Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold871
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: 93194
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:327 original size:19 final size:19
Alignment explanation
Indices: 305--344 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
295 AATATTTTAT
305 TAAAT-TAATTATAAAAATA
1 TAAATATAA-TATAAAAATA
324 TAAATATAATATAAAAATA
1 TAAATATAATATAAAAATA
343 TA
1 TA
345 TTTAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAATATAATATAAAAATA
Found at i:11668 original size:14 final size:14
Alignment explanation
Indices: 11645--11678 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
11635 TAATATTATA
*
11645 TTATAATTATATTT
1 TTATATTTATATTT
11659 TTATATTTATATTT
1 TTATATTTATATTT
*
11673 ATATAT
1 TTATAT
11679 AATTTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATATTTATATTT
Found at i:12110 original size:18 final size:18
Alignment explanation
Indices: 12087--12129 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
12077 GAATCACATA
12087 AATTTTATATATTTTT-TT
1 AATTTTATA-ATTTTTATT
*
12105 AATTTTTTAATTTTTATT
1 AATTTTATAATTTTTATT
12123 ATATTTT
1 A-ATTTT
12130 TACACTAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 6 0.27
18 11 0.50
19 5 0.23
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
AATTTTATAATTTTTATT
Found at i:12278 original size:2 final size:2
Alignment explanation
Indices: 12271--12321 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
12261 GTTTAGAAGA
12271 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
12313 AT AT AT AT A
1 AT AT AT AT A
12322 CTTTCTCATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12721 original size:23 final size:23
Alignment explanation
Indices: 12694--12738 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
12684 TATATTTTTA
*
12694 TTATATTCAAATATATCATTAAT
1 TTATATTCAAATAAATCATTAAT
* *
12717 TTATATTTAAATAAATTATTAA
1 TTATATTCAAATAAATCATTAA
12739 ACTTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
TTATATTCAAATAAATCATTAAT
Found at i:12821 original size:27 final size:28
Alignment explanation
Indices: 12790--12855 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
12780 CTTTCATTTG
*
12790 AAAATAAAAAA-TTATTTAAATTTAAAT-
1 AAAATAAAAAACTTATTT-AATTAAAATA
*
12817 TAAATATAAAAACTTATTTAATTAAAATA
1 AAAATA-AAAAACTTATTTAATTAAAATA
12846 AAAATAAAAA
1 AAAATAAAAA
12856 TTTGCTCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
27 5 0.15
28 17 0.52
29 11 0.33
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (28 bp):
AAAATAAAAAACTTATTTAATTAAAATA
Found at i:12833 original size:29 final size:27
Alignment explanation
Indices: 12790--12855 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
12780 CTTTCATTTG
*
12790 AAAATAAAAAATTATTTAAATTTAAATTA
1 AAAATAAAAAATTATTT-AA-TTAAAATA
* *
12819 AATATAAAAACTTATTTAATTAAAATA
1 AAAATAAAAAATTATTTAATTAAAATA
12846 AAAATAAAAA
1 AAAATAAAAA
12856 TTTGCTCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 16 0.48
28 2 0.06
29 15 0.45
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
AAAATAAAAAATTATTTAATTAAAATA
Found at i:13136 original size:15 final size:15
Alignment explanation
Indices: 13087--13136 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
13077 TATCAAATTA
13087 ATTTTAAGTTTAAAAT
1 ATTTTAAGTTT-AAAT
* * *
13103 AATTTTAAATTGAATT
1 -ATTTTAAGTTTAAAT
13119 ATTTTAAGTTTAAAT
1 ATTTTAAGTTTAAAT
13134 ATT
1 ATT
13137 CAAAATGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
15 15 0.56
16 3 0.11
17 9 0.33
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
ATTTTAAGTTTAAAT
Found at i:13146 original size:29 final size:32
Alignment explanation
Indices: 13082--13152 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 32
13072 TTTTGTATCA
* *
13082 AATTAATTTTAAGTTTAAAATAATTTTAAATTG
1 AATT-ATTTTAAGTTTAAAATAATTTCAAAATG
13115 AATTATTTTAAGTTT-AAAT-A-TTCAAAATG
1 AATTATTTTAAGTTTAAAATAATTTCAAAATG
*
13144 AATAATTTT
1 AATTATTTT
13153 TTAATTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 15 0.43
30 1 0.03
31 4 0.11
32 11 0.31
33 4 0.11
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (32 bp):
AATTATTTTAAGTTTAAAATAATTTCAAAATG
Found at i:14072 original size:15 final size:14
Alignment explanation
Indices: 14046--14094 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
14036 ATAGGTTGTG
14046 AATATAATATAATTT
1 AATA-AATATAATTT
14061 AATAAATAATAATTT
1 AATAAAT-ATAATTT
* *
14076 ATTTAAATATAATTA
1 A-ATAAATATAATTT
14091 AATA
1 AATA
14095 TACAAACATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 5 0.17
15 19 0.66
16 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATAAATATAATTT
Found at i:14237 original size:19 final size:19
Alignment explanation
Indices: 14213--14251 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
14203 ATTTTAAATT
14213 AATT-AAATAAATATTAAAA
1 AATTAAAATAAA-ATTAAAA
*
14232 AATTAAAATTAAATTAAAA
1 AATTAAAATAAAATTAAAA
14251 A
1 A
14252 TATATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AATTAAAATAAAATTAAAA
Found at i:17285 original size:22 final size:22
Alignment explanation
Indices: 17237--17278 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
17227 GATGGACTGT
17237 ATTTATTACCAAGTTTTAGCCA
1 ATTTATTACCAAGTTTTAGCCA
17259 ATTTATTACCACA-TTTTAGC
1 ATTTATTACCA-AGTTTTAGC
17279 TTGTTTAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (22 bp):
ATTTATTACCAAGTTTTAGCCA
Found at i:19827 original size:13 final size:13
Alignment explanation
Indices: 19811--19843 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
19801 TTTATGTGTT
19811 TATATTATTTTTA
1 TATATTATTTTTA
19824 TATA-TATTTTTA
1 TATATTATTTTTA
*
19836 AATATTAT
1 TATATTAT
19844 AATTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATATTATTTTTA
Found at i:19962 original size:12 final size:12
Alignment explanation
Indices: 19945--19969 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19935 TTTTTATATC
19945 ATATCGTATTTT
1 ATATCGTATTTT
19957 ATATCGTATTTT
1 ATATCGTATTTT
19969 A
1 A
19970 AATTTATATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (12 bp):
ATATCGTATTTT
Found at i:22601 original size:23 final size:23
Alignment explanation
Indices: 22575--22619 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
22565 GAAAGAAGAG
22575 ATATTTTCTGTTTTAATAGTTGT
1 ATATTTTCTGTTTTAATAGTTGT
22598 ATATTTTCTGTTTTAATAGTTG
1 ATATTTTCTGTTTTAATAGTTG
22620 CAAATATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.04, G:0.13, T:0.60
Consensus pattern (23 bp):
ATATTTTCTGTTTTAATAGTTGT
Found at i:38391 original size:30 final size:32
Alignment explanation
Indices: 38357--38438 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
38347 CTAAACTATT
*
38357 ATTAATTATAAATTTAATAAA-A-TCGATATA
1 ATTAATTATAAATTTAATAAATATTAGATATA
* * *
38387 ATTAATAAAAAATTTAATAAATATTAGATGTA
1 ATTAATTATAAATTTAATAAATATTAGATATA
* *
38419 ATTACTTATAAATTTGATAA
1 ATTAATTATAAATTTAATAA
38439 TAATTGAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 19 0.45
31 1 0.02
32 22 0.52
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.40
Consensus pattern (32 bp):
ATTAATTATAAATTTAATAAATATTAGATATA
Found at i:39660 original size:5 final size:5
Alignment explanation
Indices: 39650--39686 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
39640 ATATTTTTAA
*
39650 TTATT TTATT TTATT TTAAT TTATT TTATT TTGATT T
1 TTATT TTATT TTATT TTATT TTATT TTATT TT-ATT T
39687 GATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:39996 original size:23 final size:24
Alignment explanation
Indices: 39953--40014 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 24
39943 TTAAATAATT
* *
39953 TTTAATAAA-AATTAAT-TTTTTTA
1 TTTAATAAATAA-AAATATTTTTGA
39976 TTTAATAAATAAAAATATTTTTGA
1 TTTAATAAATAAAAATATTTTTGA
**
40000 AATAA-AAATAAAAAT
1 TTTAATAAATAAAAAT
40015 TATATAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 22 0.67
24 11 0.33
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TTTAATAAATAAAAATATTTTTGA
Found at i:40082 original size:10 final size:9
Alignment explanation
Indices: 40058--40087 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
40048 GAAGAGAAAA
40058 TTATTATTT
1 TTATTATTT
40067 TTATTATTT
1 TTATTATTT
40076 TTAATTATTT
1 TT-ATTATTT
40086 TT
1 TT
40088 TAAATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTATTATTT
Found at i:40084 original size:22 final size:21
Alignment explanation
Indices: 40056--40104 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
40046 GTGAAGAGAA
*
40056 AATTATTATTTTTATTATTTTT
1 AATTATTATTTTTA-AATTTTT
40078 AATTA-T-TTTTTAAATTTTT
1 AATTATTATTTTTAAATTTTT
*
40097 ATTTATTA
1 AATTATTA
40105 AAAATAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 10 0.43
20 7 0.30
21 1 0.04
22 5 0.22
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
AATTATTATTTTTAAATTTTT
Found at i:40095 original size:18 final size:17
Alignment explanation
Indices: 40075--40124 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
40065 TTTTATTATT
40075 TTTAATTATTTTTTAAA
1 TTTAATTATTTTTTAAA
*
40092 TTT--TTATTTATTAAAA
1 TTTAATTATTT-TTTAAA
* *
40108 ATAAATTATTTTTTAAA
1 TTTAATTATTTTTTAAA
40125 AAAAAATCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
15 6 0.23
16 6 0.23
17 8 0.31
18 6 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTAATTATTTTTTAAA
Found at i:40125 original size:18 final size:18
Alignment explanation
Indices: 40095--40131 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40085 TTTTAAATTT
*
40095 TTATTTATTAAAAATAAA
1 TTATTTATTAAAAAAAAA
*
40113 TTATTTTTTAAAAAAAAA
1 TTATTTATTAAAAAAAAA
40131 T
1 T
40132 CTAAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTATTTATTAAAAAAAAA
Found at i:40236 original size:807 final size:809
Alignment explanation
Indices: 39139--40722 Score: 2092
Period size: 807 Copynumber: 2.0 Consensus size: 809
39129 TTTTACTTTT
39139 ATAATTTTTTAATAAAAATTAAGTTTATATTTAATAAATAAAAATATTTTTGAAATAAAAATAAA
1 ATAATTTTTTAATAAAAATTAAGTTTATATTTAATAAATAAAAATATTTTTGAAATAAAAATAAA
* * *
39204 AATTACAGAAAAAGTTAGTGTATTTCAAAAAATAGTGAAGAGAAAATTATTATTTTTGGCTTTTT
66 AATTACAGAAAAAATTAATGTATTTCAAAAAATAGTGAAGAGAAAATTATTATTTTTGACTTTTT
******* *
39269 TATTAATTTTTTAAAATTTTTCATTAAAAAAAACTAACATTTTTTTAATTTTTTTTTTAAAAAAA
131 TATTAATTTTTTAAAATTTTTCATTAAAAAAAACTAACATTTTTTTAAAAAAAAATCTAAAAAAA
* ** * *
39334 TCTGTTTTGCTTGATTTTTACTTTTAAAAAATTTTAAATAAAAAAATTAAGTCAAATTTAAATCG
196 TCTATTTAACTTAATTTTTACTTTTAAAAAATTTTAAATAAAAAAATTAAGTCAAATTTAAATCA
* * *
39399 ATTTTTTTTAATTAATAGCTTTATGTCAAAGATATTATGGCGATTTTGAATATCTTTGTTGATAG
261 ATTTTTTTTAATTAACAGCTTTATGTCAAAGATATTACGGCGATTTTGAATATCTTTGTTGATAA
* *
39464 TGAAACTAAGTGAGG-TCTACGATCGTGATTTTTTTAAAAAAAAAAATTGTGTTAGCTTTTTTGT
326 TGAAACTAAGTG-GGATCTACGATCGTGATTTTTTT--AAAAAAAAATTGTGTTAGCTTATTTAT
***
39528 TTTATTTCAAGAAATAAAGAAGGATTATTGAATCTGCAAACATTAGATGATTCTCTTACTTCCAA
388 AACATTTCAAGAAATAAAGAAGGATTATTGAATCTGCAAACATTAGATGATTCTCTTACTTCC-A
* * * * ** * *
39593 TGACGCCGACTTGAACGATGGATAAATTATTACTTATTTTTTTATATATATTTTTAATTATTTTA
452 TGACGCCGACTTGAACGATGGATAAATTATTAATTA-TTTTTT-TATACACTTTCAAACACTCTA
** * * * *
39658 TTTTATTTTAATTTATTTTATTTTGATTTGATATGATTTTGATTTGAATAATTGA-A-TGTGGA-
515 TTTTATTTTAATTTATACTATTTTGATTTAATATGATTTTAATTTAAATAATTAATATTGTGGAC
* * **
39720 TG-T-TATTTAAGTG-GTGAATAATTAATTAAAT-GATTGATTTTCTTTTATACTTTTAAAAATT
580 TGATATATTTAAGTGAGTAAATAATTAATTAAATAG-TTGATTTT-TTTCATACTGCTAAAAATT
39781 TT-TACTTATTTTAGTATGAATTTATTATATTGGGTCCTTTAA-TTTTATTTAAATTTATTTATA
643 TTATACTTATTTTAGTATGAATTTATTAT-TTGGGTCCTTTAATTTTTATTTAAATTTATTTATA
*
39844 ATTTAAATGTTTAGGGTTCTATATTTTAGTAAGAAATATTCCTTATATCATATGTTTAACATGTG
707 ATTTAAATGTTTAGGGTTCTATATTTTAGTAAGAAATATTCCTTATATCATAGGTTTAACATGTG
39909 TATAATAAAAATTTTAAAAATTAAATTAAAAATTTTAA
772 TATAATAAAAATTTTAAAAATTAAATTAAAAATTTTAA
* *
39947 ATAA-TTTTTAATAAAAATTAATTTTTTTATTTAATAAATAAAAATATTTTTGAAATAAAAATAA
1 ATAATTTTTTAATAAAAATTAA-GTTTATATTTAATAAATAAAAATATTTTTGAAATAAAAATAA
* * * *
40011 AAATTATATAAAAAATTAATGTATTTTAAAAAATAGTGAAGAGAAAATTATTATTTTT-ATTATT
65 AAATTACAGAAAAAATTAATGTATTTCAAAAAATAGTGAAGAGAAAATTATTATTTTTGACT-TT
**
40075 TTTAATT-ATTTTTT-AAATTTTT-ATTTATTAAAAA-TAA-ATTATTTTTTAAAAAAAAATCTA
129 TTT-ATTAATTTTTTAAAATTTTTCA-TTAAAAAAAACTAACA-T-TTTTTTAAAAAAAAATCTA
* * * *
40135 AAAAAAT-TATTTAATTTAATTTTTATTTTTTAAAAATTTTTAAATAAAAAAATT-AGATCATAT
190 AAAAAATCTATTTAACTTAATTTTTA-CTTTTAAAAAATTTTAAATAAAAAAATTAAG-TCAAAT
*
40198 TTAAATTAA-TTTTTTTATATTAACAGCTTTATGTCAAAGATATTACGGCGATTTTGAATATCTT
253 TTAAATCAATTTTTTTTA-ATTAACAGCTTTATGTCAAAGATATTACGGCGATTTTGAATATCTT
* * ** *****
40262 TGTTGATAATGAAAGTAAGTGGGATCTACTATTTTGATTTTTTTTTTTTAAAATTGTGTTAGCTT
317 TGTTGATAATGAAACTAAGTGGGATCTACGATCGTGATTTTTTTAAAAAAAAATTGTGTTAGCTT
* * *
40327 ATTTATAACATTTCAAGAAATAAAGAAGGGTTATTGAATTTGCAAACGTTAGATGATTCTCTTAC
382 ATTTATAACATTTCAAGAAATAAAGAAGGATTATTGAATCTGCAAACATTAGATGATTCTCTTAC
*
40392 TTCCATGACGCTGACTTGAACGATGGATAAATTATTAATTATTTTTTTATACACTTTCAAACACT
447 TTCCATGACGCCGACTTGAACGATGGATAAATTATTAATTATTTTTTTATACACTTTCAAACACT
* * *
40457 CTATTTTATTTTATTTTATACTATTTTGATTTAATATGATTTTAATTTAAATAATTAATATTTTT
512 CTATTTTATTTTAATTTATACTATTTTGATTTAATATGATTTTAATTTAAATAATTAATATTGTG
* **
40522 TACTTGCATCAATATTTATTTGAACAGTAAATAATTAATTAAATAGTTGATTTTTTTCATACTGC
577 GAC-TG-AT--ATATTTAAGTG---AGTAAATAATTAATTAAATAGTTGATTTTTTTCATACTGC
*
40587 TAAAATTTTTATACTTATTTTAGTATGAATTTATTATTTGGGTCCTTTAATTTTTTATTTAAATT
635 TAAAAATTTTATACTTATTTTAGTATGAATTTATTATTTGGGTCCTTTAA-TTTTTATTTAAATT
* *
40652 TATTTATAATTTAAATGTTTAGGGTTTTATATTTTAGTAAGAAATTTTCCTTATATCATAGGTTT
699 TATTTATAATTTAAATGTTTAGGGTTCTATATTTTAGTAAGAAATATTCCTTATATCATAGGTTT
40717 AACATG
764 AACATG
40723 AGTTGATTCT
Statistics
Matches: 671, Mismatches: 78, Indels: 46
0.84 0.10 0.06
Matches are distributed among these distances:
802 62 0.09
803 7 0.01
804 38 0.06
805 78 0.12
806 32 0.05
807 170 0.25
808 110 0.16
809 3 0.00
811 8 0.01
814 30 0.04
815 51 0.08
816 82 0.12
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (809 bp):
ATAATTTTTTAATAAAAATTAAGTTTATATTTAATAAATAAAAATATTTTTGAAATAAAAATAAA
AATTACAGAAAAAATTAATGTATTTCAAAAAATAGTGAAGAGAAAATTATTATTTTTGACTTTTT
TATTAATTTTTTAAAATTTTTCATTAAAAAAAACTAACATTTTTTTAAAAAAAAATCTAAAAAAA
TCTATTTAACTTAATTTTTACTTTTAAAAAATTTTAAATAAAAAAATTAAGTCAAATTTAAATCA
ATTTTTTTTAATTAACAGCTTTATGTCAAAGATATTACGGCGATTTTGAATATCTTTGTTGATAA
TGAAACTAAGTGGGATCTACGATCGTGATTTTTTTAAAAAAAAATTGTGTTAGCTTATTTATAAC
ATTTCAAGAAATAAAGAAGGATTATTGAATCTGCAAACATTAGATGATTCTCTTACTTCCATGAC
GCCGACTTGAACGATGGATAAATTATTAATTATTTTTTTATACACTTTCAAACACTCTATTTTAT
TTTAATTTATACTATTTTGATTTAATATGATTTTAATTTAAATAATTAATATTGTGGACTGATAT
ATTTAAGTGAGTAAATAATTAATTAAATAGTTGATTTTTTTCATACTGCTAAAAATTTTATACTT
ATTTTAGTATGAATTTATTATTTGGGTCCTTTAATTTTTATTTAAATTTATTTATAATTTAAATG
TTTAGGGTTCTATATTTTAGTAAGAAATATTCCTTATATCATAGGTTTAACATGTGTATAATAAA
AATTTTAAAAATTAAATTAAAAATTTTAA
Found at i:40871 original size:3 final size:3
Alignment explanation
Indices: 40863--40888 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40853 TAAAATGTAT
40863 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
40889 TGTATTATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:41142 original size:23 final size:22
Alignment explanation
Indices: 41081--41151 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 22
41071 AAAATATTAT
* *
41081 AATTTAAAATTT-AATTTAATT
1 AATTTATAATTTAAATTTAATA
41102 AATTTATTTAATCATTAATATTTAATA
1 AATTTA--TAAT--TTAA-ATTTAATA
41129 AATTTATAATTTAAATATTAATA
1 AATTTATAATTTAAAT-TTAATA
41152 TTTTTAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
21 6 0.15
22 2 0.05
23 13 0.32
25 6 0.15
26 1 0.02
27 13 0.32
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
AATTTATAATTTAAATTTAATA
Found at i:41149 original size:30 final size:30
Alignment explanation
Indices: 41072--41154 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
41062 TTAAAATATA
*
41072 AAATATTATAATTTAAA-ATTTA-ATTTAAT
1 AAAT-TTATAATTTAAATATTAATATTTAAT
*
41101 TAA-TT-T-ATTT-AATCATTAATATTTAAT
1 AAATTTATAATTTAAAT-ATTAATATTTAAT
41128 AAATTTATAATTTAAATATTAATATTT
1 AAATTTATAATTTAAATATTAATATTT
41155 TTAATATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
24 2 0.05
25 4 0.09
26 5 0.11
27 11 0.25
28 2 0.05
29 3 0.07
30 14 0.32
31 3 0.07
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (30 bp):
AAATTTATAATTTAAATATTAATATTTAAT
Found at i:42391 original size:30 final size:30
Alignment explanation
Indices: 42355--42423 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
42345 TACAAAACTA
* * *
42355 TATTTTCAATGGAATTTTTATTGGAAATAT-
1 TATTTTCAATAGAA-TTTCATCGGAAATATC
*
42385 TATTTTCCATAGAATTTCATCGGAAATATC
1 TATTTTCAATAGAATTTCATCGGAAATATC
*
42415 TACTTTCAA
1 TATTTTCAA
42424 ATACATATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 13 0.41
30 19 0.59
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (30 bp):
TATTTTCAATAGAATTTCATCGGAAATATC
Found at i:43008 original size:14 final size:14
Alignment explanation
Indices: 42989--43029 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
42979 ATAAATAGAG
42989 TAATTTATTTATTT
1 TAATTTATTTATTT
*
43003 TAATTTATTTAATT
1 TAATTTATTTATTT
*
43017 TAAATTA-TTATTT
1 TAATTTATTTATTT
43030 ATATAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TAATTTATTTATTT
Found at i:43090 original size:36 final size:37
Alignment explanation
Indices: 43010--43090 Score: 87
Period size: 36 Copynumber: 2.2 Consensus size: 37
43000 TTTTAATTTA
** *
43010 TTTAATTTAAATTATTATTTATATAATTAAAAAATAT
1 TTTAATTTAAATTATTAAATATATAATTAAAAAAAAT
*
43047 TTAAATTT-AATTA-TAAATAT-TAATATAAAAATAAAT
1 TTTAATTTAAATTATTAAATATATAAT-TAAAAA-AAAT
43083 TTTAATTT
1 TTTAATTT
43091 TTTTAATATT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
34 4 0.11
35 11 0.30
36 15 0.41
37 7 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (37 bp):
TTTAATTTAAATTATTAAATATATAATTAAAAAAAAT
Found at i:44797 original size:35 final size:35
Alignment explanation
Indices: 44758--44824 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
44748 GCATAATCTT
44758 ACATTCAAACCCATTACTACAGCAATTGAACCTTA
1 ACATTCAAACCCATTACTACAGCAATTGAACCTTA
* * *
44793 ACATTCATACCCATTACTATAGCAATTTAACC
1 ACATTCAAACCCATTACTACAGCAATTGAACC
44825 ATAATGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.39, C:0.28, G:0.04, T:0.28
Consensus pattern (35 bp):
ACATTCAAACCCATTACTACAGCAATTGAACCTTA
Found at i:49144 original size:19 final size:19
Alignment explanation
Indices: 49099--49202 Score: 112
Period size: 19 Copynumber: 5.7 Consensus size: 19
49089 TTTCAATAAT
* *
49099 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACATA-AGT-G
49120 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
49139 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
49158 TTGTATCGAT--ATAA---
1 TTGTATCGATACATAAGTG
* *
49172 TT-TATCGATAAATAAGTT
1 TTGTATCGATACATAAGTG
49190 TTGTATCGATACA
1 TTGTATCGATACA
49203 ATGTATCGCT
Statistics
Matches: 74, Mismatches: 3, Indels: 14
0.81 0.03 0.15
Matches are distributed among these distances:
13 7 0.09
14 2 0.03
15 4 0.05
17 4 0.05
18 2 0.03
19 38 0.51
20 3 0.04
21 14 0.19
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:49187 original size:32 final size:32
Alignment explanation
Indices: 49140--49210 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
49130 ACATAAGTGT
* *
49140 TGTATCGATACATAAGTGTTGTATCGATATAA
1 TGTATCGATAAATAAGTGTTGTATCGATACAA
* *
49172 TTTATCGATAAATAAGTTTTGTATCGATACAA
1 TGTATCGATAAATAAGTGTTGTATCGATACAA
49204 TGTATCG
1 TGTATCG
49211 CTACAAAGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (32 bp):
TGTATCGATAAATAAGTGTTGTATCGATACAA
Found at i:49257 original size:20 final size:20
Alignment explanation
Indices: 49232--49299 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
49222 CTGCCAAGAA
49232 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
49252 AATGTATCGATACA----T-
1 AATGTATCGATACATTTTTC
49267 --TGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
49285 AATGTATCGATACAT
1 AATGTATCGATACAT
49300 CTAGAAAGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 12 0.29
16 1 0.02
17 1 0.02
20 27 0.66
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:49272 original size:13 final size:13
Alignment explanation
Indices: 49254--49280 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
49244 CATTTTTCAA
49254 TGTATCGATACAT
1 TGTATCGATACAT
49267 TGTATCGATACAT
1 TGTATCGATACAT
49280 T
1 T
49281 TTTCAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:49276 original size:33 final size:33
Alignment explanation
Indices: 49234--49299 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
49224 GCCAAGAAAA
49234 TGTATCGATACATTTTTCAATGTATCGATACAT
1 TGTATCGATACATTTTTCAATGTATCGATACAT
49267 TGTATCGATACATTTTTCAATGTATCGATACAT
1 TGTATCGATACATTTTTCAATGTATCGATACAT
49300 CTAGAAAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATTTTTCAATGTATCGATACAT
Found at i:51727 original size:51 final size:51
Alignment explanation
Indices: 51493--51729 Score: 226
Period size: 51 Copynumber: 4.6 Consensus size: 51
51483 TTAAGTTTCC
* * * *
51493 CAATTTTCCACAATCGGGGATACTCCAACCTCGGTTTTATTT-TCAAAACAC
1 CAATTTTCTATAATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACAT
* * ** *
51544 CAATTTTCTATAATCGGGAATACTCCAATCCCGGTTCCATTTCCAAAACAT
1 CAATTTTCTATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACAT
* ** * *
51595 CATTTTTTCT-TAATCGGGGATACTCCAACTTCGATTTTATTTCTAAAGCAT
1 CA-ATTTTCTATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACAT
* * *** * * *
51646 CGATTTACCGCAATCGAGGATACTCCAACCCCAGTTTTTTTTCTAAAACAT
1 CAATTTTCTATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACAT
* *
51697 CAATTTTTTATAGTCGGGGATACTCCAACCCCG
1 CAATTTTCTATAATCGGGGATACTCCAACCCCG
51730 TTATTTCCGA
Statistics
Matches: 143, Mismatches: 40, Indels: 6
0.76 0.21 0.03
Matches are distributed among these distances:
50 4 0.03
51 133 0.93
52 6 0.04
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (51 bp):
CAATTTTCTATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACAT
Found at i:51768 original size:79 final size:79
Alignment explanation
Indices: 51663--51813 Score: 214
Period size: 79 Copynumber: 1.9 Consensus size: 79
51653 CCGCAATCGA
* * * *
51663 GGATACTCCAACCCCAGTTTTTTTTCTAAAACATCAATTTTTTATAGTCGGGGATACTCCAACCC
1 GGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACCC
51728 CGTTATTTCCGAAG
66 CGTTATTTCCGAAG
* * * *
51742 GGATACTCCGATCCC-GATTTTATTTCTAAATCATCGATTTTTCACAATCGGGGATACTCCAACC
1 GGATACTCCAACCCCAG-TTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACC
51806 CCGTTATT
65 CCGTTATT
51814 ATCTCCAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
78 1 0.02
79 62 0.98
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (79 bp):
GGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACCC
CGTTATTTCCGAAG
Found at i:63948 original size:12 final size:12
Alignment explanation
Indices: 63931--63955 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
63921 TCCAAATTGG
63931 GAAGGGCCATAC
1 GAAGGGCCATAC
63943 GAAGGGCCATAC
1 GAAGGGCCATAC
63955 G
1 G
63956 TAGTAAAGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.24, G:0.36, T:0.08
Consensus pattern (12 bp):
GAAGGGCCATAC
Found at i:64114 original size:1 final size:1
Alignment explanation
Indices: 64110--64158 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
64100 ATTCTTTTTC
* * * * *
64110 AAAAAAAAAACAAAAAAAAAACAAAAAACAAAAAAAAATAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
64159 GAGAGAAAAG
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.90, C:0.06, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:64125 original size:11 final size:11
Alignment explanation
Indices: 64109--64158 Score: 66
Period size: 11 Copynumber: 4.6 Consensus size: 11
64099 TATTCTTTTT
64109 CAAAAAAAAAA
1 CAAAAAAAAAA
64120 CAAAAAAAAAA
1 CAAAAAAAAAA
*
64131 CAAAAAACAAA
1 CAAAAAAAAAA
*
64142 -AAAAAATAAA
1 CAAAAAAAAAA
*
64152 GAAAAAA
1 CAAAAAA
64159 GAGAGAAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
10 9 0.25
11 27 0.75
ACGTcount: A:0.88, C:0.08, G:0.02, T:0.02
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:64137 original size:18 final size:17
Alignment explanation
Indices: 64110--64147 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
64100 ATTCTTTTTC
64110 AAAAAAAAAACAAAAAA
1 AAAAAAAAAACAAAAAA
64127 AAAACAAAAAACAAAAAA
1 AAAA-AAAAAACAAAAAA
64145 AAA
1 AAA
64148 TAAAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAACAAAAAA
Found at i:65194 original size:29 final size:29
Alignment explanation
Indices: 65161--65245 Score: 70
Period size: 28 Copynumber: 3.0 Consensus size: 29
65151 GACGCCTTTT
65161 CCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * ** *
65190 CCTTTTC--AGTCCTCA-AAG-AGCAGGACG
1 CC-TTTCAAAGCCCACACAAGTTGGTGG-CA
65217 CCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA
65246 TTTTTCAGTC
Statistics
Matches: 38, Mismatches: 12, Indels: 12
0.61 0.19 0.19
Matches are distributed among these distances:
26 7 0.18
27 6 0.16
28 12 0.32
29 6 0.16
30 7 0.18
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.21
Consensus pattern (29 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:65364 original size:116 final size:116
Alignment explanation
Indices: 65130--65852 Score: 859
Period size: 116 Copynumber: 6.2 Consensus size: 116
65120 CTCCTTTCAC
*
65130 TTTTCAGTCCTCAAAAAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
1 TTTTCAGTCCTCAAAGAGCAGGACGCC---T--TTTCAAAGCCCACACAAGTTGGTGGCA--TTT
65195 T-CAGTCCTCAAAGAGCAGGACGCC-----TTTCAAAGCCCACACAAGTTGGTGGCAT
59 TCCAGTCCTCAAAGAGCAGGACGCCTTTTTTTTCAAAGCCCACACAAGTTGGTGGCAT
*
65247 TTTTCAGTCCTCAAAGAGCAGGACGCCTTTT-AAAGCCCACACAAGTTGGTGGTATTTTCCAGTC
1 TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
*
65311 CTCAAAGAGCAGGATGCCTTTTATTTTCAAAGCCCACACAAGTTGGTGGCAT
66 CTCAAAGAGCAGGACGCCTTTT-TTTTCAAAGCCCACACAAGTTGGTGGCAT
* *
65363 TTTCCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 TTTTCAGTCCTCAAAGAGCAGGACGC-----CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
* *
65428 CAGTCCTCAAAGAGCAGGACGCCTTTTATTTTCAAAGCCCACACGAGTTGGTGGCAC
61 CAGTCCTCAAAGAGCAGGACGCCTTTT-TTTTCAAAGCCCACACAAGTTGGTGGCAT
* ** * ***
65485 CTTTCAGT-CTCCAAAGAGCAGGAAACCTTTT-AAAGCCCACACGAGTTGGTGGCACCCTCCAGT
1 TTTTCAGTCCT-CAAAGAGCAGGACGCCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
* *
65548 CCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCTACACAAGTTGGTGGCA-
65 CCTCAAAGAGCAGGACGCCTTTTT-TTTCAAAGCCCACACAAGTTGGTGGCAT
* * * *
65600 CTTCCTAGTCCTTAAAGAGCAGGACGCCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTCCAGT
1 TTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
65664 CCTCAAAGAGCAGGACGCC-----TTTCAAAGCCCACACAAGTTGGTGGCAT
65 CCTCAAAGAGCAGGACGCCTTTTTTTTCAAAGCCCACACAAGTTGGTGGCAT
* * *
65711 TTTCCAGTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCATCTTC
1 TTTTCAGTCCTCAAAGAGCAGGACGC---CT-TTT-CAAAGCCCACACAAGTTGGTGGCATTTTC
* * * *
65776 CAGTCCTCAAAGAGCAGGACACCTTTCCTTTTCAAAGCCCATACGAGTTGGTGGCACT
61 CAGTCCTCAAAGAGCAGGACGCCTTT-TTTTTCAAAGCCCACACAAGTTGGTGGCA-T
*
65834 TTTT-AGTCCTCGAAGAGCA
1 TTTTCAGTCCTCAAAGAGCA
65853 TGATGCACTT
Statistics
Matches: 534, Mismatches: 41, Indels: 57
0.84 0.06 0.09
Matches are distributed among these distances:
109 4 0.01
110 66 0.12
111 26 0.05
112 3 0.01
113 2 0.00
114 3 0.01
115 5 0.01
116 242 0.45
117 33 0.06
121 7 0.01
122 139 0.26
123 4 0.01
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (116 bp):
TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
CTCAAAGAGCAGGACGCCTTTTTTTTCAAAGCCCACACAAGTTGGTGGCAT
Found at i:65373 original size:61 final size:60
Alignment explanation
Indices: 65130--65852 Score: 835
Period size: 61 Copynumber: 12.3 Consensus size: 60
65120 CTCCTTTCAC
* *
65130 TTTT-CAGTCCTCAAAAAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT-TTTTCAAAGCCCACACAAGTTGGTGGCA
65190 CCTTTT-CAGTCCTCAAAGAGCAGGACGCC-----TTTCAAAGCCCACACAAGTTGGTGGCA
1 --TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTTTTTCAAAGCCCACACAAGTTGGTGGCA
* *
65246 TTTTTCAGTCCTCAAAGAGCAGGACGCC----TTTT-AAAGCCCACACAAGTTGGTGGTA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTTTTTCAAAGCCCACACAAGTTGGTGGCA
*
65301 TTTTCCAGTCCTCAAAGAGCAGGATGCCTTTTATTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT-TTTTCAAAGCCCACACAAGTTGGTGGCA
* *
65362 TTTTCCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT-TTTTCAAAGCCCACACAAGTTGGTGGCA
*
65423 TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTATTTTCAAAGCCCACACGAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT-TTTTCAAAGCCCACACAAGTTGGTGGCA
* ** *
65484 CCTTT-CAGT-CTCCAAAGAGCAGGAAACC----TTTT-AAAGCCCACACGAGTTGGTGGCA
1 -TTTTCCAGTCCT-CAAAGAGCAGGACGCCTTTTTTTTCAAAGCCCACACAAGTTGGTGGCA
*** * *
65539 CCCTCCAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCTACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTT-TTTCAAAGCCCACACAAGTTGGTGGCA
* * *
65600 -CTTCCTAGTCCTTAAAGAGCAGGACGCC----TCTT-AAAGCCCACACAAGTTGGTGGCA
1 TTTTCC-AGTCCTCAAAGAGCAGGACGCCTTTTTTTTCAAAGCCCACACAAGTTGGTGGCA
65655 TTTTCCAGTCCTCAAAGAGCAGGACGCC-----TTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTTTTTCAAAGCCCACACAAGTTGGTGGCA
* *
65710 TTTTCCAGTCCTCAAAGAGCAGGATG-CTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCCTTT-T-TTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
65771 TCTTCCAGTCCTCAAAGAGCAGGACACCTTTCCTTTTCAAAGCCCATACGAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCCTTT-TTTTTCAAAGCCCACACAAGTTGGTGGCA
* *
65832 CTTTT-TAGTCCTCGAAGAGCA
1 -TTTTCCAGTCCTCAAAGAGCA
65853 TGATGCACTT
Statistics
Matches: 592, Mismatches: 39, Indels: 61
0.86 0.06 0.09
Matches are distributed among these distances:
54 9 0.02
55 203 0.34
56 42 0.07
57 1 0.00
59 1 0.00
60 13 0.02
61 286 0.48
62 37 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (60 bp):
TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTTTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:66699 original size:19 final size:18
Alignment explanation
Indices: 66649--66738 Score: 84
Period size: 19 Copynumber: 5.1 Consensus size: 18
66639 TTGAATTTCA
66649 ATAA-TTTGTATCGATAC
1 ATAAGTTTGTATCGATAC
*
66666 AAACAGTAATTGTATCGATAC
1 ATA-AGT--TTGTATCGATAC
66687 ATAAGTGTTGTATCGATAC
1 ATAAGT-TTGTATCGATAC
66706 --AA---TGTATCGATAC
1 ATAAGTTTGTATCGATAC
66719 ATAAGTTTTGTATCGATAC
1 ATAAG-TTTGTATCGATAC
66738 A
1 A
66739 ATGTATCGCT
Statistics
Matches: 60, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
13 11 0.18
15 2 0.03
17 4 0.07
18 1 0.02
19 25 0.42
20 3 0.05
21 14 0.23
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.36
Consensus pattern (18 bp):
ATAAGTTTGTATCGATAC
Found at i:66713 original size:13 final size:13
Alignment explanation
Indices: 66695--66752 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
66685 ACATAAGTGT
66695 TGTATCGATACAA
1 TGTATCGATACAA
66708 TGTATCGATACATAA
1 TGTATCGATAC--AA
66723 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
*
66740 TGTATCGCTACAA
1 TGTATCGATACAA
66753 AGCTACTGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:66717 original size:32 final size:32
Alignment explanation
Indices: 66676--66751 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
66666 AAACAGTAAT
66676 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
66708 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
66740 TGTATCGCTACA
1 TGTATCGATACA
66752 AAGCTACTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:69211 original size:51 final size:51
Alignment explanation
Indices: 69155--69390 Score: 255
Period size: 51 Copynumber: 4.6 Consensus size: 51
69145 TAAGTTTCCT
* * *
69155 AATTTTCCACAATCGGGGATACTCCAACCTTGGTTTTATTT-TCAAAACACC
1 AATTTTCCATAATCGGGGATACTCCAACCTCGGTTTTATTTCT-AAAACATC
* ** *
69206 AATTTTCTATAATCGGGGATACTCCAATCC-CGGTTCCATTTCCAAAACATC
1 AATTTTCCATAATCGGGGATACTCCAA-CCTCGGTTTTATTTCTAAAACATC
* * * *
69257 AATTTTTCTTAATCGGGGATACTCCAA-CTCCGATTTTATTTCTAAAGCATC
1 AATTTTCCATAATCGGGGATACTCCAACCT-CGGTTTTATTTCTAAAACATC
* * * *
69308 GATTTACCACAATTGGGGATACTCCAAACC-CGGTTTTATTTCTAAAACATC
1 AATTTTCCATAATCGGGGATACTCC-AACCTCGGTTTTATTTCTAAAACATC
* *
69359 AATTTTTCATAGTCGGGGATACTCCAACCTCG
1 AATTTTCCATAATCGGGGATACTCCAACCTCG
69391 TTATTTCCGA
Statistics
Matches: 149, Mismatches: 29, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
49 1 0.01
50 4 0.03
51 139 0.93
52 4 0.03
53 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (51 bp):
AATTTTCCATAATCGGGGATACTCCAACCTCGGTTTTATTTCTAAAACATC
Found at i:69454 original size:79 final size:79
Alignment explanation
Indices: 69322--69474 Score: 252
Period size: 79 Copynumber: 1.9 Consensus size: 79
69312 TACCACAATT
* * *
69322 GGGGATACTCCAAACCCGGTTTTATTTCTAAAACATCAATTTTTCATAGTCGGGGATACTCCAAC
1 GGGGATACTCCAAACCCGATTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
*
69387 CTCGTTATTTCCGA
66 CCCGTTATTTCCGA
* *
69401 GGGGATACTCCAATCCCGATTTTATTTCTAAATCATCAATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAAACCCGATTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
69466 CCCGTTATT
66 CCCGTTATT
69475 ATCTCCAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 68 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (79 bp):
GGGGATACTCCAAACCCGATTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTATTTCCGA
Found at i:75117 original size:2 final size:2
Alignment explanation
Indices: 75112--75168 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
75102 TGTGTGTGTG
75112 TA TA TA 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 TA TA TA
75154 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
75169 TGTTTTGTCC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:77518 original size:22 final size:22
Alignment explanation
Indices: 77493--77538 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
77483 AAATCGCCAT
77493 TGGGGATGGTGAAAATGGGTGA
1 TGGGGATGGTGAAAATGGGTGA
77515 TGGGGATGGTGAAAATGGGTGA
1 TGGGGATGGTGAAAATGGGTGA
77537 TG
1 TG
77539 TTGGGAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.50, T:0.24
Consensus pattern (22 bp):
TGGGGATGGTGAAAATGGGTGA
Found at i:78477 original size:91 final size:90
Alignment explanation
Indices: 78258--78604 Score: 438
Period size: 90 Copynumber: 3.9 Consensus size: 90
78248 GTAATACATG
* * **
78258 GATTGTAAATGTTAGATTACAAGGGTTAGACTAATACATGAATTATATCTGAGAATCAAA---TT
1 GATTGTAAATGTCAGACTACAAGAATTAGACTAATACATGAATTATATCTGAGAATCAAATTCTT
* **
78320 TTTTATAG---AAAAAATGTTGGCT
66 TTTTATAGAAAAAAAAAAGTTGATT
* * * * * * *
78342 GATTGAAAATATCATATTACAA-ATATTAAACTAATGCATGAATTATATCTGAGAATCAGATTCT
1 GATTGTAAATGTCAGACTACAAGA-ATTAGACTAATACATGAATTATATCTGAGAATCAAATTCT
*
78406 TTTTTATAAAAGAAAAAAAAGTTGATT
65 TTTTTATAGAA-AAAAAAAAGTTGATT
* *
78433 GATTGTAAATGTCAGACTACAAGAATTAGACTAATACATTAATTATATCTAAGAATCAAATTCTT
1 GATTGTAAATGTCAGACTACAAGAATTAGACTAATACATGAATTATATCTGAGAATCAAATTCTT
*
78498 TTTAATAGAAAAAAAAAAGTTGATT
66 TTTTATAGAAAAAAAAAAGTTGATT
* * *
78523 GATTGTAAATGTCAAACTATAAGAATTAGACTAATGCATGAATTATATCTGAGAATCAAATTCTT
1 GATTGTAAATGTCAGACTACAAGAATTAGACTAATACATGAATTATATCTGAGAATCAAATTCTT
78588 TTTTATAGAAAAAAAAA
66 TTTTATAGAAAAAAAAA
78605 GACTGTAAGG
Statistics
Matches: 224, Mismatches: 30, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
84 50 0.22
87 9 0.04
90 91 0.41
91 73 0.33
92 1 0.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (90 bp):
GATTGTAAATGTCAGACTACAAGAATTAGACTAATACATGAATTATATCTGAGAATCAAATTCTT
TTTTATAGAAAAAAAAAAGTTGATT
Found at i:78664 original size:67 final size:68
Alignment explanation
Indices: 78542--78669 Score: 188
Period size: 67 Copynumber: 1.9 Consensus size: 68
78532 TGTCAAACTA
* * *
78542 TAAGAATTAGACTAATGCATGAATTATATCTGAGAATCAAATTCTTTTTTATAGAAAAAAAAAGA
1 TAAGAATTAGACTAATACATGAATTATATCTAAGAATCAAATTCTCTTTTATAGAAAAAAAAAGA
78607 CTG
66 CTG
* *
78610 TAAGGATTAGACTAATACAT-AATTATATCTAAGAATCGAATTC-CTTTTAGTAGAAAAAAA
1 TAAGAATTAGACTAATACATGAATTATATCTAAGAATCAAATTCTCTTTTA-TAGAAAAAAA
78670 GAAAATTTGA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
66 5 0.09
67 31 0.57
68 18 0.33
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.32
Consensus pattern (68 bp):
TAAGAATTAGACTAATACATGAATTATATCTAAGAATCAAATTCTCTTTTATAGAAAAAAAAAGA
CTG
Found at i:78735 original size:159 final size:157
Alignment explanation
Indices: 78457--78758 Score: 421
Period size: 159 Copynumber: 1.9 Consensus size: 157
78447 GACTACAAGA
*
78457 ATTAGACTAATACATTAATTATATCTAAGAATCAAATTCTTTTTAATAGAAAAAAAAAAGTTGAT
1 ATTAGACTAATACATTAATTATATCTAAGAATCAAATTCCTTTTAATAGAAAAAAAAAAGTTGAT
* * * *
78522 TGATTGTAAATGTCAAACTATAAGAATTAGACTAATGCATGAATTATATCTGAGAATCAAATTCT
66 TGATTATAAATATCAAACTATAAGAATTAGACTAATGCATAAATTATATCTGAGAATCAAATTCC
*
78587 TTTTTATAGAAAAAAAAAGACTGTAAGG
131 TTTTGATA-AAAAAAAAAGACTGTAAGG
* * *
78615 ATTAGACTAATACA-TAATTATATCTAAGAATCGAATTCCTTTTAGTAGAAAAAAAGAAAATTTG
1 ATTAGACTAATACATTAATTATATCTAAGAATCAAATTCCTTTTAATAG-AAAAAA-AAAAGTTG
* * * *
78679 ATTGATTATAAGTATCAGATTGCA-AAG-ATTAGACTAATGCATAAATTATATTTGAGAATCAAA
64 ATTGATTATAAATATCAAACT--ATAAGAATTAGACTAATGCATAAATTATATCTGAGAATCAAA
78742 TTCCTTTTGATAAAAAA
127 TTCCTTTTGATAAAAAA
78759 GCAGAAAAGT
Statistics
Matches: 127, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
157 31 0.24
158 25 0.20
159 67 0.53
160 3 0.02
161 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.34
Consensus pattern (157 bp):
ATTAGACTAATACATTAATTATATCTAAGAATCAAATTCCTTTTAATAGAAAAAAAAAAGTTGAT
TGATTATAAATATCAAACTATAAGAATTAGACTAATGCATAAATTATATCTGAGAATCAAATTCC
TTTTGATAAAAAAAAAAGACTGTAAGG
Found at i:78810 original size:92 final size:91
Alignment explanation
Indices: 78611--78811 Score: 237
Period size: 92 Copynumber: 2.2 Consensus size: 91
78601 AAAAGACTGT
* * *
78611 AAGGATTAGACTAATACATAATTATATCTAAGAATCGAATTCCTTTTAGTAGAAAAAAAGAAAAT
1 AAGGATTAGACTAATGCATAATTATATCTAAGAATCAAATTCCTTTTAGTAGAAAAAAAGAAAAG
*
78676 TTGATTGATTATAAGTATCAGATTGC
66 TTGATTGATTATAAATATCAGATTGC
* * * *
78702 AAAGATTAGACTAATGCATAAATTATATTTGAGAATCAAATTCCTTTT-GATA-AAAAAGCAGAA
1 AAGGATTAGACTAATGCAT-AATTATATCTAAGAATCAAATTCCTTTTAG-TAGAAAAA-AAGAA
* *
78765 AAGTTGATTGATTGTAAATATCACGGTTG-
63 AAGTTGATTGATTATAAATATCA-GATTGC
* *
78794 AAGGATGAGACAAATGCA
1 AAGGATTAGACTAATGCA
78812 GATATTTTGA
Statistics
Matches: 93, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
91 23 0.25
92 66 0.71
93 4 0.04
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (91 bp):
AAGGATTAGACTAATGCATAATTATATCTAAGAATCAAATTCCTTTTAGTAGAAAAAAAGAAAAG
TTGATTGATTATAAATATCAGATTGC
Found at i:79428 original size:163 final size:163
Alignment explanation
Indices: 79242--79564 Score: 646
Period size: 163 Copynumber: 2.0 Consensus size: 163
79232 GATGAGGATG
79242 ATGATGAAGCCATTAACCGGATTTGAAGATTTTCCTACAACAATAATTTTTATTTAAATTCATCA
1 ATGATGAAGCCATTAACCGGATTTGAAGATTTTCCTACAACAATAATTTTTATTTAAATTCATCA
79307 TTATGTAACATTTAAATAATTTTTAAAGTCAATCTCGGTTTAGCATTGAAAGCATGTGCGATGAA
66 TTATGTAACATTTAAATAATTTTTAAAGTCAATCTCGGTTTAGCATTGAAAGCATGTGCGATGAA
79372 AAAAGTGCAATAAAAACATATTAAAAAATTTTT
131 AAAAGTGCAATAAAAACATATTAAAAAATTTTT
79405 ATGATGAAGCCATTAACCGGATTTGAAGATTTTCCTACAACAATAATTTTTATTTAAATTCATCA
1 ATGATGAAGCCATTAACCGGATTTGAAGATTTTCCTACAACAATAATTTTTATTTAAATTCATCA
79470 TTATGTAACATTTAAATAATTTTTAAAGTCAATCTCGGTTTAGCATTGAAAGCATGTGCGATGAA
66 TTATGTAACATTTAAATAATTTTTAAAGTCAATCTCGGTTTAGCATTGAAAGCATGTGCGATGAA
79535 AAAAGTGCAATAAAAACATATTAAAAAATT
131 AAAAGTGCAATAAAAACATATTAAAAAATT
79565 AATAATATTA
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
163 160 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (163 bp):
ATGATGAAGCCATTAACCGGATTTGAAGATTTTCCTACAACAATAATTTTTATTTAAATTCATCA
TTATGTAACATTTAAATAATTTTTAAAGTCAATCTCGGTTTAGCATTGAAAGCATGTGCGATGAA
AAAAGTGCAATAAAAACATATTAAAAAATTTTT
Found at i:80829 original size:23 final size:23
Alignment explanation
Indices: 80782--80829 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
80772 ACCATGACCT
*
80782 TTTTTTTATTTTTTAATTTAAAA
1 TTTTTTTATTTTTTAATATAAAA
80805 TTTTTTTATTTTTTAA-ATAATAA
1 TTTTTTTATTTTTTAATATAA-AA
80828 TT
1 TT
80830 AATATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTTTTATTTTTTAATATAAAA
Found at i:81501 original size:3 final size:3
Alignment explanation
Indices: 81493--81538 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
81483 AATTTAAAAA
81493 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
81539 CAAAAAACCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:81593 original size:15 final size:15
Alignment explanation
Indices: 81573--81602 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
81563 AAAATAATAT
*
81573 TTTATTATTAAATTA
1 TTTATTATAAAATTA
81588 TTTATTATAAAATTA
1 TTTATTATAAAATTA
81603 AAATTATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTATTATAAAATTA
Found at i:81608 original size:21 final size:20
Alignment explanation
Indices: 81561--81621 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
81551 TTAATAACCG
* **
81561 TTAAAATAATA-TTTTATTA
1 TTAAAATTATATTTTTAAAA
81580 TT-AAATTAT-TTATTATAAAA
1 TTAAAATTATATT-TT-TAAAA
81600 TTAAAATTATATTTTTAAAA
1 TTAAAATTATATTTTTAAAA
81620 TT
1 TT
81622 TTTATTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
18 7 0.21
19 4 0.12
20 12 0.35
21 9 0.26
22 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAAAATTATATTTTTAAAA
Found at i:81996 original size:23 final size:23
Alignment explanation
Indices: 81952--82013 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
81942 ATCGTCAATT
*
81952 AATTCATTA-TTAAAAAAATAAA
1 AATTAATTATTTAAAAAAATAAA
* *
81974 AA-TATATTATTTAATAAATTAAA
1 AATTA-ATTATTTAAAAAAATAAA
81997 AATTAATTATTTAAAAA
1 AATTAATTATTTAAAAA
82014 CACACGCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
21 1 0.03
22 6 0.18
23 24 0.73
24 2 0.06
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
AATTAATTATTTAAAAAAATAAA
Found at i:83889 original size:16 final size:18
Alignment explanation
Indices: 83870--83905 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
83860 TAGTTGAATT
83870 AATAATTTTA-A-ATTAA
1 AATAATTTTAGATATTAA
83886 AATAATTTTAGATATTAA
1 AATAATTTTAGATATTAA
83904 AA
1 AA
83906 AAGTAGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 1 0.06
18 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
AATAATTTTAGATATTAA
Found at i:84791 original size:25 final size:24
Alignment explanation
Indices: 84731--84793 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
84721 ATCATCTTTT
* * *
84731 ATATATATTTATATATATTTAACA
1 ATATATATTTTTATATACTAAACA
* *
84755 ATAAAATTTTTTTATATACTAAACAA
1 AT-ATATATTTTTATATACTAAAC-A
84781 ATATATATTTTTA
1 ATATATATTTTTA
84794 ATTTACTTGG
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
24 2 0.07
25 25 0.83
26 3 0.10
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (24 bp):
ATATATATTTTTATATACTAAACA
Found at i:85193 original size:2 final size:2
Alignment explanation
Indices: 85186--85254 Score: 67
Period size: 2 Copynumber: 36.5 Consensus size: 2
85176 GTATGGTATC
*
85186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T CAT AT AT -T TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
* *
85227 AT GT -T AC AT -T AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
85255 AAATTTAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
1 5 0.09
2 51 0.89
3 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.52
Consensus pattern (2 bp):
AT
Found at i:85298 original size:21 final size:21
Alignment explanation
Indices: 85274--85317 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
85264 AAGATCAAGT
* *
85274 AAGATTAATAATTATTTTTAA
1 AAGATAAAAAATTATTTTTAA
85295 AAGATAAAAAATTATTTTTAA
1 AAGATAAAAAATTATTTTTAA
85316 AA
1 AA
85318 ATTTTAGGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (21 bp):
AAGATAAAAAATTATTTTTAA
Found at i:86330 original size:2 final size:2
Alignment explanation
Indices: 86323--86360 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
86313 CATTAATCAC
86323 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
86361 TATTAACGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86587 original size:30 final size:30
Alignment explanation
Indices: 86517--86587 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
86507 ACAATTATAC
*
86517 ATATGAATATAATATAAAAATAATTAAAAT
1 ATATGAATATAAAATAAAAATAATTAAAAT
86547 ATTATG-ATATAAAATAAAAA-AA-TAAACAT
1 A-TATGAATATAAAATAAAAATAATTAAA-AT
86576 GATATGAATATA
1 -ATATGAATATA
86588 TTAATATTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
28 4 0.11
29 8 0.22
30 20 0.56
31 4 0.11
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (30 bp):
ATATGAATATAAAATAAAAATAATTAAAAT
Found at i:86622 original size:32 final size:32
Alignment explanation
Indices: 86577--86653 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
86567 AATAAACATG
* **
86577 ATATGAATATATTAATATTTCAAAATCTATAT-A
1 ATATAAAT-TATTAATACATCAAAAT-TATATAA
86610 ATATAAATTATTAATACATCAAAATTATATAA
1 ATATAAATTATTAATACATCAAAATTATATAA
*
86642 ATATAAAATATT
1 ATATAAATTATT
86654 TTAAATATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
31 5 0.13
32 27 0.69
33 7 0.18
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.40
Consensus pattern (32 bp):
ATATAAATTATTAATACATCAAAATTATATAA
Found at i:88247 original size:20 final size:20
Alignment explanation
Indices: 88222--88285 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
88212 GAATTGAAGT
88222 GGGATACAAGAGAGGGATGA
1 GGGATACAAGAGAGGGATGA
88242 GGGATACAAGAGAGGGATGA
1 GGGATACAAGAGAGGGATGA
* ** *
88262 GAGATACTTGAGAGGGAAGA
1 GGGATACAAGAGAGGGATGA
88282 GGGA
1 GGGA
88286 GCCTCTATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.39, C:0.05, G:0.45, T:0.11
Consensus pattern (20 bp):
GGGATACAAGAGAGGGATGA
Found at i:88435 original size:24 final size:27
Alignment explanation
Indices: 88362--88432 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
88352 AAACAAGCCT
* *
88362 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
88390 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
*
88417 TCATTTTTGACAAACA
1 CCATTTTTGACAAACA
88433 AATTGGTGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:90854 original size:26 final size:26
Alignment explanation
Indices: 90802--90861 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
90792 GTCACCAATT
*
90802 TGTTTGTCAAAAATAGTGGTTATTTTG
1 TGTTTGTCAAAAATAGT-GTTACTTTG
90829 TGTTTGTCAAAATATAGT-TTACTTTG
1 TGTTTGTCAAAA-ATAGTGTTACTTTG
*
90855 TATTTGT
1 TGTTTGT
90862 TAAATATGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 13 0.43
27 12 0.40
28 5 0.17
ACGTcount: A:0.25, C:0.05, G:0.18, T:0.52
Consensus pattern (26 bp):
TGTTTGTCAAAAATAGTGTTACTTTG
Done.