Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011970.1 Kokia drynarioides strain JFW-HI SEQ_126968, 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: 79362
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 94 characters in sequence are not A, C, G, or T
Found at i:4787 original size:15 final size:16
Alignment explanation
Indices: 4767--4796 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4757 TAATTCAATT
4767 TAATTTTAAA-AATAA
1 TAATTTTAAATAATAA
4782 TAATTTTAAATAATA
1 TAATTTTAAATAATA
4797 TTCTTCACGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATTTTAAATAATAA
Found at i:7716 original size:31 final size:30
Alignment explanation
Indices: 7614--7718 Score: 88
Period size: 31 Copynumber: 3.5 Consensus size: 30
7604 TATACCATTA
* * *
7614 GTCACTAAACTATTGGTAAATTTTCATTTCG
1 GTCACTTAACTATTAGAAAATTTTCATTT-G
* * *
7645 GTCACTTAACTA--AAAAAAGTTACAATTTG
1 GTCACTTAACTATTAGAAAATTTTC-ATTTG
* * *
7674 GTGACTGAACTATTTGAAAATTTTCATTTG
1 GTCACTTAACTATTAGAAAATTTTCATTTG
7704 AGTCACTTAACTATT
1 -GTCACTTAACTATT
7719 CAAAAGTTTT
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
29 17 0.30
30 9 0.16
31 30 0.54
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (30 bp):
GTCACTTAACTATTAGAAAATTTTCATTTG
Found at i:9576 original size:20 final size:20
Alignment explanation
Indices: 9551--9589 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9541 ACATAAAAAT
* *
9551 TATATATGCAATGAATTAAA
1 TATATATACAATAAATTAAA
9571 TATATATACAATAAATTAA
1 TATATATACAATAAATTAA
9590 TAAAAGATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
TATATATACAATAAATTAAA
Found at i:10174 original size:59 final size:59
Alignment explanation
Indices: 10101--10226 Score: 184
Period size: 59 Copynumber: 2.1 Consensus size: 59
10091 GATATAATTG
*
10101 AATAGTTGAATGATTATTTTATAA-TTTTCATAGTTAGATGACCAAAAACT-AAATTTATT
1 AATAATTGAATGATTATTTTATAATTTTTCATAGTTAGATGA-CAAAAA-TAAAATTTATT
* *
10160 AATAATTGAATGATTATTTTATAATTTTTCATAGTTTGATGACTAAAATAAAATTTATT
1 AATAATTGAATGATTATTTTATAATTTTTCATAGTTAGATGACAAAAATAAAATTTATT
*
10219 AGTAATTG
1 AATAATTG
10227 GGTCACTGTC
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
58 1 0.02
59 44 0.72
60 16 0.26
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.44
Consensus pattern (59 bp):
AATAATTGAATGATTATTTTATAATTTTTCATAGTTAGATGACAAAAATAAAATTTATT
Found at i:13749 original size:21 final size:23
Alignment explanation
Indices: 13725--13766 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
13715 TTTGATTTCA
13725 ATTTTAA-AAT-TTTAAATATAT
1 ATTTTAATAATATTTAAATATAT
*
13746 ATTTTAATAATATTTACATAT
1 ATTTTAATAATATTTAAATAT
13767 TTTAATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 3 0.17
23 8 0.44
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTTTAATAATATTTAAATATAT
Found at i:14453 original size:18 final size:19
Alignment explanation
Indices: 14425--14462 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
14415 GATCAAAAAT
14425 AATTAAATAAATAAT-TAAA
1 AATTAAATAAA-AATATAAA
14444 AATT-AATAAAAATATAAA
1 AATTAAATAAAAATATAAA
14462 A
1 A
14463 GAATTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.17
18 11 0.61
19 4 0.22
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AATTAAATAAAAATATAAA
Found at i:19500 original size:19 final size:19
Alignment explanation
Indices: 19478--19522 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
19468 TTATATTAGG
19478 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
19497 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
19516 ATTTAAT
1 ATTTAAT
19523 TTATGTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:20960 original size:21 final size:21
Alignment explanation
Indices: 20936--20987 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
20926 TGAGACAATA
20936 CTACTGATACAAGT-ATGACTT
1 CTACTGATACAAGTCATG-CTT
* * *
20957 CTACCGAAACATGTCATGCTT
1 CTACTGATACAAGTCATGCTT
20978 CTACTGATAC
1 CTACTGATAC
20988 TAAAAACTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (21 bp):
CTACTGATACAAGTCATGCTT
Found at i:24023 original size:30 final size:30
Alignment explanation
Indices: 23987--24049 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
23977 TTGTGATGGT
* *
23987 TGTTGATTGCGTGCGATA-AGATGCGATGAC
1 TGTTGATTGCATGCGATAGAG-TGCGATCAC
24017 TGTTGATTGCATGCGATAGAGTGCGATCAC
1 TGTTGATTGCATGCGATAGAGTGCGATCAC
24047 TGT
1 TGT
24050 CGATGCAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.22, C:0.14, G:0.32, T:0.32
Consensus pattern (30 bp):
TGTTGATTGCATGCGATAGAGTGCGATCAC
Found at i:24611 original size:24 final size:24
Alignment explanation
Indices: 24584--24658 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
24574 AATTTGACTC
* *
24584 AAACAACTAAACAGATTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
24608 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
24632 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
24656 AAA
1 AAA
24659 GATTATTTCT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:28143 original size:18 final size:20
Alignment explanation
Indices: 28109--28146 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
28099 ACAAAATTAA
28109 TTTATTTCTATAATTATTTT
1 TTTATTTCTATAATTATTTT
28129 TTTATTT-TA-AATTATTTT
1 TTTATTTCTATAATTATTTT
28147 CATAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 2 0.11
20 7 0.39
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATTTCTATAATTATTTT
Found at i:31049 original size:21 final size:20
Alignment explanation
Indices: 31019--31057 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
31009 AAAATTTTAA
31019 TTAATTTTAATTACAGCTCG
1 TTAATTTTAATTACAGCTCG
*
31039 TTAATATTTAATTATAGCT
1 TTAAT-TTTAATTACAGCT
31058 TGTCAGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (20 bp):
TTAATTTTAATTACAGCTCG
Found at i:33307 original size:19 final size:18
Alignment explanation
Indices: 33283--33326 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
33273 TACCGCTTCG
33283 AATGTAGACATTTATCACC
1 AATGTAG-CATTTATCACC
** *
33302 AATGTAGTTTTTATTACC
1 AATGTAGCATTTATCACC
33320 AATGTAG
1 AATGTAG
33327 TTTTTCTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (18 bp):
AATGTAGCATTTATCACC
Found at i:33320 original size:18 final size:18
Alignment explanation
Indices: 33293--33331 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
33283 AATGTAGACA
33293 TTTATCACCAATGTAGTT
1 TTTATCACCAATGTAGTT
*
33311 TTTATTACCAATGTAGTT
1 TTTATCACCAATGTAGTT
33329 TTT
1 TTT
33332 CTAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.51
Consensus pattern (18 bp):
TTTATCACCAATGTAGTT
Found at i:36077 original size:9 final size:9
Alignment explanation
Indices: 36059--36110 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
36049 ATCAGTAAAT
36059 AATT-TTAA
1 AATTATTAA
36067 AATTATTAA
1 AATTATTAA
36076 AATTATTTTTAA
1 AATTA---TTAA
36088 AA-TA-TAA
1 AATTATTAA
36095 AATTATTAA
1 AATTATTAA
36104 AATTATT
1 AATTATT
36111 TTTTGAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
7 5 0.13
8 6 0.16
9 19 0.50
11 2 0.05
12 6 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
AATTATTAA
Found at i:36095 original size:19 final size:21
Alignment explanation
Indices: 36061--36101 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
36051 CAGTAAATAA
36061 TTTTAAAATTATTAAAATTAT
1 TTTTAAAATTATTAAAATTAT
36082 TTTTAAAA-TA-TAAAATTAT
1 TTTTAAAATTATTAAAATTAT
36101 T
1 T
36102 AAAATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
20 2 0.10
21 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTAAAATTATTAAAATTAT
Found at i:36104 original size:28 final size:30
Alignment explanation
Indices: 36064--36134 Score: 119
Period size: 28 Copynumber: 2.4 Consensus size: 30
36054 TAAATAATTT
36064 TAAAATTATTAAAATTA-TTTTTAAAAT-A
1 TAAAATTATTAAAATTATTTTTTAAAATAA
*
36092 TAAAATTATTAAAATTATTTTTTGAAATAA
1 TAAAATTATTAAAATTATTTTTTAAAATAA
36122 TAAAATTATTAAA
1 TAAAATTATTAAA
36135 TAATTTTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 17 0.43
29 9 0.22
30 14 0.35
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTTTTTAAAATAA
Found at i:36918 original size:18 final size:18
Alignment explanation
Indices: 36897--36957 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
36887 TTATGATTTT
36897 AATAATTTTATATTTAAA
1 AATAATTTTATATTTAAA
36915 AATAATTTTAAATTATTT-AA
1 AATAATTTT--A-TATTTAAA
36935 AA-AA--TTATATTTAAAA
1 AATAATTTTATATTT-AAA
36951 AATAATT
1 AATAATT
36958 AATTTTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 15
0.70 0.00 0.30
Matches are distributed among these distances:
14 5 0.14
15 1 0.03
16 4 0.11
17 4 0.11
18 9 0.26
19 2 0.06
20 5 0.14
21 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATAATTTTATATTTAAA
Found at i:36930 original size:23 final size:23
Alignment explanation
Indices: 36907--36949 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
36897 AATAATTTTA
36907 TATTT-AAAAATAAT-TTTAAAT
1 TATTTAAAAAATAATATTTAAAT
*
36928 TATTTAAAAAATTATATTTAAA
1 TATTTAAAAAATAATATTTAAA
36950 AAATAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTTAAAAAATAATATTTAAAT
Found at i:37155 original size:29 final size:28
Alignment explanation
Indices: 37113--37170 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 28
37103 AAGTTGACCT
* *
37113 AAAAAAAATTAAGG-TCAAAGTGAGCAA
1 AAAAAAAATTAAGGACCAAAGTGACCAA
37140 AAAAAAAATCATAAGGACCAAAGTGACCAA
1 AAAAAAAAT--TAAGGACCAAAGTGACCAA
37170 A
1 A
37171 CACCCAAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 9 0.35
29 5 0.19
30 12 0.46
ACGTcount: A:0.60, C:0.12, G:0.16, T:0.12
Consensus pattern (28 bp):
AAAAAAAATTAAGGACCAAAGTGACCAA
Found at i:40840 original size:20 final size:20
Alignment explanation
Indices: 40794--40842 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
40784 TAAATTTTAT
*
40794 ATTATAAAAATTTTATATTA
1 ATTATAAAAATTTTATAATA
*
40814 ATCTA-AAATATTTTA-AATA
1 AT-TATAAAAATTTTATAATA
40833 ATTATAAAAA
1 ATTATAAAAA
40843 AAAATACATA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
18 2 0.08
19 9 0.38
20 11 0.46
21 2 0.08
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTATAAAAATTTTATAATA
Found at i:42339 original size:94 final size:93
Alignment explanation
Indices: 42203--42426 Score: 244
Period size: 94 Copynumber: 2.4 Consensus size: 93
42193 AATAATTTAG
* *
42203 TATTTGTTTTTATTTTACATTC-ATTTGGATATTTGAAATTTTAAAATATATCAAAAA-ATATTC
1 TATTT-TTTTTATTTTACACTCAATTT-GATATTTGAAATTTTAAAATACATCAAAAAGATATTC
* * *
42266 AAATTTTTTGAAAAAAA-TAATTAAGCTCCTT
64 AAACTTTTTCAAAAAAAGCAATTAAG--CCTT
* * *
42297 T-TTTTTAATTTATTTTACACTCAATTTGATATTT-AAACTTTTAAAATGCATCAAAAAGGTCTT
1 TATTTTT--TTTATTTTACACTCAATTTGATATTTGAAA-TTTTAAAATACATCAAAAAGATATT
42360 CAAACTTTTTCAAAAAAAGCAATTAAGCCTT
63 CAAACTTTTTCAAAAAAAGCAATTAAGCCTT
* *
42391 TGATTTTTTTT-TTTTGCACTCAATTTGATACTTGAA
1 T-ATTTTTTTTATTTTACACTCAATTTGATATTTGAA
42427 TCGTCCTTAA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
92 2 0.02
93 26 0.23
94 48 0.43
95 23 0.21
96 12 0.11
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (93 bp):
TATTTTTTTTATTTTACACTCAATTTGATATTTGAAATTTTAAAATACATCAAAAAGATATTCAA
ACTTTTTCAAAAAAAGCAATTAAGCCTT
Found at i:42950 original size:22 final size:23
Alignment explanation
Indices: 42908--42950 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
42898 AAAAAATAAT
* *
42908 AAAAATTTAATTATTTTTTTAAA
1 AAAAATTTAATGAATTTTTTAAA
42931 AAAAATTTAA-GAATTTTTTA
1 AAAAATTTAATGAATTTTTTA
42951 TACCCTTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
AAAAATTTAATGAATTTTTTAAA
Found at i:47071 original size:29 final size:28
Alignment explanation
Indices: 47028--47092 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
47018 TGTTCTAGAA
*
47028 AATTTTTAAAA-TTTTAATTTTTTATTAT
1 AATTTTTAAAATTTTTAAATTTTT-TTAT
*
47056 ATATTTTTAGAATTTTTTAAATTTTTTTAT
1 A-ATTTTTA-AAATTTTTAAATTTTTTTAT
47086 AATTTTT
1 AATTTTT
47093 TTAAAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 1 0.03
29 13 0.41
30 7 0.22
31 11 0.34
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (28 bp):
AATTTTTAAAATTTTTAAATTTTTTTAT
Found at i:48992 original size:39 final size:39
Alignment explanation
Indices: 48949--49028 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 39
48939 TTTTTATACT
* * *
48949 TTTTTAATAATTTTAATTTTTTGAAATTTTTAAAAAT-AA
1 TTTTTAATAACTTGAA-TTTTTAAAATTTTTAAAAATCAA
* **
48988 TTTTTATTTGCTTGAATTTTTAAAATTTTTAAAAATCAA
1 TTTTTAATAACTTGAATTTTTAAAATTTTTAAAAATCAA
49027 TT
1 TT
49029 AAATGTTGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 19 0.56
39 15 0.44
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.56
Consensus pattern (39 bp):
TTTTTAATAACTTGAATTTTTAAAATTTTTAAAAATCAA
Found at i:48996 original size:29 final size:29
Alignment explanation
Indices: 48954--49012 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
48944 ATACTTTTTT
*
48954 AATAATTTTAATTT-TTTGAAATTTTTAAA
1 AATAATTTTAATTTGCTTG-AATTTTTAAA
*
48983 AATAATTTTTATTTGCTTGAATTTTTAAA
1 AATAATTTTAATTTGCTTGAATTTTTAAA
49012 A
1 A
49013 TTTTTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 24 0.89
30 3 0.11
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (29 bp):
AATAATTTTAATTTGCTTGAATTTTTAAA
Found at i:49287 original size:3 final size:3
Alignment explanation
Indices: 49281--49311 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
49271 ATAGTACGTT
*
49281 ATG ATG ATG ATG ATG ATG ATT ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
49312 ATTCTAATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:49857 original size:24 final size:24
Alignment explanation
Indices: 49812--49863 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
49802 AAATATTATT
* * * * *
49812 TTTTAATTTTTAAGGGTTAAAAGA
1 TTTTAACTTTTAAAGATCAAAACA
49836 TTTTAACTTTTAAAGATCAAAACA
1 TTTTAACTTTTAAAGATCAAAACA
49860 TTTT
1 TTTT
49864 TTTGTCAACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (24 bp):
TTTTAACTTTTAAAGATCAAAACA
Found at i:54388 original size:19 final size:20
Alignment explanation
Indices: 54332--54388 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
54322 AAATTTTTTT
54332 ATAATTATTTATTAATTTTAA
1 ATAATTATTTA-TAATTTTAA
* * *
54353 ATAATTCTTCA-ATTTTTAA
1 ATAATTATTTATAATTTTAA
*
54372 ATAATT-TTTATAGTTTT
1 ATAATTATTTATAATTTT
54389 CTATATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 3 0.10
19 18 0.60
21 9 0.30
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (20 bp):
ATAATTATTTATAATTTTAA
Found at i:65111 original size:6 final size:6
Alignment explanation
Indices: 65100--65135 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
65090 AAAATCATAC
65100 ATAAAT ATAAAT ATAAAT ATAAAT ATATAAT ATAAA
1 ATAAAT ATAAAT ATAAAT ATAAAT ATA-AAT ATAAA
65136 GTCTATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATAAAT
Found at i:65142 original size:14 final size:13
Alignment explanation
Indices: 65103--65148 Score: 60
Period size: 12 Copynumber: 3.6 Consensus size: 13
65093 ATCATACATA
65103 AATATAAATATA-
1 AATATAAATATAT
65115 AATATAAATATAT
1 AATATAAATATAT
*
65128 AATATAAAGTCTAT
1 AATATAAA-TATAT
65142 AAT-TAAA
1 AATATAAA
65149 ATAAAATAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
12 12 0.39
13 12 0.39
14 7 0.23
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (13 bp):
AATATAAATATAT
Found at i:66367 original size:26 final size:26
Alignment explanation
Indices: 66338--66408 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
66328 ATAGTTAACG
66338 GTCAACGTCAAAGTCAACGATCAACA
1 GTCAACGTCAAAGTCAACGATCAACA
* * **
66364 GTCAATGTCAAAGTCAATGATCAATG
1 GTCAACGTCAAAGTCAACGATCAACA
66390 GTCAACGGTCAACAGTCAA
1 GTCAAC-GTCAA-AGTCAA
66409 TGGGTCGAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
26 27 0.71
27 5 0.13
28 6 0.16
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (26 bp):
GTCAACGTCAAAGTCAACGATCAACA
Found at i:69769 original size:26 final size:26
Alignment explanation
Indices: 69717--69785 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 26
69707 AGACTCGAAG
*
69717 ATACTGTACTGGCTCGTAAAAGCGAT
1 ATACTGTACTGGCTCGAAAAAGCGAT
* *
69743 ATACTTTACTGGCTC-AAAAGAGTGAT
1 ATACTGTACTGGCTCGAAAA-AGCGAT
*
69769 ATACTGAACTGGGCTCG
1 ATACTGTACT-GGCTCG
69786 TATGAGTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 3 0.09
26 27 0.77
27 5 0.14
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (26 bp):
ATACTGTACTGGCTCGAAAAAGCGAT
Found at i:70794 original size:2 final size:2
Alignment explanation
Indices: 70787--70811 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
70777 GTTACAAATA
70787 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
70812 AAATCTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:74031 original size:30 final size:30
Alignment explanation
Indices: 73990--74060 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
73980 AATTTAATTC
*
73990 TTAATATTTTTATAATTATTAAATAATTAAA
1 TTAA-ATTTTTATAATTATTAAAAAATTAAA
* *
74021 TTAAATTTTTATTATTTTTAAAAAATTAAA
1 TTAAATTTTTATAATTATTAAAAAATTAAA
*
74051 GTATAATTTT
1 TTA-AATTTT
74061 ATTTTTATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 25 0.71
31 10 0.29
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (30 bp):
TTAAATTTTTATAATTATTAAAAAATTAAA
Found at i:76262 original size:14 final size:13
Alignment explanation
Indices: 76243--76280 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
76233 CTAAAAAGAT
76243 AAATCATTTTCTAG
1 AAATCATTTTCT-G
76257 AAATCATTTTCTG
1 AAATCATTTTCTG
*
76270 AAACCATTTTC
1 AAATCATTTTC
76281 AGTCCAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.42
Consensus pattern (13 bp):
AAATCATTTTCTG
Found at i:76277 original size:13 final size:14
Alignment explanation
Indices: 76247--76280 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
76237 AAAGATAAAT
*
76247 CATTTTCTAGAAAT
1 CATTTTCTAGAAAC
76261 CATTTTCT-GAAAC
1 CATTTTCTAGAAAC
76274 CATTTTC
1 CATTTTC
76281 AGTCCAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (14 bp):
CATTTTCTAGAAAC
Found at i:77078 original size:28 final size:29
Alignment explanation
Indices: 77031--77100 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 29
77021 TAGACTCTAG
* *
77031 GGTTTCAAGGTCTAGGATCAAGAATTCAA
1 GGTTTCAAGGTTTAGAATCAAGAATTCAA
*
77060 -GTTTCAAGGTTTAGAATCAAGAGTTCAA
1 GGTTTCAAGGTTTAGAATCAAGAATTCAA
77088 GGTTT-AAGGTTTA
1 GGTTTCAAGGTTTA
77101 AAGTTTATGG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 33 0.89
29 4 0.11
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (29 bp):
GGTTTCAAGGTTTAGAATCAAGAATTCAA
Found at i:77417 original size:20 final size:19
Alignment explanation
Indices: 77401--77440 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
77391 TAATTTTTAT
77401 AATATAAAATAAATTTTAAA
1 AATAT-AAATAAATTTTAAA
*
77421 AATATATATAAATTTTAAA
1 AATATAAATAAATTTTAAA
77440 A
1 A
77441 TTTTATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATATAAATAAATTTTAAA
Found at i:79036 original size:23 final size:22
Alignment explanation
Indices: 78937--79062 Score: 103
Period size: 23 Copynumber: 5.4 Consensus size: 22
78927 AGAAGTACTT
78937 AACAGTAAGCACACAAGTGCTGGGGA
1 AACAGTAAGCACACAAGTGC----GA
78963 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACA-AGTGCGA
* * * * *
78985 ATCGGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACA-AGTGCGA
*
79007 AATCAGTAGGCACACAAGGTGCGA
1 AA-CAGTAAGCACACAA-GTGCGA
79031 AACAGTAAGCACACGAAGTGCGA
1 AACAGTAAGCACAC-AAGTGCGA
79054 AACAGTAAG
1 AACAGTAAG
79063 TGCGCTAGCT
Statistics
Matches: 84, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
22 19 0.23
23 40 0.48
24 5 0.06
26 15 0.18
27 5 0.06
ACGTcount: A:0.40, C:0.22, G:0.27, T:0.11
Consensus pattern (22 bp):
AACAGTAAGCACACAAGTGCGA
Done.