Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008312.1 Hibiscus syriacus cultivar Beakdansim tig00111005_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: 1258310
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:226337 original size:15 final size:14
Alignment explanation
Indices: 226313--226343 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
226303 ATAAGTTTCC
226313 CATTGAATTTTTTT
1 CATTGAATTTTTTT
226327 CATTGGAATTTTTTT
1 CATT-GAATTTTTTT
226342 CA
1 CA
226344 GAAGTACAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.58
Consensus pattern (14 bp):
CATTGAATTTTTTT
Found at i:235172 original size:2 final size:2
Alignment explanation
Indices: 235165--235194 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
235155 ATATTCTATC
235165 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
235195 CCAATTACAT
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):
AT
Found at i:238217 original size:2 final size:2
Alignment explanation
Indices: 238210--238247 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
238200 ACATACATAC
*
238210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
238248 TAAGATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:242271 original size:2 final size:2
Alignment explanation
Indices: 242264--242295 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
242254 TTTAAAATTA
242264 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
242296 CAAAATTTAA
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:244392 original size:34 final size:29
Alignment explanation
Indices: 244312--244368 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
244302 GGAGCAGGAT
244312 GGAGTGCATGGCGACCTACAAGGTCGCCA
1 GGAGTGCATGGCGACCTACAAGGTCGCCA
244341 GGAGTGCATGGCGACCTACAAGGTCGCC
1 GGAGTGCATGGCGACCTACAAGGTCGCC
244369 CGGCTCGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.23, C:0.28, G:0.35, T:0.14
Consensus pattern (29 bp):
GGAGTGCATGGCGACCTACAAGGTCGCCA
Found at i:252720 original size:30 final size:29
Alignment explanation
Indices: 252686--252787 Score: 88
Period size: 30 Copynumber: 3.5 Consensus size: 29
252676 AACAAGGAAA
252686 ATAAATAAATAATAAAAATATGTAATAAAT
1 ATAAATAAATAATAAAAATAT-TAATAAAT
*
252716 ATAAAT-AAT-ATATATAATA-TAA-AAAT
1 ATAAATAAATAATA-AAAATATTAATAAAT
* *
252742 AATAATATATATAATAAATAATATTAATATA-
1 -ATAA-ATAAATAATAAA-AATATTAATAAAT
252773 ATAAATAATATAATA
1 ATAAATAA-ATAATA
252788 TATATACTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
26 4 0.07
27 7 0.12
28 5 0.09
29 14 0.24
30 23 0.40
31 3 0.05
32 2 0.03
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (29 bp):
ATAAATAAATAATAAAAATATTAATAAAT
Found at i:252727 original size:9 final size:9
Alignment explanation
Indices: 252684--252840 Score: 89
Period size: 9 Copynumber: 17.1 Consensus size: 9
252674 TAAACAAGGA
252684 AAATAA-AT
1 AAATAATAT
*
252692 AAATAATAA
1 AAATAATAT
*
252701 AAAT-ATGT
1 AAATAATAT
252709 -AATAAATAT
1 AAAT-AATAT
252718 AAATAATAT
1 AAATAATAT
*
252727 ATATAATAT
1 AAATAATAT
252736 AAA-AATAAT
1 AAATAAT-AT
252745 AATATATATAAT
1 AA-ATA-AT-AT
252757 AAATAATAT
1 AAATAATAT
*
252766 TAAT-ATAAT
1 AAATAAT-AT
252775 AAATAATAT
1 AAATAATAT
252784 -AAT-ATAT
1 AAATAATAT
*
252791 ATACTATATAAT
1 A-AATA-AT-AT
252803 AAAT-ATAT
1 AAATAATAT
*
252811 ACTATAATAT
1 A-AATAATAT
252821 ATAATAATA-
1 A-AATAATAT
252830 AATATAATAT
1 AA-ATAATAT
252840 A
1 A
252841 TAGATATAAT
Statistics
Matches: 117, Mismatches: 13, Indels: 36
0.70 0.08 0.22
Matches are distributed among these distances:
7 7 0.06
8 20 0.17
9 52 0.44
10 20 0.17
11 8 0.07
12 10 0.09
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (9 bp):
AAATAATAT
Found at i:252756 original size:32 final size:32
Alignment explanation
Indices: 252708--252892 Score: 134
Period size: 30 Copynumber: 5.8 Consensus size: 32
252698 TAAAAATATG
*
252708 TAATAAATATAAATAATATATATAATATAAAAA
1 TAAT-AATATATATAATATATATAATATAAAAA
* *
252741 TAATAATATATATAATA-A-ATAATATTAATA
1 TAATAATATATATAATATATATAATATAAAAA
* *
252771 TAATAA-ATAATATAATATATATACTAT-ATAA
1 TAATAATAT-ATATAATATATATAATATAAAAA
*
252802 T-A-AATATATACT-ATAATATATAATAATAAATA
1 TAATAATATATA-TAAT-ATATATAAT-ATAAAAA
* * *
252834 TAATATATAGATATAATATATGTATAATATATAAG
1 TAATA-ATATATATAATATA--TATAATATAAAAA
* *
252869 TATATAA-CTATATAGTATATATAA
1 TA-ATAATATATATAATATATATAA
252893 GAGAAAATAA
Statistics
Matches: 121, Mismatches: 16, Indels: 31
0.72 0.10 0.18
Matches are distributed among these distances:
29 9 0.07
30 36 0.30
31 7 0.06
32 26 0.21
33 5 0.04
34 14 0.12
35 15 0.12
36 9 0.07
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (32 bp):
TAATAATATATATAATATATATAATATAAAAA
Found at i:252765 original size:39 final size:40
Alignment explanation
Indices: 252710--252872 Score: 100
Period size: 44 Copynumber: 3.8 Consensus size: 40
252700 AAAATATGTA
* *
252710 ATAAATATAAATAATATATATAATATAAAAATAATAATAT-AT
1 ATAAAAAT-AATAATATATATAATA-AATAAT-ATAATATAAT
*
252752 ATAATAAATAATATTA-ATATAATAAATAATATAATATATAT
1 ATAA-AAATAATAATATATATAATAAATAATATAATATA-AT
* *
252793 ACTATATAATAA-ATATATACTATAATATATAATAATAAATATAAT
1 A-TA-AAAATAATA-ATATA-TATAATAAATAAT-AT-AATATAAT
* * *
252838 ATATAGATATAAT-ATATGTATAATATATAAGTATA
1 ATA-A-AAATAATAATATATATAATAAATAA-TATA
252873 TAACTATATA
Statistics
Matches: 99, Mismatches: 9, Indels: 26
0.74 0.07 0.19
Matches are distributed among these distances:
39 7 0.07
40 5 0.05
41 12 0.12
42 20 0.20
43 19 0.19
44 21 0.21
45 9 0.09
46 6 0.06
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (40 bp):
ATAAAAATAATAATATATATAATAAATAATATAATATAAT
Found at i:252823 original size:30 final size:28
Alignment explanation
Indices: 252716--252889 Score: 116
Period size: 26 Copynumber: 6.0 Consensus size: 28
252706 TGTAATAAAT
*
252716 ATAAATAATATATATAATATA-A-AAATA
1 ATAAAT-ATATATATAATATATATATATA
252743 AT-AATATATATAATAA-ATAATATTAATATA
1 ATAAATATATAT-ATAATAT-ATA-T-ATATA
252773 ATAAATA-ATATA-ATATATATACTATATA
1 ATAAATATATATATA-ATATATA-TATATA
252801 ATAAATATATACTAT-A-ATATATA-ATA
1 ATAAATATATA-TATAATATATATATATA
*
252827 ATAAATATAATATATAGATATA-ATATATGT
1 ATAAATAT-ATATATA-ATATATATATAT-A
252857 ATAATATATAAGTATATAACTATATAGTATATA
1 ATAA-ATAT-A-TATATAA-TATATA-TATATA
252890 TAAGAGAAAA
Statistics
Matches: 120, Mismatches: 4, Indels: 40
0.73 0.02 0.24
Matches are distributed among these distances:
25 8 0.07
26 22 0.18
27 8 0.07
28 22 0.18
29 15 0.12
30 18 0.15
31 11 0.09
32 10 0.08
33 1 0.01
34 5 0.04
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (28 bp):
ATAAATATATATATAATATATATATATA
Found at i:252859 original size:11 final size:13
Alignment explanation
Indices: 252714--252889 Score: 93
Period size: 13 Copynumber: 13.4 Consensus size: 13
252704 TATGTAATAA
*
252714 ATATAA-ATAATAT
1 ATATAATAT-ATAG
* *
252727 ATATAATATAAAA
1 ATATAATATATAG
*
252740 ATAATAATATATAT
1 AT-ATAATATATAG
252754 A-ATAAATAATATTA-
1 ATAT-AAT-ATA-TAG
*
252768 ATATAATAAATA-
1 ATATAATATATAG
*
252780 ATATAATATATAT
1 ATATAATATATAG
*
252793 ACTAT-ATA-ATAA
1 A-TATAATATATAG
*
252805 ATAT-ATACTATAAT
1 ATATAATA-TAT-AG
*
252819 ATATAATA-ATAA
1 ATATAATATATAG
252831 ATATAATATATAG
1 ATATAATATATAG
252844 ATATAATATAT-G
1 ATATAATATATAG
252856 -TATAATATATAAG
1 ATATAATATAT-AG
252869 TATATAACTATATAG
1 -ATATAA-TATATAG
252884 TATATA
1 -ATATA
252890 TAAGAGAAAA
Statistics
Matches: 135, Mismatches: 10, Indels: 34
0.75 0.06 0.19
Matches are distributed among these distances:
11 16 0.12
12 29 0.21
13 38 0.28
14 27 0.20
15 20 0.15
16 5 0.04
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (13 bp):
ATATAATATATAG
Found at i:252874 original size:39 final size:38
Alignment explanation
Indices: 252748--252889 Score: 134
Period size: 39 Copynumber: 3.7 Consensus size: 38
252738 AAATAATAAT
* *
252748 ATATATAATAAATAATAT-TA-ATATAATAAATAATATA
1 ATATATAATATATAATATATAGATATAATATAT-ATATA
* *
252785 ATATATATACTATATAATA-A-ATATATACTATAATATATA
1 ATATATA-A-TATATAATATATAGATATAATAT-ATATATA
*
252824 ATA-ATAA-ATATAATATATAGATATAATATATGTATA
1 ATATATAATATATAATATATAGATATAATATATATATA
252860 ATATATAAGTATATAACTATATAGTATATA
1 ATATATAA-TATATAA-TATATAG-ATATA
252890 TAAGAGAAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
35 8 0.09
36 10 0.11
37 21 0.24
38 5 0.06
39 29 0.33
40 9 0.10
41 5 0.06
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (38 bp):
ATATATAATATATAATATATAGATATAATATATATATA
Found at i:253112 original size:25 final size:22
Alignment explanation
Indices: 253076--253130 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
253066 TGCGATAATT
253076 AAAA-TGTT-TTGCGAGAGTTTGA
1 AAAAGTGTTGTTGCGAGAG--TGA
*
253098 AAAACGTGTTGTTGCGATAGTGA
1 AAAA-GTGTTGTTGCGAGAGTGA
253121 AAAAGTGTTG
1 AAAAGTGTTG
253131 CGATAGTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 10 0.34
23 7 0.24
24 4 0.14
25 8 0.28
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (22 bp):
AAAAGTGTTGTTGCGAGAGTGA
Found at i:253131 original size:19 final size:19
Alignment explanation
Indices: 253107--253143 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
253097 AAAAACGTGT
253107 TGTTGCGATAGTGAAAAAG
1 TGTTGCGATAGTGAAAAAG
253126 TGTTGCGATAGTGAAAAA
1 TGTTGCGATAGTGAAAAA
253144 TCCAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (19 bp):
TGTTGCGATAGTGAAAAAG
Found at i:253132 original size:44 final size:41
Alignment explanation
Indices: 253052--253133 Score: 101
Period size: 44 Copynumber: 1.9 Consensus size: 41
253042 GCAACGCGAT
* * *
253052 TTTGAAAAATGTGTTGCGATAATTAAAATGTTTTGCGAGAG
1 TTTGAAAAATGTGTTGCGATAATGAAAAAGTGTTGCGAGAG
*
253093 TTTGAAAAACGTGTTGTTGCGATAGTGAAAAAGTGTTGCGA
1 TTTGAAAAA--TG-TGTTGCGATAATGAAAAAGTGTTGCGA
253134 TAGTGAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 9 0.26
43 2 0.06
44 23 0.68
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (41 bp):
TTTGAAAAATGTGTTGCGATAATGAAAAAGTGTTGCGAGAG
Found at i:253608 original size:20 final size:20
Alignment explanation
Indices: 253550--253610 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
253540 CCACCAGTCG
253550 TTGCGATTTTGTATTATCGCA
1 TTGCGA-TTTGTATTATCGCA
* *
253571 TTGCGA-TAGTCATAATCGCA
1 TTGCGATTTGT-ATTATCGCA
253591 TTGCGATTTGTATTATCGCA
1 TTGCGATTTGTATTATCGCA
253611 ATAGTCAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
19 3 0.09
20 22 0.65
21 9 0.26
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (20 bp):
TTGCGATTTGTATTATCGCA
Found at i:253665 original size:35 final size:35
Alignment explanation
Indices: 253573--253666 Score: 125
Period size: 35 Copynumber: 2.7 Consensus size: 35
253563 TTATCGCATT
*
253573 GCGATAGTCATAATCGCATTGCGATTTGTATTATC
1 GCGATAGTCAAAATCGCATTGCGATTTGTATTATC
* * * *
253608 GCAATAGTCAGAATCACTTTGCGATTTGTATTATC
1 GCGATAGTCAAAATCGCATTGCGATTTGTATTATC
* *
253643 GCGATAGTGAAAATCGCGTTGCGA
1 GCGATAGTCAAAATCGCATTGCGA
253667 ATCTGAAAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (35 bp):
GCGATAGTCAAAATCGCATTGCGATTTGTATTATC
Found at i:253704 original size:20 final size:19
Alignment explanation
Indices: 253681--253726 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
253671 GAAAACTGAT
*
253681 TTGCGATACTAGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
253701 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
253720 TTGCGAT
1 TTGCGAT
253727 TTTGTTAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:253714 original size:19 final size:19
Alignment explanation
Indices: 253690--253728 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
253680 TTTGCGATAC
*
253690 TAGAGATCGCGTTGCGATT
1 TAGAGATCGCATTGCGATT
253709 TAGAGATCGCATTGCGATT
1 TAGAGATCGCATTGCGATT
253728 T
1 T
253729 TGTTAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (19 bp):
TAGAGATCGCATTGCGATT
Found at i:253834 original size:2 final size:2
Alignment explanation
Indices: 253820--253903 Score: 57
Period size: 2 Copynumber: 47.0 Consensus size: 2
253810 TCTATATGTA
*
253820 AT AT AT A- ACT AT AT A- AT A- AT AT AT A- AT AT AA AT AT AT A-
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
253858 AT A- AT AT AT ACT AT AT A- AT AT A- AT -T A- AT AT AT AT AT -T
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
253895 AT A- AT AT AT
1 AT AT AT AT AT
253904 TCCCGGACTA
Statistics
Matches: 66, Mismatches: 2, Indels: 28
0.69 0.02 0.29
Matches are distributed among these distances:
1 12 0.18
2 51 0.77
3 3 0.05
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:253855 original size:23 final size:24
Alignment explanation
Indices: 253813--253903 Score: 116
Period size: 23 Copynumber: 3.8 Consensus size: 24
253803 TATTTTCTCT
*
253813 ATATGTAATATATAACTATATAATA
1 ATATATAATATATAA-TATATAATA
253838 ATATATAATATA-AATATATAATA
1 ATATATAATATATAATATATAATA
* *
253861 ATATATACTATATAATATA-ATTA
1 ATATATAATATATAATATATAATA
253884 ATATAT-ATATTATAATATAT
1 ATATATAATA-TATAATATAT
253904 TCCCGGACTA
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
22 2 0.03
23 38 0.64
24 8 0.14
25 11 0.19
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (24 bp):
ATATATAATATATAATATATAATA
Found at i:253975 original size:3 final size:3
Alignment explanation
Indices: 253967--254023 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
253957 TCAAGCTTAT
253967 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
254015 GAG GAG GAG
1 GAG GAG GAG
254024 TGGGAGTCTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:254647 original size:7 final size:7
Alignment explanation
Indices: 254632--254738 Score: 82
Period size: 6 Copynumber: 17.4 Consensus size: 7
254622 TTTGTCGATA
254632 AAGAATG
1 AAGAATG
*
254639 AAGATTG
1 AAGAATG
254646 AAGAA-G
1 AAGAATG
254652 AAGAA-G
1 AAGAATG
254658 AAGAA-G
1 AAGAATG
*
254664 AA-AAAG
1 AAGAATG
254670 AAGAA-G
1 AAGAATG
*
254676 AA-AAAG
1 AAGAATG
254682 AAGAA-G
1 AAGAATG
254688 AAGAA-G
1 AAGAATG
254694 AAGAA-G
1 AAGAATG
254700 AAGAA-G
1 AAGAATG
254706 AAGAA-G
1 AAGAATG
254712 AAGAA-G
1 AAGAATG
254718 AAGAA-G
1 AAGAATG
254724 AAGAA-G
1 AAGAATG
254730 AAGAA-G
1 AAGAATG
254736 AAG
1 AAG
254739 TGAGCATCGA
Statistics
Matches: 94, Mismatches: 2, Indels: 9
0.90 0.02 0.09
Matches are distributed among these distances:
5 4 0.04
6 76 0.81
7 14 0.15
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (7 bp):
AAGAATG
Found at i:254653 original size:3 final size:3
Alignment explanation
Indices: 254645--254738 Score: 170
Period size: 3 Copynumber: 31.3 Consensus size: 3
254635 AATGAAGATT
* *
254645 GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA GAA AAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
254693 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
254739 TGAGCATCGA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:255653 original size:10 final size:10
Alignment explanation
Indices: 255628--255658 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
255618 ATTTAAAAAA
255628 TTATTATTTAT
1 TTATTATTT-T
255639 TTATTATTTT
1 TTATTATTTT
255649 TTATTATTTT
1 TTATTATTTT
255659 GCAGGGCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.55
11 9 0.45
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTATTATTTT
Found at i:261426 original size:20 final size:20
Alignment explanation
Indices: 261397--261440 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
261387 CAATCTTCAC
* *
261397 AATATATGATTTATTAATTG
1 AATATATGATCTATTAATCG
*
261417 AATATGTGATCTATTAATCG
1 AATATATGATCTATTAATCG
261437 AATA
1 AATA
261441 ATTTGAATCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (20 bp):
AATATATGATCTATTAATCG
Found at i:265455 original size:31 final size:29
Alignment explanation
Indices: 265420--265490 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
265410 TTAACAGTTG
* *
265420 GTGGTTTTATTGACATCATTTAAATAGTTAA
1 GTGGTTTGATTGACA-CAATTAAA-AGTTAA
* *
265451 GTGGTATGATTGACACAATTAAAAGTTGA
1 GTGGTTTGATTGACACAATTAAAAGTTAA
*
265480 GTGGTTGGATT
1 GTGGTTTGATT
265491 AAAATCTTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 14 0.41
30 7 0.21
31 13 0.38
ACGTcount: A:0.31, C:0.06, G:0.24, T:0.39
Consensus pattern (29 bp):
GTGGTTTGATTGACACAATTAAAAGTTAA
Found at i:265490 original size:29 final size:29
Alignment explanation
Indices: 265410--265486 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
265400 CCATTGAGTG
* * *
265410 TTAACAGTTG-GTGGTTTTATTGACATCAT
1 TTAAAAGTTGAGTGG-TTGATTGACATCAA
*
265439 TTAAATAGTTAAGTGGTATGATTGACA-CAA
1 TTAAA-AGTTGAGTGGT-TGATTGACATCAA
265469 TTAAAAGTTGAGTGGTTG
1 TTAAAAGTTGAGTGGTTG
265487 GATTAAAATC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
28 2 0.05
29 14 0.35
30 12 0.30
31 12 0.30
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.39
Consensus pattern (29 bp):
TTAAAAGTTGAGTGGTTGATTGACATCAA
Found at i:271113 original size:26 final size:26
Alignment explanation
Indices: 271070--271134 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 26
271060 AAGAGACAAA
* *
271070 AATATATTATAAGTAGATGATTGATATT
1 AATATATT-TATG-AGATGATCGATATT
*
271098 AATATCTTTATGAGATGATCGATATT
1 AATATATTTATGAGATGATCGATATT
271124 AATATATTTAT
1 AATATATTTAT
271135 TAATTTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 23 0.70
27 3 0.09
28 7 0.21
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (26 bp):
AATATATTTATGAGATGATCGATATT
Found at i:274741 original size:30 final size:29
Alignment explanation
Indices: 274687--274746 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
274677 TTTTTCTAGT
*
274687 TTTTAAATTTATTGATATTAAAATTTTAA
1 TTTTAAATTTATTAATATTAAAATTTTAA
* *
274716 TTTTAGATTTATATAATATTTAAATTTTAA
1 TTTTAAATTTAT-TAATATTAAAATTTTAA
274746 T
1 T
274747 AATAATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (29 bp):
TTTTAAATTTATTAATATTAAAATTTTAA
Found at i:274760 original size:20 final size:20
Alignment explanation
Indices: 274728--274765 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
274718 TTAGATTTAT
274728 ATAATATTTAAATTTTAATA
1 ATAATATTTAAATTTTAATA
274748 ATAAT-TTTAAAATTTTAA
1 ATAATATTT-AAATTTTAA
274766 GTTTTGGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAATATTTAAATTTTAATA
Found at i:275209 original size:14 final size:14
Alignment explanation
Indices: 275190--275226 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
275180 TTTTGGTCAT
275190 ATGTTCGTTCGTTC
1 ATGTTCGTTCGTTC
* *
275204 ATGTTCATTCGTTT
1 ATGTTCGTTCGTTC
275218 ATGTTCGTT
1 ATGTTCGTT
275227 TATATTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.11, C:0.16, G:0.19, T:0.54
Consensus pattern (14 bp):
ATGTTCGTTCGTTC
Found at i:275225 original size:24 final size:24
Alignment explanation
Indices: 275196--275244 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
275186 TCATATGTTC
*
275196 GTTCGTTCATGTTCATTCGTTTAT
1 GTTCGTTCATATTCATTCGTTTAT
* *
275220 GTTCGTTTATATTCGTTCGTTTAT
1 GTTCGTTCATATTCATTCGTTTAT
275244 G
1 G
275245 CTCATTTACG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.12, C:0.14, G:0.18, T:0.55
Consensus pattern (24 bp):
GTTCGTTCATATTCATTCGTTTAT
Found at i:275614 original size:31 final size:31
Alignment explanation
Indices: 275577--275654 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
275567 GAACGAACAT
* * *
275577 GAACGAACACGAATAAGCTATATTCCTTAAC
1 GAACGAATATGAATAAGCAATATTCCTTAAC
* *
275608 GAACGAATATGAACAAGCAATATTCCTTAAT
1 GAACGAATATGAATAAGCAATATTCCTTAAC
275639 GAACGAATATGAATAA
1 GAACGAATATGAATAA
275655 ATTTTTTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (31 bp):
GAACGAATATGAATAAGCAATATTCCTTAAC
Found at i:284416 original size:9 final size:9
Alignment explanation
Indices: 284402--284427 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
284392 ATTAAAGGAA
284402 GAAGAAGAT
1 GAAGAAGAT
284411 GAAGAAGAT
1 GAAGAAGAT
284420 GAAGAAGA
1 GAAGAAGA
284428 AAGGTCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.35, T:0.08
Consensus pattern (9 bp):
GAAGAAGAT
Found at i:293353 original size:19 final size:19
Alignment explanation
Indices: 293332--293367 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
293322 TATGCTTTTT
*
293332 TTTTATTTGAA-TTTATAG
1 TTTTATTTCAACTTTATAG
293350 TTTTATTTCAACTTTATA
1 TTTTATTTCAACTTTATA
293368 TAAAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (19 bp):
TTTTATTTCAACTTTATAG
Found at i:294985 original size:31 final size:31
Alignment explanation
Indices: 294950--295054 Score: 201
Period size: 31 Copynumber: 3.4 Consensus size: 31
294940 AAATTACGTG
294950 TTTAGTACTTAAATTATCAAGTTTGATCTGT
1 TTTAGTACTTAAATTATCAAGTTTGATCTGT
294981 TTTAGTACTTAAATTATCAAGTTTGATCTGT
1 TTTAGTACTTAAATTATCAAGTTTGATCTGT
*
295012 TTTAGTACTTAAATTATCAAGTTTGATCTAT
1 TTTAGTACTTAAATTATCAAGTTTGATCTGT
295043 TTTAGTACTTAA
1 TTTAGTACTTAA
295055 GCTTTTAATT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
31 73 1.00
ACGTcount: A:0.30, C:0.10, G:0.11, T:0.49
Consensus pattern (31 bp):
TTTAGTACTTAAATTATCAAGTTTGATCTGT
Found at i:297064 original size:21 final size:21
Alignment explanation
Indices: 297040--297089 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
297030 CTTTTTAAGG
*
297040 TTAGGGTTTATGATTTGTGGT
1 TTAGGGTTTAGGATTTGTGGT
** *
297061 TTAGATTTTAGGGTTTGTGGT
1 TTAGGGTTTAGGATTTGTGGT
297082 TTAGGGTT
1 TTAGGGTT
297090 CAAAGTTTGA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.34, T:0.52
Consensus pattern (21 bp):
TTAGGGTTTAGGATTTGTGGT
Found at i:297075 original size:14 final size:14
Alignment explanation
Indices: 297040--297089 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
297030 CTTTTTAAGG
297040 TTAGGGTTTATGAT
1 TTAGGGTTTATGAT
297054 TT-GTGGTTTA-GATT
1 TTAG-GGTTTATGA-T
* *
297068 TTAGGGTTTGTGGT
1 TTAGGGTTTATGAT
297082 TTAGGGTT
1 TTAGGGTT
297090 CAAAGTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 3 0.10
14 25 0.83
15 2 0.07
ACGTcount: A:0.14, C:0.00, G:0.34, T:0.52
Consensus pattern (14 bp):
TTAGGGTTTATGAT
Found at i:297690 original size:2 final size:2
Alignment explanation
Indices: 297683--297748 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
297673 TGAAATATTG
297683 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
297725 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
297749 TGAGGATTTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:297983 original size:60 final size:60
Alignment explanation
Indices: 297871--297984 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
297861 CTATATGATA
* *
297871 TTGCTTTGTTAAGTCCATTGACTATTAAAAGTTACAAAATGATCATTCGACTATGGAGTG
1 TTGCTTTGTTAAGTCCATGGACTATTAAAAGTTACAAAATGATCACTCGACTATGGAGTG
* * *
297931 TTGCTTTGTTGAGTCCCTCGGA-TATTAAAAGTTACAAAATGGTCAC-CTGACTAT
1 TTGCTTTGTTAAGTCCAT-GGACTATTAAAAGTTACAAAATGATCACTC-GACTAT
297985 TTATCATGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 1 0.02
60 44 0.94
61 2 0.04
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (60 bp):
TTGCTTTGTTAAGTCCATGGACTATTAAAAGTTACAAAATGATCACTCGACTATGGAGTG
Found at i:298727 original size:21 final size:21
Alignment explanation
Indices: 298685--298730 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
298675 CGGTTTAGGG
*
298685 GGTGCACCTGGATCTCCCGCA
1 GGTGCACCTGGAGCTCCCGCA
* * *
298706 GGTGCACTTGGAGCTGCTGCA
1 GGTGCACCTGGAGCTCCCGCA
298727 GGTG
1 GGTG
298731 GTAGTTCTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.28, G:0.37, T:0.22
Consensus pattern (21 bp):
GGTGCACCTGGAGCTCCCGCA
Found at i:300929 original size:60 final size:60
Alignment explanation
Indices: 300831--300979 Score: 203
Period size: 60 Copynumber: 2.5 Consensus size: 60
300821 GTATTATATG
* * *
300831 TCCCCAAACTATGACCCTCATT-TCAAACTAATCCTTAAACTTTT-ATACGTTCTAATTTCA
1 TCCCCAAACTATGACTCTCATTCT-AAATTAATCCTTAAACTTTTGAT-CATTCTAATTTCA
* *
300891 TCCCCAAACTATGACTCTCATTCTAAATTAGTCTTTAAACTTTTGATCATTCTAATTTCA
1 TCCCCAAACTATGACTCTCATTCTAAATTAATCCTTAAACTTTTGATCATTCTAATTTCA
* *
300951 TCCTCAAACTATGACTCTCATTCTTAATT
1 TCCCCAAACTATGACTCTCATTCTAAATT
300980 GGTCACCGAA
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
60 77 0.96
61 3 0.04
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.40
Consensus pattern (60 bp):
TCCCCAAACTATGACTCTCATTCTAAATTAATCCTTAAACTTTTGATCATTCTAATTTCA
Found at i:300959 original size:29 final size:29
Alignment explanation
Indices: 300861--300960 Score: 71
Period size: 29 Copynumber: 3.4 Consensus size: 29
300851 TTTCAAACTA
* *
300861 ATCCTTAAACTTTT-ATACGTTCTAATTTC
1 ATCCTCAAACTTTTGAT-CATTCTAATTTC
* * *
300890 ATCCCCAAAC-TATGACTCTCATTCTAAATT-
1 ATCCTCAAACTTTTGA---TCATTCTAATTTC
* *
300920 AGTCTTTAAACTTTTGATCATTCTAATTTC
1 A-TCCTCAAACTTTTGATCATTCTAATTTC
300950 ATCCTCAAACT
1 ATCCTCAAACT
300961 ATGACTCTCA
Statistics
Matches: 52, Mismatches: 12, Indels: 14
0.67 0.15 0.18
Matches are distributed among these distances:
28 2 0.04
29 28 0.54
30 2 0.04
31 15 0.29
32 5 0.10
ACGTcount: A:0.30, C:0.24, G:0.04, T:0.42
Consensus pattern (29 bp):
ATCCTCAAACTTTTGATCATTCTAATTTC
Found at i:300992 original size:60 final size:60
Alignment explanation
Indices: 300831--300996 Score: 176
Period size: 60 Copynumber: 2.8 Consensus size: 60
300821 GTATTATATG
* * * * *
300831 TCCCCAAACTATGACCCTCATT-TCAAACTAATC-CTTAAACTTTT-ATACGTTCTAATTTCA
1 TCCCCAAACTATGACTCTCATTCT-AAATTAGTCAC-CAAACTTTTGAT-CATTCTAATTTCA
***
300891 TCCCCAAACTATGACTCTCATTCTAAATTAGTCTTTAAACTTTTGATCATTCTAATTTCA
1 TCCCCAAACTATGACTCTCATTCTAAATTAGTCACCAAACTTTTGATCATTCTAATTTCA
* * * *
300951 TCCTCAAACTATGACTCTCATTCTTAATTGGTCACCGAACTTTTGA
1 TCCCCAAACTATGACTCTCATTCTAAATTAGTCACCAAACTTTTGA
300997 ATCTTCCAAT
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
60 88 0.97
61 3 0.03
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.39
Consensus pattern (60 bp):
TCCCCAAACTATGACTCTCATTCTAAATTAGTCACCAAACTTTTGATCATTCTAATTTCA
Found at i:303486 original size:34 final size:34
Alignment explanation
Indices: 303437--303506 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
303427 GCGGGTGGTG
*
303437 GTTAGACGGTCGTTGGCTAGTGTCAAGATATTTT
1 GTTAGACAGTCGTTGGCTAGTGTCAAGATATTTT
*
303471 GTTAGACAGTTGTTGGCTAGTGTCAAGATATTTT
1 GTTAGACAGTCGTTGGCTAGTGTCAAGATATTTT
303505 GT
1 GT
303507 CTCCATAACG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.21, C:0.10, G:0.29, T:0.40
Consensus pattern (34 bp):
GTTAGACAGTCGTTGGCTAGTGTCAAGATATTTT
Found at i:305629 original size:37 final size:37
Alignment explanation
Indices: 305588--305670 Score: 121
Period size: 37 Copynumber: 2.2 Consensus size: 37
305578 TTAATTTCGG
* *
305588 GTTTGTGTTGGGCCAGGTCGAGTTTTTTAAATATGAT
1 GTTTGAGTCGGGCCAGGTCGAGTTTTTTAAATATGAT
* * *
305625 GTTTGAGTCGGGTCGGGTCGGGTTTTTTAAATATGAT
1 GTTTGAGTCGGGCCAGGTCGAGTTTTTTAAATATGAT
305662 GTTTGAGTC
1 GTTTGAGTC
305671 AGGTCGTTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (37 bp):
GTTTGAGTCGGGCCAGGTCGAGTTTTTTAAATATGAT
Found at i:305676 original size:37 final size:37
Alignment explanation
Indices: 305603--305686 Score: 132
Period size: 37 Copynumber: 2.3 Consensus size: 37
305593 TGTTGGGCCA
* *
305603 GGTCGAGTTTTTTAAATATGATGTTTGAGTCGGGTCG
1 GGTCGGGTTTTTTAAATATGATGTTTGAGTCAGGTCG
305640 GGTCGGGTTTTTTAAATATGATGTTTGAGTCAGGTCG
1 GGTCGGGTTTTTTAAATATGATGTTTGAGTCAGGTCG
**
305677 TTTCGGGTTT
1 GGTCGGGTTT
305687 AGGTAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.17, C:0.08, G:0.32, T:0.43
Consensus pattern (37 bp):
GGTCGGGTTTTTTAAATATGATGTTTGAGTCAGGTCG
Found at i:306534 original size:71 final size:73
Alignment explanation
Indices: 306407--306608 Score: 250
Period size: 71 Copynumber: 2.7 Consensus size: 73
306397 TTGTACAATT
306407 TTTCTTACAATTCAATTATAAAATAGGGCCCCCATTTATTTAATAAGCACTATGGCAGACATGAA
1 TTTCTTACAATTCAATTATAAAATAGGGCCCCCATTTATTTAATAAGCACTATGGCAGACATGAA
306472 CGGTACAA
66 CGGTACAA
*
306480 TTTCTTACAATTCAATTATAAAATA-GG-CCCCATTTATTTAATAAGTACTATGGCAGACATGAA
1 TTTCTTACAATTCAATTATAAAATAGGGCCCCCATTTATTTAATAAGCACTATGGCAGACATGAA
* *
306543 TGTTATTGTACCATT
66 CG-----GTA-CA-A
* * *
306558 TTTCTTACCATTTAATTATAAAAT-GTGG-CCCCATTTCTTTAATAAGCACTA
1 TTTCTTACAATTCAATTATAAAATAG-GGCCCCCATTTATTTAATAAGCACTA
306609 AAAGTCGTTT
Statistics
Matches: 113, Mismatches: 7, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
71 36 0.32
72 2 0.02
73 25 0.22
76 3 0.03
77 2 0.02
78 22 0.19
79 23 0.20
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (73 bp):
TTTCTTACAATTCAATTATAAAATAGGGCCCCCATTTATTTAATAAGCACTATGGCAGACATGAA
CGGTACAA
Found at i:314888 original size:29 final size:29
Alignment explanation
Indices: 314846--314934 Score: 124
Period size: 29 Copynumber: 3.1 Consensus size: 29
314836 TACCGGGGGT
*
314846 AGGTCGCCATGCACGCCCGGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
***
314875 AGGTCGCCATGCACGCCCAGCGACCTGGT
1 AGGTCGCCATGCACGCCCAGCGACCTACC
* *
314904 AGGTCGCCATGCATGCCCTGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
314933 AG
1 AG
314935 CCAACGACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.18, C:0.40, G:0.28, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAGCGACCTACC
Found at i:315212 original size:29 final size:29
Alignment explanation
Indices: 315151--315234 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
315141 ATGAATCCTT
** * **
315151 GGTCGCCCCGAGTGCATGGCGACCTCCTT
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
* *
315180 GGTCGCCGGGCGTGCATGGCGACCTAGGA
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
*
315209 GGTCGCTGGGAGTGCATGGCGACCTA
1 GGTCGCCGGGAGTGCATGGCGACCTA
315235 TGGTTGGGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.13, C:0.30, G:0.39, T:0.18
Consensus pattern (29 bp):
GGTCGCCGGGAGTGCATGGCGACCTACGA
Found at i:327285 original size:22 final size:21
Alignment explanation
Indices: 327260--327301 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
327250 GACATGCATA
*
327260 ACATTATTACTTTGAACATATG
1 ACATTAGTACTTTG-ACATATG
327282 ACATTAGTACTTTGACATAT
1 ACATTAGTACTTTGACATAT
327302 AAGACTTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (21 bp):
ACATTAGTACTTTGACATATG
Found at i:328028 original size:21 final size:19
Alignment explanation
Indices: 327982--328029 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
327972 ACACATTAGA
327982 TAATAATTTATATATTATT
1 TAATAATTTATATATTATT
328001 TATATAATATTATAT-TTCATT
1 TA-ATAAT-TTATATATT-ATT
328022 TGAATAAT
1 T-AATAAT
328030 GGATATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 2 0.08
20 7 0.28
21 15 0.60
22 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
TAATAATTTATATATTATT
Found at i:329899 original size:14 final size:15
Alignment explanation
Indices: 329873--329901 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
329863 TAATTTTTTA
329873 ATTAAATAATAATAT
1 ATTAAATAATAATAT
329888 ATTAAA-AATAATAT
1 ATTAAATAATAATAT
329902 TTTTATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTAAATAATAATAT
Found at i:330282 original size:28 final size:28
Alignment explanation
Indices: 330250--330319 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
330240 AGTATCGGCT
330250 CGACGACATAATGTTTCAAGCATTGACA
1 CGACGACATAATGTTTCAAGCATTGACA
* * *
330278 GGACGACATAATGTTTCAAGTATTGGCA
1 CGACGACATAATGTTTCAAGCATTGACA
*
330306 CGACGATATAATGT
1 CGACGACATAATGT
330320 AAATAGCGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (28 bp):
CGACGACATAATGTTTCAAGCATTGACA
Found at i:331270 original size:16 final size:16
Alignment explanation
Indices: 331249--331281 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
331239 ATTCATTCAA
331249 ATTAATTATGCTTATG
1 ATTAATTATGCTTATG
331265 ATTAATTATGCTTATG
1 ATTAATTATGCTTATG
331281 A
1 A
331282 AAATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.48
Consensus pattern (16 bp):
ATTAATTATGCTTATG
Found at i:332436 original size:247 final size:247
Alignment explanation
Indices: 331992--332487 Score: 902
Period size: 247 Copynumber: 2.0 Consensus size: 247
331982 GCCCTTCTGG
*
331992 AAGTTGTCTTGAAGGGTCGGGTTCTTTAGTCTGGCCTTGAGAGGTCATACGTTATAAATAAAATA
1 AAGTTGTCTTGAAGAGTCGGGTTCTTTAGTCTGGCCTTGAGAGGTCATACGTTATAAATAAAATA
332057 TAACATTGTGAATAGTAGGATTTTAAAATTAAAAAGAGATAAATTTAATGAGATGAAATGAGTAT
66 TAACATTGTGAATAGTAGGATTTTAAAATTAAAAAGAGATAAATTTAATGAGATGAAATGAGTAT
** *
332122 TTATTTACTATTTGTTTAATAATTACAAAGATGATTATAAATAAGGCAAGGTGGTATTGGGAGGT
131 TTATTTACTATTTGTTTAATAATTACAAAGATGATTATAAATAAGGCAAGGTGACATTGGAAGGT
*
332187 CCTACGTTATAAATAAAATATAACATTGTGAATAGTAGGATTTTAAAATTAA
196 CCTACGTTATAAATAAAATATAACATTGTGAATAGTAGAATTTTAAAATTAA
* * *
332239 AAGTTGTCTTGTAGAGTCGGGTTTTTTAGTCTGGCCTTGAGAGGTCTTACGTTATAAATAAAATA
1 AAGTTGTCTTGAAGAGTCGGGTTCTTTAGTCTGGCCTTGAGAGGTCATACGTTATAAATAAAATA
332304 TAACATTGTGAATAGTAGGATTTTAAAATTAAAAAGAGATAAATTTAATGAGATGAAATGAGTAT
66 TAACATTGTGAATAGTAGGATTTTAAAATTAAAAAGAGATAAATTTAATGAGATGAAATGAGTAT
*
332369 TTATTTACTATTTGTTTAATAATTACAAAGATGATTATAAATAAGGTAAGGTGACATTGGAAGGT
131 TTATTTACTATTTGTTTAATAATTACAAAGATGATTATAAATAAGGCAAGGTGACATTGGAAGGT
*
332434 CCTACGTTATAAATAAAATATAATATTGTGAATAGTAGAATTTTAAAATTAA
196 CCTACGTTATAAATAAAATATAACATTGTGAATAGTAGAATTTTAAAATTAA
332486 AA
1 AA
332488 AGAGATAAAT
Statistics
Matches: 239, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
247 239 1.00
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (247 bp):
AAGTTGTCTTGAAGAGTCGGGTTCTTTAGTCTGGCCTTGAGAGGTCATACGTTATAAATAAAATA
TAACATTGTGAATAGTAGGATTTTAAAATTAAAAAGAGATAAATTTAATGAGATGAAATGAGTAT
TTATTTACTATTTGTTTAATAATTACAAAGATGATTATAAATAAGGCAAGGTGACATTGGAAGGT
CCTACGTTATAAATAAAATATAACATTGTGAATAGTAGAATTTTAAAATTAA
Found at i:332551 original size:150 final size:150
Alignment explanation
Indices: 332280--332570 Score: 555
Period size: 150 Copynumber: 1.9 Consensus size: 150
332270 TGGCCTTGAG
* *
332280 AGGTCTTACGTTATAAATAAAATATAACATTGTGAATAGTAGGATTTTAAAATTAAAAAGAGATA
1 AGGTCCTACGTTATAAATAAAATATAACATTGTGAATAGTAGAATTTTAAAATTAAAAAGAGATA
332345 AATTTAATGAGATGAAATGAGTATTTATTTACTATTTGTTTAATAATTACAAAGATGATTATAAA
66 AATTTAATGAGATGAAATGAGTATTTATTTACTATTTGTTTAATAATTACAAAGATGATTATAAA
332410 TAAGGTAAGGTGACATTGGA
131 TAAGGTAAGGTGACATTGGA
*
332430 AGGTCCTACGTTATAAATAAAATATAATATTGTGAATAGTAGAATTTTAAAATTAAAAAGAGATA
1 AGGTCCTACGTTATAAATAAAATATAACATTGTGAATAGTAGAATTTTAAAATTAAAAAGAGATA
332495 AATTTAATGAGATGAAATGAGTATTTATTTACTATTTGTTTAATAATTACAAAGATGATTATAAA
66 AATTTAATGAGATGAAATGAGTATTTATTTACTATTTGTTTAATAATTACAAAGATGATTATAAA
332560 TAAGGTAAGGT
131 TAAGGTAAGGT
332571 CAAACTTTTA
Statistics
Matches: 138, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
150 138 1.00
ACGTcount: A:0.45, C:0.04, G:0.16, T:0.36
Consensus pattern (150 bp):
AGGTCCTACGTTATAAATAAAATATAACATTGTGAATAGTAGAATTTTAAAATTAAAAAGAGATA
AATTTAATGAGATGAAATGAGTATTTATTTACTATTTGTTTAATAATTACAAAGATGATTATAAA
TAAGGTAAGGTGACATTGGA
Found at i:339265 original size:2 final size:2
Alignment explanation
Indices: 339258--339282 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
339248 TTTGGTTCGT
339258 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
339283 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:340453 original size:56 final size:58
Alignment explanation
Indices: 340340--340455 Score: 200
Period size: 56 Copynumber: 2.0 Consensus size: 58
340330 GATTTTAATT
340340 TTAATATTAAATTTTTAAATAAATTAAATATTAAATTTTTAATATTATATTATAGATA
1 TTAATATTAAATTTTTAAATAAATTAAATATTAAATTTTTAATATTATATTATAGATA
* *
340398 TTAATATT-AATTTTTAAATAAATTAACTATT-ATTTTTTAATATTATATTATAGATA
1 TTAATATTAAATTTTTAAATAAATTAAATATTAAATTTTTAATATTATATTATAGATA
340454 TT
1 TT
340456 TAATTTTATA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
56 26 0.46
57 22 0.39
58 8 0.14
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.53
Consensus pattern (58 bp):
TTAATATTAAATTTTTAAATAAATTAAATATTAAATTTTTAATATTATATTATAGATA
Found at i:340459 original size:57 final size:59
Alignment explanation
Indices: 340339--340459 Score: 203
Period size: 57 Copynumber: 2.1 Consensus size: 59
340329 TGATTTTAAT
340339 TTTAATATTAAATTTTTAAATAAATTAAATATTAAATTTTTAATATTATATTATAGATA
1 TTTAATATTAAATTTTTAAATAAATTAAATATTAAATTTTTAATATTATATTATAGATA
* *
340398 -TTAATATT-AATTTTTAAATAAATTAACTATT-ATTTTTTAATATTATATTATAGATA
1 TTTAATATTAAATTTTTAAATAAATTAAATATTAAATTTTTAATATTATATTATAGATA
340454 TTTAAT
1 TTTAAT
340460 TTTATATCAT
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
56 24 0.41
57 27 0.46
58 8 0.14
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.53
Consensus pattern (59 bp):
TTTAATATTAAATTTTTAAATAAATTAAATATTAAATTTTTAATATTATATTATAGATA
Found at i:340518 original size:20 final size:19
Alignment explanation
Indices: 340458--340519 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
340448 TAGATATTTA
*
340458 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
340477 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
340495 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
340515 ATTTT
1 ATTTT
340520 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:341159 original size:31 final size:31
Alignment explanation
Indices: 341124--341183 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
341114 TAGTTGTATG
* *
341124 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATATCAGTATTGCAAAACTAA
341155 AATTATTTAAATATCAGTATTGCAAAACT
1 AATTATTTAAATATCAGTATTGCAAAACT
341184 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATATCAGTATTGCAAAACTAA
Found at i:343091 original size:99 final size:98
Alignment explanation
Indices: 342955--343251 Score: 468
Period size: 99 Copynumber: 3.0 Consensus size: 98
342945 GAATACCATG
**
342955 AGTGGCACCTTTTATGCCGATAATGCACTTTTATGCATTTAACTTTCATTAATGGCACCTTTTAT
1 AGTGGCACCTTTTATGCCGA-AATGCACCGTTATGCATTTAACTTTCATTAATGGCACCTTTTAT
343020 GCCGAAAATGCACCGTTATGCATTTAACTTTCATT
65 GCCG-AAATGCACCGTTATGCATTTAACTTTCATT
* * *
343055 AGTGACACCTTTTATACCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTATG
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTAATGGCACCTTTTATG
*
343120 CCGAAATGCACCGTTATGCATATAACTTTCATT
66 CCGAAATGCACCGTTATGCATTTAACTTTCATT
* * * *
343153 AGTGGCACTTTTTATGTCGAAAATGCATCGTTATGCATTTAACTTTCATTAATGGTACCTTTTAT
1 AGTGGCACCTTTTATGCCG-AAATGCACCGTTATGCATTTAACTTTCATTAATGGCACCTTTTAT
*
343218 GCCGAAATGCACCGTTGTGCATTTAACTTTCATT
65 GCCGAAATGCACCGTTATGCATTTAACTTTCATT
343252 TTAGATCATT
Statistics
Matches: 181, Mismatches: 15, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
98 44 0.24
99 119 0.66
100 18 0.10
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (98 bp):
AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTAATGGCACCTTTTATG
CCGAAATGCACCGTTATGCATTTAACTTTCATT
Found at i:343097 original size:49 final size:49
Alignment explanation
Indices: 342955--343251 Score: 459
Period size: 49 Copynumber: 6.0 Consensus size: 49
342945 GAATACCATG
**
342955 AGTGGCACCTTTTATGCCGATAATGCACTTTTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCGA-AATGCACCGTTATGCATTTAACTTTCATT
*
343005 AATGGCACCTTTTATGCCGAAAATGCACCGTTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCG-AAATGCACCGTTATGCATTTAACTTTCATT
* *
343055 AGTGACACCTTTTATACCGAAATGCACCGTTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATT
*
343104 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATATAACTTTCATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATT
* * *
343153 AGTGGCACTTTTTATGTCGAAAATGCATCGTTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCG-AAATGCACCGTTATGCATTTAACTTTCATT
* * *
343203 AATGGTACCTTTTATGCCGAAATGCACCGTTGTGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATT
343252 TTAGATCATT
Statistics
Matches: 226, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
49 121 0.54
50 104 0.46
51 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (49 bp):
AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATT
Found at i:343191 original size:148 final size:149
Alignment explanation
Indices: 342955--343251 Score: 479
Period size: 148 Copynumber: 2.0 Consensus size: 149
342945 GAATACCATG
** *
342955 AGTGGCACCTTTTATGCCGATAATGCACTTTTATGCATTTAACTTTCATTAATGGCACCTTTTAT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATATAACTTTCATTAATGGCACCTTTTAT
*
343020 GCCGAAAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTATACCGAAATGCACCGT
66 GCCGAAAATGCACCGTTATGCATTTAACTTTCATTAATGACACCTTTTATACCGAAATGCACCGT
343085 TATGCATTTAACTTTCATT
131 TATGCATTTAACTTTCATT
* *
343104 AGTGGCACCTTTTATGCCGA-AATGCACCGTTATGCATATAACTTTCATTAGTGGCACTTTTTAT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATATAACTTTCATTAATGGCACCTTTTAT
* * ** *
343168 GTCGAAAATGCATCGTTATGCATTTAACTTTCATTAATGGTACCTTTTATGCCGAAATGCACCGT
66 GCCGAAAATGCACCGTTATGCATTTAACTTTCATTAATGACACCTTTTATACCGAAATGCACCGT
*
343233 TGTGCATTTAACTTTCATT
131 TATGCATTTAACTTTCATT
343252 TTAGATCATT
Statistics
Matches: 136, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
148 116 0.85
149 20 0.15
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (149 bp):
AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATATAACTTTCATTAATGGCACCTTTTAT
GCCGAAAATGCACCGTTATGCATTTAACTTTCATTAATGACACCTTTTATACCGAAATGCACCGT
TATGCATTTAACTTTCATT
Found at i:343784 original size:18 final size:18
Alignment explanation
Indices: 343761--343808 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
343751 CCTTCCTCTT
*
343761 AATATCGATACTCACATC
1 AATATCAATACTCACATC
343779 AATATCAATACTCACATC
1 AATATCAATACTCACATC
343797 AATATCAATACT
1 AATATCAATACT
343809 AATTGCAGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.44, C:0.25, G:0.02, T:0.29
Consensus pattern (18 bp):
AATATCAATACTCACATC
Found at i:345187 original size:32 final size:32
Alignment explanation
Indices: 345151--345255 Score: 104
Period size: 32 Copynumber: 3.3 Consensus size: 32
345141 TTGGGCGTAG
* *
345151 GAGCCAACCTAAGGGATTATCTTGGGGCCTGA
1 GAGCCTACCTAAGGGATTATCTTGGGGCCTCA
* * *
345183 GAGCCTACCTAAGAG-TGTATCTTGGAGCCTTA
1 GAGCCTACCTAAGGGAT-TATCTTGGGGCCTCA
* * * *
345215 GAGCCTACCCAAGGAAATACCTTGGGGCCTCA
1 GAGCCTACCTAAGGGATTATCTTGGGGCCTCA
*
345247 GAGTCTACC
1 GAGCCTACC
345256 CAAGTGTTAC
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
31 1 0.02
32 58 0.98
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.22
Consensus pattern (32 bp):
GAGCCTACCTAAGGGATTATCTTGGGGCCTCA
Found at i:346332 original size:26 final size:26
Alignment explanation
Indices: 346302--346357 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
346292 TTCGAGGTAG
*
346302 ATTTATTCATTCCAGAGCTTAAGGGT
1 ATTTAGTCATTCCAGAGCTTAAGGGT
* *
346328 ATTTAGTCATTCCAGGGCTTAGGGGT
1 ATTTAGTCATTCCAGAGCTTAAGGGT
346354 ATTT
1 ATTT
346358 TTAGGTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.39
Consensus pattern (26 bp):
ATTTAGTCATTCCAGAGCTTAAGGGT
Found at i:347592 original size:60 final size:59
Alignment explanation
Indices: 347528--347701 Score: 242
Period size: 60 Copynumber: 2.9 Consensus size: 59
347518 TAGTCGGGTA
* * *
347528 ACCATTTTGTAACTTTTAATAGTCGATGGACTTAACAAAGCAACATCCTATAGTCAAAGT
1 ACCATTTTATAACTTTTAATAGTCGAGGGACTTAACAAAG-AACATCCTATAGTCAAAGC
*
347588 ACCATTTTATAACTTTTAATAGTCGAGGGACTTAACGAAGTAACATCCTATAGTCAAAGC
1 ACCATTTTATAACTTTTAATAGTCGAGGGACTTAACAAAG-AACATCCTATAGTCAAAGC
* * *
347648 ATCATTTTACAACTTTTAATAGTCGAGGGA-TTAAACAAAGAAGTATCCTATAGT
1 ACCATTTTATAACTTTTAATAGTCGAGGGACTT-AACAAAGAA-CATCCTATAGT
347702 TGGGGGACCA
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
59 4 0.04
60 99 0.96
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (59 bp):
ACCATTTTATAACTTTTAATAGTCGAGGGACTTAACAAAGAACATCCTATAGTCAAAGC
Found at i:350740 original size:17 final size:17
Alignment explanation
Indices: 350706--350740 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
350696 TTTTAAAGAT
**
350706 AAAAACATATTATTAAC
1 AAAAACATATTAAAAAC
350723 AAAAACATATTAAAAAC
1 AAAAACATATTAAAAAC
350740 A
1 A
350741 TATAAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAACATATTAAAAAC
Found at i:352822 original size:2 final size:2
Alignment explanation
Indices: 352815--352843 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
352805 AAAAGTGAAT
352815 TA TA 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 TA TA T
352844 GTCAAGTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:356901 original size:13 final size:13
Alignment explanation
Indices: 356883--356912 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
356873 TAAAGCTGTT
356883 CTAATAGTGCCTG
1 CTAATAGTGCCTG
356896 CTAATAGTGCCTG
1 CTAATAGTGCCTG
356909 CTAA
1 CTAA
356913 GCATGTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (13 bp):
CTAATAGTGCCTG
Found at i:357278 original size:26 final size:26
Alignment explanation
Indices: 357226--357279 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
357216 AGATTACGTT
* **
357226 ATTTTACGTTAATTGTGTAGATTATA
1 ATTTTACGTTAATTCTGTAGAAAATA
357252 ATTTTACGTTAATTCTGTTA-AAAATA
1 ATTTTACGTTAATTCTG-TAGAAAATA
357278 AT
1 AT
357280 AAAAAACACG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (26 bp):
ATTTTACGTTAATTCTGTAGAAAATA
Found at i:365055 original size:22 final size:22
Alignment explanation
Indices: 365030--365158 Score: 105
Period size: 22 Copynumber: 5.9 Consensus size: 22
365020 TCAACAATTG
* *
365030 TAGATACGATGGTCGATGACTA
1 TAGATACGACGGTCGACGACTA
* *
365052 TAGATACGACGGTCGACGATTG
1 TAGATACGACGGTCGACGACTA
* * * * *
365074 TTGATACGACGATCGATGATTG
1 TAGATACGACGGTCGACGACTA
*
365096 TAGATACGACGGTCAACGACTA
1 TAGATACGACGGTCGACGACTA
* * * * *
365118 TAGATATGACGATTGACGATTG
1 TAGATACGACGGTCGACGACTA
* *
365140 TAGATATGACGGTTGACGA
1 TAGATACGACGGTCGACGA
365159 GCCTGCGCAT
Statistics
Matches: 87, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 87 1.00
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (22 bp):
TAGATACGACGGTCGACGACTA
Found at i:365080 original size:44 final size:44
Alignment explanation
Indices: 365017--365130 Score: 138
Period size: 44 Copynumber: 2.6 Consensus size: 44
365007 ATGGATGTGT
* * *
365017 CGGTCAACAATTGTAGATACGATGGTCGATGACTATAGATACGA
1 CGGTCAACGATTGTAGATACGACGATCGATGACTATAGATACGA
* * * *
365061 CGGTCGACGATTGTTGATACGACGATCGATGATTGTAGATACGA
1 CGGTCAACGATTGTAGATACGACGATCGATGACTATAGATACGA
* * *
365105 CGGTCAACGACTATAGATATGACGAT
1 CGGTCAACGATTGTAGATACGACGAT
365131 TGACGATTGT
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (44 bp):
CGGTCAACGATTGTAGATACGACGATCGATGACTATAGATACGA
Found at i:365136 original size:66 final size:66
Alignment explanation
Indices: 365026--365150 Score: 178
Period size: 66 Copynumber: 1.9 Consensus size: 66
365016 TCGGTCAACA
* * * * *
365026 ATTGTAGATACGATGGTCGATGACTATAGATACGACGGTCGACGATTGTTGATACGACGATCGAT
1 ATTGTAGATACGACGGTCAACGACTATAGATACGACGATCGACGATTGTAGATACGACGATCGAT
365091 G
66 G
* * *
365092 ATTGTAGATACGACGGTCAACGACTATAGATATGACGATTGACGATTGTAGATATGACG
1 ATTGTAGATACGACGGTCAACGACTATAGATACGACGATCGACGATTGTAGATACGACG
365151 GTTGACGAGC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 51 1.00
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.27
Consensus pattern (66 bp):
ATTGTAGATACGACGGTCAACGACTATAGATACGACGATCGACGATTGTAGATACGACGATCGAT
G
Found at i:365139 original size:44 final size:44
Alignment explanation
Indices: 365052--365152 Score: 130
Period size: 44 Copynumber: 2.3 Consensus size: 44
365042 TCGATGACTA
* * * * *
365052 TAGATACGACGGTCGACGATTGTTGATACGACGATCGATGATTG
1 TAGATACGACGGTCAACGACTATAGATACGACGATCGACGATTG
* *
365096 TAGATACGACGGTCAACGACTATAGATATGACGATTGACGATTG
1 TAGATACGACGGTCAACGACTATAGATACGACGATCGACGATTG
*
365140 TAGATATGACGGT
1 TAGATACGACGGT
365153 TGACGAGCCT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.27
Consensus pattern (44 bp):
TAGATACGACGGTCAACGACTATAGATACGACGATCGACGATTG
Found at i:366527 original size:3 final size:3
Alignment explanation
Indices: 366519--366559 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
366509 CAAACGGCTA
* *
366519 AAG AAG AAG AAG AAG AAG AAG AAC AAG AAG ATG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
366560 AGGGAATGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.66, C:0.02, G:0.29, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:367669 original size:18 final size:18
Alignment explanation
Indices: 367646--367682 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
367636 CTTGTTTCAA
367646 TGTCGGTGATGATGTCGG
1 TGTCGGTGATGATGTCGG
*
367664 TGTCGGTGTTGATGTCGG
1 TGTCGGTGATGATGTCGG
367682 T
1 T
367683 TTCTGGTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.11, G:0.43, T:0.38
Consensus pattern (18 bp):
TGTCGGTGATGATGTCGG
Found at i:370071 original size:3 final size:3
Alignment explanation
Indices: 370063--370108 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
370053 TTAATTTTAA
*
370063 TAT TAT TAT TAT TAT TAT TAAC TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT
370108 T
1 T
370109 TAATATATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.90
4 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:375319 original size:26 final size:25
Alignment explanation
Indices: 375290--375367 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
375280 AATTTTTGAC
375290 ATTCTATCTCTTTGAGACCTTGAAAT
1 ATTCT-TCTCTTTGAGACCTTGAAAT
* *
375316 A---TTCT-TTT-CGACCTTGAAAC
1 ATTCTTCTCTTTGAGACCTTGAAAT
*
375336 ATTCCCTCTCTTTGAGACCTTGAAAT
1 ATT-CTTCTCTTTGAGACCTTGAAAT
375362 ATTCTT
1 ATTCTT
375368 TCCACCTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
20 11 0.28
21 3 0.08
22 3 0.08
23 1 0.03
24 3 0.08
25 5 0.12
26 14 0.35
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.42
Consensus pattern (25 bp):
ATTCTTCTCTTTGAGACCTTGAAAT
Found at i:375328 original size:20 final size:20
Alignment explanation
Indices: 375305--375379 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
375295 ATCTCTTTGA
375305 GACCTTGAAATATTCTTTTC
1 GACCTTGAAATATTCTTTTC
* *
375325 GACCTTGAAACATTCCCTCTCTTTGA
1 GACCTTGAAATA-T---TCT-TTT-C
375351 GACCTTGAAATATTC-TTTC
1 GACCTTGAAATATTCTTTTC
*
375370 CACCTTGAAA
1 GACCTTGAAA
375380 CACTGTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 9 0.20
20 14 0.32
21 1 0.02
22 2 0.05
24 3 0.07
25 4 0.09
26 11 0.25
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (20 bp):
GACCTTGAAATATTCTTTTC
Found at i:376032 original size:11 final size:11
Alignment explanation
Indices: 376004--376041 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
375994 AAGAGCAAAG
376004 AGAAAAATCAA
1 AGAAAAATCAA
376015 AGCAAAAATCAA
1 AG-AAAAATCAA
*
376027 AGAAAAAGCAA
1 AGAAAAATCAA
376038 AGAA
1 AGAA
376042 CAAAAGAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:377658 original size:36 final size:38
Alignment explanation
Indices: 377616--377715 Score: 150
Period size: 36 Copynumber: 2.7 Consensus size: 38
377606 TTTCTTTTGT
* *
377616 AAAACAAATTTTGTCTCGCTTGAGACAGTTT-TT-TAA
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTCTTAAAA
*
377652 AAAACAAATTTTGTCTCGCTTGAGATAATTTCTTAAAA
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTCTTAAAA
*
377690 AAAACAAATTTCGTCTCGCTTGAGAC
1 AAAACAAATTTTGTCTCGCTTGAGAC
377716 CTTTTCCCTT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 29 0.51
37 2 0.04
38 26 0.46
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (38 bp):
AAAACAAATTTTGTCTCGCTTGAGACAATTTCTTAAAA
Found at i:377811 original size:105 final size:105
Alignment explanation
Indices: 377690--377988 Score: 343
Period size: 105 Copynumber: 2.9 Consensus size: 105
377680 TTTCTTAAAA
* * * *
377690 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTGGATATACAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTGGAGATACAAATTTCAAATTTGCTTCACA
* * * * *
377755 TTAAGCAAAGTTAATATCACTTGAGATTGTTGTTTCTTTT
66 TGAAACAAAATTAATATCACTTGAGATTGTTGTTTATTTC
* * ** * *
377795 AAAACAAACTTCGTCTCACTTGAGGTATTTTTCCTTTGAGATACAAATTTCAAATTTGCTTCACA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTGGAGATACAAATTTCAAATTTGCTTCACA
*
377860 TGAAACAAAATTAATCTCACTTGAGATTGTTGTTTATTTC
66 TGAAACAAAATTAATATCACTTGAGATTGTTGTTTATTTC
* * * ** * *
377900 GAAACAATTTTCGTTTCGCTTGAGACATTTT-TTTTCTGAGATACAAATTT-AAATTTG-TTGTA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTT-GGAGATACAAATTTCAAATTTGCTT-CA
*
377962 CTTGAAACAAAATTAATATCACTTGAG
64 CATGAAACAAAATTAATATCACTTGAG
377989 TTTTTCAAAA
Statistics
Matches: 164, Mismatches: 28, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
103 2 0.01
104 35 0.21
105 127 0.77
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (105 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTGGAGATACAAATTTCAAATTTGCTTCACA
TGAAACAAAATTAATATCACTTGAGATTGTTGTTTATTTC
Found at i:378164 original size:28 final size:27
Alignment explanation
Indices: 378133--378193 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
378123 ACAGTTTCTC
378133 TTGAGATAAATCTTTGAGTCTGTTCCTT
1 TTGA-ATAAATCTTTGAGTCTGTTCCTT
*
378161 TTGAATAAAAATCTTTGAGT-TGTTTCTT
1 TTGAAT--AAATCTTTGAGTCTGTTCCTT
378189 TTGAA
1 TTGAA
378194 ACAAATATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 2 0.07
28 16 0.53
29 12 0.40
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.48
Consensus pattern (27 bp):
TTGAATAAATCTTTGAGTCTGTTCCTT
Found at i:378177 original size:29 final size:29
Alignment explanation
Indices: 378140--378210 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 29
378130 CTCTTGAGAT
378140 AAATCTTTGAGTCTGTTCCTTTTGAATA-A
1 AAATCTTTGAGTCTGTTCCTTTTGAA-ACA
*
378169 AAATCTTTGAGT-TGTTTCTTTTGAAACA
1 AAATCTTTGAGTCTGTTCCTTTTGAAACA
378197 AATATCTTTGAGTC
1 AA-ATCTTTGAGTC
378211 CATTTCTGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
27 1 0.03
28 15 0.39
29 22 0.58
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45
Consensus pattern (29 bp):
AAATCTTTGAGTCTGTTCCTTTTGAAACA
Found at i:378311 original size:63 final size:63
Alignment explanation
Indices: 378204--378349 Score: 206
Period size: 63 Copynumber: 2.3 Consensus size: 63
378194 ACAAATATCT
* * *
378204 TTGAGTCCATTTCTGTTAAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTAAAAAAAAATCA
1 TTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGT-AAAAAAAATCA
* * *
378268 TTGAGTCTATTTATTTTGAAACAAAG-TTTGTCTCTCTTGAGACAATTTCGTGAAAAAAATCT
1 TTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTAAAAAAAATCA
*
378330 TTGAGT-TGTTTCTTTTGAAA
1 TTGAGTCTATTTCTTTTGAAA
378350 AAAATCTTTG
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
61 12 0.16
62 15 0.20
63 25 0.34
64 22 0.30
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.40
Consensus pattern (63 bp):
TTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTAAAAAAAATCA
Found at i:378355 original size:27 final size:28
Alignment explanation
Indices: 378318--378387 Score: 108
Period size: 27 Copynumber: 2.5 Consensus size: 28
378308 GACAATTTCG
378318 TGAAAAAAATCTTTGAGT-TGTTTCTTT
1 TGAAAAAAATCTTTGAGTCTGTTTCTTT
378345 TGAAAAAAATCTTTGAGTCTGTTTCTTT
1 TGAAAAAAATCTTTGAGTCTGTTTCTTT
*
378373 GGAAACAAAAT-TTTG
1 TGAAA-AAAATCTTTG
378388 TCTCCCTTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 18 0.45
28 17 0.43
29 5 0.12
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.43
Consensus pattern (28 bp):
TGAAAAAAATCTTTGAGTCTGTTTCTTT
Found at i:378361 original size:89 final size:92
Alignment explanation
Indices: 378255--378447 Score: 248
Period size: 89 Copynumber: 2.1 Consensus size: 92
378245 GACAATTTCG
* *
378255 TAAAAAAAAATCATTGAGTCTATTTATTTTGAAAC-AAAGTTTGTCTCTCTTGAGACAATTTC-G
1 TAAAAAAAAATCATTGAGTCTATTTATTTGGAAACAAAAGTTTGTCTCCCTTGAGACAATTTCTG
*
378318 TGAAAAAAATCTTTGAGT-TGTTTCTT
66 TGAAAAAAATCTTTGAGTATATTTCTT
** * * * *
378344 TTGAAAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTT
1 TAAAAAAAAATCATTGAGTCTATTTATTTGGAAACAAAAGTTTGTCTCCCTTGAGACAATTTC-T
* **
378409 TTGAAAATCATCTTTGAGTATATTTCTT
65 GTGAAAAAAATCTTTGAGTATATTTCTT
378437 TAAAAAAAAAT
1 TAAAAAAAAAT
378448 TAGTCTCTCT
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
89 29 0.34
90 25 0.29
92 16 0.19
93 16 0.19
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (92 bp):
TAAAAAAAAATCATTGAGTCTATTTATTTGGAAACAAAAGTTTGTCTCCCTTGAGACAATTTCTG
TGAAAAAAATCTTTGAGTATATTTCTT
Found at i:378454 original size:153 final size:156
Alignment explanation
Indices: 378162--378512 Score: 397
Period size: 153 Copynumber: 2.2 Consensus size: 156
378152 CTGTTCCTTT
378162 TGAATAAAAATCTTTGAGTTGTTTCTTTTGAAACAAATATCTTTGAGTCCATTTCTGTTAAAACA
1 TGAATAAAAATCTTTGAGTTGTTTCTTTTGAAACAAATATCTTTGAGTCCATTTCTGTTAAAACA
* * * * * *
378227 AAGTTTTGTCTCTCTTGAGACAATTTCGTAAAAAAAAATCATTGAGTCTATTTATTTTGAAACAA
66 AAATTTTGTCTCCCTTGAGACAATTTCGTAAAAAAAAATCATTGAGTATATTTACTTTAAAAAAA
* *
378292 AGTTTGTCTCTCTTGAGACAATTTCG
131 AATTAGTCTCTCTTGAGACAATTTCG
** *
378318 TGAA-AAAAATCTTTGAGTTGTTTCTTTTGAAA-AAA-ATCTTTGAGTCTGTTTCT-TTGGAAAC
1 TGAATAAAAATCTTTGAGTTGTTTCTTTTGAAACAAATATCTTTGAGTCCATTTCTGTT-AAAAC
* ** ** *
378379 AAAATTTTGTCTCCCTTGAGACAATTTCTTTTGAAAATCATCTTTGAGTATATTT-CTTTAAAAA
65 AAAATTTTGTCTCCCTTGAGACAATTTC-GTAAAAAAAAATCATTGAGTATATTTACTTTAAAAA
* * *
378443 AAAATTAGTCTCTCTTGAGATAGTTTCTAA
129 AAAATTAGTCTCTCTTGAGACAATTTC--G
* * * *
378473 TGAAAAAATAACCTTTGGGATTGTTTCCTTTGAAACAAAT
1 TGAATAAA-AATCTTTGAG-TTGTTTCTTTTGAAACAAAT
378513 TTCGTCTCAC
Statistics
Matches: 163, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
152 2 0.01
153 75 0.46
154 22 0.13
155 32 0.20
156 7 0.04
157 8 0.05
158 14 0.09
159 3 0.02
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (156 bp):
TGAATAAAAATCTTTGAGTTGTTTCTTTTGAAACAAATATCTTTGAGTCCATTTCTGTTAAAACA
AAATTTTGTCTCCCTTGAGACAATTTCGTAAAAAAAAATCATTGAGTATATTTACTTTAAAAAAA
AATTAGTCTCTCTTGAGACAATTTCG
Found at i:378879 original size:64 final size:64
Alignment explanation
Indices: 378732--378891 Score: 175
Period size: 62 Copynumber: 2.5 Consensus size: 64
378722 AAACAAGATC
* ** *
378732 ATCTTTGAGTTTGTTTCTCTGGAAACAAGGTTTTATCCCTTAAAACAGTTTCTTTTGAAGAAAA
1 ATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTATCCCTCAAAACAGTTTCTTTTGAAGAAAA
* * * * *
378796 ATC--TGAGTCTCTTTCTTTGGAAACAAAATTTTATTTCTCTCGAGACAGTTTC-TTTG-AGAAA
1 ATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTA--TCCCTCAAAACAGTTTCTTTTGAAGAAA
378857 A
64 A
*
378858 ATCTTTGAGTTTGTTTATTTGGAAAACAAAATTT
1 ATCTTTGAGTTTGTTTCTTTGG-AAACAAAATTT
378892 ACCATCTTTG
Statistics
Matches: 79, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
62 34 0.43
63 4 0.05
64 30 0.38
65 11 0.14
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (64 bp):
ATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTATCCCTCAAAACAGTTTCTTTTGAAGAAAA
Found at i:379160 original size:28 final size:28
Alignment explanation
Indices: 379128--379181 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
379118 GAAATATATC
379128 ATCTTTGAGTTTGTTT-TTCTTGAAACAA
1 ATCTTTGAGTTTGTTTCTT-TTGAAACAA
*
379156 ATCTTTGGGTTTGTTTCTTTTGAAAC
1 ATCTTTGAGTTTGTTTCTTTTGAAAC
379182 GTCATCTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (28 bp):
ATCTTTGAGTTTGTTTCTTTTGAAACAA
Found at i:379329 original size:43 final size:43
Alignment explanation
Indices: 379229--379469 Score: 189
Period size: 40 Copynumber: 5.6 Consensus size: 43
379219 CTAAATATGG
* * * *
379229 CCAGCCGTCCTCATCACGTAGAAACCGTGTCATCCCCT-G---A
1 CCAGCCATCCTCATCACGTAGGAACCGTGTCA-ACCATAGATAA
*
379269 CCAGACC-TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAG-CCATCCTCATCACGTAGGAACCGTGTCAACCATAGATAA
* * * *
379312 CCAGCCATCCTCATCACGTAGGAACCGTGTTATCATCCCTAAATATGG
1 CCAGCCATCCTCATCACGTAGGAACCGTG---TCAACCATAGATA--A
* *
379360 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCACT-G---A
1 CCAGCCATCCTCATCACGTAGGAACCGTGTCAACCA-TAGATAA
*
379400 CCAG--ATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAGCCATC-C-TCATCACGTAGGAACCGTGTCAACCATAGATAA
* *
379443 CCAGTCGTCCTCATCACGTAGGAACCG
1 CCAGCCATCCTCATCACGTAGGAACCG
379470 AGTTATCACC
Statistics
Matches: 163, Mismatches: 18, Indels: 37
0.75 0.08 0.17
Matches are distributed among these distances:
38 2 0.01
39 5 0.03
40 57 0.35
41 2 0.01
42 2 0.01
43 47 0.29
44 1 0.01
45 8 0.05
46 11 0.07
48 28 0.17
ACGTcount: A:0.26, C:0.34, G:0.19, T:0.21
Consensus pattern (43 bp):
CCAGCCATCCTCATCACGTAGGAACCGTGTCAACCATAGATAA
Found at i:379454 original size:131 final size:131
Alignment explanation
Indices: 379215--379481 Score: 464
Period size: 131 Copynumber: 2.0 Consensus size: 131
379205 TGAAATCCTT
*
379215 ATCCCTAAATATGGCCAGCCGTCCTCATCACGTAGAAACCGTGTCATCCCCTGACCAGACCTCCT
1 ATCCCTAAATATGGCCAGCCGTCCTCATCACGTAGAAACCGTGTCATCCACTGACCAGACCTCCT
*
379280 CATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTAT
66 CATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCATCCTCATCACGTAGGAACCGAGTTAT
379345 C
131 C
* * *
379346 ATCCCTAAATATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCACTGACCAGATCTCTT
1 ATCCCTAAATATGGCCAGCCGTCCTCATCACGTAGAAACCGTGTCATCCACTGACCAGACCTCCT
* *
379411 CATCACGTAGGAGCCGTGTCAACCATAGATAACCAGTCGTCCTCATCACGTAGGAACCGAGTTAT
66 CATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCATCCTCATCACGTAGGAACCGAGTTAT
379476 C
131 C
379477 A-CCCT
1 ATCCCT
379482 TCCTAAAGAT
Statistics
Matches: 129, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
130 4 0.03
131 125 0.97
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (131 bp):
ATCCCTAAATATGGCCAGCCGTCCTCATCACGTAGAAACCGTGTCATCCACTGACCAGACCTCCT
CATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCATCCTCATCACGTAGGAACCGAGTTAT
C
Found at i:379699 original size:3 final size:3
Alignment explanation
Indices: 379691--379733 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
379681 TTAATTTTAA
*
379691 TAT TAT TAT TAT TAT TAT TAAC TA- TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT T
379734 TAATATATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
2 2 0.05
3 33 0.89
4 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:379740 original size:24 final size:24
Alignment explanation
Indices: 379690--379741 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
379680 TTTAATTTTA
379690 ATATTATTATTATTATTATTAACT
1 ATATTATTATTATTATTATTAACT
379714 ATATTATTATTATTATTATTTAA-T
1 ATATTATTATTATTATTA-TTAACT
379738 ATAT
1 ATAT
379742 GTTTGCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
ATATTATTATTATTATTATTAACT
Found at i:382965 original size:32 final size:33
Alignment explanation
Indices: 382924--383016 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
382914 GGGTCGAGTT
* *
382924 TTTTTTAAGTTTGATATTCGGGTCGGGTC-GGG
1 TTTTTTAAGTGTAATATTCGGGTCGGGTCAGGG
* * *
382956 TTTTTTAAGTGTAATATTCGGGTAGGATCAGGT
1 TTTTTTAAGTGTAATATTCGGGTCGGGTCAGGG
* *
382989 TTTTTTAAATGTAATATTCAGGTCGGGT
1 TTTTTTAAGTGTAATATTCGGGTCGGGT
383017 TTAGGGTGAA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
32 25 0.49
33 26 0.51
ACGTcount: A:0.20, C:0.08, G:0.28, T:0.44
Consensus pattern (33 bp):
TTTTTTAAGTGTAATATTCGGGTCGGGTCAGGG
Found at i:382993 original size:33 final size:32
Alignment explanation
Indices: 382923--383007 Score: 107
Period size: 32 Copynumber: 2.6 Consensus size: 32
382913 TGGGTCGAGT
* * * *
382923 TTTTTTTAAGTTTGATATTCGGGTCGGGTCGG
1 TTTTTTTAAGTGTAATATTCGGGTAGGATCGG
*
382955 GTTTTTTAAGTGTAATATTCGGGTAGGATCAGG
1 TTTTTTTAAGTGTAATATTCGGGTAGGATC-GG
*
382988 TTTTTTTAAATGTAATATTC
1 TTTTTTTAAGTGTAATATTC
383008 AGGTCGGGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 25 0.56
33 20 0.44
ACGTcount: A:0.21, C:0.07, G:0.25, T:0.47
Consensus pattern (32 bp):
TTTTTTTAAGTGTAATATTCGGGTAGGATCGG
Found at i:383371 original size:258 final size:251
Alignment explanation
Indices: 383015--383487 Score: 680
Period size: 258 Copynumber: 1.9 Consensus size: 251
383005 TTCAGGTCGG
** * *
383015 GTTTAGGGTGAAAAATACCCAACCCAACATGGAAAAAAAAATAATTTTACCTTATATATTTATGA
1 GTTTAGGGTGAAAAATACCCAACCCAACA-CCAAAAAAAAATAATTTTACATTATATATTTAGGA
* * *
383080 ATAATTATAATAATACACTTCTATATATAATTTTTTTTAATTAAATCACTGTTTTTATTGAATAA
65 ATAATTACAATAATACACTTCTATATATAA-TTTTTTCAATTAAATCACTATTTTTATTGAATAA
* * *
383145 AAATAATTTTTATTATTATTTCGGGTCGGGTCGAGTTTTTAATTCATATATTCGGGTCGGGTTGG
129 AAATAA-TTTT-TTATTATTTCGGGTC--G--G-GTTTCTAATTCATATATTCGGGTCAGGTCGG
*
383210 GTAAAATTTTATTTTGGTCGGGTCGGGTTGGGTTTTTTTAAGTGTGATATTCAGGTCGAGTTTGA
187 GTAAAACTTTATTTTGGTCGGGTCGGGTTGGGTTTTTTTAAGTGTGATATTCAGGTCGAGTTTGA
* * *
383275 GTTTAGGGTGAAAAATACTCGACCCGAC-CCAAAAAAAAATAATTTTACATTATATATTTAGGAA
1 GTTTAGGGTGAAAAATACCCAACCCAACACCAAAAAAAAATAATTTTACATTATATATTTAGGAA
* *
383339 TAATTACAATATTACACCTT-TATATATAATTTTTTCAATTAAGTCACTATTTTTATTGAATAAA
66 TAATTACAATAATACA-CTTCTATATATAATTTTTTCAATTAAATCACTATTTTTATTGAATAAA
*
383403 AATAATTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCAGGTCGGGTGAAACT
130 AATAATTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCAGGTCGGGTAAAACT
*
383468 TTATTTTGGTCGGTTCGGGT
195 TTATTTTGGTCGGGTCGGGT
383488 CGAGTCTCGG
Statistics
Matches: 194, Mismatches: 18, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
250 53 0.27
251 1 0.01
253 1 0.01
255 15 0.08
256 4 0.02
257 37 0.19
258 55 0.28
259 3 0.02
260 25 0.13
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.41
Consensus pattern (251 bp):
GTTTAGGGTGAAAAATACCCAACCCAACACCAAAAAAAAATAATTTTACATTATATATTTAGGAA
TAATTACAATAATACACTTCTATATATAATTTTTTCAATTAAATCACTATTTTTATTGAATAAAA
ATAATTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCAGGTCGGGTAAAACTT
TATTTTGGTCGGGTCGGGTTGGGTTTTTTTAAGTGTGATATTCAGGTCGAGTTTGA
Found at i:383885 original size:18 final size:16
Alignment explanation
Indices: 383844--383892 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 16
383834 ATGTTTCATA
*
383844 TTCAGATTCCAATTCC
1 TTCAGATTCTAATTCC
383860 TTCAGATTCTAATTCC
1 TTCAGATTCTAATTCC
383876 TTAACAGATTCTAATTC
1 TT--CAGATTCTAATTC
383893 ACTCATTAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 17 0.57
18 13 0.43
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.41
Consensus pattern (16 bp):
TTCAGATTCTAATTCC
Found at i:384575 original size:22 final size:22
Alignment explanation
Indices: 384547--384622 Score: 95
Period size: 21 Copynumber: 3.5 Consensus size: 22
384537 TTAATTTTAT
384547 TTTATTTTAATATAGGGTTAAC
1 TTTATTTTAATATAGGGTTAAC
* **
384569 TTTA-TTTAATTTA-AATTCAA-
1 TTTATTTTAATATAGGGTT-AAC
384589 TTTATTTTAATATAGGGTTAAC
1 TTTATTTTAATATAGGGTTAAC
384611 TTTATTTTAATA
1 TTTATTTTAATA
384623 AATTAAATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
20 6 0.14
21 20 0.45
22 18 0.41
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.54
Consensus pattern (22 bp):
TTTATTTTAATATAGGGTTAAC
Found at i:385317 original size:15 final size:16
Alignment explanation
Indices: 385279--385319 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
385269 ACAGAGCCTC
*
385279 TGAATCATTCAACATT
1 TGAATCATTCAACACT
*
385295 TGAATCATTCAACGCT
1 TGAATCATTCAACACT
385311 T-AATCATTC
1 TGAATCATTC
385320 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAACACT
Found at i:385512 original size:22 final size:22
Alignment explanation
Indices: 385464--385504 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
385454 ATTAAATGAA
385464 ATTATGAGTTTGTTTATTATTT
1 ATTATGAGTTTGTTTATTATTT
385486 ATTATGAGTTTG-TTATTAT
1 ATTATGAGTTTGTTTATTAT
385505 CTGTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (22 bp):
ATTATGAGTTTGTTTATTATTT
Found at i:385681 original size:13 final size:13
Alignment explanation
Indices: 385663--385691 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
385653 TCCCTTTAGA
385663 TTTTTATTTGTAT
1 TTTTTATTTGTAT
385676 TTTTTATTTGTAT
1 TTTTTATTTGTAT
385689 TTT
1 TTT
385692 CATATATGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTTTATTTGTAT
Found at i:386551 original size:231 final size:227
Alignment explanation
Indices: 386144--386594 Score: 785
Period size: 231 Copynumber: 2.0 Consensus size: 227
386134 GTAAATTATC
* * *
386144 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
386209 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
386274 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAAT
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT--AAAAAAAT
386339 TGAAACATAAATTACATAACTTTCAAAAAAGTATA
194 TGAAACATAAATTACATAACTTT-AAAAAAGTATA
*
386374 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
386439 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
386504 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
386569 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
386595 GCAGTTATAA
Statistics
Matches: 211, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
228 4 0.02
229 30 0.14
230 36 0.17
231 141 0.67
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:386683 original size:20 final size:19
Alignment explanation
Indices: 386660--386705 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
386650 CGATATACCA
386660 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
386680 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
386700 GGTAAA
1 GGTAAA
386706 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:386849 original size:20 final size:19
Alignment explanation
Indices: 386826--386872 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
386816 CGATATAACA
386826 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
386846 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
386866 GGTAAAA
1 GGTAAAA
386873 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:386874 original size:17 final size:19
Alignment explanation
Indices: 386835--386877 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
386825 AGGTAAAAAT
386835 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
386855 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
386872 ATGATA
1 ATGATA
386878 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:389150 original size:21 final size:21
Alignment explanation
Indices: 389103--389167 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
389093 AAGACAATCA
* *
389103 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
389125 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
389145 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
389166 AG
1 AG
389168 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:389243 original size:33 final size:33
Alignment explanation
Indices: 389201--389266 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
389191 AAATAGATGG
*
389201 AGTGGTGAAAGAA-GTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGGT-GAGGTGTTAAGGGGTGA
*
389234 AGTGGTGAAAGAAGGTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGGTGAGGTGTTAAGGGGTGA
389267 TATTAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.50, T:0.21
Consensus pattern (33 bp):
AGTGGTGAAAGAAGGTGAGGTGTTAAGGGGTGA
Found at i:391082 original size:19 final size:19
Alignment explanation
Indices: 391058--391106 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
391048 AATGTAGGGT
391058 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
391077 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
391096 T-ATTTTCGTAT
1 TAATTTT-GTAT
391107 GTGAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 5 0.18
19 23 0.82
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:391569 original size:198 final size:197
Alignment explanation
Indices: 391231--392704 Score: 2708
Period size: 198 Copynumber: 7.5 Consensus size: 197
391221 GGCCAAAAGG
391231 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
391296 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATA-TTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
391361 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
391426 AAT
195 AAT
391429 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
391494 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATA-TTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
391559 ATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
391622 AAT
195 AAT
391625 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
391690 TGTCGACACTAAAATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA-CC
*
391755 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAATTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
391820 AAT
195 AAT
391823 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
391888 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATA-TTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
391953 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
392018 AAT
195 AAT
392021 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
392086 TGTCGACACTAAAATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA-CC
*
392151 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAATTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
392216 AAT
195 AAT
392219 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
* * *
392284 TGTCGACACTAATATAGTTTGTGTCGATACTAATTT--AAATATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGA-ATGAATGGAAAACAGGGTGCACC
*
392347 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAACATCATCGAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
392412 AAT
195 AAT
392415 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
* * *
392480 TGTCGACACTAATATAGTTTGTGTCGATACTAATTT--AAATATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGA-ATGAATGGAAAACAGGGTGCACC
*
392543 ATAAAGTGTCGATCCGTATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
392608 AAT
195 AAT
392611 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
392676 TGTCGACACTAATATAGTTTGTGTCGATA
66 TGTCGACACTAATATAGTTTGTGTCGATA
392705 CTAATTTAAA
Statistics
Matches: 1253, Mismatches: 17, Indels: 14
0.98 0.01 0.01
Matches are distributed among these distances:
195 32 0.03
196 519 0.41
197 53 0.04
198 617 0.49
199 32 0.03
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (197 bp):
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
AT
Found at i:391959 original size:394 final size:394
Alignment explanation
Indices: 391231--392704 Score: 2717
Period size: 394 Copynumber: 3.7 Consensus size: 394
391221 GGCCAAAAGG
391231 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
* *
391296 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAAAATAGTTTGTGTCGATA-TTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
391361 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
391426 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
195 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
391491 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGC
260 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGC
391556 ACCATAAAGTGTCGATCC-ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
325 ACCATAAAGTGTCGATCCAATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
391620 GTAAT
390 GTAAT
391625 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
391690 TGTCGACACTAAAATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCC
66 TGTCGACACTAAAATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA-CC
*
391755 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAATTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
391820 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
195 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
391885 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGC
260 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGC
391950 ACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
325 ACCATAAAGTGTCGATCCA-ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
392015 TGTAAT
389 TGTAAT
392021 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
392086 TGTCGACACTAAAATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCC
66 TGTCGACACTAAAATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA-CC
*
392151 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAATTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
392216 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
195 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
* ** *
392281 ATGTGTCGACACTAATATAGTTTGTGTCGATA-CTAATTT--AAATATGAATGGAAAACAGGGTG
260 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGA-ATGAATGGAAAACAGGGTG
*
392343 CACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAACATCATCGAACCCAAAAGTATA
324 CACCATAAAGTGTCGATCCA-ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
392408 ATGTAAT
388 ATGTAAT
392415 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
* * * *
392480 TGTCGACACTAATATAGTTTGTGTCGATACTAATTT--AAATATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAAAATAGTTTGTGTCGATATTTATTTCCAGA-ATGAATGGAAAACAGGGTGCACC
*
392543 ATAAAGTGTCGATCCGTATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
392608 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
195 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
392673 ATGTGTCGACACTAATATAGTTTGTGTCGATA
260 ATGTGTCGACACTAATATAGTTTGTGTCGATA
392705 CTAATTTAAA
Statistics
Matches: 1061, Mismatches: 14, Indels: 12
0.98 0.01 0.01
Matches are distributed among these distances:
392 164 0.15
393 55 0.05
394 495 0.47
395 4 0.00
396 343 0.32
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (394 bp):
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
TGTCGACACTAAAATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
ATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAA
TGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCA
CCATAAAGTGTCGATCCAATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAAT
Found at i:394186 original size:18 final size:18
Alignment explanation
Indices: 394165--394226 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
394155 AGCGGTCGCA
394165 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
394183 GAAGATGACGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
394201 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
394219 GAAGATGA
1 GAAGATGA
394227 TGACGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:394189 original size:6 final size:6
Alignment explanation
Indices: 394165--394250 Score: 64
Period size: 6 Copynumber: 14.3 Consensus size: 6
394155 AGCGGTCGCA
* * * * * *
394165 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * *
394213 GGCGAT GAAGAT GATGAC GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
394251 TGATCCAAAC
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:394200 original size:3 final size:3
Alignment explanation
Indices: 394180--394254 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
394170 TGAAGCTGAC
* * * * * ** *
394180 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
394228 GAC GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
394255 CCAAACAAGT
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.36, C:0.07, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:394219 original size:36 final size:36
Alignment explanation
Indices: 394168--394246 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
394158 GGTCGCAGAA
*
394168 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* * *
394204 GATGAAGCTGGCGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
394240 GATGAAG
1 GATGAAG
394247 ATGATGATCC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.20
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:394254 original size:12 final size:12
Alignment explanation
Indices: 394168--394250 Score: 94
Period size: 12 Copynumber: 6.9 Consensus size: 12
394158 GGTCGCAGAA
*
394168 GATGAAGCTGAC
1 GATGAAGATGAC
394180 GATGAAGATGAC
1 GATGAAGATGAC
*
394192 GATGATGATGAC
1 GATGAAGATGAC
* *
394204 GATGAAGCTGGC
1 GATGAAGATGAC
*
394216 GATGAAGATGAT
1 GATGAAGATGAC
* * *
394228 GACGATGATGAT
1 GATGAAGATGAC
394240 GATGAAGATGA
1 GATGAAGATGA
394251 TGATCCAAAC
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 59 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.20
Consensus pattern (12 bp):
GATGAAGATGAC
Done.