Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold168
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: 2098754
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
File 6 of 16
Found at i:607761 original size:3 final size:3
Alignment explanation
Indices: 607755--607795 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
607745 TAAATAATAT
607755 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
607796 TTGCTCTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:608330 original size:19 final size:18
Alignment explanation
Indices: 608288--608345 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
608278 TAATACAATT
*
608288 TATAATAATTTATATATAA
1 TATAA-AATTTACATATAA
*
608307 AATAAAATTTACATACTAA
1 TATAAAATTTACATA-TAA
*
608326 TATAAATTTTA-AT-TAA
1 TATAAAATTTACATATAA
608342 TATA
1 TATA
608346 CATTTTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
16 7 0.21
18 11 0.32
19 16 0.47
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TATAAAATTTACATATAA
Found at i:608357 original size:15 final size:16
Alignment explanation
Indices: 608323--608357 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
608313 ATTTACATAC
608323 TAATATAAATTTTAAT
1 TAATATAAATTTTAAT
*
608339 TAATATACATTTT-AT
1 TAATATAAATTTTAAT
608354 TAAT
1 TAAT
608358 TTTAAAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATATAAATTTTAAT
Found at i:608497 original size:9 final size:9
Alignment explanation
Indices: 608483--608512 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
608473 TAATAAAATA
608483 TAAATTTTT
1 TAAATTTTT
608492 TAAATTTTT
1 TAAATTTTT
608501 TAAATTTTT
1 TAAATTTTT
608510 TAA
1 TAA
608513 TATAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TAAATTTTT
Found at i:608764 original size:34 final size:33
Alignment explanation
Indices: 608686--608835 Score: 115
Period size: 34 Copynumber: 4.6 Consensus size: 33
608676 ACATTAGCAT
608686 AATATTATAAA-ATAATTAAAAA--TATAA-ATA
1 AATA-TATAAATATAATTAAAAATTTATAATATA
608716 ATATGATATGAATATATAATTAAAAATTTATAATATA
1 A-AT-ATAT-AA-ATATAATTAAAAATTTATAATATA
608753 AAT-TATAAATAT-ATT-AAAATTTATATATATAA
1 AATATATAAATATAATTAAAAATTTATA-ATAT-A
* * *
608785 AATATTTTAAATATGATT-ATAA--TATAATA-A
1 AATA-TATAAATATAATTAAAAATTTATAATATA
608815 AATATATAAATATAATATAAA
1 AATATATAAATATAAT-TAAA
608836 TTATTAAATT
Statistics
Matches: 100, Mismatches: 5, Indels: 29
0.75 0.04 0.22
Matches are distributed among these distances:
29 10 0.10
30 17 0.17
31 13 0.13
32 14 0.14
33 7 0.07
34 22 0.22
35 6 0.06
36 7 0.07
37 4 0.04
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (33 bp):
AATATATAAATATAATTAAAAATTTATAATATA
Found at i:608776 original size:18 final size:19
Alignment explanation
Indices: 608754--608843 Score: 75
Period size: 20 Copynumber: 4.9 Consensus size: 19
608744 TATAATATAA
608754 ATTATAAATATATTAAAAT
1 ATTATAAATATATTAAAAT
608773 -TTAT--ATATA-TAAAAT
1 ATTATAAATATATTAAAAT
* *
608788 ATTTTAAATATGATTATAAT
1 ATTATAAATAT-ATTAAAAT
*
608808 ATAATAAA-ATATATAAATAT
1 ATTATAAATATAT-TAAA-AT
*
608828 AATATAAAT-TATTAAA
1 ATTATAAATATATTAAA
608844 TTTAATTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
15 6 0.11
16 8 0.14
18 10 0.18
19 10 0.18
20 22 0.39
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (19 bp):
ATTATAAATATATTAAAAT
Found at i:608780 original size:16 final size:15
Alignment explanation
Indices: 608738--608787 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
608728 TATATAATTA
608738 AAAATTTATA-ATAT
1 AAAATTTATATATAT
*
608752 -AAATTATAAATATATT
1 AAAATT-TATATATA-T
608768 AAAATTTATATATAT
1 AAAATTTATATATAT
608783 AAAAT
1 AAAAT
608788 ATTTTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
13 5 0.17
14 3 0.10
15 9 0.30
16 8 0.27
17 5 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAAATTTATATATAT
Found at i:608787 original size:25 final size:29
Alignment explanation
Indices: 608684--608834 Score: 109
Period size: 29 Copynumber: 5.1 Consensus size: 29
608674 TTACATTAGC
* * *
608684 ATAATATTATAAAATA-ATTAAAAATATAA
1 ATAATATAATAAAATATATTAAATATAT-T
* *
608713 ATAATATGATATGAATATATAATTAAAAAT-TT
1 ATAATAT-A-AT-AAAATAT-ATTAAATATATT
608745 ATAATATAAATTATAAATATATTAAA-AT-TT
1 ATAATAT-AA-TA-AAATATATTAAATATATT
*
608775 AT-ATAT-ATAAAATATTTTAAATATGATT
1 ATAATATAATAAAATATATTAAATAT-ATT
*
608803 ATAATATAATAAAATATA-TAAATATAAT
1 ATAATATAATAAAATATATTAAATATATT
608831 ATAA
1 ATAA
608835 ATTATTAAAT
Statistics
Matches: 102, Mismatches: 8, Indels: 25
0.76 0.06 0.19
Matches are distributed among these distances:
25 11 0.11
26 4 0.04
27 1 0.01
28 10 0.10
29 22 0.22
30 15 0.15
31 10 0.10
32 19 0.19
33 1 0.01
34 9 0.09
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
ATAATATAATAAAATATATTAAATATATT
Found at i:609195 original size:20 final size:20
Alignment explanation
Indices: 609147--609221 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 20
609137 TTATTTAAGG
*
609147 TTATATAAATTTT-TATATTT
1 TTATATTAATTTTATAT-TTT
*
609167 TGATAATTAATTTTATATTTT
1 TTAT-ATTAATTTTATATTTT
*
609188 TTATATT-ATATTTATGTTATAT
1 TTATATTAAT-TTTATATT-T-T
609210 TTATA-TAATTTT
1 TTATATTAATTTT
609222 TAATTAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
19 2 0.04
20 13 0.29
21 19 0.42
22 11 0.24
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (20 bp):
TTATATTAATTTTATATTTT
Found at i:609207 original size:11 final size:11
Alignment explanation
Indices: 609178--609252 Score: 66
Period size: 11 Copynumber: 6.9 Consensus size: 11
609168 GATAATTAAT
609178 TTTATATT-T-
1 TTTATATTATA
609187 TTTATATTATA
1 TTTATATTATA
*
609198 TTTATGTTATA
1 TTTATATTATA
* *
609209 TTTATATAATT
1 TTTATATTATA
*
609220 TTTA-ATTAAATT
1 TTTATATT--ATA
609232 TTTATATTATA
1 TTTATATTATA
*
609243 TTTGTATTAT
1 TTTATATTAT
609253 GTATTAATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
9 8 0.15
10 3 0.06
11 33 0.61
12 7 0.13
13 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (11 bp):
TTTATATTATA
Found at i:609263 original size:28 final size:28
Alignment explanation
Indices: 609232--609291 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
609222 TAATTAAATT
*
609232 TTTATATTATA-TTTGT-ATTATGTATTAA
1 TTTAT-TTATATTTTATCATTATG-ATTAA
*
609260 TTTATTTTTATTTTATCATTATGATTAA
1 TTTATTTATATTTTATCATTATGATTAA
609288 TTTA
1 TTTA
609292 AAAAATTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 4 0.14
28 18 0.64
29 6 0.21
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (28 bp):
TTTATTTATATTTTATCATTATGATTAA
Found at i:609267 original size:34 final size:33
Alignment explanation
Indices: 609193--609275 Score: 85
Period size: 34 Copynumber: 2.5 Consensus size: 33
609183 ATTTTTTATA
* * *
609193 TTATATTTATGTTATATTTATATAATTTTTAAT
1 TTATTTTTATATTATATTTATATAATTATTAAT
* * *
609226 TAAATTTTTATATTATATTTGTATTATGTATTAAT
1 T-TATTTTTATATTATATTTATATAAT-TATTAAT
*
609261 TTATTTTTATTTTAT
1 TTATTTTTATATTAT
609276 CATTATGATT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
33 1 0.03
34 32 0.80
35 7 0.17
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (33 bp):
TTATTTTTATATTATATTTATATAATTATTAAT
Found at i:609721 original size:25 final size:24
Alignment explanation
Indices: 609673--609721 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
609663 CGATCACTTA
*
609673 AAAAAATTTAAAAAATACTATATT
1 AAAAAATTTAAAAAATAATATATT
609697 AAAAAATTTAAATAATATAAT-TATT
1 AAAAAATTTAAA-AA-ATAATATATT
609722 TTTATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 12 0.55
25 6 0.27
26 4 0.18
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAAAATTTAAAAAATAATATATT
Found at i:610175 original size:16 final size:17
Alignment explanation
Indices: 610147--610179 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
610137 ATTAAATATA
610147 TTTAAATAATTTAATTT
1 TTTAAATAATTTAATTT
610164 TTTAAA-AATTTAATTT
1 TTTAAATAATTTAATTT
610180 ACATGAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAAATAATTTAATTT
Found at i:610359 original size:3 final size:3
Alignment explanation
Indices: 610351--610387 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
610341 AATTTAAATA
610351 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
610388 TCGATGGCGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:610845 original size:22 final size:24
Alignment explanation
Indices: 610796--610845 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 24
610786 TAAATTTTCT
610796 ATTTAA-AAAATTATTATTTTATA
1 ATTTAATAAAATTATTATTTTATA
*
610819 A--TAATAAAATTTTTA-TTTA-A
1 ATTTAATAAAATTATTATTTTATA
610839 ATTTAAT
1 ATTTAAT
610846 TATAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
20 2 0.09
21 7 0.30
22 13 0.57
23 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTTAATAAAATTATTATTTTATA
Found at i:610893 original size:19 final size:17
Alignment explanation
Indices: 610857--610895 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
610847 ATAAAATATA
*
610857 TAAATATTTATATTTTT
1 TAAATATTTATATATTT
610874 TAAATATTTTAATATATTT
1 TAAATA-TTT-ATATATTT
610893 TAA
1 TAA
610896 TAATGAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 3 0.16
19 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAAATATTTATATATTT
Found at i:611097 original size:26 final size:27
Alignment explanation
Indices: 611068--611137 Score: 83
Period size: 26 Copynumber: 2.6 Consensus size: 27
611058 TTTTATTTTT
611068 ATAAGT-AATTTTATATTAATATTA-AA
1 ATAAGTAAATTTTATATTAAT-TTATAA
* *
611094 ATAA-TAAATTTTATAATAATTTATAT
1 ATAAGTAAATTTTATATTAATTTATAA
611120 ATAAGATAAATTTTATAT
1 ATAAG-TAAATTTTATAT
611138 ATTAATATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 4 0.11
26 22 0.59
28 11 0.30
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (27 bp):
ATAAGTAAATTTTATATTAATTTATAA
Found at i:611136 original size:18 final size:19
Alignment explanation
Indices: 611113--611153 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
611103 TTTATAATAA
611113 TTTATATA-TAAGATAAAT
1 TTTATATATTAAGATAAAT
*
611131 TTTATATATTAATATAAAT
1 TTTATATATTAAGATAAAT
611150 TTTA
1 TTTA
611154 ATTAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTATATATTAAGATAAAT
Found at i:611145 original size:26 final size:27
Alignment explanation
Indices: 611079--611148 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 27
611069 TAAGTAATTT
611079 TATATTAATATTAAAATAATAAATTTTA
1 TATATTAATA-TAAAATAATAAATTTTA
* * *
611107 TAATAATTTATATATAA-GATAAATTTTA
1 T-AT-ATTAATATAAAATAATAAATTTTA
611135 TATATTAATATAAA
1 TATATTAATATAAA
611149 TTTTAATTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
26 9 0.26
27 2 0.06
28 12 0.34
29 6 0.17
30 6 0.17
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (27 bp):
TATATTAATATAAAATAATAAATTTTA
Found at i:611299 original size:41 final size:41
Alignment explanation
Indices: 611249--611326 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
611239 AATAGTTAAT
** * *
611249 TAATATTAAAATTGTAAAA-ATAAATATTATTTTTTAATTTA
1 TAATATT-AAATAATAAAATATAAATATAAATTTTTAATTTA
611290 TAATATTAAATAATAAAATATAAATATAAATTTTTAA
1 TAATATTAAATAATAAAATATAAATATAAATTTTTAA
611327 AATATTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 9 0.28
41 23 0.72
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (41 bp):
TAATATTAAATAATAAAATATAAATATAAATTTTTAATTTA
Found at i:611367 original size:17 final size:16
Alignment explanation
Indices: 611327--611370 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
611317 AAATTTTTAA
*
611327 AATATTTTT--AATAT
1 AATATTTTTAAAAAAT
611341 AATATTTTTAAAAAAT
1 AATATTTTTAAAAAAT
611357 AATATTTTTTAAAA
1 AATA-TTTTTAAAA
611371 GTTTTCTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.35
16 8 0.31
17 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATATTTTTAAAAAAT
Found at i:611472 original size:31 final size:28
Alignment explanation
Indices: 611436--611497 Score: 70
Period size: 31 Copynumber: 2.1 Consensus size: 28
611426 TAAGTAACAT
* *
611436 ATTTTTAATAGATTTAATAATTTTAAATATA
1 ATTTTTAATAG-TATAA-AATTATAAA-ATA
*
611467 ATTTTTATTAGTATAAAATTATAAAATA
1 ATTTTTAATAGTATAAAATTATAAAATA
611495 ATT
1 ATT
611498 AAAAATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 8 0.29
30 4 0.14
31 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (28 bp):
ATTTTTAATAGTATAAAATTATAAAATA
Found at i:611500 original size:17 final size:17
Alignment explanation
Indices: 611480--611513 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
611470 TTTATTAGTA
*
611480 TAAAATTATAAAATAAT
1 TAAAAATATAAAATAAT
611497 TAAAAATATAAAATAAT
1 TAAAAATATAAAATAAT
611514 GAATACATAT
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):
TAAAAATATAAAATAAT
Found at i:611558 original size:31 final size:32
Alignment explanation
Indices: 611520--611585 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 32
611510 TAATGAATAC
611520 ATATTAAAATTT-TATAATATAA-ATTATT-AAT
1 ATATTAAAATTTATAT-ATATAATATT-TTAAAT
611551 ATATTAAAATTTATATATATAATATTTTAAAT
1 ATATTAAAATTTATATATATAATATTTTAAAT
611583 ATA
1 ATA
611586 ATTATAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
31 20 0.62
32 12 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
ATATTAAAATTTATATATATAATATTTTAAAT
Found at i:611573 original size:23 final size:23
Alignment explanation
Indices: 611547--611619 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
611537 TATAAATTAT
*
611547 TAATATATTAAAATTTATATATA
1 TAATATATTAAAATATATATATA
*
611570 TAATAT-TTTAAATATA-AT-TA
1 TAATATATTAAAATATATATATA
* * *
611590 TAATATAATAAAATATATAAACA
1 TAATATATTAAAATATATATATA
611613 TAATATA
1 TAATATA
611620 AATTATCTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
20 8 0.20
21 10 0.24
22 9 0.22
23 14 0.34
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATATATTAAAATATATATATA
Found at i:611584 original size:14 final size:14
Alignment explanation
Indices: 611528--611587 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 14
611518 ACATATTAAA
611528 ATTTTATAATATAA-
1 ATTTTA-AATATAAT
*
611542 ATTATTAATATATTAAA
1 ATT-TTAA-ATA-TAAT
*
611559 ATTTATATATATAAT
1 ATTT-TAAATATAAT
611574 ATTTTAAATATAAT
1 ATTTTAAATATAAT
611588 TATAATATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 13 0.34
15 13 0.34
16 7 0.18
17 5 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTTAAATATAAT
Found at i:611596 original size:43 final size:46
Alignment explanation
Indices: 611520--611618 Score: 125
Period size: 43 Copynumber: 2.2 Consensus size: 46
611510 TAATGAATAC
* * *
611520 ATAT-TAAAATTTTATAATATAAATTATTAATATATTAAAATTTAT
1 ATATATAATATTTTATAATATAAATTATTAATATAATAAAATATAT
611565 ATATATAATATTTTA-AATAT-AATTA-TAATATAATAAAATATAT
1 ATATATAATATTTTATAATATAAATTATTAATATAATAAAATATAT
* *
611608 AAACATAATAT
1 ATATATAATAT
611619 AAATTATCTA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 25 0.52
44 5 0.10
45 9 0.19
46 9 0.19
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (46 bp):
ATATATAATATTTTATAATATAAATTATTAATATAATAAAATATAT
Found at i:611623 original size:93 final size:90
Alignment explanation
Indices: 611470--611653 Score: 205
Period size: 93 Copynumber: 2.0 Consensus size: 90
611460 AAATATAATT
* *
611470 TTTATTAGTATAAAATTATAAAATAATTAAAAATATAAAATAATGAATACATATTAAAATTTTAT
1 TTTATTAGTATAAAATTATAAAATAATTAAAAATATAAAATAATGAATACATAATAAAATTATAT
611535 AATATAAATTATTAATATA-TTAAAA
66 AATATAAATT-TTAATATATTTAAAA
* * *
611560 TTTATATA-TATAATATTTTAAATATAATTATAATATAATAAAATATAT-AA-ACATAATATAAA
1 TTTAT-TAGTATAAAATTATAAA-ATAATTA-AAAAT-ATAAAATA-ATGAATACATAATA-AAA
* * *
611622 TTATCTAATTTAAATTTTTATATATTTAAAA
60 TTATATAATATAAATTTTAATATATTTAAAA
611653 T
1 T
611654 AAATAAAAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
90 17 0.22
91 9 0.11
92 18 0.23
93 33 0.42
94 2 0.03
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (90 bp):
TTTATTAGTATAAAATTATAAAATAATTAAAAATATAAAATAATGAATACATAATAAAATTATAT
AATATAAATTTTAATATATTTAAAA
Found at i:611934 original size:18 final size:18
Alignment explanation
Indices: 611915--611949 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
611905 ATGAGAAAAT
611915 TTTTA-TATTTATATTTA
1 TTTTATTATTTATATTTA
*
611932 TTTTATTTTTTATATTTA
1 TTTTATTATTTATATTTA
611950 AAATATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATTATTTATATTTA
Found at i:612336 original size:23 final size:23
Alignment explanation
Indices: 612261--612337 Score: 75
Period size: 23 Copynumber: 3.2 Consensus size: 23
612251 TTTTATATAA
612261 TAATTATTT-TTTTATATAAATTT
1 TAATTATTTATTTTATAT-AATTT
* * *
612284 GAATATATTTATATATTCTATCATTT
1 TAAT-TATTTAT-T-TTATATAATTT
*
612310 TAATTATTTATTTTATATTATTT
1 TAATTATTTATTTTATATAATTT
612333 TAATT
1 TAATT
612338 TATTATATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
23 17 0.39
24 6 0.14
25 8 0.18
26 8 0.18
27 5 0.11
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (23 bp):
TAATTATTTATTTTATATAATTT
Found at i:612353 original size:23 final size:23
Alignment explanation
Indices: 612280--612353 Score: 60
Period size: 23 Copynumber: 3.1 Consensus size: 23
612270 TTTTATATAA
* *
612280 ATTTGAATATATTTATATATTCTAT
1 ATTTTAAT-TATTTATATAATCT-T
* * *
612305 CATTTTAATTATTTATTTTATATT
1 -ATTTTAATTATTTATATAATCTT
612329 ATTTTAATT-TATTATATAATCTT
1 ATTTTAATTAT-TTATATAATCTT
612352 AT
1 AT
612354 CATTTTGCTT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
22 1 0.03
23 20 0.51
24 1 0.03
25 10 0.26
26 7 0.18
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (23 bp):
ATTTTAATTATTTATATAATCTT
Found at i:612355 original size:49 final size:49
Alignment explanation
Indices: 612261--612359 Score: 130
Period size: 49 Copynumber: 2.0 Consensus size: 49
612251 TTTTATATAA
*
612261 TAATTATTTTTTTATATAAATTTGAATATATTTATATATTCTATCATTT
1 TAATTATTTTTTTATATAAATTTGAATATATTTATATAATCTATCATTT
* * *
612310 TAATTATTTATTTTATAT-TATTTTAATTTA-TTATATAATCTTATCATTT
1 TAATTATTT-TTTTATATAAATTTGAATATATTTATATAATC-TATCATTT
612359 T
1 T
612360 GCTTATAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
48 9 0.20
49 27 0.61
50 8 0.18
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (49 bp):
TAATTATTTTTTTATATAAATTTGAATATATTTATATAATCTATCATTT
Found at i:612372 original size:49 final size:50
Alignment explanation
Indices: 612270--612387 Score: 116
Period size: 49 Copynumber: 2.4 Consensus size: 50
612260 ATAATTATTT
* * * * **
612270 TTTTATATAAAT-TTGAATATATTTATATATTCTATCATTTTAATTATTTA
1 TTTTATATATATCTTTAATTTA-TTATATAATCTATCATTTTAATTATAAA
**
612320 TTTTATAT-TAT-TTTAATTTATTATATAATCTTATCATTTTGCTTATAAA
1 TTTTATATATATCTTTAATTTATTATATAATC-TATCATTTTAATTATAAA
*
612369 TTTTTTATATATCTTTAAT
1 TTTTATATATATCTTTAAT
612388 AATTAATTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
48 9 0.16
49 30 0.54
50 11 0.20
51 6 0.11
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (50 bp):
TTTTATATATATCTTTAATTTATTATATAATCTATCATTTTAATTATAAA
Found at i:612454 original size:23 final size:22
Alignment explanation
Indices: 612391--612455 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
612381 CTTTAATAAT
*
612391 TAATTAATTTAATTATATTTAAAG
1 TAATTAATTTAATT-TA-TTAAAA
*
612415 T-ATTAA-TT-ATTTTTTAAAA
1 TAATTAATTTAATTTATTAAAA
612434 TAATTAATTTAAATTTATTAAA
1 TAATTAATTT-AATTTATTAAA
612456 TTACATATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
19 6 0.18
20 6 0.18
21 5 0.15
22 2 0.06
23 14 0.41
24 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TAATTAATTTAATTTATTAAAA
Found at i:613003 original size:22 final size:20
Alignment explanation
Indices: 612975--613022 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
612965 TTCACACAAT
*
612975 TTATTTATTTAAATTTAAATAA
1 TTATTTATTT-AA-TTAAAAAA
*
612997 TTATTTATTTTATTAAAAAA
1 TTATTTATTTAATTAAAAAA
613017 TTATTT
1 TTATTT
613023 TTATATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.54
21 1 0.04
22 10 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATTTATTTAATTAAAAAA
Found at i:613047 original size:21 final size:21
Alignment explanation
Indices: 613021--613062 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
613011 AAAAAATTAT
*
613021 TTTTAT-ATTAATATTTATATA
1 TTTTATAATTAA-AATTATATA
613042 TTTTATAATTAAAATTATATA
1 TTTTATAATTAAAATTATATA
613063 AGTGAGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTATAATTAAAATTATATA
Found at i:613614 original size:29 final size:30
Alignment explanation
Indices: 613577--613640 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
613567 TATTATAAAT
* *
613577 AAATATTAAGAATAATTTTTTAT-TTTTAA
1 AAATTTTAAAAATAATTTTTTATATTTTAA
613606 AAATTTTAAAAATAATTTTTTATATTTTAA
1 AAATTTTAAAAATAATTTTTTATATTTTAA
613636 AAATT
1 AAATT
613641 AATTCTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 21 0.66
30 11 0.34
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (30 bp):
AAATTTTAAAAATAATTTTTTATATTTTAA
Found at i:613623 original size:22 final size:23
Alignment explanation
Indices: 613598--613649 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
613588 ATAATTTTTT
613598 ATTTTTAAAAATTTTAAAAA-TA
1 ATTTTTAAAAATTTTAAAAATTA
* *
613620 ATTTTT-TATATTTTAAAAATTA
1 ATTTTTAAAAATTTTAAAAATTA
613642 ATTCTTTA
1 ATT-TTTA
613650 TTTCACCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 11 0.44
22 11 0.44
23 3 0.12
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTTTTAAAAATTTTAAAAATTA
Found at i:613650 original size:22 final size:21
Alignment explanation
Indices: 613608--613650 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
613598 ATTTTTAAAA
*
613608 ATTTTAAAAATAATTTTTTAT
1 ATTTTAAAAATAATTCTTTAT
613629 ATTTTAAAAATTAATTCTTTAT
1 ATTTTAAAAA-TAATTCTTTAT
613651 TTCACCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTAAAAATAATTCTTTAT
Found at i:614691 original size:28 final size:26
Alignment explanation
Indices: 614651--614754 Score: 86
Period size: 28 Copynumber: 3.8 Consensus size: 26
614641 TTTAAAAATA
*
614651 AAAAAGTA-TAAATATTAAATTTAGAT
1 AAAAATTATTAAATATTAAATTTA-AT
*
614677 AAAAATCTATTAAATATTATATTTTTAA-
1 AAAAAT-TATTAAATATTA-A-ATTTAAT
* *
614705 AAAAATTACCTAAAATATTAAATATAAT
1 AAAAATTA--TTAAATATTAAATTTAAT
614733 AAAAAATTATTAAAATATTAAA
1 -AAAAATTATT-AAATATTAAA
614755 AATATAAATA
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
26 5 0.08
27 9 0.14
28 26 0.41
29 19 0.30
30 4 0.06
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (26 bp):
AAAAATTATTAAATATTAAATTTAAT
Found at i:614735 original size:17 final size:17
Alignment explanation
Indices: 614715--614823 Score: 77
Period size: 17 Copynumber: 6.3 Consensus size: 17
614705 AAAAATTACC
614715 TAAAATATTAAATATAA
1 TAAAATATTAAATATAA
*
614732 TAAAAAATTATTAAA-ATAT
1 T--AAAA-TATTAAATATAA
614751 TAAAA-ATATAAATATAATA
1 TAAAATAT-TAAATAT-A-A
*
614770 TAAATATATTAAATATAT
1 TAAA-ATATTAAATATAA
614788 TAAAAT-TT--ATATAA
1 TAAAATATTAAATATAA
*
614802 TATAAATATT-AATATAT
1 TA-AAATATTAAATATAA
614819 TAAAA
1 TAAAA
614824 CTTTTATAAT
Statistics
Matches: 75, Mismatches: 5, Indels: 25
0.71 0.05 0.24
Matches are distributed among these distances:
14 7 0.09
15 6 0.08
16 11 0.15
17 16 0.21
18 5 0.07
19 13 0.17
20 15 0.20
21 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAATATTAAATATAA
Found at i:614755 original size:36 final size:35
Alignment explanation
Indices: 614715--614823 Score: 129
Period size: 36 Copynumber: 3.1 Consensus size: 35
614705 AAAAATTACC
*
614715 TAAAATATTAAATATAATAAAAAATTATTAAAATAT
1 TAAAATATTAAATATAAT-ATAAATTATTAAAATAT
614751 TAAAA-ATATAAATATAATATAAATATATTAAATATAT
1 TAAAATAT-TAAATATAATATAAAT-TATTAAA-ATAT
*
614788 TAAAAT-TT--ATATAATATAAA-TATTAATATAT
1 TAAAATATTAAATATAATATAAATTATTAAAATAT
614819 TAAAA
1 TAAAA
614824 CTTTTATAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 13
0.82 0.02 0.16
Matches are distributed among these distances:
31 9 0.13
32 6 0.09
34 12 0.18
35 7 0.10
36 23 0.34
37 10 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (35 bp):
TAAAATATTAAATATAATATAAATTATTAAAATAT
Found at i:614769 original size:11 final size:11
Alignment explanation
Indices: 614755--614817 Score: 58
Period size: 11 Copynumber: 5.5 Consensus size: 11
614745 AAATATTAAA
614755 AATATAAATAT
1 AATATAAATAT
614766 AATATAAATAT
1 AATATAAATAT
614777 -AT-TAAATAT
1 AATATAAATAT
* *
614786 ATTAAAATTTATAT
1 AATATAA---ATAT
614800 AATATAAATATT
1 AATATAAATA-T
614812 AATATA
1 AATATA
614818 TTAAAACTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
9 7 0.17
10 3 0.07
11 16 0.38
12 7 0.17
14 9 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AATATAAATAT
Found at i:614803 original size:28 final size:28
Alignment explanation
Indices: 614719--614838 Score: 86
Period size: 28 Copynumber: 4.1 Consensus size: 28
614709 ATTACCTAAA
* * *
614719 ATATTAAATATAATAAAAAATTAT-TAAA
1 ATATTAAATAT-ATTAAAATTTATATAAT
* *
614747 ATATTAAAAATA-T-AAATATAATATAAAT
1 ATATTAAATATATTAAAAT-TTATAT-AAT
614775 ATATTAAATATATTAAAATTTATATAAT
1 ATATTAAATATATTAAAATTTATATAAT
*
614803 ATAAATATTAATATATTAAAACTTT-TATAATT
1 AT--AT-TAAATATATTAAAA-TTTATATAA-T
614835 ATAT
1 ATAT
614839 AATATTTTAA
Statistics
Matches: 74, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
25 3 0.04
26 3 0.04
27 2 0.03
28 28 0.38
29 6 0.08
30 8 0.11
31 18 0.24
32 6 0.08
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (28 bp):
ATATTAAATATATTAAAATTTATATAAT
Found at i:614819 original size:31 final size:33
Alignment explanation
Indices: 614775--614844 Score: 101
Period size: 31 Copynumber: 2.2 Consensus size: 33
614765 TAATATAAAT
614775 ATATTAAATATATTAAAA-TTTATATAA-TATA-A
1 ATATT-AATATATTAAAACTTT-TATAATTATATA
614807 ATATTAATATATTAAAACTTTTATAATTATATA
1 ATATTAATATATTAAAACTTTTATAATTATATA
614840 ATATT
1 ATATT
614845 TTAAATAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
31 17 0.49
32 12 0.34
33 6 0.17
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (33 bp):
ATATTAATATATTAAAACTTTTATAATTATATA
Found at i:614874 original size:20 final size:20
Alignment explanation
Indices: 614836--614875 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
614826 TTTATAATTA
* * *
614836 TATAATATTTTAAATAATAT
1 TATAATACTTAAAAAAATAT
614856 TATAATACTTAAAAAAATAT
1 TATAATACTTAAAAAAATAT
614876 AATACAGAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TATAATACTTAAAAAAATAT
Found at i:615115 original size:17 final size:19
Alignment explanation
Indices: 615087--615121 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
615077 ATAAATTTTA
615087 AATTATTTTAAT-TTAAAT
1 AATTATTTTAATATTAAAT
615105 AATTA-TTTAATATTAAA
1 AATTATTTTAATATTAAA
615122 AATAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTATTTTAATATTAAAT
Found at i:619729 original size:17 final size:17
Alignment explanation
Indices: 619703--619736 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
619693 TTTATAAAAA
619703 TATTTAAATA-AAAATT
1 TATTTAAATATAAAATT
619719 TATTATAAATATAAAATT
1 TATT-TAAATATAAAATT
619737 AAAGATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 6 0.38
18 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTTAAATATAAAATT
Found at i:620946 original size:36 final size:36
Alignment explanation
Indices: 620845--620946 Score: 86
Period size: 36 Copynumber: 2.9 Consensus size: 36
620835 TGGTTAGAAT
**
620845 TATTA-TTTAAATAATAAA-AAATATTTTTATTTAAA
1 TATTATTTTAAATAATAAATAAAT-TTTAAATTTAAA
* * ** *
620880 T-TTAATTATAAATATTAATATAAA-AATAAATTTTAA
1 TATT-ATTTTAAATAATAA-ATAAATTTTAAATTTAAA
620916 TATTATTTTAAATAATAAATAAATTTTAAAT
1 TATTATTTTAAATAATAAATAAATTTTAAAT
620947 CAATTTAAAT
Statistics
Matches: 50, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
34 2 0.04
35 7 0.14
36 35 0.70
37 3 0.06
38 3 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (36 bp):
TATTATTTTAAATAATAAATAAATTTTAAATTTAAA
Found at i:620952 original size:29 final size:27
Alignment explanation
Indices: 620876--620956 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 27
620866 TATTTTTATT
620876 TAAA-TTTAATTATAAATATTAATATAAAAA
1 TAAATTTTAA-TAT-AAT-TTAA-ATAAAAA
*
620906 TAAATTTTAATATTATTTTAAATAATAAA
1 TAAATTTTAATA-TAATTTAAATAA-AAA
620935 TAAATTTTAA-ATCAATTTAAAT
1 TAAATTTTAATAT-AATTTAAAT
620957 TTAACTTAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
27 1 0.02
28 13 0.29
29 17 0.38
30 8 0.18
31 6 0.13
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (27 bp):
TAAATTTTAATATAATTTAAATAAAAA
Found at i:621371 original size:20 final size:22
Alignment explanation
Indices: 621337--621378 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
621327 AAGGAGAAAC
621337 AGAAGGGAGGAAAAAGAAAGAA
1 AGAAGGGAGGAAAAAGAAAGAA
621359 AGAAGGGA-G-AAAAGAAAGAA
1 AGAAGGGAGGAAAAAGAAAGAA
621379 GAAAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.55
21 1 0.05
22 8 0.40
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (22 bp):
AGAAGGGAGGAAAAAGAAAGAA
Found at i:622588 original size:10 final size:10
Alignment explanation
Indices: 622560--622590 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
622550 ATACACACAC
*
622560 ATATATATAT
1 ATATATATGT
622570 ATATATATGT
1 ATATATATGT
622580 ATATATATGT
1 ATATATATGT
622590 A
1 A
622591 GTGATGGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (10 bp):
ATATATATGT
Found at i:623654 original size:21 final size:21
Alignment explanation
Indices: 623628--623672 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
623618 AAGTGATTCA
*
623628 TGGTATATTTTTCATAACAAT
1 TGGTATATTTTTCATAAAAAT
*
623649 TGGTATATTTTTCCTAAAAAT
1 TGGTATATTTTTCATAAAAAT
623670 TGG
1 TGG
623673 ATGTCGTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47
Consensus pattern (21 bp):
TGGTATATTTTTCATAAAAAT
Found at i:627915 original size:15 final size:15
Alignment explanation
Indices: 627870--627916 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
627860 TAAATTTTTT
*
627870 TTAAATATATAAAATA
1 TTAAATATAT-ATATA
627886 TTAAATATA-ATTATA
1 TTAAATATATA-TATA
627901 TTAAATATATATATA
1 TTAAATATATATATA
627916 T
1 T
627917 CTAATAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 1 0.04
15 17 0.61
16 10 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATATATATA
Found at i:628286 original size:23 final size:22
Alignment explanation
Indices: 628259--628303 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
628249 CGGTTGATTA
628259 AATTAATTTA-AATATATTAAATT
1 AATTAATTTATAAT-T-TTAAATT
628282 AATTAATTTATAATTTTAAATT
1 AATTAATTTATAATTTTAAATT
628304 TTTAAACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.33
23 11 0.52
24 3 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATTAATTTATAATTTTAAATT
Found at i:628509 original size:13 final size:13
Alignment explanation
Indices: 628493--628536 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
628483 TTTTAAAATT
*
628493 TTTTATTTATTAA
1 TTTTATATATTAA
*
628506 TTTTATAAATTAA
1 TTTTATATATTAA
*
628519 TTTAATATACTTAA
1 TTTTATATA-TTAA
628533 TTTT
1 TTTT
628537 TAAAATTTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 18 0.72
14 7 0.28
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTTATATATTAA
Found at i:628942 original size:2 final size:2
Alignment explanation
Indices: 628935--628960 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
628925 GTCCGCTCGA
628935 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
628961 TTTTGCTGAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:629686 original size:21 final size:21
Alignment explanation
Indices: 629645--629686 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
629635 TAGATATAAG
629645 TATAAAAAATAACTTTCAAAA
1 TATAAAAAATAACTTTCAAAA
*
629666 TATATAAAAATAA-TTTGAAAA
1 TATA-AAAAATAACTTTCAAAA
629687 AAAAGTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (21 bp):
TATAAAAAATAACTTTCAAAA
Found at i:629687 original size:22 final size:21
Alignment explanation
Indices: 629645--629687 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
629635 TAGATATAAG
*
629645 TATAAAAAATAACTTTCAAAA
1 TATAAAAAATAACTTTAAAAA
629666 TATATAAAAATAA-TTTGAAAAA
1 TATA-AAAAATAACTTT-AAAAA
629688 AAAGTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (21 bp):
TATAAAAAATAACTTTAAAAA
Found at i:630358 original size:16 final size:16
Alignment explanation
Indices: 630327--630366 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
630317 ATGATATTAT
*
630327 TTATATAATTTTAAAAA
1 TTATA-AATTTAAAAAA
630344 TTATAAATTTAAAAAA
1 TTATAAATTTAAAAAA
*
630360 TTTTAAA
1 TTATAAA
630367 ATATAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTATAAATTTAAAAAA
Found at i:631126 original size:12 final size:11
Alignment explanation
Indices: 631111--631161 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
631101 TGCAATAAAA
631111 TATTTTAATAAT
1 TATTTT-ATAAT
631123 TATTTTATAATT
1 TATTTTATAA-T
* *
631135 TAGTTTATTAT
1 TATTTTATAAT
631146 TATTATTATAA-
1 TATT-TTATAAT
631157 TATTT
1 TATTT
631162 ATTATGTACT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 1 0.03
11 12 0.36
12 20 0.61
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TATTTTATAAT
Found at i:631162 original size:21 final size:21
Alignment explanation
Indices: 631121--631183 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 21
631111 TATTTTAATA
631121 ATTATT-TTATAATTTAGTTTATT
1 ATTATTATTATAA--TA-TTTATT
631144 ATTATTATTATAATATTTATT
1 ATTATTATTATAATATTTATT
*
631165 ATGTACTA-TATAATCATTT
1 AT-TATTATTATAAT-ATTT
631184 TAAATATAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
21 14 0.39
22 10 0.28
23 6 0.17
24 6 0.17
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (21 bp):
ATTATTATTATAATATTTATT
Found at i:631868 original size:11 final size:11
Alignment explanation
Indices: 631853--631941 Score: 60
Period size: 11 Copynumber: 8.1 Consensus size: 11
631843 TTACCTTATA
631853 AAATTAAATAT
1 AAATTAAATAT
* *
631864 TAATTAAAAAT
1 AAATTAAATAT
*
631875 AAAATAAA-AT
1 AAATTAAATAT
*
631885 AAAATAAA-AT
1 AAATTAAATAT
631895 AAATTAAAT-T
1 AAATTAAATAT
**
631905 ATTTTTAAACTTAT
1 A-AATTAAA--TAT
631919 AAATTAAA-ATT
1 AAATTAAATA-T
631930 AAATTAAATAT
1 AAATTAAATAT
631941 A
1 A
631942 TTTAATTATT
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
10 22 0.35
11 31 0.50
12 1 0.02
13 6 0.10
14 2 0.03
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (11 bp):
AAATTAAATAT
Found at i:631878 original size:5 final size:5
Alignment explanation
Indices: 631870--631902 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
631860 ATATTAATTA
*
631870 AAAAT AAAAT AAAAT AAAAT AAAAT AAATT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
631903 TTATTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:631995 original size:31 final size:31
Alignment explanation
Indices: 631924--631983 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
631914 CTTATAAATT
**
631924 AAAATTAAATTAAATATATTTAATTATTGTC
1 AAAATTAAATTAAATATATTTAATTAAAGTC
631955 AAAATTAAATTAAATTATATTTAA-TAAAG
1 AAAATTAAATTAAA-TATATTTAATTAAAG
631984 ATCAGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (31 bp):
AAAATTAAATTAAATATATTTAATTAAAGTC
Found at i:633933 original size:25 final size:25
Alignment explanation
Indices: 633905--633979 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 25
633895 AATATAAATA
633905 ATTTATAAAATTA-ATTAAATTTTTT
1 ATTT-TAAAATTATATTAAATTTTTT
* * *
633930 ATTTT-TAATTAATATTAAAATTTTA
1 ATTTTAAAATT-ATATTAAATTTTTT
*
633955 ATTTTAAATTTATATTAAATTTTTT
1 ATTTTAAAATTATATTAAATTTTTT
633980 TCATAAATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
23 4 0.10
24 2 0.05
25 31 0.77
26 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTTAAAATTATATTAAATTTTTT
Found at i:634096 original size:19 final size:20
Alignment explanation
Indices: 634053--634101 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
634043 TTAATTAAAT
* *
634053 AATTTTAAATATTTTAATTT
1 AATTTTAAATATTTAAATTA
*
634073 TATTTTAAATA-TTAAATTA
1 AATTTTAAATATTTAAATTA
634092 AATTTTAAAT
1 AATTTTAAAT
634102 TAAATTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTTTAAATATTTAAATTA
Found at i:634107 original size:12 final size:12
Alignment explanation
Indices: 634077--634107 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
634067 TAATTTTATT
*
634077 TTAAATATTAAA
1 TTAAATTTTAAA
634089 TTAAATTTTAAA
1 TTAAATTTTAAA
634101 TTAAATT
1 TTAAATT
634108 CAAAGTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TTAAATTTTAAA
Found at i:634863 original size:22 final size:22
Alignment explanation
Indices: 634798--634876 Score: 86
Period size: 22 Copynumber: 3.3 Consensus size: 22
634788 TTTTCTATTA
*
634798 ATAAAAAATTTTAATGTTATAAGT
1 ATAAAAAATTTTAA--TTATAATT
*
634822 ACAAAATAAATTATGTAATTATAATT
1 A-TAAA-AAATT-T-TAATTATAATT
634848 ATAAAAAATTTTAATTATAATT
1 ATAAAAAATTTTAATTATAATT
634870 ATAAAAA
1 ATAAAAA
634877 TCCTTAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
22 18 0.38
23 1 0.02
24 6 0.12
25 6 0.12
26 13 0.27
27 1 0.02
28 3 0.06
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (22 bp):
ATAAAAAATTTTAATTATAATT
Found at i:635118 original size:16 final size:18
Alignment explanation
Indices: 635064--635118 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 18
635054 TGATTTGAAA
635064 TAAATTAAATATTAATATTTT
1 TAAATT-AA-ATTAA-ATTTT
*
635085 AAAATTAAATTAAA-TTT
1 TAAATTAAATTAAATTTT
635102 TAAA-TAAA-TAAATTTT
1 TAAATTAAATTAAATTTT
635118 T
1 T
635119 TTTATAATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 4 0.13
16 8 0.26
17 6 0.19
18 1 0.03
19 5 0.16
20 2 0.06
21 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATTAAATTAAATTTT
Found at i:636531 original size:14 final size:14
Alignment explanation
Indices: 636508--636564 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
636498 AATACATAAA
*
636508 TTTTTATTTTTATT
1 TTTTTCTTTTTATT
636522 TTTTTCTTTTTATT
1 TTTTTCTTTTTATT
636536 TTCCTCTT-TCTTTTATTT
1 TT--T-TTCT-TTTTA-TT
636554 TTTTTCTTTTT
1 TTTTTCTTTTT
636565 CTTTCTCTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
14 15 0.42
15 6 0.17
16 4 0.11
17 7 0.19
18 4 0.11
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTCTTTTTATT
Found at i:636549 original size:26 final size:27
Alignment explanation
Indices: 636520--636582 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
636510 TTTATTTTTA
636520 TTTT-TTTCTTTTTATTTTCCTCTT-TC
1 TTTTATTTCTTTTTATTTTCCT-TTCTC
* *
636546 TTTTATTT-TTTTTCTTTTTCTTTCTC
1 TTTTATTTCTTTTTATTTTCCTTTCTC
*
636572 TTTTCTTTCTT
1 TTTTATTTCTT
636583 CCATTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 2 0.06
26 24 0.77
27 5 0.16
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.79
Consensus pattern (27 bp):
TTTTATTTCTTTTTATTTTCCTTTCTC
Found at i:636565 original size:20 final size:20
Alignment explanation
Indices: 636509--636582 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
636499 ATACATAAAT
*
636509 TTTTATTTTTATT-TTTTTC
1 TTTTATTTTTTTTCTTTTTC
* * *
636528 -TTT-TTATTTTCCTCTTTC
1 TTTTATTTTTTTTCTTTTTC
636546 TTTTATTTTTTTTCTTTTTC
1 TTTTATTTTTTTTCTTTTTC
* *
636566 TTTCTCTTTTCTTTCTT
1 TTT-TATTTTTTTTCTT
636583 CCATTTTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
17 5 0.12
18 8 0.19
19 3 0.07
20 15 0.36
21 11 0.26
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTATTTTTTTTCTTTTTC
Found at i:636589 original size:35 final size:32
Alignment explanation
Indices: 636520--636593 Score: 85
Period size: 35 Copynumber: 2.2 Consensus size: 32
636510 TTTATTTTTA
**
636520 TTTTTTTCTTTTTATTTTCCTCTTTCTTTTAT
1 TTTTTTTCTTTTTATTTTCCTCTTTCTTCCAT
* *
636552 TTTTTTTCTTTTTCTTTCTCTTTTCTTTCTTCCAT
1 TTTTTTTCTTTTTATTT-TC--CTCTTTCTTCCAT
636587 TTTTTTT
1 TTTTTTT
636594 TTCCCAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 16 0.46
33 2 0.06
35 17 0.49
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (32 bp):
TTTTTTTCTTTTTATTTTCCTCTTTCTTCCAT
Found at i:636593 original size:38 final size:38
Alignment explanation
Indices: 636507--636595 Score: 90
Period size: 38 Copynumber: 2.3 Consensus size: 38
636497 AAATACATAA
* * *
636507 ATTTTTATTTTTATTTTTTTCTTTTTATTTTCCTCTTTC
1 ATTTTT-TTTTTATCTTTTTCTTTCTATTTTCCTCTTCC
* * *
636546 -TTTTATTTTTTTTCTTTTTCTTTCTCTTTTCTTTCTTCC
1 ATTTT-TTTTTTATCTTTTTCTTTCTATTTTC-CTCTTCC
636585 ATTTTTTTTTT
1 ATTTTTTTTTT
636596 CCCAAAAGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
38 25 0.61
39 12 0.29
40 4 0.10
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.79
Consensus pattern (38 bp):
ATTTTTTTTTTATCTTTTTCTTTCTATTTTCCTCTTCC
Found at i:636786 original size:4 final size:4
Alignment explanation
Indices: 636779--636813 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
636769 TATATATATA
636779 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
636814 ACGTTGATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:637708 original size:20 final size:20
Alignment explanation
Indices: 637683--637722 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
637673 TCTTACACAA
*
637683 TATTTTCACTTTTTCTATTT
1 TATTTTCACTTTTTCAATTT
**
637703 TATTTTTTCTTTTTCAATTT
1 TATTTTCACTTTTTCAATTT
637723 CAGTTATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.72
Consensus pattern (20 bp):
TATTTTCACTTTTTCAATTT
Found at i:640602 original size:7 final size:7
Alignment explanation
Indices: 640592--640642 Score: 57
Period size: 7 Copynumber: 6.9 Consensus size: 7
640582 AAAAAAATTA
640592 TAAATAT
1 TAAATAT
640599 TAAATAT
1 TAAATAT
*
640606 TAAATTT
1 TAAATAT
640613 TAAATTTAT
1 TAAA--TAT
640622 TAAATAT
1 TAAATAT
*
640629 TAATTAAT
1 TAAAT-AT
640637 TAAATA
1 TAAATA
640643 AATCAATTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
7 25 0.68
8 6 0.16
9 6 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TAAATAT
Found at i:641112 original size:28 final size:30
Alignment explanation
Indices: 641075--641142 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
641065 CGTCTCAAAT
*
641075 TTTTTTAAAAGACTT-AGAATAATATTTTA
1 TTTTTTAAAAGACTTAAAAATAATATTTTA
***
641104 -TTTTTAAAATTTTTAAAAATAATATTTTA
1 TTTTTTAAAAGACTTAAAAATAATATTTTA
641133 TTTTTTAAAA
1 TTTTTTAAAA
641143 ATAATTATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 11 0.33
29 13 0.39
30 9 0.27
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (30 bp):
TTTTTTAAAAGACTTAAAAATAATATTTTA
Found at i:642656 original size:30 final size:31
Alignment explanation
Indices: 642617--642677 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
642607 AAAATTTAAG
*
642617 ATCAGTTTAAATTA-ATTTAAATATTTATTTT
1 ATCAGTTTAAAATATA-TTAAATATTTATTTT
*
642648 ATCA-TTTAAAATATATTAAATTTTTATTTT
1 ATCAGTTTAAAATATATTAAATATTTATTTT
642678 TATATTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (31 bp):
ATCAGTTTAAAATATATTAAATATTTATTTT
Found at i:642892 original size:30 final size:29
Alignment explanation
Indices: 642858--642946 Score: 76
Period size: 30 Copynumber: 3.0 Consensus size: 29
642848 AAGATAAAAT
642858 AAAATAATTAGTATAATTTTTAATTTAATA
1 AAAATAATTA-TATAATTTTTAATTTAATA
***
642888 AAAATAATT-TATTAAATATAACAATTTAA-A
1 AAAATAATTATA-T-AAT-TTTTAATTTAATA
* *
642918 ATAATAATTAAATAATTTTTAA-TTAATA
1 AAAATAATTATATAATTTTTAATTTAATA
642946 A
1 A
642947 TTTTAATTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
27 4 0.09
28 7 0.15
29 4 0.09
30 22 0.48
31 9 0.20
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (29 bp):
AAAATAATTATATAATTTTTAATTTAATA
Found at i:642952 original size:13 final size:14
Alignment explanation
Indices: 642922--642957 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
642912 TTTAAAATAA
642922 TAATTAAATAATTTT
1 TAATT-AATAATTTT
642937 TAATTAATAA-TTT
1 TAATTAATAATTTT
642950 TAATTAAT
1 TAATTAAT
642958 CGAACTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 11 0.52
14 5 0.24
15 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATTAATAATTTT
Found at i:643086 original size:3 final size:3
Alignment explanation
Indices: 643078--643119 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
643068 TTTAAGATTG
643078 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
643120 ATTCAAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:643449 original size:25 final size:26
Alignment explanation
Indices: 643418--643477 Score: 95
Period size: 25 Copynumber: 2.3 Consensus size: 26
643408 AAAAAATTAA
*
643418 AATTATATTATTTTAGTTTTT-TATT
1 AATTATATTATTTTAATTTTTATATT
643443 AATTATATTATTTTAATTTTTATATT
1 AATTATATTATTTTAATTTTTATATT
643469 AATTCATAT
1 AATT-ATAT
643478 AGTACTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 20 0.62
26 8 0.25
27 4 0.12
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (26 bp):
AATTATATTATTTTAATTTTTATATT
Found at i:643682 original size:16 final size:16
Alignment explanation
Indices: 643646--643683 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
643636 AATAATTTAT
*
643646 TTTA-TTATTTTAAAA
1 TTTATTTATATTAAAA
643661 TATTATTTATATTAAAA
1 T-TTATTTATATTAAAA
643678 TTTATT
1 TTTATT
643684 AAATAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 8 0.40
17 11 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATTTATATTAAAA
Found at i:644063 original size:23 final size:24
Alignment explanation
Indices: 644023--644074 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
644013 TATACGATTG
*
644023 ATAATTTATTTTATAAAAATTATT
1 ATAATTTATTTTAAAAAAATTATT
*
644047 ATAATTT-TTTTAAAAAATTTATT
1 ATAATTTATTTTAAAAAAATTATT
644070 ATAAT
1 ATAAT
644075 ATAATTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
ATAATTTATTTTAAAAAAATTATT
Found at i:644349 original size:16 final size:16
Alignment explanation
Indices: 644330--644363 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
644320 TTTTATTAAT
* *
644330 AATTTATTTTAAATTA
1 AATTAATTTAAAATTA
644346 AATTAATTTAAAATTA
1 AATTAATTTAAAATTA
644362 AA
1 AA
644364 AAAATTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTAATTTAAAATTA
Found at i:644663 original size:14 final size:14
Alignment explanation
Indices: 644643--644677 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
644633 TTTTTAAAAA
644643 AAATTATTTTATATT
1 AAATTATTTT-TATT
644658 -AATTATTTTTATT
1 AAATTATTTTTATT
644671 AAATTAT
1 AAATTAT
644678 AAAAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
AAATTATTTTTATT
Found at i:644723 original size:33 final size:33
Alignment explanation
Indices: 644663--644727 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
644653 ATATTAATTA
644663 TTTTTATTAAATTATAAAAATAATAATATAATAAT
1 TTTTTATT-AATTATAAAAATAATAATA-AATAAT
* **
644698 TTTTTATT-ATTTTAAAAATTTTAATAAATA
1 TTTTTATTAATTATAAAAATAATAATAAATA
644728 TTTATAGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 4 0.15
33 15 0.56
35 8 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
TTTTTATTAATTATAAAAATAATAATAAATAAT
Found at i:646015 original size:2 final size:2
Alignment explanation
Indices: 646008--646033 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
645998 CCCATAAATC
646008 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
646034 GTACGATTTT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:647236 original size:27 final size:27
Alignment explanation
Indices: 647166--647236 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 27
647156 GTATTGATGA
647166 TTTTAATATATATTT-AATAATTAAAATT
1 TTTTAAT-T-TATTTAAATAATTAAAATT
*
647194 TTTTATATTTA-ATAAATAATT-AAATAT
1 TTTTA-ATTTATTTAAATAATTAAAAT-T
647221 TTTTAATTTATTTAAA
1 TTTTAATTTATTTAAA
647237 ACTCGATGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
26 10 0.27
27 19 0.51
28 6 0.16
29 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTTTAATTTATTTAAATAATTAAAATT
Found at i:648612 original size:2 final size:2
Alignment explanation
Indices: 648605--648630 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
648595 TTGAACCTAG
648605 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
648631 AAATGAAAAC
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:649266 original size:2 final size:2
Alignment explanation
Indices: 649259--649309 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
649249 TCAAGAAAAC
*
649259 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
649301 TA CA TA TA T
1 TA TA TA TA T
649310 CAGTAAATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:653347 original size:18 final size:18
Alignment explanation
Indices: 653309--653383 Score: 64
Period size: 18 Copynumber: 4.1 Consensus size: 18
653299 TATAATATGA
653309 AAATAT-AAAAATATGTAAT
1 AAATATGAAAAAT-T-TAAT
653328 AAATATGAAAAATTTAAT
1 AAATATGAAAAATTTAAT
* *
653346 AAATATAAAATAATATAA-
1 AAATATGAAA-AATTTAAT
* *
653364 ATATATGATATAATTTAAT
1 AAATATGA-AAAATTTAAT
653383 A
1 A
653384 TAGTAAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
18 25 0.54
19 15 0.33
20 6 0.13
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (18 bp):
AAATATGAAAAATTTAAT
Found at i:653416 original size:28 final size:28
Alignment explanation
Indices: 653362--653441 Score: 128
Period size: 28 Copynumber: 2.9 Consensus size: 28
653352 AAAATAATAT
*
653362 AAATA-TA-TGATATAATTTAATATAGTA
1 AAATATTATTGATATAA-TTAATGTAGTA
653389 AAATATTATTGATATAATTAATGTAGTA
1 AAATATTATTGATATAATTAATGTAGTA
653417 AAATATTATTGATATAATTAATGTA
1 AAATATTATTGATATAATTAATGTA
653442 ACACATTTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
27 5 0.10
28 37 0.74
29 8 0.16
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (28 bp):
AAATATTATTGATATAATTAATGTAGTA
Found at i:653685 original size:22 final size:22
Alignment explanation
Indices: 653657--653699 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
653647 AATATTAAAA
653657 ATATTTTTATAA-TAATATTTAT
1 ATATTTTTATAATTAA-ATTTAT
653679 ATATTTTTATAATTAAATTTA
1 ATATTTTTATAATTAAATTTA
653700 AATAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATTTTTATAATTAAATTTAT
Found at i:654237 original size:18 final size:18
Alignment explanation
Indices: 654222--654256 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
654212 TTAAAAATGA
654222 GTTTAAGTAAAAAAATAG
1 GTTTAAGTAAAAAAATAG
*
654240 GTTTATGTAAAAAAATA
1 GTTTAAGTAAAAAAATA
654257 TATTGAGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.31
Consensus pattern (18 bp):
GTTTAAGTAAAAAAATAG
Found at i:654410 original size:23 final size:22
Alignment explanation
Indices: 654380--654425 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
654370 TATTATTTAC
* * *
654380 ATTTTTAACTTTAATAAATTAA
1 ATTTTTAAATTTAAAAAACTAA
654402 ATTTATTAAATTTAAAAAACTAA
1 ATTT-TTAAATTTAAAAAACTAA
654425 A
1 A
654426 AAAAATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTTTAAATTTAAAAAACTAA
Found at i:655444 original size:27 final size:27
Alignment explanation
Indices: 655413--655468 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
655403 TTTATCAAAG
* * *
655413 ATTTAATT-TTTAAATTTTAAAAAATT
1 ATTTTATTATTTAAAATATAAAAAATT
*
655439 ATTTTATTATTTAAAATATAATAAATT
1 ATTTTATTATTTAAAATATAAAAAATT
655466 ATT
1 ATT
655469 AAAATTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTTTATTATTTAAAATATAAAAAATT
Found at i:655485 original size:16 final size:18
Alignment explanation
Indices: 655444--655485 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
655434 AAATTATTTT
655444 ATTATTTAAAATATAATAA
1 ATTA-TTAAAATATAATAA
655463 ATTATTAAAAT-TAA-AA
1 ATTATTAAAATATAATAA
*
655479 TTTATTA
1 ATTATTA
655486 TTAAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 8 0.36
17 3 0.14
18 7 0.32
19 4 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTATTAAAATATAATAA
Found at i:655485 original size:19 final size:19
Alignment explanation
Indices: 655441--655496 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
655431 AAAAAATTAT
*
655441 TTTATTATTTAAAA-TATAA
1 TTTATTA-TTAAAATTAAAA
**
655460 TAAATTATTAAAATTAAAA
1 TTTATTATTAAAATTAAAA
*
655479 TTTATTATTAAATTTAAA
1 TTTATTATTAAAATTAAA
655497 TAAAAATAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 6 0.20
19 24 0.80
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTATTATTAAAATTAAAA
Found at i:655774 original size:25 final size:25
Alignment explanation
Indices: 655739--655805 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 25
655729 TTATTTAAAA
655739 TATAATAAAATATT-AAATTTATTTT
1 TATAATAAAAT-TTAAAATTTATTTT
*
655764 TATAATTAAATTTAAAAATTTATTTAT
1 TATAATAAAATTT-AAAATTTATTT-T
*
655791 TA-AATGATAATTTAA
1 TATAAT-AAAATTTAA
655806 GACAAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
24 2 0.06
25 10 0.29
26 15 0.43
27 8 0.23
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (25 bp):
TATAATAAAATTTAAAATTTATTTT
Found at i:655782 original size:26 final size:27
Alignment explanation
Indices: 655753--655805 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
655743 ATAAAATATT
*
655753 AAATTTATTT-TTATAATTA-AATTTAA
1 AAATTTATTTATTA-AATGATAATTTAA
655779 AAATTTATTTATTAAATGATAATTTAA
1 AAATTTATTTATTAAATGATAATTTAA
655806 GACAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (27 bp):
AAATTTATTTATTAAATGATAATTTAA
Found at i:661759 original size:2 final size:2
Alignment explanation
Indices: 661746--661792 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
661736 TGACAACCTC
*
661746 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
661788 AT AT A
1 AT AT A
661793 ACAATTTCCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:665938 original size:12 final size:12
Alignment explanation
Indices: 665921--665947 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
665911 CACATACTTG
665921 CGTCCAAACATA
1 CGTCCAAACATA
665933 CGTCCAAACATA
1 CGTCCAAACATA
665945 CGT
1 CGT
665948 TAGATATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.33, G:0.11, T:0.19
Consensus pattern (12 bp):
CGTCCAAACATA
Found at i:668570 original size:14 final size:15
Alignment explanation
Indices: 668537--668581 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 15
668527 CAAAATTTAA
668537 ATTATAATATATATTT
1 ATTATAAT-TATATTT
*
668553 TTTATTATATTATATTT
1 ATTA-TA-ATTATATTT
668570 ATTATAATTATA
1 ATTATAATTATA
668582 AATGTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 6 0.24
16 5 0.20
17 12 0.48
18 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTATAATTATATTT
Found at i:669419 original size:13 final size:14
Alignment explanation
Indices: 669401--669431 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
669391 TTATTTAAAC
669401 TAAAAAA-TATTTT
1 TAAAAAAGTATTTT
669414 TAAAAAAGTATTTT
1 TAAAAAAGTATTTT
669428 TAAA
1 TAAA
669432 GCACTCGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
TAAAAAAGTATTTT
Found at i:669532 original size:15 final size:14
Alignment explanation
Indices: 669499--669549 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
669489 TAATGAAAGA
*
669499 AATATTTTAATTTT
1 AATATTTTAAATTT
*
669513 GATATTATTAAATTT
1 AATATT-TTAAATTT
*
669528 AATATTTTAATTTT
1 AATATTTTAAATTT
*
669542 TATATTTT
1 AATATTTT
669550 TAAAATTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (14 bp):
AATATTTTAAATTT
Found at i:669532 original size:29 final size:31
Alignment explanation
Indices: 669499--669562 Score: 96
Period size: 29 Copynumber: 2.1 Consensus size: 31
669489 TAATGAAAGA
669499 AATATTTTAATTTTGATATTATT-AAA-TTT
1 AATATTTTAATTTTGATATTATTAAAATTTT
* *
669528 AATATTTTAATTTTTATATTTTTAAAATTTT
1 AATATTTTAATTTTGATATTATTAAAATTTT
669559 AATA
1 AATA
669563 AATAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 21 0.68
30 3 0.10
31 7 0.23
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (31 bp):
AATATTTTAATTTTGATATTATTAAAATTTT
Found at i:669538 original size:8 final size:8
Alignment explanation
Indices: 669499--669562 Score: 50
Period size: 8 Copynumber: 8.5 Consensus size: 8
669489 TAATGAAAGA
669499 AATATTTT
1 AATATTTT
669507 -A-ATTTT
1 AATATTTT
*
669513 GATATTATT
1 AATATT-TT
669522 AA-A-TTT
1 AATATTTT
669528 AATATTTT
1 AATATTTT
669536 AAT-TTTT
1 AATATTTT
669543 -ATATTTTT
1 AATA-TTTT
*
669551 AAAATTTT
1 AATATTTT
669559 AATA
1 AATA
669563 AATAAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
6 11 0.24
7 8 0.18
8 21 0.47
9 5 0.11
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (8 bp):
AATATTTT
Found at i:669550 original size:15 final size:15
Alignment explanation
Indices: 669499--669562 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
669489 TAATGAAAGA
669499 AATA-TTTTAATTTT
1 AATATTTTTAATTTT
* * *
669513 GATATTATTAAATTT
1 AATATTTTTAATTTT
669528 AATA-TTTTAATTTT
1 AATATTTTTAATTTT
*
669542 TATATTTTTAAAATTTT
1 AATATTTTT--AATTTT
669559 AATA
1 AATA
669563 AATAAAAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
14 14 0.37
15 15 0.39
17 9 0.24
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
AATATTTTTAATTTT
Found at i:669804 original size:14 final size:14
Alignment explanation
Indices: 669785--669833 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
669775 TTACAATTTC
669785 AAATATAAAAATTA
1 AAATATAAAAATTA
* *
669799 AAATATTAAATTTA
1 AAATATAAAAATTA
669813 ATAATATAAAAATTA
1 A-AATATAAAAATTA
669828 AAATAT
1 AAATAT
669834 TTTTTTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATATAAAAATTA
Found at i:669805 original size:29 final size:29
Alignment explanation
Indices: 669773--669861 Score: 101
Period size: 29 Copynumber: 3.0 Consensus size: 29
669763 AATTTTTATT
*
669773 TATTACAATTTCA-AATATAAAAATTAAAA
1 TATTA-AATTTAATAATATAAAAATTAAAA
669802 TATTAAATTTAATAATATAAAAATTAAAA
1 TATTAAATTTAATAATATAAAAATTAAAA
** *
669831 TATT-TTTTTATTATAATAAAAAAATTAAAA
1 TATTAAATTTA--ATAATATAAAAATTAAAA
669861 T
1 T
669862 TTTATTTTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
28 10 0.19
29 25 0.47
30 18 0.34
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (29 bp):
TATTAAATTTAATAATATAAAAATTAAAA
Found at i:669809 original size:21 final size:21
Alignment explanation
Indices: 669785--669829 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
669775 TTACAATTTC
669785 AAATATAAAAAT-TAAAATATT
1 AAATATAAAAATATAAAA-ATT
* *
669806 AAATTTAATAATATAAAAATT
1 AAATATAAAAATATAAAAATT
669827 AAA
1 AAA
669830 ATATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATATAAAAATATAAAAATT
Found at i:669888 original size:14 final size:14
Alignment explanation
Indices: 669871--669939 Score: 70
Period size: 15 Copynumber: 4.9 Consensus size: 14
669861 TTTTATTTTT
669871 AAATATATAATATA
1 AAATATATAATATA
*
669885 AAATATAAAAATATA
1 AAATAT-ATAATATA
*
669900 AAAAATATAAATATA
1 AAATATAT-AATATA
*
669915 AAATAATATATTA-A
1 AAAT-ATATAATATA
669929 AAATA-ATAATA
1 AAATATATAATA
669940 AAGCGTACGA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
12 5 0.11
13 1 0.02
14 12 0.26
15 24 0.52
16 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATATATAATATA
Found at i:670656 original size:22 final size:22
Alignment explanation
Indices: 670629--670671 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
670619 ATTTAATTAA
* *
670629 TTTTAACTATATAAAATATAAC
1 TTTTAAATATATAAAAAATAAC
670651 TTTTAAATATATAAAAAATAA
1 TTTTAAATATATAAAAAATAA
670672 TATATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTAAATATATAAAAAATAAC
Found at i:671182 original size:1 final size:1
Alignment explanation
Indices: 671176--671200 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
671166 TATTATTTAG
671176 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
671201 CCCGTCGCAG
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:672659 original size:23 final size:24
Alignment explanation
Indices: 672609--672659 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
672599 AATGGTTCGA
*
672609 AATTTTTTAAATTAATTAATTTAT
1 AATTATTTAAATTAATTAATTTAT
* *
672633 -ATTATTTATATTTATT-ATTTAT
1 AATTATTTAAATTAATTAATTTAT
672655 AATTA
1 AATTA
672660 ATAAAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
AATTATTTAAATTAATTAATTTAT
Found at i:672971 original size:19 final size:19
Alignment explanation
Indices: 672916--672971 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
672906 TGTTTAATAT
672916 TAATATTATATTTATATTTAA
1 TAAT-TTATA-TTATATTTAA
*
672937 -AATTT-TAATATATTTAA
1 TAATTTATATTATATTTAA
*
672954 TAATTTATATTCTATTTA
1 TAATTTATATTATATTTA
672972 TGTTCACGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 9 0.30
18 7 0.23
19 11 0.37
20 3 0.10
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TAATTTATATTATATTTAA
Done.