Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003725.1 Kokia drynarioides strain JFW-HI SEQ_116680, 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: 57217
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:361 original size:51 final size:51
Alignment explanation
Indices: 306--471 Score: 244
Period size: 51 Copynumber: 3.3 Consensus size: 51
296 AAATTCACCC
*
306 CCATGCCCACCACCCCTGCCATTCCTACCACCATATTCACCATCACCCTTT
1 CCATGCCCACCACCCCTGCCATTCCTACTACCATATTCACCATCACCCTTT
* * *
357 CCATGCCCACCA-CCCTGGCCATTCCTACTACCACATTCATCATCACTCTTT
1 CCATGCCCACCACCCCT-GCCATTCCTACTACCATATTCACCATCACCCTTT
* * * *
408 CCATGCCCATCACCCTTGCCATTCCTACTACCATAATCACCATCACCCTTG
1 CCATGCCCACCACCCCTGCCATTCCTACTACCATATTCACCATCACCCTTT
459 CCATGCCCACCAC
1 CCATGCCCACCAC
472 AGAAACTACC
Statistics
Matches: 101, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
50 4 0.04
51 94 0.93
52 3 0.03
ACGTcount: A:0.22, C:0.48, G:0.05, T:0.24
Consensus pattern (51 bp):
CCATGCCCACCACCCCTGCCATTCCTACTACCATATTCACCATCACCCTTT
Found at i:2440 original size:17 final size:17
Alignment explanation
Indices: 2405--2440 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2395 ATTACGTATT
* *
2405 TATTTATAAATATTTAA
1 TATTTATAAACATTAAA
2422 TATTTATAAACATTAAA
1 TATTTATAAACATTAAA
2439 TA
1 TA
2441 AATAAATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTTATAAACATTAAA
Found at i:5138 original size:47 final size:47
Alignment explanation
Indices: 5047--5137 Score: 121
Period size: 47 Copynumber: 2.0 Consensus size: 47
5037 AATTAATCAA
* * * *
5047 ATTAATCGAAATAAATAAAATATATTTTTTAAACTATTATTTTTTAT
1 ATTAACCGAAATAAATAAAATATATTATATAAAATATTATTTTTTAT
**
5094 ATTAACCGAAATAAATAGTATATATTATATAAAATA-TATTTTTT
1 ATTAACCGAAATAAATAAAATATATTATATAAAATATTATTTTTT
5138 TGAACTATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
46 8 0.21
47 30 0.79
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (47 bp):
ATTAACCGAAATAAATAAAATATATTATATAAAATATTATTTTTTAT
Found at i:7958 original size:43 final size:44
Alignment explanation
Indices: 7871--7958 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 44
7861 TAAAGCTTCA
* * * * * * *
7871 GGGGACACACGGGCGTGTGTCTGACTGTGTGTGTATATTGTTTT
1 GGGGACACACGGGAGTGTGCCAGACAGTGTGTGCATACTATTTT
7915 GGGG-CACACGGGAGTGTGCCAGACAGTGTGTGCATACTATTTT
1 GGGGACACACGGGAGTGTGCCAGACAGTGTGTGCATACTATTTT
7958 G
1 G
7959 TGATTTAAGG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 33 0.89
44 4 0.11
ACGTcount: A:0.17, C:0.16, G:0.36, T:0.31
Consensus pattern (44 bp):
GGGGACACACGGGAGTGTGCCAGACAGTGTGTGCATACTATTTT
Found at i:8038 original size:56 final size:56
Alignment explanation
Indices: 7978--8086 Score: 139
Period size: 56 Copynumber: 1.9 Consensus size: 56
7968 GTACAGGGGA
* ** *
7978 CACACGGG-TCAGGAACACGGGTGTGTGCCAGACCGTGTGTGTATATTGTTTTGTGC
1 CACACGGGCT-AGGAACACGGGTGTGTGCCAGACAGTGTGAATATACTGTTTTGTGC
* * *
8034 CACACGGGCTGGGCACACGGGTGTGTGTCAGACAGTGTGAATATACTGTTTTG
1 CACACGGGCTAGGAACACGGGTGTGTGCCAGACAGTGTGAATATACTGTTTTG
8087 CAATTGCAGG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
56 44 0.98
57 1 0.02
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (56 bp):
CACACGGGCTAGGAACACGGGTGTGTGCCAGACAGTGTGAATATACTGTTTTGTGC
Found at i:8747 original size:97 final size:98
Alignment explanation
Indices: 8578--8765 Score: 238
Period size: 97 Copynumber: 1.9 Consensus size: 98
8568 GAAAAGGATG
* * *
8578 TTCGATTATCTCGATTTAAAGAAAAAGTCGCACCTAGTAAGTTTAGGTACAAATTTTCAGAATCA
1 TTCGATTATCTCGATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATCA
*
8643 GAGAT-AAAGAAACATTGCCTCGATTTAAGAATA
66 GAAATAAAAG-AACATTGCCTCGATTTAAGAATA
* ** *
8676 TTCGATTAT-TCCGATTTGAAGAAAAA-TCGTGCCTAGTAAGTTAAGGCACAAATTTTCAAAATT
1 TTCGATTATCT-CGATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATC
* * *
8739 TGAAATAAAAGAATATTGCCTCTATTT
65 AGAAATAAAAGAACATTGCCTCGATTT
8766 TAAAGTTTTT
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
97 50 0.65
98 27 0.35
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (98 bp):
TTCGATTATCTCGATTTAAAGAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATCA
GAAATAAAAGAACATTGCCTCGATTTAAGAATA
Found at i:9173 original size:88 final size:87
Alignment explanation
Indices: 9089--9551 Score: 331
Period size: 88 Copynumber: 5.3 Consensus size: 87
9079 AATCAGGATC
** * * * * *
9089 AAAAATGAAATTTTTAAAAGTTTGGGGGTAAAATGGT-AATTTTGGGAAAAATCAGGATCAAAAA
1 AAAAAT-AAATTTTTGGAAGTTCGAGGGTAAAATGGTAAATTTTTGGAAAAATAAGGGTCAAAAA
9153 TGGAATTTTAGGAATTTCAGGGGT
65 TGGAATTTTAGGAATTTCA-GGGT
* * *
9177 AAACAT-AATTTTTGGAAGTTCGAGGGTAAAATGATAAA-TTTTGGAAAAATTAGGGTCAAAAAT
1 AAAAATAAATTTTTGGAAGTTCGAGGGTAAAATGGTAAATTTTTGGAAAAATAAGGGTCAAAAAT
* *
9240 GTAATTTTAGGAAGTTCGAGGGT
66 GGAATTTTAGGAATTTC-AGGGT
* * ** *
9263 AAAAATGTAATTTTTGGGAGTTC-AGGGGTAAAATGGT-AATTTTTGG-AAAATTTGAGGTTAAA
1 AAAAAT-AAATTTTTGGAAGTTCGA-GGGTAAAATGGTAAATTTTTGGAAAAATAAG-GGTCAAA
* * *
9325 AATGGAATTATAAGAAGTTT-GGAGGT
63 AATGGAATTTTAGGAA-TTTCAG-GGT
*
9351 AAAAATATAATTTTTGGAAGTT-TAGGGT-AAATGGTAATATTTTTTTGGAAAAATAAGGGTCAA
1 AAAAATA-AATTTTTGGAAGTTCGAGGGTAAAATGGTAA-A--TTTTTGGAAAAATAAGGGTCAA
* **
9414 AAATGGAATTTTAAGAAGTTTGGGGGTT
62 AAATGGAATTTTAGGAA-TTTCAGGG-T
* * * ** **
9442 AAAACGT-AATTTTTGGAAGTTAGAGGGTAAAAAT-GT-AATTTTTAG-AAGGTTTGAGGTCAAA
1 AAAA-ATAAATTTTTGGAAGTTCGAGGGT-AAAATGGTAAATTTTTGGAAAAATAAG-GGTCAAA
* * * *
9503 AATAGAATTTTAGAAAGTTAAGGTGT
63 AATGGAATTTTAGGAATTTCAGG-GT
* *
9529 AAAAATGTAATTTTTAGAAGTTC
1 AAAAAT-AAATTTTTGGAAGTTC
9552 AAGGTCAAAA
Statistics
Matches: 306, Mismatches: 43, Indels: 52
0.76 0.11 0.13
Matches are distributed among these distances:
86 78 0.25
87 32 0.10
88 119 0.39
89 2 0.01
90 49 0.16
91 19 0.06
92 3 0.01
93 4 0.01
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (87 bp):
AAAAATAAATTTTTGGAAGTTCGAGGGTAAAATGGTAAATTTTTGGAAAAATAAGGGTCAAAAAT
GGAATTTTAGGAATTTCAGGGT
Found at i:9176 original size:59 final size:57
Alignment explanation
Indices: 8994--9179 Score: 187
Period size: 59 Copynumber: 3.2 Consensus size: 57
8984 TTGGATACTC
* * * *
8994 GGGGGTAAAATGGTAATTTT-GGAAAAGTACAAGG-TTAAAAATTGAATTTTAGACATCT
1 GGGGGTAAAATGGTAATTTTGGGAAAAAT-C-AGGATCAAAAATGGAATTTTAGA-ATTT
* * ** * *
9052 GGGGGTAATATGATAATTTTTGAAAAAAATCAGGATCAAAAATGAAATTTTTAAAAGTTT
1 GGGGGTAAAATGGTAA-TTTTGGGAAAAATCAGGATCAAAAATGGAA-TTTTAGAA-TTT
9112 GGGGGTAAAATGGTAATTTTGGGAAAAATCAGGATCAAAAATGGAATTTTAGGAATTT
1 GGGGGTAAAATGGTAATTTTGGGAAAAATCAGGATCAAAAATGGAATTTTA-GAATTT
*
9170 CAGGGGTAAA
1 -GGGGGTAAA
9180 CATAATTTTT
Statistics
Matches: 104, Mismatches: 17, Indels: 13
0.78 0.13 0.10
Matches are distributed among these distances:
58 25 0.24
59 52 0.50
60 27 0.26
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.30
Consensus pattern (57 bp):
GGGGGTAAAATGGTAATTTTGGGAAAAATCAGGATCAAAAATGGAATTTTAGAATTT
Found at i:9220 original size:29 final size:28
Alignment explanation
Indices: 9148--9609 Score: 204
Period size: 29 Copynumber: 15.8 Consensus size: 28
9138 AATCAGGATC
* * *
9148 AAAAATGGAATTTTAGGAATTTCAGGGGT
1 AAAAATGTAATTTTTGGAAGTTCA-GGGT
*
9177 AAACA--TAATTTTTGGAAGTTCGAGGGT
1 AAAAATGTAATTTTTGGAAGTTC-AGGGT
* *
9204 -AAAATGATAAATTTTGGAAAAATT-AGGGT
1 AAAAATG-TAATTTTTGG--AAGTTCAGGGT
*
9233 CAAAAATGTAATTTTAGGAAGTTCGAGGGT
1 -AAAAATGTAATTTTTGGAAGTTC-AGGGT
*
9263 AAAAATGTAATTTTTGGGAGTTCAGGGGT
1 AAAAATGTAATTTTTGGAAGTTCA-GGGT
* * *
9292 -AAAATGGTAATTTTTGGAAAATTTGAGGTT
1 AAAAAT-GTAATTTTTGG--AAGTTCAGGGT
* * ** **
9322 AAAAATGGAATTATAAGAAGTTTGGAGGT
1 AAAAATGTAATTTTTGGAAGTTCAG-GGT
* *
9351 AAAAATATAATTTTTGGAAGTTTAGGGT
1 AAAAATGTAATTTTTGGAAGTTCAGGGT
** *
9379 --AAATGGTAATATTTTTTTGGAAAAATAAGGGT
1 AAAAAT-GT-A-A--TTTTTGG-AAGTTCAGGGT
* ** **
9411 CAAAAATGGAATTTTAAGAAGTTTGGGGGT
1 -AAAAATGTAATTTTTGGAAG-TTCAGGGT
* * *
9441 TAAAACGTAATTTTTGGAAGTTAGAGGGT
1 AAAAATGTAATTTTTGGAAGTT-CAGGGT
* *
9470 AAAAATGTAATTTTTAGAAGGTT-TGAGGT
1 AAAAATGTAATTTTTGGAA-GTTCAG-GGT
* * *
9499 CAAAAATAG-AATTTTAGAAAGTTAAGGTGT
1 -AAAAAT-GTAATTTTTGGAAGTTCAGG-GT
* *
9529 AAAAATGTAATTTTTAGAAGTTCAAGGT
1 AAAAATGTAATTTTTGGAAGTTCAGGGT
* * * **
9557 CAAAATATAATTTTGGAGAAGTTTGGGGGT
1 AAAAATGTAATTTTTG-GAAG-TTCAGGGT
* *
9587 TAAAATATAATTTTTGGATAGTT
1 AAAAATGTAATTTTTGGA-AGTT
9610 TAGAGCCTTC
Statistics
Matches: 327, Mismatches: 69, Indels: 74
0.70 0.15 0.16
Matches are distributed among these distances:
26 7 0.02
27 18 0.06
28 38 0.12
29 148 0.45
30 74 0.23
31 27 0.08
32 9 0.03
33 1 0.00
34 1 0.00
35 4 0.01
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.34
Consensus pattern (28 bp):
AAAAATGTAATTTTTGGAAGTTCAGGGT
Found at i:9591 original size:59 final size:60
Alignment explanation
Indices: 9448--9601 Score: 181
Period size: 59 Copynumber: 2.6 Consensus size: 60
9438 GGTTAAAACG
* * **
9448 TAATTTTTG-GAAGTTAGAGGGTAAAAATGTAATTTTTAGAAGGTTTGAGGTCAAAAATA
1 TAATTTTAGAGAAGTTAGGGGGTAAAAATGTAATTTTTAGAAGGTTCAAGGTCAAAAATA
* * *
9507 GAATTTTAGA-AAGTTAAGGTGTAAAAATGTAATTTTTAGAA-GTTCAAGGTC-AAAATA
1 TAATTTTAGAGAAGTTAGGGGGTAAAAATGTAATTTTTAGAAGGTTCAAGGTCAAAAATA
* * * *
9564 TAATTTTGGAGAAGTTTGGGGGTTAAAATATAATTTTT
1 TAATTTTAGAGAAGTTAGGGGGTAAAAATGTAATTTTT
9602 GGATAGTTTA
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
57 14 0.18
58 30 0.38
59 35 0.44
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (60 bp):
TAATTTTAGAGAAGTTAGGGGGTAAAAATGTAATTTTTAGAAGGTTCAAGGTCAAAAATA
Found at i:10760 original size:3 final size:3
Alignment explanation
Indices: 10745--10811 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
10735 TGTTACTTAA
* * * * *
10745 TAT TAT TAA TAT TAT TAT TGT TAT TAT TATT TAT TAG TGT TAT TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
*
10791 TAA TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
10812 CAGTAATGAT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:13021 original size:2 final size:2
Alignment explanation
Indices: 13009--13041 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12999 TCGTATTGAA
*
13009 AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
13042 ATCCGTGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20716 original size:20 final size:22
Alignment explanation
Indices: 20672--20717 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
20662 ATTTAATTGT
20672 TTTATTTTTTTACATTATTTCTC
1 TTTATTTTTTTACA-TATTTCTC
*
20695 TTTATTTTTTT-C-TATTTTTC
1 TTTATTTTTTTACATATTTCTC
20715 TTT
1 TTT
20718 CTTATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
22 1 0.05
23 11 0.50
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTTTTTACATATTTCTC
Found at i:22190 original size:21 final size:21
Alignment explanation
Indices: 22148--22190 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
22138 ATTTCTCAAT
*
22148 TAGGGTTACTTCGCATATGTA
1 TAGGGTTACTTCGCATACGTA
*
22169 TAGGGTTATTTCAGCAT-CGTA
1 TAGGGTTACTTC-GCATACGTA
22190 T
1 T
22191 GGTCTATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (21 bp):
TAGGGTTACTTCGCATACGTA
Found at i:24675 original size:17 final size:17
Alignment explanation
Indices: 24642--24724 Score: 103
Period size: 17 Copynumber: 4.8 Consensus size: 17
24632 AATCCAATTT
*
24642 TTTATTTTTAAATTTTAA
1 TTTA-TTTTAAATTTAAA
24660 TTTATTTTTAAATTTAAA
1 TTTA-TTTTAAATTTAAA
* * *
24678 TTCATTTTGAGTTTAAA
1 TTTATTTTAAATTTAAA
*
24695 TTTATTTTAAATTTGAA
1 TTTATTTTAAATTTAAA
24712 TTTATTTTAAATT
1 TTTATTTTAAATT
24725 AAAAAATTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
17 37 0.65
18 20 0.35
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (17 bp):
TTTATTTTAAATTTAAA
Found at i:26592 original size:28 final size:29
Alignment explanation
Indices: 26529--26839 Score: 194
Period size: 29 Copynumber: 10.8 Consensus size: 29
26519 TCCTGAATTG
* * * *
26529 TCCAAAAGTTATATTTTGACCCTTAAAATT
1 TCCAAAAATTACATTTTGACCC-CAAACTT
*
26559 TCTAAAAATTACA-TTTGACCCCAAACTT
1 TCCAAAAATTACATTTTGACCCCAAACTT
* *
26587 T-CTAAAATTACATTTTGACCTCAAACTT
1 TCCAAAAATTACATTTTGACCCCAAACTT
**
26615 TCCAAAAATTACATTTTG-CCCTTGAACTT
1 TCCAAAAATTACATTTTGACCC-CAAACTT
* * * *
26644 TACAAAAATTACAATTTTAACCCTAAAATT
1 TCCAAAAATTAC-ATTTTGACCCCAAACTT
26674 TCCAAAAATTACATTTT-A-CCCATGAAC-T
1 TCCAAAAATTACATTTTGACCCCA--AACTT
*** **
26702 TCCAAAAATTACATTTTGACCTTGATTTT
1 TCCAAAAATTACATTTTGACCCCAAACTT
** * * *
26731 TATAAAAATAATATTTTTGCCCCCAAACTT
1 TCCAAAAATTACA-TTTTGACCCCAAACTT
** *
26761 T-CAAAAATTACCATTTT-ACCCCTGGA-TG
1 TCCAAAAATTA-CATTTTGACCCC-AAACTT
* * *
26789 TCCAAAAATTACATTTTTG-CCCTAAAGTG
1 TCCAAAAATTACA-TTTTGACCCCAAACTT
26818 TCCAAAAATTACCATTTT-ACCC
1 TCCAAAAATTA-CATTTTGACCC
26840 TCGGGCATCC
Statistics
Matches: 218, Mismatches: 44, Indels: 39
0.72 0.15 0.13
Matches are distributed among these distances:
27 12 0.06
28 52 0.24
29 105 0.48
30 46 0.21
31 3 0.01
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.36
Consensus pattern (29 bp):
TCCAAAAATTACATTTTGACCCCAAACTT
Found at i:26718 original size:87 final size:86
Alignment explanation
Indices: 26529--26811 Score: 281
Period size: 87 Copynumber: 3.3 Consensus size: 86
26519 TCCTGAATTG
* * * *
26529 TCCAAAAGTTATATTTTGACCCTTAAAATTT-CTAAAAATTAC-A-TTTGACCCCAAACTTTCTA
1 TCCAAAAATTACATTTTG-CCCTTGAAATTTAC-AAAAATTACAATTTTGACCCCAAACTTTCAA
26591 AAATTACATTTTGACCTCA--AACTT
64 AAATTACATTTT-ACC-CATGAAC-T
* * * *
26615 TCCAAAAATTACATTTTGCCCTTGAACTTTACAAAAATTACAATTTTAACCCTAAAATTTCCAAA
1 TCCAAAAATTACATTTTGCCCTTGAAATTTACAAAAATTACAATTTTGACCCCAAACTTT-CAAA
26680 AATTACATTTTACCCATGAACT
65 AATTACATTTTACCCATGAACT
* ** * * * * *
26702 TCCAAAAATTACATTTTGACCTTGATTTTTATAAAAATAATATTTTTGCCCCCAAACTTTCAAAA
1 TCCAAAAATTACATTTTGCCCTTGAAATTTACAAAAATTACAATTTTGACCCCAAACTTTCAAAA
* *
26767 ATTACCATTTTACCCCTGGA-T
66 ATTA-CATTTTACCCATGAACT
26788 GTCCAAAAATTACATTTTTGCCCT
1 -TCCAAAAATTACA-TTTTGCCCT
26812 AAAGTGTCCA
Statistics
Matches: 166, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
85 19 0.11
86 30 0.18
87 92 0.55
88 25 0.15
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.37
Consensus pattern (86 bp):
TCCAAAAATTACATTTTGCCCTTGAAATTTACAAAAATTACAATTTTGACCCCAAACTTTCAAAA
ATTACATTTTACCCATGAACT
Found at i:26850 original size:29 final size:27
Alignment explanation
Indices: 26762--26863 Score: 73
Period size: 29 Copynumber: 3.6 Consensus size: 27
26752 CCCAAACTTT
*
26762 CAAAAATTACCATTTTACCC-CTGGATGTC
1 CAAAAATTA-CATTTTACCCTCAGGA--TC
* *
26791 CAAAAATTACATTTTTGCCCTAAAGTG-TC
1 CAAAAATTACA-TTTTACCCT-CAG-GATC
*
26820 CAAAAATTACCATTTTACCCTCGGGCATC
1 CAAAAATTA-CATTTTACCCTCAGG-ATC
*
26849 CAAAAATCACATTTT
1 CAAAAATTACATTTT
26864 TGACTCCGTT
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
27 1 0.02
28 9 0.15
29 45 0.76
30 2 0.03
31 1 0.02
32 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.31
Consensus pattern (27 bp):
CAAAAATTACATTTTACCCTCAGGATC
Found at i:28497 original size:10 final size:10
Alignment explanation
Indices: 28484--28525 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
28474 AATCGGATAA
28484 TTTATATTTT
1 TTTATATTTT
*
28494 TTTATTGTTTT
1 TTTA-TATTTT
28505 TTTATATTTT
1 TTTATATTTT
*
28515 TATATATTTT
1 TTTATATTTT
28525 T
1 T
28526 AAACAATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTATATTTT
Found at i:30174 original size:20 final size:20
Alignment explanation
Indices: 30145--30185 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
30135 AAAAAATCTA
30145 TTAAAAACGTTTACCAAAAG
1 TTAAAAACGTTTACCAAAAG
* *
30165 TTAAATACGTTTATCAAAAG
1 TTAAAAACGTTTACCAAAAG
30185 T
1 T
30186 AAACCCATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (20 bp):
TTAAAAACGTTTACCAAAAG
Found at i:30993 original size:5 final size:5
Alignment explanation
Indices: 30983--31014 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
30973 CTTCAAAAAA
30983 AGAAG AGAAG AGAAG AGAAG AGAA- AG-AG AGAA
1 AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG AGAA
31015 AGCCATGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
3 1 0.04
4 4 0.16
5 20 0.80
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
AGAAG
Found at i:39156 original size:25 final size:24
Alignment explanation
Indices: 39128--39187 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 24
39118 AATCTCCATT
**
39128 AAGCTCAAGTCTAGCTTTGAGTCTC
1 AAGCTCAAGTCTAGAGTTGAG-CTC
* * *
39153 AAGCCTCAAATTTTGAGTTGAGCTC
1 AAG-CTCAAGTCTAGAGTTGAGCTC
39178 AAGCTCAAGT
1 AAGCTCAAGT
39188 TTCTTACCGC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 6 0.21
25 9 0.32
26 13 0.46
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (24 bp):
AAGCTCAAGTCTAGAGTTGAGCTC
Found at i:43779 original size:3 final size:3
Alignment explanation
Indices: 43771--43822 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
43761 GGGAATCGTG
43771 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
43819 AAT A
1 AAT A
43823 TGTTTTATAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:50827 original size:15 final size:15
Alignment explanation
Indices: 50804--50841 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
50794 TCATCTCCCC
*
50804 TTGAGTCCACTACAA
1 TTGACTCCACTACAA
*
50819 TTGACTCCACTACCA
1 TTGACTCCACTACAA
50834 TTGACTCC
1 TTGACTCC
50842 TCCGGAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.26, C:0.34, G:0.11, T:0.29
Consensus pattern (15 bp):
TTGACTCCACTACAA
Found at i:52317 original size:72 final size:72
Alignment explanation
Indices: 52236--52375 Score: 264
Period size: 72 Copynumber: 1.9 Consensus size: 72
52226 ATTGATACCA
52236 ATTTGAGCTTCAATGTTTTG-AAAATTTGAACAAAAATCAAAAGTATCAATACCCTTAACAAAGC
1 ATTTGAGCTTCAATGTTTTGCAAAA-TTGAACAAAAATCAAAAGTATCAATACCCTTAACAAAGC
52300 ATCGATAC
65 ATCGATAC
52308 ATTTGAGCTTCAATGTTTTGCAAAATTGAACAAAAATCAAAAGTATCAATACCCTTAACAAAGCA
1 ATTTGAGCTTCAATGTTTTGCAAAATTGAACAAAAATCAAAAGTATCAATACCCTTAACAAAGCA
52373 TCG
66 TCG
52376 TTACTTCTCA
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
72 63 0.94
73 4 0.06
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (72 bp):
ATTTGAGCTTCAATGTTTTGCAAAATTGAACAAAAATCAAAAGTATCAATACCCTTAACAAAGCA
TCGATAC
Found at i:55775 original size:55 final size:54
Alignment explanation
Indices: 55647--55790 Score: 173
Period size: 56 Copynumber: 2.6 Consensus size: 54
55637 AAAAATTACA
* * ** *
55647 TGGCCGACACCATATTTTTTGTCAGACAAAAAAAATTTGGTGTTGGTCATGTGT
1 TGGCCGACACCATATTTTTTATCAGAAAAAAAAAATTTGGTAATGGTCATGTAT
55701 TGGCCGACACCAGTATTTTTTATCAGGAAAAAAAAAATTTGGTAATGGTCAT-TCAT
1 TGGCCGACACCA-TATTTTTTATCA-GAAAAAAAAAATTTGGTAATGGTCATGT-AT
* * * *
55757 TGGTCGACACCATCTTTTTTATCTGATAAAAAAA
1 TGGCCGACACCATATTTTTTATCAGAAAAAAAAA
55791 TTATTTTTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
54 21 0.27
55 22 0.28
56 35 0.45
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (54 bp):
TGGCCGACACCATATTTTTTATCAGAAAAAAAAAATTTGGTAATGGTCATGTAT
Found at i:55840 original size:57 final size:58
Alignment explanation
Indices: 55754--55903 Score: 223
Period size: 56 Copynumber: 2.6 Consensus size: 58
55744 AATGGTCATT
* * *
55754 CATTGGTCGACACCATCTTTTTTATCTGATAAAAAAATTATTTTTTTTGTTGGCCATG
1 CATTGGTCGACACCATCTTTTTTATCTGATAAAAAAATGATTTTTTGTGTTGGCAATG
* * *
55812 CATTGATCGACACTA-CCTTTTTATCTGAT-AAAAAATGATTTTTTGTGTTGGCAATG
1 CATTGGTCGACACCATCTTTTTTATCTGATAAAAAAATGATTTTTTGTGTTGGCAATG
55868 CATTGGTCGACACCATCTTTTTTATCTGACTAAAAA
1 CATTGGTCGACACCATCTTTTTTATCTGA-TAAAAA
55904 TTTAAATTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
56 37 0.46
57 25 0.31
58 14 0.17
59 4 0.05
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (58 bp):
CATTGGTCGACACCATCTTTTTTATCTGATAAAAAAATGATTTTTTGTGTTGGCAATG
Found at i:55964 original size:75 final size:75
Alignment explanation
Indices: 55871--56018 Score: 196
Period size: 75 Copynumber: 2.0 Consensus size: 75
55861 GGCAATGCAT
* * *
55871 TGGTCGACACCATCTTTTTTATCTGACTAAAAA-TTT-AAATTTTTTTTGGTGTTGGCCATTGC-
1 TGGTCAACACCATCTTTTTTATCTGAC-AAAAAGTTTCAAA-TTTTTTGGGTGTTGACCA-TGCA
*
55933 TTGGTCGACACAA
63 TTCGTCGACACAA
55946 TGGTCAACACCA-CATTTTTTATCTGACAAAAAGTTTCAAATTTTTTGGGTGTTGACCATGCATT
1 TGGTCAACACCATC-TTTTTTATCTGACAAAAAGTTTCAAATTTTTTGGGTGTTGACCATGCATT
56010 CGTCGACAC
65 CGTCGACAC
56019 CACCGTTTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
74 9 0.14
75 53 0.82
76 3 0.05
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.39
Consensus pattern (75 bp):
TGGTCAACACCATCTTTTTTATCTGACAAAAAGTTTCAAATTTTTTGGGTGTTGACCATGCATTC
GTCGACACAA
Found at i:56068 original size:59 final size:60
Alignment explanation
Indices: 55984--56120 Score: 172
Period size: 59 Copynumber: 2.3 Consensus size: 60
55974 AAAAGTTTCA
* * * *
55984 AATTTTTTGGGTGTTGACCATGCATTCGTCGACACC-AC-CGTTTTTATCTGATAAAAAAT
1 AATTTTTTTGGTGTTGGCCATGCATTCGCCGACACCAACACGTTTTTATCAGAT-AAAAAT
* * **
56043 AATTTTTTTTGTGTTGGCCATGCATTGGCCGACACCAACATTTTTTTATCAGATAAAAAT
1 AATTTTTTTGGTGTTGGCCATGCATTCGCCGACACCAACACGTTTTTATCAGATAAAAAT
56103 -ATTTTTTTGGTGTTGGCC
1 AATTTTTTTGGTGTTGGCC
56121 GACACCACTT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 48 0.72
60 8 0.12
61 11 0.16
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.41
Consensus pattern (60 bp):
AATTTTTTTGGTGTTGGCCATGCATTCGCCGACACCAACACGTTTTTATCAGATAAAAAT
Found at i:56158 original size:48 final size:48
Alignment explanation
Indices: 56067--56158 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
56057 TGGCCATGCA
**
56067 TTGGCCGACACCAACATTTTTTTATCAGATAAAAATATTTTTTTGGTG
1 TTGGCCGACACCAACATTTTTTTATCAGATAAAAATAAATTTTTGGTG
*
56115 TTGGCCGACACC-AC-TTTTTTTATCTGATAAAAAAATAAATTTTT
1 TTGGCCGACACCAACATTTTTTTATCAGAT--AAAAATAAATTTTT
56159 TTTTTATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
46 13 0.33
47 2 0.05
48 24 0.62
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (48 bp):
TTGGCCGACACCAACATTTTTTTATCAGATAAAAATAAATTTTTGGTG
Found at i:57178 original size:2 final size:2
Alignment explanation
Indices: 57171--57217 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
57161 CCAGTAGAAG
57171 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57213 AT AT A
1 AT AT A
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.