Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold47
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: 2157611
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 149227 characters in sequence are not A, C, G, or T
File 12 of 15
Found at i:1518727 original size:32 final size:32
Alignment explanation
Indices: 1518686--1518748 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1518676 TAGCTAATTA
*
1518686 TGTATCGATACAATACTTATGTATGGATACAT
1 TGTATCGATACAAAACTTATGTATGGATACAT
*
1518718 TGTATCGATACAAAACTTATGTATTGATACA
1 TGTATCGATACAAAACTTATGTATGGATACA
1518749 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATGGATACAT
Found at i:1527747 original size:24 final size:22
Alignment explanation
Indices: 1527719--1527769 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1527709 AATATTATAT
*
1527719 AATATATACTTAATTTTATTTA
1 AATATATACTCAATTTTATTTA
1527741 AATATATACTCAATTTTATTTA
1 AATATATACTCAATTTTATTTA
*
1527763 AACATAT
1 AATATAT
1527770 TAAGACTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (22 bp):
AATATATACTCAATTTTATTTA
Found at i:1530490 original size:51 final size:51
Alignment explanation
Indices: 1530427--1530542 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 51
1530417 AAATAAAAGG
* ** *
1530427 GTTGAAGTATCCCTGATTATAGAAA-ATTGGTGTTTTAAAAATAAAATCGGA
1 GTTGGAGTATCCCCAATTATA-AAATATTGGTATTTTAAAAATAAAATCGGA
* * *
1530478 GTTGGAGTATCCCCAATTGTAAAATTTTGGTATTTTAAAAATAAAATCGGG
1 GTTGGAGTATCCCCAATTATAAAATATTGGTATTTTAAAAATAAAATCGGA
*
1530529 GTTCGAGTATCCCC
1 GTTGGAGTATCCCC
1530543 TCGAAAATAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 3 0.05
51 53 0.95
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (51 bp):
GTTGGAGTATCCCCAATTATAAAATATTGGTATTTTAAAAATAAAATCGGA
Found at i:1532980 original size:25 final size:24
Alignment explanation
Indices: 1532927--1532981 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
1532917 CCAAAATTCA
1532927 GAAAAATCTGACATGTCCTTTGGT
1 GAAAAATCTGACATGTCCTTTGGT
1532951 GAAAAATCTGACATGTCCTTTGGT
1 GAAAAATCTGACATGTCCTTTGGT
1532975 GAAAAAT
1 GAAAAAT
1532982 GACATTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Consensus pattern (24 bp):
GAAAAATCTGACATGTCCTTTGGT
Found at i:1533182 original size:20 final size:20
Alignment explanation
Indices: 1533157--1533252 Score: 131
Period size: 20 Copynumber: 4.8 Consensus size: 20
1533147 AAAAATGCCT
1533157 AAATGTATCGATACATTGTA
1 AAATGTATCGATACATTGTA
1533177 AAATGTATCGATACATTGTA
1 AAATGTATCGATACATTGTA
*
1533197 AAATGTATCGATACAATG-A
1 AAATGTATCGATACATTGTA
* * * *
1533216 GCAATATATCGATACAATGCA
1 -AAATGTATCGATACATTGTA
1533237 AAATGTATCGATACAT
1 AAATGTATCGATACAT
1533253 CTGGGTAAAC
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
19 1 0.01
20 66 0.97
21 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (20 bp):
AAATGTATCGATACATTGTA
Found at i:1533314 original size:13 final size:13
Alignment explanation
Indices: 1533267--1533296 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1533257 GTAAACCCAG
1533267 AATGTATCGATAC
1 AATGTATCGATAC
1533280 AATGTATCGATAC
1 AATGTATCGATAC
1533293 AATG
1 AATG
1533297 AACAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1534418 original size:34 final size:34
Alignment explanation
Indices: 1534375--1534442 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
1534365 CATATTAATC
1534375 TTGGATAGTATTTTTACTAAAATCCTCATTGAAT
1 TTGGATAGTATTTTTACTAAAATCCTCATTGAAT
*
1534409 TTGGATAGTATTTTTACTAAAATCCTTATTGAAT
1 TTGGATAGTATTTTTACTAAAATCCTCATTGAAT
1534443 AGGATATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (34 bp):
TTGGATAGTATTTTTACTAAAATCCTCATTGAAT
Found at i:1535084 original size:34 final size:34
Alignment explanation
Indices: 1535046--1535114 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
1535036 GCATATTAAT
1535046 TTTGGATAGTATTTTTACTAAAATCCTTATTGAA
1 TTTGGATAGTATTTTTACTAAAATCCTTATTGAA
1535080 TTTGGATAGTATTTTTACTAAAATCCTTATTGAA
1 TTTGGATAGTATTTTTACTAAAATCCTTATTGAA
1535114 T
1 T
1535115 AGGATTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.48
Consensus pattern (34 bp):
TTTGGATAGTATTTTTACTAAAATCCTTATTGAA
Found at i:1535807 original size:29 final size:29
Alignment explanation
Indices: 1535751--1535813 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
1535741 AATGAAATTC
** *
1535751 AATTTCATAAATAATTTTGATTTGATGCG
1 AATTTCATAAATAATTTTGATTCAATGCA
*
1535780 AATTT-ATAAATATTTTTGAATTCAATGCA
1 AATTTCATAAATAATTTTG-ATTCAATGCA
1535809 AATTT
1 AATTT
1535814 TCTTTTTGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 12 0.41
29 17 0.59
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (29 bp):
AATTTCATAAATAATTTTGATTCAATGCA
Found at i:1542323 original size:28 final size:27
Alignment explanation
Indices: 1542283--1542337 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 27
1542273 GTCCTTGAAG
1542283 TTACCTGCAACCATTCAAGGGCAATCTC
1 TTACCTGCAACCATTCAAGGG-AATCTC
1542311 TTACCTGCAACCATTCAAGGGAATCTC
1 TTACCTGCAACCATTCAAGGGAATCTC
1542338 GTACTTGCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (27 bp):
TTACCTGCAACCATTCAAGGGAATCTC
Found at i:1544617 original size:22 final size:22
Alignment explanation
Indices: 1544603--1544644 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1544593 ATTATTTAAG
1544603 TTAAAT-ATATTAATTTTAAAA
1 TTAAATCATATTAATTTTAAAA
*
1544624 TTAAATCATATTAAATTTAAA
1 TTAAATCATATTAATTTTAAA
1544645 TAAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAAATCATATTAATTTTAAAA
Found at i:1547439 original size:18 final size:20
Alignment explanation
Indices: 1547402--1547439 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1547392 AAATTCAATT
1547402 TGGGAAAAGTAATCAGATTGG
1 TGGGAAAAG-AATCAGATTGG
1547423 TGGGAAAA-AATCA-ATTG
1 TGGGAAAAGAATCAGATTG
1547440 ATTTGGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
21 8 0.47
ACGTcount: A:0.42, C:0.05, G:0.29, T:0.24
Consensus pattern (20 bp):
TGGGAAAAGAATCAGATTGG
Found at i:1547861 original size:17 final size:17
Alignment explanation
Indices: 1547835--1547875 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1547825 ATATGATATG
1547835 AATATAATATAAAAAAT
1 AATATAATATAAAAAAT
*
1547852 AATATTATATAAAAAAT
1 AATATAATATAAAAAAT
1547869 AATATAA
1 AATATAA
1547876 ATTTTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AATATAATATAAAAAAT
Found at i:1548020 original size:24 final size:26
Alignment explanation
Indices: 1547975--1548055 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 26
1547965 TCATTTTTAA
1547975 TTTAATAA-TATTATAGATAAATATTATT
1 TTTAA-AATTATTATA-A-AAATATTATT
1548003 TTTAAAATT-TT-TAAAAATATT-TT
1 TTTAAAATTATTATAAAAATATTATT
* *
1548026 TTAAAAAATTATTATAAAAA-ATAATT
1 TT-TAAAATTATTATAAAAATATTATT
1548052 TTTA
1 TTTA
1548056 CTTTTTGAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
23 4 0.09
24 13 0.29
25 6 0.13
26 12 0.27
27 4 0.09
28 6 0.13
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (26 bp):
TTTAAAATTATTATAAAAATATTATT
Found at i:1548160 original size:17 final size:16
Alignment explanation
Indices: 1548128--1548189 Score: 51
Period size: 16 Copynumber: 3.9 Consensus size: 16
1548118 AAATATATAA
*
1548128 ATATAT-TAAAAT-TT
1 ATATATATAAATTATT
1548142 ATATAATATAAATTATT
1 ATAT-ATATAAATTATT
*
1548159 AT-TATACTAAAAT-TT
1 ATATATA-TAAATTATT
1548174 ATATATATATAATTAT
1 ATATATATA-AATTAT
1548190 GATACTAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
14 4 0.11
15 11 0.29
16 18 0.47
17 5 0.13
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATATATAAATTATT
Found at i:1548173 original size:32 final size:32
Alignment explanation
Indices: 1548100--1548189 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
1548090 TTTTAAATTT
* * *
1548100 TAAAATTATAAATAACATAAATATATAAATATAT
1 TAAAATT-TATATAATATAAAT-TATAAATATAC
* *
1548134 TAAAATTTATATAATATAAATTATTATTATAC
1 TAAAATTTATATAATATAAATTATAAATATAC
1548166 TAAAATTTATAT-ATATATAATTAT
1 TAAAATTTATATAATATA-AATTAT
1548190 GATACTAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
31 5 0.10
32 26 0.52
33 12 0.24
34 7 0.14
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (32 bp):
TAAAATTTATATAATATAAATTATAAATATAC
Found at i:1548182 original size:18 final size:17
Alignment explanation
Indices: 1548118--1548185 Score: 63
Period size: 18 Copynumber: 4.1 Consensus size: 17
1548108 TAAATAACAT
* *
1548118 AAATATATAAATATATTA
1 AAATTTATATATATA-TA
1548136 AAATTTATATA-ATAT-
1 AAATTTATATATATATA
1548151 AAA-TTAT-TATTATACTA
1 AAATTTATATA-TATA-TA
1548168 AAATTTATATATATATA
1 AAATTTATATATATATA
1548185 A
1 A
1548186 TTATGATACT
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
13 2 0.05
14 4 0.10
15 6 0.14
16 2 0.05
17 9 0.21
18 17 0.40
19 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTTATATATATATA
Found at i:1548187 original size:15 final size:15
Alignment explanation
Indices: 1548128--1548187 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
1548118 AAATATATAA
1548128 ATATAT-TAAAATTT
1 ATATATATAAAATTT
*
1548142 ATATAATATAAATTATT
1 ATAT-ATATAAAAT-TT
1548159 AT-TATACTAAAATTT
1 ATATATA-TAAAATTT
*
1548174 ATATATATATAATT
1 ATATATATAAAATT
1548188 ATGATACTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 4 0.11
15 15 0.39
16 15 0.39
17 4 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATATATAAAATTT
Found at i:1548189 original size:29 final size:31
Alignment explanation
Indices: 1548129--1548216 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 31
1548119 AATATATAAA
* *
1548129 TATATTAAAATTTATATAATATAAATTATTAT
1 TATACTAAAATTTATATAATAT-AATAATTAT
1548161 TATACTAAAATTTATAT-ATAT-ATAATTAT
1 TATACTAAAATTTATATAATATAATAATTAT
* * *
1548190 GATACTAATATGTTATAATAACATAAT
1 TATACTAAAAT-TTAT-ATAATATAAT
1548217 CAGACTTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
29 16 0.34
30 4 0.09
31 6 0.13
32 19 0.40
33 2 0.04
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (31 bp):
TATACTAAAATTTATATAATATAATAATTAT
Found at i:1548519 original size:23 final size:23
Alignment explanation
Indices: 1548460--1548521 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 23
1548450 AAATTCAATT
*
1548460 TTTTAAAAAAAATTATTATTTAA
1 TTTTAATAAAAATTATTATTTAA
1548483 --TTAATAAAAA-TATT-TTTATA
1 TTTTAATAAAAATTATTATTTA-A
1548503 TTTTAATAAAAATTATTAT
1 TTTTAATAAAAATTATTAT
1548522 ATATAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
19 4 0.12
20 5 0.15
21 9 0.27
22 10 0.30
23 4 0.12
24 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTAATAAAAATTATTATTTAA
Found at i:1548523 original size:20 final size:20
Alignment explanation
Indices: 1548460--1548523 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 20
1548450 AAATTCAATT
*
1548460 TTTTAAAAAAAATTATTAT-
1 TTTTAATAAAAATTATTATA
*
1548479 TTAATTAATAAAAATATTTTTATA
1 TT--TTAAT-AAAA-ATTATTATA
1548503 TTTTAATAAAAATTATTATA
1 TTTTAATAAAAATTATTATA
1548523 T
1 T
1548524 ATAAAAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 2 0.05
20 9 0.24
21 8 0.22
22 9 0.24
23 7 0.19
24 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTAATAAAAATTATTATA
Found at i:1548527 original size:16 final size:18
Alignment explanation
Indices: 1548508--1548547 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1548498 TTATATTTTA
*
1548508 ATAAAAA-TTAT-TATAT
1 ATAAAAATTTATATAAAT
1548524 ATAAAAATTTATATAAAT
1 ATAAAAATTTATATAAAT
1548542 ATAAAA
1 ATAAAA
1548548 TATCTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 4 0.19
18 10 0.48
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAAAATTTATATAAAT
Found at i:1548590 original size:17 final size:18
Alignment explanation
Indices: 1548552--1548592 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1548542 ATAAAATATC
* *
1548552 TTAAAAATATTTATAACA
1 TTAATAATATATATAACA
1548570 -TAATAATATATATAA-A
1 TTAATAATATATATAACA
1548586 TTAATAA
1 TTAATAA
1548593 AAATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAATAATATATATAACA
Found at i:1549217 original size:20 final size:20
Alignment explanation
Indices: 1549165--1549219 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
1549155 AAATTCTTTT
*
1549165 TAAG-TAATATTTTATATAA
1 TAAGATAATATTTTATACAA
* *
1549184 T-TGATAATATTTTTATGCAA
1 TAAGATAATA-TTTTATACAA
1549204 TAAGATAATATTTTAT
1 TAAGATAATATTTTAT
1549220 CTACTACTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 1 0.03
19 6 0.21
20 15 0.52
21 7 0.24
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (20 bp):
TAAGATAATATTTTATACAA
Found at i:1549373 original size:21 final size:21
Alignment explanation
Indices: 1549291--1549392 Score: 101
Period size: 20 Copynumber: 5.1 Consensus size: 21
1549281 CAGCTGAAGG
*
1549291 TAATATTTTATATAATTTTAA
1 TAATATTTTATATAATTATAA
**
1549312 TAA-AAATTAT-T-ATTA-AA
1 TAATATTTTATATAATTATAA
*
1549329 TAATATTTTATATAACTCATAA
1 TAATATTTTATATAA-TTATAA
*
1549351 T-AT-TTTTATGTAA-TATAA
1 TAATATTTTATATAATTATAA
1549369 TAATATTTTATATAATTATAA
1 TAATATTTTATATAATTATAA
1549390 TAA
1 TAA
1549393 AAGTATATCA
Statistics
Matches: 64, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
17 5 0.08
18 13 0.20
19 4 0.06
20 24 0.38
21 15 0.23
22 3 0.05
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (21 bp):
TAATATTTTATATAATTATAA
Found at i:1553458 original size:2 final size:2
Alignment explanation
Indices: 1553451--1553485 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1553441 ATGATCTTTT
* *
1553451 TA TA TA TA TA TA TG TG TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1553486 TTACATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1553832 original size:13 final size:13
Alignment explanation
Indices: 1553814--1553845 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1553804 TAATTAACTC
1553814 AATAAATATCAAT
1 AATAAATATCAAT
*
1553827 AATAAATATTAAT
1 AATAAATATCAAT
1553840 AATAAA
1 AATAAA
1553846 AAATATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (13 bp):
AATAAATATCAAT
Found at i:1557289 original size:20 final size:20
Alignment explanation
Indices: 1557262--1557311 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
1557252 ATGGAGGTGT
*
1557262 TGAACATGTCAT-AAATGCA
1 TGAACATGGCATAAAATGCA
*
1557281 TGAAGCATGGCTTAAAATGCA
1 TGAA-CATGGCATAAAATGCA
1557302 TGAATCATGG
1 TGAA-CATGG
1557312 GCTGTTAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 4 0.15
20 6 0.23
21 16 0.62
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (20 bp):
TGAACATGGCATAAAATGCA
Found at i:1558226 original size:52 final size:52
Alignment explanation
Indices: 1558148--1558348 Score: 332
Period size: 52 Copynumber: 3.9 Consensus size: 52
1558138 CGAAATATGA
*
1558148 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
*
1558200 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
* *
1558252 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
**
1558304 AAATTTGCCTGCATGTATCGATACAAAG-ATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGTAT-AGTGTATCGATACA
1558349 ATGTATCGAT
Statistics
Matches: 141, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
51 2 0.01
52 139 0.99
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
Found at i:1558355 original size:13 final size:13
Alignment explanation
Indices: 1558337--1558361 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1558327 CAAAGATCAG
1558337 TGTATCGATACAA
1 TGTATCGATACAA
1558350 TGTATCGATACA
1 TGTATCGATACA
1558362 TTTAAGTGAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1558439 original size:33 final size:33
Alignment explanation
Indices: 1558402--1558468 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1558392 AGTAGCTTAA
1558402 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1558435 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1558468 A
1 A
1558469 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1558442 original size:13 final size:13
Alignment explanation
Indices: 1558424--1558448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1558414 CAAAAAAATA
1558424 TGTATCGATACAT
1 TGTATCGATACAT
1558437 TGTATCGATACA
1 TGTATCGATACA
1558449 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1560856 original size:20 final size:20
Alignment explanation
Indices: 1560831--1560885 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1560821 CTGCCAAGGA
1560831 AATGTATCGATACATT-ACTC
1 AATGTATCGATACATTGA-TC
1560851 AATGTATCGATACATTGATC
1 AATGTATCGATACATTGATC
**
1560871 TTTGTATCGATACAT
1 AATGTATCGATACAT
1560886 CTAGGAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (20 bp):
AATGTATCGATACATTGATC
Found at i:1563840 original size:22 final size:23
Alignment explanation
Indices: 1563806--1563850 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1563796 TCGAAAAAAA
*
1563806 AAAAAAAAGAAAG-GGGCTTTCC
1 AAAAAAAACAAAGTGGGCTTTCC
* *
1563828 AAAAAAACCAAAGTGGGTTTTCC
1 AAAAAAAACAAAGTGGGCTTTCC
1563851 GATTGAGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.18
Consensus pattern (23 bp):
AAAAAAAACAAAGTGGGCTTTCC
Found at i:1564257 original size:12 final size:13
Alignment explanation
Indices: 1564205--1564263 Score: 57
Period size: 14 Copynumber: 4.5 Consensus size: 13
1564195 AAATTTAGGT
1564205 AAAAAAGAAAGAAG
1 AAAAAAGAAA-AAG
* * * *
1564219 GAAGATGAAGAAG
1 AAAAAAGAAAAAG
1564232 AAAGAAAGAAAAAG
1 AAA-AAAGAAAAAG
1564246 AAAAAA-AAAAAG
1 AAAAAAGAAAAAG
1564258 AAAAAA
1 AAAAAA
1564264 TATGAAATGG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
12 12 0.33
13 8 0.22
14 16 0.44
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:1572077 original size:30 final size:31
Alignment explanation
Indices: 1572037--1572094 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
1572027 GTACTGTGAC
*
1572037 CTTTTCAAAGTCCACGACTCAGTGGCATTTT
1 CTTTTCAAAGTCCACAACTCAGTGGCATTTT
*
1572068 CTTTT-AAAGTCCACAACTCCGTGGCAT
1 CTTTTCAAAGTCCACAACTCAGTGGCAT
1572095 CCTTTTAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.33
Consensus pattern (31 bp):
CTTTTCAAAGTCCACAACTCAGTGGCATTTT
Found at i:1572129 original size:46 final size:46
Alignment explanation
Indices: 1572062--1572150 Score: 169
Period size: 46 Copynumber: 1.9 Consensus size: 46
1572052 GACTCAGTGG
*
1572062 CATTTTCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTTCA
1 CATTTTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTTCA
1572108 CATTTTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGT
1 CATTTTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGT
1572151 CCCCAACTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.38
Consensus pattern (46 bp):
CATTTTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTTCA
Found at i:1572157 original size:27 final size:27
Alignment explanation
Indices: 1572114--1572554 Score: 702
Period size: 27 Copynumber: 16.1 Consensus size: 27
1572104 TTCACATTTT
1572114 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
1572142 CTTTTAAGTCCCCAACTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* **
1572169 CTTTCAAGTCCACAACTCCGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1572196 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1572223 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
1572251 TTTTTAAGTCCACAACTCCGTGGCCCC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1572278 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1572305 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1572332 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1572360 CTTTTAAGTCCACAACTCCGTGGCCCC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1572387 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
1572415 CTTTTAAGTCCACAGCTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1572442 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
1572470 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1572497 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
1572524 CTTTTAAGTCCACAAGTCAGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1572551 CTTT
1 CTTT
1572555 CAAAGCCCAC
Statistics
Matches: 382, Mismatches: 27, Indels: 9
0.91 0.06 0.02
Matches are distributed among these distances:
27 275 0.72
28 107 0.28
ACGTcount: A:0.21, C:0.35, G:0.15, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1572280 original size:55 final size:55
Alignment explanation
Indices: 1572114--1572578 Score: 722
Period size: 55 Copynumber: 8.5 Consensus size: 55
1572104 TTCACATTTT
* *
1572114 CTTTTAAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCCCAACTTCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
* * *
1572169 CTTTCAAGTCCACAACTCCGTGGCAT-TCTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
* *
1572223 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGCCCC
1 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
*
1572278 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
*
1572332 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCCCC
1 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
* *
1572387 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAGCTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
1572442 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
* * *
1572497 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAAGTCAGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
* * * *
1572551 CTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTT-TAAGTCCACAACTCCGTGGCATC
1572579 TTTTCAAAGT
Statistics
Matches: 378, Mismatches: 27, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
54 150 0.40
55 227 0.60
56 1 0.00
ACGTcount: A:0.22, C:0.35, G:0.15, T:0.28
Consensus pattern (55 bp):
CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1572282 original size:82 final size:82
Alignment explanation
Indices: 1572114--1572578 Score: 711
Period size: 82 Copynumber: 5.7 Consensus size: 82
1572104 TTCACATTTT
* * *
1572114 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCCCAACTTCGTGGCA-CCCTTTCAAGT
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGT
**
1572178 CCACAACTCCGTGGCATT
65 CCACAACTCCGTGGCACC
* *
1572196 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTC
*
1572261 CACAACTCCGTGGCCCC
66 CACAACTCCGTGGCACC
1572278 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCAT-CCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTC
1572342 CACAACTCCGTGGCATCC
66 CACAACTCCGTGGCA-CC
*
1572360 CTTTTAAGTCCACAACTCCGTGGCCCCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTC
* *
1572425 CACAGCTCCGTGGCATC
66 CACAACTCCGTGGCACC
1572442 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGT
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGT
1572506 CCACAACTCCGTGGCACC
65 CCACAACTCCGTGGCACC
* * * * * * *
1572524 CTTTTAAGTCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTT-TAAGTCCACAACTCCGTGGCATC
1572579 TTTTCAAAGT
Statistics
Matches: 353, Mismatches: 24, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
81 73 0.21
82 227 0.64
83 53 0.15
ACGTcount: A:0.22, C:0.35, G:0.15, T:0.28
Consensus pattern (82 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTC
CACAACTCCGTGGCACC
Found at i:1572740 original size:32 final size:32
Alignment explanation
Indices: 1572534--1575333 Score: 3834
Period size: 32 Copynumber: 90.8 Consensus size: 32
1572524 CTTTTAAGTC
* *
1572534 CACAAGTCAGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * * *
1572562 CACAAGTCAGTGGC-A-TCTTTTCAAAGTCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1572592 CACAAGTTGGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1572620 CACAAGTCAGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1572648 CACAAGTCGGTGGCAATCTATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
1572678 CACAAGTTAGTGGC-A-TCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1572708 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1572740 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1572772 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1572804 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1572836 CACAAGTCGGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1572867 CATAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1572899 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1572931 CACAAGTCGGTGGCAACCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * * *
1572961 CACAAGTCAGTGGC-A-TCTTTTCAAAGTCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1572991 CACAAGTTGGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1573019 CACAAGTCAGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1573047 CACAAGTCGGTGGCAATCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
1573077 CACAAGTTAGTGGC-A-TCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1573107 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1573139 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1573171 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1573203 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1573235 CACAAGTCGGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1573266 CATAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1573298 CACAAGTCGGTGGCAACCCATTTCAAAGTCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1573330 CACAAGTTGGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1573358 CACAAGTCAGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1573386 CACAAGTCGGTGGCAATCTATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
1573416 CACAAGTTAGTGGC-A-TCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1573446 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1573478 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1573510 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1573542 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1573574 CACAAGTCGGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1573605 CATAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1573637 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1573669 CACAAGTCGGTGGCAACCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * * *
1573699 CACAAGTCAGTGGC-A-TCTTTTCAAAGTCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1573729 CACAAGTTGGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1573757 CACAAGTCAGTGGC-ATCC-TTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1573787 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1573819 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1573851 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1573883 CACAAGTCGGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1573914 CATAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1573946 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1573978 CACAAGTCGGTGGCAACCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * * *
1574008 CACAAGTCAGTGGC-A-TCTTTTCAAAGTCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1574038 CACAAGTTGGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1574066 CACAAGTCAGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1574094 CACAAGTCGGTGGCAATCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
1574124 CACAAGTTAGTGGC-A-TCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1574154 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1574186 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1574218 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1574250 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1574282 CACAAGTCGGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1574313 CATAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1574345 CACAAGTCGGTGGCAACCCATTTCAAAGTCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1574377 CACAAGTTGGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1574405 CACAAGTCAGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1574433 CACAAGTCGGTGGCAATCTATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
1574463 CACAAGTTAGTGGC-A-TCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1574493 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1574525 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1574557 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1574589 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1574621 CACAAGTCGGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1574652 CATAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1574684 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1574716 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1574748 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1574780 CACAAGTCGGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1574811 CATAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1574843 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1574875 CACAAGTCGGTGGCAACCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * * *
1574905 CACAAGTCAGTGGC-A-TCTTTTCAAAGTCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1574935 CACAAGTTGGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1574963 CACAAGTCAGTGGC-ATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1574991 CACAAGTCGGTGGCAATCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
1575021 CACAAGTTAGTGGC-A-TCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1575051 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1575083 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1575115 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1575147 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1575179 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1575211 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1575243 CACAAGTCGGTGGCGACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1575275 CACAAGTCGGGGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** ** *
1575307 TGCAAGTTAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
1575334 TCACCATTTT
Statistics
Matches: 2548, Mismatches: 161, Indels: 122
0.90 0.06 0.04
Matches are distributed among these distances:
27 1 0.00
28 368 0.14
29 69 0.03
30 390 0.15
31 238 0.09
32 1482 0.58
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.18
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:1573295 original size:399 final size:405
Alignment explanation
Indices: 1572534--1575333 Score: 4074
Period size: 399 Copynumber: 7.0 Consensus size: 405
1572524 CTTTTAAGTC
** * *
1572534 CACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGTCCACACAAGT
1 CACAAGTTGGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAAGT
* *
1572599 TGGTGGC-ATCC-TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAG-CC-CACAAGTCGGTG
66 CGGTGGCAATCCATTTCAAAGCCCACAAGTCAGTGGCATCCTTCCAAAGCCCACACAAGTCGGTG
* * ** * *
1572660 GCAATCTATTTCAAAG-CC-CACAAGTTAGTGGCA-TCATTCCAAAGCCCACACAAGTCGGTGGC
131 GCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACCCATTTCAAAGCCCACACAAGTCGGTGGC
*
1572722 AACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCA
196 AACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCA
*
1572787 ACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGC-A
261 ACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAA
* *
1572851 CCCATTTCAAAGCCCACATAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAAC
326 CCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAAC
*
1572916 CCATTTCAAAGCCCA
391 CCATTTCAAAGTCCA
* * * *
1572931 CACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGTCCACACAA
1 CACAAGTTGGTGGC-ATCC-TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAA
* *
1572996 GTTGGTGGC-ATCC-TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAG-CC-CACAAGTCGG
64 GTCGGTGGCAATCCATTTCAAAGCCCACAAGTCAGTGGCATCCTTCCAAAGCCCACACAAGTCGG
* ** * *
1573057 TGGCAATCCATTTCAAAG-CC-CACAAGTTAGTGGCA-TCATTCCAAAGCCCACACAAGTCGGTG
129 TGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACCCATTTCAAAGCCCACACAAGTCGGTG
*
1573119 GCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGG
194 GCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGG
*
1573184 CAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGC
259 CAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGC
*
1573249 -ACCCATTTCAAAGCCCACATAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCA
324 AACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCA
1573313 ACCCATTTCAAAGTCCA
389 ACCCATTTCAAAGTCCA
1573330 CACAAGTTGGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAG-CC-CACAAGT
1 CACAAGTTGGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAAGT
* * *
1573393 CGGTGGCAATCTATTTCAAAGCCCACAAGTTAGTGGCATCATTCCAAAGCCCACACAAGTCGGTG
66 CGGTGGCAATCCATTTCAAAGCCCACAAGTCAGTGGCATCCTTCCAAAGCCCACACAAGTCGGTG
1573458 GCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGG
131 GCAACCCATTTCAAAGCCCACACAAGTCGGTGGC-ACCCATTTCAAAGCCCACACAAGTCGGTGG
1573523 CAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGC
195 CAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGC
* *
1573588 -ACCCATTTCAAAGCCCACATAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCA
260 AACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCA
*
1573652 ACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAG-CC-CACAAGTCAGTGGC-A
325 ACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAA
* *
1573714 -TCTTTTCAAAGTCCA
390 CCCATTTCAAAGTCCA
1573729 CACAAGTTGGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAAGT
1 CACAAGTTGGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAAGT
* * *
1573794 CGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTC
66 CGGTGGCAATCCATTTCAAAG-CC-CACAAGTCAGTGGC-ATCC-TTCCAAAGCCCACACAAGTC
*
1573859 GGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACCCATTTCAAAGCCCACATAAGTCGG
127 GGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACCCATTTCAAAGCCCACACAAGTCGG
1573924 TGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGT
192 TGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGT
* * * * *
1573989 GGCAACCCATTTCAAAG-CC-CACAAGTCAGTGGC-A-TCTTTTCAAAGTCCACACAAGTTGGTG
257 GGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTG
* * *
1574050 GC-ATCC-TTTCAAAG-CC-CACAAGTCAGTGGC-ATCC-TTTCAAAG-CC-CACAAGTCGGTGG
322 GCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGG
*
1574107 CAATCCATTTCAAAG-CC-
387 CAACCCATTTCAAAGTCCA
* * * * *
1574124 CACAAGTTAGTGGCATCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACAC
1 CACAAGTTGGTGGCATCCTTTCAAAG-CC-CACAAGTCAGTGGC-ATCC-TTTCAAAGCCCACAC
* * *
1574189 AAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCCACACA
62 AAGTCGGTGGCAATCCATTTCAAAG-CC-CACAAGTCAGTGGC-ATCC-TTCCAAAGCCCACACA
*
1574254 AGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACCCATTTCAAAGCCCACATAAG
123 AGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACCCATTTCAAAGCCCACACAAG
* *
1574319 TCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGTCCACACAAGT
188 TCGGTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGT
* * * *
1574384 TGGTGGC-ATCC-TTTCAAAG-CC-CACAAGTCAGTGGC-ATCC-TTTCAAAG-CC-CACAAGTC
253 CGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTC
* * ** * *
1574441 GGTGGCAATCTATTTCAAAG-CC-CACAAGTTAGTGGC-A-TCATTCCAAAGCCCACACAAGTCG
318 GGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCG
*
1574502 GTGGCAACCCATTTCAAAGCCCA
383 GTGGCAACCCATTTCAAAGTCCA
* * * * *
1574525 CACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCCAC
1 CACAAGTTGGTGGC-ATCC-TTTCAAAG-CC-CACAAGTCAGTGGC-ATCC-TTTCAAAGCCCAC
* * * * *
1574590 ACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACCCATTTCAAAGCCCACAT
60 ACAAGTCGGTGGCAATCCATTTCAAAG-CC-CACAAGTCAGTGGCATCC-TTCCAAAGCCCACAC
1574655 AAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACA
122 AAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGC-ACCCATTTCAAAGCCCACACA
1574720 AGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAA
186 AGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAA
* *
1574785 GTCGGTGGC-ACCCATTTCAAAGCCCACATAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAG
251 GTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAG
1574849 TCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAG-CC-CACAAGT
316 TCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGT
* * *
1574912 CAGTGGC-A-TCTTTTCAAAGTCCA
381 CGGTGGCAACCCATTTCAAAGTCCA
1574935 CACAAGTTGGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAG-CC-CACAAGT
1 CACAAGTTGGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAAGT
* *
1574998 CGGTGGCAATCCATTTCAAAGCCCACAAGTTAGTGGCATCATTCCAAAGCCCACACAAGTCGGTG
66 CGGTGGCAATCCATTTCAAAGCCCACAAGTCAGTGGCATCCTTCCAAAGCCCACACAAGTCGGTG
1575063 GCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGG
131 GCAACCCATTTCAAAGCCCACACAAGTCGGTGGC-ACCCATTTCAAAGCCCACACAAGTCGGTGG
1575128 CAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGC
195 CAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGC
*
1575193 AACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCG
260 AACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCA
* * * ** **
1575258 ACCCTTTTCAAAGCCCACACAAGTCGGGGGCAACCCATTTAAAAGCCCATGCAAGTTAGTGGCAA
325 ACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAA
*
1575323 CCCTTTTCAAA
390 CCCATTTCAAA
1575334 TCACCATTTT
Statistics
Matches: 2241, Mismatches: 111, Indels: 95
0.92 0.05 0.04
Matches are distributed among these distances:
395 72 0.03
396 19 0.01
397 180 0.08
398 19 0.01
399 884 0.39
400 127 0.06
401 91 0.04
402 167 0.07
403 343 0.15
404 122 0.05
405 76 0.03
406 25 0.01
407 5 0.00
408 15 0.01
409 5 0.00
410 51 0.02
411 3 0.00
412 25 0.01
413 3 0.00
414 9 0.00
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.18
Consensus pattern (405 bp):
CACAAGTTGGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAAGT
CGGTGGCAATCCATTTCAAAGCCCACAAGTCAGTGGCATCCTTCCAAAGCCCACACAAGTCGGTG
GCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACCCATTTCAAAGCCCACACAAGTCGGTGGC
AACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCA
ACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAA
CCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAAC
CCATTTCAAAGTCCA
Found at i:1575417 original size:45 final size:47
Alignment explanation
Indices: 1575366--1575484 Score: 127
Period size: 49 Copynumber: 2.5 Consensus size: 47
1575356 GTCCGATATT
*
1575366 GCTGGCCTTGAATCAGCATATTGG-CACCTTT-CTAAGCCCAATGTC
1 GCTGGCCTTGAATCAGCACATTGGCCACCTTTCCTAAGCCCAATGTC
* * * *
1575411 GCTGGCCTTGAGTCAGCACATTGGTCCACTTTTCCCTTAGCCCGATGTC
1 GCTGGCCTTGAATCAGCACATTGG-CCACCTTT-CCTAAGCCCAATGTC
* *
1575460 GCTGACCTTGAAAT-GGCACATTGGC
1 GCTGGCCTTG-AATCAGCACATTGGC
1575485 ATTCCTCTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
45 22 0.36
47 6 0.10
48 1 0.02
49 30 0.49
50 2 0.03
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.29
Consensus pattern (47 bp):
GCTGGCCTTGAATCAGCACATTGGCCACCTTTCCTAAGCCCAATGTC
Found at i:1576207 original size:22 final size:23
Alignment explanation
Indices: 1576173--1576217 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1576163 GATCGAAAAA
*
1576173 AAAAAAAAGAAAG-GGGCTTTCC
1 AAAAAAAACAAAGTGGGCTTTCC
* *
1576195 AAAAAAACCAAAGTGGGTTTTCC
1 AAAAAAAACAAAGTGGGCTTTCC
1576218 GATTGAGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.18
Consensus pattern (23 bp):
AAAAAAAACAAAGTGGGCTTTCC
Found at i:1576613 original size:17 final size:17
Alignment explanation
Indices: 1576593--1576628 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1576583 AAGGAAGATG
* *
1576593 AAGAAGAAAGAAAGAAA
1 AAGAAAAAAAAAAGAAA
1576610 AAGAAAAAAAAAAGAAA
1 AAGAAAAAAAAAAGAAA
1576627 AA
1 AA
1576629 ATATGAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:1582806 original size:21 final size:21
Alignment explanation
Indices: 1582782--1582837 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
1582772 TATTTTATTT
1582782 TTATTTTTATTTATAATATAA
1 TTATTTTTATTTATAATATAA
* *
1582803 TTATTATTATTTAT-ATTTAA
1 TTATTTTTATTTATAATATAA
*
1582823 TTA-TTTTATATATAA
1 TTATTTTTATTTATAA
1582838 AAGTAGGGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 8 0.27
20 9 0.30
21 13 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTTTTATTTATAATATAA
Found at i:1582827 original size:35 final size:31
Alignment explanation
Indices: 1582762--1582837 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 31
1582752 CATAATATAA
* *
1582762 TTAATATTATTATTTTATTTTTATTTTTATT
1 TTAATATAATTATTTTATTTATATTTTTATT
1582793 TATAATATAATTATTATTATTTATATTTAATTATT
1 T-TAATATAATTATT-TTATTTATATTT--TTATT
1582828 TTATATATAA
1 TTA-ATATAA
1582838 AAGTAGGGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
31 1 0.03
32 12 0.32
33 11 0.29
34 2 0.05
35 12 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (31 bp):
TTAATATAATTATTTTATTTATATTTTTATT
Found at i:1582827 original size:41 final size:35
Alignment explanation
Indices: 1582756--1582837 Score: 101
Period size: 38 Copynumber: 2.2 Consensus size: 35
1582746 TTTGATCATA
1582756 ATATAATTAATATTATTATTTTATTTTTATTTTTAT
1 ATATAATTAATATTATTATTTTATTTTTA-TTTTAT
*
1582792 TTATAATATAATTATTATTATTTATATTTAATTATTTTAT
1 ATATAAT-TAA-TATTATTATTT-TATTT--TTATTTTAT
1582832 ATATAA
1 ATATAA
1582838 AAGTAGGGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
36 6 0.15
37 3 0.08
38 11 0.28
39 5 0.13
40 11 0.28
41 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (35 bp):
ATATAATTAATATTATTATTTTATTTTTATTTTAT
Found at i:1582938 original size:24 final size:24
Alignment explanation
Indices: 1582911--1582964 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1582901 GTTGAATTGT
*
1582911 TTTGTCTTGTCAGTCACGCTGTTC
1 TTTGTCTTGTCACTCACGCTGTTC
*
1582935 TTTGTCTTGTCACTCGCGCTGTTC
1 TTTGTCTTGTCACTCACGCTGTTC
1582959 TGTTGT
1 T-TTGT
1582965 AGATGTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.06, C:0.24, G:0.22, T:0.48
Consensus pattern (24 bp):
TTTGTCTTGTCACTCACGCTGTTC
Found at i:1586241 original size:2 final size:2
Alignment explanation
Indices: 1586234--1586265 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1586224 GAAGTACTTC
1586234 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1586266 TACCCAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1593690 original size:21 final size:21
Alignment explanation
Indices: 1593666--1593706 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1593656 AGACAAATAG
*
1593666 TACTCCACAACAGGTGGAGTA
1 TACTCCAAAACAGGTGGAGTA
1593687 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1593707 TTCAACAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTA
Found at i:1595609 original size:27 final size:27
Alignment explanation
Indices: 1595579--1595648 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
1595569 GTCAACAATG
1595579 TTTGTCAAAAATTGTGGTT-ATTTTATA
1 TTTGTCAAAAATTGTGGTTCATTTT-TA
* *
1595606 TTTGTCAAAAA-TGATGGTTCCTTTTTT
1 TTTGTCAAAAATTG-TGGTTCATTTTTA
1595633 TTTGTCAAAAATTGTG
1 TTTGTCAAAAATTGTG
1595649 ACTTGTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 2 0.05
27 30 0.79
28 6 0.16
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.50
Consensus pattern (27 bp):
TTTGTCAAAAATTGTGGTTCATTTTTA
Found at i:1596330 original size:19 final size:19
Alignment explanation
Indices: 1596273--1596331 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
1596263 AGTATTAAAT
*
1596273 ATAATA-AATATTTTAAAAA
1 ATAATATAATA-TTTAATAA
*
1596292 ATAATAT-ATATTTATCTAA
1 ATAATATAATATTTA-ATAA
*
1596311 ATAGTATAATATTTAATAA
1 ATAATATAATATTTAATAA
1596330 AT
1 AT
1596332 TAAAAATTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 4 0.12
19 22 0.67
20 7 0.21
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
ATAATATAATATTTAATAA
Found at i:1598297 original size:28 final size:26
Alignment explanation
Indices: 1598236--1598310 Score: 98
Period size: 28 Copynumber: 2.8 Consensus size: 26
1598226 GTAGAATGTT
*
1598236 ATTTATTT-AAATTTGAATTTATTTA
1 ATTTATTTAAAATTTAAATTTATTTA
1598261 ATTTATTTAAAATTTAAATTTATTTTTA
1 ATTTATTTAAAATTTAAATTTA--TTTA
**
1598289 ATTTATTTAGTATTTAAATTTA
1 ATTTATTTAAAATTTAAATTTA
1598311 CATTCGATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
25 8 0.18
26 12 0.27
28 24 0.55
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (26 bp):
ATTTATTTAAAATTTAAATTTATTTA
Found at i:1598308 original size:17 final size:16
Alignment explanation
Indices: 1598236--1598310 Score: 53
Period size: 17 Copynumber: 4.3 Consensus size: 16
1598226 GTAGAATGTT
* *
1598236 ATTTATTTAAATTTGA
1 ATTTATTTATATTTAA
1598252 ATTTATTTAATTTATTTAAA
1 ATTTATTT-A--TATTT-AA
*
1598272 ATTTAAATTTAT-TTTTA
1 ATTT--ATTTATATTTAA
1598289 ATTTATTTAGTATTTAA
1 ATTTATTTA-TATTTAA
1598306 ATTTA
1 ATTTA
1598311 CATTCGATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
15 5 0.11
16 9 0.19
17 15 0.32
18 3 0.06
19 5 0.11
20 5 0.11
21 1 0.02
22 4 0.09
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
ATTTATTTATATTTAA
Found at i:1598320 original size:28 final size:28
Alignment explanation
Indices: 1598236--1598321 Score: 79
Period size: 28 Copynumber: 3.2 Consensus size: 28
1598226 GTAGAATGTT
* *
1598236 ATTTATTT-AAATTTGAATTT--ATTTA
1 ATTTATTTAAAATTTAAATTTACATTCA
** *
1598261 ATTTATTTAAAATTTAAATTTATTTTTA
1 ATTTATTTAAAATTTAAATTTACATTCA
** *
1598289 ATTTATTTAGTATTTAAATTTACATTCG
1 ATTTATTTAAAATTTAAATTTACATTCA
1598317 ATTTA
1 ATTTA
1598322 ATGGGTAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
25 8 0.16
26 11 0.22
28 31 0.62
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.58
Consensus pattern (28 bp):
ATTTATTTAAAATTTAAATTTACATTCA
Found at i:1598358 original size:17 final size:17
Alignment explanation
Indices: 1598331--1598375 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1598321 AATGGGTAAT
*
1598331 ATTTATCAAATATCTAA
1 ATTTATTAAATATCTAA
* *
1598348 ATTTTTTAAATATTTAA
1 ATTTATTAAATATCTAA
1598365 ATTTATTAAAT
1 ATTTATTAAAT
1598376 TAAATTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTATTAAATATCTAA
Found at i:1601640 original size:24 final size:22
Alignment explanation
Indices: 1601613--1601667 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 22
1601603 AAAATAATAT
1601613 AATAAACTCAACATAATATATTTA
1 AATAAA-TCAACATAATATA-TTA
*
1601637 AATACAATTAACATAATATATTA
1 AATA-AATCAACATAATATATTA
1601660 ATATAAAT
1 A-ATAAAT
1601668 ATTACATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 7 0.25
24 19 0.68
25 2 0.07
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (22 bp):
AATAAATCAACATAATATATTA
Found at i:1603024 original size:25 final size:25
Alignment explanation
Indices: 1602996--1603048 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1602986 TTTTTAAAAT
* *
1602996 TTTAATTTTTAATTTTTTTCTATTA
1 TTTAATTTTTAATATTTTTCAATTA
* *
1603021 TTTAATTTTTTATATTTTTGAATTA
1 TTTAATTTTTAATATTTTTCAATTA
1603046 TTT
1 TTT
1603049 TCAAATGACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (25 bp):
TTTAATTTTTAATATTTTTCAATTA
Found at i:1603031 original size:17 final size:16
Alignment explanation
Indices: 1603000--1603050 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 16
1602990 TAAAATTTTA
1603000 ATTTTTAATTTTTTTCT
1 ATTTTTAA-TTTTTTCT
*
1603017 ATTATTTAATTTTTTAT
1 ATT-TTTAATTTTTTCT
1603034 ATTTTTGAATTATTTTC
1 ATTTTT-AATT-TTTTC
1603051 AAATGACATG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 3 0.10
17 17 0.59
18 9 0.31
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (16 bp):
ATTTTTAATTTTTTCT
Found at i:1604781 original size:16 final size:17
Alignment explanation
Indices: 1604743--1604782 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1604733 TGAATTACAA
1604743 TTAAATTTGTTTAAGTG
1 TTAAATTTGTTTAAGTG
*
1604760 TTAAATTTGTTTTAGT-
1 TTAAATTTGTTTAAGTG
1604776 TTAAATT
1 TTAAATT
1604783 AAATTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (17 bp):
TTAAATTTGTTTAAGTG
Found at i:1604985 original size:14 final size:14
Alignment explanation
Indices: 1604966--1604992 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1604956 CCATGTTAAC
1604966 TATATATAAATAAA
1 TATATATAAATAAA
1604980 TATATATAAATAA
1 TATATATAAATAA
1604993 GATTAGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TATATATAAATAAA
Found at i:1608365 original size:42 final size:40
Alignment explanation
Indices: 1608279--1608367 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 40
1608269 GGTATAACTA
* *
1608279 AAATTTTAAACTAACAAATATATTTATTGATAGCTAAACAT
1 AAATTTTAAACTAACAAATATATTTATTGATA-CAAAAAAT
*
1608320 AAATTATTAAATTAACAAATATATTTATTGATTA-AAAAAATT
1 AAATT-TTAAACTAACAAATATATTTATTGA-TACAAAAAA-T
1608362 AAATTT
1 AAATTT
1608368 GAAAATTAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
41 10 0.24
42 30 0.71
43 2 0.05
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (40 bp):
AAATTTTAAACTAACAAATATATTTATTGATACAAAAAAT
Found at i:1608374 original size:42 final size:41
Alignment explanation
Indices: 1608290--1608376 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 41
1608280 AATTTTAAAC
* * *
1608290 TAACAAATATATTTATTGATAGCTAAACATAAATTATTAAAT
1 TAACAAATATATTTATTGATA-CAAAAAATAAATTATAAAAT
1608332 TAACAAATATATTTATTGATTA-AAAAAATTAAATT-TGAAAAT
1 TAACAAATATATTTATTGA-TACAAAAAA-TAAATTAT-AAAAT
1608374 TAA
1 TAA
1608377 ATTAAATCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
41 5 0.13
42 32 0.82
43 2 0.05
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (41 bp):
TAACAAATATATTTATTGATACAAAAAATAAATTATAAAAT
Found at i:1609427 original size:17 final size:17
Alignment explanation
Indices: 1609407--1609440 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1609397 TCAAATAAAT
1609407 AAATATAAAAAATTTAA
1 AAATATAAAAAATTTAA
*
1609424 AAATATAATAAATTTAA
1 AAATATAAAAAATTTAA
1609441 TTGATTATGT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATATAAAAAATTTAA
Found at i:1609515 original size:20 final size:22
Alignment explanation
Indices: 1609485--1609525 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1609475 AATTTATGTT
*
1609485 TAAATGTAATT-CTAAAAAAAA
1 TAAATGTAATTAATAAAAAAAA
1609506 TAAA-GTAATTAATAAAAAAA
1 TAAATGTAATTAATAAAAAAA
1609526 TTACAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (22 bp):
TAAATGTAATTAATAAAAAAAA
Found at i:1609991 original size:21 final size:20
Alignment explanation
Indices: 1609964--1610013 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
1609954 AAAATTTTGA
1609964 ATTCAAAGT-GTTAAAATTAAT
1 ATTCAAA-TAGTT-AAATTAAT
*
1609985 TTTCAAATCAGTTAAATTAAT
1 ATTCAAAT-AGTTAAATTAAT
1610006 ATTCAAAT
1 ATTCAAAT
1610014 GAGATTTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.04
21 21 0.84
22 3 0.12
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (20 bp):
ATTCAAATAGTTAAATTAAT
Found at i:1610533 original size:21 final size:21
Alignment explanation
Indices: 1610483--1610601 Score: 81
Period size: 21 Copynumber: 5.9 Consensus size: 21
1610473 AATAATAAAC
*
1610483 AATTAAATATATTATATTTTT
1 AATTAAATATATTATATTTAT
*
1610504 AATTTAATATATTATATATTAT
1 AATTAAATATATTATAT-TTAT
*
1610526 -ATTAAATATA-AATATTTA-
1 AATTAAATATATTATATTTAT
*
1610544 ACGATTATAT-TA-T-TATTTAT
1 A--ATTAAATATATTATATTTAT
* * *
1610564 AAATAAATATATTAAAATTAT
1 AATTAAATATATTATATTTAT
* *
1610585 ATTTAAAAATA-TATATT
1 AATTAAATATATTATATT
1610602 ATACTGTGAT
Statistics
Matches: 75, Mismatches: 15, Indels: 17
0.70 0.14 0.16
Matches are distributed among these distances:
18 5 0.07
19 11 0.15
20 12 0.16
21 44 0.59
22 3 0.04
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (21 bp):
AATTAAATATATTATATTTAT
Found at i:1610573 original size:60 final size:59
Alignment explanation
Indices: 1610490--1610601 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 59
1610480 AACAATTAAA
* * * * *
1610490 TATATTATATTTTTAATTTAATATATTATATATTATA-TTAAATATAAATATTTAACGAT
1 TATATTATATTTATAAATAAATATATTA-AAATTATATTTAAAAATAAATATTTAACGAT
*
1610549 TATATTATTATTTATAAATAAATATATTAAAATTATATTTAAAAATATATATT
1 TATATTA-TATTTATAAATAAATATATTAAAATTATATTTAAAAATAAATATT
1610602 ATACTGTGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
59 14 0.31
60 31 0.69
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (59 bp):
TATATTATATTTATAAATAAATATATTAAAATTATATTTAAAAATAAATATTTAACGAT
Found at i:1610586 original size:13 final size:13
Alignment explanation
Indices: 1610570--1610602 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1610560 TTATAAATAA
*
1610570 ATATATTAAAATT
1 ATATATTAAAAAT
1610583 ATAT-TTAAAAAT
1 ATATATTAAAAAT
1610595 ATATATTA
1 ATATATTA
1610603 TACTGTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATATATTAAAAAT
Found at i:1610587 original size:33 final size:34
Alignment explanation
Indices: 1610505--1610587 Score: 93
Period size: 33 Copynumber: 2.5 Consensus size: 34
1610495 TATATTTTTA
*
1610505 ATTTAATATATTATA-TATTATATTAAATATAAAT
1 ATTTAACA-ATTATATTATTATATTAAATATAAAT
*
1610539 ATTTAACGATTATATTATTAT-TTATAA-ATAAAT
1 ATTTAACAATTATATTATTATATTA-AATATAAAT
1610572 ATATTAA-AATTATATT
1 AT-TTAACAATTATATT
1610588 TAAAAATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 25 0.58
34 18 0.42
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (34 bp):
ATTTAACAATTATATTATTATATTAAATATAAAT
Found at i:1610591 original size:25 final size:25
Alignment explanation
Indices: 1610555--1610602 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
1610545 CGATTATATT
1610555 ATTATTTATAAATAA-ATATATTAAA
1 ATTATTTATAAA-AATATATATTAAA
1610580 ATTATATT-TAAAAATATATATTA
1 ATTAT-TTATAAAAATATATATTA
1610603 TACTGTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 2 0.10
25 17 0.81
26 2 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
ATTATTTATAAAAATATATATTAAA
Found at i:1611149 original size:16 final size:15
Alignment explanation
Indices: 1611128--1611188 Score: 86
Period size: 16 Copynumber: 3.9 Consensus size: 15
1611118 TATTTTATTT
1611128 TAATAAATCAAATATA
1 TAATAAAT-AAATATA
*
1611144 TAATAAATAAATATTC
1 TAATAAATAAATA-TA
1611160 TAATAAATCAAATATA
1 TAATAAAT-AAATATA
1611176 TAATAAATAAATA
1 TAATAAATAAATA
1611189 GTAAAAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
15 10 0.24
16 26 0.63
17 5 0.12
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (15 bp):
TAATAAATAAATATA
Found at i:1611169 original size:32 final size:32
Alignment explanation
Indices: 1611123--1611188 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
1611113 TTTTTTATTT
*
1611123 TATTTTAATAAATCAAATATATAATAAATAAA
1 TATTCTAATAAATCAAATATATAATAAATAAA
1611155 TATTCTAATAAATCAAATATATAATAAATAAA
1 TATTCTAATAAATCAAATATATAATAAATAAA
1611187 TA
1 TA
1611189 GTAAAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (32 bp):
TATTCTAATAAATCAAATATATAATAAATAAA
Found at i:1612903 original size:16 final size:16
Alignment explanation
Indices: 1612868--1612900 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1612858 AAAAATATAA
*
1612868 TTATTTTTATTTTATT
1 TTATTTTTATTATATT
1612884 TTATTTTT-TTATATT
1 TTATTTTTATTATATT
1612899 TT
1 TT
1612901 TATCAACTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (16 bp):
TTATTTTTATTATATT
Found at i:1613769 original size:23 final size:23
Alignment explanation
Indices: 1613743--1613871 Score: 63
Period size: 23 Copynumber: 5.7 Consensus size: 23
1613733 ATTCGTTTAA
1613743 ATTAAATGAAT-TGATTTATAAAC
1 ATTAAATGAATAT-ATTTATAAAC
* *
1613766 ATTAAATAAATATATTTTTAAAC
1 ATTAAATGAATATATTTATAAAC
* * * * *
1613789 ATATAATTGAACATGTTTGTAAATA
1 AT-TAAATGAATATATTTATAAA-C
* *
1613814 ATTAAA--AATATATTCATAAAT
1 ATTAAATGAATATATTTATAAAC
* * *
1613835 AATAAATTAAT-TAATTA-AAA-
1 ATTAAATGAATATATTTATAAAC
* *
1613855 AATAAATAAATATATTT
1 ATTAAATGAATATATTT
1613872 TTTAATTTAA
Statistics
Matches: 81, Mismatches: 19, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
20 10 0.12
21 12 0.15
22 14 0.17
23 24 0.30
24 19 0.23
25 2 0.02
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (23 bp):
ATTAAATGAATATATTTATAAAC
Found at i:1614019 original size:10 final size:10
Alignment explanation
Indices: 1614004--1614037 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1613994 TTTATATTTT
1614004 TAAATAATAA
1 TAAATAATAA
1614014 TAAATAATAA
1 TAAATAATAA
* *
1614024 TTAATAATAT
1 TAAATAATAA
1614034 TAAA
1 TAAA
1614038 AAATTATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
TAAATAATAA
Found at i:1614031 original size:20 final size:20
Alignment explanation
Indices: 1614006--1614051 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1613996 TATATTTTTA
*
1614006 AATAATAATAAATAATAATT
1 AATAATAATAAAAAATAATT
* *
1614026 AATAATATTAAAAAATTATT
1 AATAATAATAAAAAATAATT
1614046 AA-AATA
1 AATAATA
1614052 CGATAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AATAATAATAAAAAATAATT
Found at i:1625698 original size:1 final size:1
Alignment explanation
Indices: 1625692--1625716 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1625682 ATTACTCAGA
1625692 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
1625717 TCTTATTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1628251 original size:16 final size:16
Alignment explanation
Indices: 1628222--1628263 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1628212 ATTTTGGATT
* *
1628222 TTTTCTTTTTAGTATG
1 TTTTCATTTCAGTATG
1628238 TTTTCATTTCAGTATG
1 TTTTCATTTCAGTATG
1628254 TTTTCATTTC
1 TTTTCATTTC
1628264 TTTTGTAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.14, C:0.12, G:0.10, T:0.64
Consensus pattern (16 bp):
TTTTCATTTCAGTATG
Found at i:1632603 original size:29 final size:30
Alignment explanation
Indices: 1632548--1632608 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 30
1632538 AGAAAAAGAA
1632548 AGAAAATACATGAAAGATAGGCATCAGATC
1 AGAAAATACATGAAAGATAGGCATCAGATC
1632578 AGAAAATACATG-AAGATAGGCATCAGATC
1 AGAAAATACATGAAAGATAGGCATCAGATC
1632607 AG
1 AG
1632609 CACTTGGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.49, C:0.13, G:0.21, T:0.16
Consensus pattern (30 bp):
AGAAAATACATGAAAGATAGGCATCAGATC
Found at i:1638368 original size:15 final size:13
Alignment explanation
Indices: 1638346--1638394 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
1638336 AAAAATAGTA
1638346 ATTT-AATAAATT
1 ATTTAAATAAATT
1638358 ATTTCAAAATAAACTT
1 ATTT--AAATAAA-TT
*
1638374 ATTTTAATAAATT
1 ATTTAAATAAATT
1638387 ATTTAAAT
1 ATTTAAAT
1638395 TTTAATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 4 0.13
13 9 0.29
14 6 0.19
15 6 0.19
16 6 0.19
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTAAATAAATT
Found at i:1638410 original size:18 final size:19
Alignment explanation
Indices: 1638374--1638410 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1638364 AAATAAACTT
*
1638374 ATTTTAATAAATTATTTAA
1 ATTTTAATAAATAATTTAA
1638393 ATTTTAAT-AATAATTTAA
1 ATTTTAATAAATAATTTAA
1638411 TTTATTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTTAATAAATAATTTAA
Found at i:1639193 original size:2 final size:2
Alignment explanation
Indices: 1639188--1639221 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1639178 CAAAAGTGTG
1639188 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1639222 TTTTTAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1641720 original size:28 final size:31
Alignment explanation
Indices: 1641663--1641725 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
1641653 CTCGGATTAT
*
1641663 AATTTAATAATAAAAATAATATAT-TTATTTA
1 AATTTAATAATAAAAATAATATATAAT-TTTA
*
1641694 AATTTAATTATAAAAAT-ATATA-AATTTTA
1 AATTTAATAATAAAAATAATATATAATTTTA
1641723 AAT
1 AAT
1641726 CTTTCTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 7 0.24
30 6 0.21
31 16 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
AATTTAATAATAAAAATAATATATAATTTTA
Found at i:1647178 original size:8 final size:9
Alignment explanation
Indices: 1647155--1647180 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1647145 TGTTTCTGCC
1647155 TCTTTTTCT
1 TCTTTTTCT
1647164 TCTTTTTCT
1 TCTTTTTCT
1647173 TCTTTTTC
1 TCTTTTTC
1647181 ATCTCCAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TCTTTTTCT
Found at i:1652566 original size:25 final size:25
Alignment explanation
Indices: 1652532--1652579 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
1652522 CCATGTATTC
1652532 TAGTTCTCTGTGGTTATTCACCCAT
1 TAGTTCTCTGTGGTTATTCACCCAT
1652557 TAGTTCTCTGTGGTTATTCACCC
1 TAGTTCTCTGTGGTTATTCACCC
1652580 TAAACCATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (25 bp):
TAGTTCTCTGTGGTTATTCACCCAT
Found at i:1658643 original size:23 final size:22
Alignment explanation
Indices: 1658601--1658647 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
1658591 TTAAATAAGT
*
1658601 ATATTATTTAATTATTATTTGA
1 ATATTATTTAATTATAATTTGA
1658623 ATATTATCTTAA-TATAAATTTGA
1 ATATTAT-TTAATTAT-AATTTGA
1658646 AT
1 AT
1658648 TAGATAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (22 bp):
ATATTATTTAATTATAATTTGA
Found at i:1663730 original size:4 final size:4
Alignment explanation
Indices: 1663721--1663755 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
1663711 GCATATGAAC
*
1663721 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TATA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
1663756 GTACCTCTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:1668383 original size:20 final size:20
Alignment explanation
Indices: 1668358--1668395 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1668348 TGAAAGAATT
*
1668358 AAAAAAAT-TATTATTTTTA
1 AAAAAAATATTTTATTTTTA
1668377 AAAAAAATATTTTATTTTT
1 AAAAAAATATTTTATTTTT
1668396 TTTTTTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAAAAATATTTTATTTTTA
Found at i:1669251 original size:18 final size:19
Alignment explanation
Indices: 1669199--1669250 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
1669189 ATTTTTAATT
*
1669199 AATA-AAAAATCTCAAATCA
1 AATATAAAAAT-TAAAATCA
* *
1669218 AAT-TTAAATTTAAAATCA
1 AATATAAAAATTAAAATCA
1669236 AATATAAAAATTAAA
1 AATATAAAAATTAAA
1669251 TAAATTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (19 bp):
AATATAAAAATTAAAATCA
Found at i:1669637 original size:1 final size:1
Alignment explanation
Indices: 1669598--1669627 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
1669588 GAGCCAGCAG
*
1669598 CCCCCGCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1669628 AACTACCCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.97, G:0.03, T:0.00
Consensus pattern (1 bp):
C
Found at i:1674420 original size:5 final size:5
Alignment explanation
Indices: 1674410--1674441 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
1674400 ATAAAGAATC
1674410 AATTG AATTG AATTG AATTG AATTG AATTG AA
1 AATTG AATTG AATTG AATTG AATTG AATTG AA
1674442 CTTTCAGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.38
Consensus pattern (5 bp):
AATTG
Found at i:1678175 original size:19 final size:20
Alignment explanation
Indices: 1678134--1678177 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1678124 TATATATTTA
1678134 ATTTTTTTTAAAAAATTATT
1 ATTTTTTTTAAAAAATTATT
1678154 ATTTATTTTT-AAAAATTA-T
1 ATTT-TTTTTAAAAAATTATT
1678173 ATTTT
1 ATTTT
1678178 ATATTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.04
19 5 0.22
20 12 0.52
21 5 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTTTTTTAAAAAATTATT
Found at i:1678178 original size:20 final size:20
Alignment explanation
Indices: 1678134--1678184 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1678124 TATATATTTA
*
1678134 ATTTT-TTTTAAAAAATTAT
1 ATTTTATTTTTAAAAATTAT
1678153 -TATTTATTTTTAAAAATTAT
1 AT-TTTATTTTTAAAAATTAT
*
1678173 ATTTTATATTTA
1 ATTTTATTTTTA
1678185 TATTAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 1 0.04
19 3 0.11
20 22 0.81
21 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTTATTTTTAAAAATTAT
Found at i:1678526 original size:29 final size:30
Alignment explanation
Indices: 1678484--1678541 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
1678474 TAATGAAAAA
*
1678484 AATATTTTAATTTTTTTA-TTATTAAATTT
1 AATATTTTAATTTTTATACTTATTAAATTT
*
1678513 AATATTTTAATTTTTATACTTTTTAAATT
1 AATATTTTAATTTTTATACTTATTAAATT
1678542 ATAACAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (30 bp):
AATATTTTAATTTTTATACTTATTAAATTT
Found at i:1678790 original size:14 final size:14
Alignment explanation
Indices: 1678773--1678822 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
1678763 TATAATTTAA
1678773 AAAATATAAATATT
1 AAAATATAAATATT
1678787 AAAATATTAAAT-TT
1 AAAATA-TAAATATT
*
1678801 AATAATATAAAAATT
1 AA-AATATAAATATT
1678816 AAAATAT
1 AAAATAT
1678823 TTCATTCACT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 19 0.59
15 13 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATATAAATATT
Found at i:1678793 original size:8 final size:8
Alignment explanation
Indices: 1678780--1678823 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
1678770 TAAAAAATAT
1678780 AAATATTA
1 AAATATTA
1678788 AAATATT-
1 AAATATTA
1678795 AAAT-TTA
1 AAATATTA
1678802 ATAATA-TA
1 A-AATATTA
1678810 AAA-ATTA
1 AAATATTA
1678817 AAATATT
1 AAATATT
1678824 TCATTCACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
6 3 0.10
7 12 0.39
8 16 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AAATATTA
Found at i:1678810 original size:29 final size:31
Alignment explanation
Indices: 1678760--1678823 Score: 96
Period size: 29 Copynumber: 2.1 Consensus size: 31
1678750 ATTTTTTATT
*
1678760 TATTATAATTTAAAAAATATAAATATTAAAA
1 TATTATAATTTAAAAAATATAAAAATTAAAA
*
1678791 TATTA-AATTT-AATAATATAAAAATTAAAA
1 TATTATAATTTAAAAAATATAAAAATTAAAA
1678820 TATT
1 TATT
1678824 TCATTCACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 21 0.68
30 5 0.16
31 5 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
TATTATAATTTAAAAAATATAAAAATTAAAA
Found at i:1679405 original size:14 final size:14
Alignment explanation
Indices: 1679386--1679412 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1679376 AAATTGCTCC
1679386 CATGGCAGATGAAT
1 CATGGCAGATGAAT
1679400 CATGGCAGATGAA
1 CATGGCAGATGAA
1679413 AGAATAGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.30, T:0.19
Consensus pattern (14 bp):
CATGGCAGATGAAT
Found at i:1679631 original size:22 final size:23
Alignment explanation
Indices: 1679586--1679631 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1679576 ATTCAAATAT
* *
1679586 TTATAATTTTTTTTATTTTTAAA
1 TTATAATTTTTTTTATATTAAAA
1679609 TTATAA-TTTTTTTATATTAAAA
1 TTATAATTTTTTTTATATTAAAA
1679631 T
1 T
1679632 AAATAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTATAATTTTTTTTATATTAAAA
Found at i:1687845 original size:15 final size:14
Alignment explanation
Indices: 1687820--1687870 Score: 66
Period size: 16 Copynumber: 3.4 Consensus size: 14
1687810 AAACTTAATA
1687820 AAAATATTAAATTATT
1 AAAA-ATTAAATT-TT
1687836 AAAAATTAAATTTT
1 AAAAATTAAATTTT
1687850 AAAAATATATAATTTT
1 AAAAAT-TA-AATTTT
1687866 AAAAA
1 AAAAA
1687871 ATATAATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.24
15 10 0.30
16 15 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAAATTAAATTTT
Found at i:1687872 original size:17 final size:16
Alignment explanation
Indices: 1687818--1687877 Score: 74
Period size: 15 Copynumber: 3.9 Consensus size: 16
1687808 CAAAACTTAA
1687818 TAAAAATAT-TAAATTAT
1 TAAAAATATAT-AATT-T
1687835 TAAAAAT-TA-AATTT
1 TAAAAATATATAATTT
1687849 TAAAAATATATAATTT
1 TAAAAATATATAATTT
1687865 TAAAAA-ATATAAT
1 TAAAAATATATAAT
1687878 ATATATTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.20
15 13 0.32
16 12 0.30
17 7 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAAAATATATAATTT
Found at i:1692181 original size:2 final size:2
Alignment explanation
Indices: 1692174--1692203 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1692164 ACCCTTAAAA
*
1692174 AG AG AG AG CG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1692204 TTTGAAGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1694288 original size:2 final size:2
Alignment explanation
Indices: 1694281--1694306 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1694271 ACCCTTAAAA
1694281 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
1694307 TTTGAAGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1695052 original size:29 final size:28
Alignment explanation
Indices: 1695020--1695081 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
1695010 AATTTTATAA
*
1695020 TAAAAGAAATATTTTAATATTTATGTTAT
1 TAAAAGAAATATTTTAATATTTATATT-T
*** *
1695049 TAAATTTAATATTTTAATTTTTATATTT
1 TAAAAGAAATATTTTAATATTTATATTT
1695077 TAAAA
1 TAAAA
1695082 ATTTAATAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (28 bp):
TAAAAGAAATATTTTAATATTTATATTT
Found at i:1695065 original size:14 final size:14
Alignment explanation
Indices: 1695027--1695080 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
1695017 TAATAAAAGA
1695027 AATATTTTAATATTT
1 AATATTTTAA-ATTT
*
1695042 -ATGTTATTAAATTT
1 AATATT-TTAAATTT
*
1695056 AATATTTTAATTTT
1 AATATTTTAAATTT
*
1695070 TATATTTTAAA
1 AATATTTTAAA
1695081 AATTTAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 24 0.75
15 8 0.25
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
AATATTTTAAATTT
Found at i:1695221 original size:22 final size:22
Alignment explanation
Indices: 1695187--1695244 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
1695177 TTTATATCAC
1695187 ATAATATAATTTTAATAATATTTAA
1 ATAATAT--TTTTAATAATA-TTAA
*
1695212 ATAAT-TTTTTAATATTATTAA
1 ATAATATTTTTAATAATATTAA
*
1695233 TTAATATTTTTA
1 ATAATATTTTTA
1695245 TTTATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 8 0.27
22 16 0.53
24 1 0.03
25 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATAATATTTTTAATAATATTAA
Found at i:1695250 original size:23 final size:21
Alignment explanation
Indices: 1695196--1695254 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
1695186 CATAATATAA
*
1695196 TTTTAATAATATTTAAATAATT
1 TTTTAATATTA-TTAAATAATT
*
1695218 TTTTAATATTATTAATTAATAT
1 TTTTAATATTATTAAATAAT-T
*
1695240 TTTTATTTATTATTA
1 TTTTA-ATATTATTA
1695255 CAAAATTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.25
22 16 0.50
23 8 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTAATATTATTAAATAATT
Found at i:1695477 original size:26 final size:27
Alignment explanation
Indices: 1695441--1695522 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 27
1695431 ATTTACATAT
* *
1695441 TTTAAAAATTTATCATCTA-AT-TTAAA
1 TTTAAATATTTAT-ATATATATATTAAA
1695467 TTTAAATATTTATATATATATATTAAA
1 TTTAAATATTTATATATATATATTAAA
* * * *
1695494 TATAAATATTAAATATAAATATTTTAAA
1 TTTAAATATT-TATATATATATATTAAA
1695522 T
1 T
1695523 AAAAAATTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
25 4 0.09
26 14 0.30
27 14 0.30
28 15 0.32
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
TTTAAATATTTATATATATATATTAAA
Found at i:1695502 original size:13 final size:13
Alignment explanation
Indices: 1695462--1695516 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
1695452 ATCATCTAAT
*
1695462 TTAAATTTAAATA
1 TTAAATATAAATA
* *
1695475 TTTATATATATATA
1 -TTAAATATAAATA
1695489 TTAAATATAAATA
1 TTAAATATAAATA
1695502 TTAAATATAAATA
1 TTAAATATAAATA
1695515 TT
1 TT
1695517 TTAAATAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
13 26 0.72
14 10 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TTAAATATAAATA
Found at i:1695525 original size:26 final size:27
Alignment explanation
Indices: 1695462--1695523 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
1695452 ATCATCTAAT
* * *
1695462 TTAAATTTAAATATTTATATATATATA
1 TTAAATATAAATATTAATATAAATATA
*
1695489 TTAAATATAAATATTAAATATAAATATT
1 TTAAATATAAATATT-AATATAAATATA
1695517 TTAAATA
1 TTAAATA
1695524 AAAAATTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 14 0.47
28 16 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TTAAATATAAATATTAATATAAATATA
Found at i:1695753 original size:12 final size:11
Alignment explanation
Indices: 1695714--1695766 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
1695704 ATAATATTAA
1695714 ATTTTTAAAATT
1 ATTTTT-AAATT
*
1695726 TTTATTTAAATT
1 ATT-TTTAAATT
1695738 ATTTTTAAATT
1 ATTTTTAAATT
*
1695749 GATTTGTAAATTT
1 -ATTTTTAAA-TT
1695762 ATTTT
1 ATTTT
1695767 ATTATTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 8 0.24
12 21 0.62
13 5 0.15
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (11 bp):
ATTTTTAAATT
Found at i:1695826 original size:22 final size:20
Alignment explanation
Indices: 1695781--1695827 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
1695771 TTAAAAATAA
*
1695781 AAAATATATATTTTTATATT
1 AAAATTTATATTTTTATATT
1695801 --AATTTATATATTTTATAATT
1 AAAATTTATAT-TTTTAT-ATT
1695821 AAAATTT
1 AAAATTT
1695828 TAAAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
18 8 0.36
19 6 0.27
20 3 0.14
22 5 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AAAATTTATATTTTTATATT
Found at i:1695862 original size:48 final size:48
Alignment explanation
Indices: 1695756--1695863 Score: 112
Period size: 48 Copynumber: 2.2 Consensus size: 48
1695746 ATTGATTTGT
* * *
1695756 AAATTTATTTTATTATTAAAAATAAAAAATATATATTTTTATATTAAT
1 AAATATATTTTATAATTAAAAATAAAAAATATATATTTTTATATTAAA
** * **
1695804 TTATATATTTTATAATTAAAATTTTAAAA-ATATATTTTTATTATTTAAA
1 AAATATATTTTATAATTAAAAATAAAAAATATATATTTTTA-TA-TTAAA
1695853 AAATA-ATTTTA
1 AAATATATTTTA
1695864 ACCATATATA
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
47 11 0.23
48 30 0.62
49 7 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (48 bp):
AAATATATTTTATAATTAAAAATAAAAAATATATATTTTTATATTAAA
Found at i:1696169 original size:26 final size:25
Alignment explanation
Indices: 1696117--1696170 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
1696107 TAAATAAAAA
* **
1696117 TAAATTTACTTTTCATATTTACTTT
1 TAAATTTAATTTTCATATTTAAATT
*
1696142 TAAATTTAATTATTTATATTTAAATT
1 TAAATTTAATT-TTCATATTTAAATT
1696168 TAA
1 TAA
1696171 TATAAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (25 bp):
TAAATTTAATTTTCATATTTAAATT
Found at i:1696222 original size:22 final size:23
Alignment explanation
Indices: 1696159--1696233 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 23
1696149 AATTATTTAT
1696159 ATTTAAATTTAATATAAATT-AAA
1 ATTTAAA-TTAATATAAATTAAAA
* * *
1696182 AGTTAAA-AAATATATATTAAAA
1 ATTTAAATTAATATAAATTAAAA
**
1696204 ATTTAAATTAAT-TAAATTAATT
1 ATTTAAATTAATATAAATTAAAA
1696226 ATTTAAAT
1 ATTTAAAT
1696234 CAAATATTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
21 9 0.21
22 24 0.57
23 9 0.21
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (23 bp):
ATTTAAATTAATATAAATTAAAA
Found at i:1698460 original size:21 final size:21
Alignment explanation
Indices: 1698434--1698475 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1698424 CCTGATCAAG
1698434 ACTTCATTGATCATGTACTTT
1 ACTTCATTGATCATGTACTTT
1698455 ACTTCATTGATCATGTACTTT
1 ACTTCATTGATCATGTACTTT
1698476 TACTGCTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.48
Consensus pattern (21 bp):
ACTTCATTGATCATGTACTTT
Found at i:1700319 original size:2 final size:2
Alignment explanation
Indices: 1700314--1700347 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1700304 CTAAAAAAAG
1700314 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1700348 AAACAGAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1700932 original size:24 final size:24
Alignment explanation
Indices: 1700905--1700951 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1700895 CTCCCAAAGG
*
1700905 CTCGCTAAGATTTTCCGCAGGCAT
1 CTCGCCAAGATTTTCCGCAGGCAT
* *
1700929 CTCGCCATGATTTTCCGCTGGCA
1 CTCGCCAAGATTTTCCGCAGGCA
1700952 CCTTGATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.32, G:0.21, T:0.30
Consensus pattern (24 bp):
CTCGCCAAGATTTTCCGCAGGCAT
Done.