Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011791.1 Kokia drynarioides strain JFW-HI SEQ_126786, 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: 172411
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 45 characters in sequence are not A, C, G, or T
Found at i:2375 original size:14 final size:12
Alignment explanation
Indices: 2347--2372 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2337 TATAAAAAGC
2347 TTAAAACTATTT
1 TTAAAACTATTT
2359 TTAAAACTATTT
1 TTAAAACTATTT
2371 TT
1 TT
2373 TTATATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (12 bp):
TTAAAACTATTT
Found at i:2503 original size:2 final size:2
Alignment explanation
Indices: 2496--2526 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2486 TTAAAATTAT
2496 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2527 TAAATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6808 original size:89 final size:89
Alignment explanation
Indices: 6709--6877 Score: 295
Period size: 89 Copynumber: 1.9 Consensus size: 89
6699 AATAAAATTT
*
6709 TGTTTCTTTCTCAATTTCA-ATCACAAATTAAAAAAGACTTTCCATCAAAGTTTCACTTTAATAA
1 TGTTTCTTTCTCAATTT-AGATCACAAATTAAAAAAGACTTTCCATCAAAATTTCACTTTAATAA
6773 AAAAGATCGTAAGAATGCTAGATTC
65 AAAAGATCGTAAGAATGCTAGATTC
*
6798 TGTTTCTTTCTTAATTTAGATCACAAATTAAAAAAGACTTTCCATCAAAATTTCACTTTAATAAA
1 TGTTTCTTTCTCAATTTAGATCACAAATTAAAAAAGACTTTCCATCAAAATTTCACTTTAATAAA
*
6863 AAAGATTGTAAGAAT
66 AAAGATCGTAAGAAT
6878 ACTAATGGGT
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
88 1 0.01
89 75 0.99
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (89 bp):
TGTTTCTTTCTCAATTTAGATCACAAATTAAAAAAGACTTTCCATCAAAATTTCACTTTAATAAA
AAAGATCGTAAGAATGCTAGATTC
Found at i:7450 original size:15 final size:12
Alignment explanation
Indices: 7420--7444 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7410 AAATTTAAAT
7420 AAAAATTATTTA
1 AAAAATTATTTA
7432 AAAAATTATTTA
1 AAAAATTATTTA
7444 A
1 A
7445 TCAAAATTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAAATTATTTA
Found at i:8212 original size:29 final size:28
Alignment explanation
Indices: 8179--8247 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 28
8169 AGTAAAAATA
8179 TTTTATAATAGTCAAAATTA-AATTGTAAT
1 TTTTATAATAGT-AAAATTATAATT-TAAT
* *
8208 TTTTATAAGAGTAAAATTATAATTTTAT
1 TTTTATAATAGTAAAATTATAATTTAAT
8236 TATTT-TAATAGT
1 T-TTTATAATAGT
8248 TTATATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 17 0.49
29 18 0.51
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.49
Consensus pattern (28 bp):
TTTTATAATAGTAAAATTATAATTTAAT
Found at i:10433 original size:13 final size:14
Alignment explanation
Indices: 10409--10439 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
10399 GTCGGATCGG
10409 TTGGGCTTGAAGCT
1 TTGGGCTTGAAGCT
10423 TTGGG-TTGAAGCT
1 TTGGGCTTGAAGCT
10436 TTGG
1 TTGG
10440 CTAAACGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.13, C:0.10, G:0.39, T:0.39
Consensus pattern (14 bp):
TTGGGCTTGAAGCT
Found at i:20020 original size:40 final size:40
Alignment explanation
Indices: 19954--20576 Score: 508
Period size: 40 Copynumber: 15.9 Consensus size: 40
19944 TGAACAATGG
*
19954 TTTCAATCTGCCCTATGATTGGGGTAAGAGATTGGATGAT
1 TTTCAATCTGCCCCATGATTGGGGTAAGAGATTGGATGAT
* * * *** * *
19994 TTTTAATTTGCCCCAAGATCAAGGTAAGAGATTAGATGGT
1 TTTCAATCTGCCCCATGATTGGGGTAAGAGATTGGATGAT
* * ***
20034 TTTCAATCTGTCCTATGACCAGGGTAAGAGATTGGATGAT
1 TTTCAATCTGCCCCATGATTGGGGTAAGAGATTGGATGAT
*
20074 TTTCAATTTGCCCCATGATTGGGGTAAGAGATTGG-TG-T
1 TTTCAATCTGCCCCATGATTGGGGTAAGAGATTGGATGAT
* ** *
20112 TTTCAATCTACCTTATGATTGGGGTAAGAGATTGAATGAT
1 TTTCAATCTGCCCCATGATTGGGGTAAGAGATTGGATGAT
* ** * *
20152 TTTCAATCTGCCCTATGATTAAGGTAAGAGATTAGATG-G
1 TTTCAATCTGCCCCATGATTGGGGTAAGAGATTGGATGAT
* * * *
20191 CTACAATCTGCCCTATAATTGGGGTAAGAGATTGG-T-AT
1 TTTCAATCTGCCCCATGATTGGGGTAAGAGATTGGATGAT
* * *
20229 TTTCAATTTGCCTCATGATTAGGGTAAGAGATTGGATGA-
1 TTTCAATCTGCCCCATGATTGGGGTAAGAGATTGGATGAT
* * * * *
20268 CTGCAATTTACACCATGATTGGGGTAAGAGATTGG-TG-T
1 TTTCAATCTGCCCCATGATTGGGGTAAGAGATTGGATGAT
* * * *** * *
20306 TTTTAATCTGCCCTATGATCGACATAAGAGATTAGATGGT
1 TTTCAATCTGCCCCATGATTGGGGTAAGAGATTGGATGAT
* *
20346 TTTCAATCTTCCCCATGATCGGGGTAAGAGATTGG-T-AT
1 TTTCAATCTGCCCCATGATTGGGGTAAGAGATTGGATGAT
* *
20384 TTTTAATCTACCCCATGATTGGGGTAAGAGATTGGAGTG-T
1 TTTCAATCTGCCCCATGATTGGGGTAAGAGATTGGA-TGAT
* * * *
20424 CTTCAATCTACCCTC-TAATTAGGGTAAGAGATTGGAT--T
1 TTTCAATCTGCCC-CATGATTGGGGTAAGAGATTGGATGAT
* *
20462 TTTCAATCTGCCCCATGATCGAGGTAAGAGATTGG-TG-T
1 TTTCAATCTGCCCCATGATTGGGGTAAGAGATTGGATGAT
* ** *
20500 GTCTTTAATCTGCCCTTTGATCGGGGTAAGAGATTGG-TG-T
1 -T-TTCAATCTGCCCCATGATTGGGGTAAGAGATTGGATGAT
* * * *
20540 GCCTTCAATCTGCCCCATGGTCGGGGTAAGATATTGG
1 --TTTCAATCTGCCCCATGATTGGGGTAAGAGATTGG
20577 TGTGTCTTCA
Statistics
Matches: 466, Mismatches: 100, Indels: 34
0.78 0.17 0.06
Matches are distributed among these distances:
37 2 0.00
38 147 0.32
39 68 0.15
40 248 0.53
41 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (40 bp):
TTTCAATCTGCCCCATGATTGGGGTAAGAGATTGGATGAT
Found at i:20156 original size:78 final size:78
Alignment explanation
Indices: 19954--20656 Score: 502
Period size: 78 Copynumber: 9.0 Consensus size: 78
19944 TGAACAATGG
* * * * *
19954 TTTCAATCTGCCCTATGATTGGGGTAAGAGATTGGATGATTTTTAATTTGCCCCAAGATCAAGGT
1 TTTCAATCTACCCTATGATTGGGGTAAGAGATT-GATGATTTTCAATCTGCCCCATGATCGAGGT
*
20019 AAGAGATTAGATGGT
65 AAGAGATTAGGT-GT
** *** * * *
20034 TTTCAATCTGTCCTATGACCAGGGTAAGAGATTGGATGATTTTCAATTTGCCCCATGATTGGGGT
1 TTTCAATCTACCCTATGATTGGGGTAAGAGATT-GATGATTTTCAATCTGCCCCATGATCGAGGT
20099 AAGAGATT-GGTGT
65 AAGAGATTAGGTGT
* * **
20112 TTTCAATCTACCTTATGATTGGGGTAAGAGATTGAATGATTTTCAATCTGCCCTATGATTAAGGT
1 TTTCAATCTACCCTATGATTGGGGTAAGAGATTG-ATGATTTTCAATCTGCCCCATGATCGAGGT
* *
20177 AAGAGATTAGATGG
65 AAGAGATTAGGTGT
* * * * * * * *
20191 CTACAATCTGCCCTATAATTGGGGTAAGAGATTGGT-ATTTTCAATTTGCCTCATGAT-TAGGGT
1 TTTCAATCTACCCTATGATTGGGGTAAGAGATTGATGATTTTCAATCTGCCCCATGATCGA-GGT
*
20254 AAGAGATT-GGATGA
65 AAGAGATTAGG-TGT
* * * * * * **
20268 CTGCAATTTACACC-ATGATTGGGGTAAGAGATTGGTG-TTTTTAATCTGCCCTATGATCGACAT
1 TTTCAATCTAC-CCTATGATTGGGGTAAGAGATTGATGATTTTCAATCTGCCCCATGATCGAGGT
*
20331 AAGAGATTAGATGGT
65 AAGAGATTAGGT-GT
* * * * * * * *
20346 TTTCAATCTTCCCCATGATCGGGGTAAGAGATTGGT-ATTTTTAATCTACCCCATGATTGGGGTA
1 TTTCAATCTACCCTATGATTGGGGTAAGAGATTGATGATTTTCAATCTGCCCCATGATCGAGGTA
*
20410 AGAGATTGGAGTGT
66 AGAGATTAG-GTGT
* * * *
20424 CTTCAATCTACCCTCTAATTAGGGTAAGAGATTG--GATTTTTCAATCTGCCCCATGATCGAGGT
1 TTTCAATCTACCCTATGATTGGGGTAAGAGATTGATGA-TTTTCAATCTGCCCCATGATCGAGGT
20487 AAGAGATT-GGTGT
65 AAGAGATTAGGTGT
* * * * * * * *
20500 GTCTTTAATCTGCCCTTTGATCGGGGTAAGAGATTGGTG-TGCCTTCAATCTGCCCCATGGTCGG
1 -T-TTCAATCTACCCTATGATTGGGGTAAGAGATTGATGAT--TTTCAATCTGCCCCATGATCGA
*
20564 GGTAAGATATT-GGTGT
62 GGTAAGAGATTAGGTGT
* * * * * * * * * *
20580 GTCTTCAATTTGCCCTCTAACTAGGGTAAAAGATTG--GATGCTTCAATTTACCCCATGATC-AG
1 -T-TTCAATCTACCCTATGATTGGGGTAAGAGATTGATGAT-TTTCAATCTGCCCCATGATCGAG
20642 AGTAAGAGATT-GGTG
63 -GTAAGAGATTAGGTG
20657 CATAGCTTCG
Statistics
Matches: 505, Mismatches: 96, Indels: 46
0.78 0.15 0.07
Matches are distributed among these distances:
76 6 0.01
77 92 0.18
78 244 0.48
79 36 0.07
80 127 0.25
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (78 bp):
TTTCAATCTACCCTATGATTGGGGTAAGAGATTGATGATTTTCAATCTGCCCCATGATCGAGGTA
AGAGATTAGGTGT
Found at i:20178 original size:118 final size:116
Alignment explanation
Indices: 19955--20594 Score: 540
Period size: 118 Copynumber: 5.4 Consensus size: 116
19945 GAACAATGGT
* * * * **
19955 TTCAATCTGCCCTATGATTGGGGTAAGAGATTGGATGATTTTTAATTTGCCCCAAGATCAAGGTA
1 TTCAATCTGCCCCATGATTGGGGTAAGAGATTGG-TG-TTTTCAATCTGCCCCATGATCGGGGTA
* * *** *
20020 AGAGATTAGATGGTTTTCAATCTGTCCTATGACCAGGGTAAGAGATTGGATGATT
64 AGAGATT-GATGATTTTCAATCTGCCCTATGATTGGGGTAAGAGATTGGATG-TC
* * ** *
20075 TTCAATTTGCCCCATGATTGGGGTAAGAGATTGGTGTTTTCAATCTACCTTATGATTGGGGTAAG
1 TTCAATCTGCCCCATGATTGGGGTAAGAGATTGGTGTTTTCAATCTGCCCCATGATCGGGGTAAG
** * *
20140 AGATTGAATGATTTTCAATCTGCCCTATGATTAAGGTAAGAGATTAGATGGC
66 AGATTG-ATGATTTTCAATCTGCCCTATGATTGGGGTAAGAGATTGGATGTC
* * * * * * **
20192 TACAATCTGCCCTATAATTGGGGTAAGAGATTGGTATTTTCAATTTGCCTCATGATTAGGGTAAG
1 TTCAATCTGCCCCATGATTGGGGTAAGAGATTGGTGTTTTCAATCTGCCCCATGATCGGGGTAAG
* * * * *
20257 AGATTGGATGA-CTGCAATTTACACC-ATGATTGGGGTAAGAGATTGG-TGTT
66 AGATT-GATGATTTTCAATCTGC-CCTATGATTGGGGTAAGAGATTGGATGTC
* * * *** * *
20307 TTTAATCTGCCCTATGATCGACATAAGAGATTAGATGGTTTTCAATCTTCCCCATGATCGGGGTA
1 TTCAATCTGCCCCATGATTGGGGTAAGAGATT-GGT-GTTTTCAATCTGCCCCATGATCGGGGTA
* * * *
20372 AGAGATTGGT-ATTTTTAATCTACCCCATGATTGGGGTAAGAGATTGGAGTGTC
64 AGAGATTGATGATTTTCAATCTGCCCTATGATTGGGGTAAGAGATTGGA-TGTC
* * * *
20425 TTCAATCTACCCTC-TAATTAGGGTAAGAGATTGGAT-TTTTCAATCTGCCCCATGATCGAGGTA
1 TTCAATCTGCCC-CATGATTGGGGTAAGAGATTGG-TGTTTTCAATCTGCCCCATGATCGGGGTA
* * * *
20488 AGAGATTGGTG-TGTCTTTAATCTGCCCTTTGATCGGGGTAAGAGATTGG-TGTGCC
64 AGAGATTGATGAT-T-TTCAATCTGCCCTATGATTGGGGTAAGAGATTGGATGT--C
* * * *
20543 TTCAATCTGCCCCATGGTCGGGGTAAGATATTGGTGTGTCTTCAATTTGCCC
1 TTCAATCTGCCCCATGATTGGGGTAAGAGATTGGTGT-T-TTCAATCTGCCC
20595 TCTAACTAGG
Statistics
Matches: 420, Mismatches: 80, Indels: 40
0.78 0.15 0.07
Matches are distributed among these distances:
115 30 0.07
116 96 0.23
117 101 0.24
118 147 0.35
119 3 0.01
120 43 0.10
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (116 bp):
TTCAATCTGCCCCATGATTGGGGTAAGAGATTGGTGTTTTCAATCTGCCCCATGATCGGGGTAAG
AGATTGATGATTTTCAATCTGCCCTATGATTGGGGTAAGAGATTGGATGTC
Found at i:20652 original size:38 final size:39
Alignment explanation
Indices: 19955--20654 Score: 488
Period size: 40 Copynumber: 17.9 Consensus size: 39
19945 GAACAATGGT
* * *
19955 TTCAATCTGCCCTATGATTGGGGTAAGAGATTGGATGATT
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATG-TC
* * * ** * *
19995 TTTAATTTGCCCCAAGATCAAGGTAAGAGATTAGATGGTT
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT-GTC
* * * * *
20035 TTCAATCTGTCCTATGACCAGGGTAAGAGATTGGATGATT
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATG-TC
* * *
20075 TTCAATTTGCCCCATGATTGGGGTAAGAGATTGG-TGTT
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGTC
* ** * * *
20113 TTCAATCTACCTTATGATTGGGGTAAGAGATTGAATGATT
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATG-TC
* *** * *
20153 TTCAATCTGCCCTATGATTAAGGTAAGAGATTAGATGGC
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGTC
* * * *
20192 TACAATCTGCCCTATAATTGGGGTAAGAGATTGGTAT-T-
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGG-ATGTC
* * ** *
20230 TTCAATTTGCCTCATGATTAGGGTAAGAGATTGGATGAC
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGTC
* * * * * *
20269 TGCAATTTACACCATGATTGGGGTAAGAGATTGG-TGTT
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGTC
* * *** * *
20307 TTTAATCTGCCCTATGATCGACATAAGAGATTAGATGGTT
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT-GTC
*
20347 TTCAATCTTCCCCATGATCGGGGTAAGAGATTGGTAT-T-
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGG-ATGTC
* * *
20385 TTTAATCTACCCCATGATTGGGGTAAGAGATTGGAGTGTC
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGA-TGTC
* * ** *
20425 TTCAATCTACCCTC-TAATTAGGGTAAGAGATTGGAT-TT
1 TTCAATCTGCCC-CATGATCGGGGTAAGAGATTGGATGTC
* *
20463 TTCAATCTGCCCCATGATCGAGGTAAGAGATTGGTGTGTC
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGG-ATGTC
* **
20503 TTTAATCTGCCCTTTGATCGGGGTAAGAGATTGG-TGTGCC
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGT--C
* * *
20543 TTCAATCTGCCCCATGGTCGGGGTAAGATATTGGTGTGTC
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGG-ATGTC
* * * *
20583 TTCAATTTGCCCTC-T-AACTAGGGTAAAAGATTGGATG-C
1 TTCAATCTGCCC-CATGATC-GGGGTAAGAGATTGGATGTC
* * * *
20621 TTCAATTTACCCCATGATCAGAGTAAGAGATTGG
1 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
20655 TGCATAGCTT
Statistics
Matches: 528, Mismatches: 107, Indels: 52
0.77 0.16 0.08
Matches are distributed among these distances:
37 5 0.01
38 173 0.33
39 73 0.14
40 269 0.51
41 5 0.01
42 3 0.01
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (39 bp):
TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGTC
Found at i:21024 original size:50 final size:50
Alignment explanation
Indices: 20972--21212 Score: 180
Period size: 50 Copynumber: 4.9 Consensus size: 50
20962 TCTCATCTTG
* * **
20972 TCTTCTAAGGTACCGGGTTCGTCATTATGGTCTCAACCTTTCCCTTCATG
1 TCTTCTAAGGTACCGGGTTCGTCATTACGGCCTCAACCTTTCCCTTCACA
* * * ** * *
21022 TCTTC-ATGGTACAGGGTCCACCGTTACGGCCTCAACCTTTCCCGTCACA
1 TCTTCTAAGGTACCGGGTTCGTCATTACGGCCTCAACCTTTCCCTTCACA
** * *
21071 TCTTCTAATATACCGGGTTCGTGATTGCGGCCTCAACCTTTCCCTTCACA
1 TCTTCTAAGGTACCGGGTTCGTCATTACGGCCTCAACCTTTCCCTTCACA
* * ** * **** * **
21121 TCATCTAAGGTACCAGGTTCACCCTTGTTTCCTCAACATTTCCCTTCTTA
1 TCTTCTAAGGTACCGGGTTCGTCATTACGGCCTCAACCTTTCCCTTCACA
* * * * *
21171 TCTTC-ATGATATCGGGTTCGCCATTGCGGCCTCAACCTTTCC
1 TCTTCTAAGGTACCGGGTTCGTCATTACGGCCTCAACCTTTCC
21213 TATTACATCT
Statistics
Matches: 143, Mismatches: 47, Indels: 3
0.74 0.24 0.02
Matches are distributed among these distances:
49 65 0.45
50 78 0.55
ACGTcount: A:0.17, C:0.32, G:0.16, T:0.34
Consensus pattern (50 bp):
TCTTCTAAGGTACCGGGTTCGTCATTACGGCCTCAACCTTTCCCTTCACA
Found at i:22193 original size:11 final size:10
Alignment explanation
Indices: 22179--22225 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 10
22169 CTCTCCTCTT
22179 TTTTTTGTTTC
1 TTTTTT-TTTC
22190 TTTTTTTTGTC
1 TTTTTTTT-TC
22201 TTTTCTTTTTC
1 TTTT-TTTTTC
*
22212 -TTTTTCTTC
1 TTTTTTTTTC
22221 TTTTT
1 TTTTT
22226 AGGTGAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
9 5 0.16
10 9 0.28
11 14 0.44
12 4 0.12
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:22210 original size:16 final size:13
Alignment explanation
Indices: 22175--22199 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22165 CGACCTCTCC
22175 TCTTTTTTTTGTT
1 TCTTTTTTTTGTT
22188 TCTTTTTTTTGT
1 TCTTTTTTTTGT
22200 CTTTTCTTTT
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:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (13 bp):
TCTTTTTTTTGTT
Found at i:23100 original size:18 final size:18
Alignment explanation
Indices: 23077--23118 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
23067 TGCTTTATTT
23077 TCTTTTCTTCTTC-TTCT-C
1 TCTTTT-TT-TTCTTTCTCC
23095 TCTTTTTTTTCTTTCTCC
1 TCTTTTTTTTCTTTCTCC
23113 TCTTTT
1 TCTTTT
23119 AATAGTGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.14
17 6 0.27
18 13 0.59
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (18 bp):
TCTTTTTTTTCTTTCTCC
Found at i:28764 original size:20 final size:18
Alignment explanation
Indices: 28732--28786 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
28722 GCAATAAAAA
*
28732 GGTCTCAGGCAGAGGAGAG
1 GGTCTCGGGCAGAGGA-AG
* *
28751 GTTTCTTGGGCAGAGGAAG
1 G-GTCTCGGGCAGAGGAAG
28770 GGTCTCGGGCAGAGGAA
1 GGTCTCGGGCAGAGGAA
28787 ACATCTCGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 14 0.47
19 4 0.13
20 12 0.40
ACGTcount: A:0.24, C:0.15, G:0.45, T:0.16
Consensus pattern (18 bp):
GGTCTCGGGCAGAGGAAG
Found at i:28793 original size:18 final size:18
Alignment explanation
Indices: 28758--28796 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
28748 GAGGTTTCTT
***
28758 GGGCAGAGGAAGGGTCTC
1 GGGCAGAGGAAACATCTC
28776 GGGCAGAGGAAACATCTC
1 GGGCAGAGGAAACATCTC
28794 GGG
1 GGG
28797 AGTCAAAGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.18, G:0.46, T:0.10
Consensus pattern (18 bp):
GGGCAGAGGAAACATCTC
Found at i:36204 original size:16 final size:17
Alignment explanation
Indices: 36183--36214 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
36173 GAAGAAGCTA
36183 CAAGAGAAAAA-AAAAG
1 CAAGAGAAAAAGAAAAG
36199 CAAGAGAAAAAGAAAA
1 CAAGAGAAAAAGAAAA
36215 AGAAGAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.75, C:0.06, G:0.19, T:0.00
Consensus pattern (17 bp):
CAAGAGAAAAAGAAAAG
Found at i:36216 original size:18 final size:17
Alignment explanation
Indices: 36183--36230 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
36173 GAAGAAGCTA
36183 CAAGAGAAAA-AAAAAG
1 CAAGAGAAAAGAAAAAG
36199 CAAGAGAAAAAGAAAAAG
1 CAAGAG-AAAAGAAAAAG
36217 -AAGAAGGAAAAGAA
1 CAAG-A-GAAAAGAA
36231 GAGGAGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.21
17 7 0.25
18 14 0.50
19 1 0.04
ACGTcount: A:0.73, C:0.04, G:0.23, T:0.00
Consensus pattern (17 bp):
CAAGAGAAAAGAAAAAG
Found at i:37290 original size:7 final size:6
Alignment explanation
Indices: 37268--37320 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
37258 TCAAACGCAT
**
37268 AAAGAA AAAGAA AAA-AA TGA-AA AAAGAA AAA-AA AAAGAA AAA-AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
37312 AAAGAA AAA
1 AAAGAA AAA
37321 AATATATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 16 0.40
6 24 0.60
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:37290 original size:8 final size:7
Alignment explanation
Indices: 37268--37321 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
37258 TCAAACGCAT
37268 AAAG-AA
1 AAAGAAA
37274 AAAGAAAA
1 AAAG-AAA
37282 AAATGAAA
1 AAA-GAAA
37290 AAAGAAA
1 AAAGAAA
*
37297 AAAAAAA
1 AAAGAAA
*
37304 GAAAAAAA
1 -AAAGAAA
37312 AAAGAAA
1 AAAGAAA
37319 AAA
1 AAA
37322 ATATATATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
6 4 0.10
7 19 0.45
8 18 0.43
9 1 0.02
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (7 bp):
AAAGAAA
Found at i:37301 original size:11 final size:11
Alignment explanation
Indices: 37268--37322 Score: 76
Period size: 11 Copynumber: 5.0 Consensus size: 11
37258 TCAAACGCAT
37268 AAAGAAAAAGAA
1 AAAGAAAAA-AA
**
37280 AAA-AATGAAA
1 AAAGAAAAAAA
37290 AAAGAAAAAAA
1 AAAGAAAAAAA
37301 AAAGAAAAAAA
1 AAAGAAAAAAA
37312 AAAGAAAAAAA
1 AAAGAAAAAAA
37323 TATATATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
10 5 0.13
11 30 0.79
12 3 0.08
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:41923 original size:15 final size:15
Alignment explanation
Indices: 41886--41934 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
41876 TCTTGTAGTT
* *
41886 TTTATTTAATTTCAA
1 TTTATTTTATTTTAA
*
41901 TTTATTTTATTTTAC
1 TTTATTTTATTTTAA
41916 TTTATTTTTATTTTTAA
1 TTTA-TTTTA-TTTTAA
41933 TT
1 TT
41935 CACTCTAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 16 0.57
16 5 0.18
17 7 0.25
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATTTTATTTTAA
Found at i:42119 original size:15 final size:15
Alignment explanation
Indices: 42099--42131 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
42089 GCATTTAATT
42099 TTTAGTTGTTATTTA
1 TTTAGTTGTTATTTA
42114 TTTAGTTGTTATTTA
1 TTTAGTTGTTATTTA
42129 TTT
1 TTT
42132 TCGTGACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.70
Consensus pattern (15 bp):
TTTAGTTGTTATTTA
Found at i:42401 original size:20 final size:20
Alignment explanation
Indices: 42365--42402 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42355 ACATATTTTC
*
42365 TTTTATTTTTTATTTATTCA
1 TTTTATTTTTTAGTTATTCA
42385 TTTTATTATTTT-GTTATT
1 TTTTATT-TTTTAGTTATT
42403 TTTATGCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTATTTTTTAGTTATTCA
Found at i:43595 original size:21 final size:22
Alignment explanation
Indices: 43551--43593 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
43541 AGTTATCCCC
*
43551 TAATTTTAATTAAAAAATTATT
1 TAATTTCAATTAAAAAATTATT
43573 TAATTTCAA-TAAAAAA-TATT
1 TAATTTCAATTAAAAAATTATT
43593 T
1 T
43594 TACTCTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 7 0.35
22 8 0.40
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATTTCAATTAAAAAATTATT
Found at i:50472 original size:17 final size:15
Alignment explanation
Indices: 50450--50483 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
50440 ACTCTAAAAA
50450 TTTAAAAATATATATTT
1 TTTAAAAA-AT-TATTT
50467 TTTAAAAAATTATTT
1 TTTAAAAAATTATTT
50482 TT
1 TT
50484 AGTCGTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 2 0.12
17 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAAAAAATTATTT
Found at i:53382 original size:23 final size:23
Alignment explanation
Indices: 53356--53415 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
53346 TTTATTAACA
53356 AATATTTCAATTAAATAT-TTAAT
1 AATATTTCAATTAAAT-TGTTAAT
*
53379 AATATTTTCAA-TATATTGTTAAT
1 AATA-TTTCAATTAAATTGTTAAT
53402 AA-ATATTCAATTAA
1 AATAT-TTCAATTAA
53416 TTCATAAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
21 1 0.03
22 7 0.23
23 17 0.55
24 6 0.19
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (23 bp):
AATATTTCAATTAAATTGTTAAT
Found at i:57234 original size:16 final size:16
Alignment explanation
Indices: 57213--57243 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
57203 TTGTGGATCC
57213 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
57229 CATTTTATCTTTATT
1 CATTTTACCTTTATT
57244 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:60206 original size:16 final size:15
Alignment explanation
Indices: 60180--60214 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
60170 TCAGTCACAT
*
60180 GAAAAAAAAGAAGAA
1 GAAAAAAAAGAAAAA
60195 GAAAAGAAAAGAAAAA
1 GAAAA-AAAAGAAAAA
60211 GAAA
1 GAAA
60215 TATATTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
GAAAAAAAAGAAAAA
Found at i:60699 original size:37 final size:37
Alignment explanation
Indices: 60649--60726 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
60639 TTACTACTAA
* * *
60649 TGTCGCTGCATGAGCACTTCTAGATTGCGCCCAAAAC
1 TGTCGCTGCATGAGCACTTCTAAATTACACCCAAAAC
* *
60686 TGTCGCTGCATGAGCATTTCTAAATTACACCCAAAAT
1 TGTCGCTGCATGAGCACTTCTAAATTACACCCAAAAC
60723 TGTC
1 TGTC
60727 ATCATAAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (37 bp):
TGTCGCTGCATGAGCACTTCTAAATTACACCCAAAAC
Found at i:60801 original size:38 final size:37
Alignment explanation
Indices: 60748--60831 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 37
60738 ATTTTTGGAA
* *
60748 TGCACCCAAGACTATCGCTACATAAATATTCTTCAAAT
1 TGCACCCAAAACTATCGCTACATAAACATTCTTC-AAT
* * * *
60786 TGCATCCAAAACTATCTCTGCATAAGCATTCTTCAAT
1 TGCACCCAAAACTATCGCTACATAAACATTCTTCAAT
60823 TGCACCCAA
1 TGCACCCAA
60832 GAATGTCGAT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
37 11 0.28
38 28 0.72
ACGTcount: A:0.35, C:0.29, G:0.08, T:0.29
Consensus pattern (37 bp):
TGCACCCAAAACTATCGCTACATAAACATTCTTCAAT
Found at i:62807 original size:21 final size:23
Alignment explanation
Indices: 62757--62815 Score: 79
Period size: 21 Copynumber: 2.7 Consensus size: 23
62747 TAAAAACATG
* *
62757 ACTTGTTTCGGTAGAAGTGTCTC
1 ACTTGTATCGGTAGAACTGTCTC
62780 A-TTGTATCGGTAGAACT-T-TC
1 ACTTGTATCGGTAGAACTGTCTC
62800 ACTTGTATCGGTAGAA
1 ACTTGTATCGGTAGAA
62816 GTCTGCACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.09
21 15 0.45
22 14 0.42
23 1 0.03
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (23 bp):
ACTTGTATCGGTAGAACTGTCTC
Found at i:67167 original size:31 final size:29
Alignment explanation
Indices: 67130--67189 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
67120 GAGACCACTT
*
67130 CGTAACAAAATGATAACATAAGTGACTAAAA
1 CGTAAC-AAATCA-AACATAAGTGACTAAAA
**
67161 CGTAACATTTCAAACATAAGTGACTAAAA
1 CGTAACAAATCAAACATAAGTGACTAAAA
67190 TATAATCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 17 0.65
30 3 0.12
31 6 0.23
ACGTcount: A:0.52, C:0.15, G:0.12, T:0.22
Consensus pattern (29 bp):
CGTAACAAATCAAACATAAGTGACTAAAA
Found at i:69612 original size:16 final size:15
Alignment explanation
Indices: 69577--69614 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
69567 ATCGATAAAT
69577 TTAAAAATTATATTA
1 TTAAAAATTATATTA
69592 TTAAAATATTA-ATTA
1 TTAAAA-ATTATATTA
69607 TATAAAAA
1 T-TAAAAA
69615 CATATCGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAAAAATTATATTA
Found at i:69674 original size:7 final size:7
Alignment explanation
Indices: 69641--69684 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
69631 ATCCCTCCCT
*
69641 ATTATAA
1 ATTATAG
*
69648 ATTATTG
1 ATTATAG
*
69655 ATTATTG
1 ATTATAG
69662 ATTATAG
1 ATTATAG
*
69669 ATTATAT
1 ATTATAG
69676 ATTATAG
1 ATTATAG
69683 AT
1 AT
69685 AAAAGCATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (7 bp):
ATTATAG
Found at i:69708 original size:89 final size:89
Alignment explanation
Indices: 69605--69769 Score: 303
Period size: 89 Copynumber: 1.9 Consensus size: 89
69595 AAATATTAAT
69605 TATATAAAAACATATCGAAGTATATAATCCCTCCCTATTATAAATTATTGATTATTGATTATAGA
1 TATATAAAAACATATCGAAGTATATAATCCCTCCCTATTATAAATTATTGATTATTGATTATAGA
*
69670 TTATATATTATAGATAAAAGCATA
66 TTATAGATTATAGATAAAAGCATA
* *
69694 TATATAAAAACATATCGAAGTATATAATCCCTCCCTATTATATATTATTGATTATTGATTATTGA
1 TATATAAAAACATATCGAAGTATATAATCCCTCCCTATTATAAATTATTGATTATTGATTATAGA
69759 TTATAGATTAT
66 TTATAGATTAT
69770 TGATTATTGA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 73 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (89 bp):
TATATAAAAACATATCGAAGTATATAATCCCTCCCTATTATAAATTATTGATTATTGATTATAGA
TTATAGATTATAGATAAAAGCATA
Found at i:69747 original size:7 final size:7
Alignment explanation
Indices: 69737--69780 Score: 79
Period size: 7 Copynumber: 6.3 Consensus size: 7
69727 CCTATTATAT
69737 ATTATTG
1 ATTATTG
69744 ATTATTG
1 ATTATTG
69751 ATTATTG
1 ATTATTG
*
69758 ATTATAG
1 ATTATTG
69765 ATTATTG
1 ATTATTG
69772 ATTATTG
1 ATTATTG
69779 AT
1 AT
69781 AAAAGCATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (7 bp):
ATTATTG
Found at i:70176 original size:5 final size:5
Alignment explanation
Indices: 70166--70191 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
70156 CTGTTTGTAA
70166 TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT T
70192 GATTCGATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:74595 original size:12 final size:13
Alignment explanation
Indices: 74576--74620 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
74566 AAATATTTTT
74576 TATTTTTTGAAAA
1 TATTTTTTGAAAA
74589 T-TTTTTTGAAAA
1 TATTTTTTGAAAA
* *
74601 TATTTTATAAAAA
1 TATTTTTTGAAAA
74614 CTATTTT
1 -TATTTT
74621 CAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 12 0.43
13 10 0.36
14 6 0.21
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (13 bp):
TATTTTTTGAAAA
Found at i:75408 original size:6 final size:6
Alignment explanation
Indices: 75397--75424 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
75387 CTTTGAAAGC
75397 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
75425 TCGACAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:75951 original size:31 final size:32
Alignment explanation
Indices: 75916--75980 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 32
75906 AATTTTATTA
*
75916 TTTTAATAATTTTTAAAAGATTAAA-TA-AAT
1 TTTTTATAATTTTTAAAAGATTAAAGTATAAT
* *
75946 TTTTTATTATTTTTAAAGGATTAAAGTATAAT
1 TTTTTATAATTTTTAAAAGATTAAAGTATAAT
75978 TTT
1 TTT
75981 ATCATTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 22 0.73
31 2 0.07
32 6 0.20
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (32 bp):
TTTTTATAATTTTTAAAAGATTAAAGTATAAT
Found at i:75960 original size:30 final size:33
Alignment explanation
Indices: 75924--75999 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 33
75914 TATTTTAATA
*
75924 ATTTTTAAAAGATTAAA-TA-AATTTT-TTATT
1 ATTTTTAAAAGATTAAAGTATAATTTTATCATT
*
75954 ATTTTTAAAGGATTAAAGTATAATTTTATCATT
1 ATTTTTAAAAGATTAAAGTATAATTTTATCATT
75987 ATTAATTTAAAAG
1 ATT--TTTAAAAG
76000 TTTATAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
30 16 0.42
31 2 0.05
32 6 0.16
33 7 0.18
35 7 0.18
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (33 bp):
ATTTTTAAAAGATTAAAGTATAATTTTATCATT
Found at i:81240 original size:5 final size:5
Alignment explanation
Indices: 81230--81256 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
81220 CAAGGCATTG
81230 TATGA TATGA TATGA TATGA TATGA TA
1 TATGA TATGA TATGA TATGA TATGA TA
81257 CGATTCGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (5 bp):
TATGA
Found at i:81267 original size:15 final size:15
Alignment explanation
Indices: 81230--81260 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
81220 CAAGGCATTG
*
81230 TATGATATGATATGA
1 TATGATATGATACGA
81245 TATGATATGATACGA
1 TATGATATGATACGA
81260 T
1 T
81261 TCGATATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (15 bp):
TATGATATGATACGA
Found at i:81616 original size:16 final size:18
Alignment explanation
Indices: 81585--81625 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
81575 TTCGGATTAA
81585 ATTTTTGTATTTTGTTTT
1 ATTTTTGTATTTTGTTTT
81603 ATTTTTG-A-TTTGTTTT
1 ATTTTTGTATTTTGTTTT
81619 -TTTTTGT
1 ATTTTTGT
81626 TTTAGTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.27
16 8 0.36
17 1 0.05
18 7 0.32
ACGTcount: A:0.10, C:0.00, G:0.12, T:0.78
Consensus pattern (18 bp):
ATTTTTGTATTTTGTTTT
Found at i:81618 original size:11 final size:11
Alignment explanation
Indices: 81587--81633 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
81577 CGGATTAAAT
81587 TTTTGTATTTTG
1 TTTTGT-TTTTG
*
81599 TTTTATTTTTG
1 TTTTGTTTTTG
*
81610 ATTTGTTTTT-
1 TTTTGTTTTTG
*
81620 TTTTGTTTTAG
1 TTTTGTTTTTG
81631 TTT
1 TTT
81634 AATTCGTCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
10 8 0.28
11 16 0.55
12 5 0.17
ACGTcount: A:0.09, C:0.00, G:0.13, T:0.79
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:81633 original size:16 final size:16
Alignment explanation
Indices: 81594--81633 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
81584 AATTTTTGTA
81594 TTTTGTTTTATTTTTG
1 TTTTGTTTTATTTTTG
*
81610 ATTTGTTTT-TTTTTG
1 TTTTGTTTTATTTTTG
81625 TTTTAGTTT
1 TTTT-GTTT
81634 AATTCGTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.07, C:0.00, G:0.12, T:0.80
Consensus pattern (16 bp):
TTTTGTTTTATTTTTG
Found at i:82255 original size:16 final size:16
Alignment explanation
Indices: 82234--82288 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
82224 ATTTGGTTCA
*
82234 CTGTAATAGAATAGAG
1 CTGTAATGGAATAGAG
82250 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
82266 TTGTAATGGAATA-AG
1 CTGTAATGGAATAGAG
82281 ACTGTAAT
1 -CTGTAAT
82289 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
15 2 0.06
16 33 0.94
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.29
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:82363 original size:44 final size:46
Alignment explanation
Indices: 82270--82364 Score: 126
Period size: 44 Copynumber: 2.1 Consensus size: 46
82260 ATAGAGTTGT
82270 AATGGAATAAGACTGTAATCAGTAATTCAATTGTTTGGTTGAATAG
1 AATGGAATAAGACTGTAATCAGTAATTCAATTGTTTGGTTGAATAG
* *
82316 AATGGAAT-AGACCTGTAAT-AGT-ATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAAGA-CTGTAATCAGTAATTCAAT-TGTTTGGTTGAATAG
82360 AATGG
1 AATGG
82365 TGCTGTAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 6 0.13
46 15 0.33
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (46 bp):
AATGGAATAAGACTGTAATCAGTAATTCAATTGTTTGGTTGAATAG
Found at i:82522 original size:58 final size:58
Alignment explanation
Indices: 82460--82584 Score: 180
Period size: 58 Copynumber: 2.2 Consensus size: 58
82450 TTTTAATAAG
* * *
82460 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATACAATTTAAT-AAAATAATAAATAATTTAATAACATTTTTAACATA
* *
82518 ATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAACATTTTTAATATA
1 ATTATTATTAAATACAATTTAATAAAATAATAAATAATTTAATAACATTTTTAACATA
*
82576 ATTGTTATT
1 ATTATTATT
82585 GTTATTAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 21 0.35
58 39 0.65
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.46
Consensus pattern (58 bp):
ATTATTATTAAATACAATTTAATAAAATAATAAATAATTTAATAACATTTTTAACATA
Found at i:88612 original size:32 final size:32
Alignment explanation
Indices: 88574--88641 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
88564 TATATAAGAC
88574 ACTATGGCCAAATGATTACAATCTTCAGTACT
1 ACTATGGCCAAATGATTACAATCTTCAGTACT
*
88606 ACTATGGCCAAATGATTACAATCTTTAGTACT
1 ACTATGGCCAAATGATTACAATCTTCAGTACT
88638 ACTA
1 ACTA
88642 GTATCTTCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (32 bp):
ACTATGGCCAAATGATTACAATCTTCAGTACT
Found at i:89934 original size:15 final size:14
Alignment explanation
Indices: 89910--89940 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
89900 CTGCTGATTG
89910 TTATTATAACTCCC
1 TTATTATAACTCCC
89924 TTATCTATAACTCCC
1 TTAT-TATAACTCCC
89939 TT
1 TT
89941 GACGTGAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (14 bp):
TTATTATAACTCCC
Found at i:109379 original size:3 final size:3
Alignment explanation
Indices: 109373--109423 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
109363 TAGTTTTTTG
*
109373 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
109421 TTA
1 TTA
109424 ATTTTAAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:112834 original size:10 final size:10
Alignment explanation
Indices: 112819--112861 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
112809 ACATTAGGAA
112819 TTTTTTATTT
1 TTTTTTATTT
112829 TTTTTTATTT
1 TTTTTTATTT
** *
112839 TTCATTGTTT
1 TTTTTTATTT
112849 TTATTTTATTT
1 TT-TTTTATTT
112860 TT
1 TT
112862 GCTTTTGTCG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 19 0.73
11 7 0.27
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.84
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:133201 original size:2 final size:2
Alignment explanation
Indices: 133194--133221 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
133184 TTGTGATTAA
133194 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
133222 GTTGTTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:136070 original size:42 final size:42
Alignment explanation
Indices: 136011--136094 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
136001 TTACCCTCCT
136011 ATAAGAAAGAATAACAAAATTTGTGGAATTGAATTCTTCATA
1 ATAAGAAAGAATAACAAAATTTGTGGAATTGAATTCTTCATA
136053 ATAAGAAAGAATAACAAAATTTGTGGAATTGAATTCTTCATA
1 ATAAGAAAGAATAACAAAATTTGTGGAATTGAATTCTTCATA
136095 GCTTGATATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (42 bp):
ATAAGAAAGAATAACAAAATTTGTGGAATTGAATTCTTCATA
Found at i:137570 original size:17 final size:16
Alignment explanation
Indices: 137550--137597 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
137540 ACTACAATGC
*
137550 AAATGTAAGAACAATTA
1 AAATGTAA-AACAATAA
*
137567 AAATGCAAAGACAATAA
1 AAATGTAAA-ACAATAA
137584 AAATGTAATAACAA
1 AAATGTAA-AACAA
137598 CTAGATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 1 0.04
17 24 0.92
18 1 0.04
ACGTcount: A:0.62, C:0.08, G:0.10, T:0.19
Consensus pattern (16 bp):
AAATGTAAAACAATAA
Found at i:144103 original size:3 final size:3
Alignment explanation
Indices: 144095--144130 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
144085 TTAAGAATAC
*
144095 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGA TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
144131 CATTGCATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.03, C:0.00, G:0.33, T:0.64
Consensus pattern (3 bp):
TGT
Found at i:152916 original size:6 final size:6
Alignment explanation
Indices: 152905--152940 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
152895 CTCCCTCACT
152905 CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC
1 CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC
152941 AATCTCTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CCTTCC
Found at i:153061 original size:21 final size:21
Alignment explanation
Indices: 153046--153092 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 21
153036 ATGGCTCCGT
153046 GAAGAGCAACGCTGGCTAAGA
1 GAAGAGCAACGCTGGCTAAGA
*
153067 GAAGAGCAGCGCTGGCTTAAAGA
1 GAAGAGCAACGCTGGC-T-AAGA
153090 GAA
1 GAA
153093 AGAATCGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.65
22 1 0.04
23 7 0.30
ACGTcount: A:0.38, C:0.17, G:0.34, T:0.11
Consensus pattern (21 bp):
GAAGAGCAACGCTGGCTAAGA
Found at i:156235 original size:9 final size:9
Alignment explanation
Indices: 156217--156259 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
156207 CTTATAAAAC
156217 TTATAATATT
1 TTAT-ATATT
*
156227 TTATTTATT
1 TTATATATT
156236 TTATATA-T
1 TTATATATT
156244 TTATATATT
1 TTATATATT
*
156253 TTTTATA
1 TTATATA
156260 AGTTTTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
8 8 0.28
9 17 0.59
10 4 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTATATATT
Found at i:156239 original size:19 final size:20
Alignment explanation
Indices: 156217--156260 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
156207 CTTATAAAAC
156217 TTATAATATTT-TAT-TTATT
1 TTATAATATTTATATATT-TT
156236 TTAT-ATATTTATATATTTT
1 TTATAATATTTATATATTTT
156255 TTATAA
1 TTATAA
156261 GTTTTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 6 0.27
19 13 0.59
20 3 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATAATATTTATATATTTT
Found at i:159437 original size:12 final size:12
Alignment explanation
Indices: 159420--159455 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
159410 TTTACTTCAC
159420 AAATCATTACAT
1 AAATCATTACAT
*
159432 AAATCATTACAC
1 AAATCATTACAT
159444 AAATCATTACAT
1 AAATCATTACAT
159456 TGGTGCTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATCATTACAT
Found at i:161326 original size:32 final size:32
Alignment explanation
Indices: 161265--161327 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
161255 GAAAGTTACG
* **
161265 GAGTAACCATTCGCACTTTTGAATGAACATGT
1 GAGTAACCATTCACACTTTTGAACAAACATGT
161297 GAGTAACCATTCACACTTTTGAACAAACATG
1 GAGTAACCATTCACACTTTTGAACAAACATG
161328 CAATTTGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (32 bp):
GAGTAACCATTCACACTTTTGAACAAACATGT
Found at i:164754 original size:20 final size:19
Alignment explanation
Indices: 164725--164764 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
164715 CTATACGTTT
164725 CGAAACATTCTAAAATTAAG
1 CGAAACATTCT-AAATTAAG
* *
164745 CGAAATATTCTGAATTAAG
1 CGAAACATTCTAAATTAAG
164764 C
1 C
164765 ACATAGTAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
CGAAACATTCTAAATTAAG
Found at i:167256 original size:20 final size:20
Alignment explanation
Indices: 167233--167284 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
167223 TGTACTTTGG
167233 TGCCCCTGTTTGCACTTCGA
1 TGCCCCTGTTTGCACTTCGA
*
167253 TGCCCCTATTTGCACTTCGA
1 TGCCCCTGTTTGCACTTCGA
167273 TGCCCCTGTTTG
1 TGCCCCTGTTTG
167285 AATCTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.10, C:0.35, G:0.19, T:0.37
Consensus pattern (20 bp):
TGCCCCTGTTTGCACTTCGA
Found at i:168227 original size:33 final size:33
Alignment explanation
Indices: 168190--168258 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
168180 AACTTACTCG
168190 ATTGGAAAATCTCTGTTTATATAACAATCAAAT
1 ATTGGAAAATCTCTGTTTATATAACAATCAAAT
168223 ATTGGAAAATCTCTGTTTATATAACAATCAAAT
1 ATTGGAAAATCTCTGTTTATATAACAATCAAAT
168256 ATT
1 ATT
168259 CATACTTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.38
Consensus pattern (33 bp):
ATTGGAAAATCTCTGTTTATATAACAATCAAAT
Found at i:171838 original size:34 final size:34
Alignment explanation
Indices: 171800--171866 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
171790 ATTTTAAATA
171800 AGTTTGAATTTA-TTCTAAATTTAAATTCATTTTG
1 AGTTTGAATTTACTT-TAAATTTAAATTCATTTTG
*
171834 AGTTTGAATTTACTTTAAATTTAAATTTATTTT
1 AGTTTGAATTTACTTTAAATTTAAATTCATTTT
171867 CAATTAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 29 0.94
35 2 0.06
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.55
Consensus pattern (34 bp):
AGTTTGAATTTACTTTAAATTTAAATTCATTTTG
Found at i:171871 original size:17 final size:17
Alignment explanation
Indices: 171806--171871 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 17
171796 AATAAGTTTG
*
171806 AATTTATTCTAAATTTA
1 AATTTATTTTAAATTTA
* * * *
171823 AATTCATTTTGAGTTTG
1 AATTTATTTTAAATTTA
*
171840 AATTTACTTTAAATTTA
1 AATTTATTTTAAATTTA
*
171857 AATTTATTTTCAATT
1 AATTTATTTTAAATT
171872 AAAAATTAAT
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.55
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Done.