Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008099.1 Hibiscus syriacus cultivar Beakdansim tig00110627_pilon, whole genome shotgun sequence
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: 767286
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 3 of 5
Found at i:365873 original size:38 final size:37
Alignment explanation
Indices: 365818--365938 Score: 136
Period size: 38 Copynumber: 3.1 Consensus size: 37
365808 ACTAAAGTTG
365818 ATATTTATATA-TGAACTATAGTTTACATATAAATTAT
1 ATATTTATATACT-AACTATAGTTTACATATAAATTAT
365855 ATAGTTTATATACTAACTATAGTTTACATATAAAATATAGTT
1 ATA-TTTATATACTAACTATAGTTTACATAT-AAAT-TA--T
* * * *
365897 GATATTTACATACGAACTATAGTTTACATATGAACTAT
1 -ATATTTATATACTAACTATAGTTTACATATAAATTAT
365935 ATAT
1 ATAT
365939 ATGAACTATA
Statistics
Matches: 73, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
37 7 0.10
38 26 0.36
39 5 0.07
40 4 0.05
41 2 0.03
42 26 0.36
43 3 0.04
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (37 bp):
ATATTTATATACTAACTATAGTTTACATATAAATTAT
Found at i:365942 original size:13 final size:13
Alignment explanation
Indices: 365924--365951 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
365914 TATAGTTTAC
365924 ATATGAACTATAT
1 ATATGAACTATAT
365937 ATATGAACTATAT
1 ATATGAACTATAT
365950 AT
1 AT
365952 TTTACATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (13 bp):
ATATGAACTATAT
Found at i:365948 original size:31 final size:32
Alignment explanation
Indices: 365910--365973 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
365900 ATTTACATAC
365910 GAAC-TATAGTTTACATATGAACTATATATAT
1 GAACATATAGTTTACATATGAACTATATATAT
* * *
365941 GAACTATATATTTTACATTTGACCTATATATAT
1 GAAC-ATATAGTTTACATATGAACTATATATAT
365974 ATATATACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 4 0.14
33 24 0.86
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (32 bp):
GAACATATAGTTTACATATGAACTATATATAT
Found at i:365970 original size:2 final size:2
Alignment explanation
Indices: 365965--366089 Score: 64
Period size: 2 Copynumber: 60.0 Consensus size: 2
365955 ACATTTGACC
*
365965 TA TA TA TA TA TA TA TA CTA TA GT- TGA TA T- TA CTA TA TA GTT TA
1 TA TA TA TA TA TA TA TA -TA TA -TA T-A TA TA TA -TA TA TA -TA TA
* * *
366008 CA TA TGA CT- TA TA TA TA TA TA CTA TA GTT TA TA TT TA TA TA T-
1 TA TA T-A -TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA
*
366050 TA TA TA T- TA TA TA TA TA AA CTA TA TA TA CTA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA
366090 ATTTACATAT
Statistics
Matches: 96, Mismatches: 10, Indels: 34
0.69 0.07 0.24
Matches are distributed among these distances:
1 6 0.06
2 75 0.78
3 14 0.15
4 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:366039 original size:20 final size:20
Alignment explanation
Indices: 365964--366089 Score: 89
Period size: 20 Copynumber: 6.0 Consensus size: 20
365954 TACATTTGAC
365964 CTATATATATATATATACTATA
1 CTATATAT-TATATATA-TATA
* *
365986 GT-TGATATTACTATATAGTTTA
1 CTAT-ATATTA-TATATA-TATA
366008 C-ATATGACTTATATATATATA
1 CTATAT-A-TTATATATATATA
*
366029 CTATAGT-TTATATTTATATA
1 CTATA-TATTATATATATATA
* *
366049 TTATATATTATATATATAAA
1 CTATATATTATATATATATA
366069 CTATATA-TACTATATAATATA
1 CTATATATTA-TATAT-ATATA
366090 ATTTACATAT
Statistics
Matches: 83, Mismatches: 11, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
19 3 0.04
20 38 0.46
21 13 0.16
22 25 0.30
23 4 0.05
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (20 bp):
CTATATATTATATATATATA
Found at i:366083 original size:34 final size:33
Alignment explanation
Indices: 366037--366111 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 33
366027 TACTATAGTT
* * *
366037 TATATTTATATATTATAT-ATTATATATATAAAC
1 TATATATATATATAATATAATT-TACATATAAAC
*
366070 TATATATACTATATAATATAATTTACATATGAAC
1 TATATATA-TATATAATATAATTTACATATAAAC
*
366104 TATTTATA
1 TATATATA
366112 AAAATCATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
33 7 0.20
34 25 0.71
35 3 0.09
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.48
Consensus pattern (33 bp):
TATATATATATATAATATAATTTACATATAAAC
Found at i:366223 original size:49 final size:50
Alignment explanation
Indices: 366170--366284 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 50
366160 AATAATTTAT
*
366170 ACTATAGTATATATAAACCATATA-T-TATATAGTTCATTAGTATATATAA
1 ACTATA-TATATATAAACCATACATTATATATAGTTCATTAGTATATATAA
* *
366219 ACTATATAATATATAAACTATACATTATATATATTTCATTAGTATATATAA
1 ACTATAT-ATATATAAACCATACATTATATATAGTTCATTAGTATATATAA
366270 ACTATATATTATATA
1 ACTATATA-TATATA
366285 GTTCATTAGT
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
48 1 0.02
49 20 0.34
50 2 0.03
51 36 0.61
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (50 bp):
ACTATATATATATAAACCATACATTATATATAGTTCATTAGTATATATAA
Found at i:366239 original size:84 final size:85
Alignment explanation
Indices: 366141--366327 Score: 247
Period size: 84 Copynumber: 2.2 Consensus size: 85
366131 ACTATAGTTG
* *
366141 ATATTTATATACTATATAAAATA-AT-TTAT-ACTATAGTATATATAAACCATATATTATATAGT
1 ATATATATAAACTATATAAAATATATATT-TCA-T-TAGTATATATAAACCATATATTATATAGT
366203 TCATTAGTATATATAAACTATAT
63 TCATTAGTATATATAAACTATAT
* ** *
366226 A-ATATATAAACTATACATTATATATATTTCATTAGTATATATAAACTATATATTATATAGTTCA
1 ATATATATAAACTATATAAAATATATATTTCATTAGTATATATAAACCATATATTATATAGTTCA
366290 TTAGTATATATAAACTATAT
66 TTAGTATATATAAACTATAT
*
366310 ATTATATGTAAACTATAT
1 A-TATATATAAACTATAT
366328 TAGTGTACTA
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
84 68 0.76
85 5 0.06
86 16 0.18
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (85 bp):
ATATATATAAACTATATAAAATATATATTTCATTAGTATATATAAACCATATATTATATAGTTCA
TTAGTATATATAAACTATAT
Found at i:366271 original size:35 final size:35
Alignment explanation
Indices: 366227--366316 Score: 148
Period size: 33 Copynumber: 2.6 Consensus size: 35
366217 AAACTATATA
* *
366227 ATATATAAACTATACATTATATATATTTCATTAGT
1 ATATATAAACTATATATTATATATAGTTCATTAGT
366262 ATATATAAACTATATA-T-TATATAGTTCATTAGT
1 ATATATAAACTATATATTATATATAGTTCATTAGT
366295 ATATATAAACTATATATTATAT
1 ATATATAAACTATATATTATAT
366317 GTAAACTATA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
33 31 0.61
34 2 0.04
35 18 0.35
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (35 bp):
ATATATAAACTATATATTATATATAGTTCATTAGT
Found at i:366363 original size:21 final size:21
Alignment explanation
Indices: 366338--366499 Score: 125
Period size: 21 Copynumber: 7.5 Consensus size: 21
366328 TAGTGTACTA
* *
366338 TATAGTTTATACTTTATAACC
1 TATAGTTTATAATTTATAAAC
*
366359 TATAGTATATAATTTATAAAC
1 TATAGTTTATAATTTATAAAC
366380 TATAGTTTATAATTTATAAAC
1 TATAGTTTATAATTTATAAAC
* *
366401 TATAGTTTATATTAATGTTAATTATC
1 TATAG-TT-TA-TAAT-TT-ATAAAC
**
366427 T-TA-ACTATAATTTATATTAA-
1 TATAGTTTATAATTTATA--AAC
* *
366447 TATAGTATATATTTTATAAAC
1 TATAGTTTATAATTTATAAAC
* *
366468 TATACTATATAATTTAT-AAC
1 TATAGTTTATAATTTATAAAC
366488 ATATAGTTTATA
1 -TATAGTTTATA
366500 TTAATATTAA
Statistics
Matches: 113, Mismatches: 17, Indels: 22
0.74 0.11 0.14
Matches are distributed among these distances:
19 2 0.02
20 8 0.07
21 74 0.65
22 14 0.12
23 2 0.02
24 4 0.04
25 4 0.04
26 5 0.04
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.48
Consensus pattern (21 bp):
TATAGTTTATAATTTATAAAC
Found at i:366457 original size:88 final size:88
Alignment explanation
Indices: 366359--366565 Score: 260
Period size: 88 Copynumber: 2.4 Consensus size: 88
366349 CTTTATAACC
* * *
366359 TATAGTATATAATTTATAAACTATAGTTTATAATTTATAA-ACTATAGTTTATATTAATGTTAA-
1 TATAGTATATAATTTATAAACTATACTATATAATTTATAACA-TATAGTTTATATTAATATTAAC
*
366422 TTATCTTA-ACTATAATTTATATTAA
65 TT-T-ATAGACTATAATTTATATTAA
*
366447 TATAGTATATATTTTATAAACTATACTATATAATTTATAACATATAGTTTATATTAATATTAACT
1 TATAGTATATAATTTATAAACTATACTATATAATTTATAACATATAGTTTATATTAATATTAACT
*
366512 TTATAGACTATATTTTATATTAA
66 TTATAGACTATAATTTATATTAA
* * * *
366535 TATTAAT-TACAAATTATAAACTATATTATAT
1 TA-TAGTATATAATTTATAAACTATACTATAT
366566 TAATATAAGT
Statistics
Matches: 104, Mismatches: 11, Indels: 8
0.85 0.09 0.07
Matches are distributed among these distances:
87 2 0.02
88 96 0.92
89 6 0.06
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (88 bp):
TATAGTATATAATTTATAAACTATACTATATAATTTATAACATATAGTTTATATTAATATTAACT
TTATAGACTATAATTTATATTAA
Found at i:366479 original size:81 final size:82
Alignment explanation
Indices: 366394--366626 Score: 203
Period size: 88 Copynumber: 2.8 Consensus size: 82
366384 GTTTATAATT
* * * *
366394 TATAAACTATAGTTTATATTAATGTTAATTATCTTA-ACTATAATTTATATTAATA-TAGTATAT
1 TATAAACTATAGTTTATATTAATATTAATTAT-ATAGACTATAATTTATATTAATATTAAT-TAC
**
366457 ATTTTATAAACTATACTATA
64 AAATTATAAACTATAC-ATA
*
366477 TAATTTATAACATATAGTTTATATTAATATTAACTT-TATAGACTATATTTTATATTAATATTAA
1 T-A--TA-AAC-TATAGTTTATATTAATATTAA-TTATATAGACTATAATTTATATTAATATTAA
*
366541 TTACAAATTATAAACTATA-TTA
60 TTACAAATTATAAACTATACATA
* * * * *
366563 TATTAA-TATAAGTTAATATTAATATTAATTATA-ATA-TATAA-TTATTTTAATATTAATTATA
1 TATAAACTAT-AGTTTATATTAATATTAATTATATAGACTATAATTTATATTAATATTAATTACA
366624 AAT
65 AAT
366627 AATTTATTAA
Statistics
Matches: 126, Mismatches: 14, Indels: 25
0.76 0.08 0.15
Matches are distributed among these distances:
78 21 0.17
79 4 0.03
80 7 0.06
81 19 0.15
82 2 0.02
83 2 0.02
84 1 0.01
85 1 0.01
86 5 0.04
87 5 0.04
88 54 0.43
89 5 0.04
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (82 bp):
TATAAACTATAGTTTATATTAATATTAATTATATAGACTATAATTTATATTAATATTAATTACAA
ATTATAAACTATACATA
Found at i:366529 original size:31 final size:31
Alignment explanation
Indices: 366480--366540 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
366470 TACTATATAA
366480 TTTATAACATATAGTTTATATTAATATTAAC
1 TTTATAACATATAGTTTATATTAATATTAAC
*
366511 TTTATAGAC-TATATTTTATATTAATATTAA
1 TTTATA-ACATATAGTTTATATTAATATTAA
366541 TTACAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (31 bp):
TTTATAACATATAGTTTATATTAATATTAAC
Found at i:366580 original size:44 final size:44
Alignment explanation
Indices: 366531--366615 Score: 111
Period size: 44 Copynumber: 1.9 Consensus size: 44
366521 ATATTTTATA
366531 TTAATATTAATTACAAATTATAA-ACTAT-ATTATATTAATATAAG
1 TTAATATTAA-TACAAATTATAATA-TATAATTATATTAATATAAG
** *
366575 TTAATATTAATATTAATTATAATATATAATTATTTTAATAT
1 TTAATATTAATACAAATTATAATATATAATTATATTAATAT
366616 TAATTATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 13 0.36
44 23 0.64
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (44 bp):
TTAATATTAATACAAATTATAATATATAATTATATTAATATAAG
Found at i:366583 original size:16 final size:16
Alignment explanation
Indices: 366562--366624 Score: 65
Period size: 16 Copynumber: 3.8 Consensus size: 16
366552 AAACTATATT
*
366562 ATATTAATATAAGTTA
1 ATATTAATATAATTTA
366578 ATATTAATATTAATTATA
1 ATATTAATA-TAATT-TA
*
366596 ATATATAAT-TATTTTA
1 ATAT-TAATATAATTTA
366612 ATATTAATTATAA
1 ATATTAA-TATAA
366625 ATAATTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
15 3 0.08
16 16 0.41
17 10 0.26
18 6 0.15
19 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATATTAATATAATTTA
Found at i:366599 original size:28 final size:26
Alignment explanation
Indices: 366495--366644 Score: 100
Period size: 28 Copynumber: 5.7 Consensus size: 26
366485 AACATATAGT
*
366495 TTATATTAATATTAACTTTATAGACTATATT
1 TTATATTAATATTAA--TTATA-A-TATA-A
*
366526 TTATATTAATATTAATTACAAATTATAAA
1 TTATATTAATATTAATTA-TAA-TAT-AA
*
366555 CTATATT-ATATTAA-TATAAGT-T-A
1 TTATATTAATATTAATTATAA-TATAA
366578 --ATATTAATATTAATTATAATATATAA
1 TTATATTAATATTAATTAT-A-ATATAA
*
366604 TTATTTTAATATTAATTATAA-ATAA
1 TTATATTAATATTAATTATAATATAA
*
366629 TT-TATTAATATAAATT
1 TTATATTAATATTAATT
366645 TTATAGGGAT
Statistics
Matches: 100, Mismatches: 9, Indels: 27
0.74 0.07 0.20
Matches are distributed among these distances:
21 5 0.05
22 7 0.07
23 4 0.04
24 14 0.14
25 9 0.09
26 5 0.05
27 3 0.03
28 23 0.23
29 13 0.13
30 2 0.02
31 15 0.15
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (26 bp):
TTATATTAATATTAATTATAATATAA
Found at i:370790 original size:13 final size:13
Alignment explanation
Indices: 370771--370808 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
370761 TAATTTAGTG
370771 ATTATAAATAA-A
1 ATTATAAATAAGA
370783 ATTTATAATATAAGA
1 A-TTATAA-ATAAGA
370798 ATTATAAATAA
1 ATTATAAATAA
370809 TATAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
ATTATAAATAAGA
Found at i:370818 original size:19 final size:19
Alignment explanation
Indices: 370787--370904 Score: 74
Period size: 19 Copynumber: 6.5 Consensus size: 19
370777 AATAAAATTT
370787 ATAATAT-AAGAATTATAA
1 ATAATATAAAGAATTATAA
370805 ATAATATAAAGAATT-TGAA
1 ATAATATAAAGAATTAT-AA
* **
370824 TTAATATAAA-AATCATATTT
1 ATAATATAAAGAAT--TATAA
**
370844 ATAATATTCA-AA-T-T--
1 ATAATATAAAGAATTATAA
370858 ATAATAT-AAGAATTATAA
1 ATAATATAAAGAATTATAA
* *
370876 AAAATATAAAGAATTGTAA
1 ATAATATAAAGAATTATAA
*
370895 TTAATATAAA
1 ATAATATAAA
370905 AACTAAATTT
Statistics
Matches: 78, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
13 1 0.01
14 9 0.12
15 1 0.01
16 2 0.03
17 1 0.01
18 17 0.22
19 36 0.46
20 10 0.13
21 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.36
Consensus pattern (19 bp):
ATAATATAAAGAATTATAA
Found at i:370954 original size:26 final size:27
Alignment explanation
Indices: 370908--370960 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
370898 ATATAAAAAC
* *
370908 TAAATTTAATTATCATAAATT-TATTA
1 TAAATTTAAATAACATAAATTATATTA
370934 TAAATTTAAAATAACAT-AATTATATTA
1 TAAATTT-AAATAACATAAATTATATTA
370961 ATTATAGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (27 bp):
TAAATTTAAATAACATAAATTATATTA
Found at i:374578 original size:35 final size:35
Alignment explanation
Indices: 374533--374653 Score: 161
Period size: 35 Copynumber: 3.4 Consensus size: 35
374523 GGTAACCAAC
374533 TTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 TTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
* **
374569 TTTGGAAAATGGGTTTCAAAGTTTGGTAAATGTTT
1 TTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
374604 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 -TTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
374641 ATTGAAAAATGAT
1 TTTGAAAAATGAT
374654 AATGGAATAA
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
35 30 0.41
36 22 0.30
37 22 0.30
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.43
Consensus pattern (35 bp):
TTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:374632 original size:37 final size:36
Alignment explanation
Indices: 374533--374650 Score: 150
Period size: 36 Copynumber: 3.3 Consensus size: 36
374523 GGTAACCAAC
374533 TTTGAAAAA-ATGATTTTCAAAGTTTGGTAAATGTTT
1 TTTGAAAAATA-GATTTTCAAAGTTTGGTAAATGTTT
* **
374569 TTTGGAAAAT-GGGTTTCAAAGTTTGGTAAATGTTT
1 TTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
* *
374604 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 -TTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
*
374641 ATTGAAAAAT
1 TTTGAAAAAT
374651 GATAATGGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
35 23 0.32
36 26 0.37
37 22 0.31
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.43
Consensus pattern (36 bp):
TTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTT
Found at i:379197 original size:36 final size:37
Alignment explanation
Indices: 379144--379227 Score: 127
Period size: 37 Copynumber: 2.3 Consensus size: 37
379134 TGGCAACCAA
379144 CTTTGAAAAAATAA-TTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATAATTTTTCAAAGTTTGGTAAATGTTT
*
379181 CTTTGAAAAATAATTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAATTTTTCAAAGTTTGGTAAATGTTT
*
379218 -GTTGAAAAAT
1 CTTTGAAAAAT
379228 GATAATGAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
36 17 0.39
37 27 0.61
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (37 bp):
CTTTGAAAAATAATTTTTCAAAGTTTGGTAAATGTTT
Found at i:389907 original size:17 final size:17
Alignment explanation
Indices: 389885--389917 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
389875 TAACATGATA
389885 AAAATCTAT-TTTAAAAC
1 AAAATCT-TGTTTAAAAC
389902 AAAATCTTGTTTAAAA
1 AAAATCTTGTTTAAAA
389918 TGATATGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (17 bp):
AAAATCTTGTTTAAAAC
Found at i:390094 original size:2 final size:2
Alignment explanation
Indices: 390087--390114 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
390077 CATGTGCCCT
390087 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
390115 ATTAGTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:390937 original size:105 final size:105
Alignment explanation
Indices: 390798--391007 Score: 411
Period size: 105 Copynumber: 2.0 Consensus size: 105
390788 GCTTTTGCCT
390798 TTCTAAGGGTTGACAACAATGTCAACCACATAACTTATTCGGCTTTCTGTGATGCTCTTACACAA
1 TTCTAAGGGTTGACAACAATGTCAACCACATAACTTATTCGGCTTTCTGTGATGCTCTTACACAA
390863 CTTCTCTTCATTCACTTTATTGAGATAATTAGTATAATTG
66 CTTCTCTTCATTCACTTTATTGAGATAATTAGTATAATTG
*
390903 TTCTAAGGGTTGACAACAATGTCAACCACATAACTTATTCGGCTTTCTGTGATGCTCTTACACAG
1 TTCTAAGGGTTGACAACAATGTCAACCACATAACTTATTCGGCTTTCTGTGATGCTCTTACACAA
390968 CTTCTCTTCATTCACTTTATTGAGATAATTAGTATAATTG
66 CTTCTCTTCATTCACTTTATTGAGATAATTAGTATAATTG
391008 CAGTGATGAA
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (105 bp):
TTCTAAGGGTTGACAACAATGTCAACCACATAACTTATTCGGCTTTCTGTGATGCTCTTACACAA
CTTCTCTTCATTCACTTTATTGAGATAATTAGTATAATTG
Found at i:395304 original size:2 final size:2
Alignment explanation
Indices: 395297--395327 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
395287 TTTAATTGAA
395297 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
395328 GAGAGGGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:405352 original size:13 final size:14
Alignment explanation
Indices: 405328--405356 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
405318 TAGGTAAACA
405328 CGGTAGAAAAAATC
1 CGGTAGAAAAAATC
405342 CGGTA-AAAAAATC
1 CGGTAGAAAAAATC
405355 CG
1 CG
405357 AATTTGACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.14
Consensus pattern (14 bp):
CGGTAGAAAAAATC
Found at i:410427 original size:17 final size:17
Alignment explanation
Indices: 410405--410441 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
410395 CAATATCTGG
410405 GGCTGCCTGCCGTGGTC
1 GGCTGCCTGCCGTGGTC
*
410422 GGCTGCCTGCCGTGTTC
1 GGCTGCCTGCCGTGGTC
410439 GGC
1 GGC
410442 CGCTGATGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.35, G:0.41, T:0.24
Consensus pattern (17 bp):
GGCTGCCTGCCGTGGTC
Found at i:410481 original size:3 final size:3
Alignment explanation
Indices: 410473--410497 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
410463 TAGCTACCTA
410473 GCT GCT GCT GCT GCT GCT GCT GCT G
1 GCT GCT GCT GCT GCT GCT GCT GCT G
410498 TCAAAACCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.36, T:0.32
Consensus pattern (3 bp):
GCT
Found at i:415010 original size:3 final size:3
Alignment explanation
Indices: 415002--415064 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
414992 GCAGTAGCAG
415002 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
415050 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
415065 AAGATAATGG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:419378 original size:21 final size:21
Alignment explanation
Indices: 419354--419414 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
419344 AACTTTGAAA
419354 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
419375 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
419389 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
419410 AAATG
1 AAATG
419415 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:419460 original size:36 final size:36
Alignment explanation
Indices: 419346--419465 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
419336 TGGTAACCAA
419346 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
419383 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* * *
419418 CTTTGAAAAATAGTTTTTCAAAGTTTAGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
419455 -GTTGAAAAATG
1 CTTTGAAAAATG
419466 ATAATGGGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
35 36 0.47
36 14 0.18
37 27 0.35
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:423852 original size:21 final size:21
Alignment explanation
Indices: 423828--423888 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
423818 AACTTTGAAA
423828 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
423849 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
*
423863 AAATAGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
423884 AAATG
1 AAATG
423889 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 9 0.30
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:423934 original size:36 final size:36
Alignment explanation
Indices: 423820--423938 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
423810 TGGTAACCAA
*
423820 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTT
423857 CTTTG-AAAATAGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
423892 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
*
423929 -GTTGAAAAAT
1 CTTTGAAAAAT
423939 GATAATGGGA
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
35 34 0.44
36 16 0.21
37 27 0.35
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:424447 original size:21 final size:20
Alignment explanation
Indices: 424406--424447 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
424396 CCCGTTATCC
*
424406 AATAAAAACCTAAAATTCCT
1 AATAAAAACCTAAAATGCCT
424426 AATAATAAACC-AAAATCGCCT
1 AATAA-AAACCTAAAAT-GCCT
424447 A
1 A
424448 TCCGATTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.55, C:0.21, G:0.02, T:0.21
Consensus pattern (20 bp):
AATAAAAACCTAAAATGCCT
Found at i:426625 original size:18 final size:17
Alignment explanation
Indices: 426602--426640 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
426592 TCCTATCACG
*
426602 TAGAAACTTGTGTATTT
1 TAGAAACTTGTCTATTT
*
426619 ATAGAAAGTTGTCTATTT
1 -TAGAAACTTGTCTATTT
426637 TAGA
1 TAGA
426641 GGGGTGCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (17 bp):
TAGAAACTTGTCTATTT
Found at i:437491 original size:16 final size:16
Alignment explanation
Indices: 437467--437506 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
437457 ATATTAAGTT
*
437467 ATATGTAACGCAAATA
1 ATATATAACGCAAATA
*
437483 ATATATAACGTAAATA
1 ATATATAACGCAAATA
*
437499 ATAAATAA
1 ATATATAA
437507 TAGATTGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.28
Consensus pattern (16 bp):
ATATATAACGCAAATA
Found at i:443610 original size:45 final size:47
Alignment explanation
Indices: 443525--443619 Score: 122
Period size: 45 Copynumber: 2.1 Consensus size: 47
443515 TTTGAGTCAT
* * *
443525 TTATTTTTATTTTTCGAATAAATGCATGTGAACTATATATCATGCGG
1 TTATGTTTATTTTTCGAATAAATGCATGCGAACTAGATATCATGCGG
* * *
443572 TTATGTTTATTTTTTGAA-CAA-GCATGCGAATTAGATATCATGCGG
1 TTATGTTTATTTTTCGAATAAATGCATGCGAACTAGATATCATGCGG
443617 TTA
1 TTA
443620 GGATTTCTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 24 0.57
46 2 0.05
47 16 0.38
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (47 bp):
TTATGTTTATTTTTCGAATAAATGCATGCGAACTAGATATCATGCGG
Found at i:453141 original size:9 final size:9
Alignment explanation
Indices: 453123--453193 Score: 54
Period size: 9 Copynumber: 7.4 Consensus size: 9
453113 AAAGGGGAGA
453123 AAAAATAATG
1 AAAAA-AATG
453133 AAAAAAATG
1 AAAAAAATG
*
453142 AAAAGAAGA-A
1 AAAA-AA-ATG
453152 AAGAAAAATG
1 AA-AAAAATG
*
453162 GAAAAAATG
1 AAAAAAATG
*
453171 AAAAATGATG
1 AAAAA-AATG
*
453181 GAAAAAATG
1 AAAAAAATG
453190 AAAA
1 AAAA
453194 GAAAAAAAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
9 26 0.54
10 19 0.40
11 3 0.06
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.11
Consensus pattern (9 bp):
AAAAAAATG
Found at i:453145 original size:19 final size:18
Alignment explanation
Indices: 453123--453193 Score: 54
Period size: 19 Copynumber: 3.7 Consensus size: 18
453113 AAAGGGGAGA
453123 AAAAATAATGAAAAAAATG
1 AAAAA-AATGAAAAAAATG
*
453142 AAAAGAAGA-AAAGAAAAATG
1 AAAA-AA-ATGAA-AAAAATG
* *
453162 GAAAAAATGAAAAATGATG
1 AAAAAAATGAAAAA-AATG
*
453181 GAAAAAATGAAAA
1 AAAAAAATGAAAA
453194 GAAAAAAAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
18 4 0.09
19 27 0.63
20 12 0.28
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.11
Consensus pattern (18 bp):
AAAAAAATGAAAAAAATG
Found at i:453170 original size:29 final size:28
Alignment explanation
Indices: 453120--453174 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
453110 AAAAAAGGGG
*
453120 AGAAAAAATAATGAAAAAAATGAAAAGA
1 AGAAAAAAAAATGAAAAAAATGAAAAGA
*
453148 AGAAAAGAAAAATGGAAAAAATGAAAA
1 AGAAAA-AAAAATGAAAAAAATGAAAA
453175 ATGATGGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (28 bp):
AGAAAAAAAAATGAAAAAAATGAAAAGA
Found at i:453211 original size:27 final size:26
Alignment explanation
Indices: 453181--453260 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 26
453171 AAAAATGATG
453181 GAAAAAATGA-AAAGAAAAAAAGAAACA
1 GAAAAAATGAGAAAG-AAAAAAGAAA-A
* * *
453208 GAAACAATGAGGACGAAAAAAGAAAA
1 GAAAAAATGAGAAAGAAAAAAGAAAA
* *
453234 GAAAAAATAATGAAAAAGAAAAAGAAA
1 GAAAAAATGA-GAAAGA-AAAAAGAAA
453261 TAAAAGGGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
26 9 0.21
27 22 0.52
28 11 0.26
ACGTcount: A:0.74, C:0.04, G:0.17, T:0.05
Consensus pattern (26 bp):
GAAAAAATGAGAAAGAAAAAAGAAAA
Found at i:454321 original size:16 final size:17
Alignment explanation
Indices: 454284--454318 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
454274 AGGTTTCCCA
454284 AAGATAGTTGAAGATTG
1 AAGATAGTTGAAGATTG
454301 AAGATA-TTGAAGCATTG
1 AAGATAGTTGAAG-ATTG
454318 A
1 A
454319 GATGAAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.43, C:0.03, G:0.26, T:0.29
Consensus pattern (17 bp):
AAGATAGTTGAAGATTG
Found at i:454888 original size:109 final size:109
Alignment explanation
Indices: 454696--454997 Score: 329
Period size: 109 Copynumber: 2.8 Consensus size: 109
454686 TTGAGATTGT
** * * * *
454696 TCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCAAGTTCTATACTCTCTGAAGG
1 TCTCTGAAGGAATAGAGAGCAAACCCGTTT-ATGAAGATTGTTCGAGTTCTATACTCCCTGAAAG
* * **
454761 AATAGAGAGCAGACCCGTTTGTTGAAGATTGTTCGAGT-TCTATAC
65 AATAGGGAGCAGACCCGTTTATTGAAGATCATTCGAGTCT-TATAC
* * * *
454806 TCTCTGAAGGAATAGAGAACATACCCGTTTATGAAGATTGTTTGAGTTCTATACTCCCTGAACGA
1 TCTCTGAAGGAATAGAGAGCAAACCCGTTTATGAAGATTGTTCGAGTTCTATACTCCCTGAAAGA
*
454871 ATAGGGAGCAGACCCGTTTATTGAAGATCATTTGAGTCTTATAC
66 ATAGGGAGCAGACCCGTTTATTGAAGATCATTCGAGTCTTATAC
* * * * * * * *
454915 TCCCTGAATGAATGGGGAGCAAACACATTTACCGAAGATTGTTCGAG-TCTTATACTCCTTGAAA
1 TCTCTGAAGGAATAGAGAGCAAACCCGTTTA-TGAAGATTGTTCGAGTTC-TATACTCCCTGAAA
* *
454979 GAATGGGGAGCGGACCCGT
64 GAATAGGGAGCAGACCCGT
454998 CATTTGAAGA
Statistics
Matches: 162, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
109 92 0.57
110 70 0.43
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (109 bp):
TCTCTGAAGGAATAGAGAGCAAACCCGTTTATGAAGATTGTTCGAGTTCTATACTCCCTGAAAGA
ATAGGGAGCAGACCCGTTTATTGAAGATCATTCGAGTCTTATAC
Found at i:454916 original size:55 final size:55
Alignment explanation
Indices: 454699--454997 Score: 316
Period size: 55 Copynumber: 5.5 Consensus size: 55
454689 AGATTGTTCT
* * * *
454699 CTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCAAGTTCTATACTCT
1 CTGAAGGAATAGAGAGCAGACCCGTTTATTGAAGATTGTTCGAGTTCTATACTCC
* *
454754 CTGAAGGAATAGAGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTTCTATACTCT
1 CTGAAGGAATAGAGAGCAGACCCGTTTATTGAAGATTGTTCGAGTTCTATACTCC
* * *
454809 CTGAAGGAATAGAGAACATACCCGTTTA-TGAAGATTGTTTGAGTTCTATACTCC
1 CTGAAGGAATAGAGAGCAGACCCGTTTATTGAAGATTGTTCGAGTTCTATACTCC
* * ** *
454863 CTGAACGAATAGGGAGCAGACCCGTTTATTGAAGATCATTTGAG-TCTTATACTCC
1 CTGAAGGAATAGAGAGCAGACCCGTTTATTGAAGATTGTTCGAGTTC-TATACTCC
* * * * * * **
454918 CTGAATGAATGGGGAGCAAACACATTTACCGAAGATTGTTCGAG-TCTTATACTCC
1 CTGAAGGAATAGAGAGCAGACCCGTTTATTGAAGATTGTTCGAGTTC-TATACTCC
* * * * *
454973 TTGAAAGAATGGGGAGCGGACCCGT
1 CTGAAGGAATAGAGAGCAGACCCGT
454998 CATTTGAAGA
Statistics
Matches: 213, Mismatches: 29, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
54 50 0.23
55 163 0.77
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (55 bp):
CTGAAGGAATAGAGAGCAGACCCGTTTATTGAAGATTGTTCGAGTTCTATACTCC
Found at i:458575 original size:12 final size:12
Alignment explanation
Indices: 458557--458586 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
458547 GATAATAAGT
458557 CCAAACTCAAAC
1 CCAAACTCAAAC
*
458569 TCAAACTCAAAC
1 CCAAACTCAAAC
458581 CCAAAC
1 CCAAAC
458587 CCATACCCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.40, G:0.00, T:0.10
Consensus pattern (12 bp):
CCAAACTCAAAC
Found at i:470303 original size:2 final size:2
Alignment explanation
Indices: 470296--470324 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
470286 TTATAATTCT
470296 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
470325 GATTGAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:491273 original size:9 final size:9
Alignment explanation
Indices: 491259--491357 Score: 72
Period size: 9 Copynumber: 10.3 Consensus size: 9
491249 GCTGCTGGAA
491259 ACCGGTTTG
1 ACCGGTTTG
*
491268 ACCGGTTTTCA
1 ACCGG-TTT-G
491279 ACCGGTTTTG
1 ACCGG-TTTG
*
491289 ACCGGTTTA
1 ACCGGTTTG
*
491298 ACCGATTTG
1 ACCGGTTTG
491307 ACCGGTTTCG
1 ACCGGTTT-G
* *
491317 ACCGATTCG
1 ACCGGTTTG
*
491326 AACCGTTTTG
1 -ACCGGTTTG
*
491336 ACCGGTCTG
1 ACCGGTTTG
*
491345 AACCAGTTTG
1 -ACCGGTTTG
491355 ACC
1 ACC
491358 AGTCTGACCC
Statistics
Matches: 71, Mismatches: 14, Indels: 10
0.75 0.15 0.11
Matches are distributed among these distances:
9 33 0.46
10 29 0.41
11 9 0.13
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:491333 original size:19 final size:19
Alignment explanation
Indices: 491288--491339 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
491278 AACCGGTTTT
* *
491288 GACCGGTTT-AACCGATTT
1 GACCGGTTTCGACCGATTC
491306 GACCGGTTTCGACCGATTC
1 GACCGGTTTCGACCGATTC
*
491325 GAACC-GTTTTGACCG
1 G-ACCGGTTTCGACCG
491340 GTCTGAACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 9 0.31
19 17 0.59
20 3 0.10
ACGTcount: A:0.19, C:0.27, G:0.25, T:0.29
Consensus pattern (19 bp):
GACCGGTTTCGACCGATTC
Found at i:491380 original size:14 final size:14
Alignment explanation
Indices: 491363--491392 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
491353 TGACCAGTCT
491363 GACCCGACCCGACC
1 GACCCGACCCGACC
491377 GACCCGACCCGACC
1 GACCCGACCCGACC
491391 GA
1 GA
491393 TGACCCGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.53, G:0.23, T:0.00
Consensus pattern (14 bp):
GACCCGACCCGACC
Found at i:491414 original size:17 final size:17
Alignment explanation
Indices: 491362--491401 Score: 59
Period size: 14 Copynumber: 2.5 Consensus size: 17
491352 TTGACCAGTC
491362 TGACCCGACCCGACC--
1 TGACCCGACCCGACCGA
491377 -GACCCGACCCGACCGA
1 TGACCCGACCCGACCGA
491393 TGACCCGAC
1 TGACCCGAC
491402 TTGACCGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 14 0.64
17 8 0.36
ACGTcount: A:0.23, C:0.50, G:0.23, T:0.05
Consensus pattern (17 bp):
TGACCCGACCCGACCGA
Found at i:493188 original size:16 final size:17
Alignment explanation
Indices: 493157--493190 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
493147 CGTATCGCTG
*
493157 ACAAAATTTTACTATTC
1 ACAAAATTTCACTATTC
493174 ACAAAA-TTCACTATTC
1 ACAAAATTTCACTATTC
493190 A
1 A
493191 TATGAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:496825 original size:19 final size:19
Alignment explanation
Indices: 496801--496858 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 19
496791 TAAGAGGGAG
496801 GAAAAATATAATAATAATA
1 GAAAAATATAATAATAATA
496820 GAAAAA-AT-A-AATAAT-
1 GAAAAATATAATAATAATA
496835 GTAAATGAATATAATAATAA-A
1 G-AAA--AATATAATAATAATA
496856 GAA
1 GAA
496859 GTAAAGAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 13
0.71 0.00 0.29
Matches are distributed among these distances:
15 1 0.03
16 9 0.28
17 1 0.03
18 4 0.12
19 8 0.25
20 3 0.09
21 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (19 bp):
GAAAAATATAATAATAATA
Found at i:496876 original size:37 final size:37
Alignment explanation
Indices: 496805--496876 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
496795 AGGGAGGAAA
* *
496805 AATATAATAATAATAGAAAAAATAAATAATGTAAATG
1 AATATAATAATAATAGAAAAAAGAAATAAGGTAAATG
* *
496842 AATATAATAATAA-AGAAGTAAAGAAATAGGGTAAA
1 AATATAATAATAATAGAA-AAAAGAAATAAGGTAAA
496877 ATACAAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 4 0.13
37 26 0.87
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (37 bp):
AATATAATAATAATAGAAAAAAGAAATAAGGTAAATG
Found at i:496902 original size:8 final size:8
Alignment explanation
Indices: 496889--496927 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
496879 ACAAAATGTG
496889 TACATATA
1 TACATATA
496897 TACATATA
1 TACATATA
*
496905 TATATATA
1 TACATATA
*
496913 TATATATA
1 TACATATA
496921 -ACATATA
1 TACATATA
496928 AGTGACATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 6 0.21
8 23 0.79
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (8 bp):
TACATATA
Found at i:498200 original size:41 final size:41
Alignment explanation
Indices: 498150--498228 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
498140 ATGAAATTAG
*
498150 TACTAATATATATATGTGAATATTATAAAAGTGTGGAGTAA
1 TACTAATATATATATGTAAATATTATAAAAGTGTGGAGTAA
498191 TACTAATATATATATGTAAATATTATAAAAGTGTGGAG
1 TACTAATATATATATGTAAATATTATAAAAGTGTGGAG
498229 ACGAAATTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.44, C:0.03, G:0.16, T:0.37
Consensus pattern (41 bp):
TACTAATATATATATGTAAATATTATAAAAGTGTGGAGTAA
Found at i:498839 original size:105 final size:105
Alignment explanation
Indices: 498602--499304 Score: 1235
Period size: 105 Copynumber: 6.7 Consensus size: 105
498592 GTATATAGCT
* **** * *
498602 CCTTCGTCGCGAAGTTGAACTTATACTGTCTTGAGTCCAATATCCCTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* * * * *
498667 GGCTCTGAAGTTGGGAAGTTATTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTC
*
498708 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCATTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
498773 GGCTCTGATATTGAGAAATGTTTGTTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTC
*
498813 CTTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
498878 GGCTCTGAAATTGGGAAATGTTTGTTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTC
498918 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
498983 GGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTC
499023 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
499088 GGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTC
499128 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
499193 GGCTCTGAAATTGAGAAACGTTTGTTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTC
*
499233 CCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
499298 GGCTCTG
66 GGCTCTG
499305 GGTAAAACCT
Statistics
Matches: 575, Mismatches: 22, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
105 504 0.88
106 71 0.12
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
GGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTC
Found at i:505142 original size:65 final size:65
Alignment explanation
Indices: 505038--505171 Score: 268
Period size: 65 Copynumber: 2.1 Consensus size: 65
505028 ACTCGCTGTG
505038 CTTCAAGATCTTGAGGAACTCTTTAGCTTCTTCCTCCTTTATAGGTTCATTGACGACTAGCACAT
1 CTTCAAGATCTTGAGGAACTCTTTAGCTTCTTCCTCCTTTATAGGTTCATTGACGACTAGCACAT
505103 CTTCAAGATCTTGAGGAACTCTTTAGCTTCTTCCTCCTTTATAGGTTCATTGACGACTAGCACAT
1 CTTCAAGATCTTGAGGAACTCTTTAGCTTCTTCCTCCTTTATAGGTTCATTGACGACTAGCACAT
505168 CTTC
1 CTTC
505172 TTTGAATGGC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 69 1.00
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.37
Consensus pattern (65 bp):
CTTCAAGATCTTGAGGAACTCTTTAGCTTCTTCCTCCTTTATAGGTTCATTGACGACTAGCACAT
Found at i:509605 original size:20 final size:20
Alignment explanation
Indices: 509567--509610 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
509557 ATGGTTAGTA
*
509567 AAATAAAAATAAATGGAAAT
1 AAATAAAAATAAATAGAAAT
509587 AAATAAAAATAACA-AGAAAT
1 AAATAAAAATAA-ATAGAAAT
509607 AAAT
1 AAAT
509611 GGCAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (20 bp):
AAATAAAAATAAATAGAAAT
Found at i:510953 original size:37 final size:37
Alignment explanation
Indices: 510882--510953 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
510872 GGGAGGAAAA
* *
510882 AATATAATAATAATAGAAAAAATAAATAATGTAAATG
1 AATATAATAATAATAGAAAAAAGAAATAAGGTAAATG
* *
510919 AATATAATAATAA-AGAAGTAAAGAAATAGGGTAAA
1 AATATAATAATAATAGAA-AAAAGAAATAAGGTAAA
510954 ATACAAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 4 0.13
37 26 0.87
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (37 bp):
AATATAATAATAATAGAAAAAAGAAATAAGGTAAATG
Found at i:512273 original size:41 final size:41
Alignment explanation
Indices: 512223--512301 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
512213 ATGAAATTAG
* *
512223 TACTAATATATATATGTGAATATTATAAAAGTGTGGAGTAA
1 TACTAATATATATATATAAATATTATAAAAGTGTGGAGTAA
512264 TACTAATATATATATATAAATATTATAAAAGTGTGGAG
1 TACTAATATATATATATAAATATTATAAAAGTGTGGAG
512302 ACGAAATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.37
Consensus pattern (41 bp):
TACTAATATATATATATAAATATTATAAAAGTGTGGAGTAA
Found at i:515587 original size:12 final size:12
Alignment explanation
Indices: 515570--515604 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
515560 CATAACAGAG
515570 GCAACACTTCTA
1 GCAACACTTCTA
515582 GCAACACTTCTA
1 GCAACACTTCTA
* *
515594 GTATCACTTCT
1 GCAACACTTCT
515605 TCAACCGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (12 bp):
GCAACACTTCTA
Found at i:521714 original size:22 final size:22
Alignment explanation
Indices: 521671--521714 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
521661 CAAAATCAAA
* *
521671 TTAAAATAAAAATGATAGAAAT
1 TTAAAAGAAAAATCATAGAAAT
521693 TTAAAAGAAAATATCATA-AAAT
1 TTAAAAGAAAA-ATCATAGAAAT
521715 ATGGAGCTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (22 bp):
TTAAAAGAAAAATCATAGAAAT
Found at i:529222 original size:27 final size:28
Alignment explanation
Indices: 529166--529222 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
529156 GAAAAAATTG
**
529166 AATATTTTAGGTATGTATTTTGATCAAA
1 AATATTTTAGGTACCTATTTTGATCAAA
529194 AATATTTTAGGTACCTA-TTTGATCAAA
1 AATATTTTAGGTACCTATTTTGATCAAA
529221 AA
1 AA
529223 GATAAGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (28 bp):
AATATTTTAGGTACCTATTTTGATCAAA
Found at i:532455 original size:17 final size:18
Alignment explanation
Indices: 532435--532469 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
532425 TATTAATGGA
532435 GTAAAA-AAATAAAAAAG
1 GTAAAAGAAATAAAAAAG
*
532452 GTAAAAGAAATTAAAAAG
1 GTAAAAGAAATAAAAAAG
532470 AATAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (18 bp):
GTAAAAGAAATAAAAAAG
Found at i:532553 original size:36 final size:36
Alignment explanation
Indices: 532506--532598 Score: 109
Period size: 36 Copynumber: 2.6 Consensus size: 36
532496 TAGTATTTAC
* * *
532506 TAAAACAAATAAAAATAATAAATATATAATACTAAA
1 TAAAATAAATAAAAAAAATAAATACATAATACTAAA
* * *
532542 TAAAATAAATAAAAAAAAGATATACATAATATTAAA
1 TAAAATAAATAAAAAAAATAAATACATAATACTAAA
532578 -AAAAT-AATAGAAAAAAATAAA
1 TAAAATAAATA-AAAAAAATAAA
532599 ATAAAGTAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
34 4 0.08
35 14 0.29
36 30 0.62
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (36 bp):
TAAAATAAATAAAAAAAATAAATACATAATACTAAA
Found at i:532565 original size:32 final size:32
Alignment explanation
Indices: 532503--532565 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
532493 AAGTAGTATT
* *
532503 TACTAAAACAAATAAAAATAATAAATATATAA
1 TACTAAAACAAATAAAAATAAAAAAGATATAA
532535 TACTAAATA-AAATAAATAA-AAAAAAGATATA
1 TACTAAA-ACAAATAAA-AATAAAAAAGATATA
532566 CATAATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 24 0.89
33 3 0.11
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.24
Consensus pattern (32 bp):
TACTAAAACAAATAAAAATAAAAAAGATATAA
Found at i:532617 original size:2 final size:2
Alignment explanation
Indices: 532610--532634 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
532600 TAAAGTAAAA
532610 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
532635 ATTAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:532791 original size:25 final size:25
Alignment explanation
Indices: 532746--532793 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
532736 TTAATATATC
* *
532746 TATATATATATATAATGATATAAGA
1 TATATATATATAAAATAATATAAGA
532771 TATATATA-ATAAAAATAATATAA
1 TATATATATAT-AAAATAATATAA
532794 TATAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 18 0.90
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
TATATATATATAAAATAATATAAGA
Found at i:534358 original size:110 final size:109
Alignment explanation
Indices: 534163--534420 Score: 314
Period size: 110 Copynumber: 2.4 Consensus size: 109
534153 GTATTATTCT
* * *
534163 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTC----TGAAACTGGGAAATTGTTTGTTG
1 GAGTTCAATATCCTTCGT-GTGAAGTTGAAATTGGCTCTGAATGAAACTGGAAAATTGTTTGTTG
*
534224 ACAGCCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTC
65 ACAACCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTC
*
534269 GAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACT-GAAAAGTTGTTTGTT
1 GAGTTCAATATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAATGAAACTGGAAAA-TTGTTTGTT
* ** * *
534333 GACAATCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTT
64 GACAACCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTC
*
534379 GAG-TCTAATAT-ATCTCGTTGTGAAGTTGAAATTGGCTCTGAA
1 GAGTTC-AATATCCT-TCG-TGTGAAGTTGAAATTGGCTCTGAA
534421 ACTGGGAAGC
Statistics
Matches: 131, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
106 33 0.25
107 1 0.01
109 7 0.05
110 90 0.69
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (109 bp):
GAGTTCAATATCCTTCGTGTGAAGTTGAAATTGGCTCTGAATGAAACTGGAAAATTGTTTGTTGA
CAACCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTC
Found at i:535255 original size:67 final size:66
Alignment explanation
Indices: 535137--535303 Score: 214
Period size: 65 Copynumber: 2.5 Consensus size: 66
535127 AAGATATATG
* * * **
535137 TTGTTTCATGA-AAACGGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTTAAGGGAAATAAATTCAAAGA-
535201 TT
65 TT
535203 TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTT-AGGTGAAATAAATTCAAAG
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTTAAGG-GAAATAAATTCAAAG
535266 ATT
64 ATT
* * *
535269 TTGTTTCAAGGGAAACTGTCTTAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
535304 CTTAGTTCCA
Statistics
Matches: 90, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
65 31 0.34
66 7 0.08
67 31 0.34
68 21 0.23
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:535341 original size:101 final size:101
Alignment explanation
Indices: 535219--535404 Score: 273
Period size: 101 Copynumber: 1.8 Consensus size: 101
535209 TCAAGAGAAA
* ** * * *
535219 CTGTCTCAAGGGAGACAAAATTTGTTTTAGGTGAAATAAATTCAAAGATTTTGTTTCAAGGGAAA
1 CTGTCTCAAGGGAGACAAAATTTGTTTCAAATAAAACAAATTCAAAGAATTTGTTTCAAGGGAAA
*
535284 CTGTCTTAAGAGAGACAAAACTTAGTTCCAAAATAT
66 CTGTCTCAAGAGAGACAAAACTTAGTTCCAAAATAT
** * *
535320 CTGTCTCAAGGGAGATGAAATTTGTTTCAAATAAAACATATTCAAATAATTTGTTTCAAGGGAAA
1 CTGTCTCAAGGGAGACAAAATTTGTTTCAAATAAAACAAATTCAAAGAATTTGTTTCAAGGGAAA
535385 CTGTCTCAAGAGAGACAAAA
66 CTGTCTCAAGAGAGACAAAA
535405 TTTGTTTCAA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
101 74 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (101 bp):
CTGTCTCAAGGGAGACAAAATTTGTTTCAAATAAAACAAATTCAAAGAATTTGTTTCAAGGGAAA
CTGTCTCAAGAGAGACAAAACTTAGTTCCAAAATAT
Found at i:535414 original size:36 final size:36
Alignment explanation
Indices: 535367--535559 Score: 204
Period size: 36 Copynumber: 5.5 Consensus size: 36
535357 ATATTCAAAT
535367 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
535403 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGA
1 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
* * * *
535439 AATTTATTTCAAGGGAAAATGTTTTC-A-A-TG----
1 AATTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAA
* * * *
535469 -TTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAA
1 AATT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
535505 AATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAA
1 AA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
535542 AATTCGTTTCAAGGGAAA
1 AATTTGTTTCAAGGGAAA
535560 TGTTTTCAAT
Statistics
Matches: 128, Mismatches: 18, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
29 5 0.04
30 15 0.12
32 1 0.01
34 1 0.01
35 1 0.01
36 70 0.55
37 33 0.26
38 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (36 bp):
AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
Found at i:535425 original size:101 final size:102
Alignment explanation
Indices: 535205--535634 Score: 426
Period size: 102 Copynumber: 4.2 Consensus size: 102
535195 GAAGATTTTG
* * * * * *
535205 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTT-TAGGTGAAATAAATTCAAAGATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGG-AAAATATATTC-AATATT
* *
535269 T-TGTTTCAAGGGAAACTGTCTTAAGAGAGACAAAACTT
64 TATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
* * * ** ** * *
535307 AGTTCCAA---AATATCTGTCTCAAGGGAGATGAAATTTGTTTCAAATAAAACATATTCAAATAA
1 TGTTTCAAGGGAA-A-CTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAATATATTC-AATAT
*
535369 TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
63 TTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
* * * * *
535407 TGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTATTTCAAGGGAAAATGTTTTCAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAA-GGAAAATATATTCAATATTT
* * *
535472 ATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
65 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
* * * * * *
535510 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAATATATTCAATATTTA
* *
535575 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAATA-TT
66 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
*
535611 TCGTTTCAAGGGAAACTATCTCAA
1 T-GTTTCAAGGGAAACTGTCTCAA
535635 ACAAGATAAA
Statistics
Matches: 283, Mismatches: 35, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
99 2 0.01
100 9 0.03
101 107 0.38
102 121 0.43
103 44 0.16
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAATATATTCAATATTTA
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
Found at i:535531 original size:37 final size:36
Alignment explanation
Indices: 535473--535559 Score: 120
Period size: 37 Copynumber: 2.4 Consensus size: 36
535463 TCAATGTTTA
* * * *
535473 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
535510 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
*
535546 CGTTTCAAGGGAAA
1 TGTTTCAAGGGAAA
535560 TGTTTTCAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 15 0.33
37 30 0.67
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
Found at i:535646 original size:102 final size:102
Alignment explanation
Indices: 535371--535634 Score: 431
Period size: 102 Copynumber: 2.6 Consensus size: 102
535361 TCAAATAATT
* * *
535371 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGA
* *
535436 CGAAATTTATTTCAAGGGAAAATGTTTTCAATGTTTA
66 CAAAATTCATTTCAAGGGAAAATGTTTTCAATGTTTA
*
535473 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
535538 ACAAAATTCGTTTCAAGGG-AAATGTTTTCAATGTTTA
65 ACAAAATTCATTTCAAGGGAAAATGTTTTCAATGTTTA
*
535575 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAATATTTCGTTTCAAGGGAAACTATCTCAA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT-GTTTCAAGGGAAACTATCTCAA
535635 ACAAGATAAA
Statistics
Matches: 151, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
101 3 0.02
102 103 0.68
103 45 0.30
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGA
CAAAATTCATTTCAAGGGAAAATGTTTTCAATGTTTA
Found at i:537306 original size:14 final size:13
Alignment explanation
Indices: 537277--537305 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
537267 TTTTCTTCAA
537277 TTTTC-CTTTGTT
1 TTTTCTCTTTGTT
537289 TTTTCTCTTTGTT
1 TTTTCTCTTTGTT
537302 TTTT
1 TTTT
537306 TTTCTTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:537308 original size:16 final size:16
Alignment explanation
Indices: 537287--537317 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
537277 TTTTCCTTTG
537287 TTTTTTCTCTTTGTTT
1 TTTTTTCTCTTTGTTT
*
537303 TTTTTTCTTTTTGTT
1 TTTTTTCTCTTTGTT
537318 CTGATTGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (16 bp):
TTTTTTCTCTTTGTTT
Found at i:540461 original size:18 final size:17
Alignment explanation
Indices: 540429--540475 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
540419 TATTAATGGA
540429 GTAAAAAAATAAAAAAG
1 GTAAAAAAATAAAAAAG
*
540446 GTAAAAGAAATTAAAAAG
1 GTAAAA-AAATAAAAAAG
540464 G-AATAAAAATAA
1 GTAA-AAAAATAA
540476 TGTATACACA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (17 bp):
GTAAAAAAATAAAAAAG
Found at i:540592 original size:14 final size:14
Alignment explanation
Indices: 540573--540612 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
540563 CATGATATTA
540573 AAAAAAAATAATAG
1 AAAAAAAATAATAG
540587 AAAAAAAATAA-AG
1 AAAAAAAATAATAG
* *
540600 TAAAAATATAATA
1 AAAAAAAATAATA
540613 TATATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (14 bp):
AAAAAAAATAATAG
Found at i:540765 original size:9 final size:9
Alignment explanation
Indices: 540735--540781 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
540725 TTAATACATC
540735 TATATATAA
1 TATATATAA
540744 TGATATA-AGA
1 T-ATATATA-A
540754 TATATATAA
1 TATATATAA
*
540763 TATAAATAA
1 TATATATAA
540772 TATAATATAA
1 TAT-ATATAA
540782 AAAAAAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 19 0.59
10 13 0.41
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (9 bp):
TATATATAA
Found at i:540776 original size:14 final size:15
Alignment explanation
Indices: 540736--540782 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
540726 TAATACATCT
*
540736 ATATATAATGATATAA
1 ATATAT-ATAATATAA
540752 GATATATATAATATAA
1 -ATATATATAATATAA
540768 ATA-ATATAATATAA
1 ATATATATAATATAA
540782 A
1 A
540783 AAAAAAGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 12 0.41
15 3 0.10
16 8 0.28
17 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (15 bp):
ATATATATAATATAA
Found at i:540824 original size:36 final size:37
Alignment explanation
Indices: 540750--540834 Score: 102
Period size: 36 Copynumber: 2.3 Consensus size: 37
540740 ATAATGATAT
* *
540750 AAGATATATATAATATAAATAATATAATATAAAAAAA
1 AAGATATATATAATATAAATAAAAGAATATAAAAAAA
**
540787 AAGA-ATATAGTAA-ATAAATAAAAGAATATAATTAAA
1 AAGATATATA-TAATATAAATAAAAGAATATAAAAAAA
*
540823 AATATATATATA
1 AAGATATATATA
540835 GGGAACGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
36 29 0.71
37 12 0.29
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (37 bp):
AAGATATATATAATATAAATAAAAGAATATAAAAAAA
Found at i:546281 original size:26 final size:27
Alignment explanation
Indices: 546250--546303 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
546240 AAATGAAAAT
* *
546250 TCAAATGTACGAAGAGT-GGTTTGAAG
1 TCAAATGTACAAAGAGTAGGTTCGAAG
546276 TCAAATGTACAAAGAGTAGGTTCGAAG
1 TCAAATGTACAAAGAGTAGGTTCGAAG
546303 T
1 T
546304 TGGGATGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.37, C:0.09, G:0.28, T:0.26
Consensus pattern (27 bp):
TCAAATGTACAAAGAGTAGGTTCGAAG
Found at i:547892 original size:109 final size:109
Alignment explanation
Indices: 547701--547919 Score: 420
Period size: 109 Copynumber: 2.0 Consensus size: 109
547691 TCTAATCTAT
547701 TTCCCCCTTGGTTTTCTTGGCTTTTATTTCTCTTAATGGACTGTGTTTTGAGAAATTCAACTTCA
1 TTCCCCCTTGGTTTTCTTGGCTTTTATTTCTCTTAATGGACTGTGTTTTGAGAAATTCAACTTCA
547766 TATCAGAGTTTGTAATTTGGATAAATGGTTCTGCTATGATTATA
66 TATCAGAGTTTGTAATTTGGATAAATGGTTCTGCTATGATTATA
*
547810 TTCCCCCTTGGTTTTCTTGGCTTTTATTTCTCTTAATGGACTGTGTTTTGAGTAATTCAACTTCA
1 TTCCCCCTTGGTTTTCTTGGCTTTTATTTCTCTTAATGGACTGTGTTTTGAGAAATTCAACTTCA
*
547875 TATCAGATTTTGTAATTTGGATAAATGGTTCTGCTATGATTATA
66 TATCAGAGTTTGTAATTTGGATAAATGGTTCTGCTATGATTATA
547919 T
1 T
547920 AGTTCTACAT
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 108 1.00
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.47
Consensus pattern (109 bp):
TTCCCCCTTGGTTTTCTTGGCTTTTATTTCTCTTAATGGACTGTGTTTTGAGAAATTCAACTTCA
TATCAGAGTTTGTAATTTGGATAAATGGTTCTGCTATGATTATA
Found at i:548793 original size:20 final size:21
Alignment explanation
Indices: 548756--548795 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
548746 GAAAACTCCC
* *
548756 GAAACGGAATAAGGTTAAAAG
1 GAAACGGAACAAGATTAAAAG
548777 GAAA-GGAACAAGATTAAAA
1 GAAACGGAACAAGATTAAAA
548796 AAAAACCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.57, C:0.05, G:0.25, T:0.12
Consensus pattern (21 bp):
GAAACGGAACAAGATTAAAAG
Found at i:551869 original size:35 final size:35
Alignment explanation
Indices: 551830--551941 Score: 170
Period size: 35 Copynumber: 3.2 Consensus size: 35
551820 AAAACATTCC
551830 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
551865 TCAATTTCATTCTAAACCCTAAATTCCAAAAAAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* * * *
551900 TCAATTACATTCTAAAACCCAAATTCTAAAATATT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
551935 TCAATTT
1 TCAATTT
551942 AAGGAGGAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:552575 original size:51 final size:51
Alignment explanation
Indices: 552518--552619 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
552508 CAAATCAGAA
552518 ATATTTATTTTTAAATAAATG-ATTATTATCATATTCTTACTATTGAAAAAT
1 ATATTTATTTTT-AATAAATGAATTATTATCATATTCTTACTATTGAAAAAT
552569 ATATTTATTTTTAATAAATGAATTATTATCATATTCTTACTATTGAAAAAT
1 ATATTTATTTTTAATAAATGAATTATTATCATATTCTTACTATTGAAAAAT
552620 TTTCATGTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
50 8 0.16
51 42 0.84
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (51 bp):
ATATTTATTTTTAATAAATGAATTATTATCATATTCTTACTATTGAAAAAT
Found at i:552577 original size:25 final size:25
Alignment explanation
Indices: 552542--552625 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 25
552532 ATAAATGATT
552542 ATTATCATATTCTTACTATTGAAAA
1 ATTATCATATTCTTACTATTGAAAA
* * * * **
552567 ATATAT-TTATTTTTAATAAATGAATT
1 AT-TATCATATTCTTACT-ATTGAAAA
552593 ATTATCATATTCTTACTATTGAAAA
1 ATTATCATATTCTTACTATTGAAAA
*
552618 ATTTTCAT
1 ATTATCAT
552626 GTCTTTAAAT
Statistics
Matches: 43, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
25 25 0.58
26 18 0.42
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (25 bp):
ATTATCATATTCTTACTATTGAAAA
Found at i:552767 original size:35 final size:33
Alignment explanation
Indices: 552725--552837 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 33
552715 AAAAAAGATA
* * *
552725 GAAATTGAAGTATTTAAGAATTTGGGTTTTAGAAA
1 GAAATTGAATTATTT-GGAATTTGGG-TTTAGAAT
*
552760 GTAATTGAATTATTTTGGAATTTAGGGTTTAGAAT
1 GAAATTGAATTA-TTTGGAATTT-GGGTTTAGAAT
552795 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTA-TTTGGAATTTG-GGTTTAGAAT
552830 GAAATTGA
1 GAAATTGA
552838 GGATTGTTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
34 1 0.01
35 62 0.90
36 6 0.09
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (33 bp):
GAAATTGAATTATTTGGAATTTGGGTTTAGAAT
Found at i:553704 original size:20 final size:20
Alignment explanation
Indices: 553679--553732 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
553669 GACCAACAAA
553679 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
553699 TTCGCAAAC-C-AGTTTTCAAT
1 TTCGC-AACGCGA-ATTCCAAT
553719 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
553733 ATGTAAATCG
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
19 4 0.15
20 19 0.70
21 4 0.15
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:553773 original size:21 final size:21
Alignment explanation
Indices: 553749--553848 Score: 128
Period size: 21 Copynumber: 4.8 Consensus size: 21
553739 ATCGCATTAT
*
553749 GATTTTCCAAATTCACGTTGC
1 GATTTTCCAAATTCGCGTTGC
553770 GATTTTCCAAATTCGCGTTGC
1 GATTTTCCAAATTCGCGTTGC
* *
553791 GATTTTCTAAATCCGCGTTGC
1 GATTTTCCAAATTCGCGTTGC
* * **
553812 GATTTTCTAAATCCGATTTGC
1 GATTTTCCAAATTCGCGTTGC
*
553833 GATATTCCAAATTCGC
1 GATTTTCCAAATTCGC
553849 AACGCGATAG
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 70 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (21 bp):
GATTTTCCAAATTCGCGTTGC
Found at i:553865 original size:20 final size:20
Alignment explanation
Indices: 553840--553955 Score: 162
Period size: 20 Copynumber: 5.8 Consensus size: 20
553830 TGCGATATTC
*
553840 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
*
553860 CAAATTCTCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
553880 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
*
553900 CAAATTCGCAACGTGAAAGT
1 CAAATTCGCAACGCGAAAGT
* **
553920 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAAAGT
553939 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
553956 TTTAATTTCG
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
19 17 0.20
20 69 0.80
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:553958 original size:20 final size:20
Alignment explanation
Indices: 553840--553969 Score: 142
Period size: 20 Copynumber: 6.6 Consensus size: 20
553830 TGCGATATTC
553840 CAAATTCGCAACGCG-ATAGT
1 CAAATTCGCAACGCGAAT-GT
* *
553860 CAAATTCTCAACGCGAAAGT
1 CAAATTCGCAACGCGAATGT
553880 CAAATTCGCAACGCG-ATAGT
1 CAAATTCGCAACGCGAAT-GT
* *
553900 CAAATTCGCAACGTGAAAGT
1 CAAATTCGCAACGCGAATGT
* *
553920 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATGT
553939 CAAATTCGCAACGCGAAT-T
1 CAAATTCGCAACGCGAATGT
* *
553958 TAATTTCGCAAC
1 CAAATTCGCAAC
553970 ACAAATGTTT
Statistics
Matches: 95, Mismatches: 11, Indels: 9
0.83 0.10 0.08
Matches are distributed among these distances:
19 29 0.31
20 64 0.67
21 2 0.02
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATGT
Found at i:554133 original size:16 final size:16
Alignment explanation
Indices: 554112--554142 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
554102 ATCTCTATTT
554112 TTTTTACATAATTTTA
1 TTTTTACATAATTTTA
*
554128 TTTTTATATAATTTT
1 TTTTTACATAATTTT
554143 TCAATGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTACATAATTTTA
Found at i:554897 original size:24 final size:24
Alignment explanation
Indices: 554839--554885 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
554829 AGTCAGTATT
*
554839 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
554863 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
554886 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:557197 original size:17 final size:18
Alignment explanation
Indices: 557165--557199 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
557155 AAGCAAAAGG
557165 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
557183 AAATC-AAATCTCAATCA
1 AAATCAAAATCGCAATCA
557200 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:557578 original size:20 final size:20
Alignment explanation
Indices: 557553--557610 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
557543 AAAATCGTGT
*
557553 TGCGAATCTGACTTTCGCGC
1 TGCGAATTTGACTTTCGCGC
557573 TGCGAATTTGACTTTCGCGC
1 TGCGAATTTGACTTTCGCGC
557593 TGCGAATTTGACTTTCGC
1 TGCGAATTTGACTTTCGC
557611 AACGCTTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.26, G:0.24, T:0.34
Consensus pattern (20 bp):
TGCGAATTTGACTTTCGCGC
Found at i:557634 original size:34 final size:34
Alignment explanation
Indices: 557585--557678 Score: 143
Period size: 34 Copynumber: 2.8 Consensus size: 34
557575 CGAATTTGAC
*
557585 TTTCGCGCTGCGAATTTGACTTTCGCAACGCTTA
1 TTTCGCGTTGCGAATTTGACTTTCGCAACGCTTA
* * *
557619 TTTCGCGTTGAGAATTTAACTATCGCAACGCTTA
1 TTTCGCGTTGCGAATTTGACTTTCGCAACGCTTA
*
557653 TTTCGCGTTGCGAATTTGATTTTCGC
1 TTTCGCGTTGCGAATTTGACTTTCGC
557679 GTTGCGAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 52 1.00
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.38
Consensus pattern (34 bp):
TTTCGCGTTGCGAATTTGACTTTCGCAACGCTTA
Found at i:557678 original size:20 final size:20
Alignment explanation
Indices: 557653--557690 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
557643 GCAACGCTTA
557653 TTTCGCGTTGCGAATTTGAT
1 TTTCGCGTTGCGAATTTGAT
557673 TTTCGCGTTGCGAATTTG
1 TTTCGCGTTGCGAATTTG
557691 TACCTTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.16, G:0.26, T:0.45
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAT
Found at i:561482 original size:19 final size:20
Alignment explanation
Indices: 561458--561504 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
561448 AAAATCGTAA
561458 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCAGTTTCGCGT
*
561477 TGCGATTTTCATTTTCGCGT
1 TGCGATTTTCAGTTTCGCGT
*
561497 TACGATTT
1 TGCGATTT
561505 AGGGTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.13, C:0.17, G:0.21, T:0.49
Consensus pattern (20 bp):
TGCGATTTTCAGTTTCGCGT
Found at i:561786 original size:22 final size:22
Alignment explanation
Indices: 561761--561818 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
561751 GATGGAGATA
561761 GACGGATTTCGTCGGAAATAGG
1 GACGGATTTCGTCGGAAATAGG
* * * * *
561783 GACGAATTTCTTTGGAGATGGG
1 GACGGATTTCGTCGGAAATAGG
*
561805 GACGGATGTCGTCG
1 GACGGATTTCGTCG
561819 TAGAGAGTGA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.14, G:0.38, T:0.26
Consensus pattern (22 bp):
GACGGATTTCGTCGGAAATAGG
Found at i:561992 original size:21 final size:21
Alignment explanation
Indices: 561955--562020 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
561945 CTTTCGCGTT
*
561955 GCGAATTT-GACTATCGCAAC
1 GCGAATTTGGAATATCGCAAC
561975 GCGAATTTGGAATATCGCAAC
1 GCGAATTTGGAATATCGCAAC
* *
561996 GCGAATTTGGAAAATCGCAAT
1 GCGAATTTGGAATATCGCAAC
562017 GCGA
1 GCGA
562021 TTTACATAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 8 0.19
21 34 0.81
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (21 bp):
GCGAATTTGGAATATCGCAAC
Found at i:562077 original size:20 final size:21
Alignment explanation
Indices: 562030--562100 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 21
562020 ATTTACATAG
562030 TCGCGTTGCGAAATTGGAAAC
1 TCGCGTTGCGAAATTGGAAAC
* *
562051 TAG-GTTGCGAAATTGG-AAT
1 TCGCGTTGCGAAATTGGAAAC
* *
562070 TCGCGTTGC-AAATTTGAGA-
1 TCGCGTTGCGAAATTGGAAAC
*
562089 TCGCATTGCGAA
1 TCGCGTTGCGAA
562101 TTTGTTGTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
19 18 0.44
20 21 0.51
21 2 0.05
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (21 bp):
TCGCGTTGCGAAATTGGAAAC
Found at i:562380 original size:17 final size:18
Alignment explanation
Indices: 562350--562383 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
562340 ATTTTAAAGA
*
562350 AATTTAAGTTTTTTTTAC
1 AATTTAAGTCTTTTTTAC
562368 AATTTAA-TCTTTTTTA
1 AATTTAAGTCTTTTTTA
562384 GAAAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (18 bp):
AATTTAAGTCTTTTTTAC
Found at i:563276 original size:24 final size:24
Alignment explanation
Indices: 563239--563294 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
563229 TTCACACTGG
* *
563239 CCATGCACGTGCCATTTACATTAA
1 CCATGCATGGGCCATTTACATTAA
563263 CCATGCATGGGCCATTTACATTAA
1 CCATGCATGGGCCATTTACATTAA
563287 CCATGCAT
1 CCATGCAT
563295 TCTCTTGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (24 bp):
CCATGCATGGGCCATTTACATTAA
Found at i:567885 original size:20 final size:20
Alignment explanation
Indices: 567847--567885 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
567837 TGTGGAACCT
* *
567847 TATGGAAGAGTGTGGAAGAA
1 TATGGAAGAGAGTGAAAGAA
*
567867 TATGGAAGGGAGTGAAAGA
1 TATGGAAGAGAGTGAAAGA
567886 GTGTAGAGCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.41, T:0.18
Consensus pattern (20 bp):
TATGGAAGAGAGTGAAAGAA
Found at i:576369 original size:34 final size:34
Alignment explanation
Indices: 576294--576369 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 34
576284 CATCCAGCTT
* * *
576294 AAATTTTTTATTTATTATATATTTTAGATTTTTTA
1 AAATTTTTTATTAATAATATATTTTA-ATTTCTTA
*
576329 ATATTTTTTATTAATAATATATATTT-ATTTCTTA
1 AAATTTTTTATTAATAATATAT-TTTAATTTCTTA
576363 AAATTTT
1 AAATTTT
576370 ATAAATTAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
34 13 0.37
35 19 0.54
36 3 0.09
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (34 bp):
AAATTTTTTATTAATAATATATTTTAATTTCTTA
Found at i:591171 original size:28 final size:28
Alignment explanation
Indices: 591127--591212 Score: 163
Period size: 28 Copynumber: 3.1 Consensus size: 28
591117 CCTTGCAGAC
*
591127 AAAATACAAGTTCTATAGCTTTTGAAGT
1 AAAATACAAGTTGTATAGCTTTTGAAGT
591155 AAAATACAAGTTGTATAGCTTTTGAAGT
1 AAAATACAAGTTGTATAGCTTTTGAAGT
591183 AAAATACAAGTTGTATAGCTTTTGAAGT
1 AAAATACAAGTTGTATAGCTTTTGAAGT
591211 AA
1 AA
591213 TTAAGGATCA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (28 bp):
AAAATACAAGTTGTATAGCTTTTGAAGT
Found at i:592846 original size:21 final size:21
Alignment explanation
Indices: 592820--592876 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 21
592810 TTAAAGAAGG
592820 AGAATAGAAGAACGGAGATAA
1 AGAATAGAAGAACGGAGATAA
592841 AGAATAGAAGAAAAAACGGAGATAA
1 AGAATAGAAG----AACGGAGATAA
*
592866 AGAAGAGAAGA
1 AGAATAGAAGA
592877 GAGGTTCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
21 11 0.35
25 20 0.65
ACGTcount: A:0.61, C:0.04, G:0.28, T:0.07
Consensus pattern (21 bp):
AGAATAGAAGAACGGAGATAA
Found at i:595649 original size:18 final size:18
Alignment explanation
Indices: 595637--595671 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
595627 AAGAACGGAG
*
595637 ATAAGGAAGAGAAGAGAA
1 ATAAAGAAGAGAAGAGAA
595655 ATAAAGAAGAGAAGAGA
1 ATAAAGAAGAGAAGAGA
595672 GGTTCAAGAG
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:0.63, C:0.00, G:0.31, T:0.06
Consensus pattern (18 bp):
ATAAAGAAGAGAAGAGAA
Found at i:596242 original size:69 final size:69
Alignment explanation
Indices: 596154--596294 Score: 255
Period size: 69 Copynumber: 2.0 Consensus size: 69
596144 TCAGTCTCAT
*
596154 AGAGAGATTTTATGATCCACAATCCGGTGAAGTCCTTATCGATGGCATCAAGTCCTAGAATGTCG
1 AGAGAGATTTTATGATCCACAATCCGGTGAAGTCCTTATCGATGGCACCAAGTCCTAGAATGTCG
596219 TTAG
66 TTAG
*
596223 AGAGAGATTTTATGATCCACAATCCGGTGAAGTCCTTATCTATGGCACCAAGTCCTAGAATGTCG
1 AGAGAGATTTTATGATCCACAATCCGGTGAAGTCCTTATCGATGGCACCAAGTCCTAGAATGTCG
*
596288 TTGG
66 TTAG
596292 AGA
1 AGA
596295 AATCTATCAG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (69 bp):
AGAGAGATTTTATGATCCACAATCCGGTGAAGTCCTTATCGATGGCACCAAGTCCTAGAATGTCG
TTAG
Found at i:598544 original size:11 final size:11
Alignment explanation
Indices: 598528--598552 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
598518 GTGCTTAGAA
598528 TGGGGTTATTG
1 TGGGGTTATTG
598539 TGGGGTTATTG
1 TGGGGTTATTG
598550 TGG
1 TGG
598553 AGAAAGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.48, T:0.44
Consensus pattern (11 bp):
TGGGGTTATTG
Found at i:600960 original size:30 final size:30
Alignment explanation
Indices: 600924--601014 Score: 173
Period size: 30 Copynumber: 3.0 Consensus size: 30
600914 TCAGAGGGCC
*
600924 TGAAAAGATTTCTAGCAATGGAACAAAGGG
1 TGAAAAGATTTCTAGCAATGGCACAAAGGG
600954 TGAAAAGATTTCTAGCAATGGCACAAAGGG
1 TGAAAAGATTTCTAGCAATGGCACAAAGGG
600984 TGAAAAGATTTCTAGCAATGGCACAAAGGG
1 TGAAAAGATTTCTAGCAATGGCACAAAGGG
601014 T
1 T
601015 TTTTCCGGTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.41, C:0.12, G:0.26, T:0.21
Consensus pattern (30 bp):
TGAAAAGATTTCTAGCAATGGCACAAAGGG
Found at i:604025 original size:34 final size:35
Alignment explanation
Indices: 603987--604080 Score: 102
Period size: 34 Copynumber: 2.7 Consensus size: 35
603977 TTTACGGACG
* *
603987 TTAAATGAACATTAAACGAATATGTTTA-TGAATA
1 TTAAATGAACACTAAACGAATATGTTTATTGAACA
* * * *
604021 TTAAATAAACGCTAAACGAATAT-ATTATTGAACG
1 TTAAATGAACACTAAACGAATATGTTTATTGAACA
* *
604055 TTAAATGAACACTAAATGAACATGTT
1 TTAAATGAACACTAAACGAATATGTT
604081 CACGAATGAA
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
33 3 0.06
34 43 0.91
35 1 0.02
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.32
Consensus pattern (35 bp):
TTAAATGAACACTAAACGAATATGTTTATTGAACA
Found at i:604090 original size:16 final size:16
Alignment explanation
Indices: 604069--604099 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
604059 ATGAACACTA
*
604069 AATGAACATGTTCACG
1 AATGAACATATTCACG
604085 AATGAACATATTCAC
1 AATGAACATATTCAC
604100 AAACACTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (16 bp):
AATGAACATATTCACG
Found at i:604169 original size:30 final size:32
Alignment explanation
Indices: 604129--604206 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 32
604119 TCGTGAATGT
*
604129 TAAACAAACGAACACGAA-A-AATATCAAAAA
1 TAAATAAACGAACACGAACACAATATCAAAAA
* *
604159 TAAATAAACGAACACGAACACGATATTAAAAA
1 TAAATAAACGAACACGAACACAATATCAAAAA
*
604191 T--TTAAACGAACACGAA
1 TAAATAAACGAACACGAA
604207 TCGAACATGA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 31 0.74
31 1 0.02
32 10 0.24
ACGTcount: A:0.60, C:0.17, G:0.09, T:0.14
Consensus pattern (32 bp):
TAAATAAACGAACACGAACACAATATCAAAAA
Found at i:604832 original size:17 final size:16
Alignment explanation
Indices: 604803--604907 Score: 76
Period size: 17 Copynumber: 6.6 Consensus size: 16
604793 TAAACATGAA
604803 AATAAATAATAATAAT
1 AATAAATAATAATAAT
604819 AAT-AATAA-AATAAT
1 AATAAATAATAATAAT
* * *
604833 AAATTAAAGGAAAAAATAAA
1 -AA-TAAA--TAATAATAAT
*
604853 AATAAATAAAAATAAAT
1 AATAAATAATAAT-AAT
604870 AATAAATAATAATAA-
1 AATAAATAATAATAAT
*
604885 AA-AAATAA-AAAAAT
1 AATAAATAATAATAAT
*
604899 AACAAATAA
1 AATAAATAA
604908 AAAAATACTG
Statistics
Matches: 74, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
13 4 0.05
14 14 0.19
15 15 0.20
16 12 0.16
17 16 0.22
18 4 0.05
19 4 0.05
20 5 0.07
ACGTcount: A:0.75, C:0.01, G:0.02, T:0.22
Consensus pattern (16 bp):
AATAAATAATAATAAT
Found at i:604855 original size:6 final size:6
Alignment explanation
Indices: 604791--604910 Score: 70
Period size: 6 Copynumber: 19.3 Consensus size: 6
604781 TAAATCACAG
* * * *
604791 AATAAA CATGAA AATAAA TAATAAT AATAAT AAT-AA AATAATA AATTAAA
1 AATAAA AATAAA AATAAA -AATAAA AATAAA AATAAA AATAA-A AA-TAAA
*
604841 GGA-AAA AATAAA AAT--A AATAAA AATAAA TAATAAA TAATAATA AA-AAA
1 -AATAAA AATAAA AATAAA AATAAA AATAAA -AATAAA -AATAA-A AATAAA
*
604889 ATAAAAA AATAACA AATAAA AA
1 A-ATAAA AATAA-A AATAAA AA
604911 AATACTGAAA
Statistics
Matches: 92, Mismatches: 9, Indels: 26
0.72 0.07 0.20
Matches are distributed among these distances:
4 4 0.04
5 7 0.08
6 43 0.47
7 33 0.36
8 5 0.05
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.21
Consensus pattern (6 bp):
AATAAA
Found at i:604857 original size:50 final size:49
Alignment explanation
Indices: 604801--604912 Score: 138
Period size: 50 Copynumber: 2.3 Consensus size: 49
604791 AATAAACATG
* * *
604801 AAAATAAATAATAAT-AATAATAATAAAATAATAAATTAAAGGAAAAAATA
1 AAAATAAATAAAAATAAATAATAA-AAAATAATAAA-AAAAGAAAAAAATA
* *
604851 AAAATAAATAAAAATAAATAATAAATAATAATAAAAAAATAAAAAAATA
1 AAAATAAATAAAAATAAATAATAAAAAATAATAAAAAAAGAAAAAAATA
604900 ACAAATAAA-AAAA
1 A-AAATAAATAAAA
604913 TACTGAAACT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
49 16 0.29
50 31 0.56
51 8 0.15
ACGTcount: A:0.77, C:0.01, G:0.02, T:0.21
Consensus pattern (49 bp):
AAAATAAATAAAAATAAATAATAAAAAATAATAAAAAAAGAAAAAAATA
Done.