Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014188.1 Kokia drynarioides strain JFW-HI SEQ_129221, 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: 87413
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Warning! 129 characters in sequence are not A, C, G, or T
Found at i:740 original size:22 final size:22
Alignment explanation
Indices: 715--760 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
705 TAAATTATTT
*
715 AATTGAAATTCAAGTAGAAAAA
1 AATTGAAATTCAAGTAAAAAAA
* * *
737 AATTTAAATTGAGGTAAAAAAA
1 AATTGAAATTCAAGTAAAAAAA
759 AA
1 AA
761 ATGTTTTCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.61, C:0.02, G:0.13, T:0.24
Consensus pattern (22 bp):
AATTGAAATTCAAGTAAAAAAA
Found at i:6092 original size:21 final size:21
Alignment explanation
Indices: 6054--6093 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6044 TGGACTAATT
**
6054 ATTTTAAAAATACTATTTAAA
1 ATTTTAAAAATAAAATTTAAA
*
6075 ATTTTTAAAATAAAATTTA
1 ATTTTAAAAATAAAATTTA
6094 TTTTATTGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTTAAAAATAAAATTTAAA
Found at i:8135 original size:26 final size:26
Alignment explanation
Indices: 8099--8150 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
8089 GGAAAGGTTG
*
8099 CACCTGGTAAGTTAAGGCAAAAATTT
1 CACCTAGTAAGTTAAGGCAAAAATTT
*
8125 CACCTAGTAAGTTAAGGCACAAATTT
1 CACCTAGTAAGTTAAGGCAAAAATTT
8151 TTGAAACTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (26 bp):
CACCTAGTAAGTTAAGGCAAAAATTT
Found at i:8532 original size:29 final size:28
Alignment explanation
Indices: 8500--8937 Score: 226
Period size: 29 Copynumber: 14.9 Consensus size: 28
8490 TTTTTAGACA
8500 TTCGGGAGTAAAAATGGAATTTTTGGAGT
1 TTCGGG-GTAAAAATGGAATTTTTGGAGT
** * * * *
8529 TTCGCAGTCCAAAAT--AGTTTTTAGACAT
1 TTCGGGGT-AAAAATGGAATTTTTGGA-GT
* * ***
8557 CTGGGGGT-AAAATGGTAATTTTCAAAAGT
1 TTCGGGGTAAAAATGG-AATTTT-TGGAGT
* * *
8586 TTCGGGATCAAAAATGGAAATTTTGGAGG
1 TTCGGGGT-AAAAATGGAATTTTTGGAGT
* * *
8615 TTCAAGGGTAAAAATGTATTTTTTTGGAAGT
1 TTC-GGGGTAAAAATGGA-ATTTTTGG-AGT
* * * *
8646 TTCAGGGTTGAAAATGAAATTTTTAGAAG-
1 TTC-GGGGTAAAAATGGAATTTTT-GGAGT
* *
8675 ATCAGGGGTAAAAATGGAATTTTTTGAAGTT
1 TTC-GGGGTAAAAATGGAA-TTTTTGGAG-T
* * * *
8706 TTAGGGTTAAAAATGGATTTTTTAGAAG-
1 TTCGGGGTAAAAATGGAATTTTT-GGAGT
*
8734 TTCGAGGGTCAAAATGGAATTTTTGGAAGT
1 TTCG-GGGTAAAAATGGAATTTTTGG-AGT
*
8764 TT-GGGGTAAAAAAATGGGATTTTTGGAAGT
1 TTCGGGGT--AAAAATGGAATTTTTGG-AGT
** *
8794 TTCAAAGGTCAAAATGGAATTTTTGGAAGT
1 TTC-GGGGTAAAAATGGAATTTTTGG-AGT
** *
8824 TTAAGGGTAAAAATGAGATTTTTTGGAGT
1 TTCGGGGTAAAAATG-GAATTTTTGGAGT
*
8853 TTCGGGGTCGAAAATGGAATTTTTGGAAG-
1 TTCGGGGT-AAAAATGGAATTTTTGG-AGT
*
8882 TTCGAGGGTAAAAATGGGATTTTTGGAAG-
1 TTCG-GGGTAAAAATGGAATTTTTGG-AGT
*
8911 TTCGGGGGTAAAAACGGAATTTTTGGA
1 TTC-GGGGTAAAAATGGAATTTTTGGA
8938 CAGTTTATAG
Statistics
Matches: 316, Mismatches: 65, Indels: 57
0.72 0.15 0.13
Matches are distributed among these distances:
26 5 0.02
27 8 0.03
28 16 0.05
29 148 0.47
30 111 0.35
31 25 0.08
32 3 0.01
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (28 bp):
TTCGGGGTAAAAATGGAATTTTTGGAGT
Found at i:8653 original size:30 final size:29
Alignment explanation
Indices: 8582--8943 Score: 308
Period size: 29 Copynumber: 12.2 Consensus size: 29
8572 TAATTTTCAA
*
8582 AAGTTTC-GGGATCAAAAATGGAAATTTTGG
1 AAGTTTCAGGG-T-AAAAATGGAATTTTTGG
* * *
8612 -AGGTTCAAGGGTAAAAATGTATTTTTTTGG
1 AAGTTTC-AGGGTAAAAATGGA-ATTTTTGG
* * *
8642 AAGTTTCAGGGTTGAAAATGAAATTTTTAG
1 AAGTTTCAGGG-TAAAAATGGAATTTTTGG
* *
8672 AAG-ATCAGGGGTAAAAATGGAATTTTTTG
1 AAGTTTCA-GGGTAAAAATGGAATTTTTGG
* * *
8701 AAGTTTTAGGGTTAAAAATGGATTTTTTAG
1 AAGTTTCAGGG-TAAAAATGGAATTTTTGG
*
8731 AAG-TTCGAGGGTCAAAATGGAATTTTTGG
1 AAGTTTC-AGGGTAAAAATGGAATTTTTGG
* *
8760 AAGTTT-GGGGTAAAAAAATGGGATTTTTGG
1 AAGTTTCAGGGT--AAAAATGGAATTTTTGG
* *
8790 AAGTTTCAAAGGTCAAAATGGAATTTTTGG
1 AAGTTTC-AGGGTAAAAATGGAATTTTTGG
* *
8820 AAGTTTAAGGGTAAAAATGAGATTTTTTGG
1 AAGTTTCAGGGTAAAAATG-GAATTTTTGG
* *
8850 -AGTTTCGGGGTCGAAAATGGAATTTTTGG
1 AAGTTTCAGGGT-AAAAATGGAATTTTTGG
*
8879 AAG-TTCGAGGGTAAAAATGGGATTTTTGG
1 AAGTTTC-AGGGTAAAAATGGAATTTTTGG
* *
8908 AAG-TTCGGGGGTAAAAACGGAATTTTTGG
1 AAGTTTC-AGGGTAAAAATGGAATTTTTGG
8937 ACAGTTT
1 A-AGTTT
8944 ATAGACCTCC
Statistics
Matches: 270, Mismatches: 42, Indels: 39
0.77 0.12 0.11
Matches are distributed among these distances:
28 4 0.01
29 130 0.48
30 115 0.43
31 18 0.07
32 3 0.01
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.34
Consensus pattern (29 bp):
AAGTTTCAGGGTAAAAATGGAATTTTTGG
Found at i:8691 original size:89 final size:86
Alignment explanation
Indices: 8595--8934 Score: 301
Period size: 89 Copynumber: 3.8 Consensus size: 86
8585 TTTCGGGATC
* * * *
8595 AAAAATGGAAATTTTGGAGGTTCAAGGGTAAAAATGTATTTTTTTGGAAGTTTCAGGGTTGAAAA
1 AAAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGGA-TTTTTTGGAAGTTTCAGGG-TAAAAA
8660 TGAAATTTTTAGAAGATCAGGGGT-
64 TGAAATTTTTAGAAG-TC-GGGGTA
* ** * *
8684 AAAAATGGAATTTTTTGAAGTTTTAGGGTTAAAAATGGATTTTTTAGAAG-TTCGAGGGTCAAAA
1 AAAAATGGAATTTTTGGAAGTTCAAGGG-TAAAAATGGATTTTTTGGAAGTTTC-AGGGTAAAAA
* * *
8748 TGGAATTTTTGGAAGTTTGGGGTAA
64 TGAAATTTTTAGAAG-TCGGGGT-A
* * * * *
8773 AAAAATGGGATTTTTGGAAGTTTCAAAGGTCAAAATGGAATTTTTGGAAGTTTAAGGGTAAAAAT
1 AAAAATGGAATTTTTGGAAG-TTCAAGGGTAAAAATGGATTTTTTGGAAGTTTCAGGGTAAAAAT
* * * *
8838 GAGATTTTTTGGAGTTTCGGGGTC
65 GAAATTTTTAGAAG--TCGGGGTA
* * *
8862 GAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGGA-TTTTTGGAAG-TTCGGGGGTAAAAA
1 AAAAATGGAATTTTTGGAAGTTCAAGGGTAAAAAT-GGATTTTTTGGAAGTTTC-AGGGTAAAAA
* *
8925 CGGAATTTTT
64 TGAAATTTTT
8935 GGACAGTTTA
Statistics
Matches: 204, Mismatches: 38, Indels: 19
0.78 0.15 0.07
Matches are distributed among these distances:
87 7 0.03
88 60 0.29
89 114 0.56
90 23 0.11
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (86 bp):
AAAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGGATTTTTTGGAAGTTTCAGGGTAAAAATG
AAATTTTTAGAAGTCGGGGTA
Found at i:8705 original size:59 final size:58
Alignment explanation
Indices: 8475--8943 Score: 316
Period size: 59 Copynumber: 7.9 Consensus size: 58
8465 GGAAGTTCGA
**
8475 GGTTAAAAGATGAAATTTTTAGACA-TTCGGGAGTAAAAATGGAATTTTTGG-AGTTTC-G
1 GGTTAAAA-ATGGGATTTTTAGA-AGTTCGGG-GTAAAAATGGAATTTTTGGAAGTTTCAG
* ** * * ***
8533 CAGTCCAAAAT-AG-TTTTTAGACA-TCTGGGGGT-AAAATGGTAATTTTCAAAAGTTTC-G
1 -GGTTAAAAATGGGATTTTTAGA-AGT-TCGGGGTAAAAATGG-AATTTTTGGAAGTTTCAG
* * * * * * * *
8590 GGATCAAAAATGGAAATTTTGGAGGTTCAAGGGTAAAAATGTATTTTTTTGGAAGTTTCAG
1 GG-TTAAAAATGGGATTTTTAGAAGTTC-GGGGTAAAAATGGA-ATTTTTGGAAGTTTCAG
* ** * * *
8651 GGTTGAAAATGAAATTTTTAGAAGATCAGGGGTAAAAATGGAATTTTTTGAAGTTTTAG
1 GGTTAAAAATGGGATTTTTAGAAGTTC-GGGGTAAAAATGGAATTTTTGGAAGTTTCAG
* *
8710 GGTTAAAAAT-GGATTTTTTAGAAGTTCGAGGGTCAAAATGGAATTTTTGGAAGTTT-GG
1 GGTTAAAAATGGGA-TTTTTAGAAGTTCG-GGGTAAAAATGGAATTTTTGGAAGTTTCAG
* * ** * *
8768 GGTAAAAAAATGGGATTTTTGGAAGTTTCAAAGGTCAAAATGGAATTTTTGGAAGTTTAAG
1 GGT-TAAAAATGGGATTTTTAGAAG-TTC-GGGGTAAAAATGGAATTTTTGGAAGTTTCAG
* * * *
8829 GG-TAAAAATGAGATTTTTTGGAGTTTCGGGGTCGAAAATGGAATTTTTGGAAG-TTCGAG
1 GGTTAAAAATGGGATTTTTAGAAG-TTCGGGGT-AAAAATGGAATTTTTGGAAGTTTC-AG
* *
8888 GG-TAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAACGGAATTTTTGGACAGTTT
1 GGTTAAAAATGGGATTTTTAGAAGTTC-GGGGTAAAAATGGAATTTTTGGA-AGTTT
8944 ATAGACCTCC
Statistics
Matches: 328, Mismatches: 59, Indels: 45
0.76 0.14 0.10
Matches are distributed among these distances:
55 7 0.02
56 20 0.06
57 19 0.06
58 33 0.10
59 161 0.49
60 82 0.25
61 6 0.02
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.34
Consensus pattern (58 bp):
GGTTAAAAATGGGATTTTTAGAAGTTCGGGGTAAAAATGGAATTTTTGGAAGTTTCAG
Found at i:10115 original size:3 final size:3
Alignment explanation
Indices: 10109--10143 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
10099 TTATTAATGT
10109 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
10144 TTATTATTAT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:10148 original size:3 final size:3
Alignment explanation
Indices: 10142--10167 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10132 ATAATAATAA
10142 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
10168 ATGCTATCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:10915 original size:17 final size:17
Alignment explanation
Indices: 10873--10943 Score: 79
Period size: 17 Copynumber: 4.1 Consensus size: 17
10863 TAATTGGACT
* *
10873 TTTAATTTTGAAATTAAA
1 TTTAAATTT-AAAATAAA
* * *
10891 TTTTAATTTAAGATTAA
1 TTTAAATTTAAAATAAA
10908 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
10925 TCTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
10942 TT
1 TT
10944 AAAAAAAAGG
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
17 36 0.84
18 7 0.16
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:11774 original size:114 final size:114
Alignment explanation
Indices: 11574--11896 Score: 502
Period size: 114 Copynumber: 2.8 Consensus size: 114
11564 CCACTTTTCA
*
11574 GTATCTCATCAGGAAGCTAACCTTTTATTGGTTCGCCCTGCTTCTCAGTATCTCATCAGGAAGCT
1 GTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGCCCTGCTTCTCAGTATCTCATCAGGAAGCT
* *
11639 GAGATTCGAAGATTTGCTCACATTGAGCCCTGTGTTGATATACTTCTCT
66 GGGATTCGAAGATTTGCTCACATTGAGCCCTGAGTTGATATACTTCTCT
*
11688 GTATCTCATCAGGGAGCTAACCTTTTATTGCTTCGCCCTGCTTCTCAGTATCTCATCAGGAAGCT
1 GTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGCCCTGCTTCTCAGTATCTCATCAGGAAGCT
* * *
11753 GGGATTCGAAGATTTGCTCACATGGAGCCTTGAGTTGGTATACTTCTCT
66 GGGATTCGAAGATTTGCTCACATTGAGCCCTGAGTTGATATACTTCTCT
* * ** *
11802 GTACCTCATCAAGAAGCTAACCGTTTTATTATTTCGACCTGCTTCTCAGTATCTCATCAGGAAGC
1 GTATCTCATCAGGAAGCTAACC-TTTTATTGCTTCGCCCTGCTTCTCAGTATCTCATCAGGAAGC
* * *
11867 TGGGGTTCGAAGATTTGCTCGCTTTGAGCC
65 TGGGATTCGAAGATTTGCTCACATTGAGCC
11897 TCATTTCATT
Statistics
Matches: 191, Mismatches: 17, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
114 126 0.66
115 65 0.34
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (114 bp):
GTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGCCCTGCTTCTCAGTATCTCATCAGGAAGCT
GGGATTCGAAGATTTGCTCACATTGAGCCCTGAGTTGATATACTTCTCT
Found at i:34472 original size:3 final size:3
Alignment explanation
Indices: 34466--34500 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
34456 ATAATAATAA
*
34466 TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
34501 ATGCTATCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:35083 original size:30 final size:30
Alignment explanation
Indices: 35022--35083 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
35012 NNNNNNNNNN
* * **
35022 CATGCGCTACCGTCCCACGGTCCTCCGGTG
1 CATGCGCTACCGCCCCACAGTCCTCAAGTG
* *
35052 CATGCGCTGCCGCCCCGCAGTCCTCAAGTG
1 CATGCGCTACCGCCCCACAGTCCTCAAGTG
35082 CA
1 CA
35084 CCCGTCACTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.13, C:0.44, G:0.26, T:0.18
Consensus pattern (30 bp):
CATGCGCTACCGCCCCACAGTCCTCAAGTG
Found at i:35547 original size:3 final size:3
Alignment explanation
Indices: 35541--35575 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
35531 ATAATAATAA
*
35541 TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
35576 ATGCTATCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:36303 original size:6 final size:6
Alignment explanation
Indices: 36281--36361 Score: 82
Period size: 6 Copynumber: 14.0 Consensus size: 6
36271 TAATTGGACT
*
36281 TTTAAT TTTGAAA -TTAAA TTTAAA TTTAAA -TTAAA TTTAAA TTTAAGA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A
* *
36329 -TT-AA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
36362 ATAAATTAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
4 1 0.02
5 15 0.23
6 45 0.70
7 3 0.05
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:36313 original size:17 final size:17
Alignment explanation
Indices: 36281--36368 Score: 115
Period size: 17 Copynumber: 5.1 Consensus size: 17
36271 TAATTGGACT
*
36281 TTTAATTTTGAAATTAAA
1 TTTAAATTT-AAATTAAA
36299 TTTAAATTTAAATTAAA
1 TTTAAATTTAAATTAAA
36316 TTTAAATTTAAGATT-AA
1 TTTAAATTTAA-ATTAAA
*
36333 TTTAAATTTAAAATAAA
1 TTTAAATTTAAATTAAA
* *
36350 TCTAAATTTAAAATAAA
1 TTTAAATTTAAATTAAA
36367 TT
1 TT
36369 AAAAAAAGGG
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
16 2 0.03
17 51 0.80
18 11 0.17
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:36314 original size:11 final size:11
Alignment explanation
Indices: 36291--36368 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
36281 TTTAATTTTG
36291 AAATTAAATTT
1 AAATTAAATTT
36302 AAATTTAAA-TT
1 AAA-TTAAATTT
36313 AAATTTAAATTT
1 AAA-TTAAATTT
36325 AAGATT-AATTT
1 AA-ATTAAATTT
*
36336 AAATTTAAA-AT
1 AAA-TTAAATTT
36347 AAATCTAAATTT
1 AAAT-TAAATTT
*
36359 AAAATAAATT
1 AAATTAAATT
36369 AAAAAAAGGG
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
10 2 0.04
11 37 0.65
12 17 0.30
13 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:41979 original size:52 final size:52
Alignment explanation
Indices: 41894--42133 Score: 340
Period size: 52 Copynumber: 4.6 Consensus size: 52
41884 TAAATGCAAA
* *
41894 AAGGTCTGATGACTATGTGTTATCGTGAGTATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * *
41946 AAGG-CTCGATGACTATGTGTCATCGTGAGTATATAAATCCTCTACAGATTAT
1 AAGGTC-CGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
*
41998 GAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * * * *
42050 GAGGTCCGATGACTATGTGTCATTGTGAGCATATGGATCCTTTTATGGATT-T
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCC-TTTACGGATTAT
*
42102 AAGGTCCGATGACTTTGTGTCATCGTGAGTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTAT
42134 TAAATGGGAA
Statistics
Matches: 168, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
51 1 0.01
52 157 0.93
53 10 0.06
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (52 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
Found at i:43738 original size:6 final size:6
Alignment explanation
Indices: 43716--43781 Score: 57
Period size: 6 Copynumber: 11.2 Consensus size: 6
43706 TTGGACTTTC
**
43716 ATTTAA ATTCT-A A-TTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTTAAA
1 ATTTAA ATT-TAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA
**
43763 AGATAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA A
43782 ATAAATTTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
4 1 0.02
5 6 0.13
6 35 0.74
7 5 0.11
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:43772 original size:19 final size:18
Alignment explanation
Indices: 43730--43789 Score: 88
Period size: 17 Copynumber: 3.4 Consensus size: 18
43720 AAATTCTAAT
43730 TAAATTTAAATTT-AAAG
1 TAAATTTAAATTTAAAAG
*
43747 CAAATTTAAATTTAAAAG
1 TAAATTTAAATTTAAAAG
43765 ATAAATTTAAATTTAAAA-
1 -TAAATTTAAATTTAAAAG
43783 TAAATTT
1 TAAATTT
43790 GAATCAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
17 19 0.49
18 4 0.10
19 16 0.41
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (18 bp):
TAAATTTAAATTTAAAAG
Found at i:43783 original size:13 final size:12
Alignment explanation
Indices: 43716--43781 Score: 57
Period size: 11 Copynumber: 5.6 Consensus size: 12
43706 TTGGACTTTC
43716 ATTTAAATTCT-A
1 ATTTAAATT-TAA
43728 A-TTAAATTTAA
1 ATTTAAATTTAA
**
43739 ATTTAAA-GCAA
1 ATTTAAATTTAA
43750 ATTTAAATTTAAA
1 ATTTAAATTT-AA
**
43763 AGATAAATTTAA
1 ATTTAAATTTAA
43775 ATTTAAA
1 ATTTAAA
43782 ATAAATTTGA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
10 1 0.02
11 18 0.43
12 13 0.31
13 10 0.24
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (12 bp):
ATTTAAATTTAA
Found at i:43787 original size:17 final size:17
Alignment explanation
Indices: 43716--43789 Score: 87
Period size: 17 Copynumber: 4.2 Consensus size: 17
43706 TTGGACTTTC
*
43716 ATTTAAATTCT-AATTAA
1 ATTTAAATT-TAAAATAA
**
43733 ATTTAAATTTAAAGCAA
1 ATTTAAATTTAAAATAA
43750 ATTTAAATTTAAAAGATAA
1 ATTTAAATTT-AAA-ATAA
43769 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
43786 ATTT
1 ATTT
43790 GAATCAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
16 1 0.02
17 31 0.62
18 6 0.12
19 12 0.24
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:45423 original size:22 final size:21
Alignment explanation
Indices: 45397--45437 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
45387 ACATTTTGTC
*
45397 TTTATTTATTTTCATTGATATT
1 TTTATTTATTTGCA-TGATATT
45419 TTTATTTATTTGCATGATA
1 TTTATTTATTTGCATGATA
45438 CATTTTCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.63
Consensus pattern (21 bp):
TTTATTTATTTGCATGATATT
Found at i:45443 original size:22 final size:22
Alignment explanation
Indices: 45397--45443 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
45387 ACATTTTGTC
* *
45397 TTTATTTATTTTCATTGATATT
1 TTTATTTATTTGCATTGATAAT
45419 TTTATTTATTTGCA-TGATACAT
1 TTTATTTATTTGCATTGATA-AT
45441 TTT
1 TTT
45444 CTTAAATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.64
Consensus pattern (22 bp):
TTTATTTATTTGCATTGATAAT
Found at i:49573 original size:6 final size:6
Alignment explanation
Indices: 49562--49600 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
49552 TGATCAAAAT
* * *
49562 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
49601 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:56164 original size:23 final size:23
Alignment explanation
Indices: 56116--56287 Score: 190
Period size: 23 Copynumber: 7.5 Consensus size: 23
56106 TATACGGAAC
* *
56116 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
56138 -AACAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
56160 AAACAGAGAGTACACAAAGTAC-
1 AAACAGAGAGCACACAAAGTGCT
*
56182 AAATCAGAGAGCACACAAAGTGTT
1 AAA-CAGAGAGCACACAAAGTGCT
*
56206 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
56229 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
56252 AATAACAGAGAGCACGA-GATGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
56277 AAACAGAGAGC
1 AAACAGAGAGC
56288 GCGCTAATGT
Statistics
Matches: 129, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
21 11 0.09
22 11 0.09
23 86 0.67
24 4 0.03
25 16 0.12
26 1 0.01
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:56198 original size:46 final size:46
Alignment explanation
Indices: 56116--56263 Score: 210
Period size: 46 Copynumber: 3.2 Consensus size: 46
56106 TATACGGAAC
56116 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACACAAAGTGCT
1 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT
* *
56160 AAACAGAGAGTACACAAAGTACAAATCAGAGAGCACACAAAGTGTT
1 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT
* * * *
56206 AATCAGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT
56252 AATAACAGAGAG
1 -A-AACAGAGAG
56264 CACGAGATGT
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
44 13 0.14
45 10 0.11
46 59 0.65
47 1 0.01
48 8 0.09
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.12
Consensus pattern (46 bp):
AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT
Found at i:62702 original size:23 final size:23
Alignment explanation
Indices: 62654--62825 Score: 190
Period size: 23 Copynumber: 7.5 Consensus size: 23
62644 TATACGGAAC
* *
62654 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
62676 -AACAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
62698 AAACAGAGAGTACACAAAGTAC-
1 AAACAGAGAGCACACAAAGTGCT
*
62720 AAATCAGAGAGCACACAAAGTGTT
1 AAA-CAGAGAGCACACAAAGTGCT
*
62744 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
62767 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
62790 AATAACAGAGAGCACGA-GATGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
62815 AAACAGAGAGC
1 AAACAGAGAGC
62826 GCGCTAATGT
Statistics
Matches: 129, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
21 11 0.09
22 11 0.09
23 86 0.67
24 4 0.03
25 16 0.12
26 1 0.01
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:62736 original size:46 final size:46
Alignment explanation
Indices: 62654--62801 Score: 210
Period size: 46 Copynumber: 3.2 Consensus size: 46
62644 TATACGGAAC
62654 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACACAAAGTGCT
1 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT
* *
62698 AAACAGAGAGTACACAAAGTACAAATCAGAGAGCACACAAAGTGTT
1 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT
* * * *
62744 AATCAGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT
62790 AATAACAGAGAG
1 -A-AACAGAGAG
62802 CACGAGATGT
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
44 13 0.14
45 10 0.11
46 59 0.65
47 1 0.01
48 8 0.09
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.12
Consensus pattern (46 bp):
AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT
Found at i:66621 original size:18 final size:18
Alignment explanation
Indices: 66598--66638 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
66588 CCAATTGCTA
66598 GGGCCCGACCCGAAAAAT
1 GGGCCCGACCCGAAAAAT
66616 GGGCCCGACCCGAAAAAT
1 GGGCCCGACCCGAAAAAT
66634 GGGCC
1 GGGCC
66639 TAAAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.34, G:0.32, T:0.05
Consensus pattern (18 bp):
GGGCCCGACCCGAAAAAT
Found at i:68153 original size:9 final size:9
Alignment explanation
Indices: 68139--68211 Score: 58
Period size: 9 Copynumber: 7.6 Consensus size: 9
68129 ACATGGACCA
68139 AAAAATTTT
1 AAAAATTTT
68148 AAAAATTGTT
1 AAAAATT-TT
*
68158 AAAAAATATT
1 -AAAAATTTT
68168 AAAAATATCTAT
1 AAAAAT-T-T-T
*
68180 AAAAATTGT
1 AAAAATTTT
68189 AAAAATATTT
1 AAAAAT-TTT
*
68199 -AAAATTAT
1 AAAAATTTT
68207 AAAAA
1 AAAAA
68212 AATAACTGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
8 2 0.04
9 29 0.56
10 6 0.12
11 8 0.15
12 7 0.13
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (9 bp):
AAAAATTTT
Found at i:68159 original size:10 final size:10
Alignment explanation
Indices: 68139--68194 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
68129 ACATGGACCA
68139 AAAAATT-TT
1 AAAAATTGTT
68148 AAAAATTGTT
1 AAAAATTGTT
* *
68158 AAAAAATATT
1 AAAAATTGTT
*
68168 AAAAATATCTAT
1 AAAAAT-TGT-T
68180 AAAAATTG-T
1 AAAAATTGTT
68189 AAAAAT
1 AAAAAT
68195 ATTTAAAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 14 0.36
10 15 0.38
11 3 0.08
12 7 0.18
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.34
Consensus pattern (10 bp):
AAAAATTGTT
Found at i:68183 original size:21 final size:19
Alignment explanation
Indices: 68139--68211 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 19
68129 ACATGGACCA
*
68139 AAAAATTTTAAAAAT-TGTT
1 AAAAATATTAAAAATAT-TT
68158 AAAAAATATTAAAAATATCTAT
1 -AAAAATATTAAAAATAT-T-T
68180 AAAAAT-TGTAAAAATATTT
1 AAAAATAT-TAAAAATATTT
*
68199 AAAATTA-TAAAAA
1 AAAAATATTAAAAA
68212 AATAACTGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 6 0.13
19 6 0.13
20 16 0.35
21 17 0.37
22 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (19 bp):
AAAAATATTAAAAATATTT
Found at i:68214 original size:50 final size:50
Alignment explanation
Indices: 68138--68265 Score: 131
Period size: 50 Copynumber: 2.6 Consensus size: 50
68128 AACATGGACC
* * *
68138 AAAAAAT-TTTAAAAATTGTTAAAAAAT-A-TTAAAAATATCTATAAAAATTGT
1 AAAAAATATTTAAAAATTATAAAAAAATAACTGAAAAA-AT-T-TAAAAA-TGT
* *
68189 -AAAAATATTT-AAAATTATAAAAAAATAACTGAAGAAATTTAAGAATGT
1 AAAAAATATTTAAAAATTATAAAAAAATAACTGAAAAAATTTAAAAATGT
68237 AAACAAATATTTAAAAATTATAAAAAAAT
1 AAA-AAATATTTAAAAATTATAAAAAAAT
68266 TCAAGATACA
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
48 3 0.05
49 7 0.11
50 29 0.44
51 22 0.33
52 5 0.08
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (50 bp):
AAAAAATATTTAAAAATTATAAAAAAATAACTGAAAAAATTTAAAAATGT
Found at i:69930 original size:26 final size:26
Alignment explanation
Indices: 69900--69989 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 26
69890 GTTATTAAAT
69900 TTTAATAAAATTATTATTAAATATAA
1 TTTAATAAAATTATTATTAAATATAA
* * ** *
69926 TTTAATAAAAATAAATAATTTAACCATAT
1 TTTAAT-AAAAT-TATTA-TTAAATATAA
* ** *
69955 TTTAACATGATTATTATTAAATACAA
1 TTTAATAAAATTATTATTAAATATAA
69981 TTTAATAAA
1 TTTAATAAA
69990 TAGTATATAA
Statistics
Matches: 44, Mismatches: 17, Indels: 6
0.66 0.25 0.09
Matches are distributed among these distances:
26 18 0.41
27 8 0.18
28 6 0.14
29 12 0.27
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (26 bp):
TTTAATAAAATTATTATTAAATATAA
Found at i:78804 original size:52 final size:52
Alignment explanation
Indices: 78742--78928 Score: 277
Period size: 52 Copynumber: 3.6 Consensus size: 52
78732 AAATGCAAAA
* * *
78742 AGGTCTGATGACTATGTGTCATTGTGAGTATATGAATCCTTTACGAATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
78794 AGGTCCGATGACTATGTATCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
78846 AGGTCCTATGACTATGTGTCATCGTGAGTATATGGATCCTTTTACGGATT-TA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCC-TTTACGGATTATG
* *
78898 AGGTCCGATGACTTTGTGTCATCATGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
78929 TAAATGAGAA
Statistics
Matches: 123, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
52 113 0.92
53 10 0.08
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:79923 original size:21 final size:20
Alignment explanation
Indices: 79876--79924 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
79866 GAGTAACTTA
79876 TTAATAAATAAAAATATAAT
1 TTAATAAATAAAAATATAAT
*
79896 TTCATAATATAAAAATAT-AT
1 TTAATAA-ATAAAAATATAAT
79916 TTGAATAAA
1 TT-AATAAA
79925 AAGTTGGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
TTAATAAATAAAAATATAAT
Found at i:83512 original size:19 final size:18
Alignment explanation
Indices: 83445--83535 Score: 78
Period size: 19 Copynumber: 4.9 Consensus size: 18
83435 TATCTTGGAT
* *
83445 TTTTTTATAATTTTAAAA
1 TTTTTTACAATTTTTAAA
*
83463 TATATGTTTAC-ATTTTTTAA
1 T-T-T-TTTACAATTTTTAAA
83483 TTTTTT-CAATTATTTAAA
1 TTTTTTACAATT-TTTAAA
* *
83501 TTTTTTATAATTTTAAATA
1 TTTTTTACAATTTTTAA-A
83520 TTTTTTACAATTTTTA
1 TTTTTTACAATTTTTA
83536 TAGATATTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 13
0.73 0.10 0.16
Matches are distributed among these distances:
16 1 0.02
17 6 0.10
18 17 0.29
19 21 0.36
20 9 0.16
21 4 0.07
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (18 bp):
TTTTTTACAATTTTTAAA
Found at i:83575 original size:9 final size:9
Alignment explanation
Indices: 83469--83576 Score: 76
Period size: 9 Copynumber: 11.3 Consensus size: 9
83459 AAAATATATG
*
83469 TTTACATTT
1 TTTAAATTT
83478 TTT-AATTT
1 TTTAAATTT
* *
83486 TTTCAATTA
1 TTTAAATTT
83495 TTTAAATTT
1 TTTAAATTT
83504 TTTATAA-TT
1 TTTA-AATTT
*
83513 TTAAATATTT
1 TTTAA-ATTT
83523 TTTACAATTT
1 TTTA-AATTT
*
83533 TTATAGATATT
1 TT-TAAAT-TT
83544 TTTAATGATTT
1 TTTAA--ATTT
*
83555 TTTAACAATT
1 TTTAA-ATTT
83565 TTTAAATTT
1 TTTAAATTT
83574 TTT
1 TTT
83577 TGGTCCGTGG
Statistics
Matches: 79, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
8 8 0.10
9 30 0.38
10 25 0.32
11 14 0.18
12 2 0.03
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTAAATTT
Done.