Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold293
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: 1704560
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 3 of 12
Found at i:322939 original size:32 final size:32
Alignment explanation
Indices: 322903--322965 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
322893 ATTTGAATTT
*
322903 AAAATAATTCAAA-TCAAAAGCTGTTTAAACTC
1 AAAATAATTCAAACTCAAAA-CTATTTAAACTC
* *
322935 AAAATAATTTAAACTCCAAACTATTTAAACT
1 AAAATAATTCAAACTCAAAACTATTTAAACT
322966 TAAGATTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 22 0.81
33 5 0.19
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (32 bp):
AAAATAATTCAAACTCAAAACTATTTAAACTC
Found at i:322947 original size:16 final size:16
Alignment explanation
Indices: 322926--322965 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
322916 TCAAAAGCTG
322926 TTTAAACT-CAAAATAA
1 TTTAAACTCCAAAAT-A
*
322942 TTTAAACTCCAAACTA
1 TTTAAACTCCAAAATA
322958 TTTAAACT
1 TTTAAACT
322966 TAAGATTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.35
Consensus pattern (16 bp):
TTTAAACTCCAAAATA
Found at i:323157 original size:21 final size:20
Alignment explanation
Indices: 323133--323175 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
323123 TATATGTCTA
323133 TATGAGATAAAATAATAATTT
1 TATGAGA-AAAATAATAATTT
* **
323154 TATGATAAAAATGTTAATTT
1 TATGAGAAAAATAATAATTT
323174 TA
1 TA
323176 CTTTTATACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (20 bp):
TATGAGAAAAATAATAATTT
Found at i:324929 original size:21 final size:23
Alignment explanation
Indices: 324894--324955 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 23
324884 TGATTCAATA
*
324894 AAATAAATATTTAAATTTAATTT
1 AAATAAATATTTAAAATTAATTT
324917 AAAT-AAT-TTTAAAATTAA--T
1 AAATAAATATTTAAAATTAATTT
*
324936 AAATTAA-ATTTAAAA-TAATT
1 AAATAAATATTTAAAATTAATT
324956 CAAACTCAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
19 8 0.24
20 9 0.26
21 10 0.29
22 3 0.09
23 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATAAATATTTAAAATTAATTT
Found at i:324967 original size:30 final size:30
Alignment explanation
Indices: 324905--324967 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
324895 AATAAATATT
* * *
324905 TAAATTTAATTTAAATAATTTTAAAATTAA
1 TAAATTAAATTTAAATAATTTCAAAATCAA
*
324935 TAAATTAAATTTAAAATAA-TTCAAACTCAA
1 TAAATTAAATTT-AAATAATTTCAAAATCAA
324965 TAA
1 TAA
324968 TTTTAATATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 22 0.79
31 6 0.21
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (30 bp):
TAAATTAAATTTAAATAATTTCAAAATCAA
Found at i:325010 original size:16 final size:16
Alignment explanation
Indices: 324991--325040 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
324981 CTAAAATTAT
324991 TTAAATATAAAATAAC
1 TTAAATATAAAATAAC
*
325007 TTAAAT-TCAAAATAAA
1 TTAAATAT-AAAATAAC
* *
325023 TAAAATATATAATAAC
1 TTAAATATAAAATAAC
325039 TT
1 TT
325041 TAACTTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 1 0.04
16 25 0.93
17 1 0.04
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAAATATAAAATAAC
Found at i:325437 original size:14 final size:14
Alignment explanation
Indices: 325420--325470 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
325410 TAATAAAATA
*
325420 ATATAAATATTTTG
1 ATATAAATATTTTC
*
325434 ATATAAATATTTTT
1 ATATAAATATTTTC
*
325448 ATATAATTATTTTC
1 ATATAAATATTTTC
325462 ATATAAATA
1 ATATAAATA
325471 CTTAAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (14 bp):
ATATAAATATTTTC
Found at i:325759 original size:15 final size:15
Alignment explanation
Indices: 325722--325764 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
325712 ATCTTTTAAC
* *
325722 TTTAAAATATTTATT
1 TTTAATATATATATT
325737 TTTAATATATATATT
1 TTTAATATATATATT
325752 TATT-ATATATATA
1 T-TTAATATATATA
325765 AAATAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 23 0.92
16 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAATATATATATT
Found at i:325800 original size:33 final size:33
Alignment explanation
Indices: 325740--325802 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
325730 ATTTATTTTT
*
325740 AATATATATATTTATTATATATATAAAATAAAA
1 AATATATATATTTATTAAATATATAAAATAAAA
*
325773 AATATATA-ATTTTTTAAATATATTAAAATA
1 AATATATATATTTATTAAATATA-TAAAATA
325803 TTTTTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
AATATATATATTTATTAAATATATAAAATAAAA
Found at i:325835 original size:20 final size:20
Alignment explanation
Indices: 325769--325834 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
325759 TATATAAAAT
*
325769 AAAAAATATATAAT-TTTTTA
1 AAAAAAT-TAAAATATTTTTA
* *
325789 AATATATTAAAATATTTTTA
1 AAAAAATTAAAATATTTTTA
325809 AAAAAATTAAATATATTTTTA
1 AAAAAATTAAA-ATATTTTTA
325830 TAAAA
1 -AAAA
325835 TATATATCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
19 5 0.13
20 20 0.53
21 9 0.24
22 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAAAATTAAAATATTTTTA
Found at i:326805 original size:26 final size:27
Alignment explanation
Indices: 326748--326805 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
326738 GTTGACAAAG
*
326748 ATTTTTATTTTTTTAAAAAAATTATTT
1 ATTTTAATTTTTTTAAAAAAATTATTT
**
326775 A-TTTAATTTTTTTAAATCAATT-TTT
1 ATTTTAATTTTTTTAAAAAAATTATTT
326800 ATTTTA
1 ATTTTA
326806 TTCTTTGATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 4 0.15
26 22 0.81
27 1 0.04
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (27 bp):
ATTTTAATTTTTTTAAAAAAATTATTT
Found at i:327063 original size:36 final size:37
Alignment explanation
Indices: 326965--327073 Score: 95
Period size: 36 Copynumber: 3.0 Consensus size: 37
326955 AATATATATT
* *
326965 TATATATAAATATATATAATA--AAAACATATT--TACA
1 TATATATATATA-ATATAATATTAAAA-ATATTAATAAA
** *
327000 TATATATATATAATATTTTATTAAAAATTTTAA-AAA
1 TATATATATATAATATAATATTAAAAATATTAATAAA
*
327036 TATATATATAT-ATATAAATATTTAAAATATTAATAAA
1 TATATATATATAATAT-AATATTAAAAATATTAATAAA
327073 T
1 T
327074 TTAAAATAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
34 6 0.10
35 19 0.32
36 30 0.51
37 4 0.07
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (37 bp):
TATATATATATAATATAATATTAAAAATATTAATAAA
Found at i:328805 original size:21 final size:23
Alignment explanation
Indices: 328781--328826 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
328771 TTATAATTAA
328781 ATTTAAAT-A-AAAATAAATTTT
1 ATTTAAATGATAAAATAAATTTT
*
328802 ATTTAAATGATAATATAAATTTT
1 ATTTAAATGATAAAATAAATTTT
328825 AT
1 AT
328827 AACTCAAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.36
22 1 0.05
23 13 0.59
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTTAAATGATAAAATAAATTTT
Found at i:329291 original size:59 final size:58
Alignment explanation
Indices: 329189--329303 Score: 178
Period size: 59 Copynumber: 2.0 Consensus size: 58
329179 GCAGCGAGGA
*
329189 GATTCGATAATAATGGCGGACCCCATCATGTAAAAGTCACATCGTTTCTCAATCATAC
1 GATTCGATAATAATGGCGGACCCCAACATGTAAAAGTCACATCGTTTCTCAATCATAC
* *
329247 GATTCG-TCAATAATGGCGGAATCTCAACATGTAAAAGTCACATCGTTTCTCAATCAT
1 GATTCGAT-AATAATGGCGG-ACCCCAACATGTAAAAGTCACATCGTTTCTCAATCAT
329304 GCGGGCAAGG
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
57 1 0.02
58 17 0.33
59 34 0.65
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (58 bp):
GATTCGATAATAATGGCGGACCCCAACATGTAAAAGTCACATCGTTTCTCAATCATAC
Found at i:333698 original size:5 final size:5
Alignment explanation
Indices: 333688--333720 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
333678 GTAGCTACTT
*
333688 AAAGA AAAGA AATGA AAAGA AAAGA AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
333721 CTTTATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:334671 original size:14 final size:13
Alignment explanation
Indices: 334646--334675 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
334636 TTATTATTTA
334646 ATTAAAAATAAAT
1 ATTAAAAATAAAT
334659 ATTAAATAATAAAT
1 ATTAAA-AATAAAT
334673 ATT
1 ATT
334676 TTATGTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTAAAAATAAAT
Found at i:338465 original size:61 final size:61
Alignment explanation
Indices: 338370--338488 Score: 202
Period size: 61 Copynumber: 2.0 Consensus size: 61
338360 TGATATGTTG
* * *
338370 ATTTGACTTTGTGTCCATGATTCTAAGTGTTTGAATAATCTTTGATGTTATAGGCTTGGTA
1 ATTTGACTTTGAGTCCATGATTCTAAGTGTTTGAACAATCTTTAATGTTATAGGCTTGGTA
*
338431 ATTTGACTTTGAGTCCATGATTTTAAGTGTTTGAACAATCTTTAATGTTATAGGCTTG
1 ATTTGACTTTGAGTCCATGATTCTAAGTGTTTGAACAATCTTTAATGTTATAGGCTTG
338489 ATTTTGATGA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.45
Consensus pattern (61 bp):
ATTTGACTTTGAGTCCATGATTCTAAGTGTTTGAACAATCTTTAATGTTATAGGCTTGGTA
Found at i:339333 original size:13 final size:13
Alignment explanation
Indices: 339317--339341 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
339307 ATAAAAAAAA
339317 TTCATAATTAAAT
1 TTCATAATTAAAT
339330 TTCATAATTAAA
1 TTCATAATTAAA
339342 AATCCAAAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTCATAATTAAAT
Found at i:345116 original size:22 final size:20
Alignment explanation
Indices: 345089--345138 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
345079 ATCAAATAAT
*
345089 TTTTAAATTTAATTTAATTCAA
1 TTTTAAATTTAA-TAAATT-AA
345111 TTTTAAAATTTAATAAATTAA
1 TTTT-AAATTTAATAAATTAA
345132 TTTTAAA
1 TTTTAAA
345139 ATAACTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 3 0.12
21 6 0.23
22 9 0.35
23 8 0.31
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTTAAATTTAATAAATTAA
Found at i:345135 original size:21 final size:22
Alignment explanation
Indices: 345085--345140 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 22
345075 CTTCATCAAA
* *
345085 TAATTTTTAAATTTAATTTAAT
1 TAATTTTAAAATTTAATTAAAT
345107 TCAATTTTAAAATTTAA-TAAAT
1 T-AATTTTAAAATTTAATTAAAT
345129 TAATTTTAAAAT
1 TAATTTTAAAAT
345141 AACTTAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 11 0.35
22 6 0.19
23 14 0.45
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATTTTAAAATTTAATTAAAT
Found at i:345694 original size:16 final size:16
Alignment explanation
Indices: 345673--345723 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
345663 ATTAAATTCT
345673 TTTAAAATAATTTAAA
1 TTTAAAATAATTTAAA
*
345689 TTTAAAATTATTTAAA
1 TTTAAAATAATTTAAA
* *
345705 TATAAAATTAACTTAAA
1 TTTAAAA-TAATTTAAA
345722 TT
1 TT
345724 AATTAAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 21 0.72
17 8 0.28
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTAAAATAATTTAAA
Found at i:346651 original size:15 final size:17
Alignment explanation
Indices: 346633--346700 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
346623 TTTAAATTTT
*
346633 ATTAAAA-T-TTTATTA
1 ATTAAAATTATTTAATA
346648 ATTATAAATTATTTAATA
1 ATTA-AAATTATTTAATA
*
346666 ATTAAATTTATTTAATA
1 ATTAAAATTATTTAATA
*
346683 AATAAATATT-TTTAATA
1 ATTAAA-ATTATTTAATA
346700 A
1 A
346701 GAAAAAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
15 4 0.09
16 3 0.07
17 26 0.58
18 12 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTAAAATTATTTAATA
Found at i:350082 original size:17 final size:19
Alignment explanation
Indices: 350055--350090 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
350045 AAAAGATTTG
350055 TTTGATAAATA-TTAAAAA
1 TTTGATAAATATTTAAAAA
350073 TTTG-TAAATATTTAAAAA
1 TTTGATAAATATTTAAAAA
350091 AATTCTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (19 bp):
TTTGATAAATATTTAAAAA
Found at i:352947 original size:240 final size:240
Alignment explanation
Indices: 352524--353006 Score: 840
Period size: 240 Copynumber: 2.0 Consensus size: 240
352514 GAGGTGCGTC
* * * *
352524 TGACTTAATATCACTCGTGATTGAGAATTTATATGTCAAGATAAGGGATATTTTCTCGAGTAAAG
1 TGACTTAATATCACTCGCGATTGAGAATTTATATGGCAAGAGAAGGGATATTTTCTCGACTAAAG
* * *
352589 TGGGGAAGATTGGTAGATGAATCGCATATCTAATTAATCTTCGCCGGTCACCATAAAGTGGTCGA
66 TGGGGAAGATTGGCAGATGAATCGCATAACTAATTAATCTTCGACGGTCACCATAAAGTGGTCGA
352654 AGTTTTGGAGTCACCACCGATCATTTCAGGCTAGGTATGATCAGATGCCTATTGAAACTTATGTT
131 AGTTTTGGAGTCACCACCGATCATTTCAGGCTAGGTATGATCAGATGCCTATTGAAACTTATGTT
352719 TTGAGTTATGAAACTCGAAACATCGATCACATAGTCTATATAATT
196 TTGAGTTATGAAACTCGAAACATCGATCACATAGTCTATATAATT
* *
352764 TGACTTAATATCCCTCGCGATTGAGAATTTATATGGCAAGAGAAGGGATATTTTCTCGACTGAAG
1 TGACTTAATATCACTCGCGATTGAGAATTTATATGGCAAGAGAAGGGATATTTTCTCGACTAAAG
* *
352829 TGGGGACGATTGGCAGATGAATCGCATAACTAATTGATCTTCGACGGTCACCATAAAGTGGTCGA
66 TGGGGAAGATTGGCAGATGAATCGCATAACTAATTAATCTTCGACGGTCACCATAAAGTGGTCGA
*
352894 AGTTTTGGAGTCACCACCGATCATTTCTGGCTAGGTATGATCAGATGCCTATTGAAACTTATGTT
131 AGTTTTGGAGTCACCACCGATCATTTCAGGCTAGGTATGATCAGATGCCTATTGAAACTTATGTT
* *
352959 TTGAGTTATGAAACTTGAAACATCGATCACATGGTCTATATAATT
196 TTGAGTTATGAAACTCGAAACATCGATCACATAGTCTATATAATT
353004 TGA
1 TGA
353007 ATATTCATCA
Statistics
Matches: 229, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
240 229 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (240 bp):
TGACTTAATATCACTCGCGATTGAGAATTTATATGGCAAGAGAAGGGATATTTTCTCGACTAAAG
TGGGGAAGATTGGCAGATGAATCGCATAACTAATTAATCTTCGACGGTCACCATAAAGTGGTCGA
AGTTTTGGAGTCACCACCGATCATTTCAGGCTAGGTATGATCAGATGCCTATTGAAACTTATGTT
TTGAGTTATGAAACTCGAAACATCGATCACATAGTCTATATAATT
Found at i:356177 original size:9 final size:9
Alignment explanation
Indices: 356158--356194 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
356148 TCACTTCAAC
356158 TAAACATAAA
1 TAAA-ATAAA
356168 TAAAATAAA
1 TAAAATAAA
356177 TAAAATAAA
1 TAAAATAAA
*
356186 TAAACTAAA
1 TAAAATAAA
356195 GACAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 22 0.85
10 4 0.15
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (9 bp):
TAAAATAAA
Found at i:357880 original size:24 final size:24
Alignment explanation
Indices: 357848--357919 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
357838 TGCTTAAATA
*
357848 AATTTTTTTCACTTTTTTCTTTTC
1 AATTTTTTTCACTTTTTTTTTTTC
*
357872 AATTTTTTTCAATTTTCTTTTTTTC
1 AATTTTTTTCACTTTT-TTTTTTTC
**
357897 TCTTTTTTTC-CTTATTTTTTTTT
1 AATTTTTTTCACTT-TTTTTTTTT
357920 ACTTTTCATT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 24 0.59
25 17 0.41
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (24 bp):
AATTTTTTTCACTTTTTTTTTTTC
Found at i:357925 original size:21 final size:22
Alignment explanation
Indices: 357901--357947 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
357891 TTTTTCTCTT
*
357901 TTTTTCCTTAT-TTTTTTTTAC
1 TTTTTCATTATCTTTTTTTTAC
* *
357922 -TTTTCATTTTCTTTTTTTTTC
1 TTTTTCATTATCTTTTTTTTAC
357943 TTTTT
1 TTTTT
357948 ATTTCAAGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 8 0.38
21 9 0.43
22 4 0.19
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTCATTATCTTTTTTTTAC
Found at i:372799 original size:27 final size:28
Alignment explanation
Indices: 372769--372833 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 28
372759 ACATAAAATG
*
372769 TTTAAATGAAAA-TTTCACATGT-AAAAA
1 TTTAAAT-AAAATTTTCACAAGTGAAAAA
*
372796 TTT-AATAAAATTTTCACAAGTGAAAAG
1 TTTAAATAAAATTTTCACAAGTGAAAAA
*
372823 TTTAAAAAAAA
1 TTTAAATAAAA
372834 GTCTCATATG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 4 0.12
26 12 0.38
27 10 0.31
28 6 0.19
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (28 bp):
TTTAAATAAAATTTTCACAAGTGAAAAA
Found at i:372830 original size:25 final size:25
Alignment explanation
Indices: 372777--372832 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
372767 TGTTTAAATG
*
372777 AAAATTTCACATGTAAAAATTTAAT
1 AAAATTTCACAAGTAAAAATTTAAT
* *
372802 AAAATTTTCACAAGTGAAAAGTTTAAA
1 AAAA-TTTCACAAGT-AAAAATTTAAT
372829 AAAA
1 AAAA
372833 AGTCTCATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 4 0.15
26 9 0.35
27 13 0.50
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (25 bp):
AAAATTTCACAAGTAAAAATTTAAT
Found at i:372880 original size:27 final size:26
Alignment explanation
Indices: 372850--372903 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
372840 TATGTGAGAG
*
372850 TTAAGTAAAAAATG-TACATGTAAAAAT
1 TTAA-TAAAAAATGTTAAAT-TAAAAAT
*
372877 TTAATTAAAAATGTTAAATTAAAAAT
1 TTAATAAAAAATGTTAAATTAAAAAT
372903 T
1 T
372904 CTATGCATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (26 bp):
TTAATAAAAAATGTTAAATTAAAAAT
Found at i:372923 original size:27 final size:29
Alignment explanation
Indices: 372882--372942 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 29
372872 AAAATTTAAT
*
372882 TAAAAATGTTAAATTAAAAATTCTATGCA
1 TAAAAATGTTAAATTAAAAATTCTATACA
*
372911 TAAAAAT-TT-AATTAAAAATTTTATACA
1 TAAAAATGTTAAATTAAAAATTCTATACA
372938 TAAAA
1 TAAAA
372943 GATTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 21 0.70
28 2 0.07
29 7 0.23
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (29 bp):
TAAAAATGTTAAATTAAAAATTCTATACA
Found at i:373202 original size:21 final size:22
Alignment explanation
Indices: 373156--373196 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
373146 TAAAGTATTC
373156 ATACTTGTGCCATAAAATATAG
1 ATACTTGTGCCATAAAATATAG
373178 ATACTT-TGCCATAAAATAT
1 ATACTTGTGCCATAAAATAT
373197 CAATACCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (22 bp):
ATACTTGTGCCATAAAATATAG
Found at i:374967 original size:30 final size:30
Alignment explanation
Indices: 374931--374987 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
374921 AGTAAATTTA
374931 TTATTATAAAATAAATTAA-TAAAAATATAT
1 TTATTATAAAAT-AATTAATTAAAAATATAT
**
374961 TTATTATAGCATAATTAATTAAAAATA
1 TTATTATAAAATAATTAATTAAAAATA
374988 AGTAATTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (30 bp):
TTATTATAAAATAATTAATTAAAAATATAT
Found at i:375069 original size:13 final size:13
Alignment explanation
Indices: 375041--375074 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
375031 TTTTATTTAA
375041 ATTTTAATTCATTT
1 ATTTT-ATTCATTT
*
375055 ATTTTATTTATTT
1 ATTTTATTCATTT
375068 ATTTTAT
1 ATTTTAT
375075 AACATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTTTATTCATTT
Found at i:376200 original size:2 final size:2
Alignment explanation
Indices: 376187--376225 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
376177 TTAATGATGA
* * *
376187 AT AT AC AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
376226 AAAGAGAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:380228 original size:33 final size:31
Alignment explanation
Indices: 380173--380233 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
380163 ATTTGATATT
* * *
380173 TATATCTTTTAAATATTTAAAAATAAATGAG
1 TATAACTTTCAAATATTTAAAAAGAAATGAG
380204 TATAACTTTCAAATATATATAAAAAGAAAT
1 TATAACTTTCAAATAT-T-TAAAAAGAAAT
380234 TTAAAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.56
32 1 0.04
33 10 0.40
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (31 bp):
TATAACTTTCAAATATTTAAAAAGAAATGAG
Found at i:382767 original size:73 final size:73
Alignment explanation
Indices: 382681--382817 Score: 186
Period size: 73 Copynumber: 1.9 Consensus size: 73
382671 AGTTAAATAC
* * * * * **
382681 TCAAAGGTTAATAAAAATTGTTTATTGAATATGCCAAAA-AATAATGATAATAAATAGTAAAAAC
1 TCAAAGATCAATAAAAATAGATTATTAAATATGCCAAAAGAA-AACAATAATAAATAGTAAAAAC
382745 GTCAATCAT
65 GTCAATCAT
*
382754 TCAAAGATCAATAAAAATAGATTATTAAATATGCCAAAAGAAAACAATAATAAATGGTAAAAAC
1 TCAAAGATCAATAAAAATAGATTATTAAATATGCCAAAAGAAAACAATAATAAATAGTAAAAAC
382818 ATTAATCACA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 53 0.96
74 2 0.04
ACGTcount: A:0.55, C:0.09, G:0.10, T:0.26
Consensus pattern (73 bp):
TCAAAGATCAATAAAAATAGATTATTAAATATGCCAAAAGAAAACAATAATAAATAGTAAAAACG
TCAATCAT
Found at i:383542 original size:2 final size:2
Alignment explanation
Indices: 383535--383570 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
383525 TGTTATAATA
383535 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
383571 CTTTCCATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:385854 original size:2 final size:2
Alignment explanation
Indices: 385847--385882 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
385837 CGGTAACCTC
385847 TA TA TA TA TA 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 TA TA TA TA TA
385883 CACACACACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:387688 original size:2 final size:2
Alignment explanation
Indices: 387681--387715 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
387671 TGGTTTTAAA
387681 AT AT 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 AT AT A
387716 GATAGTTAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:387969 original size:18 final size:17
Alignment explanation
Indices: 387946--388015 Score: 56
Period size: 18 Copynumber: 4.1 Consensus size: 17
387936 AAAAGTGTTG
387946 TATATTATTAAATTTTAA
1 TATATTA-TAAATTTTAA
387964 TATATTA-ATAA-TTT-A
1 TATATTATA-AATTTTAA
* *
387979 TGTTTTATAAATTTTAA
1 TATATTATAAATTTTAA
*
387996 TATATTTATATATTTATAA
1 TATA-TTATAAATTT-TAA
388015 T
1 T
388016 TTTTTATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
15 8 0.20
16 8 0.20
17 5 0.12
18 16 0.39
19 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
TATATTATAAATTTTAA
Found at i:388008 original size:10 final size:9
Alignment explanation
Indices: 387981--388046 Score: 54
Period size: 8 Copynumber: 7.7 Consensus size: 9
387971 ATAATTTATG
*
387981 TTTTATAAA
1 TTTTATATA
387990 TTTTA-ATA
1 TTTTATATA
387998 TATTTATATA
1 T-TTTATATA
388008 -TTTATA-A
1 TTTTATATA
388015 TTTT-T-TA
1 TTTTATATA
388022 TTTTATAT-
1 TTTTATATA
388030 TTTATATCATA
1 TTT-TAT-ATA
388041 TTTTAT
1 TTTTAT
388047 TTATGTCATA
Statistics
Matches: 47, Mismatches: 1, Indels: 17
0.72 0.02 0.26
Matches are distributed among these distances:
7 7 0.15
8 16 0.34
9 13 0.28
10 8 0.17
11 3 0.06
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTATATA
Found at i:388010 original size:8 final size:8
Alignment explanation
Indices: 387963--388036 Score: 52
Period size: 7 Copynumber: 9.8 Consensus size: 8
387953 TTAAATTTTA
*
387963 ATATATTA
1 ATATATTT
387971 ATA-ATTT
1 ATATATTT
*
387978 ATGT-TTT
1 ATATATTT
*
387985 ATAAATTTT
1 ATATA-TTT
387994 AATATATTT
1 -ATATATTT
388003 ATATATTT
1 ATATATTT
388011 ATA-ATTT
1 ATATATTT
*
388018 -TTTATTT
1 ATATATTT
388025 -TATATTT
1 ATATATTT
388032 -TATAT
1 ATATAT
388037 CATATTTTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
6 1 0.02
7 29 0.54
8 14 0.26
9 6 0.11
10 4 0.07
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (8 bp):
ATATATTT
Found at i:388021 original size:18 final size:18
Alignment explanation
Indices: 387981--388022 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
387971 ATAATTTATG
387981 TTTTATAAATTTTAATAT
1 TTTTATAAATTTTAATAT
* *
387999 ATTTATATATTTATAAT-T
1 TTTTATAAATTT-TAATAT
388017 TTTTAT
1 TTTTAT
388023 TTTATATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTATAAATTTTAATAT
Found at i:388024 original size:7 final size:7
Alignment explanation
Indices: 387946--388036 Score: 56
Period size: 8 Copynumber: 11.7 Consensus size: 7
387936 AAAAGTGTTG
387946 TATATTAT
1 TATATT-T
*
387954 TAAATTT
1 TATATTT
387961 TAATATATT
1 T-ATAT-TT
* *
387970 AATAATT
1 TATATTT
*
387977 TATGTTT
1 TATATTT
387984 TATAAATTT
1 TAT--ATTT
387993 TAATATATT
1 T-ATAT-TT
388002 TATATATT
1 TATAT-TT
388010 TATAATTT
1 TAT-ATTT
*
388018 TTTATTT
1 TATATTT
388025 TATATTT
1 TATATTT
388032 TATAT
1 TATAT
388037 CATATTTTAT
Statistics
Matches: 66, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
7 26 0.39
8 27 0.41
9 11 0.17
10 2 0.03
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (7 bp):
TATATTT
Found at i:388026 original size:32 final size:33
Alignment explanation
Indices: 387946--388018 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 33
387936 AAAAGTGTTG
* *
387946 TATATTAT-TAAATTTTAATATATTAATA-ATT
1 TATATTTTATAAATTTTAATATATTTATATATT
*
387977 TATGTTTTATAAATTTTAATATATTTATATATT
1 TATATTTTATAAATTTTAATATATTTATATATT
388010 TATAATTTT
1 TAT-ATTTT
388019 TTATTTTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 6 0.17
32 19 0.54
33 6 0.17
34 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (33 bp):
TATATTTTATAAATTTTAATATATTTATATATT
Found at i:388047 original size:24 final size:23
Alignment explanation
Indices: 388000--388082 Score: 69
Period size: 27 Copynumber: 3.3 Consensus size: 23
387990 TTTTAATATA
*
388000 TTTATATATTTATAATTTTTTAT
1 TTTATATATTTATAATATTTTAT
388023 TTTATAT-TTTATATCATATTTTAT
1 TTTATATATTTATA--ATATTTTAT
*
388047 TTATGTCATATTTATATAGTATATTTAT
1 TT-TAT-ATATTTATA-A-TAT-TTTAT
*
388075 GTTATATA
1 TTTATATA
388083 AAATGAGTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
22 6 0.12
23 7 0.15
24 10 0.21
25 2 0.04
26 6 0.12
27 11 0.23
28 6 0.12
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (23 bp):
TTTATATATTTATAATATTTTAT
Found at i:388049 original size:23 final size:22
Alignment explanation
Indices: 387998--388082 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 22
387988 AATTTTAATA
*
387998 TATTTATATATTTATAATTTTT
1 TATTTATATATTTATAATATTT
388020 TATTT-TATATTTTATATCATATTT
1 TATTTATATA-TTTATA--ATATTT
388044 TATTTATGTCATATTTATATAGTATATT
1 TATTTA--T-ATATTTATA-A-TAT-TT
388072 TATGTTATATA
1 TAT-TTATATA
388083 AAATGAGTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
21 4 0.08
22 11 0.22
24 10 0.20
26 4 0.08
27 11 0.22
28 8 0.16
29 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (22 bp):
TATTTATATATTTATAATATTT
Found at i:388314 original size:34 final size:34
Alignment explanation
Indices: 388247--388462 Score: 292
Period size: 34 Copynumber: 6.4 Consensus size: 34
388237 TGCTGTTGTG
* * *
388247 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
388280 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
388314 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
388347 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
388381 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
388415 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
388449 TGTTGATTAAATGG
1 TGTTGATTAAATGG
388463 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 40 0.25
34 122 0.75
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:388428 original size:68 final size:67
Alignment explanation
Indices: 388247--388464 Score: 319
Period size: 67 Copynumber: 3.2 Consensus size: 67
388237 TGCTGTTGTG
* * * * *
388247 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
388312 AT
66 AT
* * * *
388314 TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
388379 AT
66 AT
* * *
388381 TGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
388446 CAT
65 CAT
388449 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
388465 GTTTTTACCA
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 73 0.54
68 61 0.46
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (67 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
AT
Found at i:388792 original size:19 final size:19
Alignment explanation
Indices: 388768--388824 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 19
388758 TTGGTTGTCG
*
388768 AGGTACTATTCACGTATAT
1 AGGTACTATTCACGTATAC
*
388787 AGGTACTATTCACATATAC
1 AGGTACTATTCACGTATAC
* *
388806 GGGTACTATTCAAGTATAC
1 AGGTACTATTCACGTATAC
388825 GGTTACTGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (19 bp):
AGGTACTATTCACGTATAC
Found at i:388825 original size:19 final size:19
Alignment explanation
Indices: 388769--388831 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
388759 TGGTTGTCGA
* **
388769 GGTACTATTCACGTATATA
1 GGTACTATTCAAGTATACG
388788 GGTACTATTCACA-TATACG
1 GGTACTATTCA-AGTATACG
388807 GGTACTATTCAAGTATACG
1 GGTACTATTCAAGTATACG
*
388826 GTTACT
1 GGTACT
388832 GTACACGTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 1 0.03
19 37 0.97
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (19 bp):
GGTACTATTCAAGTATACG
Found at i:392966 original size:34 final size:34
Alignment explanation
Indices: 392897--393114 Score: 296
Period size: 34 Copynumber: 6.5 Consensus size: 34
392887 AAGTGGGAGA
* * *
392897 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
392930 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
392964 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
392997 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
393031 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
393065 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
393099 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
393115 TGGTTTTTAC
Statistics
Matches: 164, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 42 0.26
34 122 0.74
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:393080 original size:68 final size:67
Alignment explanation
Indices: 392897--393116 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
392887 AAGTGGGAGA
* * * * *
392897 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
392962 CC
66 CC
* * * *
392964 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
393029 CC
66 CC
* * *
393031 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
393096 GCC
65 GCC
393099 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
393117 GTTTTTACCA
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:393697 original size:33 final size:33
Alignment explanation
Indices: 393660--393731 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 33
393650 TTTAAAAGTG
393660 TTATATATTATTAAATTTTAACATATTAATA-AT
1 TTATATATTA-TAAATTTTAACATATTAATATAT
* * *
393693 TTATATTTTATAAATTTTAATATATTTATATAT
1 TTATATATTATAAATTTTAACATATTAATATAT
393726 TTATAT
1 TTATAT
393732 TATATTTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
32 18 0.51
33 17 0.49
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (33 bp):
TTATATATTATAAATTTTAACATATTAATATAT
Found at i:393708 original size:32 final size:34
Alignment explanation
Indices: 393660--393746 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 34
393650 TTTAAAAGTG
*
393660 TTATATATTATTAAATTTTAACATATTAATA-AT
1 TTATATTTTATTAAATTTTAACATATTAATATAT
* *
393693 TTATATTTTA-TAAATTTTAATATATTTATATAT
1 TTATATTTTATTAAATTTTAACATATTAATATAT
*
393726 TTATATTATATTTATAATTTT
1 TTATATTTTA-TTA-AATTTT
393747 TTATTTTATA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
32 18 0.39
33 20 0.43
35 2 0.04
36 6 0.13
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (34 bp):
TTATATTTTATTAAATTTTAACATATTAATATAT
Found at i:393722 original size:18 final size:18
Alignment explanation
Indices: 393661--393746 Score: 74
Period size: 18 Copynumber: 4.9 Consensus size: 18
393651 TTAAAAGTGT
393661 TATATATTATTAAATTTTAA
1 TATAT-TTA-TAAATTTTAA
* *
393681 CATATTAAT-AA-TTT-A
1 TATATTTATAAATTTTAA
393696 TAT-TTTATAAATTTTAA
1 TATATTTATAAATTTTAA
* *
393713 TATATTTATATATTTATAT
1 TATATTTATAAATTT-TAA
393732 TATATTTAT-AATTTT
1 TATATTTATAAATTTT
393747 TTATTTTATA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
14 4 0.07
15 5 0.09
16 6 0.11
17 7 0.13
18 15 0.28
19 13 0.24
20 4 0.07
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (18 bp):
TATATTTATAAATTTTAA
Found at i:393732 original size:14 final size:13
Alignment explanation
Indices: 393713--393774 Score: 67
Period size: 14 Copynumber: 4.8 Consensus size: 13
393703 TAAATTTTAA
393713 TATATTTATATATT
1 TATATTT-TATATT
393727 TATA--TTATATT
1 TATATTTTATATT
*
393738 TATAATTTTTTATTT
1 TAT-ATTTTATA-TT
393753 TATATTTTATA-T
1 TATATTTTATATT
393765 TATATTTTAT
1 TATATTTTAT
393775 TTATTTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
11 9 0.21
12 13 0.31
14 15 0.36
15 5 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATATTTTATATT
Found at i:393749 original size:38 final size:36
Alignment explanation
Indices: 393693--393789 Score: 119
Period size: 33 Copynumber: 2.7 Consensus size: 36
393683 TATTAATAAT
*
393693 TTATATTTTATAAATTTTAATATATTTATATATTTATA
1 TTATATTTTATAATTTTTAATAT-TTTATAT-TTTATA
393731 TTATA-TTTATAATTTTT--TATTTTATATTTTATA
1 TTATATTTTATAATTTTTAATATTTTATATTTTATA
*
393764 TTATATTTTATTTATTTTTTAATATT
1 TTATATTTTA--TAATTTTTAATATT
393790 ATGTTTATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
33 11 0.21
34 11 0.21
35 3 0.06
36 7 0.13
37 11 0.21
38 9 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (36 bp):
TTATATTTTATAATTTTTAATATTTTATATTTTATA
Found at i:393788 original size:19 final size:20
Alignment explanation
Indices: 393691--393799 Score: 75
Period size: 19 Copynumber: 5.4 Consensus size: 20
393681 CATATTAATA
393691 ATTTATATTTTATAA-ATTTT
1 ATTTATATTTT-TAATATTTT
* *
393711 A-ATATATTTAT-ATA-TTT
1 ATTTATATTTTTAATATTTT
* *
393728 ATATTATATTTATAATTTTTT
1 AT-TTATATTTTTAATATTTT
393749 ATTTTATATTTTATATTATATTTT
1 A-TTTATATTTT-TA--ATATTTT
*
393773 ATTTAT-TTTTTAATATTAT
1 ATTTATATTTTTAATATTTT
*
393792 GTTTATAT
1 ATTTATAT
393800 AATATAATCA
Statistics
Matches: 71, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
17 5 0.07
18 2 0.03
19 27 0.38
20 4 0.06
21 14 0.20
22 7 0.10
23 5 0.07
24 7 0.10
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (20 bp):
ATTTATATTTTTAATATTTT
Found at i:393788 original size:24 final size:24
Alignment explanation
Indices: 393713--393791 Score: 76
Period size: 24 Copynumber: 3.3 Consensus size: 24
393703 TAAATTTTAA
*
393713 TATATTTATATATTTATATTATA-TT
1 TATA-TTATAT-TTTATTTTATATTT
*
393738 TATA--ATTTTTTATTTTATATTT
1 TATATTATATTTTATTTTATATTT
*
393760 TATATTATATTTTA-TTTATTTTT
1 TATATTATATTTTATTTTATATTT
393783 TAATATTAT
1 T-ATATTAT
393792 GTTTATATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
21 10 0.22
22 9 0.20
23 9 0.20
24 14 0.30
25 4 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
TATATTATATTTTATTTTATATTT
Found at i:403014 original size:20 final size:20
Alignment explanation
Indices: 402989--403065 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
402979 GTAAAAAGAT
402989 AGAATATATCGATATATTGA
1 AGAATATATCGATATATTGA
* *
403009 AGAATATATCGATACATTCA
1 AGAATATATCGATATATTGA
* *
403029 TA-CATGTATCGATATATTGA
1 -AGAATATATCGATATATTGA
* * *
403049 AAAATGTATCAATATAT
1 AGAATATATCGATATAT
403066 CTGGGTAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (20 bp):
AGAATATATCGATATATTGA
Found at i:405529 original size:22 final size:22
Alignment explanation
Indices: 405502--405543 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
405492 TTAATAATAT
*
405502 ATAATATAATA-TTATTTTTTGG
1 ATAATA-AATAGTTAATTTTTGG
405524 ATAATAAATAGTTAATTTTT
1 ATAATAAATAGTTAATTTTT
405544 AACATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
ATAATAAATAGTTAATTTTTGG
Found at i:405853 original size:19 final size:19
Alignment explanation
Indices: 405829--405912 Score: 73
Period size: 19 Copynumber: 4.3 Consensus size: 19
405819 TAATAAATTG
*
405829 TATTAATTTAAGTAT-TTAA
1 TATTAATATAA-TATATTAA
405848 TATTAATATAATATATTAA
1 TATTAATATAATATATTAA
* *
405867 TATTAA-ATATTTTATTAAA
1 TATTAATATAATATATT-AA
* *
405886 TATTACTATTTAAAATATTAA
1 TATTA--ATATAATATATTAA
405907 TATTAA
1 TATTAA
405913 AAATTAATAA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.21
19 28 0.53
21 8 0.15
22 6 0.11
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (19 bp):
TATTAATATAATATATTAA
Found at i:405876 original size:13 final size:13
Alignment explanation
Indices: 405836--405921 Score: 86
Period size: 13 Copynumber: 6.5 Consensus size: 13
405826 TTGTATTAAT
*
405836 TTAAGTATTTAATA
1 TTAA-TATTAAATA
405850 TTAATA-TAATATA
1 TTAATATTAA-ATA
405863 TTAATATTAAATA
1 TTAATATTAAATA
*
405876 TT-TTATTAAATA
1 TTAATATTAAATA
*
405888 TTACTATTTAAAATA
1 TTAATA-TT-AAATA
*
405903 TTAATATTAAAAA
1 TTAATATTAAATA
405916 TTAATA
1 TTAATA
405922 ATTTAACGAG
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
12 13 0.21
13 28 0.45
14 11 0.18
15 10 0.16
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (13 bp):
TTAATATTAAATA
Found at i:406062 original size:23 final size:23
Alignment explanation
Indices: 406036--406100 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
406026 ATAATAACTA
*
406036 TAATATTTTAAATATTAATATAT
1 TAATATTTTAAATATTAATATAG
* *
406059 TAATGTTTT-AATAATAA-ATAG
1 TAATATTTTAAATATTAATATAG
* *
406080 TATTATTTTAAGTATTTAATA
1 TAATATTTTAAATA-TTAATA
406101 GCAATATATT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
21 10 0.31
22 10 0.31
23 11 0.34
24 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.51
Consensus pattern (23 bp):
TAATATTTTAAATATTAATATAG
Found at i:406076 original size:29 final size:29
Alignment explanation
Indices: 406044--406100 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
406034 TATAATATTT
*
406044 TAAATATTAATATATTAATGT-TTTAATAA
1 TAAATAGTAATATATTAA-GTATTTAATAA
* *
406073 TAAATAGTATTATTTTAAGTATTTAATA
1 TAAATAGTAATATATTAAGTATTTAATA
406101 GCAATATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (29 bp):
TAAATAGTAATATATTAAGTATTTAATAA
Found at i:408683 original size:26 final size:25
Alignment explanation
Indices: 408626--408711 Score: 86
Period size: 26 Copynumber: 3.4 Consensus size: 25
408616 AGTCACCAAT
* * *
408626 TTTGACAAAC-AACAAGCCACCATT
1 TTTGACAAACAAAAAATCCACCATA
*
408650 TTTTACAAACAAAAATATCCACCATA
1 TTTGACAAACAAAAA-ATCCACCATA
408676 TTTGACAAATACAAAGAAAT-CACCATA
1 TTTGAC-AA-ACAAA-AAATCCACCATA
408703 TTTGACAAA
1 TTTGACAAA
408712 TACAAAGGGT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
24 9 0.17
25 4 0.08
26 15 0.29
27 15 0.29
28 7 0.13
29 2 0.04
ACGTcount: A:0.48, C:0.22, G:0.06, T:0.24
Consensus pattern (25 bp):
TTTGACAAACAAAAAATCCACCATA
Found at i:410660 original size:21 final size:22
Alignment explanation
Indices: 410622--410667 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
410612 ATTTGTTGAA
**
410622 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGTTGCGGAGTACT
410643 ACTCCACCTGTTGCGGAGTACT
1 ACTCCACCTGTTGCGGAGTACT
410665 ACT
1 ACT
410668 TGTCTGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (22 bp):
ACTCCACCTGTTGCGGAGTACT
Found at i:413179 original size:26 final size:25
Alignment explanation
Indices: 413122--413207 Score: 77
Period size: 27 Copynumber: 3.4 Consensus size: 25
413112 AGTCACAAAT
* ** *
413122 TTTGACAAAC-AACAAGCCACCATT
1 TTTGACAAACAAAGAAATCACCATA
*
413146 TTTTACAAACAAA-AATATTCACCATA
1 TTTGACAAACAAAGAA-A-TCACCATA
413172 TTTGACAAATACAAAGAAATCACCATA
1 TTTGAC-AA-ACAAAGAAATCACCATA
413199 TTTGACAAA
1 TTTGACAAA
413208 TACAAAGGGT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
24 11 0.22
25 3 0.06
26 13 0.25
27 16 0.31
28 6 0.12
29 2 0.04
ACGTcount: A:0.48, C:0.21, G:0.06, T:0.26
Consensus pattern (25 bp):
TTTGACAAACAAAGAAATCACCATA
Found at i:417244 original size:15 final size:16
Alignment explanation
Indices: 417216--417251 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
417206 ATTTTAAAAT
417216 TTTAAATAAAAAAGTA
1 TTTAAATAAAAAAGTA
417232 TTTAAAT-AAAAAGTA
1 TTTAAATAAAAAAGTA
417247 TTTAA
1 TTTAA
417252 TATTTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (16 bp):
TTTAAATAAAAAAGTA
Found at i:417361 original size:24 final size:25
Alignment explanation
Indices: 417307--417372 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
417297 TTTTGTATTT
417307 TAATAATATATTATTA-ATATTAACAA
1 TAATAATATATT-TTATA-ATTAACAA
* *
417333 AAATAATATATTTTATAATTGA-AA
1 TAATAATATATTTTATAATTAACAA
417357 TAATAA-ATA-TTTATAA
1 TAATAATATATTTTATAA
417373 AATATTGTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
22 7 0.19
23 3 0.08
24 7 0.19
25 7 0.19
26 12 0.33
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
TAATAATATATTTTATAATTAACAA
Found at i:418450 original size:3 final size:3
Alignment explanation
Indices: 418442--418470 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
418432 TTTAATGCAA
418442 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
418471 GTTTTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:418505 original size:2 final size:2
Alignment explanation
Indices: 418494--418528 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
418484 ATGCACCTTC
418494 AT AT -T 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
418529 TAAAATTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:422916 original size:25 final size:25
Alignment explanation
Indices: 422854--422923 Score: 99
Period size: 24 Copynumber: 2.8 Consensus size: 25
422844 AATAAAAATT
*
422854 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
422878 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
*
422903 AGCCTCC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
422924 CAAAGAAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 21 0.50
25 21 0.50
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:422969 original size:27 final size:28
Alignment explanation
Indices: 422908--422978 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 28
422898 AAACAAGCCT
* *
422908 CCATATTTGACAAATACAAAGAAAACCA
1 CCATTTTTGACAAACACAAAGAAAACCA
*
422936 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGAAAACCA
422963 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
422979 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.23
Consensus pattern (28 bp):
CCATTTTTGACAAACACAAAGAAAACCA
Found at i:422981 original size:24 final size:24
Alignment explanation
Indices: 422856--422981 Score: 92
Period size: 24 Copynumber: 4.9 Consensus size: 24
422846 TAAAAATTAG
* *
422856 CCACCAATTTTGACAAACAACA-AG
1 CCACCATTTTTGACAAACAA-ATAA
* * *
422880 CCACCAATTTTGACAAATAAACAA
1 CCACCATTTTTGACAAACAAATAA
* * *
422904 GCCTCCATATTTGACAAATACAAAGAAAA
1 -CCACCATTTTTGAC-AA-AC-AA-ATAA
422933 CCACCATTTTTGACAAACACAAAATAA
1 CCACCATTTTTGAC-AA-AC-AAATAA
422960 CCACCATTTTTGACAAACAAAT
1 CCACCATTTTTGACAAACAAAT
422982 GGGTGGCTTT
Statistics
Matches: 85, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
23 1 0.01
24 24 0.28
25 13 0.15
26 4 0.05
27 18 0.21
28 22 0.26
29 3 0.04
ACGTcount: A:0.47, C:0.25, G:0.06, T:0.21
Consensus pattern (24 bp):
CCACCATTTTTGACAAACAAATAA
Found at i:427477 original size:24 final size:24
Alignment explanation
Indices: 427449--427572 Score: 88
Period size: 27 Copynumber: 4.8 Consensus size: 24
427439 TAAAAATTAG
427449 CCACCAATTTTGACAAACAACAAA
1 CCACCAATTTTGACAAACAACAAA
* *
427473 CCACCAATTTTGACAAATAAACAAG
1 CCACCAATTTTGACAAA-CAACAAA
** *
427498 CCTTC-ATATTTGACAAATACAAAGGAAA
1 CCACCAAT-TTTGAC-AA-AC-AA-CAAA
* *
427526 CCACCATTTTTGACAAACACAAAATAA
1 CCACCAATTTTGAC-AA-ACAACA-AA
*
427553 CCACCATTTTTGACAAACAA
1 CCACCAATTTTGACAAACAA
427573 ATGGGTGGCT
Statistics
Matches: 80, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
24 19 0.24
25 18 0.22
26 5 0.06
27 21 0.26
28 16 0.20
29 1 0.01
ACGTcount: A:0.47, C:0.25, G:0.06, T:0.22
Consensus pattern (24 bp):
CCACCAATTTTGACAAACAACAAA
Found at i:427562 original size:27 final size:27
Alignment explanation
Indices: 427506--427571 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
427496 AGCCTTCATA
*
427506 TTTGACAAATACAAAGGAAACCACCATT
1 TTTGACAAACACAAA-GAAACCACCATT
427534 TTTGACAAACACAAA-ATAACCACCATT
1 TTTGACAAACACAAAGA-AACCACCATT
427561 TTTGACAAACA
1 TTTGACAAACA
427572 AATGGGTGGC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 1 0.03
27 21 0.58
28 14 0.39
ACGTcount: A:0.47, C:0.23, G:0.08, T:0.23
Consensus pattern (27 bp):
TTTGACAAACACAAAGAAACCACCATT
Found at i:427574 original size:24 final size:24
Alignment explanation
Indices: 427449--427574 Score: 92
Period size: 24 Copynumber: 4.9 Consensus size: 24
427439 TAAAAATTAG
*
427449 CCACCAATTTTGACAAACAACA-AA
1 CCACCATTTTTGACAAACAA-ATAA
* * *
427473 CCACCAATTTTGACAAATAAACAA
1 CCACCATTTTTGACAAACAAATAA
** * *
427497 GCCTTCATATTTGACAAATACAAAGGAAA
1 -CCACCATTTTTGAC-AA-ACAAA--TAA
427526 CCACCATTTTTGACAAACACAAAATAA
1 CCACCATTTTTGAC-AA-AC-AAATAA
427553 CCACCATTTTTGACAAACAAAT
1 CCACCATTTTTGACAAACAAAT
427575 GGGTGGCTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
23 1 0.01
24 25 0.30
25 12 0.14
26 4 0.05
27 20 0.24
28 16 0.19
29 5 0.06
ACGTcount: A:0.47, C:0.25, G:0.06, T:0.22
Consensus pattern (24 bp):
CCACCATTTTTGACAAACAAATAA
Found at i:428453 original size:2 final size:2
Alignment explanation
Indices: 428446--428470 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
428436 CTAGTGTATT
428446 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
428471 TTGATTAAAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:429700 original size:27 final size:29
Alignment explanation
Indices: 429660--429716 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
429650 ATAATTTTTA
*
429660 TTATAAATATTAATA-AATTT-ATCAAAT
1 TTATAAATAATAATACAATTTCATCAAAT
*
429687 TTATATATAATAATACAATTTGCATCAAAT
1 TTATAAATAATAATACAATTT-CATCAAAT
429717 GACTACTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.52
28 5 0.20
30 7 0.28
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (29 bp):
TTATAAATAATAATACAATTTCATCAAAT
Found at i:429952 original size:17 final size:17
Alignment explanation
Indices: 429930--429965 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
429920 TATTATTTTA
429930 AATAAA-TGAAAAACTAT
1 AATAAATTGAAAAA-TAT
429947 AATAAATTGAAAAATAT
1 AATAAATTGAAAAATAT
429964 AA
1 AA
429966 GTGTTGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (17 bp):
AATAAATTGAAAAATAT
Found at i:430171 original size:12 final size:12
Alignment explanation
Indices: 430154--430180 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
430144 ATAGTTTTGG
430154 ATAAAAATTAAA
1 ATAAAAATTAAA
430166 ATAAAAATTAAA
1 ATAAAAATTAAA
430178 ATA
1 ATA
430181 TTTTATTTGT
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
ATAAAAATTAAA
Found at i:434845 original size:15 final size:16
Alignment explanation
Indices: 434825--434866 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
434815 TATATATAAA
434825 TATAAATTTTAAAAT-
1 TATAAATTTTAAAATC
*
434840 TATAAATATTTAATATC
1 TATAAAT-TTTAAAATC
*
434857 TAAAAATTTT
1 TATAAATTTT
434867 GAATATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 7 0.30
16 10 0.43
17 6 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TATAAATTTTAAAATC
Found at i:434863 original size:17 final size:19
Alignment explanation
Indices: 434841--434883 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
434831 TTTTAAAATT
*
434841 ATAAATATTT-AATATCTA
1 ATAAATATTTGAATATCAA
434859 A-AAAT-TTTGAATATCAA
1 ATAAATATTTGAATATCAA
434876 ATAAATAT
1 ATAAATAT
434884 AAAAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 3 0.14
17 12 0.57
18 5 0.24
19 1 0.05
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (19 bp):
ATAAATATTTGAATATCAA
Found at i:435625 original size:2 final size:2
Alignment explanation
Indices: 435618--435647 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
435608 TTGTACAAAT
435618 TA TA 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 TA TA
435648 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:435652 original size:2 final size:2
Alignment explanation
Indices: 435647--435681 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
435637 ATATATATAT
*
435647 AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
435682 CTAAACTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:436617 original size:16 final size:16
Alignment explanation
Indices: 436592--436625 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
436582 AATATACAAA
436592 TTTTTTTTA-TTTTCT
1 TTTTTTTTATTTTTCT
436607 TTTTCTTTTATTTTTCT
1 TTTT-TTTTATTTTTCT
436624 TT
1 TT
436626 CTTCCATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 5 0.29
17 8 0.47
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTTTTATTTTTCT
Found at i:449152 original size:7 final size:7
Alignment explanation
Indices: 449142--449172 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
449132 AAAAATTTTA
449142 TTTTATT
1 TTTTATT
*
449149 TTTTATA
1 TTTTATT
449156 TTTTATT
1 TTTTATT
449163 TTTTATT
1 TTTTATT
449170 TTT
1 TTT
449173 ATTAAGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTATT
Found at i:449159 original size:14 final size:14
Alignment explanation
Indices: 449140--449175 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
449130 ATAAAAATTT
449140 TATTTTATTTTTTA
1 TATTTTATTTTTTA
449154 TATTTTATTTTTTA
1 TATTTTATTTTTTA
449168 T-TTTTATT
1 TATTTTATT
449176 AAGAAATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TATTTTATTTTTTA
Found at i:450393 original size:16 final size:16
Alignment explanation
Indices: 450356--450394 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
450346 ATATTTATAT
450356 TTATTTAATTTATTTA
1 TTATTTAATTTATTTA
** *
450372 AAATTTAATTTTTTTA
1 TTATTTAATTTATTTA
450388 TTATTTA
1 TTATTTA
450395 CTTATTAGTT
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTTAATTTATTTA
Found at i:450825 original size:9 final size:9
Alignment explanation
Indices: 450811--450865 Score: 60
Period size: 9 Copynumber: 6.3 Consensus size: 9
450801 AGGACGAATT
450811 AAAATAATA
1 AAAATAATA
* *
450820 AAAATATTT
1 AAAATAATA
450829 AAAATAATA
1 AAAATAATA
*
450838 AAAAT-TTA
1 AAAATAATA
*
450846 AATAT-ATA
1 AAAATAATA
450854 AAAATAATA
1 AAAATAATA
450863 AAA
1 AAA
450866 TTATTAATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
8 12 0.32
9 25 0.68
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AAAATAATA
Found at i:450832 original size:18 final size:18
Alignment explanation
Indices: 450809--450859 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
450799 CAAGGACGAA
450809 TTAAAATAATAAAAATAT
1 TTAAAATAATAAAAATAT
450827 TTAAAATAAT-AAAA-AT
1 TTAAAATAATAAAAATAT
450843 TT-AAATATATAAAAATA
1 TTAAAATA-ATAAAAATA
450860 ATAAAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.17
16 6 0.20
17 8 0.27
18 11 0.37
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TTAAAATAATAAAAATAT
Found at i:450846 original size:16 final size:16
Alignment explanation
Indices: 450809--450858 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 16
450799 CAAGGACGAA
450809 TTAAAATAATAAAAATAT
1 TTAAAATAAT-AAAA-AT
450827 TTAAAATAATAAAAAT
1 TTAAAATAATAAAAAT
450843 TT-AAATATATAAAAAT
1 TTAAAATA-ATAAAAAT
450859 AATAAAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 4 0.13
18 10 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAAAATAATAAAAAT
Found at i:451037 original size:2 final size:2
Alignment explanation
Indices: 451030--451093 Score: 64
Period size: 2 Copynumber: 34.0 Consensus size: 2
451020 ATTATAAATC
* *
451030 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T- TA -A CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
451070 TA T- TA -A CA TT TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
451094 ATTTGACGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
1 4 0.08
2 48 0.92
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:451687 original size:24 final size:25
Alignment explanation
Indices: 451626--451691 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 25
451616 CAAGTTATTA
*
451626 TATGTTTATTTAAATTTTGACACAT
1 TATGTTTATTTAAAATTTGACACAT
451651 TAATGATTCTTTATTTAAAATTTGACACAT
1 T-ATG----TTTATTTAAAATTTGACACAT
451681 T-TGTTTATTTA
1 TATGTTTATTTA
451692 TATTATGTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
24 8 0.23
25 1 0.03
26 3 0.09
28 2 0.06
30 21 0.60
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.53
Consensus pattern (25 bp):
TATGTTTATTTAAAATTTGACACAT
Found at i:452083 original size:24 final size:25
Alignment explanation
Indices: 452056--452102 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
452046 TATATAAATT
*
452056 TTTACATATTAATA-ATTTATTTTA
1 TTTAAATATTAATATATTTATTTTA
*
452080 TTTAAATTTTAATATATTTATTT
1 TTTAAATATTAATATATTTATTT
452103 ACTCGTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTAAATATTAATATATTTATTTTA
Found at i:452144 original size:17 final size:19
Alignment explanation
Indices: 452112--452146 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
452102 TACTCGTATC
452112 ATATTATATAATTATATTT
1 ATATTATATAATTATATTT
452131 ATATTATA-AA-TATATT
1 ATATTATATAATTATATT
452147 AAGATACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTATATAATTATATTT
Found at i:452305 original size:21 final size:23
Alignment explanation
Indices: 452271--452315 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
452261 GCAAATTATT
452271 AATACTATTATTAT-ATTTTTAA
1 AATACTATTATTATAATTTTTAA
*
452293 AATA-TATTTTTATAAATTTTTAA
1 AATACTATTATTAT-AATTTTTAA
452316 TTTGTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 4 0.20
23 8 0.40
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
AATACTATTATTATAATTTTTAA
Found at i:453987 original size:19 final size:21
Alignment explanation
Indices: 453922--453990 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
453912 GTACTGTTTA
*
453922 TTTAAT-TAAAATTATTTAAA-
1 TTTAATATAAAA-TATATAAAT
453942 TTTAATTATAAAATATATAAAT
1 TTTAA-TATAAAATATATAAAT
*
453964 ATTAATATAAAA-ATA-AAAT
1 TTTAATATAAAATATATAAAT
453983 TTTAATAT
1 TTTAATAT
453991 TTTAAATAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 11 0.26
20 8 0.19
21 15 0.35
22 9 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTAATATAAAATATATAAAT
Found at i:455063 original size:16 final size:17
Alignment explanation
Indices: 455044--455080 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
455034 TGTTTACAAT
455044 TTATTTTATGTA-TATA
1 TTATTTTATGTATTATA
*
455060 TTATTTTTTGTATTATA
1 TTATTTTATGTATTATA
455077 TTAT
1 TTAT
455081 ATTTTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (17 bp):
TTATTTTATGTATTATA
Found at i:455076 original size:17 final size:17
Alignment explanation
Indices: 455044--455091 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
455034 TGTTTACAAT
*
455044 TTATTTTATGTA-TATA
1 TTATTTTTTGTATTATA
455060 TTATTTTTTGTATTATA
1 TTATTTTTTGTATTATA
* *
455077 TTATATTTTATATTA
1 TTATTTTTTGTATTA
455092 CATTTTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (17 bp):
TTATTTTTTGTATTATA
Found at i:462025 original size:17 final size:19
Alignment explanation
Indices: 461992--462029 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
461982 GACTATAAAA
461992 TACATATCATATTATTTAT
1 TACATATCATATTATTTAT
462011 TACATAT-AT-TTATTTAT
1 TACATATCATATTATTTAT
462028 TA
1 TA
462030 AAGACATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.53
18 2 0.11
19 7 0.37
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (19 bp):
TACATATCATATTATTTAT
Found at i:462687 original size:24 final size:23
Alignment explanation
Indices: 462655--462700 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
462645 ACAAAAAAAT
*
462655 ATTTAATTTATATTTATTTTAATA
1 ATTTAATTTAAATTT-TTTTAATA
*
462679 ATTTTATTTAAATTTTTTTAAT
1 ATTTAATTTAAATTTTTTTAAT
462701 TAAATAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTTAATTTAAATTTTTTTAATA
Found at i:462862 original size:16 final size:15
Alignment explanation
Indices: 462834--462874 Score: 73
Period size: 16 Copynumber: 2.7 Consensus size: 15
462824 TTAAAAAGTG
462834 TAGTACATTACTGTA
1 TAGTACATTACTGTA
462849 TAGTACAGTTACTGTA
1 TAGTACA-TTACTGTA
462865 TAGTACATTA
1 TAGTACATTA
462875 TAGATGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (15 bp):
TAGTACATTACTGTA
Found at i:468310 original size:2 final size:2
Alignment explanation
Indices: 468303--468333 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
468293 TATCTCTAAC
*
468303 AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
468334 AGTATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:468339 original size:10 final size:11
Alignment explanation
Indices: 468304--468345 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
468294 ATCTCTAACA
468304 TATATATATA-
1 TATATATATAG
468314 TATATATATAG
1 TATATATATAG
468325 -ATATATATAAG
1 TATATATAT-AG
*
468336 TATAAATATA
1 TATATATATA
468346 AAAAAAGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 18 0.64
11 3 0.11
12 7 0.25
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (11 bp):
TATATATATAG
Found at i:468368 original size:15 final size:17
Alignment explanation
Indices: 468333--468369 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
468323 AGATATATAT
468333 AAGTATAAATATAAAAA
1 AAGTATAAATATAAAAA
*
468350 AAGT-TAAAT-TAACAA
1 AAGTATAAATATAAAAA
468365 AAGTA
1 AAGTA
468370 ATTATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 9 0.50
16 5 0.28
17 4 0.22
ACGTcount: A:0.65, C:0.03, G:0.08, T:0.24
Consensus pattern (17 bp):
AAGTATAAATATAAAAA
Found at i:470839 original size:2 final size:2
Alignment explanation
Indices: 470832--470857 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
470822 GCTTTAAAGC
470832 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
470858 GAAATGTTTA
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:472781 original size:15 final size:14
Alignment explanation
Indices: 472760--472792 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
472750 AATATTTAAA
*
472760 ATTTTTTAAACCAT
1 ATTTTTTTAACCAT
472774 ATTTTTTTAACCAT
1 ATTTTTTTAACCAT
472788 ATTTT
1 ATTTT
472793 AAAGTTCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTTTTTTAACCAT
Found at i:474184 original size:21 final size:20
Alignment explanation
Indices: 474149--474197 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
474139 AATTAAAAAA
474149 TTAA-TTAAAAATTTAAATT
1 TTAAGTTAAAAATTTAAATT
*
474168 TTAAGTTAAATAATTTAAGTT
1 TTAAGTTAAA-AATTTAAATT
474189 TTGAAGTTA
1 TT-AAGTTA
474198 TTTGAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.15
20 5 0.19
21 11 0.42
22 6 0.23
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (20 bp):
TTAAGTTAAAAATTTAAATT
Found at i:477431 original size:12 final size:11
Alignment explanation
Indices: 477388--477437 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 11
477378 TAATTTATTT
477388 AAAAAAAAAGG
1 AAAAAAAAAGG
* *
477399 AGAAAAGAGAGAG
1 A-AAAAAAAAG-G
477412 AAAAAAAAAGG
1 AAAAAAAAAGG
477423 AAAAGAAAAAGG
1 AAAA-AAAAAGG
477435 AAA
1 AAA
477438 TTATAATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
11 6 0.19
12 24 0.75
13 2 0.06
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGG
Found at i:478275 original size:17 final size:17
Alignment explanation
Indices: 478255--478292 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
478245 AAAAAAGAAT
478255 TAAAAACAAA-AATTAAA
1 TAAAAACAAATAATT-AA
*
478272 TAAAAATAAATAATTAA
1 TAAAAACAAATAATTAA
478289 TAAA
1 TAAA
478293 TGATATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAAAACAAATAATTAA
Found at i:483700 original size:20 final size:21
Alignment explanation
Indices: 483677--483716 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
483667 AAAAATTAAA
*
483677 ATATTTTAT-ATTATATTTAT
1 ATATTTTATAATTAAATTTAT
483697 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
483717 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:484229 original size:21 final size:22
Alignment explanation
Indices: 484204--484253 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
484194 ACTTAAAATT
*
484204 TTTTTATTTATAAAATT-TATA
1 TTTTTATTAATAAAATTATATA
*
484225 TTTTTA-TAATATAATTATATA
1 TTTTTATTAATAAAATTATATA
484246 TGTTTTAT
1 T-TTTTAT
484254 AAGAATACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 8 0.33
21 11 0.46
22 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTTATTAATAAAATTATATA
Found at i:484265 original size:23 final size:21
Alignment explanation
Indices: 484217--484271 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
484207 TTATTTATAA
*
484217 AATT-TATATTTTTATAATAT
1 AATTATATATTTTTATAAAAT
484237 AATTATATATGTTTTATAAGAAT
1 AATTATATAT-TTTTATAA-AAT
*
484260 ACTTATA-ATTTT
1 AATTATATATTTT
484272 ATTTTATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 4 0.13
21 8 0.27
22 10 0.33
23 8 0.27
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (21 bp):
AATTATATATTTTTATAAAAT
Found at i:484387 original size:15 final size:15
Alignment explanation
Indices: 484367--484406 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
484357 AAATATATTC
484367 AATTAATAAAAATTA
1 AATTAATAAAAATTA
*
484382 AATTAA-AAATATTA
1 AATTAATAAAAATTA
484396 AA--AATAAAAAT
1 AATTAATAAAAAT
484407 ATATAATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 2 0.09
13 5 0.23
14 9 0.41
15 6 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AATTAATAAAAATTA
Found at i:484916 original size:2 final size:2
Alignment explanation
Indices: 484909--484940 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
484899 AATGAAGGAA
484909 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
484941 TATCTAGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:488577 original size:33 final size:31
Alignment explanation
Indices: 488502--488577 Score: 118
Period size: 34 Copynumber: 2.4 Consensus size: 31
488492 TTAAATAATA
488502 CTAATTTAA-TTAAAAAAAGTGTACAAAAGG
1 CTAATTTAAGTTAAAAAAAGTGTACAAAAGG
488532 CTAAATTTAAGTTATAATAAAAGTGTACAAAAGG
1 CT-AATTTAAGTTA-AA-AAAAGTGTACAAAAGG
488566 CTAATTTAAGTT
1 CTAATTTAAGTT
488578 TATTAACTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
30 2 0.05
31 7 0.17
32 3 0.07
33 12 0.29
34 18 0.43
ACGTcount: A:0.49, C:0.07, G:0.13, T:0.32
Consensus pattern (31 bp):
CTAATTTAAGTTAAAAAAAGTGTACAAAAGG
Done.