Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010443.1 Kokia drynarioides strain JFW-HI SEQ_125334, 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: 67938
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 54 characters in sequence are not A, C, G, or T
Found at i:71 original size:7 final size:7
Alignment explanation
Indices: 46--85 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
36 TTGATATTAA
46 TAATAA-
1 TAATAAT
52 TAAT-AT
1 TAATAAT
58 TAATAAT
1 TAATAAT
*
65 TATTAAT
1 TAATAAT
72 TAATAAT
1 TAATAAT
79 TAATAAT
1 TAATAAT
86 AAAAAAACGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
5 1 0.03
6 8 0.27
7 21 0.70
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TAATAAT
Found at i:75 original size:14 final size:14
Alignment explanation
Indices: 41--85 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
31 ATGTTTTGAT
* *
41 ATTAATAATAATAA
1 ATTAATAATTATTA
55 TATTAATAATTATTA
1 -ATTAATAATTATTA
*
70 ATTAATAATTAATA
1 ATTAATAATTATTA
84 AT
1 AT
86 AAAAAAACGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTAATAATTATTA
Found at i:1295 original size:59 final size:59
Alignment explanation
Indices: 1202--1813 Score: 868
Period size: 59 Copynumber: 10.4 Consensus size: 59
1192 GGAGGTCCTT
* * * *
1202 GAACTTTCCAAAAATCACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGGCCCC
1 GAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * * *
1261 AAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCTC
1 GAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * * *
1320 GAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAACCCCA-TTTTGACCCT
1 GAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * *
1378 AAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCAATTTTGACCCC
1 GAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * *
1437 GAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTC
1 GAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * *
1496 GAACCTTCTAAAAATTACCATTTTATCCCCGAACTTCCAAAAACCCCATTTTTGACCCC
1 GAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
*
1555 AAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
1 GAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* ** *
1614 AAACCTTCCAAAAATTACCATTTTACCCTTGAACTTCCAAAAATCGCATTTTTGACCCC
1 GAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * * *
1673 GAACCTTCTAAAAATTATCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTC
1 GAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * * * * **
1732 GAATCTTCTAAAAATTACCATTTTACCCTCGAACTTTCAAAAATCCTATTTTTGATTCC
1 GAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
*
1791 GAACATTCC-AAAATTACCATTTT
1 GAACCTTCCAAAAATTACCATTTT
1814 GCCACTCCGT
Statistics
Matches: 497, Mismatches: 55, Indels: 3
0.90 0.10 0.01
Matches are distributed among these distances:
58 64 0.13
59 433 0.87
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (59 bp):
GAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
Found at i:2178 original size:95 final size:96
Alignment explanation
Indices: 2052--2241 Score: 237
Period size: 95 Copynumber: 2.0 Consensus size: 96
2042 AAACTTTAAT
*
2052 ATCGAGGCAATATTCTTTTACTTCGGGTTCCGAAA-ATTTGCGCCTTAACTCACTAGATGCAA-A
1 ATCGAGGCAATATTCTTTTACTTCGGATTCCGAAATA-TTGCGCCTTAACTCACTAGATGCAACA
* *
2115 TTTTTTCAAATCGA-AGTAATCGAATACCCTTA
65 TTTCTTCAAATCGAGA-TAATCAAATACCCTTA
* * *
2147 ATCGAGGCAATGTT-TTCTTATCTTC-GATTCCGAAATATTGCGCCTTAACTTACTAGGTGCAAC
1 ATCGAGGCAATATTCTT-TTA-CTTCGGATTCCGAAATATTGCGCCTTAACTCACTAGATGCAAC
* *
2210 CTTTCTTCAAATCGAGATAATCAAATATCCTT
64 ATTTCTTCAAATCGAGATAATCAAATACCCTT
2242 CTCGCAAAAG
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
94 2 0.02
95 48 0.59
96 31 0.38
97 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (96 bp):
ATCGAGGCAATATTCTTTTACTTCGGATTCCGAAATATTGCGCCTTAACTCACTAGATGCAACAT
TTCTTCAAATCGAGATAATCAAATACCCTTA
Found at i:4018 original size:16 final size:16
Alignment explanation
Indices: 3966--4026 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
3956 AATAATACAT
*
3966 AATAAATAACATATTTA
1 AATAAATAA-ATTTTTA
* *
3983 ATGTAAAT-AATATTTAA
1 A-ATAAATAAAT-TTTTA
4000 AATAAATAAATTTTTA
1 AATAAATAAATTTTTA
4016 AATAAA-AAATT
1 AATAAATAAATT
4027 AAAACTATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
15 5 0.14
16 17 0.47
17 9 0.25
18 5 0.14
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
AATAAATAAATTTTTA
Found at i:4607 original size:24 final size:24
Alignment explanation
Indices: 4576--4621 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
4566 ATAACTTTAT
*
4576 TTTATTAT-GAAAATAAAAAATGG
1 TTTATTATAAAAAATAAAAAATGG
*
4599 TTTACTTATAAAAAATTAAAAAT
1 TTTA-TTATAAAAAATAAAAAAT
4622 AACTTAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 4 0.21
25 11 0.58
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (24 bp):
TTTATTATAAAAAATAAAAAATGG
Found at i:4812 original size:23 final size:23
Alignment explanation
Indices: 4773--4822 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
4763 TAATAATTTT
**
4773 AAATTAAATTATAAATATTTTAA
1 AAATTAAATTATAAATATGATAA
*
4796 AAATTAACTTA-ATAATATGATAA
1 AAATTAAATTATA-AATATGATAA
4819 AAAT
1 AAAT
4823 AAAAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (23 bp):
AAATTAAATTATAAATATGATAA
Found at i:5406 original size:15 final size:15
Alignment explanation
Indices: 5371--5418 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
5361 AAAATAAAAA
*
5371 TAAAATTTAAATTAAT
1 TAAAAATTAAATT-AT
*
5387 AAAAAATATAAA-TAT
1 TAAAAAT-TAAATTAT
5402 TAAAAATTAAATTAT
1 TAAAAATTAAATTAT
5417 TA
1 TA
5419 TTTGAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 4 0.15
15 13 0.48
16 6 0.22
17 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAAATTAAATTAT
Found at i:8948 original size:16 final size:16
Alignment explanation
Indices: 8896--8956 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
8886 AATAATACAT
*
8896 AATAAATAACATATTTA
1 AATAAATAA-ATTTTTA
* *
8913 ATGTAAAT-AATATTTAA
1 A-ATAAATAAAT-TTTTA
8930 AATAAATAAATTTTTA
1 AATAAATAAATTTTTA
8946 AATAAA-AAATT
1 AATAAATAAATT
8957 AAAACTATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
15 5 0.14
16 17 0.47
17 9 0.25
18 5 0.14
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
AATAAATAAATTTTTA
Found at i:9537 original size:24 final size:24
Alignment explanation
Indices: 9506--9551 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
9496 ATAACTTTAT
*
9506 TTTATTAT-GAAAATAAAAAATGG
1 TTTATTATAAAAAATAAAAAATGG
*
9529 TTTACTTATAAAAAATTAAAAAT
1 TTTA-TTATAAAAAATAAAAAAT
9552 AACTTAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 4 0.21
25 11 0.58
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (24 bp):
TTTATTATAAAAAATAAAAAATGG
Found at i:9742 original size:23 final size:23
Alignment explanation
Indices: 9703--9752 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
9693 TAATAATTTT
**
9703 AAATTAAATTATAAATATTTTAA
1 AAATTAAATTATAAATATGATAA
*
9726 AAATTAACTTA-ATAATATGATAA
1 AAATTAAATTATA-AATATGATAA
9749 AAAT
1 AAAT
9753 AAAAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (23 bp):
AAATTAAATTATAAATATGATAA
Found at i:10336 original size:15 final size:15
Alignment explanation
Indices: 10301--10348 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
10291 AAAATAAAAA
*
10301 TAAAATTTAAATTAAT
1 TAAAAATTAAATT-AT
*
10317 AAAAAATATAAA-TAT
1 TAAAAAT-TAAATTAT
10332 TAAAAATTAAATTAT
1 TAAAAATTAAATTAT
10347 TA
1 TA
10349 TTTGAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 4 0.15
15 13 0.48
16 6 0.22
17 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAAATTAAATTAT
Found at i:12597 original size:31 final size:31
Alignment explanation
Indices: 12559--12617 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
12549 TATTTGAGTT
*
12559 AATTAAGTTATTTGGATAAACTCGAATAAAA
1 AATTAAGTTATTTAGATAAACTCGAATAAAA
* * *
12590 AATTAAGTTTTTTAGTTTAACTCGAATA
1 AATTAAGTTATTTAGATAAACTCGAATA
12618 TGAATTACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (31 bp):
AATTAAGTTATTTAGATAAACTCGAATAAAA
Found at i:12743 original size:21 final size:21
Alignment explanation
Indices: 12701--12743 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12691 ACCTTTTCTA
* **
12701 AAGTTAAAAGTCAAAATTATT
1 AAGTTAAAAGGCAAAACCATT
12722 AAGTTAAAAGGCAAAACCATT
1 AAGTTAAAAGGCAAAACCATT
12743 A
1 A
12744 TATTGTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACCATT
Found at i:14488 original size:15 final size:15
Alignment explanation
Indices: 14468--14521 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
14458 ATACTACAAA
14468 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
14483 ATATTTATAATTATAAT
1 ATATTTATTA-T-TAAT
*
14500 AAATATTTATTATTAGT
1 --ATATTTATTATTAAT
14517 ATATT
1 ATATT
14522 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:14736 original size:25 final size:26
Alignment explanation
Indices: 14701--14753 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
14691 TATTAAAATA
14701 AAAATAAAAATTA-AATAATT-TATT
1 AAAATAAAAATTATAATAATTATATT
*
14725 AAAATAACAAATTATATTAATTATATT
1 AAAATAA-AAATTATAATAATTATATT
14752 AA
1 AA
14754 TAATTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 7 0.28
25 6 0.24
26 6 0.24
27 6 0.24
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
AAAATAAAAATTATAATAATTATATT
Found at i:14756 original size:25 final size:23
Alignment explanation
Indices: 14702--14753 Score: 59
Period size: 26 Copynumber: 2.1 Consensus size: 23
14692 ATTAAAATAA
14702 AAATAAAAATTAAATAATTTATT
1 AAATAAAAATTAAATAATTTATT
*
14725 AAAATAACAAATTATATTAATTATATT
1 -AAATAA-AAATTA-AATAATT-TATT
14752 AA
1 AA
14754 TAATTTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 6 0.25
25 6 0.25
26 8 0.33
27 4 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATAAAAATTAAATAATTTATT
Found at i:22108 original size:13 final size:13
Alignment explanation
Indices: 22090--22123 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
22080 CCTCCCTTAG
22090 GAAATTTCATT-T
1 GAAATTTCATTCT
22102 CGAAATTTCATTCT
1 -GAAATTTCATTCT
22116 GAAATTTC
1 GAAATTTC
22124 TTACTAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 19 0.95
14 1 0.05
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (13 bp):
GAAATTTCATTCT
Found at i:34904 original size:68 final size:68
Alignment explanation
Indices: 34809--34936 Score: 170
Period size: 68 Copynumber: 1.9 Consensus size: 68
34799 AGCTGATATA
* * *
34809 TGGTCTTACACCTGTAATCCTCATGTTTAATGTCCCGAC-GAACTCTATTGGTTTTAATAGAAAA
1 TGGTATTACACCTATAATCCTCATGTTTAATGTCCCGACAG-ACTCCATTGGTTTTAATAGAAAA
34873 GATT
65 GATT
* * *
34877 TGGTATTACACTTATAATCC-CTATGTTTAATGTCCTGACAGACTCCATTGGTTTTCATAG
1 TGGTATTACACCTATAATCCTC-ATGTTTAATGTCCCGACAGACTCCATTGGTTTTAATAG
34937 TAGAGCTATG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
67 1 0.02
68 50 0.96
69 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (68 bp):
TGGTATTACACCTATAATCCTCATGTTTAATGTCCCGACAGACTCCATTGGTTTTAATAGAAAAG
ATT
Found at i:36419 original size:109 final size:109
Alignment explanation
Indices: 36225--36433 Score: 269
Period size: 109 Copynumber: 1.9 Consensus size: 109
36215 CAAAAAAAAA
* * *
36225 TTATCGATTTTAAATAGGATATTCATCTATTGAGGTTCAAGGAAAAATCATACCAAACACGTTAG
1 TTATCGACTTTAAATAGGATACTCATCTATTGAGGTTCAAAGAAAAATCATACCAAACACGTTAG
* * * *
36290 GACACAATTTTTCGAGTTCCCTAAAATAACAGAACGTTGAGTAT
66 GACACAATTTCTCGAATTCCCAAAAATAAAAGAACGTTGAGTAT
* * **
36334 TTATCGACTTTAAATAGGATACTCAAT-TATTTAGGTTCAAAGAAAAATCATACCCAGTACGTTA
1 TTATCGACTTTAAATAGGATACTC-ATCTATTGAGGTTCAAAGAAAAATCATACCAAACACGTT-
**
36398 AGG-CATGATTTCTCGAATTCCCAAAAATAAAAGAAC
64 AGGACACAATTTCTCGAATTCCCAAAAATAAAAGAAC
36434 ATTGCCTCGA
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
109 80 0.94
110 5 0.06
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.30
Consensus pattern (109 bp):
TTATCGACTTTAAATAGGATACTCATCTATTGAGGTTCAAAGAAAAATCATACCAAACACGTTAG
GACACAATTTCTCGAATTCCCAAAAATAAAAGAACGTTGAGTAT
Found at i:36868 original size:3 final size:3
Alignment explanation
Indices: 36857--36928 Score: 137
Period size: 3 Copynumber: 24.3 Consensus size: 3
36847 CAATTAAGTA
36857 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
36904 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
36929 TGTTAATCAA
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 66 0.97
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:37043 original size:18 final size:16
Alignment explanation
Indices: 37017--37059 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 16
37007 ACATAGCATG
37017 AAATAAAAATAAATGAGA
1 AAAT-AAAATAAATGA-A
37035 TAAATAAAATAAATGAA
1 -AAATAAAATAAATGAA
37052 AAATAAAA
1 AAATAAAA
37060 AGAAAGGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.33
17 1 0.04
18 11 0.46
19 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (16 bp):
AAATAAAATAAATGAA
Found at i:38304 original size:46 final size:46
Alignment explanation
Indices: 38230--38429 Score: 200
Period size: 46 Copynumber: 4.5 Consensus size: 46
38220 ACTTCTGTGA
* * *
38230 GATGGTAGCTTCAATC-TGCCCCTCTTGATATAGGTGTAAAAGATTA
1 GATGGTGGCTTCAATCTTGCCCCTCTTGAT-TAGGGGTAAAAGATTG
*
38276 GATAGTGGCTTCAATCTTG-CCCTCTTGATTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTTGCCCCTCTTGATTAGGGGTAAAAGATTG
* * * *
38321 GATGGTTGCTTTAAT-TTGTCCATCTTGATTAGGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTTGCCCCTCTTGATTA-GGGGTAAAAGATTG
* * * *
38367 GATGGTGGTTTCAA-CTTG-CCC-CATGGTT-GGGGTAAGAGATTG
1 GATGGTGGCTTCAATCTTGCCCCTCTTGATTAGGGGTAAAAGATTG
* *
38409 GATGATGTCTTCAATC-TGCCC
1 GATGGTGGCTTCAATCTTGCCC
38430 TATGATCGGG
Statistics
Matches: 130, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
42 26 0.20
43 3 0.02
44 8 0.06
45 39 0.30
46 52 0.40
47 2 0.02
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.34
Consensus pattern (46 bp):
GATGGTGGCTTCAATCTTGCCCCTCTTGATTAGGGGTAAAAGATTG
Found at i:38412 original size:42 final size:41
Alignment explanation
Indices: 38353--38941 Score: 503
Period size: 42 Copynumber: 14.4 Consensus size: 41
38343 TCTTGATTAG
* * *
38353 GGGGTAAAAGATTGGATGGTGGT-TTCAACTTGCCCCATGGTT
1 GGGGTAAGAGATTGGATGAT-GTCTTCAA-TTGCCCCATGGTC
* *
38395 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCTATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAAT-TGCCCCATGGTC
* *
38437 GGGGTGAGAGATTGGATGA---CTTCAATTTACCCCATGGTC
1 GGGGTAAGAGATTGGATGATGTCTTCAA-TTGCCCCATGGTC
* * * *
38476 GGGTTAAGAGATTGGATGATGTCTTCAATCTACCCCATGATT
1 GGGGTAAGAGATTGGATGATGTCTTCAAT-TGCCCCATGGTC
* * *
38518 GAGGTAAGAGATTGGATGATGTCTTCAATTTGCCTCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAA-TTGCCCCATGGTC
* **
38560 AGGGTAAGAGATT--A-GATGGGTTCAATTTGCCCCATGGTC
1 GGGGTAAGAGATTGGATGATGTCTTCAA-TTGCCCCATGGTC
* * *
38599 GGGGTAACAGATT-GA--ATGACTTTAATTTGCCCCATGGTC
1 GGGGTAAGAGATTGGATGATGTCTTCAA-TTGCCCCATGGTC
* * * * * **
38638 GAGGTAAGAGATTGAACGATGTTTTCAATCTACCCCATGACC
1 GGGGTAAGAGATTGGATGATGTCTTCAAT-TGCCCCATGGTC
* * *
38680 GAGGTAAGAGATTGAATGGTGTCTTCAATTTGCCCCATGGT-
1 GGGGTAAGAGATTGGATGATGTCTTCAA-TTGCCCCATGGTC
*
38721 TGGGTAAGAGATTGGATGATGTCTTCAATATGCCCCATGGTC
1 GGGGTAAGAGATTGGATGATGTCTTCAAT-TGCCCCATGGTC
* * *
38763 -GGGTAAGAGATTGAACGATGTCTTCAATCTGCCCCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAAT-TGCCCCATGGTC
* * *
38804 GGGGTAAGAGATTGGATGATGTCTTTAATCTGCACCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAAT-TGCCCCATGGTC
* * * *
38846 GAGGTAAGAGATT--A-GATGGCTTCAATTTACCTCATGGTC
1 GGGGTAAGAGATTGGATGATGTCTTCAA-TTGCCCCATGGTC
* * * * *
38885 GGGGTAAGAGA-TCG--GATGTCTTTAATCTACACCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAAT-TGCCCCATGGTC
38924 GGGGTAAGAGATTGGATG
1 GGGGTAAGAGATTGGATG
38942 GTAGCTTTGT
Statistics
Matches: 453, Mismatches: 70, Indels: 48
0.79 0.12 0.08
Matches are distributed among these distances:
38 2 0.00
39 152 0.34
40 9 0.02
41 77 0.17
42 211 0.47
43 2 0.00
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (41 bp):
GGGGTAAGAGATTGGATGATGTCTTCAATTGCCCCATGGTC
Found at i:38491 original size:81 final size:80
Alignment explanation
Indices: 38376--38941 Score: 570
Period size: 81 Copynumber: 7.0 Consensus size: 80
38366 GGATGGTGGT
* * *
38376 TTCAACTTGCCCCATGGTTGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCTATGATCGGGG
1 TTCAATTTGCCCCATGG-TCGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGG
*
38441 TGAGAGATTGGATGAC
65 TAAGAGATTGGATGAC
* * * *
38457 TTCAATTTACCCCATGGTCGGGTTAAGAGATTGGATGATGTCTTCAATCTACCCCATGATTGAGG
1 TTCAATTTGCCCCATGGTCGGG-TAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGG
38522 TAAGAGATTGGATGATGTC
65 TAAGAGATTGGATGA---C
* * ** * *
38541 TTCAATTTGCCTCATGATCAGGGTAAGAGATT--A-GATGGGTTCAATTTGCCCCATGGTCGGGG
1 TTCAATTTGCCCCATGGTC-GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGG
* *
38603 TAACAGATTGAATGAC
65 TAAGAGATTGGATGAC
* * * * * * *
38619 TTTAATTTGCCCCATGGTCGAGGTAAGAGATTGAACGATGTTTTCAATCTACCCCATGACCGAGG
1 TTCAATTTGCCCCATGGTCG-GGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGG
* *
38684 TAAGAGATTGAATGGTGTC
65 TAAGAGATTG---GATGAC
* * *
38703 TTCAATTTGCCCCATGGTTGGGTAAGAGATTGGATGATGTCTTCAATATGCCCCATGGTC-GGGT
1 TTCAATTTGCCCCATGGTCGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGT
*
38767 AAGAGATTGAACGATGTC
66 AAGAGATTG---GATGAC
* * * * *
38785 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGTCTTTAATCTGCACCATGATCGAGG
1 TTCAATTTGCCCCATGGTC-GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGG
* *
38850 TAAGAGATTAGATGGC
65 TAAGAGATTGGATGAC
* * * * * *
38866 TTCAATTTACCTCATGGTCGGGGTAAGAGA-TCG--GATGTCTTTAATCTACACCATGATCGGGG
1 TTCAATTTGCCCCATGGTC-GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGG
38928 TAAGAGATTGGATG
65 TAAGAGATTGGATG
38942 GTAGCTTTGT
Statistics
Matches: 407, Mismatches: 64, Indels: 31
0.81 0.13 0.06
Matches are distributed among these distances:
77 1 0.00
78 68 0.17
80 7 0.02
81 164 0.40
82 36 0.09
83 70 0.17
84 58 0.14
85 3 0.01
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (80 bp):
TTCAATTTGCCCCATGGTCGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGT
AAGAGATTGGATGAC
Found at i:40230 original size:12 final size:12
Alignment explanation
Indices: 40202--40244 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
40192 TCTCGGCCTC
*
40202 TCTTTTTTCATT
1 TCTTTTTTCTTT
40214 T-TTTTTTCTTT
1 TCTTTTTTCTTT
*
40225 TCTTTTCTCTTT
1 TCTTTTTTCTTT
40237 TCTTTTTT
1 TCTTTTTT
40245 TCGGGGTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (12 bp):
TCTTTTTTCTTT
Found at i:41904 original size:29 final size:29
Alignment explanation
Indices: 41851--41906 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
41841 TAATGATTGT
*
41851 TGAAAATGAGAAACGACGAATTGAAAACG
1 TGAAAATGAGAAACGACGAAATGAAAACG
41880 TGAAAGAT-AGAAACGAC-AAGATGAAAA
1 TGAAA-ATGAGAAACGACGAA-ATGAAAA
41907 TTTCCCGACC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 2 0.08
29 20 0.83
30 2 0.08
ACGTcount: A:0.55, C:0.09, G:0.23, T:0.12
Consensus pattern (29 bp):
TGAAAATGAGAAACGACGAAATGAAAACG
Found at i:42238 original size:28 final size:28
Alignment explanation
Indices: 42186--42240 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
42176 AAATGAGCAT
* *
42186 CATGACCTTTGGGTTAACAGGGAGTAAG
1 CATGACCTTTGGGTCAACAAGGAGTAAG
*
42214 CATGACCTTTGGGTCAACAATGAGTAA
1 CATGACCTTTGGGTCAACAAGGAGTAA
42241 ATCGGATATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.25
Consensus pattern (28 bp):
CATGACCTTTGGGTCAACAAGGAGTAAG
Found at i:43537 original size:16 final size:16
Alignment explanation
Indices: 43516--43546 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
43506 AAAAGGGTAA
43516 AACTGCCTTTGTTTTC
1 AACTGCCTTTGTTTTC
43532 AACTGCCTTTGTTTT
1 AACTGCCTTTGTTTT
43547 TAAACAAATG
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:0.23, G:0.13, T:0.52
Consensus pattern (16 bp):
AACTGCCTTTGTTTTC
Found at i:47288 original size:109 final size:109
Alignment explanation
Indices: 47165--47380 Score: 306
Period size: 109 Copynumber: 2.0 Consensus size: 109
47155 AAACAAAGAA
* * * * * * *
47165 TATTTATCTATTTTAAATAGGATATTCAATTATTTAGGTTCAAGGAAAAATCATACACAATACAT
1 TATTTATCAATTTTAAATAAGATACTCAATTATTTAGGTTCAAAGAAAAACCATACACAAAACAG
* *
47230 TAGGGCACAATTTCTCGAATTCCCTAAAATAACAGAACATTGAG
66 TAGGGCACAATTTCTCGAATTCCCAAAAATAAAAGAACATTGAG
* *
47274 TATTTATCAATTTTAAATAAGATACTCAATTATTTAGGTTCAAAGAAAAACCATACCCAAAACGG
1 TATTTATCAATTTTAAATAAGATACTCAATTATTTAGGTTCAAAGAAAAACCATACACAAAACAG
* * *
47339 TATGGCACAATTTCTCGAATTTCCAAAAATAAAATAACATTG
66 TAGGGCACAATTTCTCGAATTCCCAAAAATAAAAGAACATTG
47381 CCTTGATTTT
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
109 93 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (109 bp):
TATTTATCAATTTTAAATAAGATACTCAATTATTTAGGTTCAAAGAAAAACCATACACAAAACAG
TAGGGCACAATTTCTCGAATTCCCAAAAATAAAAGAACATTGAG
Found at i:47817 original size:3 final size:3
Alignment explanation
Indices: 47811--47881 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
47801 CAATTAAGTA
47811 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
47859 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
47882 GTTAATCAAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:47984 original size:18 final size:16
Alignment explanation
Indices: 47958--48000 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 16
47948 ACATAGCATG
47958 AAATAAAAATAAATGAGA
1 AAAT-AAAATAAATGA-A
47976 TAAATAAAATAAATGAA
1 -AAATAAAATAAATGAA
47993 AAATAAAA
1 AAATAAAA
48001 AGAAAGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.33
17 1 0.04
18 11 0.46
19 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (16 bp):
AAATAAAATAAATGAA
Found at i:48418 original size:15 final size:16
Alignment explanation
Indices: 48393--48422 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
48383 GAATTAAAGA
48393 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
48409 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
48423 CATAGGGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:48422 original size:22 final size:22
Alignment explanation
Indices: 48371--48412 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
48361 CTAAGGAAAA
48371 ATAAAAG-AAATAGAATTAAAG
1 ATAAAAGAAAATAGAATTAAAG
48392 ATAAAAGAAAATAGAATTAAA
1 ATAAAAGAAAATAGAATTAAA
48413 AGAAATAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAAAAGAAAATAGAATTAAAG
Found at i:48427 original size:22 final size:20
Alignment explanation
Indices: 48368--48427 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 20
48358 GATCTAAGGA
48368 AAAATAAAAGAAATAGAATT
1 AAAATAAAAGAAATAGAATT
48388 AAAGATAAAAGAAAATAGAATT
1 AAA-ATAAAAG-AAATAGAATT
*
48410 AAAAGAAATAGAACATAG
1 AAAATAAA-AGAA-ATAG
48428 GGAATTCGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
20 3 0.09
21 13 0.37
22 19 0.54
ACGTcount: A:0.68, C:0.02, G:0.13, T:0.17
Consensus pattern (20 bp):
AAAATAAAAGAAATAGAATT
Found at i:49248 original size:30 final size:29
Alignment explanation
Indices: 49210--49286 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 29
49200 AGATAAACAT
49210 AAATTAAATACAAATAAATAATAT-CTTTA
1 AAATTAAATACAAATAAA-AATATACTTTA
* * *
49239 AATATTAAATCCTAATAAAAATATATTTTA
1 AA-ATTAAATACAAATAAAAATATACTTTA
*
49269 AAATAAAATA-AAATAAAA
1 AAATTAAATACAAATAAAA
49287 CCAAGTCTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.17
29 13 0.32
30 20 0.50
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (29 bp):
AAATTAAATACAAATAAAAATATACTTTA
Found at i:56644 original size:34 final size:33
Alignment explanation
Indices: 56601--56673 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 33
56591 TTGGTATTAT
*
56601 ATAAATATAT-AATTTAGATTTTTAAAATAATTTA
1 ATAAATATATAAATTT-GATTATTAAAA-AATTTA
* *
56635 ATAAATATATAAATTTTATTATTACAAAATTTA
1 ATAAATATATAAATTTGATTATTAAAAAATTTA
56668 ATAAAT
1 ATAAAT
56674 TATTGTACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
33 12 0.34
34 18 0.51
35 5 0.14
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (33 bp):
ATAAATATATAAATTTGATTATTAAAAAATTTA
Found at i:58359 original size:17 final size:17
Alignment explanation
Indices: 58339--58398 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
58329 AATAAATAAA
*
58339 AAATATATAAAATTATT
1 AAATATATAAAATAATT
*
58356 AAATAT-TAAAATAAAAT
1 AAATATATAAAAT-AATT
* *
58373 AAATATTTAAAAAAATT
1 AAATATATAAAATAATT
58390 AAA-ATATAA
1 AAATATATAA
58399 TATGGGTGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 11 0.31
17 20 0.56
18 5 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATATATAAAATAATT
Found at i:58365 original size:27 final size:30
Alignment explanation
Indices: 58304--58395 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 30
58294 TAAAATAATT
*
58304 TTAAAATAACTATATAAAAATTTTTAATAA
1 TTAAAATAACTATATAAAAATTTTAAATAA
*
58334 ATAAAA-AA-TATAT-AAAATTATTAAAT-A
1 TTAAAATAACTATATAAAAATT-TTAAATAA
* * *
58361 TTAAAATAA--A-ATAAATATTTAAAAAAA
1 TTAAAATAACTATATAAAAATTTTAAATAA
58388 TTAAAATA
1 TTAAAATA
58396 TAATATGGGT
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
26 6 0.12
27 27 0.52
28 12 0.23
29 2 0.04
30 5 0.10
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (30 bp):
TTAAAATAACTATATAAAAATTTTAAATAA
Found at i:59814 original size:96 final size:96
Alignment explanation
Indices: 59643--59817 Score: 219
Period size: 96 Copynumber: 1.8 Consensus size: 96
59633 TTTGATTATC
** * * * * *
59643 TCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGTGCAATATTTCGGAATCGAAGATAAGAAA
1 TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAACCCAAAATAAGAAA
*
59708 ACATCGCCTCGATTAAGGGTATTCGATTGCT
66 ACATCACCTCGATTAAGGGTATTCGATTGCT
*
59739 TCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAA-ATTTTCGAAACCCAAAATAA-AA
1 TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATA-TTTCGAAACCCAAAATAAGAA
* *
59802 GAATATTACCTCGATT
65 -AACATCACCTCGATT
59818 TTGAAGTTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
95 3 0.05
96 63 0.95
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (96 bp):
TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAACCCAAAATAAGAAA
ACATCACCTCGATTAAGGGTATTCGATTGCT
Found at i:60178 original size:29 final size:27
Alignment explanation
Indices: 60127--60520 Score: 281
Period size: 29 Copynumber: 13.4 Consensus size: 27
60117 AAAAGGGTAA
* *
60127 TTTTGGTAGATTCAGGGTCAAAAATGAGAT
1 TTTTGGAAG-TTCGGGGT-AAAAATG-GAT
60157 TTTTGGAAGTTCAGGGGT-AAAATGGTAAT
1 TTTTGGAAGTTC-GGGGTAAAAATGG--AT
60186 TTTTGGAAGTTTCGGGGTCAAAAATGGAAT
1 TTTTGGAAG-TTCGGGGT-AAAAATGG-AT
*
60216 TTTTGGAAGTTTGGGGGT-AAAATGGTAAT
1 TTTTGGAAG-TTCGGGGTAAAAATGG--AT
***
60245 TTTTGGAAGGTTTCATAGTAAAAAATGGGAT
1 TTTTGGAA-G-TTCGGGGT-AAAAAT-GGAT
* *
60276 TTTAGGAAGTTCGGGGTTAAAATGGTATT
1 TTTTGGAAGTTCGGGGTAAAAATGG-A-T
60305 TTTTGGAAGTTTCGGGGTCAAAAATGGGAT
1 TTTTGGAAG-TTCGGGGT-AAAAAT-GGAT
* * *
60335 TTTTGGAAGCTCGAGGGTAAAATTGTAAT
1 TTTTGGAAGTTCG-GGGTAAAAATG-GAT
* ** *
60364 TTTTGAAAGTTTTAGGGTTAAAATGGGAT
1 TTTTGGAAG-TTCGGGGTAAAAAT-GGAT
*
60393 TTTTGGAAGTTCGAGG-ATAAAATGGTAAT
1 TTTTGGAAGTTCGGGGTA-AAAATGG--AT
*
60422 TTTTGGAAGTTTCGGGGTCAAAAATGGAA
1 TTTTGGAAG-TTCGGGGT-AAAAATGGAT
**
60451 TTTTGGAAGTTCGGGGATAAAATATTAAT
1 TTTTGGAAGTTCGGGG-TAAAA-ATGGAT
60480 TTTTGGAAGGTTCGGGGTTAAAAATGGGAT
1 TTTTGGAA-GTTCGGGG-TAAAAAT-GGAT
60510 TTTTGGAAGTT
1 TTTTGGAAGTT
60521 TAGNNNNNNN
Statistics
Matches: 297, Mismatches: 37, Indels: 61
0.75 0.09 0.15
Matches are distributed among these distances:
27 5 0.02
28 40 0.13
29 118 0.40
30 95 0.32
31 29 0.10
32 8 0.03
33 2 0.01
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.36
Consensus pattern (27 bp):
TTTTGGAAGTTCGGGGTAAAAATGGAT
Found at i:60207 original size:59 final size:58
Alignment explanation
Indices: 60112--60520 Score: 509
Period size: 59 Copynumber: 7.0 Consensus size: 58
60102 AAACATTCGG
* * * * *
60112 GGGGTAAAAGGGTAA-TTTTGGTAGATTCAGGGTCAAAAATGAGATTTTTGGAAGTTC
1 GGGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
* *
60169 AGGGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTG
1 -GGGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG-TTC
*** * *
60229 GGGGTAAAATGGTAATTTTTGGAAGGTTTCATAGTAAAAAATGGGATTTTAGGAAGTTC
1 GGGGTAAAATGGTAATTTTTGGAA-GTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
* *
60288 GGGGTTAAAATGGTATTTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGCTC
1 GGGG-TAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
* * ** *
60347 GAGGGTAAAATTGTAATTTTTGAAAGTTTTAGGGT-TAAAATGGGATTTTTGGAAGTTC
1 G-GGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
* *
60405 GAGGATAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAAT-GGAATTTTGGAAGTTC
1 G-GGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
** * *
60463 GGGGATAAAATATTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTT
1 GGGG-TAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
60521 TAGNNNNNNN
Statistics
Matches: 302, Mismatches: 41, Indels: 15
0.84 0.11 0.04
Matches are distributed among these distances:
57 2 0.01
58 114 0.38
59 137 0.45
60 49 0.16
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
Found at i:63173 original size:34 final size:33
Alignment explanation
Indices: 63130--63202 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 33
63120 TTGGTATTAT
*
63130 ATAAATATAT-AATTTAGATTTTTAAAATAATTTA
1 ATAAATATATAAATTT-GATTATTAAAA-AATTTA
* *
63164 ATAAATATATAAATTTTATTATTACAAAATTTA
1 ATAAATATATAAATTTGATTATTAAAAAATTTA
63197 ATAAAT
1 ATAAAT
63203 TATTGTACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
33 12 0.34
34 18 0.51
35 5 0.14
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (33 bp):
ATAAATATATAAATTTGATTATTAAAAAATTTA
Found at i:64888 original size:17 final size:17
Alignment explanation
Indices: 64868--64927 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
64858 AATAAATAAA
*
64868 AAATATATAAAATTATT
1 AAATATATAAAATAATT
*
64885 AAATAT-TAAAATAAAAT
1 AAATATATAAAAT-AATT
* *
64902 AAATATTTAAAAAAATT
1 AAATATATAAAATAATT
64919 AAA-ATATAA
1 AAATATATAA
64928 TATGGGTGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 11 0.31
17 20 0.56
18 5 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATATATAAAATAATT
Found at i:64894 original size:27 final size:30
Alignment explanation
Indices: 64833--64924 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 30
64823 TAAAATAATT
*
64833 TTAAAATAACTATATAAAAATTTTTAATAA
1 TTAAAATAACTATATAAAAATTTTAAATAA
*
64863 ATAAAA-AA-TATAT-AAAATTATTAAAT-A
1 TTAAAATAACTATATAAAAATT-TTAAATAA
* * *
64890 TTAAAATAA--A-ATAAATATTTAAAAAAA
1 TTAAAATAACTATATAAAAATTTTAAATAA
64917 TTAAAATA
1 TTAAAATA
64925 TAATATGGGT
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
26 6 0.12
27 27 0.52
28 12 0.23
29 2 0.04
30 5 0.10
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (30 bp):
TTAAAATAACTATATAAAAATTTTAAATAA
Found at i:66343 original size:96 final size:96
Alignment explanation
Indices: 66172--66346 Score: 219
Period size: 96 Copynumber: 1.8 Consensus size: 96
66162 TTTGATTATC
** * * * * *
66172 TCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGTGCAATATTTCGGAATCGAAGATAAGAAA
1 TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAACCCAAAATAAGAAA
*
66237 ACATCGCCTCGATTAAGGGTATTCGATTGCT
66 ACATCACCTCGATTAAGGGTATTCGATTGCT
*
66268 TCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAA-ATTTTCGAAACCCAAAATAA-AA
1 TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATA-TTTCGAAACCCAAAATAAGAA
* *
66331 GAATATTACCTCGATT
65 -AACATCACCTCGATT
66347 TTGAAGTTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
95 3 0.05
96 63 0.95
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (96 bp):
TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAACCCAAAATAAGAAA
ACATCACCTCGATTAAGGGTATTCGATTGCT
Found at i:66736 original size:59 final size:58
Alignment explanation
Indices: 66641--67344 Score: 729
Period size: 59 Copynumber: 12.0 Consensus size: 58
66631 AAACATTCGG
* * * * * *
66641 GGGGTAAAAGGGTAA-TTTTGGTAGATTCAGGGTCAAAAATGAGATTTTTGGAAGTTC
1 GGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTC
* * * *
66698 AGGGGTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTG
1 -GGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAG-TTC
*** * *
66758 GGGGTAAAATGGTAATTTTTGGAAGGTTTCATAGTAAAAAATGGGATTTTAGGAAGTTC
1 GGGGTAAAATGGTAATTTTTGGAAGG-TTCGGGGTTAAAAATGGGATTTTTGGAAGTTC
* * * *
66817 GGGGTTAAAATGGTATTTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGCTC
1 GGGG-TAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTC
* * * **
66876 GAGGGTAAAATTGTAATTTTTGAAAGTTTTAGGGTT-AAAATGGGATTTTTGGAAGTTC
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTC
* * * *
66934 GAGGATAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAAT-GGAATTTTGGAAGTTC
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTC
**
66992 GGGGATAAAATATTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTT-
1 GGGG-TAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTC
** * ** * *
67050 -TAGTGACCTCCGGGGTAA-TTTTGGAAGGTTCGGGGTTAAAAATGAGATTTTTGGAAGTTTG
1 GGGGTAAAAT----GGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAG-TTC
* * *
67111 GGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGAGATTTTTGGAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAG-TTC
* *
67170 GGGGTAAAAAATGG-GATTTTTGGAAGGTTCGGGGTTAAAAATGAGATTTTTGGAAGTTC
1 GGGGT--AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTC
*
67229 GAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTT
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTC
* **********
67288 AGNNNNNNNNNNTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTT
1 GGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTT
67345 TAGGGACCTC
Statistics
Matches: 552, Mismatches: 74, Indels: 40
0.83 0.11 0.06
Matches are distributed among these distances:
56 3 0.01
57 3 0.01
58 172 0.31
59 266 0.48
60 97 0.18
61 7 0.01
62 4 0.01
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.35
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTC
Found at i:66748 original size:30 final size:29
Alignment explanation
Indices: 66656--67287 Score: 490
Period size: 30 Copynumber: 21.4 Consensus size: 29
66646 AAAAGGGTAA
* * *
66656 TTTTGGTAGATTCAGGGTCAAAAAT-GAGAT
1 TTTTGGAAGTTTCGGGGT-AAAAATGGA-AT
66686 TTTTGGAAG-TTCAGGGGT-AAAATGGTAAT
1 TTTTGGAAGTTTC-GGGGTAAAAATGG-AAT
66715 TTTTGGAAGTTTCGGGGTCAAAAATGGAAT
1 TTTTGGAAGTTTCGGGGT-AAAAATGGAAT
*
66745 TTTTGGAAGTTTGGGGGT-AAAATGGTAAT
1 TTTTGGAAGTTTCGGGGTAAAAATGG-AAT
*** *
66774 TTTTGGAAGGTTTCATAGTAAAAAATGGGAT
1 TTTTGGAA-GTTTCGGGGT-AAAAATGGAAT
* * *
66805 TTTAGGAAG-TTCGGGGTTAAAATGGTATT
1 TTTTGGAAGTTTCGGGGTAAAAATGG-AAT
*
66834 TTTTGGAAGTTTCGGGGTCAAAAATGGGAT
1 TTTTGGAAGTTTCGGGGT-AAAAATGGAAT
* * *
66864 TTTTGGAAG-CTCGAGGGTAAAATTGTAAT
1 TTTTGGAAGTTTCG-GGGTAAAAATGGAAT
* ** * *
66893 TTTTGAAAGTTTTAGGGTTAAAATGGGAT
1 TTTTGGAAGTTTCGGGGTAAAAATGGAAT
*
66922 TTTTGGAAG-TTCGAGG-ATAAAATGGTAAT
1 TTTTGGAAGTTTCGGGGTA-AAAATGG-AAT
66951 TTTTGGAAGTTTCGGGGTCAAAAATGGAA-
1 TTTTGGAAGTTTCGGGGT-AAAAATGGAAT
*
66980 TTTTGGAAG-TTCGGGGATAAAATAT-TAAT
1 TTTTGGAAGTTTCGGGG-TAAAA-ATGGAAT
* *
67009 TTTTGGAAGGTTCGGGGTTAAAAATGGGAT
1 TTTTGGAAGTTTCGGGG-TAAAAATGGAAT
* * ********
67039 TTTTGGAAGTTTAGTGACCTCCGGGGTAA-
1 TTTTGGAAGTTTCGGGGTAAAAATGG-AAT
*
67068 TTTTGGAAGGTTCGGGGTTAAAAAT-GAGAT
1 TTTTGGAAGTTTCGGGG-TAAAAATGGA-AT
*
67098 TTTTGGAAGTTTGGGGGT-AAAATGGTAAT
1 TTTTGGAAGTTTCGGGGTAAAAATGG-AAT
* *
67127 TTTTGGAAGGTTCGAGGTTAAAAAT-GAGAT
1 TTTTGGAAGTTTCG-GGGTAAAAATGGA-AT
* *
67157 TTTTGGAAGTTTGGGGGTAAAAAATGGGAT
1 TTTTGGAAGTTTCGGGGT-AAAAATGGAAT
*
67187 TTTTGGAAGGTTCGGGGTTAAAAAT-GAGAT
1 TTTTGGAAGTTTCGGGG-TAAAAATGGA-AT
67217 TTTTGGAAG-TTCGAGGGT-AAAATGGTAAT
1 TTTTGGAAGTTTCG-GGGTAAAAATGG-AAT
* *
67246 TTTTGGAAGGTTCGGGGTTAAAAATGGGAT
1 TTTTGGAAGTTTCGGGG-TAAAAATGGAAT
67276 TTTTGGAAGTTT
1 TTTTGGAAGTTT
67288 AGNNNNNNNN
Statistics
Matches: 479, Mismatches: 79, Indels: 88
0.74 0.12 0.14
Matches are distributed among these distances:
28 54 0.11
29 175 0.37
30 198 0.41
31 44 0.09
32 8 0.02
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.35
Consensus pattern (29 bp):
TTTTGGAAGTTTCGGGGTAAAAATGGAAT
Done.