Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008740.1 Hibiscus syriacus cultivar Beakdansim tig00111827_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 261820
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:7022 original size:20 final size:21
Alignment explanation
Indices: 6976--7029 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
6966 ACACGCAGCG
6976 AAGGGATCGATCCGTTTTGAA
1 AAGGGATCGATCCGTTTTGAA
*
6997 AAGGGATCGATCCGTTTTG-T
1 AAGGGATCGATCCGTTTTGAA
7017 AAGGGATCGATCC
1 AAGGGATCGATCC
7030 TGTGCAATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (21 bp):
AAGGGATCGATCCGTTTTGAA
Found at i:13127 original size:32 final size:32
Alignment explanation
Indices: 13055--13127 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 32
13045 TTATAAATGT
* * *
13055 TAATATTATTGGTACTACACTAGTATCGACAC
1 TAATAATATTGATACTACAATAGTATCGACAC
* * * **
13087 TGACAATATTGATACTACAATAGTATTGGTAC
1 TAATAATATTGATACTACAATAGTATCGACAC
13119 TAATAATAT
1 TAATAATAT
13128 CAGTATCACT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (32 bp):
TAATAATATTGATACTACAATAGTATCGACAC
Found at i:13221 original size:20 final size:20
Alignment explanation
Indices: 13187--13239 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
13177 TATTGATACT
** *
13187 AATATCAATGTTACAGGAAC
1 AATATCAATACTACAAGAAC
*
13207 AATATCAATACTACAAGAAT
1 AATATCAATACTACAAGAAC
*
13227 AATATCGATACTA
1 AATATCAATACTA
13240 TAATCTAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.26
Consensus pattern (20 bp):
AATATCAATACTACAAGAAC
Found at i:14610 original size:15 final size:15
Alignment explanation
Indices: 14590--14620 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
14580 TTCATTTTCC
14590 TTGTAATTCAAAGCA
1 TTGTAATTCAAAGCA
14605 TTGTAATTCAAAGCA
1 TTGTAATTCAAAGCA
14620 T
1 T
14621 GCCAATCTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (15 bp):
TTGTAATTCAAAGCA
Found at i:18783 original size:17 final size:17
Alignment explanation
Indices: 18752--18790 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
18742 ATAACATTAT
*
18752 TACTACAATAATATTGG
1 TACTACAATAATATTGA
*
18769 TACTACAATAGTATTGA
1 TACTACAATAATATTGA
18786 TACTA
1 TACTA
18791 ATGATATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (17 bp):
TACTACAATAATATTGA
Found at i:18798 original size:32 final size:31
Alignment explanation
Indices: 18762--18896 Score: 87
Period size: 32 Copynumber: 4.3 Consensus size: 31
18752 TACTACAATA
18762 ATATTGGTACTACAATAGTATTGATACTAATG
1 ATATTGGTACTACAATAGTATTGATACTAA-G
* * * **
18794 ATATTTGTTCTAAAATAGTATCAATACTGACAG
1 ATATTGGTACTACAATAGTATTGATACT-A-AG
* * ** *
18827 -TATTAGTACTAGAATAGTAAAG-TACTAAC
1 ATATTGGTACTACAATAGTATTGATACTAAG
* *
18856 ATTATTGGTACTACAA-ATGTATTGGTACTAAT
1 A-TATTGGTACTACAATA-GTATTGATACTAAG
18888 AGTATTGGT
1 A-TATTGGT
18897 GTTACAAGAA
Statistics
Matches: 79, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
29 1 0.01
30 2 0.03
31 20 0.25
32 53 0.67
33 2 0.03
34 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.37
Consensus pattern (31 bp):
ATATTGGTACTACAATAGTATTGATACTAAG
Found at i:18868 original size:15 final size:15
Alignment explanation
Indices: 18848--18896 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
18838 GAATAGTAAA
*
18848 GTACTAACATTATTG
1 GTACTAAAATTATTG
18863 GTACTACAAATGTATTG
1 GTACTA-AAAT-TATTG
* *
18880 GTACTAATAGTATTG
1 GTACTAAAATTATTG
18895 GT
1 GT
18897 GTTACAAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 13 0.45
16 5 0.17
17 11 0.38
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (15 bp):
GTACTAAAATTATTG
Found at i:24936 original size:22 final size:24
Alignment explanation
Indices: 24903--24950 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 24
24893 ATAAGGAAGA
24903 TATTTTGATTTC-TTTA-TTATCT
1 TATTTTGATTTCATTTATTTATCT
24925 TATTTT-ATTTTCAATTTATTTATCT
1 TATTTTGA-TTTC-ATTTATTTATCT
24950 T
1 T
24951 TTGTTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
21 1 0.05
22 10 0.45
24 4 0.18
25 7 0.32
ACGTcount: A:0.21, C:0.08, G:0.02, T:0.69
Consensus pattern (24 bp):
TATTTTGATTTCATTTATTTATCT
Found at i:34821 original size:69 final size:69
Alignment explanation
Indices: 34735--34873 Score: 251
Period size: 69 Copynumber: 2.0 Consensus size: 69
34725 TAAACCTCTT
* *
34735 TGAACACTAGTTTCAGCCTCATTCTCAACAATCGGTAAAAGTTCCTCTTGCAGATCACCAAGAGC
1 TGAACACTAGTTTCAGCCTCATTCCCAACAATCGGTAAAAGTTCCTCTTGCAGATCACAAAGAGC
34800 TTCC
66 TTCC
*
34804 TGAACACTAGTTTCAGCCTCATTCCCAACAATCGGTAGAAGTTCCTCTTGCAGATCACAAAGAGC
1 TGAACACTAGTTTCAGCCTCATTCCCAACAATCGGTAAAAGTTCCTCTTGCAGATCACAAAGAGC
34869 TTCC
66 TTCC
34873 T
1 T
34874 AAGACATGAC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (69 bp):
TGAACACTAGTTTCAGCCTCATTCCCAACAATCGGTAAAAGTTCCTCTTGCAGATCACAAAGAGC
TTCC
Found at i:37301 original size:19 final size:21
Alignment explanation
Indices: 37260--37301 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
37250 AAATATATTA
*
37260 ATTTATATATATTAATAAGAT
1 ATTTATATATATTAATAAAAT
*
37281 ATTTATTTAT-TTAA-AAAAT
1 ATTTATATATATTAATAAAAT
37300 AT
1 AT
37302 CAGAAAAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 6 0.32
20 4 0.21
21 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
ATTTATATATATTAATAAAAT
Found at i:39136 original size:3 final size:3
Alignment explanation
Indices: 39117--39182 Score: 87
Period size: 3 Copynumber: 21.3 Consensus size: 3
39107 TTGTAATATT
* **
39117 TAA TCAA TAA TATA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TTT
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39164 TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
39183 TTTAAATTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:39154 original size:21 final size:21
Alignment explanation
Indices: 39122--39187 Score: 114
Period size: 21 Copynumber: 3.1 Consensus size: 21
39112 ATATTTAATC
*
39122 AATAATATATAATAATAATATT
1 AATAATA-ATAATAATAATTTT
39144 AATAATAATAATAATAATTTT
1 AATAATAATAATAATAATTTT
39165 AATAATAATAATAATAATTTT
1 AATAATAATAATAATAATTTT
39186 AA
1 AA
39188 ATTTAAAATG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
21 36 0.84
22 7 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATAATAATAATAATAATTTT
Found at i:39366 original size:45 final size:45
Alignment explanation
Indices: 39315--39980 Score: 1001
Period size: 45 Copynumber: 14.8 Consensus size: 45
39305 GATGGAAATG
* *
39315 TTGAAAACATCATGCACCGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
39360 TTGAAAACATCATA-CACTGAAGGGCTTACAGATGACCCGAAGGTTT
1 TTGAAAACATCA-AGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
* * * *
39406 TTGAAAACATCATGCAGTAAAGGGCTTACAGATGACCCAAAGGTTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
* * *
39452 TTGAAAACATCATGCACTGAAGGGATTACAGATTACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* *
39497 TTGAAGACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* * *
39542 TTGAAGACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* ** *
39587 TTGAAAACATCAAGCAATGAAGAACTTATAGATGACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* * *
39632 TTGAAGACATCAAGCACTGAAGGACTTACAGATAACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* *
39677 TTGAAGACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* *
39722 TTGAAAACATCAAGCACTGAAGGACTTACAGATGACCTGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* *
39767 TTGAAGACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* * * *
39812 TTGAAGACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
39857 TTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
39902 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
39947 TTGAAAATATCAAGCACTGAAGGGCTTACAGATG
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATG
39981 TGAGAAATAG
Statistics
Matches: 571, Mismatches: 47, Indels: 6
0.92 0.08 0.01
Matches are distributed among these distances:
45 490 0.86
46 81 0.14
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (45 bp):
TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
Found at i:40605 original size:22 final size:22
Alignment explanation
Indices: 40580--40659 Score: 85
Period size: 22 Copynumber: 3.6 Consensus size: 22
40570 AATAAAGCTT
40580 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
40602 TCATCTTT--AAAGAGATAGGCTA
1 TCATCTTTGAAAAGAGA-A-TCTA
* *
40624 TCATCTTTGAAGAA-ATAGTCTA
1 TCATCTTTGAA-AAGAGAATCTA
40646 TCATCTTTGAAAAG
1 TCATCTTTGAAAAG
40660 TGTAGATGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
20 7 0.15
21 3 0.06
22 33 0.69
24 3 0.06
25 2 0.04
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:41092 original size:54 final size:54
Alignment explanation
Indices: 41028--41177 Score: 145
Period size: 54 Copynumber: 2.9 Consensus size: 54
41018 TGACTGGTTC
* * * *
41028 GTAAAACATTTGTCAATACATTCATCATCTCATGTGGTTTATGCTCAGATGCTA
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGCACAGATGCTA
* * * *
41082 GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCACAGATGC--
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGCACAGATGCTA
* * *
41134 -T-----ATTTAACAACACATTCATCATTTCATGTGACTTATGCACAGAT
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGCACAGAT
41178 TTCTGGTCAG
Statistics
Matches: 83, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
46 38 0.46
51 1 0.01
54 44 0.53
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGCACAGATGCTA
Found at i:41173 original size:46 final size:46
Alignment explanation
Indices: 41089--41177 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
41079 CTAGTAAAAC
* * * * *
41089 ATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCACAGATGCT
1 ATTTAACAACACATTCATCATTTCATGTGACTTATGCACAGATGCT
41135 ATTTAACAACACATTCATCATTTCATGTGACTTATGCACAGAT
1 ATTTAACAACACATTCATCATTTCATGTGACTTATGCACAGAT
41178 TTCTGGTCAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (46 bp):
ATTTAACAACACATTCATCATTTCATGTGACTTATGCACAGATGCT
Found at i:44841 original size:32 final size:32
Alignment explanation
Indices: 44800--44861 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
44790 GAAGAAATGA
*
44800 TTGTTATGCTCATCTTATAGAGATACTTCTCG
1 TTGTTATGCTCATCTCATAGAGATACTTCTCG
* * *
44832 TTGTTATGCTTATCTCGTAGAGATATTTCT
1 TTGTTATGCTCATCTCATAGAGATACTTCT
44862 TGTGTCTGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (32 bp):
TTGTTATGCTCATCTCATAGAGATACTTCTCG
Found at i:45339 original size:9 final size:8
Alignment explanation
Indices: 45318--45391 Score: 60
Period size: 8 Copynumber: 8.9 Consensus size: 8
45308 CTTGTTTCAA
45318 TTTTTTTC
1 TTTTTTTC
* *
45326 CTTTTATC
1 TTTTTTTC
*
45334 TTTTTTTG
1 TTTTTTTC
*
45342 TATTTTTCC
1 T-TTTTTTC
45351 TTTTTTTC
1 TTTTTTTC
45359 TTTTTTT-
1 TTTTTTTC
*
45366 TTCCTTTTCC
1 TT--TTTTTC
45376 TTTTTTTC
1 TTTTTTTC
45384 TTCTTTTT
1 TT-TTTTT
45392 TTTAAGTATA
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
7 2 0.04
8 32 0.63
9 15 0.29
10 2 0.04
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.80
Consensus pattern (8 bp):
TTTTTTTC
Found at i:45364 original size:17 final size:16
Alignment explanation
Indices: 45318--45391 Score: 60
Period size: 17 Copynumber: 4.4 Consensus size: 16
45308 CTTGTTTCAA
* *
45318 TTTTTTTCCTTTTATC
1 TTTTTTTCTTTTTTTC
* *
45334 TTTTTTTGTATTTTTCC
1 TTTTTTTCT-TTTTTTC
45351 TTTTTTTCTTTTTTT-
1 TTTTTTTCTTTTTTTC
*
45366 TTCCTTTTCCTTTTTTTC
1 TT--TTTTTCTTTTTTTC
45384 TTCTTTTT
1 TT-TTTTT
45392 TTTAAGTATA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
15 2 0.04
16 12 0.26
17 30 0.65
18 2 0.04
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.80
Consensus pattern (16 bp):
TTTTTTTCTTTTTTTC
Found at i:45373 original size:25 final size:25
Alignment explanation
Indices: 45321--45393 Score: 94
Period size: 25 Copynumber: 2.9 Consensus size: 25
45311 GTTTCAATTT
* * *
45321 TTTTCC-TTTTATCTTTTTTTGTAT
1 TTTTCCTTTTTTTCTTTTTTTTTAC
*
45345 TTTTCCTTTTTTTCTTTTTTTTTCC
1 TTTTCCTTTTTTTCTTTTTTTTTAC
45370 TTTTCCTTTTTTTCTTCTTTTTTT
1 TTTTCCTTTTTTTCTT-TTTTTTT
45394 TAAGTATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.14
25 30 0.70
26 7 0.16
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.79
Consensus pattern (25 bp):
TTTTCCTTTTTTTCTTTTTTTTTAC
Found at i:45381 original size:19 final size:19
Alignment explanation
Indices: 45344--45382 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
45334 TTTTTTTGTA
*
45344 TTTTTCCTTTTTTTCTTTT
1 TTTTTCCTTTTCTTCTTTT
45363 TTTTTCCTTTTC--CTTTT
1 TTTTTCCTTTTCTTCTTTT
45380 TTT
1 TTT
45383 CTTCTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
19 11 0.58
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTCCTTTTCTTCTTTT
Found at i:51455 original size:2 final size:2
Alignment explanation
Indices: 51448--51494 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
51438 ATTTAAACCA
* *
51448 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51490 AT AT A
1 AT AT A
51495 ATAAAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52639 original size:21 final size:21
Alignment explanation
Indices: 52613--52667 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
52603 GTGGAAGCTT
52613 CGGTGAGTCACCAAGGCTATG
1 CGGTGAGTCACCAAGGCTATG
52634 CGGTGAGTCACCAAGGCTATG
1 CGGTGAGTCACCAAGGCTATG
*
52655 CGGTGACTCACCA
1 CGGTGAGTCACCA
52668 TATAGCTTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.27, G:0.31, T:0.18
Consensus pattern (21 bp):
CGGTGAGTCACCAAGGCTATG
Found at i:52987 original size:3 final size:3
Alignment explanation
Indices: 52968--53035 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
52958 TTTTAATATT
* *
52968 TAA TAAA TAA TATA TAA TAA TAA TAT TAA TAA TTA TAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
53015 TAA TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
53036 ATTTAAATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:53007 original size:18 final size:18
Alignment explanation
Indices: 52968--53035 Score: 91
Period size: 18 Copynumber: 3.7 Consensus size: 18
52958 TTTTAATATT
*
52968 TAATAAATAATATATAATAA
1 TAAT-AATAATA-ATTATAA
*
52988 TAATATTAATAATTATAA
1 TAATAATAATAATTATAA
*
53006 TAATAATAATAATTTTAA
1 TAATAATAATAATTATAA
53024 TAATAATAATAA
1 TAATAATAATAA
53036 ATTTAAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
18 34 0.77
19 6 0.14
20 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATAATAATAATTATAA
Found at i:53040 original size:18 final size:18
Alignment explanation
Indices: 52965--53041 Score: 81
Period size: 18 Copynumber: 4.3 Consensus size: 18
52955 GCTTTTTAAT
52965 ATTTAATAAATAAT-ATATA
1 ATTTAAT-AATAATAATA-A
*
52984 A--TAATAATATTAAT-A
1 ATTTAATAATAATAATAA
52999 ATTATAATAATAATAATAA
1 ATT-TAATAATAATAATAA
*
53018 TTTTAATAATAATAATAA
1 ATTTAATAATAATAATAA
53036 ATTTAA
1 ATTTAA
53042 ATTTAAAATG
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
15 2 0.04
16 5 0.10
17 6 0.12
18 32 0.65
19 4 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTAATAATAATAATAA
Found at i:63218 original size:16 final size:16
Alignment explanation
Indices: 63197--63227 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
63187 GAGTTTGTTA
63197 AGCTTTTCTGTTATGT
1 AGCTTTTCTGTTATGT
63213 AGCTTTTCTGTTATG
1 AGCTTTTCTGTTATG
63228 CATTCAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.19, T:0.55
Consensus pattern (16 bp):
AGCTTTTCTGTTATGT
Found at i:65513 original size:17 final size:16
Alignment explanation
Indices: 65482--65515 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
65472 CACGTGAGGA
65482 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
65498 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
65515 T
1 T
65516 ACTATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:76138 original size:17 final size:17
Alignment explanation
Indices: 76113--76148 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
76103 ATGAACTAAA
*
76113 TTTATTCAAATCAAATT
1 TTTAATCAAATCAAATT
*
76130 TTTAATCAAATCTAATT
1 TTTAATCAAATCAAATT
76147 TT
1 TT
76149 ACTCGCCACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTAATCAAATCAAATT
Found at i:76639 original size:3 final size:3
Alignment explanation
Indices: 76631--76665 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
76621 CATACCTACT
76631 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
76666 TAGCAAAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:85901 original size:28 final size:29
Alignment explanation
Indices: 85859--85915 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
85849 TCACTCCCCG
* *
85859 TAAAATC-AACCAAAATCATGACAAATCAA
1 TAAAATCAAACAAAAATC-TAACAAATCAA
85888 TAAAA-CAAACAAAAATCTAACAAATCAA
1 TAAAATCAAACAAAAATCTAACAAATCAA
85916 CCACTCCTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.63, C:0.19, G:0.02, T:0.16
Consensus pattern (29 bp):
TAAAATCAAACAAAAATCTAACAAATCAA
Found at i:86782 original size:27 final size:24
Alignment explanation
Indices: 86751--86825 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 24
86741 GAAAATGAAA
86751 ATAAAATATTTTTAAATTAAGTTAAT
1 ATAAAATATTTTT-AA-TAAGTTAAT
**
86777 AGTAAAATATAATTAATAAGTTAAT
1 A-TAAAATATTTTTAATAAGTTAAT
*
86802 ATAAAA-ATATTT--TAAGTTAAT
1 ATAAAATATTTTTAATAAGTTAAT
86823 ATA
1 ATA
86826 TATAAAATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
21 12 0.27
23 5 0.11
24 5 0.11
25 10 0.22
26 3 0.07
27 10 0.22
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.41
Consensus pattern (24 bp):
ATAAAATATTTTTAATAAGTTAAT
Found at i:87213 original size:19 final size:19
Alignment explanation
Indices: 87189--87232 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
87179 GAGGATTATG
87189 AATAAAAATGAAAATATAA
1 AATAAAAATGAAAATATAA
*
87208 AATAAAAATGAAAATATAT
1 AATAAAAATGAAAATATAA
87227 AATAAA
1 AATAAA
87233 TCGGGTATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (19 bp):
AATAAAAATGAAAATATAA
Found at i:87965 original size:21 final size:21
Alignment explanation
Indices: 87850--87965 Score: 58
Period size: 21 Copynumber: 5.6 Consensus size: 21
87840 GCGAAATAAA
*
87850 AATCGCAACGCGATCTT-CAG
1 AATCGCAACGCGATTTTCCAG
** * *
87870 AATCGCAAATC-AGTTCCCAG
1 AATCGCAACGCGATTTTCCAG
* ** *
87890 AATCGCAACGCGATTATGAAT
1 AATCGCAACGCGATTTTCCAG
* ** *
87911 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
** *
87931 AATTCGCATTGCGATTTTCCAT
1 AA-TCGCAACGCGATTTTCCAG
87953 AATCGCAACGCGA
1 AATCGCAACGCGA
87966 ACATATAAAT
Statistics
Matches: 68, Mismatches: 24, Indels: 7
0.69 0.24 0.07
Matches are distributed among these distances:
19 2 0.03
20 23 0.34
21 41 0.60
22 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:88015 original size:40 final size:40
Alignment explanation
Indices: 87971--88189 Score: 196
Period size: 40 Copynumber: 5.4 Consensus size: 40
87961 CGCGAACATA
* *
87971 TAAATCGCAACGCGATTCAG-ACTATCGCAACGAGTATCCG
1 TAAATCGCAACGCGATTCAGTA-AATCGCAACGCGTATCCG
* * * *
88011 TAAATCGCAACGACAATAC-GTAAAATCACAACGCGTATCTG
1 TAAATCGCAACG-CGATTCAGT-AAATCGCAACGCGTATCCG
* * * *
88052 TAAATCGCAACGAGAAT-ACGTAAATCGCAACGCATATCTG
1 TAAATCGCAACGCGATTCA-GTAAATCGCAACGCGTATCCG
* * *
88092 TAAATCGCAACGAGAAT-ACGTAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGATTCA-GTAAATCGCAACGCGTATCCG
* * *
88132 TAAATCGCAACGACAATAC-GTAAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-CGATTCAGT-AAATCGCAACGCGTATCCG
88173 TAAATCGCAACGCGATT
1 TAAATCGCAACGCGATT
88190 TTTAAAGCTC
Statistics
Matches: 150, Mismatches: 21, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
40 85 0.57
41 64 0.43
42 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (40 bp):
TAAATCGCAACGCGATTCAGTAAATCGCAACGCGTATCCG
Found at i:88017 original size:20 final size:20
Alignment explanation
Indices: 87994--88184 Score: 186
Period size: 20 Copynumber: 9.4 Consensus size: 20
87984 GATTCAGACT
87994 ATCGCAACGAGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
** *
88014 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
* * *
88035 ATCACAACGCGTATCTGTAA
1 ATCGCAACGAGTATCCGTAA
* *
88055 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
*
88075 ATCGCAACGCA-TATCTGTAA
1 ATCGCAACG-AGTATCCGTAA
* *
88095 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
* *
88115 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
** *
88135 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
* *
88156 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
88176 ATCGCAACG
1 ATCGCAACG
88185 CGATTTTTAA
Statistics
Matches: 132, Mismatches: 35, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
19 1 0.01
20 101 0.77
21 30 0.23
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:88055 original size:41 final size:40
Alignment explanation
Indices: 87994--88184 Score: 283
Period size: 40 Copynumber: 4.7 Consensus size: 40
87984 GATTCAGACT
*
87994 ATCGCAACGAGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGACAATACGT-AA
* * *
88035 ATCACAACGCGTATCTGTAAATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAA
* * *
88075 ATCGCAACGCATATCTGTAAATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAA
*
88115 ATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGACAATACGT-AA
*
88156 ATCGCAATGCGTATCCGTAAATCGCAACG
1 ATCGCAACGCGTATCCGTAAATCGCAACG
88185 CGATTTTTAA
Statistics
Matches: 139, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 74 0.53
41 65 0.47
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (40 bp):
ATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAA
Found at i:88807 original size:21 final size:21
Alignment explanation
Indices: 88746--88858 Score: 139
Period size: 21 Copynumber: 5.6 Consensus size: 21
88736 TTTTAAACTT
88746 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
88766 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
88786 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
88807 AAAATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
*
88828 AAAATCGCAAC--GCGAAATG
1 AAAATCGCAACGAGAGAAATG
88847 AAAATCGCAACG
1 AAAATCGCAACG
88859 CGAAACCAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
19 18 0.21
20 30 0.36
21 36 0.43
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.12
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:88846 original size:19 final size:19
Alignment explanation
Indices: 88746--88874 Score: 123
Period size: 21 Copynumber: 6.5 Consensus size: 19
88736 TTTTAAACTT
**
88746 AAAATCGCAACATGAAAATG
1 AAAATCGCAACGCG-AAATG
*
88766 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
** *
88786 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC--GCGAAATG
*
88807 AAAATCGCAACGAGAGAAATG
1 AAAATCGCAAC--GCGAAATG
88828 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
**
88847 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATG
88866 AAAATCGCA
1 AAAATCGCA
88875 TTGCGATTTT
Statistics
Matches: 97, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
19 33 0.34
20 28 0.29
21 35 0.36
22 1 0.01
ACGTcount: A:0.50, C:0.20, G:0.19, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:88880 original size:19 final size:19
Alignment explanation
Indices: 88828--88874 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
88818 GAGAGAAATG
**
88828 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACC
88847 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
88866 AAAATCGCA
1 AAAATCGCA
88875 TTGCGATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.49, C:0.26, G:0.17, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:88940 original size:20 final size:20
Alignment explanation
Indices: 88875--88963 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 20
88865 CAAAATCGCA
88875 TTGCGATTTTCATTT-CGCG
1 TTGCGATTTTCATTTCCGCG
*
88894 TTGCGA--TT-A--T-CTCG
1 TTGCGATTTTCATTTCCGCG
**
88908 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTTCCGCG
*
88928 TTGCGATTTTCA-TTCTCTCG
1 TTGCGATTTTCATTTC-CGCG
88948 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
88964 AACCAAAAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 10 0.18
20 28 0.50
21 3 0.05
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTCATTTCCGCG
Found at i:91010 original size:21 final size:21
Alignment explanation
Indices: 90986--91052 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
90976 TCATTCCTCG
90986 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
91007 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
91028 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
91049 AGAG
1 AGAG
91053 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:92420 original size:14 final size:14
Alignment explanation
Indices: 92401--92436 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
92391 ATTGTTTAAT
92401 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
92415 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
92429 TGATTTGT
1 TGATTTGT
92437 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:92573 original size:19 final size:19
Alignment explanation
Indices: 92538--92590 Score: 88
Period size: 19 Copynumber: 2.7 Consensus size: 19
92528 AAAACAGACT
92538 ATCGCAACGCGGAAATGAAA
1 ATCGCAACGC-GAAATGAAA
*
92558 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
92577 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
92591 CTTTTATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 22 0.71
20 9 0.29
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:92620 original size:19 final size:18
Alignment explanation
Indices: 92592--92630 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
92582 AACGCGAAAC
92592 TTTTATTTCGCATTGCGA
1 TTTTATTTCGCATTGCGA
92610 TTTTCATTTCGCATTGCGA
1 TTTT-ATTTCGCATTGCGA
92629 TT
1 TT
92631 CCTCGTTGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.15, C:0.18, G:0.15, T:0.51
Consensus pattern (18 bp):
TTTTATTTCGCATTGCGA
Found at i:92659 original size:20 final size:20
Alignment explanation
Indices: 92636--92685 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
92626 CGATTCCTCG
*
92636 TTGCGATAGTCATTTCCGCA
1 TTGCGATAGTCAATTCCGCA
92656 TTGCGATAGTCAATTCCGCA
1 TTGCGATAGTCAATTCCGCA
*
92676 TTGTGATAGT
1 TTGCGATAGT
92686 TAAATGAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAATTCCGCA
Found at i:92928 original size:19 final size:19
Alignment explanation
Indices: 92904--92949 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
92894 AGAGGAAAAT
92904 ATGAAAATCACAATGCGAA
1 ATGAAAATCACAATGCGAA
*
92923 ATGAAAATCGCAATGCGAA
1 ATGAAAATCACAATGCGAA
92942 ATGAAAAT
1 ATGAAAAT
92950 TTCGCGTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.52, C:0.13, G:0.17, T:0.17
Consensus pattern (19 bp):
ATGAAAATCACAATGCGAA
Found at i:93011 original size:33 final size:33
Alignment explanation
Indices: 92954--93087 Score: 133
Period size: 33 Copynumber: 3.8 Consensus size: 33
92944 GAAAATTTCG
92954 CGTTGCGATTTTCATTTTTGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTTGCATTGCGATTCACT
*
92988 CGTTGCGATTTTCATTTTGCATTGCGATTTTCATTT
1 CGTTGCGATTTTCATTTTGCATTGCGA--TTCA-CT
*** *
93024 CGCATTGCGATTTTCATTTCATATTGCGATTCTCT
1 CG--TTGCGATTTTCATTTTGCATTGCGATTCACT
** *
93059 CGTTGCGATAGTCATTTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTT-GCATTGCGAT
93088 AGTCAATTCC
Statistics
Matches: 82, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
33 26 0.32
34 21 0.26
35 7 0.09
36 6 0.07
38 22 0.27
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTTGCATTGCGATTCACT
Found at i:93043 original size:19 final size:19
Alignment explanation
Indices: 92948--93054 Score: 116
Period size: 19 Copynumber: 5.8 Consensus size: 19
92938 CGAAATGAAA
*
92948 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
92967 ATTTTTGCATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
92985 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
93001 ATTTTGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
93020 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
**
93039 ATTTCATATTGCGATT
1 ATTTCGCATTGCGATT
93055 CTCTCGTTGC
Statistics
Matches: 73, Mismatches: 9, Indels: 12
0.78 0.10 0.13
Matches are distributed among these distances:
14 6 0.08
16 6 0.08
17 2 0.03
18 4 0.05
19 44 0.60
20 11 0.15
ACGTcount: A:0.16, C:0.19, G:0.17, T:0.49
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:93074 original size:71 final size:72
Alignment explanation
Indices: 92948--93087 Score: 194
Period size: 72 Copynumber: 1.9 Consensus size: 72
92938 CGAAATGAAA
* * **
92948 ATTTCGCGTTGCGATTTTCATTTTTGCATTGCGATTCACTCGTTGCGATTTTCATTTT-GCATTG
1 ATTTCGCATTGCGATTTTCATTTAT-CATTGCGATTCACTCGTTGCGATAGTCATTTTCGCATTG
93012 CGATTTTC
65 CGATTTTC
* *
93020 ATTTCGCATTGCGATTTTCATTTCAT-ATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTG
1 ATTTCGCATTGCGATTTTCATTT-ATCATTGCGATTCACTCGTTGCGATAGTCATTTTCGCATTG
93084 CGAT
65 CGAT
93088 AGTCAATTCC
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
71 28 0.47
72 31 0.52
73 1 0.02
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.46
Consensus pattern (72 bp):
ATTTCGCATTGCGATTTTCATTTATCATTGCGATTCACTCGTTGCGATAGTCATTTTCGCATTGC
GATTTTC
Found at i:93084 original size:20 final size:20
Alignment explanation
Indices: 93059--93113 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
93049 GCGATTCTCT
* *
93059 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTCCG
93079 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
* *
93099 CATTACGATAGTCAA
1 CGTTGCGATAGTCAA
93114 ATGAATGTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCCG
Found at i:95545 original size:24 final size:24
Alignment explanation
Indices: 95511--95564 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
95501 CTGAAAAATC
95511 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
95535 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
95559 ATCAAA
1 ATCAAA
95565 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:96439 original size:20 final size:19
Alignment explanation
Indices: 96418--96678 Score: 157
Period size: 20 Copynumber: 12.9 Consensus size: 19
96408 GCGATAGTCA
*
96418 GAATCTCGTTGCGATTTAC
1 GAATCGCGTTGCGATTTAC
*
96437 AGATTCGCGTTGCGATTTAC
1 -GAATCGCGTTGCGATTTAC
*
96457 GGATACGCGTTGCGATTTTAC
1 GAAT-CGCGTTGCGA-TTTAC
* *
96478 GTATTGTCGTTGCGATTTAC
1 GAATCG-CGTTGCGATTTAC
* *
96498 GGATACGCATTGCGATTTAC
1 GAAT-CGCGTTGCGATTTAC
* * *
96518 GTATTCTCGTTGCAATTTAC
1 G-AATCGCGTTGCGATTTAC
96538 -AGATACGCGTTGCGATTTAC
1 GA-AT-CGCGTTGCGATTTAC
* * *
96558 GTATTCTCGTTGCGATTTAT
1 G-AATCGCGTTGCGATTTAC
* *
96578 GGATACGCGTTGTGATTTTAC
1 GAAT-CGCGTTGCGA-TTTAC
* *
96599 GTATTGTCGTTGCGATTTAC
1 GAATCG-CGTTGCGATTTAC
*
96619 GGATACGCGTTGCGATTTTAC
1 GAAT-CGCGTTGCGA-TTTAC
* * *
96640 GGATACTCGTTGCGATAGT-C
1 GAAT-CGCGTTGCGAT-TTAC
*
96660 AGAATCGCGTTGTGATTTA
1 -GAATCGCGTTGCGATTTA
96679 TATGTTCGCG
Statistics
Matches: 188, Mismatches: 36, Indels: 34
0.73 0.14 0.13
Matches are distributed among these distances:
18 1 0.01
19 5 0.03
20 124 0.66
21 57 0.30
22 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (19 bp):
GAATCGCGTTGCGATTTAC
Found at i:96468 original size:40 final size:40
Alignment explanation
Indices: 96424--96716 Score: 299
Period size: 40 Copynumber: 7.2 Consensus size: 40
96414 GTCAGAATCT
96424 CGTTGCGATTTACAG-ATTCGCGTTGCGATTTACGGATACG
1 CGTTGCGATTTAC-GTATTCGCGTTGCGATTTACGGATACG
96464 CGTTGCGATTTTACGTATT-GTCGTTGCGATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCG-CGTTGCGATTTACGGATACG
* * * *
96505 CATTGCGATTTACGTATTCTCGTTGCAATTTACAGATACG
1 CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
* *
96545 CGTTGCGATTTACGTATTCTCGTTGCGATTTATGGATACG
1 CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
*
96585 CGTTGTGATTTTACGTATT-GTCGTTGCGATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCG-CGTTGCGATTTACGGATACG
* * * * *
96626 CGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-ATCG
1 CGTTGCGA-TTTACGTATTCGCGTTGCGAT-TTACGGATA-CG
* ** * * ** *
96667 CGTTGTGATTTATATGTTCGCGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
96707 CGTTGCGATT
1 CGTTGCGATT
96717 ATGGAAAATC
Statistics
Matches: 214, Mismatches: 28, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
39 1 0.00
40 111 0.52
41 101 0.47
42 1 0.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
Found at i:96582 original size:121 final size:122
Alignment explanation
Indices: 96424--96716 Score: 389
Period size: 121 Copynumber: 2.4 Consensus size: 122
96414 GTCAGAATCT
96424 CGTTGCGATTTACAGATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTT
1 CGTTGCGATTTACAGATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTT
* *
96489 GCGATTTACGGATACGCATTGCGA-TTTACGTATTCTCGTTGCAATTTACAGATACG
66 GCGATTTACGGATACGCATTGCGATTTTACGGATACTCGTTGCAATTTACAGATACG
* * *
96545 CGTTGCGATTTAC-GTATTCTCGTTGCGATTTATGGATACGCGTTGTGATTTTACGTATTGTCGT
1 CGTTGCGATTTACAG-ATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGT
* * *
96609 TGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-ATCG
65 TGCGATTTACGGATACGCATTGCGATTTTACGGATACTCGTTGCAAT-TTACAGATA-CG
* * * ** *
96667 CGTTGTGATTTATATG-TTCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACA-GATTCGCGTTGCGATTTACGGATACGCGTTGCGATT
96717 ATGGAAAATC
Statistics
Matches: 149, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
120 1 0.01
121 84 0.56
122 62 0.42
123 1 0.01
124 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (122 bp):
CGTTGCGATTTACAGATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTT
GCGATTTACGGATACGCATTGCGATTTTACGGATACTCGTTGCAATTTACAGATACG
Found at i:96671 original size:41 final size:41
Alignment explanation
Indices: 96424--96655 Score: 337
Period size: 41 Copynumber: 5.7 Consensus size: 41
96414 GTCAGAATCT
*
96424 CGTTGCGA-TTTACAG-ATTCGCGTTGCGATTTACGGATACG
1 CGTTGCGATTTTAC-GTATTCTCGTTGCGATTTACGGATACG
*
96464 CGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
* * *
96505 CATTGCGA-TTTACGTATTCTCGTTGCAATTTACAGATACG
1 CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
*
96545 CGTTGCGA-TTTACGTATTCTCGTTGCGATTTATGGATACG
1 CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
* *
96585 CGTTGTGATTTTACGTATTGTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
* *
96626 CGTTGCGATTTTACGGATACTCGTTGCGAT
1 CGTTGCGATTTTACGTATTCTCGTTGCGAT
96656 AGTCAGAATC
Statistics
Matches: 172, Mismatches: 17, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
40 81 0.47
41 91 0.53
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
Found at i:96687 original size:20 final size:20
Alignment explanation
Indices: 96664--96716 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
96654 ATAGTCAGAA
* *
96664 TCGCGTTGTGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
96684 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
96704 TCGCGTTGCGATT
1 TCGCGTTGCGATT
96717 ATGGAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:96691 original size:81 final size:81
Alignment explanation
Indices: 96424--96716 Score: 299
Period size: 81 Copynumber: 3.6 Consensus size: 81
96414 GTCAGAATCT
* *
96424 CGTTGCGATTTACA-GATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGT
1 CGTTGCGATTTACATG-TTCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGT
* *
96488 TGCGATTTACGGATACG
65 TGCGATTCACGAATACG
* * * * *
96505 CATTGCGATTTACGTATTCTCGTTGCAATTTACAGATACGCGTTGCGA-TTTACGTATTCTCGTT
1 CGTTGCGATTTACATGTTCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTT
* * *
96569 GCGATTTATGGATACG
66 GCGATTCACGAATACG
* * * * * *
96585 CGTTGTGATTTTACGTATT-GTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCG
1 CGTTGCGA-TTTACATGTTCG-CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCG
96649 TTGCGATAGTCA-GAAT-CG
64 TTGCGAT--TCACGAATACG
* * * * *
96667 CGTTGTGATTTATATGTTCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACATGTTCGCGTTGCGATTTACAGATACGCGTTGCGATT
96717 ATGGAAAATC
Statistics
Matches: 181, Mismatches: 24, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
80 36 0.20
81 110 0.61
82 30 0.17
83 3 0.02
84 2 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (81 bp):
CGTTGCGATTTACATGTTCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTT
GCGATTCACGAATACG
Found at i:97284 original size:2 final size:2
Alignment explanation
Indices: 97277--97309 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
97267 ATATTTTGTG
97277 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
97310 CTATTCATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:97849 original size:17 final size:17
Alignment explanation
Indices: 97823--97860 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
97813 CGCAAACCAA
97823 TTTTTATCTTTAAAA-TG
1 TTTTTATC-TTAAAATTG
*
97840 TTTTTTTCTTAAAATTG
1 TTTTTATCTTAAAATTG
97857 TTTT
1 TTTT
97861 AAAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (17 bp):
TTTTTATCTTAAAATTG
Found at i:99011 original size:68 final size:68
Alignment explanation
Indices: 98936--99072 Score: 229
Period size: 68 Copynumber: 2.0 Consensus size: 68
98926 TCACTTGTAC
* *
98936 TAACTCATTTCTTCTTATTTTTTGTGTCACTTTTCACTTTTTTGAATTGGATCATTGTTGAACCA
1 TAACTCATTTCTTCTTATTTTTTGTATCAATTTTCACTTTTTTGAATTGGATCATTGTTGAACCA
99001 ACT
66 ACT
* * *
99004 TAACTCATTTTTTCTTATTTTTTGTATCAATTTTCATTTTTTTGCATTGGATCATTGTTGAACCA
1 TAACTCATTTCTTCTTATTTTTTGTATCAATTTTCACTTTTTTGAATTGGATCATTGTTGAACCA
99069 ACT
66 ACT
99072 T
1 T
99073 TTGATTTTGA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.53
Consensus pattern (68 bp):
TAACTCATTTCTTCTTATTTTTTGTATCAATTTTCACTTTTTTGAATTGGATCATTGTTGAACCA
ACT
Found at i:106467 original size:2 final size:2
Alignment explanation
Indices: 106460--106490 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
106450 TTTAAAAATT
*
106460 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
106491 TTGTGTCAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:106729 original size:15 final size:15
Alignment explanation
Indices: 106702--106744 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
106692 TATAATTGTC
*
106702 AATATAAATTATATAT
1 AATAAAAATTATAT-T
*
106718 AA-AAATATTATATT
1 AATAAAAATTATATT
106732 AATAAAAATTATA
1 AATAAAAATTATA
106745 AATTCTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 3 0.13
15 18 0.78
16 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATAAAAATTATATT
Found at i:110915 original size:27 final size:27
Alignment explanation
Indices: 110863--110915 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
110853 AAATACTTTA
* *
110863 GGTCATTTTACACTTTAGGGATATTTT
1 GGTCATTTTAAACTTTAGGGACATTTT
110890 GGTCATTTTAAACTTTAAGGG-CATTT
1 GGTCATTTTAAACTTT-AGGGACATTT
110916 CTATAAATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (27 bp):
GGTCATTTTAAACTTTAGGGACATTTT
Found at i:115969 original size:14 final size:14
Alignment explanation
Indices: 115950--115976 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
115940 TTAACTTTTC
115950 GGTCAAAGTCAACT
1 GGTCAAAGTCAACT
115964 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
115977 GGGTTGACTC
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:0.22, G:0.22, T:0.19
Consensus pattern (14 bp):
GGTCAAAGTCAACT
Found at i:116012 original size:15 final size:14
Alignment explanation
Indices: 115979--116046 Score: 55
Period size: 15 Copynumber: 4.7 Consensus size: 14
115969 AAGTCAACGG
115979 GTTGACTCAGACGA
1 GTTGACTCAGACGA
* *
115993 GTTGACTTAGACCTA
1 GTTGACTCAGA-CGA
* *
116008 GTTGACTCAGATGG
1 GTTGACTCAGACGA
* *
116022 GTTAACTCCGATCGA
1 GTTGACTCAGA-CGA
*
116037 TTTGACTCAG
1 GTTGACTCAG
116047 TGACTGGACT
Statistics
Matches: 39, Mismatches: 13, Indels: 3
0.71 0.24 0.05
Matches are distributed among these distances:
14 19 0.49
15 20 0.51
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:121880 original size:21 final size:21
Alignment explanation
Indices: 121856--121895 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
121846 GAGAAATTAT
*
121856 TTTTAAAATATATAAATGATG
1 TTTTAAAATATAAAAATGATG
*
121877 TTTTAAAATTTAAAAATGA
1 TTTTAAAATATAAAAATGA
121896 AAACAAACTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (21 bp):
TTTTAAAATATAAAAATGATG
Found at i:125730 original size:20 final size:21
Alignment explanation
Indices: 125705--125764 Score: 86
Period size: 20 Copynumber: 2.8 Consensus size: 21
125695 TTTGGTGCAG
*
125705 AGGGAATCGATTCCCCCTTT-
1 AGGGAACCGATTCCCCCTTTA
125725 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATTCCCCCTTT-A
125747 AGGGGAACCGATTCCCCC
1 A-GGGAACCGATTCCCCC
125765 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 19 0.53
22 1 0.03
23 16 0.44
ACGTcount: A:0.22, C:0.33, G:0.23, T:0.22
Consensus pattern (21 bp):
AGGGAACCGATTCCCCCTTTA
Found at i:127352 original size:12 final size:12
Alignment explanation
Indices: 127335--127363 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
127325 AGATGAGCCT
127335 GAGCAGCCCGAA
1 GAGCAGCCCGAA
127347 GAGCAGCCCGAA
1 GAGCAGCCCGAA
127359 GAGCA
1 GAGCA
127364 AGCACAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.31, G:0.34, T:0.00
Consensus pattern (12 bp):
GAGCAGCCCGAA
Found at i:128043 original size:13 final size:13
Alignment explanation
Indices: 128025--128049 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
128015 AGGGGGAGTA
128025 ATTTCAAAATTTG
1 ATTTCAAAATTTG
128038 ATTTCAAAATTT
1 ATTTCAAAATTT
128050 CAAAATCTTA
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:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
ATTTCAAAATTTG
Found at i:129294 original size:2 final size:2
Alignment explanation
Indices: 129287--129319 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
129277 TTTCGTAAAT
129287 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
129320 TGTAGATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:140992 original size:18 final size:16
Alignment explanation
Indices: 140964--140997 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
140954 CTCAAGCCTT
140964 TAAAATAACATATAACA
1 TAAAATAACATA-AACA
140981 TAAAAGTAACATAAACA
1 TAAAA-TAACATAAACA
140998 CCATGAGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.65, C:0.12, G:0.03, T:0.21
Consensus pattern (16 bp):
TAAAATAACATAAACA
Found at i:143912 original size:19 final size:19
Alignment explanation
Indices: 143888--143936 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
143878 ATGTAATTAG
143888 TGTACCGATACCCCTAGGC
1 TGTACCGATACCCCTAGGC
143907 TGTACCGATACCCCTAGGC
1 TGTACCGATACCCCTAGGC
143926 TGTACCGATAC
1 TGTACCGATAC
143937 ACTTAGTCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.22
Consensus pattern (19 bp):
TGTACCGATACCCCTAGGC
Found at i:145204 original size:117 final size:117
Alignment explanation
Indices: 145060--145277 Score: 280
Period size: 117 Copynumber: 1.9 Consensus size: 117
145050 GTATTCTTTT
* * * *
145060 GAAAGCTAAAATAGACTTGGAAAATCAAAATGAAATGTTGAAA-AAGGAGTTAGAGCTTTCAAAA
1 GAAAGCTAAAATAGACTTGGAAAATCAAAATGAAATATT-AAAGAAGGAGTTACAACTCTCAAAA
* *
145124 ATGAAATCTGAATACT-TTGATAAAGAAATTTTCGAATTAAACAAACTTCTTCTA
65 ATGAAATCTGAA-ACTATTGAAAAAGAAAATTTC-AATTAAACAAACTTCTTCTA
* * * *
145178 GAAA-CTAAAATGGATTTTGAAAATCAAAATGAAATATTAAAGAAGGATTTACAACTCTCAAAAA
1 GAAAGCTAAAATAGACTTGGAAAATCAAAATGAAATATTAAAGAAGGAGTTACAACTCTCAAAAA
* *
145242 TGAAATTTGAAAGTATTGAAAAAGAAAATTTCAATT
66 TGAAATCTGAAACTATTGAAAAAGAAAATTTCAATT
145278 TGAAAGTTAA
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
116 9 0.10
117 73 0.85
118 4 0.05
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (117 bp):
GAAAGCTAAAATAGACTTGGAAAATCAAAATGAAATATTAAAGAAGGAGTTACAACTCTCAAAAA
TGAAATCTGAAACTATTGAAAAAGAAAATTTCAATTAAACAAACTTCTTCTA
Found at i:149168 original size:21 final size:22
Alignment explanation
Indices: 149136--149198 Score: 58
Period size: 23 Copynumber: 2.9 Consensus size: 22
149126 ATCCATACCC
*
149136 CCTTG-ATATGTATCGATACA-
1 CCTTGAATGTGTATCGATACAT
* *
149156 CCTTGAATGTGTACCTATACATT
1 CCTTGAATGTGTATCGATACA-T
* *
149179 CCTTTAATGTGTATTGATAC
1 CCTTGAATGTGTATCGATAC
149199 CCCCCAGGGG
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 5 0.15
21 12 0.36
23 16 0.48
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (22 bp):
CCTTGAATGTGTATCGATACAT
Found at i:149831 original size:15 final size:16
Alignment explanation
Indices: 149807--149837 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
149797 ATTTTTTTAA
149807 TATATATATATATAAT
1 TATATATATATATAAT
149823 TATAT-TATATATAAT
1 TATATATATATATAAT
149838 CCGGGTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATATATATATATAAT
Found at i:163465 original size:20 final size:21
Alignment explanation
Indices: 163419--163466 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
163409 CCCTATTTAA
163419 CCCAAAAGCCTTATTGAGGTC
1 CCCAAAAGCCTTATTGAGGTC
163440 CCCAAAAGCCTTATTGAGGT-
1 CCCAAAAGCCTTATTGAGGTC
163460 CCCAAAA
1 CCCAAAA
163467 CATTATTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (21 bp):
CCCAAAAGCCTTATTGAGGTC
Found at i:166762 original size:24 final size:25
Alignment explanation
Indices: 166718--166764 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
166708 AAAAATGAGT
*
166718 AAATAAACATACAAGGATTGAATTA
1 AAATAAACATAAAAGGATTGAATTA
166743 AAATAAA-ATAAAATGG-TTGAAT
1 AAATAAACATAAAA-GGATTGAAT
166765 AATAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.26
Consensus pattern (25 bp):
AAATAAACATAAAAGGATTGAATTA
Found at i:176609 original size:24 final size:24
Alignment explanation
Indices: 176577--176625 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
176567 AAGTGGGAGA
*
176577 TTGTTAAAAGTCCAAATTGGCAGC
1 TTGTTAAAAGCCCAAATTGGCAGC
176601 TTGTTAAAAGCCCAAATTGGCAGC
1 TTGTTAAAAGCCCAAATTGGCAGC
176625 T
1 T
176626 GCAAATTGAG
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:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (24 bp):
TTGTTAAAAGCCCAAATTGGCAGC
Found at i:176946 original size:34 final size:34
Alignment explanation
Indices: 176886--176952 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
176876 TCTTGAAGAG
*
176886 TTATTTTCTCCTTTTTATCGAAAGAGAA-TTGTTA
1 TTATTTTCTCCTTTTGATCG-AAGAGAAGTTGTTA
176920 TTATTTTCTCCTTGTTAGATCG-AGAGAAGTTGT
1 TTATTTTCTCCTT-TT-GATCGAAGAGAAGTTGT
176953 AATTCCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 19 0.66
35 6 0.21
36 4 0.14
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (34 bp):
TTATTTTCTCCTTTTGATCGAAGAGAAGTTGTTA
Found at i:178388 original size:24 final size:24
Alignment explanation
Indices: 178361--178407 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
178351 TTTGTGACAC
* *
178361 GTTTTCTTTGTTCTTATGGCATGT
1 GTTTTCTCTGCTCTTATGGCATGT
178385 GTTTTCTCTGCTCTTATGGCATG
1 GTTTTCTCTGCTCTTATGGCATG
178408 ATCCTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.09, C:0.17, G:0.21, T:0.53
Consensus pattern (24 bp):
GTTTTCTCTGCTCTTATGGCATGT
Found at i:178892 original size:10 final size:10
Alignment explanation
Indices: 178877--178908 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
178867 ACATTAGTTC
178877 TTTTCTTTTT
1 TTTTCTTTTT
178887 TTTTCTTTTT
1 TTTTCTTTTT
178897 TTTT-TTTTT
1 TTTTCTTTTT
178906 TTT
1 TTT
178909 GCTTCTATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:178894 original size:15 final size:14
Alignment explanation
Indices: 178874--178908 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
178864 GTTACATTAG
178874 TTCTTTTCTTTTTTT
1 TTCTTTT-TTTTTTT
178889 TTCTTTTTTTTTTT
1 TTCTTTTTTTTTTT
178903 TT-TTTT
1 TTCTTTT
178909 GCTTCTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.20
14 9 0.45
15 7 0.35
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (14 bp):
TTCTTTTTTTTTTT
Found at i:184343 original size:27 final size:28
Alignment explanation
Indices: 184305--184363 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
184295 TGAAAAATAA
*
184305 ATAAATAAATATTAAAATA-ATTTA-TAT
1 ATAAAAAAATA-TAAAATATATTTATTAT
184332 ATAAAAAAATATAAAATATTATTTATTAT
1 ATAAAAAAATATAAAATA-TATTTATTAT
184361 ATA
1 ATA
184364 TATATATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 7 0.25
27 10 0.36
28 5 0.18
29 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
ATAAAAAAATATAAAATATATTTATTAT
Found at i:184504 original size:27 final size:28
Alignment explanation
Indices: 184434--184504 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
184424 TAAAACAATA
184434 AAAATACAATTAT-ATATTTAAAAGTAGT
1 AAAATA-AATTATAATATTTAAAAGTAGT
* * *
184462 AAAATAAATGAAAATATTTAAAATTAGT
1 AAAATAAATTATAATATTTAAAAGTAGT
* *
184490 -GACTAAATTATAATA
1 AAAATAAATTATAATA
184505 AAATTAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
27 15 0.43
28 20 0.57
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (28 bp):
AAAATAAATTATAATATTTAAAAGTAGT
Found at i:185780 original size:3 final size:3
Alignment explanation
Indices: 185774--185828 Score: 78
Period size: 3 Copynumber: 18.7 Consensus size: 3
185764 TAATATTTAT
*
185774 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
185820 TAAA TAA TA
1 T-AA TAA TA
185829 TTTAAATGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 4 0.09
3 41 0.87
4 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:186197 original size:120 final size:120
Alignment explanation
Indices: 185970--186255 Score: 384
Period size: 120 Copynumber: 2.4 Consensus size: 120
185960 TGAATAAATT
* * * *
185970 CTTCTTTTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCCGCTGG---GGATGATGTTGACCT
1 CTTCTTATTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTGGAAAGGATGATGTTAACCT
* * * *
186032 ATTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGTTCTTCTCATTATGAA
65 ATTTCCTTCTGTGATAAAATCATTCAAAAGGTTGAACAAGCTCTTCTCATTATGAA
** *
186088 CTTCTTATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGTTTGATGTTAATCTA
1 CTTCTTATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGTTAACCTA
* * *
186153 TTTGCTTCTGTGATAAAATTATGT-AAAAGGTTGAACAAGCTCTTCTCATTGTGAA
66 TTTCCTTCTGTGATAAAATCAT-TCAAAAGGTTGAACAAGCTCTTCTCATTATGAA
*
186208 CTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAA
1 CTTCTTATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
186256 AGCTGATCCA
Statistics
Matches: 149, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
117 5 0.03
118 38 0.26
119 11 0.07
120 94 0.63
121 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.42
Consensus pattern (120 bp):
CTTCTTATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGTTAACCTA
TTTCCTTCTGTGATAAAATCATTCAAAAGGTTGAACAAGCTCTTCTCATTATGAA
Found at i:186513 original size:113 final size:110
Alignment explanation
Indices: 186177--186690 Score: 677
Period size: 113 Copynumber: 4.6 Consensus size: 110
186167 AAAATTATGT
** *
186177 AAAAGGTTGAACAAGCTCTTCTCATTGTGAA-CTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
* *
186241 GAAC-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGC
66 GAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAAC
186285 AAAAGGTTGAACAAATTCTTCTCATTATGAAT-TTCTTCTTCTTCAGATGACGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATCTTCTTCTTCTTCAGAT---GAGTTCTTCTCAT
* * * * * * *
186349 TATGAACTCTAC-CTGGCAATGTTAATCCATCAAATGATGAATTTAAAC
63 TATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAAC
186397 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA--TCTTCTT-CTTCTTCAGATGAGTTCTTCTCAT
*
186462 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC
63 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAAC
*
186510 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA--TCTTCTT-CTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
186575 TACGAACTTCCTCTGG-AAAGTTTGACCCATCAATTGATGGTTTTGAAC
63 TATGAACTTTCTCTGGAAAAG-CTGATCCATCAAATGATGGATTTGAAC
186623 AAATA-GTTGAACAAATTCTTCTCATTATGAAT-TTCTTC-T-TTCAGATGAGTTCTTCTCATTA
1 AAA-AGGTTGAACAAATTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
186684 TGAACTT
65 TGAACTT
186691 CTTCTTCTTC
Statistics
Matches: 362, Mismatches: 31, Indels: 27
0.86 0.07 0.06
Matches are distributed among these distances:
107 27 0.07
108 45 0.12
109 1 0.00
110 5 0.01
111 21 0.06
112 65 0.18
113 180 0.50
114 2 0.01
115 5 0.01
116 11 0.03
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (110 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAAC
Found at i:186660 original size:17 final size:17
Alignment explanation
Indices: 186638--186726 Score: 60
Period size: 17 Copynumber: 5.1 Consensus size: 17
186628 GTTGAACAAA
*
186638 TTCTTCTCATTATGAAT
1 TTCTTCTCATTATGAAC
* *
186655 TTCTTCTTTCA-GATG-AG
1 TTCTTC--TCATTATGAAC
186672 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
*
186689 TTCTTCTTC-TTCA-GATGAG
1 TTCTTC-TCATT-ATGA--AC
186708 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
186725 TT
1 TT
186727 TCTCTGGAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 20
0.68 0.07 0.24
Matches are distributed among these distances:
15 3 0.05
16 3 0.05
17 27 0.48
18 9 0.16
19 14 0.25
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.49
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:186681 original size:34 final size:36
Alignment explanation
Indices: 186638--186729 Score: 152
Period size: 36 Copynumber: 2.6 Consensus size: 36
186628 GTTGAACAAA
186638 TTCTTCTCATTATGAATTTCTTC-T-TTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
*
186672 TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
186708 TTCTTCTCATTATGAACTTTCT
1 TTCTTCTCATTATGAA-TTTCT
186730 CTGGAAAAGC
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
34 22 0.42
35 1 0.02
36 26 0.49
37 4 0.08
ACGTcount: A:0.20, C:0.21, G:0.10, T:0.50
Consensus pattern (36 bp):
TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
Found at i:186726 original size:143 final size:149
Alignment explanation
Indices: 186525--186839 Score: 437
Period size: 143 Copynumber: 2.1 Consensus size: 149
186515 GTTGAACAAA
186525 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTCTG
1 TTCTTCTCATTATGAA---CTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTCTG
* * * *
186590 G-AAAGTTTGACCCATCAATTGATGGTTTTGAACAAATAGTTGAACAAATTCTTCTCATTATGAA
63 GAAAAG-CTGACCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAA
186654 -T-TTCTT-C-T-TTCAGATGAG
127 CTCTTCTTCCTTCTTCAGATGAG
* * *
186672 TTCTTCTCATTATGAACTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1 TTCTTCTCATTATGAACTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTCTGGAA
* * *
186736 AAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTC
66 AAGCTGACCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAAC-TC
*
186801 TTCTTCCTTCTTTAGATGAG
130 TTCTTCCTTCTTCAGATGAG
186821 TTCTTCTCATTATGAACTT
1 TTCTTCTCATTATGAACTT
186840 TCTCTGGAAA
Statistics
Matches: 150, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
143 88 0.59
144 10 0.07
145 1 0.01
146 5 0.03
147 17 0.11
148 1 0.01
149 28 0.19
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (149 bp):
TTCTTCTCATTATGAACTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTCTGGAA
AAGCTGACCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTCT
TCTTCCTTCTTCAGATGAG
Found at i:186869 original size:113 final size:109
Alignment explanation
Indices: 186670--186874 Score: 356
Period size: 113 Copynumber: 1.8 Consensus size: 109
186660 CTTTCAGATG
186670 AGTTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
1 AGTTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
*
186735 AAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACA
66 AAAGCTGATCCATCAAATGATGGATTTGAACAAAAAGTTGAACA
*
186779 AGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTT-CTTC---AGATGAGTTCTTCTCATTATGAACTTTCTC
186844 TGGAAAAGCTGATCCATCAAATGATGGATTT
62 TGGAAAAGCTGATCCATCAAATGATGGATTT
186875 TAATCTTTGC
Statistics
Matches: 90, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
109 26 0.29
110 4 0.04
113 60 0.67
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (109 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
AAAGCTGATCCATCAAATGATGGATTTGAACAAAAAGTTGAACA
Found at i:187824 original size:93 final size:93
Alignment explanation
Indices: 187665--188047 Score: 662
Period size: 93 Copynumber: 4.1 Consensus size: 93
187655 CTTATTTCTA
* * * *
187665 CTATGAACACATTCATCTT-TCAAATCCAATGATTGG-TTCTGTGGTTTCATACCAAACCAGATC
1 CTATGAGCACATTCATCTTCT-AAATTCAATGATTGGTTTTTG-GGGTTCATACCAAACCAGATC
*
187728 AGATAACTCAAAGAACACTTTCAGAAGATG
64 AGATAACTCAAAGAACACTTCCAGAAGATG
187758 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
*
187823 ATAACTCAAAGAACACTTCCAGAAAATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
*
187851 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
*
187916 ATAACTCAAAGAACACTTCTAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
187944 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
188009 ATAACTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
188037 CTATGAGCACA
1 CTATGAGCACA
188048 CGGCACTTGT
Statistics
Matches: 277, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
93 272 0.98
94 5 0.02
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (93 bp):
CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
ATAACTCAAAGAACACTTCCAGAAGATG
Found at i:189093 original size:46 final size:46
Alignment explanation
Indices: 189042--189138 Score: 133
Period size: 46 Copynumber: 2.1 Consensus size: 46
189032 TGACCCCCCC
*
189042 TTTTTTTCTCTCTTTCTTTCTTTTT-CTCTTTTTTCCCTTTTTTTTA
1 TTTTTTTCTCTCTTTCTTTCTTTTTAAT-TTTTTTCCCTTTTTTTTA
* * * *
189088 TTTTTTTCTTTCTTTCTTTTTTTTTAATTTTTTTCTCTTTTTTTTC
1 TTTTTTTCTCTCTTTCTTTCTTTTTAATTTTTTTCCCTTTTTTTTA
189134 TTTTT
1 TTTTT
189139 CTTTTTTTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.80
Consensus pattern (46 bp):
TTTTTTTCTCTCTTTCTTTCTTTTTAATTTTTTTCCCTTTTTTTTA
Found at i:189145 original size:27 final size:26
Alignment explanation
Indices: 189041--189146 Score: 90
Period size: 28 Copynumber: 3.9 Consensus size: 26
189031 TTGACCCCCC
* *
189041 CTTTTTTTCTCTCTTTCTTTCTTTTTCT
1 CTTTTTTT-TCT-TTTTTTTTTTTTTCT
**
189069 CTTTTTTCCCTTTTTTTTATTTTTT-T
1 CTTTTTTTTCTTTTTTTT-TTTTTTCT
189095 CTTTCTTTCTT-TTTTTTTAATTTTTTTCT
1 CTTT-TTT-TTCTTTTTTT--TTTTTTTCT
*
189124 CTTTTTTTTCTTTTTCTTTTTTT
1 CTTTTTTTTCTTTTTTTTTTTTT
189147 CTTCAAGCAT
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
26 17 0.27
27 19 0.30
28 22 0.34
29 6 0.09
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (26 bp):
CTTTTTTTTCTTTTTTTTTTTTTTCT
Found at i:189149 original size:8 final size:8
Alignment explanation
Indices: 189052--189149 Score: 72
Period size: 8 Copynumber: 11.5 Consensus size: 8
189042 TTTTTTTCTC
*
189052 TCTTTCTT
1 TCTTTTTT
*
189060 TCTTTTTC
1 TCTTTTTT
189068 TCTTTTTT
1 TCTTTTTT
*
189076 CCCTTTTTTT
1 -TC-TTTTTT
*
189086 TATTTTTT
1 TCTTTTTT
189094 TCTTTCTTT
1 TCTTT-TTT
*
189103 CTTTTTTTT
1 -TCTTTTTT
*
189112 TAATTTTTT
1 T-CTTTTTT
189121 TCTCTTTTT
1 TCT-TTTTT
189130 T-TTCTTTT
1 TCTT-TTTT
189138 TCTTTTTT
1 TCTTTTTT
189146 TCTT
1 TCTT
189150 CAAGCATAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
7 1 0.01
8 39 0.54
9 22 0.31
10 10 0.14
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (8 bp):
TCTTTTTT
Found at i:196511 original size:15 final size:15
Alignment explanation
Indices: 196488--196519 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
196478 TGAAATGAAT
196488 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
196503 AATGTATGTATGCAA
1 AATGAATGTATGCAA
196518 AA
1 AA
196520 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:199318 original size:88 final size:82
Alignment explanation
Indices: 199165--199338 Score: 197
Period size: 88 Copynumber: 2.0 Consensus size: 82
199155 ATTTCAAAAT
* * *
199165 TATAATTATATAAAAAAATATTTATTTATTTAAAAATATCAGAAAAGGACTTCTAGGTACCTTAA
1 TATAATTATATAAAAAAATATATATTTATTTAAAAATATCAGAAAAGGACATCCAGGTA-CTTAA
*
199230 GACAGCTCTTTTCTTCGA
65 GACAGCCCTTTTCTTCGA
* *
199248 TATATATTATAATAAAAAAATTATAATATTTAATTTTAAAATATCAGAATAGGACATCCAGTTGT
1 TATA-ATTAT-ATAAAAAAA-TAT-ATATTT-ATTTAAAAATATCAGAAAAGGACATCCAG--GT
* *
199313 A-TTAAGACTGCCCTTTTCTTTGA
59 ACTTAAGACAGCCCTTTTCTTCGA
199336 TAT
1 TAT
199339 TGAAAAATAA
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
83 4 0.05
84 5 0.07
85 9 0.12
86 3 0.04
87 5 0.07
88 47 0.62
90 3 0.04
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (82 bp):
TATAATTATATAAAAAAATATATATTTATTTAAAAATATCAGAAAAGGACATCCAGGTACTTAAG
ACAGCCCTTTTCTTCGA
Found at i:199962 original size:15 final size:15
Alignment explanation
Indices: 199942--199973 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
199932 GGCTATTTAA
199942 GCCCGAAACTGGCTG
1 GCCCGAAACTGGCTG
199957 GCCCGAAACTGGCTG
1 GCCCGAAACTGGCTG
199972 GC
1 GC
199974 TCTCATTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.34, G:0.34, T:0.12
Consensus pattern (15 bp):
GCCCGAAACTGGCTG
Found at i:200822 original size:3 final size:3
Alignment explanation
Indices: 200816--200859 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
200806 TAATATTTAT
*
200816 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TGAA TGA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA
200860 TAAAGAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:217535 original size:20 final size:20
Alignment explanation
Indices: 217510--217547 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
217500 TAGGTTTGAG
* *
217510 TATCGATATTTGATGAACAA
1 TATCGATACTAGATGAACAA
217530 TATCGATACTAGATGAAC
1 TATCGATACTAGATGAAC
217548 TAGGAAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (20 bp):
TATCGATACTAGATGAACAA
Found at i:218376 original size:19 final size:18
Alignment explanation
Indices: 218336--218371 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
218326 TAAAACTATC
*
218336 ACATGATATTTATATAAA
1 ACATGATATTAATATAAA
218354 ACAT-ATATTAATATAAA
1 ACATGATATTAATATAAA
218371 A
1 A
218372 TACATCCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.36
Consensus pattern (18 bp):
ACATGATATTAATATAAA
Found at i:221833 original size:107 final size:106
Alignment explanation
Indices: 221291--222043 Score: 1076
Period size: 106 Copynumber: 7.0 Consensus size: 106
221281 TGTACTATTC
* * * *
221291 TGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTTTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
*
221356 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
221397 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGATACTGGGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
*
221462 ACCAGCCGTCCCTTCGTTGTGAAGTTTAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
221503 CGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTTTGAAACTGGGAAATTGTTTGTTGAGA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
221568 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
221609 TGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
* *
221674 ACCAACCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
** * * * *
221715 TGAGTCCAATATCCTTTACTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTTGTTGAT
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTG-TTTGTTGAC
* * * *
221780 GACCAGTCGTCCCTTCATTATGAAGTTGAACTTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
221822 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTTGTTGAC
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTG-TTTGTTGAC
* *
221887 GACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * ** * *
221929 TAAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAATGAAACT-TAAAAGTGGTTTAT
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC----TGAAACTGGGAAA-TTGTTTGT
* *
221993 TGACAACCAACCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
61 TGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
*
222039 CGAGT
1 TGAGT
222044 GGCACGATAT
Statistics
Matches: 590, Mismatches: 51, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
106 349 0.59
107 183 0.31
110 51 0.09
111 7 0.01
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.36
Consensus pattern (106 bp):
TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:222360 original size:14 final size:14
Alignment explanation
Indices: 222341--222367 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
222331 CTAAAATCTG
222341 TCTGGAATCTTGAC
1 TCTGGAATCTTGAC
222355 TCTGGAATCTTGA
1 TCTGGAATCTTGA
222368 AGTTTCGATC
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:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (14 bp):
TCTGGAATCTTGAC
Found at i:223046 original size:58 final size:58
Alignment explanation
Indices: 222983--223095 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
222973 CTTTTGTTCT
* * *
222983 TTTTTCTCTTTTTC-ATTTTTTCAATTTAGGGTGCCCTTTCGGGTTTTCACCCTAAACG
1 TTTTTC-CTTTTTCTATTTTTTCAACTTAGGATGCCCTTTCAGGTTTTCACCCTAAACG
* * *
223041 TTTTTCCTTTTTCTTTTTTTTCGACTTAGGATGCCCTTTCAGGTTTTCATCCTAA
1 TTTTTCCTTTTTCTATTTTTTCAACTTAGGATGCCCTTTCAGGTTTTCACCCTAA
223096 GCGAAGTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
57 7 0.15
58 41 0.85
ACGTcount: A:0.13, C:0.22, G:0.12, T:0.52
Consensus pattern (58 bp):
TTTTTCCTTTTTCTATTTTTTCAACTTAGGATGCCCTTTCAGGTTTTCACCCTAAACG
Found at i:240610 original size:106 final size:106
Alignment explanation
Indices: 240488--240682 Score: 284
Period size: 106 Copynumber: 1.8 Consensus size: 106
240478 CACACCAATA
* * * * *
240488 TTTTGGGTGTTGTGTTGTTTAAAGTGCATG-AGAAGTTTGTATTGATTAAAATATTATTTACTTT
1 TTTTGGGTGTTATGTTGTTTAAAGTGAATGCA-AAGGTTATAATGATTAAAATATTATTTACTTT
*
240552 TAACTTTTACATAATCTTTTCTTCAATGTTGCCCAACCATTT
65 TAACTTTTACATAATCATTTCTTCAATGTTGCCCAACCATTT
* * *
240594 TTTTTGGTGTTATGTTGTTTAACGTGAATGCAAAGGTTATAATGATTAAAATATTATTTATTTTT
1 TTTTGGGTGTTATGTTGTTTAAAGTGAATGCAAAGGTTATAATGATTAAAATATTATTTACTTTT
*
240659 AACTTTTACATCATCATTTCTTCA
66 AACTTTTACATAATCATTTCTTCA
240683 CCTTTTTAAT
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
106 77 0.99
107 1 0.01
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (106 bp):
TTTTGGGTGTTATGTTGTTTAAAGTGAATGCAAAGGTTATAATGATTAAAATATTATTTACTTTT
AACTTTTACATAATCATTTCTTCAATGTTGCCCAACCATTT
Found at i:241173 original size:25 final size:23
Alignment explanation
Indices: 241119--241175 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
241109 ATATTATATT
*
241119 AAATTTGTGTAATTTAAATTATG
1 AAATTTGTGTAATTAAAATTATG
*
241142 AATATTTGTTTAATTAATAATTATTG
1 AA-ATTTGTGTAATTAA-AATTA-TG
*
241168 TAATTTGT
1 AAATTTGT
241176 AAATTTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 2 0.07
24 12 0.43
25 11 0.39
26 3 0.11
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (23 bp):
AAATTTGTGTAATTAAAATTATG
Found at i:246300 original size:17 final size:17
Alignment explanation
Indices: 246275--246308 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
246265 AATGAAATAA
*
246275 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
246292 AAATAAAATAACCAAAT
1 AAATAAAATAAACAAAT
246309 TGGGATAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:247021 original size:24 final size:24
Alignment explanation
Indices: 246994--247111 Score: 80
Period size: 24 Copynumber: 4.7 Consensus size: 24
246984 CCTAAATCCT
246994 AATTAAAATACTAAAACCTATTTA
1 AATTAAAATACTAAAACCTATTTA
** * *
247018 AATTAAAATACCTAAAACAAAGATAA
1 AATTAAAATA-CTAAAACCTA-TTTA
* *
247044 AATATAAAA-A-TAATATCCTAAAACTT-
1 AAT-TAAAATACTAA-AACCT---ATTTA
247070 AATTAAAATACTAAAACCTATTTA
1 AATTAAAATACTAAAACCTATTTA
*
247094 AACTAAAATACCTAAAAC
1 AATTAAAATA-CTAAAAC
247112 AAAGATAAAT
Statistics
Matches: 71, Mismatches: 12, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
23 3 0.04
24 22 0.31
25 22 0.31
26 14 0.20
27 9 0.13
28 1 0.01
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.27
Consensus pattern (24 bp):
AATTAAAATACTAAAACCTATTTA
Found at i:247034 original size:75 final size:76
Alignment explanation
Indices: 246912--247120 Score: 325
Period size: 76 Copynumber: 2.8 Consensus size: 76
246902 TAAAACATTT
* * * *
246912 TAAATCCTAATTAAAA-ACTTAAAA-CTATTTAAACTAAAATACCTAAAATAAAAATAATAT-TT
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
246974 AAAATAATATCC
65 AAAATAATATCC
*
246986 TAAATCCTAATTAAAATACTAAAACCTATTTAAATTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
247051 AAATAATATCC
66 AAATAATATCC
* *
247062 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAA
247121 TATGATGTTT
Statistics
Matches: 124, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
74 21 0.17
75 34 0.27
76 69 0.56
ACGTcount: A:0.58, C:0.13, G:0.01, T:0.28
Consensus pattern (76 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
AAATAATATCC
Found at i:249202 original size:5 final size:5
Alignment explanation
Indices: 249192--249238 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
249182 TGTTCAGAGA
* * * *
249192 AAAAT AAAAT AAAAT TAATT AAAAT AAAAT -AAAT AGAAT GAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
249239 GTTCGCTGAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:255642 original size:75 final size:74
Alignment explanation
Indices: 255535--255745 Score: 325
Period size: 74 Copynumber: 2.8 Consensus size: 74
255525 TAAAAGATCT
* * *
255535 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAACAAAAATAATATTTA
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAAATAA-AATAA
255599 AAATAATATCC
64 AAATAATATCC
*
255610 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATAAAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAAATAAAATAAAA
255675 ATAATATCC
66 ATAATATCC
* * * *
255684 TAAAACTTAATTAAAATACTAAAACATATTTAAACTAAAATACCTAAAACAAATATAAAATA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAAATAAAATA
255746 TAATGTTTAA
Statistics
Matches: 127, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
74 77 0.61
75 50 0.39
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.27
Consensus pattern (74 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAAATAAAATAAAA
ATAATATCC
Found at i:255668 original size:25 final size:24
Alignment explanation
Indices: 255621--255742 Score: 79
Period size: 25 Copynumber: 5.0 Consensus size: 24
255611 AAATCCTAAT
** *
255621 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACAAATATAAAC
* *
255645 TAAAATACCTAAAACAAAGATAAAA
1 TAAAATA-CTAAAACAAATATAAAC
* * *
255670 TAAAA-A-TAATATCCTAAA-ACTTAAT
1 TAAAATACTAA-A-AC-AAATA-TAAAC
* *
255695 TAAAATACTAAAACATATTTAAAC
1 TAAAATACTAAAACAAATATAAAC
255719 TAAAATACCTAAAACAAATATAAA
1 TAAAATA-CTAAAACAAATATAAA
255743 ATATAATGTT
Statistics
Matches: 74, Mismatches: 15, Indels: 17
0.70 0.14 0.16
Matches are distributed among these distances:
22 3 0.04
23 1 0.01
24 22 0.30
25 43 0.58
26 2 0.03
27 3 0.04
ACGTcount: A:0.61, C:0.13, G:0.01, T:0.25
Consensus pattern (24 bp):
TAAAATACTAAAACAAATATAAAC
Found at i:256757 original size:14 final size:14
Alignment explanation
Indices: 256738--256777 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
256728 CACGTTTAGA
256738 TTTAAA-AAAATGTT
1 TTTAAATAAAAT-TT
*
256752 TTTAAATAATATTT
1 TTTAAATAAAATTT
256766 TTTAAATAAAAT
1 TTTAAATAAAAT
256778 ATTATAAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
TTTAAATAAAATTT
Found at i:259659 original size:16 final size:16
Alignment explanation
Indices: 259596--259662 Score: 53
Period size: 20 Copynumber: 3.7 Consensus size: 16
259586 ATCTTTTAAC
*
259596 AAATAAAATAAAGAAAG
1 AAATAAAATAAAG-ATG
259613 AAATTTTAAAATAAAGAGTG
1 AAA---TAAAATAAAGA-TG
259633 AACATATAAAATAAAGATG
1 -A-A-ATAAAATAAAGATG
259652 AAATAAAATAA
1 AAATAAAATAA
259663 TAGTAATTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
16 9 0.21
17 4 0.10
18 1 0.02
19 3 0.07
20 22 0.52
21 1 0.02
22 1 0.02
23 1 0.02
ACGTcount: A:0.67, C:0.01, G:0.10, T:0.21
Consensus pattern (16 bp):
AAATAAAATAAAGATG
Found at i:259664 original size:19 final size:20
Alignment explanation
Indices: 259620--259664 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
259610 AAGAAATTTT
*
259620 AAAATAAAGAGTGAACATAT
1 AAAATAAAGAGTGAACATAA
259640 AAAATAAAGA-TGAA-ATAA
1 AAAATAAAGAGTGAACATAA
259658 AATAATA
1 AA-AATA
259665 GTAATTTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 5 0.22
19 8 0.35
20 10 0.43
ACGTcount: A:0.67, C:0.02, G:0.11, T:0.20
Consensus pattern (20 bp):
AAAATAAAGAGTGAACATAA
Found at i:261801 original size:17 final size:18
Alignment explanation
Indices: 261779--261815 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
261769 AGATTCGGTC
*
261779 TTGTTTTTA-TTTTTTCT
1 TTGTTTTAATTTTTTTCT
261796 TTGTTTTAATTTTTTTCT
1 TTGTTTTAATTTTTTTCT
261814 TT
1 TT
261816 TTGGG
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:0.08, C:0.05, G:0.05, T:0.81
Consensus pattern (18 bp):
TTGTTTTAATTTTTTTCT
Done.