Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013905.1 Kokia drynarioides strain JFW-HI SEQ_128934, 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: 97681
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 26 characters in sequence are not A, C, G, or T
Found at i:4496 original size:31 final size:31
Alignment explanation
Indices: 4458--4525 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
4448 TCCTTCCCTT
4458 TTCTTTCAGCTAAAATCCCTCTTATAATTCA
1 TTCTTTCAGCTAAAATCCCTCTTATAATTCA
4489 TTCTTTCAGCTAAAATCCCTCTTATAATTCA
1 TTCTTTCAGCTAAAATCCCTCTTATAATTCA
*
4520 TACTTT
1 TTCTTT
4526 TAGCATTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.28, C:0.25, G:0.03, T:0.44
Consensus pattern (31 bp):
TTCTTTCAGCTAAAATCCCTCTTATAATTCA
Found at i:8091 original size:102 final size:102
Alignment explanation
Indices: 7922--8118 Score: 270
Period size: 102 Copynumber: 1.9 Consensus size: 102
7912 CAGAACCTTT
* * * * * **
7922 TGTAACACATTATTCTTGAGGAATAATTGAATAATGGATAGAGCCTTTTCATCGAGTTATTTTTA
1 TGTAACACATTATTCGTGAGGAATAATTGAATAACGAATAGAGCCTTTTCATCAAATTATTCCTA
*
7987 TTCTAACTGATCCTTATTTGC-GAGTTTCTTAACCTCA
66 TTCTAACTGATCCATATTTGCAG-GTTTCTTAACCTCA
* *
8024 TGTAACACATTATTCGTGAGGCATAATTGAATAACGAATAGAGCCTTTTCATCAAATTCTTCCTA
1 TGTAACACATTATTCGTGAGGAATAATTGAATAACGAATAGAGCCTTTTCATCAAATTATTCCTA
* *
8089 TTCTAATTTATCCATATTTGCAGGTTTCTT
66 TTCTAACTGATCCATATTTGCAGGTTTCTT
8119 TCCCGTAATG
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
102 81 0.99
103 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.41
Consensus pattern (102 bp):
TGTAACACATTATTCGTGAGGAATAATTGAATAACGAATAGAGCCTTTTCATCAAATTATTCCTA
TTCTAACTGATCCATATTTGCAGGTTTCTTAACCTCA
Found at i:9468 original size:30 final size:30
Alignment explanation
Indices: 9434--9493 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
9424 TATAATTTGG
* * *
9434 CACATGGTCGTGTG-CCTAGCCCGTGTGGCT
1 CACATGGCCATGTGTCC-AGCCCATGTGGCT
9464 CACATGGCCATGTGTCCAGCCCATGTGGCT
1 CACATGGCCATGTGTCCAGCCCATGTGGCT
9494 TCTAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.13, C:0.32, G:0.30, T:0.25
Consensus pattern (30 bp):
CACATGGCCATGTGTCCAGCCCATGTGGCT
Found at i:13094 original size:23 final size:23
Alignment explanation
Indices: 13048--13095 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
13038 TAGCAGTTAC
* * *
13048 TAAGTAGTTGTAATTAGTTACTG
1 TAAGCAGTTGTAATCAATTACTG
*
13071 TAAGCAGTTGTAATCAATTGCTG
1 TAAGCAGTTGTAATCAATTACTG
13094 TA
1 TA
13096 TAAATATGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (23 bp):
TAAGCAGTTGTAATCAATTACTG
Found at i:14888 original size:21 final size:22
Alignment explanation
Indices: 14864--14928 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
14854 ATATTATATT
* *
14864 ATATTATTATATAATTAT-TAA
1 ATATTATTATAAAATAATATAA
*
14885 ATATTAATATAAAATAATATAA
1 ATATTATTATAAAATAATATAA
* *
14907 ATATTATTTTAAAA-AATTTAA
1 ATATTATTATAAAATAATATAA
14928 A
1 A
14929 AACTAATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATTATTATAAAATAATATAA
Found at i:23250 original size:49 final size:49
Alignment explanation
Indices: 23178--23276 Score: 164
Period size: 49 Copynumber: 2.0 Consensus size: 49
23168 TACTTCTCTC
23178 ACATTCCATTTCTCTTCATTCCTTAAGGTATAGTATAATATTCATGAGT
1 ACATTCCATTTCTCTTCATTCCTTAAGGTATAGTATAATATTCATGAGT
* *
23227 ACATTCCTTTTCT-TTCCATTCCTTAAGGTATAGTATAGTATTCATGAGT
1 ACATTCCATTTCTCTT-CATTCCTTAAGGTATAGTATAATATTCATGAGT
23276 A
1 A
23277 AAATAATCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
48 2 0.04
49 45 0.96
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.43
Consensus pattern (49 bp):
ACATTCCATTTCTCTTCATTCCTTAAGGTATAGTATAATATTCATGAGT
Found at i:24988 original size:21 final size:21
Alignment explanation
Indices: 24959--25000 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
24949 AAAGTAGGAA
*
24959 ATGGTAATAATACAAAGTATT
1 ATGGAAATAATACAAAGTATT
24980 ATGGAAATAATACAAAGTATT
1 ATGGAAATAATACAAAGTATT
25001 CAATAAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.31
Consensus pattern (21 bp):
ATGGAAATAATACAAAGTATT
Found at i:25326 original size:19 final size:20
Alignment explanation
Indices: 25272--25326 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 20
25262 TATAAAAGTT
* * *
25272 TACAAGAAAATATTGATAAA
1 TACAAGAATATAGTGAAAAA
**
25292 TA-AAGCGTATAGTGAAAAA
1 TACAAGAATATAGTGAAAAA
25311 TACAAGAATATA-TGAA
1 TACAAGAATATAGTGAA
25327 TTTTATTGTC
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.24
Consensus pattern (20 bp):
TACAAGAATATAGTGAAAAA
Found at i:25805 original size:28 final size:29
Alignment explanation
Indices: 25765--25830 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
25755 CTACGTGTAT
*
25765 TTAGCACTTTGTGTGCTCTCTGTTCTA-A
1 TTAGCACTTTGTGTACTCTCTGTTCTATA
* *
25793 TTAGCACTTTGTGTATTCTCTGTTTTATA
1 TTAGCACTTTGTGTACTCTCTGTTCTATA
*
25822 ATAGCACTT
1 TTAGCACTT
25831 CAGTGCTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 24 0.73
29 9 0.27
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.48
Consensus pattern (29 bp):
TTAGCACTTTGTGTACTCTCTGTTCTATA
Found at i:26991 original size:55 final size:55
Alignment explanation
Indices: 26932--27039 Score: 153
Period size: 55 Copynumber: 2.0 Consensus size: 55
26922 CTATATAGAC
** * *
26932 TTCACATACCTTATATGATGCCATAGTCCCAGACTAGGTCTTACACGATATGGTT
1 TTCACATACCCCATATAATGCCATAGTCCCAGACTAGGTCTTACACGACATGGTT
* * *
26987 TTCACATTCCCCATATAATTCCATAGTCCTAGACTAGGTCTTACACGACATGG
1 TTCACATACCCCATATAATGCCATAGTCCCAGACTAGGTCTTACACGACATGG
27040 CCTTTGCTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (55 bp):
TTCACATACCCCATATAATGCCATAGTCCCAGACTAGGTCTTACACGACATGGTT
Found at i:27702 original size:21 final size:21
Alignment explanation
Indices: 27678--27731 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
27668 TTTGTGATAG
*
27678 TTCTACCGATACAAGT-GTAAC
1 TTCTACCGATACAAGTCAT-AC
* * *
27699 TTCTACAGAAACAAGTCATGC
1 TTCTACCGATACAAGTCATAC
27720 TTCTACCGATAC
1 TTCTACCGATAC
27732 TAAAAACTCC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATAC
Found at i:28049 original size:13 final size:13
Alignment explanation
Indices: 28033--28058 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28023 CGTTACATTT
28033 TAGTACTAGATGC
1 TAGTACTAGATGC
28046 TAGTACTAGATGC
1 TAGTACTAGATGC
28059 CTACTTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
TAGTACTAGATGC
Found at i:28459 original size:25 final size:25
Alignment explanation
Indices: 28423--28492 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
28413 CTTCTAGAAT
* *
28423 TTAGCTCATACGAGCCCAGATAAGG
1 TTAGCTCTTACGAGCCCAAATAAGG
28448 TTAGCTCTTACGAGCCCAAATAAGG
1 TTAGCTCTTACGAGCCCAAATAAGG
*
28473 TTAGCTCTTACAAGCCCAAA
1 TTAGCTCTTACGAGCCCAAA
28493 CAGAGTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (25 bp):
TTAGCTCTTACGAGCCCAAATAAGG
Found at i:31930 original size:33 final size:33
Alignment explanation
Indices: 31893--31956 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
31883 AAATTTGCAA
*
31893 GGTCTTAAGGTGAAATAACATCATGTATAGGTT
1 GGTCTTAAGGTGAAATAACAGCATGTATAGGTT
31926 GGTCTTAAGGTGAAATAACAGCATGTATAGG
1 GGTCTTAAGGTGAAATAACAGCATGTATAGG
31957 CTGTAGAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (33 bp):
GGTCTTAAGGTGAAATAACAGCATGTATAGGTT
Found at i:35070 original size:22 final size:23
Alignment explanation
Indices: 35040--35082 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
35030 TAAAGTGGGT
35040 CATGCAAATTAAATTAATTAAAG
1 CATGCAAATTAAATTAATTAAAG
* *
35063 CATG-AAATTATATTATTTAA
1 CATGCAAATTAAATTAATTAA
35083 TGGACATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (23 bp):
CATGCAAATTAAATTAATTAAAG
Found at i:35585 original size:16 final size:15
Alignment explanation
Indices: 35559--35588 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
35549 ATCCATCATT
35559 TCTTCATTCTCTCAA
1 TCTTCATTCTCTCAA
35574 TCTTCTATTCTCTCA
1 TCTTC-ATTCTCTCA
35589 TTTCTCTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (15 bp):
TCTTCATTCTCTCAA
Found at i:46343 original size:13 final size:13
Alignment explanation
Indices: 46325--46349 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46315 TAAGTATGAA
46325 ATGCTAAAAATGC
1 ATGCTAAAAATGC
46338 ATGCTAAAAATG
1 ATGCTAAAAATG
46350 ATACAAAAGA
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:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
ATGCTAAAAATGC
Found at i:46710 original size:19 final size:17
Alignment explanation
Indices: 46686--46729 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 17
46676 ATTCTTTCCT
46686 TTTTCTTTCTTTTATCAAC
1 TTTTCTTTCTTTT-TC-AC
*
46705 TTTTCTTTCTTTTTCTC
1 TTTTCTTTCTTTTTCAC
46722 TTTTCTTT
1 TTTTCTTT
46730 TCATTATGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 9 0.38
18 2 0.08
19 13 0.54
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTCTTTCTTTTTCAC
Found at i:54477 original size:17 final size:17
Alignment explanation
Indices: 54457--54503 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
54447 ATATTATTAA
**
54457 TGTCATTGCATTTTTAT
1 TGTCATTGCATTTACAT
* *
54474 TGTCACTGCATCTACAT
1 TGTCATTGCATTTACAT
54491 TGTCATTGCATTT
1 TGTCATTGCATTT
54504 CCATATATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (17 bp):
TGTCATTGCATTTACAT
Found at i:60350 original size:15 final size:15
Alignment explanation
Indices: 60330--60361 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
60320 TTCTTCCTTC
60330 TCTTCTTCCTTTTCT
1 TCTTCTTCCTTTTCT
*
60345 TCTTCTTCTTTTTCT
1 TCTTCTTCCTTTTCT
60360 TC
1 TC
60362 ATCCTTCTCT
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
TCTTCTTCCTTTTCT
Found at i:60350 original size:27 final size:27
Alignment explanation
Indices: 60320--60372 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
60310 TAGGTTCAGT
* *
60320 TTCTTCCTTCTCTTCTTCCTTTTCTTC
1 TTCTTCCTTCTCTTCATCCTTCTCTTC
* *
60347 TTCTTCTTTTTCTTCATCCTTCTCTT
1 TTCTTCCTTCTCTTCATCCTTCTCTT
60373 GATCACCTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (27 bp):
TTCTTCCTTCTCTTCATCCTTCTCTTC
Found at i:60359 original size:12 final size:12
Alignment explanation
Indices: 60320--60372 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
60310 TAGGTTCAGT
*
60320 TTCTTCCTTCTC
1 TTCTTCCTTTTC
60332 TTCTTCCTTTTC
1 TTCTTCCTTTTC
60344 TTCTTCTTCTTTTTC
1 TTCTTC--C-TTTTC
* *
60359 TTCATCCTTCTC
1 TTCTTCCTTTTC
60371 TT
1 TT
60373 GATCACCTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
12 23 0.66
13 1 0.03
14 1 0.03
15 10 0.29
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTCCTTTTC
Found at i:69812 original size:16 final size:16
Alignment explanation
Indices: 69787--69828 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
69777 AATACATCAT
69787 TTCTTC-ATTCTCTCA
1 TTCTTCTATTCTCTCA
69802 TTCTTCTATTCTCTCA
1 TTCTTCTATTCTCTCA
69818 TT-TCTCTATTC
1 TTCT-TCTATTC
69829 ATTCCCACGC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.12, C:0.31, G:0.00, T:0.57
Consensus pattern (16 bp):
TTCTTCTATTCTCTCA
Found at i:74054 original size:20 final size:20
Alignment explanation
Indices: 74029--74154 Score: 110
Period size: 20 Copynumber: 6.3 Consensus size: 20
74019 AAAGGAAAAA
* *
74029 GTGCCCTTGTTTGCACCTCG
1 GTGCCCTTATTTGCACTTCG
* * * *
74049 GTGCCCCTATATACACTTCA
1 GTGCCCTTATTTGCACTTCG
*
74069 GTGTCCTTATTTGCACATT-G
1 GTGCCCTTATTTGCAC-TTCG
* * *
74089 GTACCCCTATTTGCACTTTG
1 GTGCCCTTATTTGCACTTCG
* *
74109 GTGCCCTTGTTTGCACTTTG
1 GTGCCCTTATTTGCACTTCG
* *
74129 GTGCCTTTATTTGCACTTCA
1 GTGCCCTTATTTGCACTTCG
74149 GTGCCC
1 GTGCCC
74155 CTGTTATGCA
Statistics
Matches: 82, Mismatches: 22, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
19 2 0.02
20 78 0.95
21 2 0.02
ACGTcount: A:0.13, C:0.29, G:0.19, T:0.39
Consensus pattern (20 bp):
GTGCCCTTATTTGCACTTCG
Found at i:75553 original size:38 final size:38
Alignment explanation
Indices: 75508--75594 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 38
75498 GAAATCCTTG
*
75508 TTATAATTATTGTAATTA-TAATTTAT-GATCAAATATTA
1 TTATAATTATTGTAA--AGTAATTTATCGATCAAACATTA
* *
75546 TTATAATTATTGTAAAGTAATTTTTCGGTCAAACATTA
1 TTATAATTATTGTAAAGTAATTTATCGATCAAACATTA
*
75584 TTATAGTTATT
1 TTATAATTATT
75595 ATATTCAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 1 0.02
37 7 0.16
38 35 0.81
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (38 bp):
TTATAATTATTGTAAAGTAATTTATCGATCAAACATTA
Found at i:76059 original size:4 final size:4
Alignment explanation
Indices: 76052--76078 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
76042 TATATATATA
76052 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
76079 ATGGATTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:76759 original size:21 final size:21
Alignment explanation
Indices: 76735--76802 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
76725 AAATGGTATG
76735 ATTTGATTATGTTTTTAGGTT
1 ATTTGATTATGTTTTTAGGTT
* * *
76756 ATTTG-TTCA--TATTAAGACTT
1 ATTTGATT-ATGTTTTTAG-GTT
*
76776 GTGTTGATTATGTTTTTAGGTT
1 AT-TTGATTATGTTTTTAGGTT
76798 ATTTG
1 ATTTG
76803 TTCATATTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
19 5 0.15
20 5 0.15
21 13 0.39
22 5 0.15
23 5 0.15
ACGTcount: A:0.21, C:0.03, G:0.19, T:0.57
Consensus pattern (21 bp):
ATTTGATTATGTTTTTAGGTT
Found at i:76785 original size:42 final size:42
Alignment explanation
Indices: 76737--76822 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
76727 ATGGTATGAT
76737 TTGATTATGTTTTTAGGTTATTTGTTCATATTAAGACTTGTG
1 TTGATTATGTTTTTAGGTTATTTGTTCATATTAAGACTTGTG
76779 TTGATTATGTTTTTAGGTTATTTGTTCATATTAAGACTTGTG
1 TTGATTATGTTTTTAGGTTATTTGTTCATATTAAGACTTGTG
76821 TT
1 TT
76823 AAGGAAATGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.21, C:0.05, G:0.19, T:0.56
Consensus pattern (42 bp):
TTGATTATGTTTTTAGGTTATTTGTTCATATTAAGACTTGTG
Found at i:84235 original size:37 final size:37
Alignment explanation
Indices: 84184--84256 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
84174 AAAATATCAC
*
84184 TTGTATCTAAAAATACCAATAAAGC-ATTCAAGTTCAT
1 TTGTATCTAAAAATACCAATAAAACAATT-AAGTTCAT
*
84221 TTGTATCTATAAATACCAATAAAACAATTAAGTTCA
1 TTGTATCTAAAAATACCAATAAAACAATTAAGTTCA
84257 ATCAAAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 30 0.91
38 3 0.09
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (37 bp):
TTGTATCTAAAAATACCAATAAAACAATTAAGTTCAT
Found at i:93683 original size:17 final size:17
Alignment explanation
Indices: 93661--93724 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 17
93651 TAAAATTATA
93661 TAATAAATATATAAAAT
1 TAATAAATATATAAAAT
* * *
93678 TAATAATTATTTAAAAC
1 TAATAAATATATAAAAT
* *
93695 T-ATAAA-ATTTAAATT
1 TAATAAATATATAAAAT
93710 TAAT-AATAATATAAA
1 TAATAAAT-ATATAAA
93725 TATATAATGA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
15 10 0.27
16 6 0.16
17 21 0.57
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATAAATATATAAAAT
Found at i:93731 original size:32 final size:33
Alignment explanation
Indices: 93658--93731 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 33
93648 TACTAAAATT
* *
93658 ATATAATAAATATATAAAATTAATAATTATTTAA
1 ATAT-ATAAATATATAAAATTAATAATAATATAA
* *
93692 A-ACTATAAA-ATTTAAATTTAATAATAATATAA
1 ATA-TATAAATATATAAAATTAATAATAATATAA
93724 ATATATAA
1 ATATATAA
93732 TGACATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
32 25 0.74
33 7 0.21
34 2 0.06
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
ATATATAAATATATAAAATTAATAATAATATAA
Found at i:93885 original size:38 final size:40
Alignment explanation
Indices: 93830--93908 Score: 101
Period size: 38 Copynumber: 2.0 Consensus size: 40
93820 ATTACTAATA
*
93830 AATTTATTTTTAATGA-TTTGAGAATTAAGGTTTTACTTTT
1 AATTTATTTTTAATGATTTTG-GAATTAAGATTTTACTTTT
* *
93870 AATTT-TTTTT-ATGATTTTGGAATTTATATTTTACTTTT
1 AATTTATTTTTAATGATTTTGGAATTAAGATTTTACTTTT
93908 A
1 A
93909 GTGTTTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 21 0.60
39 9 0.26
40 5 0.14
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (40 bp):
AATTTATTTTTAATGATTTTGGAATTAAGATTTTACTTTT
Found at i:94863 original size:2 final size:2
Alignment explanation
Indices: 94856--94882 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
94846 ATATTAATAC
94856 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
94883 ACTATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:95030 original size:17 final size:17
Alignment explanation
Indices: 95008--95094 Score: 86
Period size: 17 Copynumber: 5.1 Consensus size: 17
94998 CAAACTCCTT
95008 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
*
95025 TTAAATTT-GTTTAAAA
1 TTAAATTTATTTTAAAA
* *
95041 TTTTAATTTATTTTAAAT
1 -TTAAATTTATTTTAAAA
* **
95059 TTAAATTTAATTTAAGT
1 TTAAATTTATTTTAAAA
* *
95076 TTAAAATTATTTTCAAA
1 TTAAATTTATTTTAAAA
95093 TT
1 TT
95095 TAAAATTATC
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
16 7 0.12
17 43 0.77
18 6 0.11
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:95078 original size:6 final size:6
Alignment explanation
Indices: 95007--95098 Score: 52
Period size: 6 Copynumber: 16.0 Consensus size: 6
94997 CCAAACTCCT
* * * * *
95007 TTTAAA TTT-AT TTTAAA ATTAAA TTT--G TTTAAAA TTTTAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
* * *
95052 TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA ATT-AT TTTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
95099 ATTATCATAA
Statistics
Matches: 63, Mismatches: 15, Indels: 16
0.67 0.16 0.17
Matches are distributed among these distances:
4 3 0.05
5 16 0.25
6 37 0.59
7 7 0.11
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:95086 original size:34 final size:34
Alignment explanation
Indices: 95007--95103 Score: 115
Period size: 34 Copynumber: 2.8 Consensus size: 34
94997 CCAAACTCCT
* *
95007 TTTAAATTTATTTTAAAATTAAATTTGTTTAAAA
1 TTTAAATTTATTTTAAATTTAAATTTATTTAAAA
* *
95041 TTTTAATTTATTTTAAATTTAAATTTAATTT-AAG
1 TTTAAATTTATTTTAAATTTAAATTT-ATTTAAAA
* *
95075 TTTAAAATTATTTTCAAATTTAAAATTAT
1 TTTAAATTTATTTT-AAATTTAAATTTAT
95104 CATAAATTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
34 40 0.74
35 14 0.26
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTAAAA
Found at i:95112 original size:17 final size:18
Alignment explanation
Indices: 95075--95117 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
95065 TTAATTTAAG
**
95075 TTTAAAATTATTTTCAAA
1 TTTAAAATTATCATCAAA
95093 TTTAAAATTATCAT-AAA
1 TTTAAAATTATCATCAAA
95110 TTTAAAAT
1 TTTAAAAT
95118 AAATAAAGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAAAATTATCATCAAA
Found at i:95114 original size:35 final size:34
Alignment explanation
Indices: 95007--95117 Score: 91
Period size: 34 Copynumber: 3.2 Consensus size: 34
94997 CCAAACTCCT
* * ** *
95007 TTTAAATTTATTTTAAAATT-AAATTTGTTTAAAA
1 TTTAAAATTATTTTAAATTTAAAATTAATAT-AAA
* * * * *
95041 TTTTAATTTATTTTAAATTTAAATTTAATTTAAG
1 TTTAAAATTATTTTAAATTTAAAATTAATATAAA
95075 TTTAAAATTATTTTCAAATTTAAAATT-ATCATAAA
1 TTTAAAATTATTTT-AAATTTAAAATTAAT-ATAAA
95110 TTTAAAAT
1 TTTAAAAT
95118 AAATAAAGCC
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
34 34 0.54
35 29 0.46
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (34 bp):
TTTAAAATTATTTTAAATTTAAAATTAATATAAA
Found at i:96994 original size:58 final size:58
Alignment explanation
Indices: 96922--97146 Score: 276
Period size: 58 Copynumber: 3.9 Consensus size: 58
96912 CTAAATTGTT
*
96922 CAAAAATTCCATTTTTACCC-CTGAACTTCCAAAAATCCCA-TTTTAACCTCGAAACTTT
1 CAAAAATTCCATTTTTACCCTC-GAACTTCCAAAAATCCCATTTTTAACC-CGAAACTTC
* * * *
96980 CAAAAATTCTATTTTTACCCTCGAATTTCCAAAAATCCAATTTTTAACCCCAAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAA-CCCGAAACTTC
* * * * *
97039 CAAAAA-TCTCATTTTTACCCCCAAACTTTCAAAAATCCCATTTTTGACCCGAAACCTC
1 CAAAAATTC-CATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCGAAACTTC
* * *
97097 CAAAAATCCCATTTTTACCCTCGAACTTCTAAAAATCCCATTTTTGACCC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCC
97147 CGAATTTTCC
Statistics
Matches: 143, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
58 89 0.62
59 52 0.36
60 2 0.01
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (58 bp):
CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCGAAACTTC
Found at i:97150 original size:29 final size:28
Alignment explanation
Indices: 96922--97150 Score: 235
Period size: 29 Copynumber: 7.9 Consensus size: 28
96912 CTAAATTGTT
*
96922 CAAAAATTCCATTTTTACCCCTGAACTTC
1 CAAAAATCCCATTTTTACCCC-GAACTTC
* * *
96951 CAAAAATCCCATTTTAACCTCGAAACTTT
1 CAAAAATCCCATTTTTACCCCG-AACTTC
* * *
96980 CAAAAATTCTATTTTTACCCTCGAATTTC
1 CAAAAATCCCATTTTTACCC-CGAACTTC
* *
97009 CAAAAATCCAATTTTTAACCCCAAAACTTC
1 CAAAAATCCCATTTTT-ACCCC-GAACTTC
* * *
97039 CAAAAATCTCATTTTTACCCCCAAACTTT
1 CAAAAATCCCATTTTTA-CCCCGAACTTC
*
97068 CAAAAATCCCATTTTTGA-CCCGAAACCTC
1 CAAAAATCCCATTTTT-ACCCCG-AACTTC
97097 CAAAAATCCCATTTTTACCCTCGAACTTC
1 CAAAAATCCCATTTTTACCC-CGAACTTC
*
97126 TAAAAATCCCATTTTTGACCCCGAA
1 CAAAAATCCCATTTTT-ACCCCGAA
97151 TTTTCCCAAA
Statistics
Matches: 167, Mismatches: 23, Indels: 20
0.80 0.11 0.10
Matches are distributed among these distances:
28 5 0.03
29 126 0.75
30 36 0.22
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.31
Consensus pattern (28 bp):
CAAAAATCCCATTTTTACCCCGAACTTC
Found at i:97162 original size:117 final size:117
Alignment explanation
Indices: 96922--97147 Score: 312
Period size: 117 Copynumber: 1.9 Consensus size: 117
96912 CTAAATTGTT
** * *
96922 CAAAAAT-TCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTAACCTCGAAACTTTCAAAAA
1 CAAAAATCT-CATTTTTACCCCCAAACTTCCAAAAATCCCATTTTAACCTCGAAACCTCCAAAAA
* * *
96986 TTCTATTTTTACCCTCGAATTTCCAAAAATCCAATTTTTAACCCCAAAACTTC
65 TCCCATTTTTACCCTCGAACTTCCAAAAATCCAATTTTTAACCCCAAAACTTC
* *
97039 CAAAAATCTCATTTTTACCCCCAAACTTTCAAAAATCCCATTTTTGACC-CGAAACCTCCAAAAA
1 CAAAAATCTCATTTTTACCCCCAAACTTCCAAAAATCCCA-TTTTAACCTCGAAACCTCCAAAAA
* * *
97103 TCCCATTTTTACCCTCGAACTTCTAAAAATCCCATTTTTGACCCC
65 TCCCATTTTTACCCTCGAACTTCCAAAAATCCAATTTTTAACCCC
97148 GAATTTTCCC
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
117 87 0.92
118 8 0.08
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.32
Consensus pattern (117 bp):
CAAAAATCTCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTAACCTCGAAACCTCCAAAAAT
CCCATTTTTACCCTCGAACTTCCAAAAATCCAATTTTTAACCCCAAAACTTC
Done.