Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014393.1 Kokia drynarioides strain JFW-HI SEQ_129431, 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: 65812
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:8668 original size:201 final size:198
Alignment explanation
Indices: 8297--8915 Score: 754
Period size: 201 Copynumber: 3.1 Consensus size: 198
8287 AAATGGTTAG
* *
8297 CTTCCTAATAAGATACAGAGAA-ATATACCAACTCTGAGCTCGATGTGAGCAAATCTTCGAATCC
1 CTTCCTAATGAGATACAGAGAAGA-ATACCAACTC-GAGCTCAATGTGAGCAAATCTTCGAA-CC
* * ** *
8361 CAGCTTCCTGATGAGATACTAAGAAGCAGAGCGAATTAAT-AAAAGGTTAGCTTCCTGATAAGAT
63 CAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGAT
* *
8425 ACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAGTAAGG
128 ACTGAGAAGTA-ACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAGG
*
8490 CGGTCAT
192 AGGTCAT
* * *
8497 CTTCCTAATGAGATACAAAGAAGAATACCAACTCGAGGCTCAATGCGAGCAAATCTTCGAACCTT
1 CTTCCTAATGAGATACAGAGAAGAATACCAACTCGA-GCTCAATGTGAGCAAATCTTCGAACC-C
* * *
8562 AGCTTCTTGATGAGATATTGAGAAGTAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGATA
64 AGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGATA
*
8627 CTGAGAAGTGAACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAGGA
129 CTGAGAAGT-AACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAGGA
*
8692 GATCAT
193 GGTCAT
* * *
8698 CTTCCTGATGAGATACAGAGAAGTATACC-A----A-CTCAATGTGAGCAAATCTTCGACCCCCA
1 CTTCCTAATGAGATACAGAGAAGAATACCAACTCGAGCTCAATGTGAGCAAATCTTCGA-ACCCA
* * *
8757 GCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAATGTTAACTTCTTGATGAGATA-
65 GCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGATAC
* * * * * * ** *
8821 TGGAGAAGTAACCAAATCCATCTTTCTGATGAAACACAGAGAAGTGGATCAAAACAAGTGA-TAT
130 T-GAGAAGTAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAGGA-
*
8885 GGTCCT
193 GGTCAT
* *
8891 CTTCCTGATGAGATACTGAGAAGAA
1 CTTCCTAATGAGATACAGAGAAGAA
8916 GGCCAAGTCA
Statistics
Matches: 367, Mismatches: 44, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
192 1 0.00
193 71 0.19
194 87 0.24
195 2 0.01
196 1 0.00
199 4 0.01
200 85 0.23
201 115 0.31
202 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.23
Consensus pattern (198 bp):
CTTCCTAATGAGATACAGAGAAGAATACCAACTCGAGCTCAATGTGAGCAAATCTTCGAACCCAG
CTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGATACT
GAGAAGTAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAGGAGGT
CAT
Found at i:9866 original size:19 final size:20
Alignment explanation
Indices: 9819--9867 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
9809 TCTTTTACTG
*
9819 TATTAATGATT-AACATTAA
1 TATTAATTATTAAACATTAA
*
9838 TATT-AGTATTAAACA-TAA
1 TATTAATTATTAAACATTAA
9856 TATTAATTATTA
1 TATTAATTATTA
9868 TTAATTACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (20 bp):
TATTAATTATTAAACATTAA
Found at i:10929 original size:30 final size:29
Alignment explanation
Indices: 10874--11245 Score: 308
Period size: 30 Copynumber: 12.6 Consensus size: 29
10864 TTCGAGGTCA
* * *
10874 AAAAAGGGATTTTTAGATG-TTTGGGGTT
1 AAAAATGGATTTTTGGAAGTTTTGGGGTT
* *
10902 AAAAATGGACCTTTTGAAAGTTTTGGGGTT
1 AAAAATGGA-TTTTTGGAAGTTTTGGGGTT
* *
10932 AAAAATGGGATTTTTGGTAG-TTCGAGGG-T
1 AAAAAT-GGATTTTTGGAAGTTTTG-GGGTT
10961 AAAAATGGAATTTTTGGAAGTTTTGGGGTT
1 AAAAATGG-ATTTTTGGAAGTTTTGGGGTT
* ** * **
10991 AAAATTGAGATTTTTAAAAGCTTCAGGGTT
1 AAAAATG-GATTTTTGGAAGTTTTGGGGTT
*
11021 AAAAATGGGATTTTTGGAAGTTTTGGGATT
1 AAAAAT-GGATTTTTGGAAGTTTTGGGGTT
** * *
11051 AAAAATTGGATTTTTAAAAG-TTCGAGAG-T
1 AAAAA-TGGATTTTTGGAAGTTTTG-GGGTT
*
11080 AAAAATGGGATTTTTGGAAGTTTTTGGGTT
1 AAAAAT-GGATTTTTGGAAGTTTTGGGGTT
* *
11110 AAAAATGGGATTTTTAGAAG-TTTGATGG-T
1 AAAAAT-GGATTTTTGGAAGTTTTG-GGGTT
* *
11139 AAAAATGGGATTTTTGGAAGTTTCGAGGTT
1 AAAAAT-GGATTTTTGGAAGTTTTGGGGTT
* * *
11169 AAAAATAGGATTTTTGGAAGCTTCGGGGTA
1 AAAAAT-GGATTTTTGGAAGTTTTGGGGTT
* * *
11199 AAAAAGGGATTTTTGGAAGTTTCGAGGTT
1 AAAAATGGATTTTTGGAAGTTTTGGGGTT
11228 AAAAATGGGATTTTTGGA
1 AAAAAT-GGATTTTTGGA
11246 CAATTTAGGA
Statistics
Matches: 277, Mismatches: 49, Indels: 34
0.77 0.14 0.09
Matches are distributed among these distances:
28 11 0.04
29 101 0.36
30 159 0.57
31 6 0.02
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.37
Consensus pattern (29 bp):
AAAAATGGATTTTTGGAAGTTTTGGGGTT
Found at i:10942 original size:59 final size:59
Alignment explanation
Indices: 10873--11242 Score: 442
Period size: 59 Copynumber: 6.3 Consensus size: 59
10863 ATTCGAGGTC
* * * * *
10873 AAAAAAGGGATTTTTAGATGTTTG-GGGTTAAAAAT-GGACCTTTTGAAAGTTTTGGGGTT
1 AAAAATGGGATTTTTAGAAGTTCGAGGG-TAAAAATGGGA-TTTTTGGAAGTTTTGGGGTT
* * *
10932 AAAAATGGGATTTTTGGTAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTT
1 AAAAATGGGATTTTTAGAAGTTCGAGGGTAAAAATGGGATTTTTGGAAGTTTTGGGGTT
* * * *
10991 AAAATTGAGATTTTTAAAAGCTTC-AGGGTTAAAAATGGGATTTTTGGAAGTTTTGGGATT
1 AAAAATGGGATTTTTAGAAG-TTCGAGGG-TAAAAATGGGATTTTTGGAAGTTTTGGGGTT
* * * *
11051 AAAAATTGGATTTTTAAAAGTTCGAGAGTAAAAATGGGATTTTTGGAAGTTTTTGGGTT
1 AAAAATGGGATTTTTAGAAGTTCGAGGGTAAAAATGGGATTTTTGGAAGTTTTGGGGTT
* * * *
11110 AAAAATGGGATTTTTAGAAGTTTGATGGTAAAAATGGGATTTTTGGAAGTTTCGAGGTT
1 AAAAATGGGATTTTTAGAAGTTCGAGGGTAAAAATGGGATTTTTGGAAGTTTTGGGGTT
* * * * *
11169 AAAAATAGGATTTTTGGAAGCTTCG-GGGTAAAAAAGGGATTTTTGGAAGTTTCGAGGTT
1 AAAAATGGGATTTTTAGAAG-TTCGAGGGTAAAAATGGGATTTTTGGAAGTTTTGGGGTT
11228 AAAAATGGGATTTTT
1 AAAAATGGGATTTTT
11243 GGACAATTTA
Statistics
Matches: 270, Mismatches: 35, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
59 210 0.78
60 60 0.22
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.37
Consensus pattern (59 bp):
AAAAATGGGATTTTTAGAAGTTCGAGGGTAAAAATGGGATTTTTGGAAGTTTTGGGGTT
Found at i:11020 original size:89 final size:89
Alignment explanation
Indices: 10864--11245 Score: 377
Period size: 89 Copynumber: 4.3 Consensus size: 89
10854 TTTGAGAAAA
* * * * * *
10864 TTCGA-GGTCAAAAAAGGGATTTTTAGATGTTT-GGGGTTAAAAATG-GACCTTTTGAAAGTTTT
1 TTCGAGGGT-AAAAATGGGATTTTTGGAAGTTTCGGGGTTAAAAATGAGA-TTTTTGGAAG-CTT
* *
10926 GGGGTTAAAAATGGGATTTTTGGTAG-
63 CGGGTTAAAAATGGGATTTTTGGAAGT
* * * **
10952 TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAATTGAGATTTTTAAAAGCTTCAG
1 TTCGAGGGTAAAAATGGGATTTTTGGAAGTTTCGGGGTTAAAAATGAGATTTTTGGAAGCTTC-G
11017 GGTTAAAAATGGGATTTTTGGAAGT
65 GGTTAAAAATGGGATTTTTGGAAGT
* * * ** * * *
11042 TTTG-GGATTAAAAATTGGATTTTTAAAAG-TTCGAGAG-TAAAAATGGGATTTTTGGAAGTTTT
1 TTCGAGG-GTAAAAATGGGATTTTTGGAAGTTTCG-GGGTTAAAAATGAGATTTTTGGAAG-CTT
* *
11104 TGGGTTAAAAATGGGATTTTTAGAAGT
63 CGGGTTAAAAATGGGATTTTTGGAAGT
* *
11131 TT-GATGGTAAAAATGGGATTTTTGGAAGTTTCGAGGTTAAAAAT-AGGATTTTTGGAAGCTTCG
1 TTCGAGGGTAAAAATGGGATTTTTGGAAGTTTCGGGGTTAAAAATGA-GATTTTTGGAAGCTTCG
* *
11194 GGGTAAAAAAGGGATTTTTGGAAGT
65 GGTTAAAAATGGGATTTTTGGAAGT
*
11219 TTCGAGGTTAAAAATGGGATTTTTGGA
1 TTCGAGGGTAAAAATGGGATTTTTGGA
11246 CAATTTAGGA
Statistics
Matches: 241, Mismatches: 40, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
88 73 0.30
89 142 0.59
90 26 0.11
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.37
Consensus pattern (89 bp):
TTCGAGGGTAAAAATGGGATTTTTGGAAGTTTCGGGGTTAAAAATGAGATTTTTGGAAGCTTCGG
GTTAAAAATGGGATTTTTGGAAGT
Found at i:12420 original size:3 final size:3
Alignment explanation
Indices: 12414--12482 Score: 86
Period size: 3 Copynumber: 23.3 Consensus size: 3
12404 ATTATTAAAA
* * *
12414 ATT ATT ATT ATT AGT GTC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
12462 ATT ATT A-T ATA AAT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
12483 ATAATGTAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:13171 original size:18 final size:17
Alignment explanation
Indices: 13150--13189 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
13140 TAAGAATGTA
13150 ATTTGGACTTTTGTAATT
1 ATTTGGACTTTT-TAATT
13168 ATTTTGGACTTTTTAATT
1 A-TTTGGACTTTTTAATT
13186 -TTTG
1 ATTTG
13190 TATTTTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 4 0.19
18 6 0.29
19 11 0.52
ACGTcount: A:0.20, C:0.05, G:0.15, T:0.60
Consensus pattern (17 bp):
ATTTGGACTTTTTAATT
Found at i:13222 original size:17 final size:17
Alignment explanation
Indices: 13204--13350 Score: 150
Period size: 18 Copynumber: 8.4 Consensus size: 17
13194 TTAGCTTTAT
* * *
13204 TTTAAATTTATAGTAAT
1 TTTAAATTTAAAATAAA
13221 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
13239 TTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAA
13256 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
13273 TTTAAATTTTTAAACAAA
1 TTTAAA-TTTAAAATAAA
*
13291 TTTAATTTTTAAAATAAA
1 TTTAA-ATTTAAAATAAA
* *
13309 TTTAAATTTTTAAACAAA
1 TTTAAA-TTTAAAATAAA
*
13327 TTTAATTTTTAAAATAAA
1 TTTAA-ATTTAAAATAAA
13345 TTTAAA
1 TTTAAA
13351 GGGAGTTCGA
Statistics
Matches: 106, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
17 37 0.35
18 69 0.65
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:13244 original size:18 final size:18
Alignment explanation
Indices: 13221--13350 Score: 165
Period size: 18 Copynumber: 7.3 Consensus size: 18
13211 TTATAGTAAT
*
13221 TTTAAATTTGAAAATAAA
1 TTTAAATTTTAAAATAAA
* *
13239 TTTAAA-CTTAAATTAAA
1 TTTAAATTTTAAAATAAA
13256 TTTAAA-TTTAAAATAAA
1 TTTAAATTTTAAAATAAA
* *
13273 TTTAAATTTTTAAACAAA
1 TTTAAATTTTAAAATAAA
*
13291 TTTAATTTTTAAAATAAA
1 TTTAAATTTTAAAATAAA
* *
13309 TTTAAATTTTTAAACAAA
1 TTTAAATTTTAAAATAAA
*
13327 TTTAATTTTTAAAATAAA
1 TTTAAATTTTAAAATAAA
13345 TTTAAA
1 TTTAAA
13351 GGGAGTTCGA
Statistics
Matches: 94, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
17 29 0.31
18 65 0.69
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (18 bp):
TTTAAATTTTAAAATAAA
Found at i:13260 original size:11 final size:11
Alignment explanation
Indices: 13222--13280 Score: 66
Period size: 11 Copynumber: 5.2 Consensus size: 11
13212 TATAGTAATT
13222 TTAAATTTGAAA
1 TTAAATTT-AAA
*
13234 ATAAATTTAAA
1 TTAAATTTAAA
13245 CTTAAA-TTAAA
1 -TTAAATTTAAA
13256 TTTAAATTTAAA
1 -TTAAATTTAAA
*
13268 ATAAATTTAAA
1 TTAAATTTAAA
13279 TT
1 TT
13281 TTTAAACAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 24 0.60
12 16 0.40
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:13317 original size:6 final size:6
Alignment explanation
Indices: 13221--13281 Score: 65
Period size: 6 Copynumber: 10.5 Consensus size: 6
13211 TTATAGTAAT
* *
13221 TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
13268 -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTT
13282 TTAAACAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
5 12 0.26
6 31 0.67
7 3 0.07
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:14264 original size:207 final size:207
Alignment explanation
Indices: 13908--14495 Score: 989
Period size: 207 Copynumber: 2.8 Consensus size: 207
13898 ATCCGCTTCT
* * *
13908 CGAATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCGTCTATTGTTTCGACCTACTTCT
1 CGAATTTGGTTCACTTCTCAGTATCTCATCTGGAAGCTAACCGTCTATTGCTTCGACCTACTTCT
* * * *
13973 CTGTATCTCATCAAGAAGCTAGGGTTCGAAGATTTTGCTCGCTTTGAGCGTAAGCCCTGATTTGG
66 CGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAGCGTAGGCCCTGATTTGG
* * *
14038 TCTTCTTCTCAGTATCTCACTAGGAATATGACCGCGTCGTTTGTTTCAATTCGCTTCTCTGTATC
131 TCTTCTTCTCAGCATCTCACTAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTATC
*
14103 TTATCAGGAAGA
196 TCATCAGGAAGA
14115 CGAATTTGGTTCACTTCTCAGTATCTCATCTGGAAGCTAACCGTCTATTGCTTCGACCTACTTCT
1 CGAATTTGGTTCACTTCTCAGTATCTCATCTGGAAGCTAACCGTCTATTGCTTCGACCTACTTCT
* *
14180 CGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAACGTAGGTCCTGATTTGG
66 CGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAGCGTAGGCCCTGATTTGG
*
14245 TCTTCTTCTCAGCATCTCACTAGGAAGATGACCGCGTCGTTTGTTTCAATCCGTTTCTCTGTATC
131 TCTTCTTCTCAGCATCTCACTAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTATC
14310 TCATCAGGAAGA
196 TCATCAGGAAGA
*
14322 CGAAATTT-GTTCACTTCTCAGTATCTCATCTGGAAGCTAACCGTCTATTGCTTCGACCTGCTTC
1 CG-AATTTGGTTCACTTCTCAGTATCTCATCTGGAAGCTAACCGTCTATTGCTTCGACCTACTTC
* *
14386 TCGGGATCTCATCAGGAAGCTGAGGTTCGAAGATTTTGCTCGCTTTGAGCGTAGGCCCTGATTTG
65 TCGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAGCGTAGGCCCTGATTTG
* *
14451 GTCTTCTTCTCAGCCTCTCACTAAGAAGATGACCGCGTCGTTTGT
130 GTCTTCTTCTCAGCATCTCACTAGGAAGATGACCGCGTCGTTTGT
14496 GGGTATCGCA
Statistics
Matches: 359, Mismatches: 21, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
207 354 0.99
208 5 0.01
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (207 bp):
CGAATTTGGTTCACTTCTCAGTATCTCATCTGGAAGCTAACCGTCTATTGCTTCGACCTACTTCT
CGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAGCGTAGGCCCTGATTTGG
TCTTCTTCTCAGCATCTCACTAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTATC
TCATCAGGAAGA
Found at i:15719 original size:17 final size:17
Alignment explanation
Indices: 15697--15734 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
15687 ACTACAATAA
15697 ACCGATCATCATGGTAC
1 ACCGATCATCATGGTAC
15714 ACCGATCATCATGGTAC
1 ACCGATCATCATGGTAC
15731 ACCG
1 ACCG
15735 GTACGTCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (17 bp):
ACCGATCATCATGGTAC
Found at i:17542 original size:2 final size:2
Alignment explanation
Indices: 17535--17580 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
17525 GAATAGATTA
17535 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
17577 AT AT
1 AT AT
17581 TATTTAAGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18379 original size:17 final size:17
Alignment explanation
Indices: 18346--18379 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
18336 AGAAAAAAAG
18346 AAAAGAAAAAGGAGTGA
1 AAAAGAAAAAGGAGTGA
18363 AAAAGGAAAAAGG-GTGA
1 AAAA-GAAAAAGGAGTGA
18380 CCTTTCATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.32, T:0.06
Consensus pattern (17 bp):
AAAAGAAAAAGGAGTGA
Found at i:24486 original size:8 final size:8
Alignment explanation
Indices: 24475--24517 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
24465 CTTTTGTTTT
24475 TTTAATTA
1 TTTAATTA
24483 TTTAATTA
1 TTTAATTA
24491 TTTAATTA
1 TTTAATTA
24499 TTT--TTA
1 TTTAATTA
24505 TTT--TTA
1 TTTAATTA
24511 TTTAATT
1 TTTAATT
24518 GAATTACACA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.36
8 21 0.64
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTAATTA
Found at i:24884 original size:19 final size:20
Alignment explanation
Indices: 24857--24894 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
24847 AAGATTTTAA
*
24857 ATAAGTTTTTTT-TAATTTT
1 ATAACTTTTTTTATAATTTT
24876 ATAACTTTTTTTATAATTT
1 ATAACTTTTTTTATAATTT
24895 ATTAGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (20 bp):
ATAACTTTTTTTATAATTTT
Found at i:24905 original size:19 final size:18
Alignment explanation
Indices: 24883--24926 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
24873 TTTATAACTT
24883 TTTTTATAATTTATTAGAA
1 TTTTTATAATTT-TTAGAA
*
24902 TTTTTAT-ATTTTTATAA
1 TTTTTATAATTTTTAGAA
*
24919 TATTTATA
1 TTTTTATA
24927 TGTTTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 11 0.50
18 4 0.18
19 7 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTTATAATTTTTAGAA
Found at i:24924 original size:9 final size:9
Alignment explanation
Indices: 24883--24986 Score: 63
Period size: 9 Copynumber: 11.6 Consensus size: 9
24873 TTTATAACTT
24883 TTTTTATAA
1 TTTTTATAA
*
24892 TTTATTAGAA
1 TTT-TTATAA
24902 TTTTTAT-A
1 TTTTTATAA
24910 TTTTTATAA
1 TTTTTATAA
* *
24919 TATTTATATG
1 TTTTTATA-A
*
24929 TTTTTATTA
1 TTTTTATAA
*
24938 TTTTAATAAA
1 TTTTTAT-AA
* *
24948 TATATATCAA
1 TTTTTAT-AA
*
24958 TTTTAATAA
1 TTTTTATAA
24967 -TTTTAT--
1 TTTTTATAA
*
24973 TTTTTGTAA
1 TTTTTATAA
24982 TTTTT
1 TTTTT
24987 TAAATAAATT
Statistics
Matches: 70, Mismatches: 18, Indels: 14
0.69 0.18 0.14
Matches are distributed among these distances:
7 5 0.07
8 13 0.19
9 27 0.39
10 25 0.36
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:24932 original size:27 final size:27
Alignment explanation
Indices: 24902--24954 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
24892 TTTATTAGAA
* *
24902 TTTTTA-TATTTTTATAATATTTATATG
1 TTTTTATTATTTTAATAA-ATATATATG
24929 TTTTTATTATTTTAATAAATATATAT
1 TTTTTATTATTTTAATAAATATATAT
24955 CAATTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (27 bp):
TTTTTATTATTTTAATAAATATATATG
Found at i:24940 original size:17 final size:17
Alignment explanation
Indices: 24885--24932 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
24875 TATAACTTTT
* *
24885 TTTATAATTTATTAGAATT
1 TTTAT-ATTT-TTATAATA
24904 TTTATATTTTTATAATA
1 TTTATATTTTTATAATA
24921 TTTATATGTTTT
1 TTTATAT-TTTT
24933 TATTATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 13 0.50
18 8 0.31
19 5 0.19
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTATATTTTTATAATA
Found at i:24961 original size:29 final size:27
Alignment explanation
Indices: 24900--24971 Score: 65
Period size: 29 Copynumber: 2.6 Consensus size: 27
24890 AATTTATTAG
* *
24900 AATTTTTA-TATTTTTATAATATTTAT
1 AATTTTTATTATTTTAATAATATATAT
*
24926 ATGTTTTTATTATTTTAATAAATATATAT
1 A-ATTTTTATTATTTTAAT-AATATATAT
* *
24955 CAATTTTAATAATTTTA
1 -AATTTTTATTATTTTA
24972 TTTTTTGTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
26 1 0.03
27 6 0.17
28 8 0.22
29 20 0.56
30 1 0.03
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (27 bp):
AATTTTTATTATTTTAATAATATATAT
Found at i:35856 original size:20 final size:21
Alignment explanation
Indices: 35822--35861 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
35812 TTTTAATTTA
35822 TTTTTTTTTCATTCTCTTTTGC
1 TTTTTTTTT-ATTCTCTTTTGC
*
35844 TTTTTTTTT-TTCTGTTTT
1 TTTTTTTTTATTCTCTTTT
35862 TCTCTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.03, C:0.12, G:0.05, T:0.80
Consensus pattern (21 bp):
TTTTTTTTTATTCTCTTTTGC
Found at i:36166 original size:17 final size:16
Alignment explanation
Indices: 36142--36183 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
36132 CAAAATTAAA
36142 TTATAATTTTAT-TAT
1 TTATAATTTTATATAT
36157 TT-TAATAATTTATATAT
1 TTATAAT--TTTATATAT
36174 TTATAATTTT
1 TTATAATTTT
36184 TAAAAAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 4 0.17
15 2 0.09
16 8 0.35
17 5 0.22
18 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATAATTTTATATAT
Found at i:37009 original size:23 final size:23
Alignment explanation
Indices: 36983--37052 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
36973 CACAACTCTA
36983 TCTTTCATACTTAAGAGCTATAT
1 TCTTTCATACTTAAGAGCTATAT
* * * * *
37006 TC-TT--GACTTGCATAACTCTA-
1 TCTTTCATACTT-AAGAGCTATAT
37026 TCTTTCATACTTAAGAGCTATAT
1 TCTTTCATACTTAAGAGCTATAT
37049 TCTT
1 TCTT
37053 GACTTGCATA
Statistics
Matches: 32, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
20 6 0.19
21 8 0.25
22 8 0.25
23 10 0.31
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (23 bp):
TCTTTCATACTTAAGAGCTATAT
Found at i:37024 original size:43 final size:43
Alignment explanation
Indices: 36976--37074 Score: 198
Period size: 43 Copynumber: 2.3 Consensus size: 43
36966 TATATAACAC
36976 AACTCTATCTTTCATACTTAAGAGCTATATTCTTGACTTGCAT
1 AACTCTATCTTTCATACTTAAGAGCTATATTCTTGACTTGCAT
37019 AACTCTATCTTTCATACTTAAGAGCTATATTCTTGACTTGCAT
1 AACTCTATCTTTCATACTTAAGAGCTATATTCTTGACTTGCAT
37062 AACTCTATCTTTC
1 AACTCTATCTTTC
37075 CGTTCATATC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.42
Consensus pattern (43 bp):
AACTCTATCTTTCATACTTAAGAGCTATATTCTTGACTTGCAT
Found at i:37069 original size:23 final size:23
Alignment explanation
Indices: 37000--37069 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
36990 TACTTAAGAG
37000 CTATATTCTTGACTTGCATAACT
1 CTATATTCTTGACTTGCATAACT
* * *
37023 CTATCTTTCAT-ACTT--A-AGA-G
1 CTAT-ATTCTTGACTTGCATA-ACT
37043 CTATATTCTTGACTTGCATAACT
1 CTATATTCTTGACTTGCATAACT
37066 CTAT
1 CTAT
37070 CTTTCCGTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 4 0.12
20 9 0.26
21 2 0.06
22 2 0.06
23 13 0.38
24 4 0.12
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.43
Consensus pattern (23 bp):
CTATATTCTTGACTTGCATAACT
Found at i:40053 original size:23 final size:23
Alignment explanation
Indices: 40027--40094 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
40017 TTCGTTTAAC
*
40027 TTAATCGAACATGCTCACGAACA
1 TTAATCGAACATGTTCACGAACA
* * * *
40050 TTAAACAAACATATTCATGAACA
1 TTAATCGAACATGTTCACGAACA
* *
40073 TATAATTGAACACGTTCACGAA
1 T-TAATCGAACATGTTCACGAA
40095 TAATGTTAAT
Statistics
Matches: 33, Mismatches: 11, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
23 19 0.58
24 14 0.42
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:40210 original size:12 final size:12
Alignment explanation
Indices: 40193--40237 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
40183 ATAAATGAAC
40193 TATAAACGAGCT
1 TATAAACGAGCT
*
40205 TATAAACGAGCC
1 TATAAACGAGCT
* *
40217 AACAAACGAGCT
1 TATAAACGAGCT
*
40229 TTTAAACGA
1 TATAAACGA
40238 ACTTGTTCGT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (12 bp):
TATAAACGAGCT
Found at i:41692 original size:18 final size:16
Alignment explanation
Indices: 41661--41704 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
41651 GGTTTAGAGT
*
41661 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
41678 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
41692 TTAAAAATTTATT
1 TTAAAAATTTATT
41705 CTCATTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:41844 original size:31 final size:30
Alignment explanation
Indices: 41809--41896 Score: 90
Period size: 29 Copynumber: 2.9 Consensus size: 30
41799 GTGACCACTT
*
41809 CGTAACAAAATACTAACATAAGTGACTAAAA
1 CGTAAC-AAATACAAACATAAGTGACTAAAA
* *
41840 CGTAAC-ATTGCAAACATAAGTGACTAAAA
1 CGTAACAAATACAAACATAAGTGACTAAAA
* *
41869 TGTAACCTAAA-ACAAACAAAAGTGACTA
1 CGTAA-C-AAATACAAACATAAGTGACTA
41897 TTTTTGTAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
29 24 0.51
30 1 0.02
31 21 0.45
32 1 0.02
ACGTcount: A:0.52, C:0.17, G:0.11, T:0.19
Consensus pattern (30 bp):
CGTAACAAATACAAACATAAGTGACTAAAA
Found at i:42669 original size:29 final size:28
Alignment explanation
Indices: 42607--42676 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 28
42597 AATTGTTTAT
*
42607 ATTTTTATAATTTTTAGAAAATTAAATTA
1 ATTTTTATTATTTTTAG-AAATTAAATTA
* *
42636 TTTTTTATTATTTTTAG-GATTAAAGTATA
1 ATTTTTATTATTTTTAGAAATTAAA-T-TA
42665 ATTTTTATTATT
1 ATTTTTATTATT
42677 AATTTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 6 0.17
28 1 0.03
29 28 0.80
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.59
Consensus pattern (28 bp):
ATTTTTATTATTTTTAGAAATTAAATTA
Found at i:42808 original size:5 final size:5
Alignment explanation
Indices: 42784--42825 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
42774 TGTAGATAAT
* *
42784 ATATA A-ATA ATATA ACTATA ATATA ATATC ATATT ATATA AT
1 ATATA ATATA ATATA A-TATA ATATA ATATA ATATA ATATA AT
42826 TGTATGATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 4 0.12
5 23 0.72
6 5 0.16
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:44687 original size:12 final size:12
Alignment explanation
Indices: 44672--44709 Score: 67
Period size: 12 Copynumber: 3.1 Consensus size: 12
44662 CTTCCCCTTC
44672 TTCTTTCTTTTT
1 TTCTTTCTTTTT
44684 TTCTTTCTCTTTT
1 TTCTTTCT-TTTT
44697 TTCTTTCTTTTT
1 TTCTTTCTTTTT
44709 T
1 T
44710 CCTTCAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 13 0.52
13 12 0.48
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTCTTTCTTTTT
Found at i:44687 original size:15 final size:14
Alignment explanation
Indices: 44677--44709 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
44667 CCTTCTTCTT
44677 TCTTTTTTTCTTTC
1 TCTTTTTTTCTTTC
44691 TC-TTTTTTCTTTC
1 TCTTTTTTTCTTTC
44704 T-TTTTT
1 TCTTTTT
44710 CCTTCAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 16 0.89
14 2 0.11
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TCTTTTTTTCTTTC
Found at i:44687 original size:24 final size:24
Alignment explanation
Indices: 44660--44714 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
44650 TTCCTTCTCC
44660 TTCTTCCCCTTCTTCTTTCTTTTT
1 TTCTTCCCCTTCTTCTTTCTTTTT
* * *
44684 TTCTTTCTCTTTTTTCTTTCTTTTT
1 TTC-TTCCCCTTCTTCTTTCTTTTT
*
44709 TCCTTC
1 TTCTTC
44715 AATTTTCGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (24 bp):
TTCTTCCCCTTCTTCTTTCTTTTT
Found at i:44949 original size:11 final size:10
Alignment explanation
Indices: 44929--44953 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
44919 TTAAATATAT
44929 AAAAATAAAA
1 AAAAATAAAA
44939 AAAAATAAAA
1 AAAAATAAAA
44949 AAAAA
1 AAAAA
44954 CACGTGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:51760 original size:21 final size:21
Alignment explanation
Indices: 51734--51781 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
51724 AAATGATAGC
* *
51734 AAAACAGTGGTAAAAAATGAA
1 AAAACAGTAGCAAAAAATGAA
*
51755 AAAACAGTAGCAAAACATGAA
1 AAAACAGTAGCAAAAAATGAA
51776 AAAACA
1 AAAACA
51782 ACAATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.65, C:0.10, G:0.15, T:0.10
Consensus pattern (21 bp):
AAAACAGTAGCAAAAAATGAA
Found at i:52246 original size:16 final size:17
Alignment explanation
Indices: 52225--52260 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
52215 TGAATTGATG
52225 AAATCT-AATATTTTAA
1 AAATCTCAATATTTTAA
*
52241 AAATCTCCATATTTTAA
1 AAATCTCAATATTTTAA
52258 AAA
1 AAA
52261 AATTTAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATCTCAATATTTTAA
Found at i:56655 original size:22 final size:23
Alignment explanation
Indices: 56612--56660 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
56602 TTTGGCATAA
*
56612 TTTATCACTTAATGTTTATATAT
1 TTTATCAATTAATGTTTATATAT
* *
56635 TTTATCAATTTAT-TTTTTATAT
1 TTTATCAATTAATGTTTATATAT
56657 TTTA
1 TTTA
56661 AAATTAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTATCAATTAATGTTTATATAT
Found at i:63365 original size:3 final size:3
Alignment explanation
Indices: 63359--63385 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
63349 GATGATGATG
63359 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
63386 TTGGGAGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:65785 original size:2 final size:2
Alignment explanation
Indices: 65780--65812 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
65770 TCTCAATTAG
65780 AT AT AT 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 AT AT AT A
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.