Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013817.1 Kokia drynarioides strain JFW-HI SEQ_128845, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 333904
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 141 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1824 original size:202 final size:202
Alignment explanation
Indices: 1463--2318 Score: 1087
Period size: 202 Copynumber: 4.2 Consensus size: 202
1453 GCGATTATCC
* * *
1463 ACAAACGATGTAGTCATCTTCTTGATGAGATACTGAGAAGAAGACCCAAACAAGGCTCAAAGTGA
1 ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCCAAACAAGGCTCAAAGTGA
* * *
1528 GCAAAATCTTCGAACCCCAGCTTCCTGATAAGACACAGAGAAGCGGGTCGAAGCAATAAAGTGGT
66 GCAAAATCTTCGAACCCCAACTTCCTGATGAGACACAGAGAAGCAGGTCGAAGCAATAAAGTGGT
* *
1593 TAGCTCCCTGATGAGATACTGAGAAGTGAACGAAATTCGCCTTCCTGATGAGATACAGAGAAGCG
131 TAGCTCCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCTTGATGAGATACAGAGAAGCG
1658 AATTGAA
196 AATTGAA
* * * * * *
1665 ACAAACTACGCGGTCATCTTCCTGATGAGACACTGAAAAGAAGACCCAAACGAGGCTCAGAGTGA
1 ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCCAAACAAGGCTCAAAGTGA
*
1730 GCAAAATCTTCGAACCCCAACTTCCTGATGAGACACAGAGAAGCGGGTCGAAGCAATAAAGTGGT
66 GCAAAATCTTCGAACCCCAACTTCCTGATGAGACACAGAGAAGCAGGTCGAAGCAATAAAGTGGT
*
1795 TAGCTCCCTGATGAGATACTG-GTAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGAGAAGC
131 TAGCTCCCTGATGAGATACTGAG-AAGTGAACCAAATTCGCCTTCTTGATGAGATACAGAGAAGC
*
1859 AAATTGAA
195 GAATTGAA
* * * *
1867 ACAAACGACGCGGTCATCTTCCTGATGAGACACTGAAAAGAAGACCCAAAAAAGG--CAAAGTGA
1 ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCCAAACAAGGCTCAAAGTGA
* * * *
1930 GCAAAATATTCGAACCCCAACTTCCTGATGAGACACTGAGAAGCAGATCGAAGCAATAAAATGGT
66 GCAAAATCTTCGAACCCCAACTTCCTGATGAGACACAGAGAAGCAGGTCGAAGCAATAAAGTGGT
* * * * * * *
1995 TAGCTTCTTGATGAGGTATTAAGAAGT-AGACCAAATTCGTCTTCTTGATGAGATACAGAGAAAC
131 TAGCTCCCTGATGAGATACTGAGAAGTGA-ACCAAATTCGCCTTCTTGATGAGATACAGAGAAGC
2059 GAATTGAA
195 GAATTGAA
* * * * *
2067 ACAAACGATGCAGTCATCTTCCTGATCAGATACTGAGAAGAACACCAAATCAAACCCACGCTCAA
1 ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACC----CAAA-CAAGGCTCAA
* * * * * * *
2132 AGCGAGCAAAATCTTCGAACCCCAACTTTCGGACGAGACACCGAGAAGCAGGTCGAAACAACAAA
61 AGTGAGCAAAATCTTCGAACCCCAACTTCCTGATGAGACACAGAGAAGCAGGTCGAAGCAATAAA
* * * * * * *
2197 -AGGTCAGC-CTCCTAATGAAATACTGAGAAGCGAACCAAACTCGTCC-TCTTGATGAGATATAG
126 GTGGTTAGCTC-CCTGATGAGATACTGAGAAGTGAACCAAATTCG-CCTTCTTGATGAGATACAG
* *
2259 AGAAGTGAATCGAA
189 AGAAGCGAATTGAA
**
2273 ACAAACGATACAGTCATCTTCCTGATGAGATACTGAGAAGAAGACC
1 ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACC
2319 AAATCAGTAA
Statistics
Matches: 573, Mismatches: 68, Indels: 22
0.86 0.10 0.03
Matches are distributed among these distances:
199 1 0.00
200 168 0.29
201 2 0.00
202 237 0.41
204 4 0.01
205 2 0.00
206 98 0.17
207 61 0.11
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (202 bp):
ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCCAAACAAGGCTCAAAGTGA
GCAAAATCTTCGAACCCCAACTTCCTGATGAGACACAGAGAAGCAGGTCGAAGCAATAAAGTGGT
TAGCTCCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCTTGATGAGATACAGAGAAGCG
AATTGAA
Found at i:2584 original size:28 final size:28
Alignment explanation
Indices: 2553--2643 Score: 123
Period size: 28 Copynumber: 3.3 Consensus size: 28
2543 TGGGCCTTTT
2553 TTTAAATTTATTTTAAATTTGATTTAAA
1 TTTAAATTTATTTTAAATTTGATTTAAA
2581 TTTAAATTTATTTTAAATTTGATTTAAA
1 TTTAAATTTATTTTAAATTTGATTTAAA
** * *
2609 TCGATATTAATTTTAAA-TTGAATTT-AA
1 TTTAAATTTATTTTAAATTTG-ATTTAAA
2636 TTTAAATT
1 TTTAAATT
2644 AAAAAAAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
27 10 0.18
28 45 0.82
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (28 bp):
TTTAAATTTATTTTAAATTTGATTTAAA
Found at i:2586 original size:17 final size:17
Alignment explanation
Indices: 2564--2600 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2554 TTAAATTTAT
2564 TTTAAATTTGA-TTTAAA
1 TTTAAATTT-ATTTTAAA
2581 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
2598 TTT
1 TTT
2601 GATTTAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 1 0.05
17 18 0.95
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:2595 original size:39 final size:39
Alignment explanation
Indices: 2552--2627 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 39
2542 CTGGGCCTTT
*
2552 TTTTAAATTT-ATTTTAAATTTGAT-TTAAATTTAAATTTA
1 TTTTAAATTTGA-TTTAAA-TCGATATTAAATTTAAATTTA
*
2591 TTTTAAATTTGATTTAAATCGATATTAATTTTAAATT
1 TTTTAAATTTGATTTAAATCGATATTAAATTTAAATT
2628 GAATTTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 4 0.12
39 28 0.85
40 1 0.03
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (39 bp):
TTTTAAATTTGATTTAAATCGATATTAAATTTAAATTTA
Found at i:2606 original size:11 final size:10
Alignment explanation
Indices: 2553--2609 Score: 50
Period size: 11 Copynumber: 5.7 Consensus size: 10
2543 TGGGCCTTTT
2553 TTTAAATTTA
1 TTTAAATTTA
2563 TTTTAAATTTGA
1 -TTTAAATTT-A
2575 TTT-AA---A
1 TTTAAATTTA
2581 TTTAAATTTA
1 TTTAAATTTA
2591 TTTTAAATTTGA
1 -TTTAAATTT-A
2603 TTTAAAT
1 TTTAAAT
2610 CGATATTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
6 4 0.10
7 2 0.05
10 3 0.08
11 28 0.72
12 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (10 bp):
TTTAAATTTA
Found at i:2635 original size:39 final size:39
Alignment explanation
Indices: 2553--2639 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 39
2543 TGGGCCTTTT
* * *
2553 TTTAAATTTATTTTAAATTTGATTTAAATTTAAATTTAT
1 TTTAAATTTATTTTAAATTCGATTTAAATTTAAATTGAA
*
2592 TTTAAATTTGA-TTTAAA-TCGATATTAATTTTAAATTGAA
1 TTTAAATTT-ATTTTAAATTCGAT-TTAAATTTAAATTGAA
2631 TTT-AATTTA
1 TTTAAATTTA
2640 AATTAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
37 1 0.02
38 9 0.21
39 31 0.74
40 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (39 bp):
TTTAAATTTATTTTAAATTCGATTTAAATTTAAATTGAA
Found at i:2643 original size:11 final size:11
Alignment explanation
Indices: 2574--2643 Score: 52
Period size: 11 Copynumber: 6.3 Consensus size: 11
2564 TTTAAATTTG
2574 ATTTAAATTTAA
1 ATTT-AATTTAA
*
2586 ATTTATTTTAA
1 ATTTAATTTAA
*
2597 ATTTGATTTAA
1 ATTTAATTTAA
**
2608 A-TCGATATTAA
1 ATTTAAT-TTAA
* * *
2619 TTTTAAATTGA
1 ATTTAATTTAA
2630 ATTTAATTTAA
1 ATTTAATTTAA
2641 ATT
1 ATT
2644 AAAAAAAATT
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
10 4 0.09
11 34 0.77
12 6 0.14
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (11 bp):
ATTTAATTTAA
Found at i:2643 original size:16 final size:16
Alignment explanation
Indices: 2596--2643 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
2586 ATTTATTTTA
* *
2596 AATTTGATTTAAATCG
1 AATTTAATTTAAATTG
2612 -ATATTAATTTTAAATTG
1 AAT-TTAA-TTTAAATTG
2629 AATTTAATTTAAATT
1 AATTTAATTTAAATT
2644 AAAAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 2 0.07
16 11 0.41
17 12 0.44
18 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (16 bp):
AATTTAATTTAAATTG
Found at i:3129 original size:11 final size:11
Alignment explanation
Indices: 3109--3167 Score: 59
Period size: 11 Copynumber: 5.3 Consensus size: 11
3099 TAATTGTTAA
3109 TATATATTTACT
1 TATATATTTA-T
3121 TAT-TATTTAT
1 TATATATTTAT
*
3131 TATATA-TTAA
1 TATATATTTAT
3141 TATGATCATTTAT
1 TAT-AT-ATTTAT
*
3154 TATCTATTTAT
1 TATATATTTAT
3165 TAT
1 TAT
3168 TTAATACGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
10 10 0.25
11 19 0.47
12 5 0.12
13 6 0.15
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (11 bp):
TATATATTTAT
Found at i:3162 original size:34 final size:32
Alignment explanation
Indices: 3105--3167 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 32
3095 TAAATAATTG
3105 TTAATATATATTTACTTATTATTTATTATATA
1 TTAATATATATTTACTTATTATTTATTATATA
3137 TTAATATGATCATTTA-TTATCTATTTATTAT
1 TTAATAT-AT-ATTTACTTAT-TATTTATTAT
3168 TTAATACGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 7 0.25
33 6 0.21
34 15 0.54
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.59
Consensus pattern (32 bp):
TTAATATATATTTACTTATTATTTATTATATA
Found at i:4314 original size:30 final size:29
Alignment explanation
Indices: 4267--4905 Score: 646
Period size: 29 Copynumber: 21.8 Consensus size: 29
4257 AAAAATTTTG
*
4267 TTTTTACCCCCAAACTTCCAAAAATCCCA
1 TTTTTACCCCAAAACTTCCAAAAATCCCA
* * *
4296 TTTTTGACCTCGAAACTTCCAAAAATTCCA
1 TTTTT-ACCCCAAAACTTCCAAAAATCCCA
* * *
4326 TCTTTACCCCTAAACTTCCTAAAATCCCA
1 TTTTTACCCCAAAACTTCCAAAAATCCCA
* * *
4355 TCTTTACCCCCAAACTTCCTAAAATCCCA
1 TTTTTACCCCAAAACTTCCAAAAATCCCA
* *
4384 TTTTTGACCCC-AAATTTCCTAAAATCCC-
1 TTTTT-ACCCCAAAACTTCCAAAAATCCCA
* *
4412 TTTTTGACCCCAAAACTTTCAAAAATTCCA
1 TTTTT-ACCCCAAAACTTCCAAAAATCCCA
*
4442 TTTTTACCCTC-GAACTTCCAAAAATCCCA
1 TTTTTACCC-CAAAACTTCCAAAAATCCCA
**
4471 TTTTTACCCCCGAACTTCCAAAAATCCCA
1 TTTTTACCCCAAAACTTCCAAAAATCCCA
** * *
4500 TTTTTGACCTTAAAAATTCCAAAAATTCCA
1 TTTTT-ACCCCAAAACTTCCAAAAATCCCA
* **
4530 TTTTTACCCCTAAACTTCCAAAAATCTGA
1 TTTTTACCCCAAAACTTCCAAAAATCCCA
* *
4559 TTTTTAACCCTAAAAACTTCCAAAAATTCCA
1 TTTTT-ACCC-CAAAACTTCCAAAAATCCCA
* *
4590 TTTTTACCCTC-GAACTTCTAAAAAATCCCA
1 TTTTTACCC-CAAAACTTC-CAAAAATCCCA
*
4620 TTTTTACCCCAAAAATTCCAAAAATCCCA
1 TTTTTACCCCAAAACTTCCAAAAATCCCA
* *
4649 TTTTTGACCCTAAAACTTCCAAAAATTCCA
1 TTTTT-ACCCCAAAACTTCCAAAAATCCCA
* *
4679 TTTTTACCCCTAAACTTTCAAAAATCCCA
1 TTTTTACCCCAAAACTTCCAAAAATCCCA
* * *
4708 -TTTTACCCTAGAATTTCCAAAAATCCCA
1 TTTTTACCCCAAAACTTCCAAAAATCCCA
* *
4736 TTTTGACCCTAAAACTTCCAAAAA-CTCCA
1 TTTTTACCCCAAAACTTCCAAAAATC-CCA
**
4765 TTTTTACCCCCGAACTTCCAAAAAATCCCA
1 TTTTTACCCCAAAACTTCC-AAAAATCCCA
* *
4795 TTTTGACCCCAAAACTTCCAAAAATTCCA
1 TTTTTACCCCAAAACTTCCAAAAATCCCA
* * *
4824 TTTTTACACCC-GAACTTTCAAAAATTCCA
1 TTTTTAC-CCCAAAACTTCCAAAAATCCCA
* * *
4853 -TTTTACCCCCAAACTCCCAAAAATCTCA
1 TTTTTACCCCAAAACTTCCAAAAATCCCA
* *
4881 TATTTGACCCTAAAACTTCCAAAAA
1 T-TTTTACCCCAAAACTTCCAAAAA
4906 ATTCATTTTT
Statistics
Matches: 512, Mismatches: 78, Indels: 39
0.81 0.12 0.06
Matches are distributed among these distances:
27 3 0.01
28 55 0.11
29 270 0.53
30 163 0.32
31 21 0.04
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31
Consensus pattern (29 bp):
TTTTTACCCCAAAACTTCCAAAAATCCCA
Found at i:4342 original size:59 final size:58
Alignment explanation
Indices: 4250--4921 Score: 627
Period size: 59 Copynumber: 11.5 Consensus size: 58
4240 GAAGGTCCCT
*** * *
4250 AACTTCCAAAAATTTTGTTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGA
1 AACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTT-ACCCCGA
* * * *
4309 AACTTCCAAAAATTCCATCTTTACCCCTAAACTTCCTAAAATCCCATCTTTACCCCCA
1 AACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTACCCCGA
* * * * *
4367 AACTTCCTAAAATCCCATTTTTGACCCC-AAATTTCCTAAAATCCC-TTTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTT-ACCCCTAAACTTCCAAAAATCCCATTTTT-ACCCCGA
* *
4425 AACTTTCAAAAATTCCATTTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTACCCCCG-
1 AACTTCCAAAAATTCCATTTTTACCCCT-AAACTTCCAAAAATCCCATTTTTA-CCCCGA
* * * * *
4483 AACTTCCAAAAATCCCATTTTTGA-CCTTAAAAATTCCAAAAATTCCATTTTTACCCCTA
1 AACTTCCAAAAATTCCATTTTT-ACCCCT-AAACTTCCAAAAATCCCATTTTTACCCCGA
* * *
4542 AACTTCCAAAAA-TCTGATTTTTAACCCTAAAAACTTCCAAAAATTCCATTTTTACCCTCG-
1 AACTTCCAAAAATTC-CATTTTTACCCCT--AAACTTCCAAAAATCCCATTTTTACCC-CGA
* * * * **
4602 AACTTCTAAAAAATCCCATTTTTACCCCAAAAATTCCAAAAATCCCATTTTTGACCCTAA
1 AACTTC-CAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTT-ACCCCGA
* *
4662 AACTTCCAAAAATTCCATTTTTACCCCTAAACTTTCAAAAATCCCA-TTTTA-CCCTA
1 AACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTACCCCGA
* * *
4718 GAATTTCCAAAAATCCCATTTTGA-CCCTAAAACTTCCAAAAA-CTCCATTTTTACCCCCG-
1 -AACTTCCAAAAATTCCATTTTTACCCCT-AAACTTCCAAAAATC-CCATTTTTA-CCCCGA
* * * *
4777 AACTTCCAAAAAATCCCATTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACACCCG-
1 AACTTCC-AAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTAC-CCCGA
* * * * * **
4836 AACTTTCAAAAATTCCA-TTTTACCCCCAAACTCCCAAAAATCTCATATTTGACCCTAA
1 AACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCAT-TTTTACCCCGA
4894 AACTTCCAAAAAATT-CATTTTTAACCCC
1 AACTTCC-AAAAATTCCATTTTT-ACCCC
4922 GAATTTTCCT
Statistics
Matches: 512, Mismatches: 70, Indels: 61
0.80 0.11 0.09
Matches are distributed among these distances:
56 11 0.02
57 67 0.13
58 144 0.28
59 219 0.43
60 54 0.11
61 16 0.03
62 1 0.00
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31
Consensus pattern (58 bp):
AACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTACCCCGA
Found at i:4987 original size:28 final size:29
Alignment explanation
Indices: 4932--4992 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 29
4922 GAATTTTCCT
*
4932 AAAATTACCATTTCACCCTCGAGAATCC-
1 AAAATTACCATTTCACCCTCCAGAATCCG
4960 AAAATTACCA-TTCTACCC-CCAGATATCCG
1 AAAATTACCATTTC-ACCCTCCAGA-ATCCG
4989 AAAA
1 AAAA
4993 GTCTCATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 7 0.24
28 18 0.62
29 4 0.14
ACGTcount: A:0.39, C:0.31, G:0.07, T:0.23
Consensus pattern (29 bp):
AAAATTACCATTTCACCCTCCAGAATCCG
Found at i:6972 original size:17 final size:17
Alignment explanation
Indices: 6941--6973 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6931 TTGAATTAGG
6941 TTGAGAAATTTATTTAA
1 TTGAGAAATTTATTTAA
6958 TTGA-AAATTTAATTTA
1 TTGAGAAATTT-ATTTA
6974 TATATAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (17 bp):
TTGAGAAATTTATTTAA
Found at i:8672 original size:2 final size:2
Alignment explanation
Indices: 8665--8690 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8655 TGGTTTTGGG
8665 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
8691 CAAATTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10240 original size:22 final size:21
Alignment explanation
Indices: 10215--10255 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
10205 TTTAAAAAAA
*
10215 TAATATTTATATTATTTTATTT
1 TAATATTTA-ATAATTTTATTT
10237 TAATATTTAATAATTTTAT
1 TAATATTTAATAATTTTAT
10256 ATATTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TAATATTTAATAATTTTATTT
Found at i:10260 original size:25 final size:25
Alignment explanation
Indices: 10232--10284 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
10222 TATATTATTT
10232 TATTTTAATATTTAAT-AATTTTATA
1 TATTTT-ATATTTAATAAATTTTATA
* * *
10257 TATTTTTTATTTATTAAATTTTTTA
1 TATTTTATATTTAATAAATTTTATA
10282 TAT
1 TAT
10285 AATCATCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
TATTTTATATTTAATAAATTTTATA
Found at i:10268 original size:16 final size:16
Alignment explanation
Indices: 10222--10282 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
10212 AAATAATATT
10222 TATATTATTTTATTTTA
1 TATATT-TTTTATTTTA
* *
10239 -ATATTTAATAATTTTA
1 TATATTT-TTTATTTTA
10255 TATATTTTTTA-TTTA
1 TATATTTTTTATTTTA
*
10270 TTAAATTTTTTAT
1 -TATATTTTTTAT
10283 ATAATCATCT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
15 5 0.14
16 24 0.69
17 6 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATATTTTTTATTTTA
Found at i:12569 original size:2 final size:2
Alignment explanation
Indices: 12562--12602 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
12552 ATATTTTAAA
*
12562 AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12603 TTTTTAAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:14217 original size:21 final size:21
Alignment explanation
Indices: 14188--14233 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
14178 TGAAAAATCA
*
14188 ATTTAATAAATAAAAATAAAT
1 ATTTAATAAACAAAAATAAAT
* * *
14209 ATTTCATAAACAAAACTAATT
1 ATTTAATAAACAAAAATAAAT
14230 ATTT
1 ATTT
14234 TAACTTTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (21 bp):
ATTTAATAAACAAAAATAAAT
Found at i:19322 original size:21 final size:20
Alignment explanation
Indices: 19281--19332 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
19271 GGAACTTTTA
19281 GTATCGGTAGTTGCTTATGTT
1 GTATCGGTAGTTGC-TATGTT
19302 GTATCGGTAGTATGC-AGTGTT
1 GTATCGGTAGT-TGCTA-TGTT
*
19323 GTATCTGTAG
1 GTATCGGTAG
19333 AACTTATTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 1 0.04
21 24 0.86
22 3 0.11
ACGTcount: A:0.17, C:0.10, G:0.31, T:0.42
Consensus pattern (20 bp):
GTATCGGTAGTTGCTATGTT
Found at i:29423 original size:22 final size:21
Alignment explanation
Indices: 29346--29424 Score: 79
Period size: 21 Copynumber: 3.6 Consensus size: 21
29336 TGATTTTATT
*
29346 TTATTATAAAGTATTTTACAACAA
1 TTATTATAAA--ATTTTAAAAC-A
* *
29370 TTATTTTAAAATTTAATAAACA
1 TTATTATAAAATTTTA-AAACA
29392 -TATTATAAAATTTTAAAACA
1 TTATTATAAAATTTTAAAACA
29412 TTATTATCAAAAT
1 TTATTAT-AAAAT
29425 AATTATAACC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
20 5 0.11
21 19 0.40
22 11 0.23
23 3 0.06
24 9 0.19
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.43
Consensus pattern (21 bp):
TTATTATAAAATTTTAAAACA
Found at i:30976 original size:9 final size:10
Alignment explanation
Indices: 30948--30975 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
30938 AAGGAAAGAA
30948 GAAAAAAAAT
1 GAAAAAAAAT
30958 GAAAAAAAAT
1 GAAAAAAAAT
30968 GAAAAAAA
1 GAAAAAAA
30976 TTTATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (10 bp):
GAAAAAAAAT
Found at i:40647 original size:29 final size:29
Alignment explanation
Indices: 40602--40659 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
40592 CATGATGTTC
*
40602 ATTTTACTTCCTGTTGACCCAAAGGTCAT
1 ATTTTACTCCCTGTTGACCCAAAGGTCAT
* * *
40631 ATTTTACTCCCTTTTGATCTAAAGGTCAT
1 ATTTTACTCCCTGTTGACCCAAAGGTCAT
40660 GCCTGTTACC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.41
Consensus pattern (29 bp):
ATTTTACTCCCTGTTGACCCAAAGGTCAT
Found at i:46818 original size:58 final size:60
Alignment explanation
Indices: 46678--46819 Score: 161
Period size: 58 Copynumber: 2.4 Consensus size: 60
46668 ATTAATGTGA
* * *
46678 TAATT-TT-AATATTAAATTTAATTTAATATTTATCTTATATATAAATATTCTATTAATT
1 TAATTATTAAATATTAAATTTAATCTAATATTTATCTTATAGATAAATATTATATTAATT
* *
46736 TAATTTATTTAATATTAAATTTAATCTAATATTTATC-T-T-GATAAGTATTATATTAATT
1 TAA-TTATTAAATATTAAATTTAATCTAATATTTATCTTATAGATAAATATTATATTAATT
*
46794 TAA-TATTAAATTGATTAAGTTTAATC
1 TAATTATTAAA-T-ATTAAATTTAATC
46820 ATAGATGAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
56 6 0.08
57 1 0.01
58 34 0.47
59 3 0.04
60 3 0.04
61 26 0.36
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.53
Consensus pattern (60 bp):
TAATTATTAAATATTAAATTTAATCTAATATTTATCTTATAGATAAATATTATATTAATT
Found at i:51037 original size:15 final size:16
Alignment explanation
Indices: 51005--51046 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
50995 GGATCTCCTA
51005 ATCTTCATAG-TACAC
1 ATCTTCATAGATACAC
*
51020 ATCTTCATAGATA-TC
1 ATCTTCATAGATACAC
*
51035 ATCCTCATAGAT
1 ATCTTCATAGAT
51047 GTCGTCATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 22 0.92
16 2 0.08
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (16 bp):
ATCTTCATAGATACAC
Found at i:52046 original size:24 final size:24
Alignment explanation
Indices: 52019--52067 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
52009 ATATGTCGGA
52019 AAAAATTCCTCGAACGTTTATGCG
1 AAAAATTCCTCGAACGTTTATGCG
*
52043 AAAAATTCCTTGAACGTTTATGCG
1 AAAAATTCCTCGAACGTTTATGCG
52067 A
1 A
52068 GTTCTACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (24 bp):
AAAAATTCCTCGAACGTTTATGCG
Found at i:53854 original size:30 final size:30
Alignment explanation
Indices: 53820--53878 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
53810 ATTAAATGGG
*
53820 AATTTTA-TGAAAATTTAGTGACTAATTTGT
1 AATTTTACTG-AAATTTAGGGACTAATTTGT
* *
53850 AATTTTACTGAAGTTTGGGGACTAATTTG
1 AATTTTACTGAAATTTAGGGACTAATTTG
53879 ATCTTTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (30 bp):
AATTTTACTGAAATTTAGGGACTAATTTGT
Found at i:54678 original size:19 final size:19
Alignment explanation
Indices: 54651--54710 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
54641 GTTGTTCGAC
* *
54651 CCAATTCATTGGCCATTGA
1 CCAAATCATTGACCATTGA
*
54670 CCAAATCATTGACCGTTGA
1 CCAAATCATTGACCATTGA
*
54689 CCAAA-CTGTTGACCATTGA
1 CCAAATC-ATTGACCATTGA
54708 CCA
1 CCA
54711 TTGACTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 1 0.03
19 34 0.97
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (19 bp):
CCAAATCATTGACCATTGA
Found at i:60258 original size:3 final size:3
Alignment explanation
Indices: 60250--60292 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
60240 TTTAATTACT
60250 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
60293 CTAGGTCTGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:68098 original size:16 final size:16
Alignment explanation
Indices: 68077--68107 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
68067 TTCACTATTA
*
68077 TGTCTTTTATATTTTT
1 TGTCTTTCATATTTTT
68093 TGTCTTTCATATTTT
1 TGTCTTTCATATTTT
68108 GCATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.06, T:0.71
Consensus pattern (16 bp):
TGTCTTTCATATTTTT
Found at i:69187 original size:23 final size:25
Alignment explanation
Indices: 69139--69186 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 25
69129 AGTTGTAGAG
69139 AGAAAATTCTCTAAAGAGATTATTTT
1 AGAAAATTCTCT-AAGAGATTATTTT
69165 AGAAAA-TCTCT-AGAGA-TATTTT
1 AGAAAATTCTCTAAGAGATTATTTT
69187 TTTGTTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
25 5 0.23
26 6 0.27
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (25 bp):
AGAAAATTCTCTAAGAGATTATTTT
Found at i:79118 original size:18 final size:18
Alignment explanation
Indices: 79074--79124 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
79064 CGAGCAACCG
*
79074 GACCAGATACGATCACAT
1 GACCAGATGCGATCACAT
79092 GACCAGATGCGATCACA-
1 GACCAGATGCGATCACAT
*
79109 GACCCAGATGCAATCA
1 GA-CCAGATGCGATCA
79125 TACAATCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 2 0.07
18 28 0.93
ACGTcount: A:0.37, C:0.29, G:0.20, T:0.14
Consensus pattern (18 bp):
GACCAGATGCGATCACAT
Found at i:85569 original size:17 final size:17
Alignment explanation
Indices: 85544--85582 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
85534 CGTGCATTTC
85544 TTTTAATTGTCAT-TGCA
1 TTTTAATTGTC-TCTGCA
*
85561 TTTTTATTGTCTCTGCA
1 TTTTAATTGTCTCTGCA
85578 TTTTA
1 TTTTA
85583 CTTATTTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 1 0.05
17 18 0.95
ACGTcount: A:0.18, C:0.13, G:0.10, T:0.59
Consensus pattern (17 bp):
TTTTAATTGTCTCTGCA
Found at i:86244 original size:2 final size:2
Alignment explanation
Indices: 86231--86282 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
86221 AAAAGATAGA
*
86231 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
86273 AT AT AT -T AT A
1 AT AT AT AT AT A
86283 CAATAAATGT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:96186 original size:34 final size:34
Alignment explanation
Indices: 96134--96201 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
96124 AAATTACAGA
* *
96134 ATGTTTATACAGATATCAAAGCACTTTTCATTTT
1 ATGTTTATAAAGAAATCAAAGCACTTTTCATTTT
96168 ATGTTTATAAAGAAATCAAAGCACTTTTCATTTT
1 ATGTTTATAAAGAAATCAAAGCACTTTTCATTTT
96202 CTTTCACGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (34 bp):
ATGTTTATAAAGAAATCAAAGCACTTTTCATTTT
Found at i:99572 original size:18 final size:18
Alignment explanation
Indices: 99555--99593 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
99545 AGATCAAAAT
99555 TAAT-ACATTAATATAAA
1 TAATAACATTAATATAAA
*
99572 TAATAATATTAATATAAA
1 TAATAACATTAATATAAA
99590 -AATA
1 TAATA
99594 GAGAAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATAACATTAATATAAA
Found at i:107256 original size:49 final size:49
Alignment explanation
Indices: 107184--107284 Score: 166
Period size: 49 Copynumber: 2.1 Consensus size: 49
107174 AAACATGGTA
* * *
107184 GTTATAATTCTTTTTGGAAAGAATATAATGTTTTTAATACTTTCCATAT
1 GTTATAATTCTCTTTGGAAAGAATATAACGTGTTTAATACTTTCCATAT
*
107233 GTTATAATTCTCTTTGGAAAGAATATAACGTGTTTAATTCTTTCCATAT
1 GTTATAATTCTCTTTGGAAAGAATATAACGTGTTTAATACTTTCCATAT
107282 GTT
1 GTT
107285 CTCTATAGGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.48
Consensus pattern (49 bp):
GTTATAATTCTCTTTGGAAAGAATATAACGTGTTTAATACTTTCCATAT
Found at i:108023 original size:12 final size:12
Alignment explanation
Indices: 108006--108035 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
107996 GAGAAGGATT
108006 AAGTAAGAATCA
1 AAGTAAGAATCA
108018 AAGTAAGAATCA
1 AAGTAAGAATCA
108030 AAGTAA
1 AAGTAA
108036 TCTAACTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.17, T:0.17
Consensus pattern (12 bp):
AAGTAAGAATCA
Found at i:111669 original size:19 final size:19
Alignment explanation
Indices: 111645--111687 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
111635 AACCCATTTG
111645 ATATTCACATCAATTTCAC
1 ATATTCACATCAATTTCAC
*
111664 ATATTCATATCAATTTCAC
1 ATATTCACATCAATTTCAC
111683 ATATT
1 ATATT
111688 TTCATATCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATTCACATCAATTTCAC
Found at i:114122 original size:19 final size:19
Alignment explanation
Indices: 114094--114155 Score: 88
Period size: 19 Copynumber: 3.3 Consensus size: 19
114084 AACCCATTTG
* * *
114094 ATATTTACATCGATTTCAT
1 ATATTCACATCAATTTCAC
114113 ATATTCACATCAATTTCAC
1 ATATTCACATCAATTTCAC
*
114132 ATATTCATATCAATTTCAC
1 ATATTCACATCAATTTCAC
114151 ATATT
1 ATATT
114156 TTCATGTCTC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.44
Consensus pattern (19 bp):
ATATTCACATCAATTTCAC
Found at i:114783 original size:106 final size:108
Alignment explanation
Indices: 114603--114806 Score: 283
Period size: 106 Copynumber: 1.9 Consensus size: 108
114593 TTAACACATC
**
114603 GGCATATGAATATGCCCACATAATCACAATATATCACTTATTAAATGCTTAACATGTATTTCATG
1 GGCATATGAATATGCCCACATAATCACAATATATCACTTATTAAATGCTTAACATGTATTTCAAA
114668 TTAGATCATAGATCTTAATAATCACATAATCACTTATCACTTA
66 TTAGATCATAGATCTTAATAATCACATAATCACTTATCACTTA
* * * *
114711 GGCATAT-AGATATGCTCGCATAATCAC-TTATTTCAC-T-TTAACATGCTTAACATGCT-TTTC
1 GGCATATGA-ATATGCCCACATAATCACAATATATCACTTATTAA-ATGCTTAACATG-TATTTC
*
114771 AAATTAGATCATAGATCTTGATAATCACATAATCAC
63 AAATTAGATCATAGATCTTAATAATCACATAATCAC
114807 ACGTTTAAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
105 4 0.05
106 50 0.58
107 9 0.10
108 23 0.27
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.35
Consensus pattern (108 bp):
GGCATATGAATATGCCCACATAATCACAATATATCACTTATTAAATGCTTAACATGTATTTCAAA
TTAGATCATAGATCTTAATAATCACATAATCACTTATCACTTA
Found at i:120089 original size:11 final size:11
Alignment explanation
Indices: 120073--120114 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
120063 ATCAAAAGCC
120073 AAAATAAATGA
1 AAAATAAATGA
*
120084 AAAATAAAAGA
1 AAAATAAATGA
120095 AAAATAAA-GA
1 AAAATAAATGA
120105 AAAATGAAAT
1 AAAAT-AAAT
120115 AATTCCTATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 7 0.25
11 21 0.75
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (11 bp):
AAAATAAATGA
Found at i:138654 original size:16 final size:15
Alignment explanation
Indices: 138632--138674 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
138622 ATAACCCAAT
*
138632 ATTATATTTTTATATA
1 ATTATATTTATAT-TA
*
138648 TTTATATTTATATTA
1 ATTATATTTATATTA
138663 ATTATATATTAT
1 ATTATAT-TTAT
138675 GTACAAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATATTTATATTA
Found at i:142718 original size:24 final size:24
Alignment explanation
Indices: 142686--142941 Score: 264
Period size: 24 Copynumber: 10.4 Consensus size: 24
142676 GGTGACGAAG
142686 CTGCTGCTGCCGCTGAAGTTCCAA
1 CTGCTGCTGCCGCTGAAGTTCCAA
142710 CTGCTGCTGCCGCTGAAGTTCCAA
1 CTGCTGCTGCCGCTGAAGTTCCAA
* *
142734 CTGCTGCTGCTGCTGTAGTTCCAA
1 CTGCTGCTGCCGCTGAAGTTCCAA
* * *
142758 CTGCTGCTGCCGCTGTAA-CTCTAG
1 CTGCTGCTGCCGCTG-AAGTTCCAA
* * *
142782 CTGCTGCTGCCGCTGTAA-CTCTAG
1 CTGCTGCTGCCGCTG-AAGTTCCAA
* *
142806 CTGCTGCTGCCGCTGTAGTTCCAG
1 CTGCTGCTGCCGCTGAAGTTCCAA
*
142830 CTGCTGCTGTCGCCGCTGAAGTTCCAG
1 CTGCTGC--T-GCCGCTGAAGTTCCAA
*
142857 CTGCTGCTGCCTCTGAAGTTCCAA
1 CTGCTGCTGCCGCTGAAGTTCCAA
* * *
142881 CTGCTGCTGTCGCTTAAGTTCCATTTG
1 CTGCTGCTGCCGCTGAAGTTCCA---A
* *
142908 TTGCTGCTGTCGCTGAAGTTCCAA
1 CTGCTGCTGCCGCTGAAGTTCCAA
*
142932 CTGCCGCTGC
1 CTGCTGCTGC
142942 TGTTGAAACT
Statistics
Matches: 201, Mismatches: 23, Indels: 16
0.84 0.10 0.07
Matches are distributed among these distances:
23 1 0.00
24 154 0.77
25 2 0.01
26 1 0.00
27 43 0.21
ACGTcount: A:0.13, C:0.32, G:0.25, T:0.30
Consensus pattern (24 bp):
CTGCTGCTGCCGCTGAAGTTCCAA
Found at i:152528 original size:33 final size:32
Alignment explanation
Indices: 152482--152547 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
152472 TATATTATTG
152482 TTTTGGTGCTTTTTACTATTTTGGTTACTTTTT
1 TTTTGGTGCTTTTTACTATTTTGG-TACTTTTT
* * * *
152515 TTTTGTTGTTTTTTACTGTTTTGGTGCTTTTT
1 TTTTGGTGCTTTTTACTATTTTGGTACTTTTT
152547 T
1 T
152548 ACTACTTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 8 0.28
33 21 0.72
ACGTcount: A:0.06, C:0.08, G:0.17, T:0.70
Consensus pattern (32 bp):
TTTTGGTGCTTTTTACTATTTTGGTACTTTTT
Found at i:152545 original size:19 final size:19
Alignment explanation
Indices: 152480--152573 Score: 67
Period size: 18 Copynumber: 5.2 Consensus size: 19
152470 ATTATATTAT
152480 TGTTTTGGTGC-TTTTTAC
1 TGTTTTGGTGCTTTTTTAC
* *
152498 TATTTTGGT--TACTTTT--
1 TGTTTTGGTGCT-TTTTTAC
*
152514 T-TTTTGTTG-TTTTTTAC
1 TGTTTTGGTGCTTTTTTAC
152531 TGTTTTGGTGCTTTTTTAC
1 TGTTTTGGTGCTTTTTTAC
** *
152550 TACTTTGGTGCTATTTTTGC
1 TGTTTTGGTGCT-TTTTTAC
152570 TGTT
1 TGTT
152574 ATTTTTGTTG
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
15 10 0.17
16 2 0.03
17 1 0.02
18 19 0.33
19 18 0.31
20 8 0.14
ACGTcount: A:0.07, C:0.10, G:0.18, T:0.65
Consensus pattern (19 bp):
TGTTTTGGTGCTTTTTTAC
Found at i:152579 original size:52 final size:51
Alignment explanation
Indices: 152480--152579 Score: 130
Period size: 52 Copynumber: 1.9 Consensus size: 51
152470 ATTATATTAT
* ** *
152480 TGTTTTGGTGCTTTTTACTATTTTGGTTACTTTTTTTTTGTTGTTTTTTAC
1 TGTTTTGGTGCTTTTTACTACTTTGGTTACTTTTTTGCTGTTATTTTTTAC
*
152531 TGTTTTGGTGCTTTTTTACTACTTTGG-TGCTATTTTTGCTGTTATTTTT
1 TGTTTTGGTGC-TTTTTACTACTTTGGTTACT-TTTTTGCTGTTATTTTT
152580 GTTGTTATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
51 14 0.33
52 28 0.67
ACGTcount: A:0.08, C:0.09, G:0.17, T:0.66
Consensus pattern (51 bp):
TGTTTTGGTGCTTTTTACTACTTTGGTTACTTTTTTGCTGTTATTTTTTAC
Found at i:152615 original size:36 final size:35
Alignment explanation
Indices: 152561--152655 Score: 127
Period size: 36 Copynumber: 2.7 Consensus size: 35
152551 ACTTTGGTGC
* * *
152561 TATTTTTGCTGTTATTTTTGTTGTTATTTTTGCTGT
1 TATTTTTGTTGTTGTTTTTGTTGTT-GTTTTGCTGT
*
152597 TATTTTTGTTGTTGTTTTTGTTATTGTTTTGCTGT
1 TATTTTTGTTGTTGTTTTTGTTGTTGTTTTGCTGT
*
152632 TATTTTTTGTTGTTGTTTTGGTTG
1 TA-TTTTTGTTGTTGTTTTTGTTG
152656 AATAGATGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 11 0.21
36 41 0.79
ACGTcount: A:0.06, C:0.03, G:0.20, T:0.71
Consensus pattern (35 bp):
TATTTTTGTTGTTGTTTTTGTTGTTGTTTTGCTGT
Found at i:152650 original size:12 final size:12
Alignment explanation
Indices: 152561--152655 Score: 102
Period size: 12 Copynumber: 7.9 Consensus size: 12
152551 ACTTTGGTGC
*
152561 TATTTTTGCTGT
1 TATTTTTGTTGT
152573 TATTTTTGTTGT
1 TATTTTTGTTGT
*
152585 TATTTTTGCTGT
1 TATTTTTGTTGT
152597 TATTTTTGTTGT
1 TATTTTTGTTGT
* *
152609 TGTTTTTGTTAT
1 TATTTTTGTTGT
* *
152621 T-GTTTTGCTGT
1 TATTTTTGTTGT
152632 TATTTTTTGTTGT
1 TA-TTTTTGTTGT
* *
152645 TGTTTTGGTTG
1 TATTTTTGTTG
152656 AATAGATGTT
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
11 8 0.12
12 52 0.75
13 9 0.13
ACGTcount: A:0.06, C:0.03, G:0.20, T:0.71
Consensus pattern (12 bp):
TATTTTTGTTGT
Found at i:155793 original size:18 final size:18
Alignment explanation
Indices: 155770--155804 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
155760 TTAGGATATT
*
155770 TTTAGGTATTTTAAGTTA
1 TTTAGGGATTTTAAGTTA
*
155788 TTTAGGGGTTTTAAGTT
1 TTTAGGGATTTTAAGTT
155805 TCTTGATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (18 bp):
TTTAGGGATTTTAAGTTA
Found at i:163432 original size:72 final size:72
Alignment explanation
Indices: 163332--163516 Score: 192
Period size: 72 Copynumber: 2.6 Consensus size: 72
163322 GTCAATTGTG
* * * * * *
163332 TTGTTGTTAGCATGATGATCAAGGGTATTAATTGTCACAAGTGTGATCTAAGTTTAAGTTGCGCC
1 TTGTTGTTAGCATGATGGTCAAAGGTATTAATTGCCACAAATGTGATCTAAGTTCAAGTTACGCC
163397 AATCGCA
66 AATCGCA
* * * * ** * **
163404 TTGTTATTAGCATGATGGTCAAAGGTATTCATTGCCTCAAATGTGGTCTGGGTTCGAGTTACGTT
1 TTGTTGTTAGCATGATGGTCAAAGGTATTAATTGCCACAAATGTGATCTAAGTTCAAGTTACGCC
* *
163469 AATTGCG
66 AATCGCA
* *
163476 TTATTGTTAGCATGATGGTCAAAGGTATTTATTGCC-CAAAT
1 TTGTTGTTAGCATGATGGTCAAAGGTATTAATTGCCACAAAT
163517 TTATTGCCCA
Statistics
Matches: 93, Mismatches: 20, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
71 5 0.05
72 88 0.95
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (72 bp):
TTGTTGTTAGCATGATGGTCAAAGGTATTAATTGCCACAAATGTGATCTAAGTTCAAGTTACGCC
AATCGCA
Found at i:163520 original size:13 final size:13
Alignment explanation
Indices: 163502--163528 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
163492 GGTCAAAGGT
163502 ATTTATTGCCCAA
1 ATTTATTGCCCAA
163515 ATTTATTGCCCAA
1 ATTTATTGCCCAA
163528 A
1 A
163529 ATATGATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (13 bp):
ATTTATTGCCCAA
Found at i:164413 original size:18 final size:18
Alignment explanation
Indices: 164373--164424 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
164363 TTTTCAGTTG
*
164373 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAATTTATT
*
164391 CAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
164409 TAATTAA--AAATTTATT
1 TAATTAATTAAATTTATT
164425 CTCATTCCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 7 0.23
18 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:181847 original size:7 final size:7
Alignment explanation
Indices: 181835--181861 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
181825 ATAAATGAAC
181835 ATTGGTA
1 ATTGGTA
181842 ATTGGTA
1 ATTGGTA
181849 ATTGGTA
1 ATTGGTA
181856 ATTGGT
1 ATTGGT
181862 TTGATTGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (7 bp):
ATTGGTA
Found at i:182972 original size:21 final size:21
Alignment explanation
Indices: 182927--182972 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
182917 CACACGGCTG
* * *
182927 TGTGCCTATCACACATAGGCG
1 TGTGCCCATCACACACAGGCA
*
182948 TGTGCCCATCACACACGGGCA
1 TGTGCCCATCACACACAGGCA
182969 TGTG
1 TGTG
182973 GGGTGTTGGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.30, G:0.26, T:0.22
Consensus pattern (21 bp):
TGTGCCCATCACACACAGGCA
Found at i:188218 original size:21 final size:23
Alignment explanation
Indices: 188178--188221 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
188168 TGAATGCAAG
*
188178 AAATGATGTAAAATTCATGATTT
1 AAATGATGTAAAATTAATGATTT
188201 AAATG-TGT-AAATTAATGATTT
1 AAATGATGTAAAATTAATGATTT
188222 GTTGTTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 3 0.15
23 5 0.25
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (23 bp):
AAATGATGTAAAATTAATGATTT
Found at i:188432 original size:18 final size:19
Alignment explanation
Indices: 188409--188488 Score: 103
Period size: 18 Copynumber: 4.4 Consensus size: 19
188399 TAGAGGGAAT
* *
188409 AGCAATACTAGCTCGT-TG
1 AGCAATACTGGCTCGTAAG
* *
188427 AGCAATACTGGCTCAT-TG
1 AGCAATACTGGCTCGTAAG
188445 AGCAATACTGG-TCGTAAG
1 AGCAATACTGGCTCGTAAG
188463 AGCAATACTGGCTCGTAAG
1 AGCAATACTGGCTCGTAAG
188482 AGCAATA
1 AGCAATA
188489 TTAGATCGCA
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
17 3 0.05
18 39 0.70
19 14 0.25
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (19 bp):
AGCAATACTGGCTCGTAAG
Found at i:189687 original size:25 final size:25
Alignment explanation
Indices: 189653--189703 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
189643 TTGTACAGCT
189653 GCAAGGAAGTTAGATCTGAGAAAAG
1 GCAAGGAAGTTAGATCTGAGAAAAG
189678 GCAAGGAAGTTAGATCTGAGAAAAG
1 GCAAGGAAGTTAGATCTGAGAAAAG
189703 G
1 G
189704 ACACTTGTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.08, G:0.33, T:0.16
Consensus pattern (25 bp):
GCAAGGAAGTTAGATCTGAGAAAAG
Found at i:193747 original size:17 final size:17
Alignment explanation
Indices: 193727--193796 Score: 68
Period size: 17 Copynumber: 4.1 Consensus size: 17
193717 TTTTAATATT
* *
193727 AATAATTTTTAATTCAA
1 AATAAATTTAAATTCAA
193744 AATAAATTTAAATTCAA
1 AATAAATTTAAATTCAA
* ** *
193761 CACGAATTTAAATTTAA
1 AATAAATTTAAATTCAA
* *
193778 AATAAATTCAAATTTAA
1 AATAAATTTAAATTCAA
193795 AA
1 AA
193797 ATTAAAAGTT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.37
Consensus pattern (17 bp):
AATAAATTTAAATTCAA
Found at i:196625 original size:23 final size:24
Alignment explanation
Indices: 196583--196628 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
196573 TAAAATAATT
* *
196583 TAATTATATTTTTTAGTTTTTTTA
1 TAATTATATTTTTGAATTTTTTTA
196607 TAATTA-ATTTTTGAATTTTTTT
1 TAATTATATTTTTGAATTTTTTT
196629 TTCAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (24 bp):
TAATTATATTTTTGAATTTTTTTA
Found at i:197283 original size:21 final size:21
Alignment explanation
Indices: 197259--197309 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
197249 ATAATAAAAG
197259 TAATATTA-ATTAAATATTAAT-
1 TAATATTATATT--ATATTAATA
197280 TAATATTATATTATATTAATA
1 TAATATTATATTATATTAATA
*
197301 TAAAATTAT
1 TAATATTAT
197310 TTCTTTTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 8 0.30
21 16 0.59
22 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATATTATATTATATTAATA
Found at i:197301 original size:11 final size:10
Alignment explanation
Indices: 197259--197299 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
197249 ATAATAAAAG
197259 TAATATTAAT
1 TAATATTAAT
197269 TAAATATTAAT
1 T-AATATTAAT
197280 TAATATTATAT
1 TAATATTA-AT
197291 T-ATATTAAT
1 TAATATTAAT
197300 ATAAAATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.07
10 14 0.48
11 13 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
TAATATTAAT
Found at i:197945 original size:31 final size:30
Alignment explanation
Indices: 197910--197972 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 30
197900 TAATAAATGT
* *
197910 AAAATTACATTTCATCCTTCTGAAAATAATA
1 AAAATTACATTTAATCCTT-TCAAAATAATA
** *
197941 AAAATTTGATTTAATCCTTTCAAAATTATA
1 AAAATTACATTTAATCCTTTCAAAATAATA
197971 AA
1 AA
197973 GATATAAGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATTACATTTAATCCTTTCAAAATAATA
Found at i:198096 original size:18 final size:20
Alignment explanation
Indices: 198070--198115 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
198060 CGCCCTTGAA
*
198070 TATAGTTATAG-T-TTTAAT
1 TATAATTATAGTTATTTAAT
198088 TATAATTATAGTTATTTAAT
1 TATAATTATAGTTATTTAAT
198108 TAATAATT
1 T-ATAATT
198116 TTTTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 10 0.42
19 1 0.04
20 7 0.29
21 6 0.25
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (20 bp):
TATAATTATAGTTATTTAAT
Found at i:198899 original size:10 final size:10
Alignment explanation
Indices: 198855--198899 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
198845 ATAATAAAAA
198855 TAATATTAAT
1 TAATATTAAT
*
198865 TAAATATTAGT
1 T-AATATTAAT
198876 TAATA-TAAT
1 TAATATTAAT
198885 ATAATATTAAT
1 -TAATATTAAT
198896 TAAT
1 TAAT
198900 TTGGTCTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 3 0.10
10 14 0.47
11 13 0.43
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (10 bp):
TAATATTAAT
Found at i:198968 original size:16 final size:17
Alignment explanation
Indices: 198947--198984 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
198937 AATATATTAT
*
198947 ATTATAAATT-AATAAA
1 ATTATAAATTAAAAAAA
198963 ATTATAAATTAAAAAAA
1 ATTATAAATTAAAAAAA
198980 ATTAT
1 ATTAT
198985 TGAATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTATAAATTAAAAAAA
Found at i:199433 original size:15 final size:15
Alignment explanation
Indices: 199415--199444 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
199405 ATTATAATTA
*
199415 TTTTATTATTAATGT
1 TTTTATTATCAATGT
199430 TTTTATTATCAATGT
1 TTTTATTATCAATGT
199445 AGTAGTTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (15 bp):
TTTTATTATCAATGT
Found at i:200147 original size:23 final size:23
Alignment explanation
Indices: 200103--200147 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
200093 TAATTAGTAA
*
200103 ATATATTTTTAAAAATTATAAAT
1 ATATATTTTTAAAAAATATAAAT
200126 ATATATTATTTAAAAAAT-TAAA
1 ATATATT-TTTAAAAAATATAAA
200148 GGTAATCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATATTTTTAAAAAATATAAAT
Found at i:202753 original size:30 final size:30
Alignment explanation
Indices: 202655--202753 Score: 85
Period size: 30 Copynumber: 3.4 Consensus size: 30
202645 TTAATATAAC
* **
202655 ATTTGGTATCTGAACTTGACATTTTTCCTA
1 ATTTGGTACCTGAACTTGATTTTTTTCCTA
* * *** *
202685 ATTTGTTACTTGAACTT--TTTTGGACCCA
1 ATTTGGTACCTGAACTTGATTTTTTTCCTA
* *
202713 ATTTGTTACCTGAAATTGATTTTTTTCCTA
1 ATTTGGTACCTGAACTTGATTTTTTTCCTA
202743 ATTTGGTACCT
1 ATTTGGTACCT
202754 AAGTTTTTTT
Statistics
Matches: 51, Mismatches: 16, Indels: 4
0.72 0.23 0.06
Matches are distributed among these distances:
28 20 0.39
30 31 0.61
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.48
Consensus pattern (30 bp):
ATTTGGTACCTGAACTTGATTTTTTTCCTA
Found at i:203082 original size:28 final size:27
Alignment explanation
Indices: 203042--203100 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 27
203032 AAAAAGTGTT
203042 AAGTTTGAGTACCAAATTGGACAAAAAA
1 AAGTTTGAGTACCAAATTGGA-AAAAAA
*
203070 AAGTTT-AGGTACCAAATTTGAAAAAAA
1 AAGTTTGA-GTACCAAATTGGAAAAAAA
203097 AAGT
1 AAGT
203101 GTTAAGTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.51, C:0.08, G:0.17, T:0.24
Consensus pattern (27 bp):
AAGTTTGAGTACCAAATTGGAAAAAAA
Found at i:203108 original size:34 final size:34
Alignment explanation
Indices: 203032--203120 Score: 84
Period size: 34 Copynumber: 2.8 Consensus size: 34
203022 CTGAATTAGG
* *
203032 AAAAAGTGTTAAGTTT-GAGTACCAAA-TTGGACA
1 AAAAAGTGTTAAGTTTAG-GTACCAAATTTGAAAA
203065 AAAAA-----AAGTTTAGGTACCAAATTTGAAAA
1 AAAAAGTGTTAAGTTTAGGTACCAAATTTGAAAA
* *
203094 AAAAAGTGTTAAGTTCATGTACCAAAT
1 AAAAAGTGTTAAGTTTAGGTACCAAAT
203121 GTTATATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
28 14 0.31
29 11 0.24
33 5 0.11
34 15 0.33
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.27
Consensus pattern (34 bp):
AAAAAGTGTTAAGTTTAGGTACCAAATTTGAAAA
Found at i:214740 original size:49 final size:48
Alignment explanation
Indices: 214683--214855 Score: 217
Period size: 49 Copynumber: 3.6 Consensus size: 48
214673 TCAAACGAGT
*
214683 AAGACCATAGCTGAAAGATGTTATGGCATCAGGATGAATAAAAATGTGA
1 AAGACCATAGCTGAAAGATGTTATGGCATC-GGATGAATAAAAATGAGA
*
214732 AAGACCATAGCTGAAAGATGTTATGGCATCGAGATGAATAAAAATAAGA
1 AAGACCATAGCTGAAAGATGTTATGGCATCG-GATGAATAAAAATGAGA
* * * * *
214781 AAGACCATAGCTAAAAGATGTTATAGTATC--ATG-ATGAAAATGAGT
1 AAGACCATAGCTGAAAGATGTTATGGCATCGGATGAATAAAAATGAGA
* * *
214826 AAGACCATGGCTGAAAAATGCTATGGCATC
1 AAGACCATAGCTGAAAGATGTTATGGCATC
214856 ATTGTAAATA
Statistics
Matches: 109, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
45 33 0.30
46 3 0.03
48 1 0.01
49 72 0.66
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.23
Consensus pattern (48 bp):
AAGACCATAGCTGAAAGATGTTATGGCATCGGATGAATAAAAATGAGA
Found at i:214857 original size:45 final size:46
Alignment explanation
Indices: 214679--214945 Score: 220
Period size: 45 Copynumber: 5.7 Consensus size: 46
214669 TGATTCAAAC
214679 GAGTAAGACCATAGCTGAAAGATGTTATGGCATCAGGATGAATAAAAAT
1 GAGTAAGACCATAGCTGAAAGATGTTATGGCATC---ATGAATAAAAAT
* *
214728 GTGAAAGACCATAGCTGAAAGATGTTATGGCATCGAGATGAATAAAAAT
1 GAGTAAGACCATAGCTGAAAGATGTTATGGCATC---ATGAATAAAAAT
* * * * * *
214777 AAGAAAGACCATAGCTAAAAGATGTTATAGTATCATG-ATGAAAAT
1 GAGTAAGACCATAGCTGAAAGATGTTATGGCATCATGAATAAAAAT
* * * * *
214822 GAGTAAGACCATGGCTGAAAAATGCTATGGCATCATTG--TAAATAG
1 GAGTAAGACCATAGCTGAAAGATGTTATGGCATCA-TGAATAAAAAT
* * * * *
214867 GACTAAGACCATAGCTGAAAGACGCTATGGCATCATTG--TAAATAG
1 GAGTAAGACCATAGCTGAAAGATGTTATGGCATCA-TGAATAAAAAT
** * * *
214912 GACAAAGACCATAGTTGAAAGACGCTATGGCATC
1 GAGTAAGACCATAGCTGAAAGATGTTATGGCATC
214946 CTTTGACAGT
Statistics
Matches: 190, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
45 111 0.58
46 5 0.03
49 74 0.39
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.22
Consensus pattern (46 bp):
GAGTAAGACCATAGCTGAAAGATGTTATGGCATCATGAATAAAAAT
Found at i:216142 original size:29 final size:29
Alignment explanation
Indices: 216105--216484 Score: 389
Period size: 29 Copynumber: 13.0 Consensus size: 29
216095 TATACATTCG
* * * *
216105 GGGGCAAAAATAGAATTTTTGGAAATTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
* *
216134 GGGATAAAAAATGGCATTTTTGGAAG-TTC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTC
* *
216163 GGGGGTAAAAATGGATTTTTTGGAAGTTTTA
1 -GGGGTAAAAATGGAATTTTTGGAAG-TTTC
* * *
216194 GGGTTAAAAGTGGGATTTTTGGAAG-TTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
216222 GAGGGTAAAAATAGG-ATTTTTGGAAGTTTC
1 G-GGGTAAAAAT-GGAATTTTTGGAAGTTTC
* *
216252 GGGTTAAAAAT-GAGATTTTTAGAAG-TTC
1 GGGGTAAAAATGGA-ATTTTTGGAAGTTTC
*
216280 GAGGGTAAAAATGGAATTTTTGGAAGTTTT
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTC
* *
216310 GGGTTAAAAATGGGATTTTTGGAAG-TTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
* *
216338 GGGGGTAAAAATGGAATGTTTGGAAGTTTT
1 -GGGGTAAAAATGGAATTTTTGGAAGTTTC
*
216368 GGGGTAAAAAATGGGATTTTTGGAAG-TTC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTC
* *
216397 GAGGTAAAAATGGAATTTTTTGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
*
216426 GGGGTTAAAAATGGGATTTTTGGAAG-TTC
1 GGGG-TAAAAATGGAATTTTTGGAAGTTTC
*
216455 GAGGGTAAAAATGGATTTTTTGGATAGTTT
1 G-GGGTAAAAATGGAATTTTTGGA-AGTTT
216485 AGGGACCTCT
Statistics
Matches: 291, Mismatches: 40, Indels: 38
0.79 0.11 0.10
Matches are distributed among these distances:
27 1 0.00
28 27 0.09
29 162 0.56
30 97 0.33
31 4 0.01
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.35
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTC
Found at i:216166 original size:59 final size:58
Alignment explanation
Indices: 216079--216484 Score: 530
Period size: 58 Copynumber: 6.9 Consensus size: 58
216069 AACTCGGGGT
* ** * * *
216079 TTAAAAATGGAATTTTTATACA-TTCGGGGGCAAAAATAGAATTTTTGGAAATTTTGGG
1 TTAAAAATGGGATTTTTGGA-AGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTGGG
* * *
216137 ATAAAAAATGGCATTTTTGGAAGTTCGGGGGTAAAAATGGATTTTTTGGAAGTTTTAGGG
1 -TTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTT-GGG
* * *
216197 TTAAAAGTGGGATTTTTGGAAGTTCGAGGGTAAAAATAGG-ATTTTTGGAAGTTTCGGG
1 TTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAAT-GGAATTTTTGGAAGTTTTGGG
* * *
216255 TTAAAAATGAGATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGG
1 TTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTGGG
*
216313 TTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATGTTTGGAAGTTTTGGGG
1 TTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTT-GGG
* * * *
216372 TAAAAAATGGGATTTTTGGAAGTTC-GAGGTAAAAATGGAATTTTTTGAAGTTTCGGGG
1 TTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTT-TGGG
* *
216430 TTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGATTTTTTGGATAGTTT
1 TTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA-AGTTT
216485 AGGGACCTCT
Statistics
Matches: 307, Mismatches: 32, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
57 2 0.01
58 158 0.51
59 137 0.45
60 10 0.03
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (58 bp):
TTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTGGG
Found at i:216303 original size:117 final size:114
Alignment explanation
Indices: 216079--216484 Score: 519
Period size: 117 Copynumber: 3.5 Consensus size: 114
216069 AACTCGGGGT
* ** * * * * *
216079 TTAAAAATGGAATTTTTATACA-TTCGGGGGCAAAAATAGAATTTTTGGAAATTTTGGGATAAAA
1 TTAAAAATGGGATTTTTGGA-AGTTCGAGGGTAAAAAT-GGATTTTTGGAAGTTTCGGG-TAAAA
* *
216143 AATGGCATTTTTGGAAGTTCGGGGGTAAAAATGGATTTTTTGGAAGTTTTAGGG
63 AATGG-ATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTT-GGG
* *
216197 TTAAAAGTGGGATTTTTGGAAGTTCGAGGGTAAAAATAGGATTTTTGGAAGTTTCGGGTTAAAAA
1 TTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAAT-GGATTTTTGGAAGTTTCGGGTAAAAAA
*
216262 TGAGATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGG
65 TG-GATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGG
* * *
216313 TTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATGTTTGGAAGTTTTGGGGTAAAAA
1 TTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG-ATTTTTGGAAG-TTTCGGGTAAAAA
* *
216378 ATGGGATTTTTGGAAGTTCGA-GGTAAAAATGGAATTTTTTGAAGTTTCGGGG
64 AT-GGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTT-TGGG
216430 TTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGATTTTTTGGATAGTTT
1 TTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGA-TTTTTGGA-AGTTT
216485 AGGGACCTCT
Statistics
Matches: 257, Mismatches: 23, Indels: 17
0.87 0.08 0.06
Matches are distributed among these distances:
115 2 0.01
116 74 0.29
117 130 0.51
118 51 0.20
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (114 bp):
TTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGATTTTTGGAAGTTTCGGGTAAAAAAT
GGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGG
Found at i:217488 original size:10 final size:10
Alignment explanation
Indices: 217473--217504 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
217463 ACTTATTATT
217473 ATAATTAATA
1 ATAATTAATA
217483 ATAATTAATA
1 ATAATTAATA
*
217493 ATAATTATTA
1 ATAATTAATA
217503 AT
1 AT
217505 GCCAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
ATAATTAATA
Found at i:218306 original size:6 final size:6
Alignment explanation
Indices: 218278--218327 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
218268 TTATAATATT
* *
218278 TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
218325 TTT
1 TTT
218328 TAAAACAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
5 8 0.21
6 27 0.71
7 3 0.08
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:218314 original size:17 final size:17
Alignment explanation
Indices: 218278--218326 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
218268 TTATAATATT
*
218278 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAATTAAA
*
218296 TTTAAACTTAAATTAAA
1 TTTAAATTTAAATTAAA
218313 TTTAAATTTAAATT
1 TTTAAATTTAAATT
218327 TTAAAACAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 20 0.71
18 8 0.29
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:218339 original size:18 final size:18
Alignment explanation
Indices: 218316--218359 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
218306 AATTAAATTT
*
218316 AAATTTAAATTTTAAAAC
1 AAATTTAAATCTTAAAAC
*
218334 AAATTT-AATCTTAAAAT
1 AAATTTAAATCTTAAAAC
218351 AAATTTAAA
1 AAATTTAAA
218360 ATGAATTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATTTAAATCTTAAAAC
Found at i:218358 original size:41 final size:41
Alignment explanation
Indices: 218278--218359 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
218268 TTATAATATT
* *
218278 TTTAAATTTGAAAATAAATTTAAACTTAAATTAAATTTAAA
1 TTTAAATTTGAAAACAAATTTAAACTTAAAATAAATTTAAA
* *
218319 TTTAAATTTTAAAACAAATTTAATCTTAAAATAAATTTAAA
1 TTTAAATTTGAAAACAAATTTAAACTTAAAATAAATTTAAA
218360 ATGAATTAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (41 bp):
TTTAAATTTGAAAACAAATTTAAACTTAAAATAAATTTAAA
Found at i:223693 original size:34 final size:34
Alignment explanation
Indices: 223650--223725 Score: 134
Period size: 34 Copynumber: 2.2 Consensus size: 34
223640 CCTAGTTGCT
223650 AGTTCAAATACTAAAATTCAGCTTTGGGTATTAC
1 AGTTCAAATACTAAAATTCAGCTTTGGGTATTAC
*
223684 AGTTCAAATACTAAAATTCAGCTTTGGGTATTGC
1 AGTTCAAATACTAAAATTCAGCTTTGGGTATTAC
*
223718 AGTACAAA
1 AGTTCAAA
223726 ACAAAACAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (34 bp):
AGTTCAAATACTAAAATTCAGCTTTGGGTATTAC
Found at i:223935 original size:70 final size:70
Alignment explanation
Indices: 223822--223958 Score: 229
Period size: 70 Copynumber: 2.0 Consensus size: 70
223812 TTATGCATTT
* * * *
223822 ATGAAAAGATCTTAGAAATATTTGTATAAACCAGAAACAGAGGAATATAATTAGAACTAAGTAAA
1 ATGAAAAGATCTTAGAAATATTTGTATAAAACAGAAACAGAGGAATAGAAATAGAACTAAGAAAA
223887 ATATC
66 ATATC
*
223892 ATGAAAAGATCTTAGAAATATTTGTATAAAATAGAAACAGAGGAATAGAAATAGAACTAAGAAAA
1 ATGAAAAGATCTTAGAAATATTTGTATAAAACAGAAACAGAGGAATAGAAATAGAACTAAGAAAA
223957 AT
66 AT
223959 TATATTTCTT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.54, C:0.07, G:0.15, T:0.24
Consensus pattern (70 bp):
ATGAAAAGATCTTAGAAATATTTGTATAAAACAGAAACAGAGGAATAGAAATAGAACTAAGAAAA
ATATC
Found at i:224574 original size:42 final size:42
Alignment explanation
Indices: 224519--224620 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 42
224509 TAGGATGAAA
** *
224519 AAAATTGAT-TTTGAGTTTAATTTAAGGGTGCTTCTTAAGAAT
1 AAAATT-ATATTTGAGTTTAATTTAAGAATACTTCTTAAGAAT
* * * *
224561 AAAATTATATTTGAGTTTAGTTTATGAATATTTTTTAAGAAT
1 AAAATTATATTTGAGTTTAATTTAAGAATACTTCTTAAGAAT
* *
224603 GAAATTATATTTGGGTTT
1 AAAATTATATTTGAGTTT
224621 CAAAATATTT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 2 0.04
42 48 0.96
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (42 bp):
AAAATTATATTTGAGTTTAATTTAAGAATACTTCTTAAGAAT
Found at i:229943 original size:28 final size:28
Alignment explanation
Indices: 229903--229959 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
229893 TTTTTCCAAT
229903 ATTGCAAAGCCACTATGCTCATTGTTGG
1 ATTGCAAAGCCACTATGCTCATTGTTGG
229931 ATTGCAAAGCCACTATGCTCATTGTTGG
1 ATTGCAAAGCCACTATGCTCATTGTTGG
229959 A
1 A
229960 GCAGAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (28 bp):
ATTGCAAAGCCACTATGCTCATTGTTGG
Found at i:233706 original size:12 final size:12
Alignment explanation
Indices: 233689--233727 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
233679 AGGAAAATGT
233689 AGAAGAGAAGGA
1 AGAAGAGAAGGA
233701 AGAAGAGAA-GA
1 AGAAGAGAAGGA
*
233712 ATTAAGAGAAGGA
1 A-GAAGAGAAGGA
233725 AGA
1 AGA
233728 TGCCCCGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.59, C:0.00, G:0.36, T:0.05
Consensus pattern (12 bp):
AGAAGAGAAGGA
Found at i:234014 original size:17 final size:18
Alignment explanation
Indices: 233983--234020 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
233973 CAAGGACAAG
* *
233983 AAAAGAAAGAGGAAGGAC
1 AAAAGAAAGAAGAAGCAC
234001 AAAAGAAA-AAGAAGCAC
1 AAAAGAAAGAAGAAGCAC
234018 AAA
1 AAA
234021 GAAGAGCACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.68, C:0.08, G:0.24, T:0.00
Consensus pattern (18 bp):
AAAAGAAAGAAGAAGCAC
Found at i:234161 original size:17 final size:18
Alignment explanation
Indices: 234127--234163 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
234117 TCTCACTTAG
*
234127 TTGTCATTGCATTTTTAT
1 TTGTCACTGCATTTTTAT
234145 TTGTCACTGCA-TTTTAT
1 TTGTCACTGCATTTTTAT
234162 TT
1 TT
234164 ATTAGTACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.16, C:0.14, G:0.11, T:0.59
Consensus pattern (18 bp):
TTGTCACTGCATTTTTAT
Found at i:238396 original size:23 final size:23
Alignment explanation
Indices: 238379--238510 Score: 201
Period size: 23 Copynumber: 5.7 Consensus size: 23
238369 ATTTACACAT
* *
238379 AAATCACATTAATCTTTAAGCAT
1 AAATCACATTAATATTTAAGCAA
*
238402 AAATCACATTAATATTTAAGCAC
1 AAATCACATTAATATTTAAGCAA
238425 AAATCACATTAATATTTAAGCAA
1 AAATCACATTAATATTTAAGCAA
*
238448 AAATCATATTAATATTTAAGCAA
1 AAATCACATTAATATTTAAGCAA
* *
238471 AAATCACATTAATATTTAAGTAC
1 AAATCACATTAATATTTAAGCAA
*
238494 AAATAACATTAATATTT
1 AAATCACATTAATATTT
238511 TAACACATTT
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 101 1.00
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (23 bp):
AAATCACATTAATATTTAAGCAA
Found at i:238960 original size:36 final size:36
Alignment explanation
Indices: 238923--239303 Score: 564
Period size: 36 Copynumber: 10.6 Consensus size: 36
238913 ACTGTCACAC
* *
238923 GGCATGAATAACATACCCTCATATTTACTATCTCAC
1 GGCATGAATAACATACCCACATATTTACTATCTCAT
* *
238959 GGCATGAATAACATACCCACATATTTACTGTCACAT
1 GGCATGAATAACATACCCACATATTTACTATCTCAT
*
238995 GGCATGAATAACATACCCACATATTTACTGTCTCAT
1 GGCATGAATAACATACCCACATATTTACTATCTCAT
* *
239031 GGCATGAATAACATACCCACATATTTACTATCACAA
1 GGCATGAATAACATACCCACATATTTACTATCTCAT
239067 GGCATGAATAACATACCCACATATTTACTATCTCAT
1 GGCATGAATAACATACCCACATATTTACTATCTCAT
** *
239103 AACATGAATAACATACTCACATATTTACTATCTCAT
1 GGCATGAATAACATACCCACATATTTACTATCTCAT
* * **
239139 GGCATGAATAACATGCCCACATATTTACTGTCAAAT
1 GGCATGAATAACATACCCACATATTTACTATCTCAT
*
239175 GGCATGAATAACATACCCACATATTTACTATCTTAT
1 GGCATGAATAACATACCCACATATTTACTATCTCAT
* * *
239211 GGCATGAATAACATACCTACATATTTACTGTCACAT
1 GGCATGAATAACATACCCACATATTTACTATCTCAT
* **
239247 GGAATGAATAACATACCCACATATTTAGGATCTCAT
1 GGCATGAATAACATACCCACATATTTACTATCTCAT
*
239283 GGGATGAATAACATACCCACA
1 GGCATGAATAACATACCCACA
239304 CATTGACTTT
Statistics
Matches: 310, Mismatches: 35, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 310 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (36 bp):
GGCATGAATAACATACCCACATATTTACTATCTCAT
Found at i:246130 original size:23 final size:23
Alignment explanation
Indices: 246104--246268 Score: 258
Period size: 23 Copynumber: 7.2 Consensus size: 23
246094 TTATGAGTCC
* * *
246104 ATTTAAACATAAATCACACTAAT
1 ATTTAAGCACAAATCACATTAAT
* *
246127 ATTTAAGAATAAATCACATTAAT
1 ATTTAAGCACAAATCACATTAAT
*
246150 ATTTAAGCACAAATCACATTTAT
1 ATTTAAGCACAAATCACATTAAT
246173 ATTTAAGCACAAATCACATTAAT
1 ATTTAAGCACAAATCACATTAAT
* *
246196 ATTTAAGCAAAAATCATATTAAT
1 ATTTAAGCACAAATCACATTAAT
246219 ATTTAAGCACAAATCACATTAAT
1 ATTTAAGCACAAATCACATTAAT
246242 ATTTAAGCACAAATCACATTAAT
1 ATTTAAGCACAAATCACATTAAT
246265 ATTT
1 ATTT
246269 TAACGCATTT
Statistics
Matches: 131, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 131 1.00
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (23 bp):
ATTTAAGCACAAATCACATTAAT
Found at i:246719 original size:36 final size:36
Alignment explanation
Indices: 246679--246950 Score: 402
Period size: 36 Copynumber: 7.6 Consensus size: 36
246669 TTCATTGTCA
*
246679 CATGGCATGAATAACATACCCACATATTTACTGTCT
1 CATGGCATGAATAACATACCCACATATTTACTATCT
* *
246715 CATGGCACGAATAACATACCCACATATTTACTGT-T
1 CATGGCATGAATAACATACCCACATATTTACTATCT
*
246750 ACATGGCATGAATAACATACCCACATATTTTCTATCT
1 -CATGGCATGAATAACATACCCACATATTTACTATCT
*
246787 CATGGCATGAATAACATACCCACATATTTACTATCA
1 CATGGCATGAATAACATACCCACATATTTACTATCT
* *
246823 CAAGGCATGAATAACATACCCACATGTTTACTATCT
1 CATGGCATGAATAACATACCCACATATTTACTATCT
* *
246859 CATGACATGAATAACATACCCACATATTTACTGTCT
1 CATGGCATGAATAACATACCCACATATTTACTATCT
** * *
246895 CATAACATGAATAGCATACCCACATATTTACTATCA
1 CATGGCATGAATAACATACCCACATATTTACTATCT
*
246931 CATGACATGAATAACATACC
1 CATGGCATGAATAACATACC
246951 TGTAACACCC
Statistics
Matches: 215, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
35 1 0.00
36 213 0.99
37 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.09, T:0.29
Consensus pattern (36 bp):
CATGGCATGAATAACATACCCACATATTTACTATCT
Found at i:251679 original size:26 final size:26
Alignment explanation
Indices: 251587--251672 Score: 145
Period size: 26 Copynumber: 3.3 Consensus size: 26
251577 ACTTAAGGTT
251587 CTCCGACCAACTCAAACTCAAGGGAC
1 CTCCGACCAACTCAAACTCAAGGGAC
*
251613 CTCCGACTAACTCAAACTCAAGGGAC
1 CTCCGACCAACTCAAACTCAAGGGAC
*
251639 CTCCGACCAACTCAAACTCAAGGGTC
1 CTCCGACCAACTCAAACTCAAGGGAC
*
251665 CTCAGACC
1 CTCCGACC
251673 CATTCAATCT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.38, G:0.15, T:0.14
Consensus pattern (26 bp):
CTCCGACCAACTCAAACTCAAGGGAC
Found at i:252067 original size:14 final size:14
Alignment explanation
Indices: 252050--252077 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
252040 CCATTGCCTA
252050 AGAAGCAAATTCGC
1 AGAAGCAAATTCGC
252064 AGAAGCAAATTCGC
1 AGAAGCAAATTCGC
252078 CCTGGTCGGT
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:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
AGAAGCAAATTCGC
Found at i:257992 original size:26 final size:25
Alignment explanation
Indices: 257963--258013 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
257953 AATTTACTCT
* * *
257963 ATTTATTTTTATTTTTATTTTTAGAA
1 ATTTAATTTT-TTTTAAATTTTAGAA
257989 ATTTAATTTTTTTTAAATTTTAGAA
1 ATTTAATTTTTTTTAAATTTTAGAA
258014 TTAAGTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (25 bp):
ATTTAATTTTTTTTAAATTTTAGAA
Found at i:269601 original size:26 final size:26
Alignment explanation
Indices: 269572--269635 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
269562 TACTAAACTG
269572 GCTCGTAAGAGCAATATACTGCACTA
1 GCTCGTAAGAGCAATATACTGCACTA
* * ** * *
269598 GCTCATAGGAGTGATATATTGCACTG
1 GCTCGTAAGAGCAATATACTGCACTA
269624 GCTCGTAAGAGC
1 GCTCGTAAGAGC
269636 GATTTACTAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (26 bp):
GCTCGTAAGAGCAATATACTGCACTA
Found at i:273167 original size:20 final size:20
Alignment explanation
Indices: 273142--273182 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
273132 GCAAATTCGA
*
273142 GGCACCAAAGTGCAAGCAGG
1 GGCACCAAAGTGCAAACAGG
* *
273162 GGCACCGAATTGCAAACAGG
1 GGCACCAAAGTGCAAACAGG
273182 G
1 G
273183 CATCTCTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.24, G:0.34, T:0.07
Consensus pattern (20 bp):
GGCACCAAAGTGCAAACAGG
Found at i:277828 original size:35 final size:35
Alignment explanation
Indices: 277785--277854 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
277775 TGGCGATGGA
277785 ATATGGGATATGGGTGTCACAGAAGAGGAAGCAAT
1 ATATGGGATATGGGTGTCACAGAAGAGGAAGCAAT
277820 ATATGGGATATGGGTGTCACAGAAGAGGAAGCAAT
1 ATATGGGATATGGGTGTCACAGAAGAGGAAGCAAT
277855 GGCTACATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.09, G:0.34, T:0.20
Consensus pattern (35 bp):
ATATGGGATATGGGTGTCACAGAAGAGGAAGCAAT
Found at i:279461 original size:73 final size:73
Alignment explanation
Indices: 279342--279488 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 73
279332 AATCAATGCC
*
279342 AAATATAAGAAGTATAGTTCTATACAGATTCTAGGCCTTAAGCCCTACACAAATCCTCTTGTTTT
1 AAATATAAGAAGTATAGTTCTATACAGATTCTAGGCCTTAAGCCCTACACAAATCCCCTTGTTTT
279407 GCCACTGT
66 GCCACTGT
279415 AAATATAAGAAGTATAGTTCTATACAGATTCTAGGCCTTAAGCCCTACACAAATCCCCTTGTTTT
1 AAATATAAGAAGTATAGTTCTATACAGATTCTAGGCCTTAAGCCCTACACAAATCCCCTTGTTTT
279480 GCCACTGT
66 GCCACTGT
279488 A
1 A
279489 TTTTATTTAT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (73 bp):
AAATATAAGAAGTATAGTTCTATACAGATTCTAGGCCTTAAGCCCTACACAAATCCCCTTGTTTT
GCCACTGT
Found at i:289768 original size:22 final size:22
Alignment explanation
Indices: 289743--289785 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
289733 ATTTTTAAGT
*
289743 AATTAATATTA-ATTATTTAAAA
1 AATTAA-ATTAGATTATATAAAA
*
289765 AATTTAATTAGATTATATAAA
1 AATTAAATTAGATTATATAAA
289786 TTAGATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
AATTAAATTAGATTATATAAAA
Found at i:289826 original size:32 final size:31
Alignment explanation
Indices: 289757--289839 Score: 76
Period size: 32 Copynumber: 2.6 Consensus size: 31
289747 AATATTAATT
* * * *
289757 ATTTAAAAAATTTAATTAGATTATATAAATTAG
1 ATTTTAAATATTTAATT--ATTTTATAAAATAG
*
289790 ATTTTAAATATTTATATTATTTTATAAAATAT
1 ATTTTAAATATTTA-ATTATTTTATAAAATAG
* *
289822 ATTTTTAATTTTTAATTA
1 ATTTTAAATATTTAATTA
289840 ATGATTTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
31 4 0.10
32 23 0.55
33 12 0.29
34 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (31 bp):
ATTTTAAATATTTAATTATTTTATAAAATAG
Found at i:293876 original size:19 final size:18
Alignment explanation
Indices: 293840--293887 Score: 87
Period size: 19 Copynumber: 2.6 Consensus size: 18
293830 GTTTAAATTG
293840 ATTTAAATTTATTTTTAA
1 ATTTAAATTTATTTTTAA
293858 ATTTAAATTTATCTTTTAA
1 ATTTAAATTTAT-TTTTAA
293877 ATTTAAATTTA
1 ATTTAAATTTA
293888 AAAATTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 12 0.41
19 17 0.59
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTAAATTTATTTTTAA
Found at i:293898 original size:6 final size:6
Alignment explanation
Indices: 293840--293889 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
293830 GTTTAAATTG
* * * *
293840 ATTTAA ATTTAT TTTTAA ATTTAA ATTTATC TTTTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA
293889 A
1 A
293890 AATTTAAATG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
6 31 0.89
7 4 0.11
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (6 bp):
ATTTAA
Found at i:294680 original size:13 final size:13
Alignment explanation
Indices: 294664--294697 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
294654 AATAAATGAC
294664 ATTAATAAATATT
1 ATTAATAAATATT
*
294677 ATTAATTAATATT
1 ATTAATAAATATT
*
294690 AGTAATAA
1 ATTAATAA
294698 TAATAAGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (13 bp):
ATTAATAAATATT
Found at i:296048 original size:59 final size:59
Alignment explanation
Indices: 295807--296049 Score: 312
Period size: 59 Copynumber: 4.1 Consensus size: 59
295797 GAGGTCTCGG
* * *
295807 AACTTCCAAAAAATTCCAATTTTGACCCCGAAACTTCCAAAAATTCTATTTTTACCCCCAA
1 AACTTCC-AAAAATTCC-ATTTTAACCCCGAAACTTCCAAAAATTCCATTTTTAACCCCAA
* * * *
295868 AACTTCCAAAAATTCCATTTTTAACCTCAAAACTTCTAAAAATTCCATTTTT-ACCCTC-G
1 AACTTCCAAAAATTCCA-TTTTAACCCCGAAACTTCCAAAAATTCCATTTTTAACCC-CAA
* *
295927 AACTTCCAAAAATTCCATTTTTACCCTC-AAACTTCCAAAAATTCCATTTTTAACCCCGA
1 AACTTCCAAAAATTCCATTTTAACCC-CGAAACTTCCAAAAATTCCATTTTTAACCCCAA
* * *
295986 AACTTCCAAGAATTCCATTTTAACCCCGAAACTTTCAAAAATTCCATTTTTAACCCTAA
1 AACTTCCAAAAATTCCATTTTAACCCCGAAACTTCCAAAAATTCCATTTTTAACCCCAA
296045 AACTT
1 AACTT
296050 AAAAAAAAAA
Statistics
Matches: 160, Mismatches: 16, Indels: 14
0.84 0.08 0.07
Matches are distributed among these distances:
58 31 0.19
59 83 0.52
60 39 0.24
61 7 0.04
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (59 bp):
AACTTCCAAAAATTCCATTTTAACCCCGAAACTTCCAAAAATTCCATTTTTAACCCCAA
Found at i:296056 original size:30 final size:30
Alignment explanation
Indices: 295807--296049 Score: 307
Period size: 30 Copynumber: 8.2 Consensus size: 30
295797 GAGGTCTCGG
* * *
295807 AACTTCCAAAAAATTCCAATTTTGACCCCGA
1 AACTTCC-AAAAATTCCATTTTTAACCCCAA
* *
295838 AACTTCCAAAAATTCTATTTTTACCCCCAA
1 AACTTCCAAAAATTCCATTTTTAACCCCAA
*
295868 AACTTCCAAAAATTCCATTTTTAACCTCAA
1 AACTTCCAAAAATTCCATTTTTAACCCCAA
* *
295898 AACTTCTAAAAATTCCATTTTT-ACCCTC-G
1 AACTTCCAAAAATTCCATTTTTAACCC-CAA
295927 AACTTCCAAAAATTCCATTTTT-ACCCTC-A
1 AACTTCCAAAAATTCCATTTTTAACCC-CAA
*
295956 AACTTCCAAAAATTCCATTTTTAACCCCGA
1 AACTTCCAAAAATTCCATTTTTAACCCCAA
* *
295986 AACTTCCAAGAATTCCA-TTTTAACCCCGA
1 AACTTCCAAAAATTCCATTTTTAACCCCAA
* *
296015 AACTTTCAAAAATTCCATTTTTAACCCTAA
1 AACTTCCAAAAATTCCATTTTTAACCCCAA
296045 AACTT
1 AACTT
296050 AAAAAAAAAA
Statistics
Matches: 190, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
29 80 0.42
30 103 0.54
31 7 0.04
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (30 bp):
AACTTCCAAAAATTCCATTTTTAACCCCAA
Found at i:296220 original size:27 final size:28
Alignment explanation
Indices: 296162--296221 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
296152 CAAATTTTCC
*
296162 CAAAATTACCATTTCACCCCCGAGAATC
1 CAAAATTACCATTTCACCCCCGAGAATA
* *
296190 CAAAATTACCATTTTACCCCCG-GTATA
1 CAAAATTACCATTTCACCCCCGAGAATA
296217 CAAAA
1 CAAAA
296222 AGTCTCATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.38, C:0.32, G:0.07, T:0.23
Consensus pattern (28 bp):
CAAAATTACCATTTCACCCCCGAGAATA
Found at i:296574 original size:96 final size:96
Alignment explanation
Indices: 296440--296614 Score: 237
Period size: 97 Copynumber: 1.8 Consensus size: 96
296430 AAAGACTTTA
* **
296440 AAATCGAGGTAATATTCTTTTATTTCGAGTTTCGGAAAT-TTGTGCCTTAACTTACTAGGTGCAA
1 AAATCGAGGCAATATTCTTTTATTTCGAG-TTCGGAAATATTGCACCTTAACTTACTAGGTGCAA
**
296504 TTTTTCTTCAAATCAAAATAATCGAATACCCT
65 CCTTTCTTCAAATCAAAATAATCGAATACCCT
* * *
296536 AAATCGAGGCAATGTTTTCTTTATCTTCGA-TTCTGAAATATTGCACCTTAACTTACTAGGTGCA
1 AAATCGAGGCAATATTCT-TTTAT-TTCGAGTTCGGAAATATTGCACCTTAACTTACTAGGTGCA
296600 ACCTTTCTTCAAATC
64 ACCTTTCTTCAAATC
296615 GAGGTAATCG
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
96 23 0.34
97 40 0.59
98 5 0.07
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (96 bp):
AAATCGAGGCAATATTCTTTTATTTCGAGTTCGGAAATATTGCACCTTAACTTACTAGGTGCAAC
CTTTCTTCAAATCAAAATAATCGAATACCCT
Found at i:298356 original size:14 final size:13
Alignment explanation
Indices: 298314--298360 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
298304 TAAATCAAGC
*
298314 TTTTCAAAAGTAT
1 TTTTCAAAAGCAT
*
298327 TTTTCAAAATCAT
1 TTTTCAAAAGCAT
* *
298340 TTTTCCAAAGCAC
1 TTTTCAAAAGCAT
298353 TTTT-AAAA
1 TTTTCAAAA
298361 ATACTTCACA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
12 3 0.11
13 25 0.89
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.43
Consensus pattern (13 bp):
TTTTCAAAAGCAT
Found at i:298467 original size:16 final size:16
Alignment explanation
Indices: 298400--298471 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
298390 CCTTAATAAT
298400 TTTGAAACTATATATA
1 TTTGAAACTATATATA
* * **
298416 TTGGAAAACTATTTCCA
1 TTTG-AAACTATATATA
* * *
298433 TTTTAGAAC-ACATAAA
1 TTTGA-AACTATATATA
298449 TTTGAAACTATATATA
1 TTTGAAACTATATATA
298465 TTTGAAA
1 TTTGAAA
298472 ACTTTTTTTG
Statistics
Matches: 40, Mismatches: 13, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
15 3 0.08
16 23 0.57
17 14 0.35
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (16 bp):
TTTGAAACTATATATA
Found at i:298526 original size:7 final size:8
Alignment explanation
Indices: 298504--298528 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
298494 TTATTTTATA
298504 AAATTTTT
1 AAATTTTT
298512 AAATTTTT
1 AAATTTTT
298520 AAATTTTT
1 AAATTTTT
298528 A
1 A
298529 TATATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
AAATTTTT
Found at i:298604 original size:18 final size:19
Alignment explanation
Indices: 298567--298603 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
298557 TTTTTAAACA
298567 TATAAAT-TTTAAAATTTT
1 TATAAATATTTAAAATTTT
*
298585 TATAAATATTTAGAATTTT
1 TATAAATATTTAAAATTTT
298604 AAAAGTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TATAAATATTTAAAATTTT
Found at i:302574 original size:22 final size:21
Alignment explanation
Indices: 302530--302574 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
302520 AATTTAGTTT
*
302530 TTTTTTTAATTAATTTAATCA
1 TTTTTTTAATTAATTTAACCA
* *
302551 TTTTTTTATTTAAATTTGACCA
1 TTTTTTTAATT-AATTTAACCA
302573 TT
1 TT
302575 AACTATTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTTTTAATTAATTTAACCA
Found at i:302762 original size:20 final size:18
Alignment explanation
Indices: 302734--302780 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
302724 TCAATAAATA
302734 ATTTAAAAATATTAAAAAGT
1 ATTTAAAAA-A-TAAAAAGT
*
302754 ATTTGAAAAATAAAAAGT
1 ATTTAAAAAATAAAAAGT
*
302772 -TATAAAAAA
1 ATTTAAAAAA
302781 AGTTTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 7 0.29
18 8 0.33
19 1 0.04
20 8 0.33
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (18 bp):
ATTTAAAAAATAAAAAGT
Found at i:303177 original size:22 final size:24
Alignment explanation
Indices: 303130--303178 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
303120 AAAAAAAAAT
*
303130 AACTAAATAACAGTTTTTTTGAATA
1 AACTAAATAACAGTTTTATT-AATA
303155 AACTAAATAACA-TTTTATT-ATA
1 AACTAAATAACAGTTTTATTAATA
303177 AA
1 AA
303179 GTCGAATTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 5 0.22
24 6 0.26
25 12 0.52
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (24 bp):
AACTAAATAACAGTTTTATTAATA
Found at i:303434 original size:24 final size:24
Alignment explanation
Indices: 303380--303464 Score: 70
Period size: 24 Copynumber: 3.7 Consensus size: 24
303370 GATTCGAAAT
**
303380 TAAATTATAATTT--TTATAGTAA
1 TAAATTATAATTTAATTATTTTAA
* *
303402 AAAAATATAATTTAATTATTTTAA
1 TAAATTATAATTTAATTATTTTAA
* * *
303426 TAAATTATATTTTTATAATTTTAA
1 TAAATTATAATTTAATTATTTTAA
*
303450 -AAATTA-AATTAAATT
1 TAAATTATAATTTAATT
303465 TTTATATTTA
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
22 16 0.33
23 6 0.12
24 26 0.54
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (24 bp):
TAAATTATAATTTAATTATTTTAA
Found at i:303458 original size:28 final size:26
Alignment explanation
Indices: 303426--303500 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
303416 ATTATTTTAA
303426 TAAATTATATTTTTATAATTTTAAAAAT
1 TAAATTATATTTTTAT-A-TTTAAAAAT
* *
303454 TAAATTAAATTTTTATATTTAGAAAT
1 TAAATTATATTTTTATATTTAAAAAT
* * *
303480 TAAAATATAATTTTATTTTTA
1 TAAATTATATTTTTATATTTA
303501 TTAATTTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 25 0.61
27 1 0.02
28 15 0.37
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (26 bp):
TAAATTATATTTTTATATTTAAAAAT
Found at i:303466 original size:27 final size:28
Alignment explanation
Indices: 303376--303495 Score: 86
Period size: 26 Copynumber: 4.7 Consensus size: 28
303366 TAAAGATTCG
*
303376 AAATTAAATTATAATTTT-TATA-GT-A
1 AAATTAAATTATAATTTTATATATTTAA
*
303401 AAA--AAA-TATAATTTAAT-TATTT--
1 AAATTAAATTATAATTTTATATATTTAA
* *
303423 TAA-TAAATTATATTTTTATA-ATTTTAA
1 AAATTAAATTATAATTTTATATA-TTTAA
*
303450 AAATTAAATTA-AATTTT-TATATTTAG
1 AAATTAAATTATAATTTTATATATTTAA
*
303476 AAATTAAAATATAATTTTAT
1 AAATTAAATTATAATTTTAT
303496 TTTTATTAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
22 12 0.16
23 8 0.11
24 10 0.14
25 6 0.08
26 16 0.22
27 14 0.19
28 8 0.11
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
AAATTAAATTATAATTTTATATATTTAA
Found at i:303481 original size:26 final size:28
Alignment explanation
Indices: 303426--303493 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
303416 ATTATTTTAA
*
303426 TAAATTATATTTTTATAATTTTAAAAAT
1 TAAATTAAATTTTTATAATTTTAAAAAT
*
303454 TAAATTAAATTTTTAT-A-TTTAGAAAT
1 TAAATTAAATTTTTATAATTTTAAAAAT
*
303480 TAAAATATAATTTT
1 TAAATTA-AATTTT
303494 ATTTTTATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 14 0.39
27 7 0.19
28 15 0.42
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (28 bp):
TAAATTAAATTTTTATAATTTTAAAAAT
Done.