
21476281 TTTGCATT-CATTCCATGCA
1 TTTGCATTGCATTCCAT-CA
*
21476300 TTTGCATTGCATTGCATCA
1 TTTGCATTGCATTCCATCA
*
21476319 TGTGCAT
1 TTTGCAT
21476326 CAAACTTCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (19 bp):
TTTGCATTGCATTCCATCA
Found at i:21480699 original size:64 final size:64
Alignment explanation
Indices: 21480624--21480751 Score: 175
Period size: 64 Copynumber: 2.0 Consensus size: 64
21480614 TCATTCATAA
* * *
21480624 CACATCTAGTTAGGAGTATTTGATTCATTTCGGTCATAGCATCCTAATTATTTGATATAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCAT
* * * * * *
21480688 CACATTTAGTTAGGAGCATTTGGTTTATTTCGATCATAGTATCTTAATTATTTGGCATAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCAT
21480752 AGATACATGA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (64 bp):
CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCAT
Found at i:21480909 original size:45 final size:44
Alignment explanation
Indices: 21480859--21481137 Score: 176
Period size: 45 Copynumber: 6.2 Consensus size: 44
21480849 ATCGAAAATG
*
21480859 ACAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGAT
1 ACAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGAT
* * * *
21480903 AGCAAGTCTTATCTTCTTGAAGTTGCAA-GAAGCAGACTGAAAGTT
1 A-CAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTG-AAGAT
* * * * * ** **
21480948 AC-AGATCTTATCTCCATGTA-TCGGCTATGGAGCAGATTTTAGCC
1 ACAAG-TCTTATCTCCCTGAAGT-TGCAATGGAGCAGACTGAAGAT
* * * * * *
21480992 ACTAGTCTTATCTTCCTGAAGTTGCAGT-AAGCAGACTAAAAATTT
1 ACAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGA--T
* * * * *
21481037 AC-AGATCTTATCTCCATGTA-TCGGCTATGGAGCAGA-TCGAAAAT
1 ACAAG-TCTTATCTCCCTGAAGT-TGCAATGGAGCAGACT-GAAGAT
*
21481081 GACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT
1 -ACAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGAT
21481126 AGCAAGTCTTAT
1 A-CAAGTCTTAT
21481138 AGGAAGCAGA
Statistics
Matches: 174, Mismatches: 43, Indels: 35
0.69 0.17 0.14
Matches are distributed among these distances:
43 11 0.06
44 50 0.29
45 99 0.57
46 14 0.08
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (44 bp):
ACAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGAT
Found at i:21480979 original size:89 final size:89
Alignment explanation
Indices: 21480885--21481122 Score: 302
Period size: 89 Copynumber: 2.7 Consensus size: 89
21480875 TGAAGTTGCA
*
21480885 ATGGAGCAGATTGAAGATAGCAAGTCTTATCTTCTTGAAGTTGCAAGAAGCAGACTGAAAGTTAC
1 ATGGAGCAGATTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAAGAAGCAGACTGAAAGTTAC
21480950 AGATCTTATCTCCATGTATCGGCT
66 AGATCTTATCTCCATGTATCGGCT
** ** * * *
21480974 ATGGAGCAGATTTTAGCCA-CTAGTCTTATCTTCCTGAAGTTGC-AGTAAGCAGACTAAAAATTT
1 ATGGAGCAGATTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAAG-AAGCAGACT-GAAAGTT
21481037 ACAGATCTTATCTCCATGTATCGGCT
64 ACAGATCTTATCTCCATGTATCGGCT
* * * * *
21481063 ATGGAGCAGATCGAAAAT-GACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA
1 ATGGAGCAGATTGAAGATAG-CAAGTCTTATCTTCCTGAAGTTGCA-AGAAGCAGACTGAA
21481123 GATAGCAAGT
Statistics
Matches: 124, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
87 2 0.02
88 31 0.25
89 58 0.47
90 24 0.19
91 8 0.06
92 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (89 bp):
ATGGAGCAGATTGAAGATAGCAAGTCTTATCTTCCTGAAGTTGCAAGAAGCAGACTGAAAGTTAC
AGATCTTATCTCCATGTATCGGCT
Found at i:21481302 original size:45 final size:44
Alignment explanation
Indices: 21481249--21481441 Score: 138
Period size: 45 Copynumber: 4.3 Consensus size: 44
21481239 TTTAGCCACT
*
21481249 AGTCTTATCTTCC-TAAAGTTGCAGGAAGCAGACTGAAAATTTACAG
1 AGTCTTATC-TCCATGAAGTTGCAGGAAGCAGACT-AAAA-TTACAG
* *
21481295 A-TCTTATCTCCATGTA-TTGGCTATGG-AGCAGA-TAGAAAATAACA-
1 AGTCTTATCTCCATGAAGTT-GC-A-GGAAGCAGACT--AAAATTACAG
* * *
21481339 AGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACT-AAA-GACAG
1 AGTCTTATCTCCATGAAGTTGCAG-GAAGCAGACTAAAATTACAG
21481382 CAAGTCTTATCTTCC-TGAAGTTGCAGGAAGCAGACTAAAAATTACAG
1 --AGTCTTATC-TCCATGAAGTTGCAGGAAGCAGACT-AAAATTACAG
21481429 A-TCTTA-CTCCATG
1 AGTCTTATCTCCATG
21481442 TATCGGCTAT
Statistics
Matches: 121, Mismatches: 8, Indels: 39
0.72 0.05 0.23
Matches are distributed among these distances:
42 6 0.05
43 7 0.06
44 22 0.18
45 58 0.48
46 22 0.18
47 6 0.05
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (44 bp):
AGTCTTATCTCCATGAAGTTGCAGGAAGCAGACTAAAATTACAG
Found at i:21481427 original size:134 final size:134
Alignment explanation
Indices: 21481138--21481615 Score: 484
Period size: 134 Copynumber: 3.6 Consensus size: 134
21481128 CAAGTCTTAT
* * * *
21481138 AGGAAGCAGACTGAAAGTTACAGATTTTATTTCCATGTATCGGCTATGGAGCAGATTAGAAATGA
1 AGGAAGCAGACTAAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATTAGAAATGA
* * ** * * ** * * *
21481203 CGAGTCTTATCTCCATCTA-TCGGCTA-TGGAGCAGATTTTAGCCACTAGTCTTATCTTCCTAAA
66 CAAGTCTTATCTCCTTGAAGT-AGCAAGTGGAGCAGATTAAAGACACAAGTCTTATCTTCCTGAA
21481266 GTTGC
130 GTTGC
* *
21481271 AGGAAGCAGACTGAAAATTTACAGATCTTATCTCCATGTATTGGCTATGGAGCAGA-TAGAAAAT
1 AGGAAGCAGACT-AAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATTAG-AAAT
* * *
21481335 AACAAGTCTTATCTCCTTGAAGTTGC-AGTGGAGCAGACTAAAGACAGCAAGTCTTATCTTCCTG
64 GACAAGTCTTATCTCCTTGAAGTAGCAAGTGGAGCAGATTAAAGACA-CAAGTCTTATCTTCCTG
21481399 AAGTTGC
128 AAGTTGC
* * ** ***
21481406 AGGAAGCAGACTAAAAATTACAGATCTTA-CTCCATGTATCGGCTATGAAGTAGATT-TTAGCCA
1 AGGAAGCAGACTAAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATTAGAAATGA
* * ** * * * * * * *
21481469 CCAGCCTTATCTGTTTGAGGTAGCAAG-AGAGCAGGTTGAAGATATAGGTCTTATCTTCCTGAAG
66 CAAGTCTTATCTCCTTGAAGTAGCAAGTGGAGCAGATTAAAGACACAAGTCTTATCTTCCTGAAG
21481533 TTGC
131 TTGC
* * * * *
21481537 AAGAAGCAGACTGAAAAGTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATTAGAACTGG
1 AGGAAGCAGACTAAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATTAGAAATGA
21481602 CAAGTCTTATCTCC
66 CAAGTCTTATCTCC
21481616 ATGTATCGTC
Statistics
Matches: 282, Mismatches: 54, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
131 48 0.17
132 57 0.20
133 51 0.18
134 91 0.32
135 35 0.12
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (134 bp):
AGGAAGCAGACTAAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATTAGAAATGA
CAAGTCTTATCTCCTTGAAGTAGCAAGTGGAGCAGATTAAAGACACAAGTCTTATCTTCCTGAAG
TTGC
Found at i:21481942 original size:17 final size:17
Alignment explanation
Indices: 21481920--21481955 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
21481910 TAAACCGACC
21481920 ACTAACTCCATCACCCT
1 ACTAACTCCATCACCCT
21481937 ACTAACTCCATCACCCT
1 ACTAACTCCATCACCCT
21481954 AC
1 AC
21481956 CTTCCACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.47, G:0.00, T:0.22
Consensus pattern (17 bp):
ACTAACTCCATCACCCT
Found at i:21482523 original size:13 final size:12
Alignment explanation
Indices: 21482499--21482531 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
21482489 TTTTTAAATA
21482499 TTATATTATTAT
1 TTATATTATTAT
21482511 TTATATATATTAT
1 TTATAT-TATTAT
21482524 TTATATTA
1 TTATATTA
21482532 AGCTATTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTATATTATTAT
Found at i:21488314 original size:13 final size:13
Alignment explanation
Indices: 21488298--21488340 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
21488288 TTTTTCTTAT
*
21488298 TTTATTTTGTTTA
1 TTTATTTTATTTA
21488311 TTTATTTTATTTA
1 TTTATTTTATTTA
* *
21488324 TTTTTTGTTATTAA
1 TTTATT-TTATTTA
21488338 TTT
1 TTT
21488341 TAAAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 17 0.65
14 9 0.35
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:21488335 original size:10 final size:9
Alignment explanation
Indices: 21488294--21488327 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
21488284 ATATTTTTTC
21488294 TTATTTTAT
1 TTATTTTAT
21488303 TT-TGTTTAT
1 TTAT-TTTAT
21488312 TTATTTTAT
1 TTATTTTAT
21488321 TTATTTT
1 TTATTTT
21488328 TTGTTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.04
9 21 0.91
10 1 0.04
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (9 bp):
TTATTTTAT
Found at i:21488425 original size:21 final size:20
Alignment explanation
Indices: 21488392--21488433 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
21488382 TTTAAATATT
*
21488392 ATTTTTAAATTATTTTTTAA
1 ATTTTGAAATTATTTTTTAA
21488412 ATTTTGAATATTATTTTTTAA
1 ATTTTGAA-ATTATTTTTTAA
21488433 A
1 A
21488434 ATTATGTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTTGAAATTATTTTTTAA
Found at i:21488513 original size:14 final size:14
Alignment explanation
Indices: 21488496--21488524 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
21488486 TTTAAATTTT
21488496 AAATATATTTTTAA
1 AAATATATTTTTAA
21488510 AAATATATTTTTAA
1 AAATATATTTTTAA
21488524 A
1 A
21488525 CAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATATATTTTTAA
Found at i:21488583 original size:34 final size:33
Alignment explanation
Indices: 21488486--21488583 Score: 99
Period size: 34 Copynumber: 2.9 Consensus size: 33
21488476 TTTTCTAAAT
*
21488486 TTTAAATTTTAAATATATTTTTAAAAATATATT
1 TTTAAATTTTAAATATATTTTTAAAAATATATA
*** * *
21488519 TTTAAACAAAATAAA-ATAATTTCAAAAATATATA
1 TTT-AA-ATTTTAAATATATTTTTAAAAATATATA
*
21488553 TTTAAATTTTAAATATTATTTTTAATAATAT
1 TTTAAATTTTAAATA-TATTTTTAAAAATAT
21488584 TTAAACATTT
Statistics
Matches: 49, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
32 5 0.10
33 6 0.12
34 33 0.67
35 5 0.10
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (33 bp):
TTTAAATTTTAAATATATTTTTAAAAATATATA
Found at i:21488601 original size:39 final size:38
Alignment explanation
Indices: 21488552--21488625 Score: 96
Period size: 40 Copynumber: 1.9 Consensus size: 38
21488542 AAAAATATAT
** *
21488552 ATTTAAA-TTTTAAATATTATTTTTAATAATATTTAAAC
1 ATTTAAATTTTTAAATAAAATTTTT-ATAAAATTTAAAC
21488590 ATTTAAAATTTTTAAATAAAATTTTTATAAAATTTA
1 ATTT-AAATTTTTAAATAAAATTTTTATAAAATTTA
21488626 TTTTAAAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 4 0.13
39 12 0.39
40 15 0.48
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (38 bp):
ATTTAAATTTTTAAATAAAATTTTTATAAAATTTAAAC
Found at i:21488688 original size:25 final size:26
Alignment explanation
Indices: 21488660--21488709 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
21488650 AAAAATAATT
*
21488660 AAAAATCATA-ATTTCAAAAATTTAG
1 AAAAATAATATATTTCAAAAATTTAG
**
21488685 AAAAATAATATATTTTTAAAATTTA
1 AAAAATAATATATTTCAAAAATTTA
21488710 AAATTTAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (26 bp):
AAAAATAATATATTTCAAAAATTTAG
Found at i:21488711 original size:7 final size:7
Alignment explanation
Indices: 21488699--21488747 Score: 62
Period size: 7 Copynumber: 6.6 Consensus size: 7
21488689 ATAATATATT
21488699 TTTAAAA
1 TTTAAAA
21488706 TTTAAAA
1 TTTAAAA
21488713 TTTAGAAA
1 TTTA-AAA
*
21488721 TATAATATA
1 TTTAA-A-A
21488730 TTTAAAA
1 TTTAAAA
21488737 TTTAAAA
1 TTTAAAA
21488744 TTTA
1 TTTA
21488748 GAAAAATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
7 24 0.65
8 8 0.22
9 5 0.14
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (7 bp):
TTTAAAA
Found at i:21488734 original size:31 final size:32
Alignment explanation
Indices: 21488676--21488754 Score: 133
Period size: 31 Copynumber: 2.5 Consensus size: 32
21488666 CATAATTTCA
21488676 AAAATTTAGAAAAATAATATATTTTTAAAATTT
1 AAAATTTAGAAAAATAATATA-TTTTAAAATTT
*
21488709 AAAATTTAGAAATATAATATA-TTTAAAATTT
1 AAAATTTAGAAAAATAATATATTTTAAAATTT
21488740 AAAATTTAGAAAAAT
1 AAAATTTAGAAAAAT
21488755 TAATTTCAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
31 24 0.55
33 20 0.45
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (32 bp):
AAAATTTAGAAAAATAATATATTTTAAAATTT
Found at i:21488783 original size:36 final size:33
Alignment explanation
Indices: 21488736--21488859 Score: 135
Period size: 36 Copynumber: 3.6 Consensus size: 33
21488726 TATATTTAAA
21488736 ATTTAAAATTTAGAAAAATTAATTTCAAAAATATAT
1 ATTTAAAATTTA-AAAAA-TAATTT-AAAAATATAT
* *
21488772 TTTTAAAATTTATAAGACATAATTTTAAAAA-ATAAT
1 ATTTAAAATTTA-AA-AAATAA-TTTAAAAATAT-AT
*
21488808 ATTCAAAATTTAAAAAATAATTTAAAAATA-AT
1 ATTTAAAATTTAAAAAATAATTTAAAAATATAT
21488840 ATTTAAAATTTTAAAAAATA
1 ATTTAAAA-TTTAAAAAATA
21488860 TATATTATAA
Statistics
Matches: 76, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
32 9 0.12
33 19 0.25
34 6 0.08
35 4 0.05
36 33 0.43
37 5 0.07
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (33 bp):
ATTTAAAATTTAAAAAATAATTTAAAAATATAT
Found at i:21488821 original size:21 final size:20
Alignment explanation
Indices: 21488795--21488836 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
21488785 AAGACATAAT
*
21488795 TTTAAAAAATAATATTCAAAA
1 TTTAAAAAATAAT-TTAAAAA
21488816 TTTAAAAAATAATTTAAAAA
1 TTTAAAAAATAATTTAAAAA
21488836 T
1 T
21488837 AATATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
TTTAAAAAATAATTTAAAAA
Found at i:21488915 original size:9 final size:9
Alignment explanation
Indices: 21488901--21488948 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
21488891 TTAATAACAA
21488901 AAAATAAAT
1 AAAATAAAT
21488910 AAAATAAAT
1 AAAATAAAT
21488919 -AAATAAAAT
1 AAAAT-AAAT
*
21488928 AAAATAAGAA
1 AAAATAA-AT
*
21488938 AAAATATAT
1 AAAATAAAT
21488947 AA
1 AA
21488949 CTTAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
8 4 0.12
9 18 0.55
10 11 0.33
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (9 bp):
AAAATAAAT
Found at i:21488918 original size:13 final size:13
Alignment explanation
Indices: 21488888--21488930 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
21488878 AAATATTTTA
* *
21488888 AAATTAATAACAAA
1 AAATAAATAA-AAT
21488902 AAATAAATAAAAT
1 AAATAAATAAAAT
21488915 AAATAAATAAAAT
1 AAATAAATAAAAT
21488928 AAA
1 AAA
21488931 ATAAGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 18 0.67
14 9 0.33
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:21488973 original size:14 final size:13
Alignment explanation
Indices: 21488952--21489010 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
21488942 TATATAACTT
21488952 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
21488965 AAAATAAAGAAAAA
1 AAAA-AAAGAAAAA
* *
21488979 GACAAAAGTTAAAAA
1 AAAAAAAG--AAAAA
**
21488994 AAAAAGTGAAAAA
1 AAAAAAAGAAAAA
21489007 AAAA
1 AAAA
21489011 GCGAAAGAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 17 0.46
14 11 0.30
15 9 0.24
ACGTcount: A:0.81, C:0.02, G:0.10, T:0.07
Consensus pattern (13 bp):
AAAAAAAGAAAAA
Found at i:21488978 original size:37 final size:37
Alignment explanation
Indices: 21488893--21488978 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 37
21488883 TTTTAAAATT
* * * *
21488893 AATAACAAAAAATAAATAAAATAAATAAATAAAATAA
1 AATAAGAAAAAATAAATAAAATAAAAAAAGAAAAAAA
* **
21488930 AATAAGAAAAAATATATAACTTAAAAAAAGAAAAAAA
1 AATAAGAAAAAATAAATAAAATAAAAAAAGAAAAAAA
21488967 AATAAAGAAAAA
1 AAT-AAGAAAAA
21488979 GACAAAAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 33 0.80
38 8 0.20
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.16
Consensus pattern (37 bp):
AATAAGAAAAAATAAATAAAATAAAAAAAGAAAAAAA
Found at i:21488998 original size:13 final size:12
Alignment explanation
Indices: 21488952--21489011 Score: 50
Period size: 12 Copynumber: 4.7 Consensus size: 12
21488942 TATATAACTT
*
21488952 AAAAAAAGAAAAA
1 AAAAAAAG-TAAA
21488965 AAAATAAAG-AAA
1 AAAA-AAAGTAAA
21488977 AAGACAAAAGTTAAA
1 AA-A-AAAAG-TAAA
*
21488992 AAAAAAAGTGAA
1 AAAAAAAGTAAA
21489004 AAAAAAAG
1 AAAAAAAG
21489012 CGAAAGAAGG
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
12 16 0.39
13 14 0.34
14 6 0.15
15 5 0.12
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.07
Consensus pattern (12 bp):
AAAAAAAGTAAA
Found at i:21490849 original size:31 final size:30
Alignment explanation
Indices: 21490809--21490868 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
21490799 TTTAATTTTA
*
21490809 TTTATTTTAATAATATATTATCCTATAAAC
1 TTTATTTTAATAATATATTATCCCATAAAC
*
21490839 TTTATATTTAATATTATATTATCCCATAAA
1 TTTAT-TTTAATAATATATTATCCCATAAA
21490869 AATTTTACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 5 0.19
31 22 0.81
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (30 bp):
TTTATTTTAATAATATATTATCCCATAAAC
Found at i:21493479 original size:28 final size:28
Alignment explanation
Indices: 21493439--21493496 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
21493429 CTATTGGAAC
21493439 AATACCAATTCCTTGAATGAAGTATAAG
1 AATACCAATTCCTTGAATGAAGTATAAG
21493467 AATACCAATTCCTTGAATGAAGTATAAG
1 AATACCAATTCCTTGAATGAAGTATAAG
21493495 AA
1 AA
21493497 AACGAAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (28 bp):
AATACCAATTCCTTGAATGAAGTATAAG
Found at i:21497337 original size:18 final size:17
Alignment explanation
Indices: 21497306--21497341 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
21497296 AAAACTAATA
*
21497306 TTTTTAAAATATTCATT
1 TTTTTAAAAAATTCATT
21497323 TTTTTATAAAAATTCATT
1 TTTTTA-AAAAATTCATT
21497341 T
1 T
21497342 AAAATTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTTAAAAAATTCATT
Found at i:21507971 original size:19 final size:19
Alignment explanation
Indices: 21507939--21508010 Score: 58
Period size: 19 Copynumber: 3.7 Consensus size: 19
21507929 TTAGAAAAAA
*
21507939 AAAATTTATTAAATTTTATT
1 AAAA-TTATAAAATTTTATT
* *
21507959 AAAATTATAAAATATTATA
1 AAAATTATAAAATTTTATT
*
21507978 AAAATATAAAAAAATTTGT-TT
1 AAAAT-T-ATAAAATTT-TATT
21507999 AAAATTA-AAAAT
1 AAAATTATAAAAT
21508011 ATATTAGAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
18 5 0.12
19 18 0.42
20 6 0.14
21 13 0.30
22 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (19 bp):
AAAATTATAAAATTTTATT
Found at i:21507979 original size:18 final size:19
Alignment explanation
Indices: 21507939--21508047 Score: 64
Period size: 20 Copynumber: 5.6 Consensus size: 19
21507929 TTAGAAAAAA
* *
21507939 AAAATTTATTAAATTTTATT
1 AAAA-TTATAAAATATTATT
21507959 AAAATTATAAAATATTA-T
1 AAAATTATAAAATATTATT
* * *
21507977 AAAAATATAAAAAAATTTGTTT
1 AAAATTAT-AAAATA-TT-ATT
21507999 AAAATTA-AAAATA-TATT
1 AAAATTATAAAATATTATT
* * *
21508016 AGAATTCTTAAAAATATT-TA
1 AAAATT-AT-AAAATATTATT
21508036 AAAATTATAAAA
1 AAAATTATAAAA
21508048 ATAAATTTAA
Statistics
Matches: 68, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
17 7 0.10
18 13 0.19
19 17 0.25
20 23 0.34
21 1 0.01
22 7 0.10
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (19 bp):
AAAATTATAAAATATTATT
Found at i:21508041 original size:20 final size:19
Alignment explanation
Indices: 21508003--21508067 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
21507993 TTGTTTAAAA
*
21508003 TTAAAAATATATTAGAATT
1 TTAAAAATATATTAAAATT
21508022 CTTAAAAATAT-TTAAAAATT
1 -TTAAAAATATATT-AAAATT
* * *
21508042 ATAAAAATAAATTTAAAATA
1 TTAAAAATATA-TTAAAATT
21508062 TTAAAA
1 TTAAAA
21508068 CTGAAATAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
19 10 0.27
20 25 0.68
21 2 0.05
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
TTAAAAATATATTAAAATT
Done.