Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_163
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: 151218
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:985 original size:30 final size:30
Alignment explanation
Indices: 951--1047 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
941 TAAACTAAAA
*
951 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
981 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
1011 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
1040 ATGAGCTA
1 -TGAGCTA
1048 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:1573 original size:21 final size:20
Alignment explanation
Indices: 1547--1586 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1537 CTCTTTAATA
1547 CCATACCATTTCATACCAATT
1 CCATACCA-TTCATACCAATT
*
1568 CCATACCATTCGTACCAAT
1 CCATACCATTCATACCAAT
1587 ACCCAAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.30
Consensus pattern (20 bp):
CCATACCATTCATACCAATT
Found at i:4652 original size:22 final size:21
Alignment explanation
Indices: 4611--4657 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
4601 TTTTATATAC
4611 TTCGATTTTTTTTTAATTTTTT
1 TTCGATTTTTTTTT-ATTTTTT
**
4633 TTCGATTTTTTAAT-TTTTTT
1 TTCGATTTTTTTTTATTTTTT
4653 TTCGA
1 TTCGA
4658 ATTTCCTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
22 12 0.52
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.72
Consensus pattern (21 bp):
TTCGATTTTTTTTTATTTTTT
Found at i:10425 original size:10 final size:10
Alignment explanation
Indices: 10410--10448 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
10400 ATATACTTCG
10410 ATTTTTTTTA
1 ATTTTTTTTA
*
10420 ATTTTTTTCA
1 ATTTTTTTTA
10430 ATTTTTTTTA
1 ATTTTTTTTA
10440 ATTTTTTTT
1 ATTTTTTTT
10449 TCGAATTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (10 bp):
ATTTTTTTTA
Found at i:10433 original size:20 final size:20
Alignment explanation
Indices: 10410--10447 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
10400 ATATACTTCG
10410 ATTTTTTTTAATTTTTTTCA
1 ATTTTTTTTAATTTTTTTCA
10430 ATTTTTTTTAATTTTTTT
1 ATTTTTTTTAATTTTTTT
10448 TTCGAATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (20 bp):
ATTTTTTTTAATTTTTTTCA
Found at i:16570 original size:19 final size:19
Alignment explanation
Indices: 16548--16585 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
16538 AACTAGCCAA
16548 GGACAACTCAAGAGTCATT
1 GGACAACTCAAGAGTCATT
16567 GGACAACTCAAGAGTCATT
1 GGACAACTCAAGAGTCATT
16586 TTCTAAGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (19 bp):
GGACAACTCAAGAGTCATT
Found at i:17301 original size:11 final size:11
Alignment explanation
Indices: 17287--17328 Score: 75
Period size: 11 Copynumber: 3.7 Consensus size: 11
17277 AAAAACTCGA
17287 AAAAAAAATTC
1 AAAAAAAATTC
17298 AAAAAAAAATTC
1 -AAAAAAAATTC
17310 AAAAAAAATTC
1 AAAAAAAATTC
17321 AAAAAAAA
1 AAAAAAAA
17329 AATTGGTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 19 0.63
12 11 0.37
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:17313 original size:23 final size:24
Alignment explanation
Indices: 17271--17329 Score: 93
Period size: 23 Copynumber: 2.5 Consensus size: 24
17261 TAGTAGTTTC
17271 TCAAAAAAAAACTCGAAAAAAAAAT
1 TCAAAAAAAAACTC-AAAAAAAAAT
*
17296 TCAAAAAAAAATTC-AAAAAAAAT
1 TCAAAAAAAAACTCAAAAAAAAAT
17319 TCAAAAAAAAA
1 TCAAAAAAAAA
17330 ATTGGTTTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 20 0.61
25 13 0.39
ACGTcount: A:0.75, C:0.10, G:0.02, T:0.14
Consensus pattern (24 bp):
TCAAAAAAAAACTCAAAAAAAAAT
Found at i:17332 original size:13 final size:12
Alignment explanation
Indices: 17271--17329 Score: 93
Period size: 12 Copynumber: 4.9 Consensus size: 12
17261 TAGTAGTTTC
*
17271 TCAAAAAAAAAC
1 TCAAAAAAAAAT
17283 TCGAAAAAAAAAT
1 TC-AAAAAAAAAT
17296 TCAAAAAAAAAT
1 TCAAAAAAAAAT
17308 TC-AAAAAAAAT
1 TCAAAAAAAAAT
17319 TCAAAAAAAAA
1 TCAAAAAAAAA
17330 ATTGGTTTCC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
11 11 0.25
12 22 0.50
13 11 0.25
ACGTcount: A:0.75, C:0.10, G:0.02, T:0.14
Consensus pattern (12 bp):
TCAAAAAAAAAT
Found at i:17686 original size:10 final size:10
Alignment explanation
Indices: 17671--17708 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
17661 GCTCGTTTCC
*
17671 AGCTCACTCG
1 AGCTCAATCG
17681 AGCTCAAGTC-
1 AGCTCAA-TCG
17691 AGCTCAATCG
1 AGCTCAATCG
17701 AGCTCAAT
1 AGCTCAAT
17709 TTAGCTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:17714 original size:20 final size:20
Alignment explanation
Indices: 17670--17707 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17660 AGCTCGTTTC
*
17670 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
17690 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
17708 TTTAGCTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:20175 original size:20 final size:20
Alignment explanation
Indices: 20146--20199 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
20136 GTTTTTTTTC
*
20146 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
20166 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
20186 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
20200 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:20181 original size:30 final size:30
Alignment explanation
Indices: 20146--20219 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
20136 GTTTTTTTTC
20146 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
20176 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
20206 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
20220 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:20209 original size:20 final size:20
Alignment explanation
Indices: 20146--20210 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
20136 GTTTTTTTTC
* * * *
20146 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
20166 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
20185 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
20206 AGCTC
1 AGCTC
20211 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:21828 original size:13 final size:14
Alignment explanation
Indices: 21810--21900 Score: 57
Period size: 13 Copynumber: 6.5 Consensus size: 14
21800 TTGGAGTAAC
21810 AAAAAAATC-AAAA
1 AAAAAAATCGAAAA
*
21823 AAAAAATTCGAAAA
1 AAAAAAATCGAAAA
* *
21837 AAAAATTTGATTGAAAA
1 AAAAA---AATCGAAAA
21854 AAAAAAATTC--AAA
1 AAAAAAA-TCGAAAA
*
21867 AAAAAAGT-G-AAA
1 AAAAAAATCGAAAA
*
21879 AAAAAAATCGAGCAA
1 AAAAAAATCGA-AAA
21894 AAAAAAA
1 AAAAAAA
21901 GGTGACAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
12 11 0.18
13 18 0.30
14 10 0.17
15 10 0.17
17 11 0.18
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (14 bp):
AAAAAAATCGAAAA
Found at i:21836 original size:14 final size:14
Alignment explanation
Indices: 21810--21900 Score: 61
Period size: 12 Copynumber: 6.5 Consensus size: 14
21800 TTGGAGTAAC
21810 AAAAAAA-TC-AAA
1 AAAAAAATTCGAAA
21822 AAAAAAATTCGAAA
1 AAAAAAATTCGAAA
21836 AAAAAATTTGATT-GAAAA
1 AAAAAA----ATTCG-AAA
21854 AAAAAAATTC--AA
1 AAAAAAATTCGAAA
*
21866 AAAAAAAGT-GAAA
1 AAAAAAATTCGAAA
21879 AAAAAAA-TCGAGCAA
1 AAAAAAATTCGA--AA
21894 AAAAAAA
1 AAAAAAA
21901 GGTGACAAAA
Statistics
Matches: 65, Mismatches: 1, Indels: 23
0.73 0.01 0.26
Matches are distributed among these distances:
12 18 0.28
13 13 0.20
14 12 0.18
15 9 0.14
17 1 0.02
18 12 0.18
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (14 bp):
AAAAAAATTCGAAA
Found at i:21927 original size:30 final size:29
Alignment explanation
Indices: 21863--21937 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 29
21853 AAAAAAAATT
*
21863 CAAAAAAAAA-GTGAAAAAAAAAATCGAG
1 CAAAAAAAAAGGTGAAAAAAAAAATCAAG
21891 CAAAAAAAAAGGTGACAAAAAAAAATCAAG
1 CAAAAAAAAAGGTGA-AAAAAAAAATCAAG
**
21921 TTAAAAAAAA-GTGAAAA
1 CAAAAAAAAAGGTGAAAA
21938 GTCTTGCGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 13 0.31
29 8 0.19
30 21 0.50
ACGTcount: A:0.71, C:0.07, G:0.13, T:0.09
Consensus pattern (29 bp):
CAAAAAAAAAGGTGAAAAAAAAAATCAAG
Found at i:22878 original size:15 final size:16
Alignment explanation
Indices: 22858--22889 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
22848 AGAAAATGAA
22858 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
22873 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
22889 A
1 A
22890 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:23004 original size:17 final size:18
Alignment explanation
Indices: 22972--23005 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22962 AAAAGAGAGT
*
22972 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
22990 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
23006 GGAGTATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:24301 original size:20 final size:20
Alignment explanation
Indices: 24272--24325 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
24262 GTTTTTTTCC
*
24272 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
24292 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
24312 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
24326 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:24307 original size:30 final size:30
Alignment explanation
Indices: 24272--24345 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
24262 GTTTTTTTCC
24272 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
24302 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
24332 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
24346 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:24335 original size:20 final size:20
Alignment explanation
Indices: 24272--24336 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
24262 GTTTTTTTCC
* * * *
24272 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
24292 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
24311 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
24332 AGCTC
1 AGCTC
24337 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:29955 original size:19 final size:19
Alignment explanation
Indices: 29933--29970 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
29923 AACTAGCCAA
29933 GGACAACTCAAGAGTCATT
1 GGACAACTCAAGAGTCATT
29952 GGACAACTCAAGAGTCATT
1 GGACAACTCAAGAGTCATT
29971 TTCTAAGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (19 bp):
GGACAACTCAAGAGTCATT
Found at i:38122 original size:14 final size:14
Alignment explanation
Indices: 38101--38138 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
38091 AGTCAAAATC
38101 AAAA-AAAAAATTG
1 AAAAGAAAAAATTG
*
38114 AAAGGAAAAAATTG
1 AAAAGAAAAAATTG
38128 AAAAGAAAAAA
1 AAAAGAAAAAA
38139 AAATTGCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 3 0.14
14 19 0.86
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (14 bp):
AAAAGAAAAAATTG
Found at i:38122 original size:15 final size:15
Alignment explanation
Indices: 38104--38139 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
38094 CAAAATCAAA
38104 AAAAAAATTG-AAAG
1 AAAAAAATTGAAAAG
*
38118 GAAAAAATTGAAAAG
1 AAAAAAATTGAAAAG
38133 AAAAAAA
1 AAAAAAA
38140 AATTGCATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (15 bp):
AAAAAAATTGAAAAG
Found at i:48829 original size:21 final size:23
Alignment explanation
Indices: 48784--48830 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
48774 TCACCTGCAA
* *
48784 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
48807 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
48828 TAA
1 TAA
48831 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:61506 original size:22 final size:22
Alignment explanation
Indices: 61478--61521 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
61468 TTTTGAACCA
61478 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
61500 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
61522 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:62174 original size:15 final size:15
Alignment explanation
Indices: 62138--62195 Score: 89
Period size: 15 Copynumber: 3.7 Consensus size: 15
62128 ACTAGCTTTT
62138 TTTTCTTTTTCACGAAA
1 TTTT-TTTTTCACG-AA
*
62155 ATTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
62170 TTTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
62185 TTTTTTTTTCA
1 TTTTTTTTTCA
62196 ACTTGATATC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
15 27 0.69
16 9 0.23
17 3 0.08
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (15 bp):
TTTTTTTTTCACGAA
Found at i:62275 original size:12 final size:13
Alignment explanation
Indices: 62238--62272 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
62228 AACCAAAAAT
62238 TTTTTTTTTTGAA
1 TTTTTTTTTTGAA
62251 TTTTTTTTTTGAA
1 TTTTTTTTTTGAA
62264 TTTTTTTTT
1 TTTTTTTTT
62273 GAAGAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.11, C:0.00, G:0.06, T:0.83
Consensus pattern (13 bp):
TTTTTTTTTTGAA
Found at i:63310 original size:21 final size:23
Alignment explanation
Indices: 63265--63311 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
63255 TCACCTGCAA
* *
63265 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
63288 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
63309 TAA
1 TAA
63312 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:70501 original size:21 final size:23
Alignment explanation
Indices: 70456--70502 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
70446 TCACCTGCAA
* *
70456 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
70479 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
70500 TAA
1 TAA
70503 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:71595 original size:16 final size:15
Alignment explanation
Indices: 71574--71630 Score: 96
Period size: 16 Copynumber: 3.7 Consensus size: 15
71564 TAGCTTCTTC
71574 TTTTTTTTCACGAAAT
1 TTTTTTTTCACG-AAT
71590 TTTTTTTTCACGAAT
1 TTTTTTTTCACGAAT
71605 TTTCTTTTTCACGAAT
1 TTT-TTTTTCACGAAT
71621 TTTTTTTTCA
1 TTTTTTTTCA
71631 ACTTGCTATC
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
15 13 0.32
16 27 0.68
ACGTcount: A:0.19, C:0.14, G:0.05, T:0.61
Consensus pattern (15 bp):
TTTTTTTTCACGAAT
Found at i:72743 original size:21 final size:23
Alignment explanation
Indices: 72698--72744 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
72688 TCACCTGCAA
* *
72698 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
72721 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
72742 TAA
1 TAA
72745 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:73837 original size:16 final size:15
Alignment explanation
Indices: 73816--73869 Score: 90
Period size: 16 Copynumber: 3.5 Consensus size: 15
73806 TAGCTTCTTC
73816 TTTTTTTTCACGAAAT
1 TTTTTTTTCACG-AAT
73832 TTTTTTTTCACGAAT
1 TTTTTTTTCACGAAT
73847 TTTCTTTTTCACGAAT
1 TTT-TTTTTCACGAAT
73863 TTTTTTT
1 TTTTTTT
73870 CAACTTGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
15 10 0.27
16 27 0.73
ACGTcount: A:0.19, C:0.13, G:0.06, T:0.63
Consensus pattern (15 bp):
TTTTTTTTCACGAAT
Found at i:74986 original size:21 final size:23
Alignment explanation
Indices: 74941--74987 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
74931 TCACCTGCAA
* *
74941 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
74964 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
74985 TAA
1 TAA
74988 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:77146 original size:20 final size:20
Alignment explanation
Indices: 77121--77165 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
77111 GCGAAAATAC
*
77121 AAAAGAAAAGAAAAATGAAA
1 AAAAGAAAAGAAAAATCAAA
*
77141 AAAAG-AAAGAAAATTCAAA
1 AAAAGAAAAGAAAAATCAAA
77160 AAAAGA
1 AAAAGA
77166 GAATGAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATCAAA
Found at i:82146 original size:61 final size:61
Alignment explanation
Indices: 82061--82182 Score: 226
Period size: 61 Copynumber: 2.0 Consensus size: 61
82051 GCTGCAGGTA
*
82061 TGATGTGAGCTTGCCTACGAACCAAATGGAGAACGAACAAGAAGCCATTAAGCTGCCCATT
1 TGATGTGAGCTTGCCTACGAACCAAATGGAGAACGAACAAGAAGCCATCAAGCTGCCCATT
*
82122 TGATGTGAGCTTGCCTACGAACCAAATGGAGAATGAACAAGAAGCCATCAAGCTGCCCATT
1 TGATGTGAGCTTGCCTACGAACCAAATGGAGAACGAACAAGAAGCCATCAAGCTGCCCATT
82183 GGTCCAATAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (61 bp):
TGATGTGAGCTTGCCTACGAACCAAATGGAGAACGAACAAGAAGCCATCAAGCTGCCCATT
Found at i:83832 original size:11 final size:12
Alignment explanation
Indices: 83816--83855 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
83806 ATTGTAGATT
83816 AAAAAATCGAAA
1 AAAAAATCGAAA
83828 AAAAAATCGAAA
1 AAAAAATCGAAA
*
83840 AAAAAATTGAAA
1 AAAAAATCGAAA
83852 AAAA
1 AAAA
83856 TTTGAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.78, C:0.05, G:0.07, T:0.10
Consensus pattern (12 bp):
AAAAAATCGAAA
Found at i:83860 original size:11 final size:11
Alignment explanation
Indices: 83816--83870 Score: 65
Period size: 11 Copynumber: 4.8 Consensus size: 11
83806 ATTGTAGATT
*
83816 AAAAAATCGAAA
1 AAAAAATTG-AA
*
83828 AAAAAATCGAAA
1 AAAAAATTG-AA
83840 AAAAAATTGAA
1 AAAAAATTGAA
*
83851 AAAAATTTGAA
1 AAAAAATTGAA
83862 AAAAAATTG
1 AAAAAATTG
83871 CATACGGTCT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
11 20 0.50
12 20 0.50
ACGTcount: A:0.71, C:0.04, G:0.09, T:0.16
Consensus pattern (11 bp):
AAAAAATTGAA
Found at i:83869 original size:12 final size:12
Alignment explanation
Indices: 83816--83867 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
83806 ATTGTAGATT
*
83816 AAAAAATCGAAA
1 AAAAAATTGAAA
*
83828 AAAAAATCGAAA
1 AAAAAATTGAAA
83840 AAAAAATTG-AA
1 AAAAAATTGAAA
*
83851 AAAAATTTGAAA
1 AAAAAATTGAAA
83863 AAAAA
1 AAAAA
83868 TTGCATACGG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
11 10 0.27
12 27 0.73
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.13
Consensus pattern (12 bp):
AAAAAATTGAAA
Found at i:93680 original size:9 final size:9
Alignment explanation
Indices: 93666--93690 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
93656 AGTTTTCGAA
93666 AAAAAAATC
1 AAAAAAATC
93675 AAAAAAATC
1 AAAAAAATC
93684 AAAAAAA
1 AAAAAAA
93691 AATTGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAATC
Found at i:94249 original size:30 final size:30
Alignment explanation
Indices: 94215--94311 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
94205 AGCTCACTCC
94215 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
94245 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
94275 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
94305 TAGCTCA
1 TAGCTCA
94312 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:104743 original size:20 final size:19
Alignment explanation
Indices: 104720--104784 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
104710 AAGCTCAAAC
104720 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
104740 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
104760 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
104780 GAGCT
1 GAGCT
104785 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:106072 original size:17 final size:18
Alignment explanation
Indices: 106050--106083 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
106040 ACAACACTCC
*
106050 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
106067 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
106084 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:107162 original size:16 final size:16
Alignment explanation
Indices: 107124--107166 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
107114 TTTTTAACTT
*
107124 GATTTTTTTTTTGGTC
1 GATTTTTTTTTTGCTC
*
107140 -ACCTTTTTTTTTGCTC
1 GA-TTTTTTTTTTGCTC
107156 GATTTTTTTTT
1 GATTTTTTTTT
107167 CACTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.07, C:0.12, G:0.12, T:0.70
Consensus pattern (16 bp):
GATTTTTTTTTTGCTC
Found at i:107173 original size:26 final size:26
Alignment explanation
Indices: 107144--107194 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
107134 TTGGTCACCT
107144 TTTTTTTTGCTCG-ATTTTTTTTTCAC
1 TTTTTTTT-CTCGAATTTTTTTTTCAC
* *
107170 TTTTTTTTTTTGAATTTTTTTTTCA
1 TTTTTTTTCTCGAATTTTTTTTTCA
107195 ATCAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.10, C:0.10, G:0.06, T:0.75
Consensus pattern (26 bp):
TTTTTTTTCTCGAATTTTTTTTTCAC
Found at i:107216 original size:15 final size:14
Alignment explanation
Indices: 107158--107218 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 14
107148 TTTTGCTCGA
*
107158 TTTTTTTTTC-ACT
1 TTTTTTTTTCGAAT
*
107171 TTTTTTTTTTGAAT
1 TTTTTTTTTCGAAT
107185 TTTTTTTTCAATC-AAT
1 TTTTTTTT---TCGAAT
107201 TTTTTTTTTCGAAAT
1 TTTTTTTTTCG-AAT
107216 TTT
1 TTT
107219 CTTATTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 11 0.28
14 10 0.26
15 6 0.15
16 11 0.28
17 1 0.03
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.72
Consensus pattern (14 bp):
TTTTTTTTTCGAAT
Found at i:108852 original size:20 final size:19
Alignment explanation
Indices: 108829--108893 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
108819 AAGCTCAAAC
108829 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
108849 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
108869 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
108889 GAGCT
1 GAGCT
108894 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:109565 original size:16 final size:17
Alignment explanation
Indices: 109546--109584 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
109536 AAAAAAAGTG
* *
109546 AAAAAAAA-TTGAGCAA
1 AAAAAAAAGGTGACCAA
109562 AAAAAAAAGGTGACCAA
1 AAAAAAAAGGTGACCAA
109579 AAAAAA
1 AAAAAA
109585 TCAAGTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.72, C:0.08, G:0.13, T:0.08
Consensus pattern (17 bp):
AAAAAAAAGGTGACCAA
Found at i:110490 original size:12 final size:13
Alignment explanation
Indices: 110454--110495 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
110444 AATAGTGAGT
*
110454 GAAAAGAAAATGAA
1 GAAAAGAAATTG-A
110468 GAAAAGAAAATTGA
1 GAAAAG-AAATTGA
110482 -AAAAGAAATTGA
1 GAAAAGAAATTGA
110494 GA
1 GA
110496 TTGAGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 7 0.28
13 6 0.24
14 7 0.28
15 5 0.20
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (13 bp):
GAAAAGAAATTGA
Found at i:110498 original size:18 final size:18
Alignment explanation
Indices: 110477--110511 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
110467 AGAAAAGAAA
110477 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
110495 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
110512 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:115322 original size:30 final size:30
Alignment explanation
Indices: 115287--115350 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
115277 AGCTTGATTT
115287 AGCTCACA-TGAGCTTAATTTAGCTCGTTTG
1 AGCTCA-ATTGAGCTTAATTTAGCTCGTTTG
* *
115317 AGCTCAATTTAGCTTACTTTAGCTCGTTTG
1 AGCTCAATTGAGCTTAATTTAGCTCGTTTG
115347 AGCT
1 AGCT
115351 TGGTTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCAATTGAGCTTAATTTAGCTCGTTTG
Found at i:122547 original size:12 final size:12
Alignment explanation
Indices: 122530--122558 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
122520 CTCACTCTCT
122530 TTTTCAATTTTC
1 TTTTCAATTTTC
122542 TTTTCAATTTTC
1 TTTTCAATTTTC
122554 TTTTC
1 TTTTC
122559 TATCTCACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTCAATTTTC
Found at i:123509 original size:17 final size:16
Alignment explanation
Indices: 123490--123521 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
123480 TGTCATGGCT
123490 TTTTTTTTAATTTCGA
1 TTTTTTTTAATTTCGA
123506 TTTTTTTTAATTTCGA
1 TTTTTTTTAATTTCGA
123522 ATATTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTTTTTTAATTTCGA
Found at i:123528 original size:17 final size:16
Alignment explanation
Indices: 123492--123529 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
123482 TCATGGCTTT
*
123492 TTTTTTAATTTCGATT
1 TTTTTTAATTTCGATA
123508 TTTTTTAATTTCGAATA
1 TTTTTTAATTTCG-ATA
123525 TTTTT
1 TTTTT
123530 CTTCTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (16 bp):
TTTTTTAATTTCGATA
Found at i:123618 original size:11 final size:11
Alignment explanation
Indices: 123604--123647 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 11
123594 ATTTGAATAC
123604 AATTTTTTTTG
1 AATTTTTTTTG
123615 AA-TTTTTTTG
1 AATTTTTTTTG
123625 AATTATTTTTTTTG
1 -A--ATTTTTTTTG
123639 AATTTTTTT
1 AATTTTTTT
123648 CCTTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 8 0.28
11 11 0.38
13 2 0.07
14 8 0.28
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:123634 original size:14 final size:13
Alignment explanation
Indices: 123606--123647 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 13
123596 TTGAATACAA
123606 TTTTTTTTGAA--
1 TTTTTTTTGAATT
123617 -TTTTTTTGAATT
1 TTTTTTTTGAATT
123629 ATTTTTTTTGAATT
1 -TTTTTTTTGAATT
123643 TTTTT
1 TTTTT
123648 CCTTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.37
13 5 0.19
14 12 0.44
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:129217 original size:9 final size:9
Alignment explanation
Indices: 129203--129237 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
129193 CGGTATTGTA
129203 AAAAAAAGG
1 AAAAAAAGG
**
129212 AAAAAAAAT
1 AAAAAAAGG
129221 AAAAAAAGG
1 AAAAAAAGG
129230 AAAAAAAG
1 AAAAAAAG
129238 AAGTGACAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (9 bp):
AAAAAAAGG
Found at i:130293 original size:6 final size:6
Alignment explanation
Indices: 130265--130404 Score: 64
Period size: 6 Copynumber: 22.3 Consensus size: 6
130255 CCATTGAGCG
* * * * * * *
130265 AGAAAA GGAAAA AGAGAT TGAAAA AGAAAT TGAAAGA AAACAAA AAGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAA-A AGA-AAA A-GAAAA
* * * * * * ** *
130316 CGAAAA AGAAAA AGAAAT TGCAAA AGAAAA AGAAAT CGAAAA AGTGAG
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
* *
130364 AGAAAA AGAAAA TGAAGAAA AGAAAA TTGAAAA AGAAAA AG
1 AGAAAA AGAAAA AG-A-AAA AGAAAA -AGAAAA AGAAAA AG
130405 CGAAAAAAGA
Statistics
Matches: 92, Mismatches: 36, Indels: 12
0.66 0.26 0.09
Matches are distributed among these distances:
6 72 0.78
7 13 0.14
8 7 0.08
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.08
Consensus pattern (6 bp):
AGAAAA
Found at i:130293 original size:18 final size:18
Alignment explanation
Indices: 130266--130359 Score: 86
Period size: 18 Copynumber: 5.4 Consensus size: 18
130256 CATTGAGCGA
* * *
130266 GAAAAGGAAAAAGAGATT
1 GAAAAAGAAAAAGAAATC
**
130284 GAAAAAGAAATTGAAA--
1 GAAAAAGAAAAAGAAATC
* *
130300 G-AAAACAAAAAGAAAAC
1 GAAAAAGAAAAAGAAATC
*
130317 GAAAAAGAAAAAGAAATT
1 GAAAAAGAAAAAGAAATC
*
130335 GCAAAAGAAAAAGAAATC
1 GAAAAAGAAAAAGAAATC
130353 GAAAAAG
1 GAAAAAG
130360 TGAGAGAAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
15 11 0.18
16 1 0.02
17 1 0.02
18 47 0.78
ACGTcount: A:0.69, C:0.04, G:0.19, T:0.07
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAATC
Found at i:130313 original size:11 final size:12
Alignment explanation
Indices: 130297--130416 Score: 75
Period size: 12 Copynumber: 9.6 Consensus size: 12
130287 AAAGAAATTG
130297 AAAGAAAAC-AA
1 AAAGAAAACGAA
130308 AAAGAAAACGAA
1 AAAGAAAACGAA
*
130320 AAAGAAAAAGAA
1 AAAGAAAACGAA
**
130332 ATTGCAAAA-GAA
1 AAAG-AAAACGAA
*
130344 AAAGAAATCGAA
1 AAAGAAAACGAA
* *
130356 AAAGTGAGA-GAA
1 AAAG-AAAACGAA
*
130368 AAAGAAAATGAAGA
1 AAAGAAAACG-A-A
*
130382 AAAGAAAATTGAA
1 AAAGAAAA-CGAA
130395 AAAGAAAAAGCGAAA
1 AAAG-AAAA-CG-AA
130410 AAAGAAA
1 AAAGAAA
130417 TTGAAAGAGA
Statistics
Matches: 86, Mismatches: 13, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
11 14 0.16
12 35 0.41
13 11 0.13
14 18 0.21
15 8 0.09
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:130386 original size:14 final size:13
Alignment explanation
Indices: 130365--130402 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
130355 AAAAGTGAGA
130365 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
130377 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
130392 GAAAAAGAAAA
1 GAAAAAGAAAA
130403 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:130416 original size:21 final size:21
Alignment explanation
Indices: 130366--130416 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
130356 AAAGTGAGAG
*
130366 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
130387 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
130408 AAAAAGAAA
1 AAAAAGAAA
130417 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:130456 original size:33 final size:33
Alignment explanation
Indices: 130419--130481 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
130409 AAAAGAAATT
130419 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
130452 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
130482 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:139107 original size:23 final size:23
Alignment explanation
Indices: 139076--139160 Score: 136
Period size: 23 Copynumber: 3.7 Consensus size: 23
139066 CACCTTTAAA
* *
139076 ACATGCATTAAATTTGGCCAGAA-
1 ACATACATTAAATTCGGCCA-AAG
139099 ACATACATTAAATTCGGCCAAAG
1 ACATACATTAAATTCGGCCAAAG
139122 ACATACATTAAATTCGGCCAAAG
1 ACATACATTAAATTCGGCCAAAG
139145 ACATACATTAAATTCG
1 ACATACATTAAATTCG
139161 TCAGGAAAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
22 2 0.03
23 57 0.97
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (23 bp):
ACATACATTAAATTCGGCCAAAG
Found at i:139402 original size:13 final size:13
Alignment explanation
Indices: 139386--139420 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
139376 TTTAAACAAA
139386 TTAATTAACTTAT
1 TTAATTAACTTAT
139399 TTAATTAACTTAT
1 TTAATTAACTTAT
*
139412 TTAACTAAC
1 TTAATTAAC
139421 AGCAACTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (13 bp):
TTAATTAACTTAT
Found at i:142157 original size:13 final size:12
Alignment explanation
Indices: 142139--142170 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
142129 ATAGGTACGT
142139 AAAAAAATTGAA
1 AAAAAAATTGAA
142151 AAAAAAATTGAA
1 AAAAAAATTGAA
142163 AAGAAAAA
1 AA-AAAAA
142171 AAAATTGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:142984 original size:15 final size:15
Alignment explanation
Indices: 142952--142985 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
142942 GTTCAACGAA
*
142952 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
142967 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
142982 GAGG
1 GAGG
142986 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:148017 original size:24 final size:25
Alignment explanation
Indices: 147964--148017 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
147954 AACAAATTCT
* *
147964 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
147989 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
148012 TTTTTT
1 TTTTTT
148018 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:150220 original size:13 final size:12
Alignment explanation
Indices: 150188--150219 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
150178 GATTTCGGAA
150188 AAATTTTTGTTG
1 AAATTTTTGTTG
150200 AAATTTTTGTTG
1 AAATTTTTGTTG
150212 AAATTTTT
1 AAATTTTT
150220 TTTACGGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.59
Consensus pattern (12 bp):
AAATTTTTGTTG
Found at i:150286 original size:12 final size:13
Alignment explanation
Indices: 150263--150288 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
150253 CTAGACCGTA
150263 TGCAATTTTTTTT
1 TGCAATTTTTTTT
150276 TGCAATTTTTTTT
1 TGCAATTTTTTTT
150289 CCTTCTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (13 bp):
TGCAATTTTTTTT
Done.