Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 131 of 173
Found at i:40006590 original size:37 final size:37
Alignment explanation
Indices: 40006523--40006606 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 37
40006513 TATATCGGTA
* *
40006523 TTTTATTTTTCAATTTAGAAATGTAGTTGTGAGGTCC
1 TTTTATTTTTCAATTTAGAAATGTAATTGTGAGCTCC
**
40006560 TTTTATTTTTCAATTTAGAGGCT-TAATTGTGAGCTCC
1 TTTTATTTTTCAATTTAGA-AATGTAATTGTGAGCTCC
*
40006597 CTTTATTTTT
1 TTTTATTTTT
40006607 TTTTGTTCAG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
37 40 0.98
38 1 0.02
ACGTcount: A:0.21, C:0.11, G:0.15, T:0.52
Consensus pattern (37 bp):
TTTTATTTTTCAATTTAGAAATGTAATTGTGAGCTCC
Found at i:40007133 original size:18 final size:20
Alignment explanation
Indices: 40007112--40007155 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 20
40007102 TTTTTAAATA
40007112 AAATTAAGTTTT-ATT-TTT
1 AAATTAAGTTTTGATTATTT
*
40007130 AAATTAATTTTTGATTAATTT
1 AAATTAAGTTTTGATT-ATTT
40007151 AAATT
1 AAATT
40007156 CAAATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 11 0.50
19 3 0.14
21 8 0.36
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
AAATTAAGTTTTGATTATTT
Found at i:40008062 original size:3 final size:3
Alignment explanation
Indices: 40008054--40008086 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
40008044 TTGTAACCTT
40008054 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40008087 ACATATCAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:40009005 original size:3 final size:3
Alignment explanation
Indices: 40008997--40009028 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
40008987 GATACGTTAA
40008997 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40009029 AAGCTTACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:40009821 original size:5 final size:5
Alignment explanation
Indices: 40009807--40009851 Score: 83
Period size: 5 Copynumber: 9.2 Consensus size: 5
40009797 GAAATCTGAG
40009807 TATA- TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT T
40009852 GAATATTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.10
5 36 0.90
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:40009891 original size:15 final size:14
Alignment explanation
Indices: 40009871--40009900 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
40009861 TATTTATTTT
40009871 TATTACATATTAATA
1 TATTACATA-TAATA
40009886 TATTACATATAATA
1 TATTACATATAATA
40009900 T
1 T
40009901 TCATACTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (14 bp):
TATTACATATAATA
Found at i:40010615 original size:69 final size:69
Alignment explanation
Indices: 40010504--40010643 Score: 205
Period size: 69 Copynumber: 2.0 Consensus size: 69
40010494 GGACTTTTAA
*
40010504 TAATCACCTTTTGGTGTTCTACGAGCTGTAGGTAGGGGAAGATTC-AGTTAAGGTACCATTAAGG
1 TAATCACCTTTTGGTGTTCTACGAGCTGCAGGTAGGGGAAGATTCGA-TTAAGGTACCATTAAGG
*
40010568 TTCTT
65 TTATT
*
40010573 TAATCACCTTTTGGTGTTCCATA-G-GCTGCAGGTAGGGGAAGATTCGATTAATGTACCATTAAG
1 TAATCACCTTTTGGTGTT-C-TACGAGCTGCAGGTAGGGGAAGATTCGATTAAGGTACCATTAAG
40010636 GTTATT
64 GTTATT
40010642 TA
1 TA
40010644 CTTTTTGGGT
Statistics
Matches: 65, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
69 60 0.92
70 3 0.05
71 2 0.03
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (69 bp):
TAATCACCTTTTGGTGTTCTACGAGCTGCAGGTAGGGGAAGATTCGATTAAGGTACCATTAAGGT
TATT
Found at i:40013037 original size:21 final size:20
Alignment explanation
Indices: 40012999--40013039 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
40012989 CTTAAATTTG
40012999 TTTGTTTAGAATTCTTTAAT
1 TTTGTTTAGAATTCTTTAAT
40013019 TTTGTCTTAGGAATT-TTTAAT
1 TTTGT-TTA-GAATTCTTTAAT
40013040 CGGAGTAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.24, C:0.05, G:0.12, T:0.59
Consensus pattern (20 bp):
TTTGTTTAGAATTCTTTAAT
Found at i:40015874 original size:16 final size:17
Alignment explanation
Indices: 40015852--40015893 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
40015842 ATCTAGTAAA
40015852 ATATTTTTATAAATTTT
1 ATATTTTTATAAATTTT
*
40015869 -TATTTTT-TTAATTTT
1 ATATTTTTATAAATTTT
40015884 ATATATTTTA
1 ATAT-TTTTA
40015894 AAAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
15 7 0.33
16 10 0.48
17 4 0.19
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATATTTTTATAAATTTT
Found at i:40016121 original size:24 final size:24
Alignment explanation
Indices: 40016093--40016148 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
40016083 ATAATGTCAC
40016093 ATGCCACAATGATATTGGTTGTGA
1 ATGCCACAATGATATTGGTTGTGA
*
40016117 ATGCCACTATGATATTGGTTGTGA
1 ATGCCACAATGATATTGGTTGTGA
40016141 ATGCCACA
1 ATGCCACA
40016149 TTAGTGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (24 bp):
ATGCCACAATGATATTGGTTGTGA
Found at i:40030419 original size:96 final size:96
Alignment explanation
Indices: 40030300--40030500 Score: 393
Period size: 96 Copynumber: 2.1 Consensus size: 96
40030290 CTTAAGAAGG
40030300 CCTTATATGGATTGAAACAGGTTTTGCAAGCTTGGTATGTGAGGATAGATGAGCACTTCACAAGT
1 CCTTATATGGATTGAAACAGGTTTTGCAAGCTTGGTATGTGAGGATAGATGAGCACTTCACAAGT
40030365 TTGAGATTTGAAAAGAGTCCTAACGAACCTA
66 TTGAGATTTGAAAAGAGTCCTAACGAACCTA
40030396 CCTTATATGGATTGAAACAGGTTTTGCAAGCTTGGTATGTGAGGATAGATGAGCACTTCACAAGT
1 CCTTATATGGATTGAAACAGGTTTTGCAAGCTTGGTATGTGAGGATAGATGAGCACTTCACAAGT
40030461 TTGAGATTTGAAAAGAGTCCTAACGAACCTA
66 TTGAGATTTGAAAAGAGTCCTAACGAACCTA
*
40030492 CCTTGTATG
1 CCTTATATG
40030501 TAAAGAAGAA
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 104 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (96 bp):
CCTTATATGGATTGAAACAGGTTTTGCAAGCTTGGTATGTGAGGATAGATGAGCACTTCACAAGT
TTGAGATTTGAAAAGAGTCCTAACGAACCTA
Found at i:40031571 original size:18 final size:17
Alignment explanation
Indices: 40031550--40031611 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
40031540 CTCGCCAAGT
40031550 TTGGCGAATCCCCTAAG
1 TTGGCGAATCCCCTAAG
* **
40031567 ATTGGTGAACTTGCC-AAG
1 -TTGGCGAA-TCCCCTAAG
40031585 TCTGGCGAATCCCCTAAG
1 T-TGGCGAATCCCCTAAG
40031603 CTTGGCGAA
1 -TTGGCGAA
40031612 CTCATGATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
17 4 0.12
18 26 0.76
19 4 0.12
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (17 bp):
TTGGCGAATCCCCTAAG
Found at i:40031591 original size:36 final size:36
Alignment explanation
Indices: 40031532--40031613 Score: 119
Period size: 36 Copynumber: 2.3 Consensus size: 36
40031522 TCATGCACAT
* * *
40031532 TTGGCGGACTCGCCAAGTTTGGCGAATCCCCTAAGA
1 TTGGCGAACTTGCCAAGTCTGGCGAATCCCCTAAGA
* *
40031568 TTGGTGAACTTGCCAAGTCTGGCGAATCCCCTAAGC
1 TTGGCGAACTTGCCAAGTCTGGCGAATCCCCTAAGA
40031604 TTGGCGAACT
1 TTGGCGAACT
40031614 CATGATAAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (36 bp):
TTGGCGAACTTGCCAAGTCTGGCGAATCCCCTAAGA
Found at i:40031801 original size:24 final size:24
Alignment explanation
Indices: 40031755--40031807 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
40031745 ATAGAATTAG
**
40031755 TATTTACTAGCATAGTATATTTGA
1 TATTTACTAGCATAAAATATTTGA
* * *
40031779 TATTTATTAGCATAAAATCTTTGT
1 TATTTACTAGCATAAAATATTTGA
40031803 TATTT
1 TATTT
40031808 CTTTCTGTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (24 bp):
TATTTACTAGCATAAAATATTTGA
Found at i:40044234 original size:103 final size:103
Alignment explanation
Indices: 40044075--40044277 Score: 379
Period size: 103 Copynumber: 2.0 Consensus size: 103
40044065 GGAAAATCTT
40044075 GTAATCTTGAGTAAACCTATGTTTACAAAGTGATTTTTGATTCAGTCTAACCTAATTAGAAGGTA
1 GTAATCTTGAGTAAACCTATGTTTACAAAGTGATTTTTGATTCAGTCTAACCTAATTAGAAGGTA
*
40044140 TTTCACTTCAATTTGATTATTCATAACCGAATTTTCTC
66 TTTCACTTCAATTTGATGATTCATAACCGAATTTTCTC
*
40044178 GTAATCTTGAGTAAACCTGTGTTTACAAAGTGATTTTTGATTCAGTCTAACCTAATTAGAAGGTA
1 GTAATCTTGAGTAAACCTATGTTTACAAAGTGATTTTTGATTCAGTCTAACCTAATTAGAAGGTA
*
40044243 TTTCACTTCAATTTGATGGTTCATAACCGAATTTT
66 TTTCACTTCAATTTGATGATTCATAACCGAATTTT
40044278 TAAGAATCAC
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 97 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (103 bp):
GTAATCTTGAGTAAACCTATGTTTACAAAGTGATTTTTGATTCAGTCTAACCTAATTAGAAGGTA
TTTCACTTCAATTTGATGATTCATAACCGAATTTTCTC
Found at i:40049039 original size:16 final size:16
Alignment explanation
Indices: 40049018--40049051 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
40049008 ATGTTTTTCC
40049018 TCCCTCTCCTTGTTGA
1 TCCCTCTCCTTGTTGA
40049034 TCCCTCTCCTTGTTGA
1 TCCCTCTCCTTGTTGA
40049050 TC
1 TC
40049052 AAAATTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.38, G:0.12, T:0.44
Consensus pattern (16 bp):
TCCCTCTCCTTGTTGA
Found at i:40053278 original size:28 final size:29
Alignment explanation
Indices: 40053224--40053279 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
40053214 AATTAAATAA
*
40053224 TAAAATATAAATATAAAATATGTTTATAC
1 TAAAATATAAATATAAAATATGATTATAC
*
40053253 TAAATTATAAATA-AAAATTAT-ATTATA
1 TAAAATATAAATATAAAA-TATGATTATA
40053280 AAAATAAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (29 bp):
TAAAATATAAATATAAAATATGATTATAC
Found at i:40054058 original size:3 final size:3
Alignment explanation
Indices: 40054052--40054087 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
40054042 AGATGATGAA
40054052 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
40054088 GTTTTGATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:40054328 original size:20 final size:19
Alignment explanation
Indices: 40054303--40054353 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
40054293 TTAATTATCC
40054303 ATTAAATAAATAACTAA-TTA
1 ATTAAATAAATAA--AACTTA
*
40054323 ATTAAACAAATAAAACTTTA
1 ATTAAATAAATAAAAC-TTA
40054343 ATTAAATAAAT
1 ATTAAATAAAT
40054354 TTTCCATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 2 0.07
20 25 0.93
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAATAAATAAAACTTA
Found at i:40057766 original size:22 final size:22
Alignment explanation
Indices: 40057741--40057785 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
40057731 GGTCAATCTC
40057741 TCAACAAAAATTAT-AAAATAAT
1 TCAA-AAAAATTATCAAAATAAT
* *
40057763 TCAAAATAATTTTCAAAATAAT
1 TCAAAAAAATTATCAAAATAAT
40057785 T
1 T
40057786 TTTAAATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (22 bp):
TCAAAAAAATTATCAAAATAAT
Found at i:40057779 original size:12 final size:12
Alignment explanation
Indices: 40057762--40057787 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40057752 TATAAAATAA
40057762 TTCAAAATAATT
1 TTCAAAATAATT
40057774 TTCAAAATAATT
1 TTCAAAATAATT
40057786 TT
1 TT
40057788 TAAATTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (12 bp):
TTCAAAATAATT
Found at i:40061568 original size:32 final size:31
Alignment explanation
Indices: 40061523--40061618 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
40061513 CTTAGATAAT
40061523 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
40061554 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
40061586 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
40061617 TT
1 TT
40061619 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:40061930 original size:4 final size:4
Alignment explanation
Indices: 40061921--40061959 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
40061911 TTCTATCCTT
40061921 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
40061960 ACTAATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 31 0.91
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:40062272 original size:19 final size:18
Alignment explanation
Indices: 40062191--40062241 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
40062181 AAAAAAAAGT
* *
40062191 AAAAAGTAAAAAGCGCAAA
1 AAAAAGCAAAAA-AGCAAA
*
40062210 AAAAAACAAAAAAGCAAA
1 AAAAAGCAAAAAAGCAAA
40062228 AAAAACGCAAAAAA
1 AAAAA-GCAAAAAA
40062242 AGAGAGTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.76, C:0.12, G:0.10, T:0.02
Consensus pattern (18 bp):
AAAAAGCAAAAAAGCAAA
Found at i:40062274 original size:10 final size:10
Alignment explanation
Indices: 40062205--40062286 Score: 62
Period size: 10 Copynumber: 8.0 Consensus size: 10
40062195 AGTAAAAAGC
40062205 GCAAAAAAAA
1 GCAAAAAAAA
*
40062215 --ACAAAAAA
1 GCAAAAAAAA
40062223 GCAAAAAAAA
1 GCAAAAAAAA
40062233 CGCAAAAAAAGA
1 -GCAAAAAAA-A
**
40062245 G-AGTAAAAAGC
1 GCA--AAAAAAA
40062256 GCAAAAAAAA
1 GCAAAAAAAA
40062266 GCAAAAAAAA
1 GCAAAAAAAA
*
40062276 ACACAAAAAAA
1 GCA-AAAAAAA
40062287 AGTTGCCTAC
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
8 7 0.12
10 25 0.44
11 18 0.32
12 7 0.12
ACGTcount: A:0.76, C:0.12, G:0.11, T:0.01
Consensus pattern (10 bp):
GCAAAAAAAA
Found at i:40062275 original size:11 final size:11
Alignment explanation
Indices: 40062217--40062288 Score: 60
Period size: 11 Copynumber: 6.6 Consensus size: 11
40062207 AAAAAAAAAC
40062217 AAAAAAGCAAA
1 AAAAAAGCAAA
*
40062228 AAAAACGCAAA
1 AAAAAAGCAAA
* *
40062239 AAAAGAG--AG
1 AAAAAAGCAAA
* *
40062248 TAAAAAGCGCAA
1 AAAAAAGC-AAA
40062260 AAAAAAGCAAA
1 AAAAAAGCAAA
40062271 AAAAAA-CACAA
1 AAAAAAGCA-AA
40062282 AAAAAAG
1 AAAAAAG
40062289 TTGCCTACCT
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
9 6 0.13
10 2 0.04
11 31 0.66
12 8 0.17
ACGTcount: A:0.75, C:0.11, G:0.12, T:0.01
Consensus pattern (11 bp):
AAAAAAGCAAA
Found at i:40066858 original size:32 final size:31
Alignment explanation
Indices: 40066813--40066908 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
40066803 CTTAGATAAT
40066813 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
40066844 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
40066876 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
40066907 TT
1 TT
40066909 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:40073251 original size:12 final size:10
Alignment explanation
Indices: 40073217--40073280 Score: 60
Period size: 11 Copynumber: 6.3 Consensus size: 10
40073207 TATTTTAGTC
*
40073217 TTTTTATAGT
1 TTTTTATAAT
*
40073227 CTTTTTAT-GT
1 -TTTTTATAAT
40073237 TTTTCTATAAT
1 TTTT-TATAAT
40073248 TTTTTATAA-
1 TTTTTATAAT
40073257 TTTTTATAAAT
1 TTTTTAT-AAT
*
40073268 TTTTTATGAT
1 TTTTTATAAT
40073278 TTT
1 TTT
40073281 AATTTTCATT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
9 11 0.23
10 17 0.36
11 19 0.40
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:40073264 original size:19 final size:19
Alignment explanation
Indices: 40073217--40073280 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 19
40073207 TATTTTAGTC
* *
40073217 TTTTTATAGTCTTTTTATGT
1 TTTTTATAAT-TTTTTATGA
*
40073237 TTTTCTATAATTTTTTATAA
1 TTTT-TATAATTTTTTATGA
40073257 TTTTTATAAATTTTTTATGA
1 TTTTTAT-AATTTTTTATGA
40073277 TTTT
1 TTTT
40073281 AATTTTCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.08
20 30 0.79
21 5 0.13
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTTTATAATTTTTTATGA
Found at i:40076350 original size:25 final size:25
Alignment explanation
Indices: 40076322--40076437 Score: 117
Period size: 25 Copynumber: 4.6 Consensus size: 25
40076312 AAGCTTTTGC
40076322 GAGCCAAATATCGGGAAGCTCAAGA
1 GAGCCAAATATCGGGAAGCTCAAGA
* *
40076347 GAGCC-ATTAATCGGGAAGCTCATGA
1 GAGCCAAAT-ATCGGGAAGCTCAAGA
* * **
40076372 GAGCTAAATAACGGGAAGCTCGTGA
1 GAGCCAAATATCGGGAAGCTCAAGA
* * * *
40076397 GAGCCAAGTATTGAGAAGCTCGAGA
1 GAGCCAAATATCGGGAAGCTCAAGA
*
40076422 GAGCCAAATATTGGGA
1 GAGCCAAATATCGGGA
40076438 CATTCATAAG
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
24 2 0.03
25 71 0.95
26 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.30, T:0.16
Consensus pattern (25 bp):
GAGCCAAATATCGGGAAGCTCAAGA
Found at i:40076383 original size:75 final size:75
Alignment explanation
Indices: 40076272--40076437 Score: 190
Period size: 75 Copynumber: 2.2 Consensus size: 75
40076262 AAGCTCTTTC
* ** ** * *
40076272 GAGCCATATAATGGGAAGCTCATGTGAACTGTATAACGGAAAGCTTTTGCGAGCCAAATATCGGG
1 GAGCCATATAATGGGAAGCTCATGAGAACTAAATAACGGAAAGCTCGTGAGAGCCAAATATCGAG
40076337 AAGCTCAAGA
66 AAGCTCAAGA
* * * *
40076347 GAGCCAT-TAATCGGGAAGCTCATGAGAGCTAAATAACGGGAAGCTCGTGAGAGCCAAGTATTGA
1 GAGCCATATAAT-GGGAAGCTCATGAGAACTAAATAACGGAAAGCTCGTGAGAGCCAAATATCGA
*
40076411 GAAGCTCGAGA
65 GAAGCTCAAGA
* *
40076422 GAGCCAAATATTGGGA
1 GAGCCATATAATGGGA
40076438 CATTCATAAG
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
74 4 0.05
75 68 0.91
76 3 0.04
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (75 bp):
GAGCCATATAATGGGAAGCTCATGAGAACTAAATAACGGAAAGCTCGTGAGAGCCAAATATCGAG
AAGCTCAAGA
Found at i:40076623 original size:21 final size:22
Alignment explanation
Indices: 40076591--40076644 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
40076581 CATGGAAATG
*
40076591 TATACAAATTAAACACA-AT-AA
1 TATACAATTTAAA-ACATATAAA
*
40076612 TATTCAATTTAAAACATATAAA
1 TATACAATTTAAAACATATAAA
40076634 TATACAATTTA
1 TATACAATTTA
40076645 GTTACACGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.11
21 13 0.46
22 12 0.43
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (22 bp):
TATACAATTTAAAACATATAAA
Found at i:40076627 original size:22 final size:22
Alignment explanation
Indices: 40076591--40076644 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
40076581 CATGGAAATG
*
40076591 TATACAAATT-AAACACAAT-AA
1 TATACAATTTAAAACA-AATAAA
* *
40076612 TATTCAATTTAAAACATATAAA
1 TATACAATTTAAAACAAATAAA
40076634 TATACAATTTA
1 TATACAATTTA
40076645 GTTACACGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (22 bp):
TATACAATTTAAAACAAATAAA
Found at i:40078904 original size:37 final size:37
Alignment explanation
Indices: 40078841--40078932 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 37
40078831 ATTCTAAAAA
*
40078841 TAATATTATTTTAATAGTTTAATATTAAATTAA-ATT
1 TAATATTATCTTAATAGTTTAATATTAAATTAATATT
* *
40078877 TAATACTTATCTTAATAGTATT-TTATTAATTTAATATT
1 TAATA-TTATCTTAATAGT-TTAATATTAAATTAATATT
*
40078915 AAAGTGATTATCTTAATA
1 TAA-T-ATTATCTTAATA
40078933 TTAAATTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
36 5 0.11
37 22 0.47
38 7 0.15
39 12 0.26
40 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (37 bp):
TAATATTATCTTAATAGTTTAATATTAAATTAATATT
Found at i:40079014 original size:21 final size:20
Alignment explanation
Indices: 40078990--40079030 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
40078980 AATAAGATTT
*
40078990 AATATTAAATTTAATCTAATA
1 AATATTAAATTAAAT-TAATA
*
40079011 AATATTATATTAAATTAATA
1 AATATTAAATTAAATTAATA
40079031 TTAAAGTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATTAAATTAAATTAATA
Found at i:40081567 original size:25 final size:25
Alignment explanation
Indices: 40081539--40081586 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
40081529 ATCTTAATAG
*
40081539 TATTTTATTAAT-TTAATATTAAAAT
1 TATTATATTAATATTAA-ATTAAAAT
*
40081564 TATTATCTTAATATTAAATTAAA
1 TATTATATTAATATTAAATTAAA
40081587 TTTAATGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TATTATATTAATATTAAATTAAAAT
Found at i:40081568 original size:20 final size:19
Alignment explanation
Indices: 40081543--40081592 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
40081533 TAATAGTATT
40081543 TTATTAATTTAATATTAAAA
1 TTATTAATTTAATATT-AAA
40081563 TTATT-ATCTTAATATTAAA
1 TTATTAAT-TTAATATTAAA
40081582 TTA--AATTTAAT
1 TTATTAATTTAAT
40081593 GTTTATCTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 5 0.18
18 2 0.07
19 8 0.29
20 13 0.46
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTAATTTAATATTAAA
Found at i:40082937 original size:34 final size:34
Alignment explanation
Indices: 40082897--40083015 Score: 139
Period size: 34 Copynumber: 3.5 Consensus size: 34
40082887 ATTATTTACT
* *
40082897 GTATTGATATGATATAGGCATATTAATTGCTATC
1 GTATTGATCTGATATAAGCATATTAATTGCTATC
* * *
40082931 GTATTGATCTGTTATAAACATATTAATTGCTACC
1 GTATTGATCTGATATAAGCATATTAATTGCTATC
** * * *
40082965 AAATTGATCTGCTATAAGCATACTAATTGTTATC
1 GTATTGATCTGATATAAGCATATTAATTGCTATC
*
40082999 GTATTGATCTGTTATAA
1 GTATTGATCTGATATAA
40083016 ACATGACATA
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 70 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (34 bp):
GTATTGATCTGATATAAGCATATTAATTGCTATC
Found at i:40098148 original size:18 final size:18
Alignment explanation
Indices: 40098127--40098162 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
40098117 TAAAAACCTT
40098127 AATATTTTTAAAATATTG
1 AATATTTTTAAAATATTG
40098145 AATATTTTTAAAATATTG
1 AATATTTTTAAAATATTG
40098163 TGTGGGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
AATATTTTTAAAATATTG
Found at i:40105414 original size:133 final size:133
Alignment explanation
Indices: 40105140--40105401 Score: 344
Period size: 133 Copynumber: 2.0 Consensus size: 133
40105130 CGCACACGGT
* * **
40105140 CATGTGTCTTATTGATTTTAAGTGCAGGATTTTTCACACGGCATCAACCTGTGACAGGGCCTGGC
1 CATGTGACTTATTGATTTTAAGTACAGGATTTTTCACACGGCATCAACCTGTGACACAGCCTGGC
* * * * *
40105205 AACACGGGCGTGTGGGGTAGCCACACAACCAGGTTTGAGGCTACACGTGCTGATCGCTTTCACAC
66 AACACGAGCGTGTGCGGTAGCCACACAACCAGATTTGAGGCTACACGAGCTGACCGCTTTCACAC
40105270 GAC
131 GAC
* * * * * *
40105273 CATGTGACTTATTGATTTTAGGTATAGGATTTTTCACACGGTATCAACTTGTTACACAGCTTGGC
1 CATGTGACTTATTGATTTTAAGTACAGGATTTTTCACACGGCATCAACCTGTGACACAGCCTGGC
* ** * *
40105338 AACATGAGCGTGTGCGGTAGCCACATGACCATATTTGAGGCTACACGAGCTGGCCGCTTTCACA
66 AACACGAGCGTGTGCGGTAGCCACACAACCAGATTTGAGGCTACACGAGCTGACCGCTTTCACA
40105402 TGGCCGTGTG
Statistics
Matches: 109, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
133 109 1.00
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (133 bp):
CATGTGACTTATTGATTTTAAGTACAGGATTTTTCACACGGCATCAACCTGTGACACAGCCTGGC
AACACGAGCGTGTGCGGTAGCCACACAACCAGATTTGAGGCTACACGAGCTGACCGCTTTCACAC
GAC
Found at i:40111153 original size:25 final size:25
Alignment explanation
Indices: 40111102--40111153 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
40111092 TTTTGTTCTC
* * *
40111102 TTTATTATTTATTTTATAACAAGTA
1 TTTAATATTTATTTAATAACAAATA
40111127 TTTAATATTTAATTTAATAA-AAATA
1 TTTAATATTT-ATTTAATAACAAATA
40111152 TT
1 TT
40111154 AATTAAAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (25 bp):
TTTAATATTTATTTAATAACAAATA
Found at i:40114935 original size:18 final size:19
Alignment explanation
Indices: 40114900--40114939 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
40114890 TCACGTCAAC
*
40114900 AAATGAATTTAAACTTAAA
1 AAATGAATTAAAACTTAAA
*
40114919 AAAT-AATTAAAATTTAAA
1 AAATGAATTAAAACTTAAA
40114937 AAA
1 AAA
40114940 AAACATTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (19 bp):
AAATGAATTAAAACTTAAA
Found at i:40115005 original size:10 final size:9
Alignment explanation
Indices: 40114970--40115006 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
40114960 GAGTTTACCC
40114970 ACAATTAAA
1 ACAATTAAA
40114979 ACAATTAAA
1 ACAATTAAA
*
40114988 AAAATTAAA
1 ACAATTAAA
40114997 ACAACTTAAA
1 ACAA-TTAAA
40115007 CACTAACCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 20 0.80
10 5 0.20
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.22
Consensus pattern (9 bp):
ACAATTAAA
Found at i:40116589 original size:81 final size:81
Alignment explanation
Indices: 40116406--40116607 Score: 359
Period size: 82 Copynumber: 2.5 Consensus size: 81
40116396 TTGAGATGGT
* *
40116406 TAACATATTTTGTTTGTTTTTTGAAATGATTTGTTGAAATGTTTGGTTAATACTTACTGCTATAG
1 TAACATATTTTGTTTGTTTTTTGAAATGATTTGTTGAAATGGTTGGTTAACACTTACTGCTATAG
40116471 GATCATTTTGTTAGCA
66 GATCATTTTGTTAGCA
40116487 TAACATATTTTGTTTGTTTTTTGAAATGATTTGTTGAAATGGTTGGTTAACATCTTACTGCTATA
1 TAACATATTTTGTTTGTTTTTTGAAATGATTTGTTGAAATGGTTGGTTAACA-CTTACTGCTATA
*
40116552 GGATCATTTTGTTAGTA
65 GGATCATTTTGTTAGCA
*
40116569 TAACATATTTTGTTTGTTTTTTAAAATGATTTGTTGAAA
1 TAACATATTTTGTTTGTTTTTTGAAATGATTTGTTGAAA
40116608 GATGTATACC
Statistics
Matches: 116, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
81 50 0.43
82 66 0.57
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.50
Consensus pattern (81 bp):
TAACATATTTTGTTTGTTTTTTGAAATGATTTGTTGAAATGGTTGGTTAACACTTACTGCTATAG
GATCATTTTGTTAGCA
Found at i:40118163 original size:121 final size:112
Alignment explanation
Indices: 40117991--40118207 Score: 294
Period size: 112 Copynumber: 1.9 Consensus size: 112
40117981 TACTCTAATA
*
40117991 TTCACGCATGGGAAAGAAAATTTTCATCAATATCCAATAAAAAATATAAAAATATAAAAAAAATC
1 TTCACACATGGGAAAGAAAATTTTCATCAATATCCAATAAAAAATATAAAAA-AT------AA--
*
40118056 CTCAATTTCTTATGAACCCTAAAACAAATCGGCTAAATATGCTTACCTGAATACAT
57 CACAATTTCTTATGAACCCTAAAACAAATCGGCTAAATATGCTTACCTGAATACAT
*
40118112 TTCACACATGGGAAAG-AAATGTTTCATCAATATCCAATTAAAAAATA-AAAAAATCACACAATT
1 TTCACACATGGGAAAGAAAAT-TTTCATCAATATCCAA-TAAAAAATATAAAAAATAACACAATT
40118175 TCTTATGAACCCTAAAACAAATCGGCTAAATAT
64 TCTTATGAACCCTAAAACAAATCGGCTAAATAT
40118208 ACAGTGACTA
Statistics
Matches: 91, Mismatches: 3, Indels: 13
0.85 0.03 0.12
Matches are distributed among these distances:
112 39 0.43
114 1 0.01
120 6 0.07
121 36 0.40
122 9 0.10
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.27
Consensus pattern (112 bp):
TTCACACATGGGAAAGAAAATTTTCATCAATATCCAATAAAAAATATAAAAAATAACACAATTTC
TTATGAACCCTAAAACAAATCGGCTAAATATGCTTACCTGAATACAT
Found at i:40119179 original size:23 final size:23
Alignment explanation
Indices: 40119135--40119179 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
40119125 ATGGATGAAA
* *
40119135 GTTAAAATATTTATATTAAACAT
1 GTTAAAATATTCATATAAAACAT
40119158 GTTAAAA-ATTCATATAATAACA
1 GTTAAAATATTCATATAA-AACA
40119180 ATTGCCATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (23 bp):
GTTAAAATATTCATATAAAACAT
Found at i:40121016 original size:38 final size:38
Alignment explanation
Indices: 40120974--40121053 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 38
40120964 TATTATGTAT
*
40120974 ATATCAAGGATGTGGAATGGAGTGGAGGAGGAGGAAAA
1 ATATCAAGGATGTGGAATGGAGTGGAGGAGAAGGAAAA
40121012 ATATCAAGGATGTGGAATGGAGTGGAGGAGAAGGAAAA
1 ATATCAAGGATGTGGAATGGAGTGGAGGAGAAGGAAAA
40121050 ATAT
1 ATAT
40121054 ATCTGAATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.41, C:0.03, G:0.39, T:0.17
Consensus pattern (38 bp):
ATATCAAGGATGTGGAATGGAGTGGAGGAGAAGGAAAA
Found at i:40124705 original size:118 final size:119
Alignment explanation
Indices: 40124493--40124717 Score: 416
Period size: 118 Copynumber: 1.9 Consensus size: 119
40124483 AAGATGGAAT
40124493 CCACCATTTTTAGGAGTGGACTGACCTGCACTGCCAAGTACCCCGGGCCAAATGCTTTCCTTGCA
1 CCACCATTTTTAGGAGTGGACTGACCTGCA---CCAAGTACCCCGGGCCAAATGCTTTCCTTGCA
40124558 GTTGTTCACAAGTATAACTTGCTCTCCATCTGCAATGAAAAAAATAAAAATAAAAAC
63 GTTGTTCACAAGTATAACTTGCTCTCCATCTGCAATGAAAAAAATAAAAATAAAAAC
40124615 CCACCATTTTTAGGAGTGGACTGACCTGCA-CAAGTACCCCGGGCCAAATGCTTTCCTTGCAGTT
1 CCACCATTTTTAGGAGTGGACTGACCTGCACCAAGTACCCCGGGCCAAATGCTTTCCTTGCAGTT
40124679 GTTCACAAGTATAACTTGCTCTCCATCTGCAATGAAAAA
66 GTTCACAAGTATAACTTGCTCTCCATCTGCAATGAAAAA
40124718 TAAAAACCCA
Statistics
Matches: 103, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
118 73 0.71
122 30 0.29
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (119 bp):
CCACCATTTTTAGGAGTGGACTGACCTGCACCAAGTACCCCGGGCCAAATGCTTTCCTTGCAGTT
GTTCACAAGTATAACTTGCTCTCCATCTGCAATGAAAAAAATAAAAATAAAAAC
Found at i:40124965 original size:19 final size:20
Alignment explanation
Indices: 40124931--40124968 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
40124921 CAGCGTCCTA
*
40124931 TCCTTTCTTTTTTTCTACTC
1 TCCTTTCTTCTTTTCTACTC
40124951 TCCTTTC-TCTTTTCTACT
1 TCCTTTCTTCTTTTCTACT
40124969 TTGATGATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.63
Consensus pattern (20 bp):
TCCTTTCTTCTTTTCTACTC
Found at i:40127452 original size:16 final size:17
Alignment explanation
Indices: 40127431--40127465 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
40127421 AATTAATTTA
*
40127431 AATTAATTAA-TTTCTC
1 AATTAAATAATTTTCTC
40127447 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
40127464 AA
1 AA
40127466 CCTAATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:40136537 original size:43 final size:42
Alignment explanation
Indices: 40136399--40136548 Score: 151
Period size: 42 Copynumber: 3.5 Consensus size: 42
40136389 AATGTGATAT
* * *
40136399 CGTGTAAGACCATGTCTGGAAC-GTTGGCATC-AATTTGAGATTTA
1 CGTGTAAGACCATGTCTGGGACAG-TGGCATCGTATAT--GA-TTA
* * *
40136443 CGTGTAAGACCATGTCTAGGACATTGGCGTCGTATATGATTA
1 CGTGTAAGACCATGTCTGGGACAGTGGCATCGTATATGATTA
* * *
40136485 CGTGTAAGACCCTGTCTGGGACAGTGGCATTGCTATTTGATTA
1 CGTGTAAGACCATGTCTGGGACAGTGGCATCG-TATATGATTA
*
40136528 CATGTAAGACCATGTCTGGGA
1 CGTGTAAGACCATGTCTGGGA
40136549 TGTTGGCATT
Statistics
Matches: 89, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
42 30 0.34
43 30 0.34
44 26 0.29
45 3 0.03
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (42 bp):
CGTGTAAGACCATGTCTGGGACAGTGGCATCGTATATGATTA
Found at i:40136556 original size:43 final size:43
Alignment explanation
Indices: 40136399--40136559 Score: 168
Period size: 43 Copynumber: 3.7 Consensus size: 43
40136389 AATGTGATAT
* *
40136399 CGTGTAAGACCATGTCTGGAACGTTGGCA-T-CAATTTGAGATTTA
1 CGTGTAAGACCATGTCTGGGACGTTGGCATTGCTATTT--GA-TTA
* * * * *
40136443 CGTGTAAGACCATGTCTAGGACATTGGCGTCG-TATATGATTA
1 CGTGTAAGACCATGTCTGGGACGTTGGCATTGCTATTTGATTA
*
40136485 CGTGTAAGACCCTGTCTGGGACAG-TGGCATTGCTATTTGATTA
1 CGTGTAAGACCATGTCTGGGAC-GTTGGCATTGCTATTTGATTA
* *
40136528 CATGTAAGACCATGTCTGGGATGTTGGCATTG
1 CGTGTAAGACCATGTCTGGGACGTTGGCATTG
40136560 TACGAGCCTT
Statistics
Matches: 96, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
42 30 0.31
43 38 0.40
44 25 0.26
45 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTGGGACGTTGGCATTGCTATTTGATTA
Found at i:40137760 original size:20 final size:20
Alignment explanation
Indices: 40137719--40137762 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40137709 ATGATTTTGG
*
40137719 AAATTAATGGTTAAGTTGTA
1 AAATTAATGCTTAAGTTGTA
*
40137739 AAATTAAATGCTTGAGTT-TA
1 AAATT-AATGCTTAAGTTGTA
40137759 AAAT
1 AAAT
40137763 GTGTCATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.43, C:0.02, G:0.16, T:0.39
Consensus pattern (20 bp):
AAATTAATGCTTAAGTTGTA
Found at i:40138030 original size:14 final size:14
Alignment explanation
Indices: 40138011--40138038 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40138001 TGGCTTGACT
40138011 TAGTAAAATGTGAA
1 TAGTAAAATGTGAA
40138025 TAGTAAAATGTGAA
1 TAGTAAAATGTGAA
40138039 GAAGAGCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (14 bp):
TAGTAAAATGTGAA
Found at i:40150493 original size:24 final size:24
Alignment explanation
Indices: 40150461--40150514 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
40150451 TGGCATAAAT
40150461 GAACAACAACAAAAATTTTCATTG
1 GAACAACAACAAAAATTTTCATTG
40150485 GAACAACAACAAAAATTTTCATTG
1 GAACAACAACAAAAATTTTCATTG
*
40150509 GCACAA
1 GAACAA
40150515 AGGATTTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.50, C:0.19, G:0.09, T:0.22
Consensus pattern (24 bp):
GAACAACAACAAAAATTTTCATTG
Found at i:40158048 original size:31 final size:31
Alignment explanation
Indices: 40158010--40158072 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
40158000 AAGAGTTAAA
40158010 GGGGTTGAGAATTGATGAAAATTGTTAAGCC
1 GGGGTTGAGAATTGATGAAAATTGTTAAGCC
40158041 GGGGTTGAGAATTGATGAAAATTGTTAAGCC
1 GGGGTTGAGAATTGATGAAAATTGTTAAGCC
40158072 G
1 G
40158073 AGATTGTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.33, T:0.29
Consensus pattern (31 bp):
GGGGTTGAGAATTGATGAAAATTGTTAAGCC
Found at i:40163343 original size:23 final size:26
Alignment explanation
Indices: 40163316--40163371 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
40163306 GCTCTTGTAT
40163316 CTTACCGTT-TT-AGCTC-G-ATAGAG
1 CTTACCGTTCTTCAGCTCAGAAT-GAG
*
40163339 CTTACCATTCTTCAGCTCAGAATGAG
1 CTTACCGTTCTTCAGCTCAGAATGAG
40163365 CTTACCG
1 CTTACCG
40163372 ATCATGGCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 8 0.30
24 2 0.07
25 5 0.19
26 10 0.37
27 2 0.07
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (26 bp):
CTTACCGTTCTTCAGCTCAGAATGAG
Found at i:40167941 original size:28 final size:28
Alignment explanation
Indices: 40167901--40167957 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
40167891 TTGCTCGGAA
*
40167901 GGATCAACTCGAGATCGACGATAGGGAG
1 GGATCAACTCGAGATCCACGATAGGGAG
40167929 GGATCAACTCGAGATCCACGATAGGGAG
1 GGATCAACTCGAGATCCACGATAGGGAG
40167957 G
1 G
40167958 TTGAATCGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.19, G:0.35, T:0.14
Consensus pattern (28 bp):
GGATCAACTCGAGATCCACGATAGGGAG
Found at i:40169558 original size:50 final size:51
Alignment explanation
Indices: 40169494--40169594 Score: 159
Period size: 52 Copynumber: 2.0 Consensus size: 51
40169484 ATAGCAGTTA
40169494 TAATTGATTTAG-ACATATCTAAATGCCTTTGAGAGCAGGTTTCATTTTAC
1 TAATTGATTTAGAACATATCTAAATGCCTTTGAGAGCAGGTTTCATTTTAC
* * *
40169544 TAATTGATTTAGACACATATCTAAATGTCTTTGAGAGCATGTTTCTTTTTA
1 TAATTGATTTAGA-ACATATCTAAATGCCTTTGAGAGCAGGTTTCATTTTA
40169595 ATATATAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 12 0.26
52 34 0.74
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (51 bp):
TAATTGATTTAGAACATATCTAAATGCCTTTGAGAGCAGGTTTCATTTTAC
Found at i:40172733 original size:40 final size:40
Alignment explanation
Indices: 40172689--40172793 Score: 120
Period size: 40 Copynumber: 2.6 Consensus size: 40
40172679 AAGCACGTTG
* * **
40172689 ACGTGGGAGTGTTTTACCCTTTGTTAGCAAAAGCGCGCTA
1 ACGTGGGAGCGCTTTACCCCGTGTTAGCAAAAGCGCGCTA
* *
40172729 ACGTGGGAGCGCTTTACCCCGTGTTAGCAAAAGCGGGCTG
1 ACGTGGGAGCGCTTTACCCCGTGTTAGCAAAAGCGCGCTA
* * * *
40172769 ACGTGAGCGCACTTTACACCGTGTT
1 ACGTGGGAGCGCTTTACCCCGTGTT
40172794 TGATTAGGGT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.21, C:0.24, G:0.30, T:0.26
Consensus pattern (40 bp):
ACGTGGGAGCGCTTTACCCCGTGTTAGCAAAAGCGCGCTA
Found at i:40172878 original size:29 final size:28
Alignment explanation
Indices: 40172835--40172900 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
40172825 GGGCTTAGGG
* *
40172835 TTAGGG-TTAGTGTTTTTGAAAAAATAAA
1 TTAGGGTTTAG-GGTTTTAAAAAAATAAA
40172863 TTAGGGTTTAGGGTTTTAAAAAAATAAA
1 TTAGGGTTTAGGGTTTTAAAAAAATAAA
*
40172891 TCAGGGTTTA
1 TTAGGGTTTA
40172901 ATTTTTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 30 0.88
29 4 0.12
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.38
Consensus pattern (28 bp):
TTAGGGTTTAGGGTTTTAAAAAAATAAA
Found at i:40172907 original size:28 final size:28
Alignment explanation
Indices: 40172846--40172907 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
40172836 TAGGGTTAGT
* * *
40172846 GTTTTTGAAAAAATAAATTAGGGTTTAG
1 GTTTTTAAAAAAATAAATCAGGGTTTAA
*
40172874 GGTTTTAAAAAAATAAATCAGGGTTTAA
1 GTTTTTAAAAAAATAAATCAGGGTTTAA
*
40172902 TTTTTT
1 GTTTTT
40172908 TTAATTGGTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.02, G:0.18, T:0.42
Consensus pattern (28 bp):
GTTTTTAAAAAAATAAATCAGGGTTTAA
Found at i:40174297 original size:59 final size:59
Alignment explanation
Indices: 40174205--40174380 Score: 201
Period size: 59 Copynumber: 3.0 Consensus size: 59
40174195 AAATCGAAAT
* * * * ** ** *
40174205 AACTCCTAATTTATTAAATGAAACAATAAAAAAATAATTTGTA-TTATCTCATTCAAAAG
1 AACTTCTATTTTATTAAATGAAACAATATAAAAATAGTTTGTACAAAAAT-ATTCAAAAC
* *
40174264 AACTTCTATTTTATTAAATGAAATAATATAAAAATAGTTTGTACAAAAATATTTAAAAC
1 AACTTCTATTTTATTAAATGAAACAATATAAAAATAGTTTGTACAAAAATATTCAAAAC
* * * *
40174323 AACTTCTGTTTTATTAAATGAAACAATATAAAAACAGTTTGTACAAATATATTAAAAA
1 AACTTCTATTTTATTAAATGAAACAATATAAAAATAGTTTGTACAAAAATATTCAAAA
40174381 AATCAATGCA
Statistics
Matches: 100, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
59 98 0.98
60 2 0.02
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (59 bp):
AACTTCTATTTTATTAAATGAAACAATATAAAAATAGTTTGTACAAAAATATTCAAAAC
Found at i:40174841 original size:12 final size:12
Alignment explanation
Indices: 40174824--40174848 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40174814 ATTTCATTCC
40174824 ACATATATATAT
1 ACATATATATAT
40174836 ACATATATATAT
1 ACATATATATAT
40174848 A
1 A
40174849 AACAGATAAC
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ACATATATATAT
Found at i:40175241 original size:47 final size:47
Alignment explanation
Indices: 40175190--40175746 Score: 913
Period size: 47 Copynumber: 11.9 Consensus size: 47
40175180 ATATTTACAA
* *
40175190 AATTGGACTGTATTTATACATCAAAACTTGACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
40175237 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
* *
40175284 ATTTGGACTGCATTTGTACATCAAAAATTGACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
*
40175331 AATTGGACTGCATTTATACGTCAAAAATTGACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
* *
40175378 AATTGGACTGC-CTTATACATCAAAAATTAACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
* * *
40175424 AATTGGACTGCATTTATACATCAAAAATTGACAACATGTACATAAAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
* *
40175471 ATTTGGACTGCATTTGTACATC-AAAATTGACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
40175517 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
* * *
40175564 ATTTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
*
40175611 AATTGGACTGCATTTATACGTCAAAAATTGACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
* *
40175658 AATTGGACTGC-CTTATACATCAAAAATTAACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
* *
40175704 AATTGGACTGCATTTGTACATCAAAATTTGACAGCATATACAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACAT
40175747 TCATTTACTC
Statistics
Matches: 471, Mismatches: 36, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
46 127 0.27
47 344 0.73
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.32
Consensus pattern (47 bp):
AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
Found at i:40175627 original size:280 final size:281
Alignment explanation
Indices: 40175192--40175746 Score: 1040
Period size: 280 Copynumber: 2.0 Consensus size: 281
40175182 ATTTACAAAA
*
40175192 TTGGACTGTATTTATACATCAAAACTTGACAGCATATACATATATAATTGGACTGCATTTATACA
1 TTGGACTGCATTTATACATCAAAACTTGACAGCATATACATATATAATTGGACTGCATTTATACA
40175257 TCAAAAATTGACAGCATATACATATATATTTGGACTGCATTTGTACATCAAAAATTGACAGCATA
66 TCAAAAATTGACAGCATATACATATATATTTGGACTGCATTTGTACATCAAAAATTGACAGCATA
40175322 TACATATATAATTGGACTGCATTTATACGTCAAAAATTGACAGCATATACATATATAATTGGACT
131 TACATATATAATTGGACTGCATTTATACGTCAAAAATTGACAGCATATACATATATAATTGGACT
40175387 GCCTTATACATCAAAAATTAACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAAT
196 GCCTTATACATCAAAAATTAACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAAT
*
40175452 TGACAACATGTACATAAATAT
261 TGACAACATATACATAAATAT
*
40175473 TTGGACTGCATTTGTACATCAAAA-TTGACAGCATATACATATATAATTGGACTGCATTTATACA
1 TTGGACTGCATTTATACATCAAAACTTGACAGCATATACATATATAATTGGACTGCATTTATACA
*
40175537 TCAAAAATTGACAGCATATACATATATATTTGGACTGCATTTGTACATCAAAATTTGACAGCATA
66 TCAAAAATTGACAGCATATACATATATATTTGGACTGCATTTGTACATCAAAAATTGACAGCATA
40175602 TACATATATAATTGGACTGCATTTATACGTCAAAAATTGACAGCATATACATATATAATTGGACT
131 TACATATATAATTGGACTGCATTTATACGTCAAAAATTGACAGCATATACATATATAATTGGACT
* *
40175667 GCCTTATACATCAAAAATTAACAGCATATACATATATAATTGGACTGCATTTGTACATCAAAATT
196 GCCTTATACATCAAAAATTAACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAAT
*
40175732 TGACAGCATATACAT
261 TGACAACATATACAT
40175747 TCATTTACTC
Statistics
Matches: 267, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
280 245 0.92
281 22 0.08
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (281 bp):
TTGGACTGCATTTATACATCAAAACTTGACAGCATATACATATATAATTGGACTGCATTTATACA
TCAAAAATTGACAGCATATACATATATATTTGGACTGCATTTGTACATCAAAAATTGACAGCATA
TACATATATAATTGGACTGCATTTATACGTCAAAAATTGACAGCATATACATATATAATTGGACT
GCCTTATACATCAAAAATTAACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAAT
TGACAACATATACATAAATAT
Found at i:40175744 original size:140 final size:141
Alignment explanation
Indices: 40175190--40175746 Score: 931
Period size: 140 Copynumber: 4.0 Consensus size: 141
40175180 ATATTTACAA
* * *
40175190 AATTGGACTGTATTTATACATCAAAACTTGACAGCATATACATATATAATTGGACTGCATTTATA
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATATAATTGGACTGCACTTATA
* *
40175255 CATCAAAAATTGACAGCATATACATATATATTTGGACTGCATTTGTACATCAAAAATTGACAGCA
66 CATCAAAAATTAACAGCATATACATATATAATTGGACTGCATTTGTACATCAAAAATTGACAGCA
40175320 TATACATATAT
131 TATACATATAT
*
40175331 AATTGGACTGCATTTATACGTCAAAAATTGACAGCATATACATATATAATTGGACTGC-CTTATA
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATATAATTGGACTGCACTTATA
* *
40175395 CATCAAAAATTAACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAATTGACAACA
66 CATCAAAAATTAACAGCATATACATATATAATTGGACTGCATTTGTACATCAAAAATTGACAGCA
* *
40175460 TGTACATAAAT
131 TATACATATAT
* * *
40175471 ATTTGGACTGCATTTGTACATC-AAAATTGACAGCATATACATATATAATTGGACTGCATTTATA
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATATAATTGGACTGCACTTATA
* * *
40175535 CATCAAAAATTGACAGCATATACATATATATTTGGACTGCATTTGTACATCAAAATTTGACAGCA
66 CATCAAAAATTAACAGCATATACATATATAATTGGACTGCATTTGTACATCAAAAATTGACAGCA
40175600 TATACATATAT
131 TATACATATAT
*
40175611 AATTGGACTGCATTTATACGTCAAAAATTGACAGCATATACATATATAATTGGACTGC-CTTATA
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATATAATTGGACTGCACTTATA
*
40175675 CATCAAAAATTAACAGCATATACATATATAATTGGACTGCATTTGTACATCAAAATTTGACAGCA
66 CATCAAAAATTAACAGCATATACATATATAATTGGACTGCATTTGTACATCAAAAATTGACAGCA
40175740 TATACAT
131 TATACAT
40175747 TCATTTACTC
Statistics
Matches: 387, Mismatches: 27, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
139 35 0.09
140 262 0.68
141 90 0.23
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.32
Consensus pattern (141 bp):
AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATATAATTGGACTGCACTTATA
CATCAAAAATTAACAGCATATACATATATAATTGGACTGCATTTGTACATCAAAAATTGACAGCA
TATACATATAT
Found at i:40176024 original size:14 final size:15
Alignment explanation
Indices: 40176000--40176034 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
40175990 TATATACATT
40176000 ACCATATAAATACTA
1 ACCATATAAATACTA
40176015 ACCATA-AAATACTA
1 ACCATATAAATACTA
40176029 ATCCAT
1 A-CCAT
40176035 GATTAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:40176773 original size:43 final size:43
Alignment explanation
Indices: 40176726--40176808 Score: 134
Period size: 43 Copynumber: 1.9 Consensus size: 43
40176716 AATCACATAC
40176726 CGATGCC-ACTGTCCCAGACAG-GGTCTTACACAAAAACACAAGT
1 CGATGCCGAC-GTCCCAGAC-GTGGTCTTACACAAAAACACAAGT
40176769 CGATGCCGACGTCCCAGACGTGGTCTTACACAAAAACACA
1 CGATGCCGACGTCCCAGACGTGGTCTTACACAAAAACACA
40176809 TATCGGAGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
42 1 0.03
43 35 0.92
44 2 0.05
ACGTcount: A:0.34, C:0.31, G:0.19, T:0.16
Consensus pattern (43 bp):
CGATGCCGACGTCCCAGACGTGGTCTTACACAAAAACACAAGT
Found at i:40183399 original size:47 final size:47
Alignment explanation
Indices: 40183348--40183950 Score: 962
Period size: 47 Copynumber: 12.9 Consensus size: 47
40183338 ATATTTACAA
* *
40183348 AATTGGACTGCACTTATACATAAAAAATTGACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
40183395 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
* * *
40183442 ATTTGGACTGCATTTGTACATAAAAAATTGACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
** * * *
40183489 AATTGGACTATAGTTATACGTCAAAAATTGATAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
* *
40183536 AATTGGACTGC-CTTATACATCAAAAATTAACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
40183582 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
* *
40183629 ATTTGGACTGCATTTGTACATC-AAAATTGACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
40183675 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
* * *
40183722 ATTTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
*
40183769 AATTGGACTGCATTTATACGTCAAAAATTGACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
* *
40183816 AATTGGACTGC-CTTATACATCAAAAATTAACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
* *
40183862 AATTGGACTGC-CTTATACATCAAAAACTGACAGCATATACATATAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
* *
40183908 AATTGGACTGCATTTGTACATCAAAATTTGACAGCATATACAT
1 AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACAT
40183951 TCATTTACTC
Statistics
Matches: 512, Mismatches: 41, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
46 173 0.34
47 339 0.66
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.32
Consensus pattern (47 bp):
AATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
Found at i:40183420 original size:93 final size:91
Alignment explanation
Indices: 40183323--40183950 Score: 763
Period size: 93 Copynumber: 6.7 Consensus size: 91
40183313 ATTTTCACAC
* * * *
40183323 CAAAATTTGGACAGCATATTTACAAAATTGGACTGCACTTATACATAAAAAATTGACAGCATATA
1 CAAAAATT-GACAGCATA-TTACAAAATTGGACTGCATTTGTACATCAAAAATTGACAGCATATA
40183388 CATATATAATTGGACTGCATTTATACAT
64 CATATATAATTGGACTGCATTTATACAT
*
40183416 CAAAAATTGACAGCATA-TACATATATATTTGGACTGCATTTGTACATAAAAAATTGACAGCATA
1 CAAAAATTGACAGCATATTACA-A-A-A-TTGGACTGCATTTGTACATCAAAAATTGACAGCATA
** * *
40183480 TACATATATAATTGGACTATAGTTATACGT
62 TACATATATAATTGGACTGCATTTATACAT
* * * *
40183510 CAAAAATTGATAGCATA-TACATATATAATTGGACTGC-CTTATACATCAAAAATTAACAGCATA
1 CAAAAATTGACAGCATATTAC--A-A-AATTGGACTGCATTTGTACATCAAAAATTGACAGCATA
40183573 TACATATATAATTGGACTGCATTTATACAT
62 TACATATATAATTGGACTGCATTTATACAT
40183603 CAAAAATTGACAGCATA-TACATATATATTTGGACTGCATTTGTACATC-AAAATTGACAGCATA
1 CAAAAATTGACAGCATATTACA-A-A-A-TTGGACTGCATTTGTACATCAAAAATTGACAGCATA
40183666 TACATATATAATTGGACTGCATTTATACAT
62 TACATATATAATTGGACTGCATTTATACAT
*
40183696 CAAAAATTGACAGCATA-TACATATATATTTGGACTGCATTTGTACATCAAAATTTGACAGCATA
1 CAAAAATTGACAGCATATTACA-A-A-A-TTGGACTGCATTTGTACATCAAAAATTGACAGCATA
*
40183760 TACATATATAATTGGACTGCATTTATACGT
62 TACATATATAATTGGACTGCATTTATACAT
* * *
40183790 CAAAAATTGACAGCATA-TACATATATAATTGGACTGC-CTTATACATCAAAAATTAACAGCATA
1 CAAAAATTGACAGCATATTAC--A-A-AATTGGACTGCATTTGTACATCAAAAATTGACAGCATA
*
40183853 TACATATATAATTGGACTGC-CTTATACAT
62 TACATATATAATTGGACTGCATTTATACAT
* *
40183882 CAAAAACTGACAGCATA-TACATATATAATTGGACTGCATTTGTACATCAAAATTTGACAGCATA
1 CAAAAATTGACAGCATATTAC--A-A-AATTGGACTGCATTTGTACATCAAAAATTGACAGCATA
40183946 TACAT
62 TACAT
40183951 TCATTTACTC
Statistics
Matches: 489, Mismatches: 33, Indels: 26
0.89 0.06 0.05
Matches are distributed among these distances:
90 4 0.01
91 6 0.01
92 54 0.11
93 245 0.50
94 168 0.34
95 2 0.00
96 10 0.02
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.32
Consensus pattern (91 bp):
CAAAAATTGACAGCATATTACAAAATTGGACTGCATTTGTACATCAAAAATTGACAGCATATACA
TATATAATTGGACTGCATTTATACAT
Found at i:40183788 original size:280 final size:279
Alignment explanation
Indices: 40183348--40183950 Score: 1071
Period size: 280 Copynumber: 2.2 Consensus size: 279
40183338 ATATTTACAA
* * *
40183348 AATTGGACTGCACTTATACATAAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATA
1 AATTGGACTGCATTTGTACAT-CAAAATTGACAGCATATACATATATAATTGGACTGCATTTATA
40183413 CATCAAAAATTGACAGCATATACATATATATTTGGACTGCATTTGTACATAAAAAATTGACAGCA
65 CATCAAAAATTGACAGCATATACATATATATTTGGACTGCATTTGTACATAAAAAATTGACAGCA
* *
40183478 TATACATATATAATTGGACTATAGTTATACGTCAAAAATTGATAGCATATACATATATAATTGGA
130 TATACATATATAATTGGACTACAGTTATACGTCAAAAATTGACAGCATATACATATATAATTGGA
*
40183543 CTGCCTTATACATCAAAAATTAACAGCATATACATATATAATTGGACTGCATTTATACATCAAAA
195 CTGCCTTATACATCAAAAATTAACAGCATATACATATATAATTGGACTGC-CTTATACATCAAAA
*
40183608 ATTGACAGCATATACATATAT
259 ACTGACAGCATATACATATAT
*
40183629 ATTTGGACTGCATTTGTACATCAAAATTGACAGCATATACATATATAATTGGACTGCATTTATAC
1 AATTGGACTGCATTTGTACATCAAAATTGACAGCATATACATATATAATTGGACTGCATTTATAC
* *
40183694 ATCAAAAATTGACAGCATATACATATATATTTGGACTGCATTTGTACATCAAAATTTGACAGCAT
66 ATCAAAAATTGACAGCATATACATATATATTTGGACTGCATTTGTACATAAAAAATTGACAGCAT
* *
40183759 ATACATATATAATTGGACTGCATTTATACGTCAAAAATTGACAGCATATACATATATAATTGGAC
131 ATACATATATAATTGGACTACAGTTATACGTCAAAAATTGACAGCATATACATATATAATTGGAC
40183824 TGCCTTATACATCAAAAATTAACAGCATATACATATATAATTGGACTGCCTTATACATCAAAAAC
196 TGCCTTATACATCAAAAATTAACAGCATATACATATATAATTGGACTGCCTTATACATCAAAAAC
40183889 TGACAGCATATACATATAT
261 TGACAGCATATACATATAT
40183908 AATTGGACTGCATTTGTACATCAAAATTTGACAGCATATACAT
1 AATTGGACTGCATTTGTACATCAAAA-TTGACAGCATATACAT
40183951 TCATTTACTC
Statistics
Matches: 308, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
279 58 0.19
280 232 0.75
281 18 0.06
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.32
Consensus pattern (279 bp):
AATTGGACTGCATTTGTACATCAAAATTGACAGCATATACATATATAATTGGACTGCATTTATAC
ATCAAAAATTGACAGCATATACATATATATTTGGACTGCATTTGTACATAAAAAATTGACAGCAT
ATACATATATAATTGGACTACAGTTATACGTCAAAAATTGACAGCATATACATATATAATTGGAC
TGCCTTATACATCAAAAATTAACAGCATATACATATATAATTGGACTGCCTTATACATCAAAAAC
TGACAGCATATACATATAT
Found at i:40184228 original size:14 final size:15
Alignment explanation
Indices: 40184204--40184238 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
40184194 TATATACATT
40184204 ACCATATAAATACTA
1 ACCATATAAATACTA
40184219 ACCATA-AAATACTA
1 ACCATATAAATACTA
40184233 ATCCAT
1 A-CCAT
40184239 GATTAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:40186332 original size:18 final size:18
Alignment explanation
Indices: 40186304--40186345 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
40186294 GAGTGGAAAA
*
40186304 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGTT
*
40186322 ATGATACATATAAGGGTT
1 AGGATACATATAAGGGTT
40186340 AGGATA
1 AGGATA
40186346 TGCACCTAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.43, C:0.05, G:0.26, T:0.26
Consensus pattern (18 bp):
AGGATACATATAAGGGTT
Found at i:40187334 original size:49 final size:49
Alignment explanation
Indices: 40187258--40187357 Score: 164
Period size: 49 Copynumber: 2.0 Consensus size: 49
40187248 GGCAATCTCC
* *
40187258 GATTTTGATTTTATTTGGTTACGTCGCCCGACACATCTCCCGATACAAT
1 GATTTTGATTTTATTTAGTTACGTCGCCCAACACATCTCCCGATACAAT
* *
40187307 GATTTTGATTTTATTTAGTTGCTTCGCCCAACACATCTCCCGATACAAT
1 GATTTTGATTTTATTTAGTTACGTCGCCCAACACATCTCCCGATACAAT
40187356 GA
1 GA
40187358 CAACAACATA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (49 bp):
GATTTTGATTTTATTTAGTTACGTCGCCCAACACATCTCCCGATACAAT
Found at i:40187969 original size:31 final size:34
Alignment explanation
Indices: 40187916--40187992 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 34
40187906 CCGACTGATA
* *
40187916 TAAAAAATT-ATA-AAAAATTATTAATTAA-A-T
1 TAAAAAATTGAAATAAAAATTATTAAATAATATT
40187946 TACAAAAA-TGAAATAAAAA-TATTAAATAATATT
1 TA-AAAAATTGAAATAAAAATTATTAAATAATATT
40187979 TAAAAAATTGAAAT
1 TAAAAAATTGAAAT
40187993 TAACTCTTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
30 3 0.08
31 16 0.41
32 11 0.28
33 9 0.23
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (34 bp):
TAAAAAATTGAAATAAAAATTATTAAATAATATT
Found at i:40194076 original size:3 final size:3
Alignment explanation
Indices: 40194068--40194112 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
40194058 ACAAATTTCA
40194068 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40194113 ACTCTTTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40199043 original size:8 final size:8
Alignment explanation
Indices: 40199030--40199085 Score: 58
Period size: 8 Copynumber: 6.4 Consensus size: 8
40199020 TGAGTTCAAA
40199030 AAAAAATC
1 AAAAAATC
40199038 AAAAAAATC
1 -AAAAAATC
40199047 AAAAAAAAATC
1 ---AAAAAATC
40199058 AAAAAATC
1 AAAAAATC
*
40199066 AAAAAATTA
1 AAAAAA-TC
40199075 AAAAAATC
1 AAAAAATC
40199083 AAA
1 AAA
40199086 GTCAAAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
8 18 0.43
9 15 0.36
11 9 0.21
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAATC
Found at i:40199043 original size:9 final size:9
Alignment explanation
Indices: 40199029--40199085 Score: 73
Period size: 9 Copynumber: 6.3 Consensus size: 9
40199019 ATGAGTTCAA
40199029 AAAAAAATC
1 AAAAAAATC
40199038 AAAAAAATC
1 AAAAAAATC
40199047 AAAAAAAAATC
1 --AAAAAAATC
40199058 -AAAAAATC
1 AAAAAAATC
*
40199066 -AAAAAATT
1 AAAAAAATC
40199074 AAAAAAATC
1 AAAAAAATC
40199083 AAA
1 AAA
40199086 GTCAAAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
8 15 0.35
9 19 0.44
11 9 0.21
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAAATC
Found at i:40199050 original size:20 final size:19
Alignment explanation
Indices: 40199025--40199071 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 19
40199015 TCTCATGAGT
40199025 TCAAAAAAAAATCAAAAAAA
1 TCAAAAAAAAATC-AAAAAA
40199045 TCAAAAAAAAATCAAAAAA
1 TCAAAAAAAAATCAAAAAA
40199064 TCAAAAAA
1 TCAAAAAA
40199072 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (19 bp):
TCAAAAAAAAATCAAAAAA
Found at i:40199080 original size:11 final size:11
Alignment explanation
Indices: 40199025--40199063 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
40199015 TCTCATGAGT
40199025 TCAAAAAAAAA
1 TCAAAAAAAAA
40199036 TC--AAAAAAA
1 TCAAAAAAAAA
40199045 TCAAAAAAAAA
1 TCAAAAAAAAA
40199056 TCAAAAAA
1 TCAAAAAA
40199064 TCAAAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.35
11 17 0.65
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (11 bp):
TCAAAAAAAAA
Found at i:40199983 original size:8 final size:8
Alignment explanation
Indices: 40199947--40199976 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
40199937 TTGAGTCAAA
40199947 AAAAAGATG
1 AAAAA-ATG
40199956 AAAAAATG
1 AAAAAATG
40199964 AAAAAATG
1 AAAAAATG
40199972 AAAAA
1 AAAAA
40199977 GTAAAAATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (8 bp):
AAAAAATG
Found at i:40199983 original size:16 final size:17
Alignment explanation
Indices: 40199946--40199983 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
40199936 TTTGAGTCAA
40199946 AAAAAAGATGAAAAAAT
1 AAAAAAGATGAAAAAAT
* *
40199963 GAAAAA-ATGAAAAAGT
1 AAAAAAGATGAAAAAAT
40199979 AAAAA
1 AAAAA
40199984 TGGAGAGGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (17 bp):
AAAAAAGATGAAAAAAT
Found at i:40201538 original size:175 final size:170
Alignment explanation
Indices: 40201157--40201887 Score: 1102
Period size: 170 Copynumber: 4.2 Consensus size: 170
40201147 GTTCATTATA
* * * * *
40201157 CAGGTCTTATTTCCCTGAGATTACGGTGGAATAGACCGAAGAATTGCAGATCTTATCTCCTTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAGATCTTATCTCCCTGAG
*
40201222 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTTCCTGAGATTACAGTGGAGCGAATTAAA
66 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGAATTAAA
40201287 GGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCAC
131 GGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCAC
40201327 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAGATCTTATCTCCCTGAG
* *
40201392 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGATATTACAGTGGAGCGGATTAAA
66 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGAATT---
*
40201457 ACCAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCGGATCGCAC
128 A--AAGGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCAC
*
40201502 CAGGTCTTATTTCCCTGAGATTACACTGGAACAGACTGAAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAGATCTTATCTCCCTGAG
* *
40201567 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAGA
66 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGAATTAAA
*
40201632 GGATCTTATCTCTCTGAAGTTATAGTAGAGCAGATCGCAC
131 GGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCAC
* * *
40201672 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGATTGAAGAATTTCAGATTTTATCTCCCTAAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAGATCTTATCTCCCTGAG
* * * *
40201737 ATTACAGCGGAGCATATTGAAGCTAGTAATCCCATCTCCTTGAGATTAAAGTGGAGCGAATTAAA
66 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGAA-T---
* ***
40201802 ATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTGT
127 -TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCAC
* * * * * *
40201847 CAGATCTTATCTCCCCGAGATTACAGCGGAGCAGATTGAAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAG
40201888 CTAGTAATCC
Statistics
Matches: 517, Mismatches: 34, Indels: 15
0.91 0.06 0.03
Matches are distributed among these distances:
170 274 0.53
171 1 0.00
172 1 0.00
173 1 0.00
175 240 0.46
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (170 bp):
CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAGATCTTATCTCCCTGAG
ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGAATTAAA
GGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCAC
Found at i:40201792 original size:345 final size:345
Alignment explanation
Indices: 40201157--40201836 Score: 1171
Period size: 345 Copynumber: 2.0 Consensus size: 345
40201147 GTTCATTATA
** * *
40201157 CAGGTCTTATTTCCCTGAGATTACGGTGGAATAGACCGAAGAATTGCAGATCTTATCTCCTTGAG
1 CAGGTCTTATTTCCCTGAGATTACACTGGAACAGACCGAAGAATTGCAGATCTTATCTCCCTGAG
*
40201222 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTTCCTGAGATTACAGTGGAGCGAATTAAA
66 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGAATTAAA
40201287 GGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCACCAGGTCTTATTTCCCTGAGATTACA
131 GGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCACCAGGTCTTATTTCCCTGAGATTACA
*
40201352 GTGGAACAGACTGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTA
196 GTGGAACAGACTGAAGAATTTCAGATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTA
* * * * *
40201417 GTAATCCTATCTCCCTGATATTACAGTGGAGCGGATTAAAACCAAGGATCTTATCTCTCTGAAGT
261 GTAATCCCATCTCCCTGAGATTAAAGTGGAGCGAATTAAAACAAAGGATCTTATCTCTCTGAAGT
40201482 TACAGTAGAGCGGATCGCAC
326 TACAGTAGAGCGGATCGCAC
* *
40201502 CAGGTCTTATTTCCCTGAGATTACACTGGAACAGACTGAAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACACTGGAACAGACCGAAGAATTGCAGATCTTATCTCCCTGAG
* *
40201567 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAGA
66 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGAATTAAA
*
40201632 GGATCTTATCTCTCTGAAGTTATAGTAGAGCAGATCGCACCAGGTCTTATTTCCCTGAGATTACA
131 GGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCACCAGGTCTTATTTCCCTGAGATTACA
* * *
40201697 GTGGAACAGATTGAAGAATTTCAGATTTTATCTCCCTAAGATTACAGCGGAGCATATTGAAGCTA
196 GTGGAACAGACTGAAGAATTTCAGATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTA
* *
40201762 GTAATCCCATCTCCTTGAGATTAAAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTCTGAAGT
261 GTAATCCCATCTCCCTGAGATTAAAGTGGAGCGAATTAAAACAAAGGATCTTATCTCTCTGAAGT
40201827 TACAGTAGAG
326 TACAGTAGAG
40201837 TAGATCGTGT
Statistics
Matches: 314, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
345 314 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (345 bp):
CAGGTCTTATTTCCCTGAGATTACACTGGAACAGACCGAAGAATTGCAGATCTTATCTCCCTGAG
ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGAATTAAA
GGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCACCAGGTCTTATTTCCCTGAGATTACA
GTGGAACAGACTGAAGAATTTCAGATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTA
GTAATCCCATCTCCCTGAGATTAAAGTGGAGCGAATTAAAACAAAGGATCTTATCTCTCTGAAGT
TACAGTAGAGCGGATCGCAC
Found at i:40202011 original size:345 final size:345
Alignment explanation
Indices: 40201161--40201933 Score: 1049
Period size: 345 Copynumber: 2.2 Consensus size: 345
40201151 ATTATACAGG
* * ** * * *
40201161 TCTTATTTCCCTGAGATTACGGTGGAATAGACCGAAGAAT-TGCAGATCTTATCTC-CTTGAGAT
1 TCTTATCTCCCCGAGATTACACTGGAACAGACTGAAGAATGT-CAGATCCTATCTCAC-TGAGAT
** * * *
40201224 TACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTTCCTGAGATTACAGTGGAGC-GAATTAAAG
64 TACAGCGGAGCAGATTGAAAATAGTAATCCTATCTCCCTGAGATTACAGTAGAGCAG-ATTAGAG
40201288 GATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCACCAGGTCTTATTTCCCTGAGATTACAG
128 GATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCACCAGGTCTTATTTCCCTGAGATTACAG
*
40201353 TGGAACAGACTGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAG
193 TGGAACAGACTGAAGAATTTCAGATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAG
* * * * *
40201418 TAATCCTATCTCCCTGATATTACAGTGGAGCGGATTAAAACCAAGGATCTTATCTCTCTGAAGTT
258 TAATCCCATCTCCCTGAGATTAAAGTGGAGCGAATTAAAACAAAGGATCTTATCTCTCTGAAGTT
* *
40201483 ACAGTAGAGCGGATCGCACCAGG
323 ACAGTAGAGCAGATCGCACCAGA
* * * * *
40201506 TCTTATTTCCCTGAGATTACACTGGAACAGACTGAAGAATTTCAGATCTTATCTCCCTGAGATTA
1 TCTTATCTCCCCGAGATTACACTGGAACAGACTGAAGAATGTCAGATCCTATCTCACTGAGATTA
** * *
40201571 CAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAGAGGAT
66 CAGCGGAGCAGATTGAAAATAGTAATCCTATCTCCCTGAGATTACAGTAGAGCAGATTAGAGGAT
*
40201636 CTTATCTCTCTGAAGTTATAGTAGAGCAGATCGCACCAGGTCTTATTTCCCTGAGATTACAGTGG
131 CTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCACCAGGTCTTATTTCCCTGAGATTACAGTGG
* * *
40201701 AACAGATTGAAGAATTTCAGATTTTATCTCCCTAAGATTACAGCGGAGCATATTGAAGCTAGTAA
196 AACAGACTGAAGAATTTCAGATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAA
* *
40201766 TCCCATCTCCTTGAGATTAAAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTCTGAAGTTACA
261 TCCCATCTCCCTGAGATTAAAGTGGAGCGAATTAAAACAAAGGATCTTATCTCTCTGAAGTTACA
* ***
40201831 GTAGAGTAGATCGTGTCAGA
326 GTAGAGCAGATCGCACCAGA
* * *
40201851 TCTTATCTCCCCGAGATTACAGC-GGAGCAGATTGAAG-CTAGT-A-ATCCTATCTCACTGAGAT
1 TCTTATCTCCCCGAGATTACA-CTGGAACAGACTGAAGAAT-GTCAGATCCTATCTCACTGAGAT
* *
40201912 TACAGTGGAGTAGATT-AAAATA
64 TACAGCGGAGCAGATTGAAAATA
40201934 AAGGATCTTA
Statistics
Matches: 387, Mismatches: 36, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
342 4 0.01
343 30 0.08
344 2 0.01
345 347 0.90
346 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (345 bp):
TCTTATCTCCCCGAGATTACACTGGAACAGACTGAAGAATGTCAGATCCTATCTCACTGAGATTA
CAGCGGAGCAGATTGAAAATAGTAATCCTATCTCCCTGAGATTACAGTAGAGCAGATTAGAGGAT
CTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCACCAGGTCTTATTTCCCTGAGATTACAGTGG
AACAGACTGAAGAATTTCAGATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAA
TCCCATCTCCCTGAGATTAAAGTGGAGCGAATTAAAACAAAGGATCTTATCTCTCTGAAGTTACA
GTAGAGCAGATCGCACCAGA
Found at i:40202163 original size:129 final size:129
Alignment explanation
Indices: 40201717--40202163 Score: 642
Period size: 129 Copynumber: 3.5 Consensus size: 129
40201707 TTGAAGAATT
* * * * * *
40201717 TCAGATTTTATCTCCCTAAGATTACAGCGGAGCATATTGAAGCTAGTAATCCCATCTCCTTGAGA
1 TCAGATCTTACCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* *
40201782 TTAAAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTG
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTG
* * *
40201846 TCAGATCTTATCTCCCCGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCACTGAGA
1 TCAGATCTTACCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
**
40201911 TTACAGTGGAGTAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTG
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTG
*
40201975 TCAGATCTTACCTCTCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGATCTTACCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* * **
40202040 TTACAGTGGAGCGGATTAAAATAAAGGATTTTATCACTCTGAAGTTACAGTAGAGTAGATCGCA
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTG
* * * * * * * * * *
40202104 TCAGGTTTTACCTCCCTGTGGTTACAGTGGAGTACATAGAAGCCAGTAATTCTATCTCCC
1 TCAGATCTTACCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCC
40202164 CGACATTGCG
Statistics
Matches: 286, Mismatches: 32, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
129 286 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (129 bp):
TCAGATCTTACCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTG
Found at i:40202250 original size:258 final size:255
Alignment explanation
Indices: 40201726--40202251 Score: 552
Period size: 258 Copynumber: 2.0 Consensus size: 255
40201716 TTCAGATTTT
* * * *
40201726 ATCTCCCTAAGATTACAGCGGAGCATATTGAAGCTAGTAATCCCATCTCCTTGAGATTAAAGTGG
1 ATCTCTCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCCATCTCCCTGAGATTAAAGTGG
* **
40201791 AGCGAATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTGTCAGATCTTA
66 AGCGAATTAAAATAAAGGATCTTATCACTCTGAAGTTACAGTAGAGTAGATCGCATCAGATCTTA
* * * * * * *
40201856 TCTCCCCGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCACTGAGATTACAGTGGA
131 CCTCCCCGAGATTACAGCGGAGCACATAGAAGCCAGTAATCCTATCTCACCGACATT--AGCGGA
** * * * * * *** **
40201921 GTAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTGTCAGATCTT
194 GTAGACCAAAACAAAGGA-CCTATCTCCCTGAAGTTACAGTAGAGCAGATAGCCACAGATCCG
* * *
40201984 ACCTCTCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGG
1 ATCTCTCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCCATCTCCCTGAGATTAAAGTGG
* * * *
40202049 AGCGGATTAAAATAAAGGATTTTATCACTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTTTTA
66 AGCGAATTAAAATAAAGGATCTTATCACTCTGAAGTTACAGTAGAGTAGATCGCATCAGATCTTA
* * * * * * *
40202114 CCTCCCTGTGGTTACAGTGGAGTACATAGAAGCCAGTAATTCTATCTCCCCGACATT-GCGGAGT
131 CCTCCCCGAGATTACAGCGGAGCACATAGAAGCCAGTAATCCTATCTCACCGACATTAGCGGAGT
* * * * * *
40202178 AGGCCAGAGCACCAATG-CCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAACCACAGATCCG
196 AGACCA-A-AACAAAGGACCTATCTCCCTGAAGTTACAGTAGAGCAGA-TAG--CCACAGATCCG
40202242 ATCTCTCTGA
1 ATCTCTCTGA
40202252 AGGGCAGTAG
Statistics
Matches: 216, Mismatches: 47, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
255 34 0.16
256 3 0.01
257 4 0.02
258 175 0.81
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (255 bp):
ATCTCTCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCCATCTCCCTGAGATTAAAGTGG
AGCGAATTAAAATAAAGGATCTTATCACTCTGAAGTTACAGTAGAGTAGATCGCATCAGATCTTA
CCTCCCCGAGATTACAGCGGAGCACATAGAAGCCAGTAATCCTATCTCACCGACATTAGCGGAGT
AGACCAAAACAAAGGACCTATCTCCCTGAAGTTACAGTAGAGCAGATAGCCACAGATCCG
Found at i:40203553 original size:3 final size:3
Alignment explanation
Indices: 40203545--40203574 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
40203535 ACAAATTTCA
*
40203545 TAT TAT TAT TAT TAT TCT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40203575 ACTCTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40205100 original size:24 final size:24
Alignment explanation
Indices: 40205073--40205124 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
40205063 TTAGTAAGTC
*
40205073 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
40205097 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
40205121 AAAT
1 AAAT
40205125 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:40207859 original size:21 final size:21
Alignment explanation
Indices: 40207835--40207913 Score: 61
Period size: 21 Copynumber: 3.6 Consensus size: 21
40207825 ATATATATTC
40207835 TTTAGAATTTTTTTAAAAAAA
1 TTTAGAATTTTTTTAAAAAAA
* *
40207856 TTTATAATTTTTTAAAATATATATA
1 TTTAGAATTTTTTTAAA-A-A-A-A
* *
40207881 TTTTAGAA-TTTTTTATAAATA
1 -TTTAGAATTTTTTTAAAAAAA
*
40207902 TTTTGAATTTTT
1 TTTAGAATTTTT
40207914 GAATTTTTTG
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
20 6 0.13
21 20 0.44
22 1 0.02
23 2 0.04
24 2 0.04
25 8 0.18
26 6 0.13
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
TTTAGAATTTTTTTAAAAAAA
Found at i:40207880 original size:19 final size:19
Alignment explanation
Indices: 40207843--40207884 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
40207833 TCTTTAGAAT
*
40207843 TTTTTTAAAAAAATTTATAA
1 TTTTTTAAAAAAATATAT-A
*
40207863 TTTTTT-AAAATATATATA
1 TTTTTTAAAAAAATATATA
40207881 TTTT
1 TTTT
40207885 AGAATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 9 0.45
20 6 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTTTAAAAAAATATATA
Found at i:40207911 original size:20 final size:21
Alignment explanation
Indices: 40207873--40207913 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
40207863 TTTTTTAAAA
*
40207873 TATATATATTTTAGAATTTTT
1 TATAAATATTTTAGAATTTTT
40207894 TATAAATATTTT-GAATTTTT
1 TATAAATATTTTAGAATTTTT
40207914 GAATTTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
TATAAATATTTTAGAATTTTT
Found at i:40207912 original size:28 final size:26
Alignment explanation
Indices: 40207824--40207902 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 26
40207814 TAACATTCTT
*
40207824 TATATATATTCTTTAGAATTTTTTTAAA
1 TATATATA-T-TTTAGAATTTTTTAAAA
*
40207852 -A-A-A-A-TTTATAATTTTTTAAAA
1 TATATATATTTTAGAATTTTTTAAAA
40207873 TATATATATTTTAGAATTTTTTATAAA
1 TATATATATTTTAGAATTTTTTA-AAA
40207900 TAT
1 TAT
40207903 TTTGAATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
21 15 0.36
22 1 0.02
23 1 0.02
24 2 0.05
25 2 0.05
26 14 0.33
27 7 0.17
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (26 bp):
TATATATATTTTAGAATTTTTTAAAA
Found at i:40213395 original size:15 final size:15
Alignment explanation
Indices: 40213375--40213411 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
40213365 CTCCGAGAGT
40213375 TGAAAACTTTATTAA
1 TGAAAACTTTATTAA
40213390 TGAAAACTTTATTAA
1 TGAAAACTTTATTAA
40213405 TGAAAAC
1 TGAAAAC
40213412 AATTGTGTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (15 bp):
TGAAAACTTTATTAA
Found at i:40216503 original size:30 final size:32
Alignment explanation
Indices: 40216443--40216506 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
40216433 CACTTATTTT
40216443 CACCTATGCCGAATGCATACACATAAATATATC
1 CACCTATGCCGAATGCA-ACACATAAATATATC
* *
40216476 CACCTATGCCGAATGCAACATATATATATAT
1 CACCTATGCCGAATGCAACACATAAATATAT
40216507 ACATATCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (32 bp):
CACCTATGCCGAATGCAACACATAAATATATC
Found at i:40216766 original size:41 final size:41
Alignment explanation
Indices: 40216721--40216917 Score: 317
Period size: 41 Copynumber: 4.8 Consensus size: 41
40216711 ACCGGCTCTT
*
40216721 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
40216762 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
40216803 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
40216844 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
40216885 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
40216918 TAACGATAAA
Statistics
Matches: 148, Mismatches: 4, Indels: 8
0.93 0.03 0.05
Matches are distributed among these distances:
39 2 0.01
40 2 0.01
41 139 0.94
42 2 0.01
43 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:40218470 original size:13 final size:13
Alignment explanation
Indices: 40218452--40218476 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40218442 CCATCGAATG
40218452 CACACAAAATAAA
1 CACACAAAATAAA
40218465 CACACAAAATAA
1 CACACAAAATAA
40218477 TATTAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:40223808 original size:16 final size:16
Alignment explanation
Indices: 40223787--40223819 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
40223777 TTCGCTGTAT
40223787 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
40223803 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
40223819 T
1 T
40223820 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.36, T:0.24
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:40223864 original size:45 final size:44
Alignment explanation
Indices: 40223799--40223888 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 44
40223789 GAATAGAGGC
**
40223799 GTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAAT
1 GTAATGGAATAGAGACGTAATAG-AAATCAACTGTTTGGTTGAAT
* ***
40223844 GTAATGGAATAGAGACGTAATAGTAATCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGACGTAATAGAAATCAACTGTTTGGTTGAAT
40223888 G
1 G
40223889 AAATAGAGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 18 0.46
45 21 0.54
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (44 bp):
GTAATGGAATAGAGACGTAATAGAAATCAACTGTTTGGTTGAAT
Found at i:40224088 original size:18 final size:16
Alignment explanation
Indices: 40224037--40224080 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
40224027 ATTTAATCAT
* *
40224037 ATTTAAACATAATTATT
1 ATTTAAATAT-ATTATA
40224054 A-TTAAATATATTATA
1 ATTTAAATATATTATA
40224069 ATTTAAATATAT
1 ATTTAAATATAT
40224081 AATTTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.25
16 17 0.71
17 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTAAATATATTATA
Found at i:40224185 original size:120 final size:120
Alignment explanation
Indices: 40224042--40224439 Score: 729
Period size: 120 Copynumber: 3.4 Consensus size: 120
40224032 ATCATATTTA
* *
40224042 AACATAATTATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
40224107 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
40224162 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
40224227 TATTCTTATATGAATTTACTCAAATCATAATATAT-ATACTATAAAATAT-AATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
40224280 AA-ATAATTATTATTAAATATATT-TAATTAAAATATATAATTTAATAAAATT-TTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
40224342 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
40224397 AACAT-ATTATTATTAAATATATTATAATT-AAATATATAATTTA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTA
40224440 TTATTAAATA
Statistics
Matches: 272, Mismatches: 2, Indels: 11
0.95 0.01 0.04
Matches are distributed among these distances:
115 46 0.17
116 42 0.15
117 59 0.22
118 13 0.05
119 14 0.05
120 98 0.36
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:40224207 original size:14 final size:15
Alignment explanation
Indices: 40224158--40224209 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40224148 ATAAAATATA
40224158 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
40224173 TATTAAATATATTAT
1 AATTAAATATATTAT
40224188 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
40224201 AATTTAATA
1 AATTAAATA
40224210 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:40224308 original size:14 final size:14
Alignment explanation
Indices: 40224275--40224325 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
40224265 CTATAAAATA
40224275 TAATTAAATA-ATT
1 TAATTAAATATATT
*
40224288 ATTATTAAATATATT
1 -TAATTAAATATATT
*
40224303 TAATTAAA-ATATA
1 TAATTAAATATATT
*
40224316 TAATTTAATA
1 TAATTAAATA
40224326 AAATTTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 11 0.35
14 17 0.55
15 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATTAAATATATT
Found at i:40224316 original size:17 final size:17
Alignment explanation
Indices: 40224296--40224329 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
40224286 TTATTATTAA
40224296 ATAT-ATTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
40224313 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
40224330 TTTAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:40224420 original size:15 final size:15
Alignment explanation
Indices: 40224400--40224454 Score: 65
Period size: 15 Copynumber: 3.4 Consensus size: 15
40224390 ATAAATTAAC
40224400 ATATTATTATTAAAT
1 ATATTATTATTAAAT
*
40224415 ATATTATAATTAAATAT
1 ATATTATTATT-AA-AT
40224432 ATAATTTATTATTAAAT
1 AT-A-TTATTATTAAAT
40224449 ATATTA
1 ATATTA
40224455 CAATTTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
15 13 0.38
16 3 0.09
17 8 0.24
18 3 0.09
19 7 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATTATTATTAAAT
Found at i:40224445 original size:19 final size:17
Alignment explanation
Indices: 40224400--40224452 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 17
40224390 ATAAATTAAC
40224400 ATATTATTATT-AA-AT
1 ATATTATTATTAAATAT
*
40224415 ATATTATAATTAAATAT
1 ATATTATTATTAAATAT
40224432 ATAATTTATTATTAAATAT
1 AT-A-TTATTATTAAATAT
40224451 AT
1 AT
40224453 TACAATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 10 0.31
16 2 0.06
17 4 0.12
18 1 0.03
19 15 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTATTATTAAATAT
Found at i:40224483 original size:16 final size:16
Alignment explanation
Indices: 40224408--40224485 Score: 56
Period size: 16 Copynumber: 4.8 Consensus size: 16
40224398 ACATATTATT
*
40224408 ATTAAATAT-ATTATA
1 ATTAAATATAATTACA
**
40224423 ATTAAATATATAATTTATT
1 ATT-AA-ATATAA-TTACA
40224442 ATTAAATAT-ATTACA
1 ATTAAATATAATTACA
40224457 ATTTAAA-ATAATTA-A
1 A-TTAAATATAATTACA
40224472 CATTAAATATAATT
1 -ATTAAATATAATT
40224486 TAATAATGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 15
0.74 0.04 0.21
Matches are distributed among these distances:
15 15 0.29
16 19 0.37
17 8 0.15
18 3 0.06
19 7 0.13
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAAATATAATTACA
Found at i:40229566 original size:13 final size:13
Alignment explanation
Indices: 40229548--40229575 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40229538 CAATACAGGC
40229548 AAGAACCGAAACA
1 AAGAACCGAAACA
40229561 AAGAACCGAAACA
1 AAGAACCGAAACA
40229574 AA
1 AA
40229576 TAATGCAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.21, G:0.14, T:0.00
Consensus pattern (13 bp):
AAGAACCGAAACA
Found at i:40232143 original size:15 final size:15
Alignment explanation
Indices: 40232108--40232149 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
40232098 TTTTTTTATA
40232108 AATTTTTA-ATAAAT
1 AATTTTTACATAAAT
*
40232122 ATATTTTTACATAAGT
1 A-ATTTTTACATAAAT
40232138 -ATTTTTACATAA
1 AATTTTTACATAA
40232150 TTTTTTTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 13 0.52
15 7 0.28
16 5 0.20
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (15 bp):
AATTTTTACATAAAT
Found at i:40232156 original size:14 final size:14
Alignment explanation
Indices: 40232123--40232149 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40232113 TTAATAAATA
40232123 TATTTTTACATAAG
1 TATTTTTACATAAG
40232137 TATTTTTACATAA
1 TATTTTTACATAA
40232150 TTTTTTTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (14 bp):
TATTTTTACATAAG
Found at i:40237336 original size:46 final size:46
Alignment explanation
Indices: 40237262--40237414 Score: 265
Period size: 46 Copynumber: 3.4 Consensus size: 46
40237252 TACATATAAT
* *
40237262 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
40237306 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
40237352 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
40237398 CACTTATCACTTTGTCA
1 CACTTATCACTTTGTCA
40237415 ACTAAAGCTA
Statistics
Matches: 104, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
44 10 0.10
45 5 0.05
46 89 0.86
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:40237420 original size:28 final size:28
Alignment explanation
Indices: 40237388--40237442 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
40237378 ATAAGTGTAG
40237388 CTAAAGCTAACACTTATCACTTTGTCAA
1 CTAAAGCTAACACTTATCACTTTGTCAA
40237416 CTAAAGCTAACACTTATCACTTTGTCA
1 CTAAAGCTAACACTTATCACTTTGTCA
40237443 CTTGATCAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (28 bp):
CTAAAGCTAACACTTATCACTTTGTCAA
Found at i:40237463 original size:74 final size:74
Alignment explanation
Indices: 40237342--40237488 Score: 285
Period size: 74 Copynumber: 2.0 Consensus size: 74
40237332 ATAAGTGTAG
*
40237342 CTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCA
1 CTAAAGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCA
40237407 CTTTGTCAA
66 CTTTGTCAA
40237416 CTAAAGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCA
1 CTAAAGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCA
40237481 CTTTGTCA
66 CTTTGTCA
40237489 CTTGATCAGA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (74 bp):
CTAAAGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCA
CTTTGTCAA
Found at i:40237469 original size:46 final size:46
Alignment explanation
Indices: 40237416--40237544 Score: 231
Period size: 46 Copynumber: 2.8 Consensus size: 46
40237406 ACTTTGTCAA
40237416 CTAAAGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CTAAAGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
40237462 CTAAAGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CTAAAGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
* * *
40237508 CTAAAGCTACCACTTATCACTTTATCTCTTGATCAGA
1 CTAAAGCTAACACTTATCACTTTGTCACTTGATCAGA
40237545 AGTACTCAAA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 80 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (46 bp):
CTAAAGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
Found at i:40237522 original size:120 final size:120
Alignment explanation
Indices: 40237296--40237530 Score: 434
Period size: 120 Copynumber: 2.0 Consensus size: 120
40237286 ATAAGTGTAG
* * *
40237296 CTAAGGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCA
1 CTAAAGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCA
40237361 CTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCAA
66 CTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCAA
40237416 CTAAAGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCA
1 CTAAAGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCA
*
40237481 CTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
66 CTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTT
40237531 ATCTCTTGAT
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 111 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (120 bp):
CTAAAGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCA
CTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCAA
Found at i:40240088 original size:18 final size:18
Alignment explanation
Indices: 40240065--40240107 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
40240055 AGGGGTAGTG
*
40240065 GGCCCAAGAGGAGCATTC
1 GGCCCAAAAGGAGCATTC
*
40240083 GGCCCAAAAGGAGCATTT
1 GGCCCAAAAGGAGCATTC
40240101 GGCCCAA
1 GGCCCAA
40240108 TATTAGTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.30, T:0.12
Consensus pattern (18 bp):
GGCCCAAAAGGAGCATTC
Found at i:40240295 original size:21 final size:21
Alignment explanation
Indices: 40240271--40240311 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40240261 TATACCCATC
40240271 AGCACACA-CATTTTGACCAGA
1 AGCACA-ATCATTTTGACCAGA
*
40240292 AGCACAATTATTTTGACCAG
1 AGCACAATCATTTTGACCAG
40240312 CCCCAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (21 bp):
AGCACAATCATTTTGACCAGA
Found at i:40246158 original size:19 final size:20
Alignment explanation
Indices: 40246121--40246162 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
40246111 AAAAAACTTT
40246121 CAAAATATAATTTTATTAAA
1 CAAAATATAATTTTATTAAA
40246141 CAAAA-ATAATATTT-TTAAA
1 CAAAATATAAT-TTTATTAAA
40246160 CAA
1 CAA
40246163 TAAGTGTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (20 bp):
CAAAATATAATTTTATTAAA
Found at i:40246637 original size:12 final size:12
Alignment explanation
Indices: 40246620--40246683 Score: 64
Period size: 11 Copynumber: 5.6 Consensus size: 12
40246610 TTTTCACAAA
40246620 CAAATTCTCTCT
1 CAAATTCTCTCT
*
40246632 CAAATTTTCTCT
1 CAAATTCTCTCT
*
40246644 CAATTTC-CTCT
1 CAAATTCTCTCT
*
40246655 CAATTTC-CT-T
1 CAAATTCTCTCT
40246665 CCAAATT-TCTCT
1 -CAAATTCTCTCT
40246677 CAAATTC
1 CAAATTC
40246684 ATATTTAATC
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
10 1 0.02
11 26 0.59
12 17 0.39
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (12 bp):
CAAATTCTCTCT
Done.