Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 322 of 322
Found at i:106856977 original size:24 final size:23
Alignment explanation
Indices: 106856948--106856995 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
106856938 GAAGAAAATA
106856948 TTTTATTTATT-AATTCATTTGATT
1 TTTTATTT-TTGAATT-ATTTGATT
*
106856972 TTTTATTTTTGAATTATTTTATT
1 TTTTATTTTTGAATTATTTGATT
106856995 T
1 T
106856996 AAAGGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTTATTTTTGAATTATTTGATT
Found at i:106862593 original size:36 final size:36
Alignment explanation
Indices: 106862543--106862652 Score: 168
Period size: 36 Copynumber: 3.1 Consensus size: 36
106862533 CCCTTCTTCT
* *
106862543 AGTCCAAGTAAGCCTCGAATTCGCAGCCCCAGCCCC
1 AGTCCTAGTCAGCCTCGAATTCGCAGCCCCAGCCCC
*
106862579 AGTCCTAGTCAGCCTCGAATTCGCAGCCCCAGCCCA
1 AGTCCTAGTCAGCCTCGAATTCGCAGCCCCAGCCCC
*
106862615 AGT-CTAAGTCAGCCTCGAATTCGCAGCCCCAGTCCC
1 AGTCCT-AGTCAGCCTCGAATTCGCAGCCCCAGCCCC
106862651 AG
1 AG
106862653 CCCCAGCCCA
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 2 0.03
36 66 0.97
ACGTcount: A:0.24, C:0.40, G:0.20, T:0.16
Consensus pattern (36 bp):
AGTCCTAGTCAGCCTCGAATTCGCAGCCCCAGCCCC
Found at i:106869031 original size:4 final size:4
Alignment explanation
Indices: 106869024--106869048 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
106869014 CTCGCGCGAG
106869024 GGCA GGCA GGCA GGCA GGCA GGCA G
1 GGCA GGCA GGCA GGCA GGCA GGCA G
106869049 CGAGCGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.52, T:0.00
Consensus pattern (4 bp):
GGCA
Found at i:106875171 original size:18 final size:18
Alignment explanation
Indices: 106875143--106875203 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
106875133 TTCTTTTCCG
*
106875143 CCCGCACCCGCACCCGCA
1 CCCGTACCCGCACCCGCA
*
106875161 CCCGTATCCGCACCCGCA
1 CCCGTACCCGCACCCGCA
*
106875179 CCCGCACCCGCA-CCGCA
1 CCCGTACCCGCACCCGCA
*
106875196 ACCGTACC
1 CCCGTACC
106875204 TTTCTGTGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
17 11 0.30
18 26 0.70
ACGTcount: A:0.18, C:0.61, G:0.16, T:0.05
Consensus pattern (18 bp):
CCCGTACCCGCACCCGCA
Found at i:106875199 original size:6 final size:6
Alignment explanation
Indices: 106875143--106875192 Score: 82
Period size: 6 Copynumber: 8.3 Consensus size: 6
106875133 TTCTTTTCCG
* *
106875143 CCCGCA CCCGCA CCCGCA CCCGTA TCCGCA CCCGCA CCCGCA CCCGCA
1 CCCGCA CCCGCA CCCGCA CCCGCA CCCGCA CCCGCA CCCGCA CCCGCA
106875191 CC
1 CC
106875193 GCAACCGTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.16, C:0.64, G:0.16, T:0.04
Consensus pattern (6 bp):
CCCGCA
Found at i:106878441 original size:21 final size:21
Alignment explanation
Indices: 106878415--106878455 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
106878405 ATCTGCTCAA
* *
106878415 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
106878436 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
106878456 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:106886027 original size:22 final size:22
Alignment explanation
Indices: 106886002--106886044 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
106885992 TGTGTCACCC
106886002 AACCTACATTATTAAACGCTTA
1 AACCTACATTATTAAACGCTTA
106886024 AACCTACATTATTAAACGCTT
1 AACCTACATTATTAAACGCTT
106886045 GAAAATAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.33
Consensus pattern (22 bp):
AACCTACATTATTAAACGCTTA
Found at i:106888065 original size:15 final size:14
Alignment explanation
Indices: 106888045--106888084 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
106888035 ATCAAATCCT
106888045 TAAATTTTAAACTTC
1 TAAATTTTAAAC-TC
*
106888060 TAAATTCTAAAACTC
1 TAAATT-TTAAACTC
106888075 TAAATTTTAA
1 TAAATTTTAA
106888085 TTCTAATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 3 0.14
15 14 0.64
16 5 0.23
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAATTTTAAACTC
Found at i:106888143 original size:14 final size:15
Alignment explanation
Indices: 106888113--106888151 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
106888103 TCCTAAATGA
*
106888113 TAAATATTAAATCTC
1 TAAATATTATATCTC
106888128 TAAATATTATAT-TC
1 TAAATATTATATCTC
106888142 TAAATATTAT
1 TAAATATTAT
106888152 TTTACTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (15 bp):
TAAATATTATATCTC
Found at i:106889451 original size:20 final size:20
Alignment explanation
Indices: 106889421--106889475 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
106889411 TTTATTATAT
*
106889421 TTGCA-TTTATTTATGTTGTG
1 TTGCATTTTATTTAT-TTGCG
106889441 TTG-ATTTTATTT-TTTGCG
1 TTGCATTTTATTTATTTGCG
*
106889459 TTGCATTTTAATTATTT
1 TTGCATTTTATTTATTT
106889476 TAATATTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 7 0.23
19 10 0.33
20 13 0.43
ACGTcount: A:0.16, C:0.05, G:0.15, T:0.64
Consensus pattern (20 bp):
TTGCATTTTATTTATTTGCG
Found at i:106897265 original size:34 final size:34
Alignment explanation
Indices: 106897217--106897283 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
106897207 TTTTGGATGA
* *
106897217 GATTTAGGCATTTCTGGGTTGAGATGTCTTATGG
1 GATTCAGGCATTTCTGGGTTGAAATGTCTTATGG
106897251 GATTCAGGCATTTCTGGGTTGAAATGTCTTATG
1 GATTCAGGCATTTCTGGGTTGAAATGTCTTATG
106897284 CATTCGAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.19, C:0.10, G:0.30, T:0.40
Consensus pattern (34 bp):
GATTCAGGCATTTCTGGGTTGAAATGTCTTATGG
Found at i:106898822 original size:10 final size:10
Alignment explanation
Indices: 106898807--106898842 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
106898797 AGAAAATTAA
106898807 TTTAATTTAT
1 TTTAATTTAT
106898817 TTTAATTTA-
1 TTTAATTTAT
*
106898826 TTAAATTTAT
1 TTTAATTTAT
106898836 TTTAATT
1 TTTAATT
106898843 AATTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTAATTTAT
Found at i:106898823 original size:19 final size:19
Alignment explanation
Indices: 106898801--106898853 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
106898791 TAATTGAGAA
*
106898801 AATTAATTTAATTTATTTT
1 AATTAATTAAATTTATTTT
*
106898820 AATTTATTAAATTTATTTT
1 AATTAATTAAATTTATTTT
106898839 AATTAATTAATATTT
1 AATTAATTAA-ATTT
106898854 CAAGAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 26 0.87
20 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTAATTAAATTTATTTT
Found at i:106898831 original size:28 final size:29
Alignment explanation
Indices: 106898786--106898842 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
106898776 TTGAAAAAAA
106898786 TATTTTAATTGAGAAAA-TTAATTTAATT
1 TATTTTAATTGAGAAAATTTAATTTAATT
* ** *
106898814 TATTTTAATTTATTAAATTTATTTTAATT
1 TATTTTAATTGAGAAAATTTAATTTAATT
106898843 AATTAATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (29 bp):
TATTTTAATTGAGAAAATTTAATTTAATT
Found at i:106901652 original size:95 final size:97
Alignment explanation
Indices: 106901521--106901717 Score: 301
Period size: 95 Copynumber: 2.0 Consensus size: 97
106901511 TTAAAAAACT
* *
106901521 TATTTTGGAAAAAATAAATTATATATAAGTTTATAACACAAGTAAAACTTTTACAATGGTAATAA
1 TATTTTGGAAAAAATAAATTATATATAACTTTATAACACAAGCAAAACTTTTACAATGGTAATAA
*
106901586 AATCT-AG-GAGCATTTAAATAATTATAATTA
66 AAGCTGAGCGAGCATTTAAATAATTATAATTA
*
106901616 TATTTTGGAAAAAA-AATTATATATATAACTTTATAACACAAGCAAAACTTTTACAATGGTAATA
1 TATTTTGGAAAAAATAAAT-TATATATAACTTTATAACACAAGCAAAACTTTTACAATGGTAATA
*
106901680 AGAGCTAGGAGCGAGCATTTAAATAATTATAATTA
65 AAAGCT--GAGCGAGCATTTAAATAATTATAATTA
106901715 TAT
1 TAT
106901718 ATTCAATTTC
Statistics
Matches: 92, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
94 3 0.03
95 61 0.66
98 2 0.02
99 26 0.28
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.35
Consensus pattern (97 bp):
TATTTTGGAAAAAATAAATTATATATAACTTTATAACACAAGCAAAACTTTTACAATGGTAATAA
AAGCTGAGCGAGCATTTAAATAATTATAATTA
Found at i:106904956 original size:95 final size:97
Alignment explanation
Indices: 106904825--106905021 Score: 301
Period size: 95 Copynumber: 2.0 Consensus size: 97
106904815 TTAAAAAACT
* *
106904825 TATTTTGGAAAAAATAAATTATATATAAGTTTATAACACAAGTAAAACTTTTACAATGGTAATAA
1 TATTTTGGAAAAAATAAATTATATATAACTTTATAACACAAGCAAAACTTTTACAATGGTAATAA
*
106904890 AATCT-AG-GAGCATTTAAATAATTATAATTA
66 AAGCTGAGCGAGCATTTAAATAATTATAATTA
*
106904920 TATTTTGGAAAAAA-AATTATATATATAACTTTATAACACAAGCAAAACTTTTACAATGGTAATA
1 TATTTTGGAAAAAATAAAT-TATATATAACTTTATAACACAAGCAAAACTTTTACAATGGTAATA
*
106904984 AGAGCTAGGAGCGAGCATTTAAATAATTATAATTA
65 AAAGCT--GAGCGAGCATTTAAATAATTATAATTA
106905019 TAT
1 TAT
106905022 ATTCAATTTC
Statistics
Matches: 92, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
94 3 0.03
95 61 0.66
98 2 0.02
99 26 0.28
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.35
Consensus pattern (97 bp):
TATTTTGGAAAAAATAAATTATATATAACTTTATAACACAAGCAAAACTTTTACAATGGTAATAA
AAGCTGAGCGAGCATTTAAATAATTATAATTA
Found at i:106909812 original size:211 final size:210
Alignment explanation
Indices: 106909264--106909888 Score: 940
Period size: 211 Copynumber: 3.0 Consensus size: 210
106909254 TGGGAACCCG
*
106909264 ATTGAAATTTCCTAGCACTTTTCATCCACAAATAGATGGGCAAATAGAGGCTGTTAACCAAAGTT
1 ATTGAAATTTTCTAGCACTTTTCATCCACAAATAGATGGGCAAATAGAGGCTGTTAACCAAAGTT
* *
106909329 TAGGAATTATGCTTAGGTGTCTTGTTTGGAATCATGTGAAGAGTTAGGATTTGGTTATTCCTCAA
66 TAGGAAATATGCTTAGGTGTCCTGTTTGGAATCATGTGAAGAGTTAGGATTTGGTTA-TCCTCAA
* * *
106909394 GATGAGTTTACATACAACTCTATGAATAGAACAATTAA-AATACACCTTTTCAAGCTATTTATGG
130 GATGAGTTTACATACAACTCTATGAATAGAACAATTAAGAAGACACCTTTTGAAGCTACTTATGG
* * *
106909458 ACTTAGACCTCAACCG
195 ACTCAAACCTCAACCA
* * * * * *
106909474 ATTGAAATTTTATGGCACTTTTCATCCAGAAATATATGGGAAAATAGAGGTTGTT-----AAGTT
1 ATTGAAATTTTCTAGCACTTTTCATCCACAAATAGATGGGCAAATAGAGGCTGTTAACCAAAGTT
* *
106909534 CAGGAAATATGCTCAGGTGT-CTGGTTTGGAATCATGTGAAGAGTTAGGATTTGGTTAGTCCTCA
66 TAGGAAATATGCTTAGGTGTCCT-GTTTGGAATCATGTGAAGAGTTAGGATTTGGTTA-TCCTCA
* * *
106909598 AGATGAGTTTACATTCAACTCTGTAAATAGAACAATTAAGAAGACACCTTTTGAAGCTACTTATG
129 AGATGAGTTTACATACAACTCTATGAATAGAACAATTAAGAAGACACCTTTTGAAGCTACTTATG
106909663 GACTCAAACCTCAACCA
194 GACTCAAACCTCAACCA
106909680 ATTGAAATTTTCTAGCACTTTTCATCCACAAATAGATGGGCAAATAGAGGCTGTTAACCAAAGTT
1 ATTGAAATTTTCTAGCACTTTTCATCCACAAATAGATGGGCAAATAGAGGCTGTTAACCAAAGTT
*
106909745 TAGGAAATATGCTTAGGTGTCCTGTTTGGAATCATATGAAGAGTTAGGATTTGGTTATCCCTCAA
66 TAGGAAATATGCTTAGGTGTCCTGTTTGGAATCATGTGAAGAGTTAGGATTTGGTTAT-CCTCAA
* * * *
106909810 GATGAGTTTACATACAACCCTTTGAATAGAACAATTAAGAAGATACCTTTTGACGCTACTTATGG
130 GATGAGTTTACATACAACTCTATGAATAGAACAATTAAGAAGACACCTTTTGAAGCTACTTATGG
106909875 ACTCAAACCTCAAC
195 ACTCAAACCTCAAC
106909889 ATGTGCTTTA
Statistics
Matches: 370, Mismatches: 36, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
204 1 0.00
205 98 0.26
206 85 0.23
210 49 0.13
211 135 0.36
212 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (210 bp):
ATTGAAATTTTCTAGCACTTTTCATCCACAAATAGATGGGCAAATAGAGGCTGTTAACCAAAGTT
TAGGAAATATGCTTAGGTGTCCTGTTTGGAATCATGTGAAGAGTTAGGATTTGGTTATCCTCAAG
ATGAGTTTACATACAACTCTATGAATAGAACAATTAAGAAGACACCTTTTGAAGCTACTTATGGA
CTCAAACCTCAACCA
Found at i:106912247 original size:12 final size:12
Alignment explanation
Indices: 106912230--106912254 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
106912220 TTCTTGCTGT
106912230 ACGACAACAACA
1 ACGACAACAACA
106912242 ACGACAACAACA
1 ACGACAACAACA
106912254 A
1 A
106912255 TAGTAATTAA
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:0.32, G:0.08, T:0.00
Consensus pattern (12 bp):
ACGACAACAACA
Found at i:106920382 original size:24 final size:24
Alignment explanation
Indices: 106920335--106920382 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
106920325 TTGTTCTGTG
* **
106920335 GCAAAGGATGAATTAACGGTAAAT
1 GCAAAGGAAGAATTAACGACAAAT
*
106920359 GCAAAGGAAGAATTGACGACAAAT
1 GCAAAGGAAGAATTAACGACAAAT
106920383 TACCCAAGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.10, G:0.25, T:0.17
Consensus pattern (24 bp):
GCAAAGGAAGAATTAACGACAAAT
Found at i:106922077 original size:17 final size:17
Alignment explanation
Indices: 106922031--106922080 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
106922021 GTTTGAAACA
*
106922031 AGTC-AAAATAACTCTC
1 AGTCAAAAATAACTATC
* *
106922047 AGTCAAGAACAACTATC
1 AGTCAAAAATAACTATC
106922064 A-TCCAAAAATAACTATC
1 AGT-CAAAAATAACTATC
106922081 GTCTTGCTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.22
Consensus pattern (17 bp):
AGTCAAAAATAACTATC
Found at i:106922472 original size:25 final size:25
Alignment explanation
Indices: 106922444--106922496 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
106922434 CTCCTATTTT
106922444 CAAAGGCATAATTTGGAGCCCTTCA
1 CAAAGGCATAATTTGGAGCCCTTCA
*
106922469 CAAAGGCTTAATTTGGAGCCCTTCA
1 CAAAGGCATAATTTGGAGCCCTTCA
106922494 CAA
1 CAA
106922497 CTAGTGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (25 bp):
CAAAGGCATAATTTGGAGCCCTTCA
Found at i:106925559 original size:17 final size:17
Alignment explanation
Indices: 106925534--106925567 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
106925524 TAAGCTAGGA
*
106925534 TAAATATAAAAATTAAT
1 TAAAAATAAAAATTAAT
*
106925551 TAAAAATAAATATTAAT
1 TAAAAATAAAAATTAAT
106925568 GATAAGAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAAATAAAAATTAAT
Found at i:106926906 original size:25 final size:23
Alignment explanation
Indices: 106926877--106926937 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 23
106926867 ACAACGTCAG
106926877 AAAAATTAAAAATTATAAAGATATTA
1 AAAAATTAAAAA-TATAAA-ATA-TA
*
106926903 AAAAA-TAAAACATATATAATATA
1 AAAAATTAAAA-ATATAAAATATA
*
106926926 AAAAATAAAAAA
1 AAAAATTAAAAA
106926938 GATCTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
23 8 0.26
24 7 0.23
25 10 0.32
26 6 0.19
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (23 bp):
AAAAATTAAAAATATAAAATATA
Found at i:106934943 original size:2 final size:2
Alignment explanation
Indices: 106934938--106934968 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
106934928 GTGCGTGAGT
106934938 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
106934969 CATATGAAGT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:106940538 original size:4 final size:4
Alignment explanation
Indices: 106940529--106940700 Score: 344
Period size: 4 Copynumber: 43.0 Consensus size: 4
106940519 GAATCCAGTT
106940529 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
106940577 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
106940625 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
106940673 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
106940701 TGAGGGAGAT
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 168 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:106944258 original size:80 final size:79
Alignment explanation
Indices: 106944121--106944278 Score: 280
Period size: 80 Copynumber: 2.0 Consensus size: 79
106944111 TCTTTTTTTT
106944121 TTTGCTTAGGAAGGGAAGTCAACAATTACCATCCTGTAGAAACATTACAGTCATTGAACAACAAA
1 TTTGCTTAGGAAGGGAAGTCAACAATTACCATCCTGTAGAAACATTACAGTCATTGAACAACAAA
106944186 GTAAGAAGGCTCCG
66 GTAAGAAGGCTCCG
* *
106944200 TTTGTTTAGGAAGGGGAAGTTAACAATTACCATCCTGTAGAAACATTACAGTCATTGAACAACAA
1 TTTGCTTAGGAA-GGGAAGTCAACAATTACCATCCTGTAGAAACATTACAGTCATTGAACAACAA
*
106944265 AGTAAGAAGTCTCC
65 AGTAAGAAGGCTCC
106944279 TATATAACTA
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
79 11 0.15
80 64 0.85
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (79 bp):
TTTGCTTAGGAAGGGAAGTCAACAATTACCATCCTGTAGAAACATTACAGTCATTGAACAACAAA
GTAAGAAGGCTCCG
Found at i:106947774 original size:88 final size:88
Alignment explanation
Indices: 106947625--106947795 Score: 306
Period size: 88 Copynumber: 1.9 Consensus size: 88
106947615 TAACCAATGG
*
106947625 CTTAAAAAGGAAAGTGGGCTCAATTTGTTAGTTTCTATCTCACAAACACAAACACTCTAACTAAA
1 CTTAAAAAGGAAAGGGGGCTCAATTTGTTAGTTTCTATCTCACAAACACAAACACTCTAACTAAA
*
106947690 AACAGGGCAAGAAAGATATATGT
66 AACAAGGCAAGAAAGATATATGT
* *
106947713 CTTAAAAAGGAAAGGGGGCTCAATTTGTTAGTTTCTATCTCACAAATACAAACACTCTAACTAGA
1 CTTAAAAAGGAAAGGGGGCTCAATTTGTTAGTTTCTATCTCACAAACACAAACACTCTAACTAAA
106947778 AACAAGGCAAGAAAGATA
66 AACAAGGCAAGAAAGATA
106947796 CTAACTAAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 79 1.00
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (88 bp):
CTTAAAAAGGAAAGGGGGCTCAATTTGTTAGTTTCTATCTCACAAACACAAACACTCTAACTAAA
AACAAGGCAAGAAAGATATATGT
Found at i:106948610 original size:15 final size:15
Alignment explanation
Indices: 106948590--106948625 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
106948580 TGTAAGGAGG
106948590 AAGAAATACAGTGTA
1 AAGAAATACAGTGTA
106948605 AAGAAATACAGTGTA
1 AAGAAATACAGTGTA
*
106948620 AGGAAA
1 AAGAAA
106948626 GGAATAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.06, G:0.22, T:0.17
Consensus pattern (15 bp):
AAGAAATACAGTGTA
Found at i:106967602 original size:23 final size:22
Alignment explanation
Indices: 106967418--106967693 Score: 126
Period size: 23 Copynumber: 12.0 Consensus size: 22
106967408 ATTGAAGAAT
* *
106967418 TTAAATGCTGTGAATTGAAGTG
1 TTAAATGCTGTAAATTGAGGTG
* * *
106967440 TTAACGTGCTGCAAATTGAAGTGTT
1 TTAA-ATGCTGTAAATTG-AG-GTG
* *
106967465 TTAAATGTTGTAAATTGAAGTGTT
1 TTAAATGCTGTAAATTG-AG-GTG
* * * **
106967489 TTAAGTACTGCAAATTGAATTG
1 TTAAATGCTGTAAATTGAGGTG
** * * *
106967511 TTTAGTTGTTGGAAATTGAGATG
1 -TTAAATGCTGTAAATTGAGGTG
*
106967534 TT-TATCGCTGT-AATTGAGGTG
1 TTAAAT-GCTGTAAATTGAGGTG
* * *
106967555 TATAAACGTTGTTAATTG-GGATG
1 T-TAAATGCTGTAAATTGAGG-TG
* *
106967578 TTAAAGTGTTGTAAGTTGAGGTG
1 TTAAA-TGCTGTAAATTGAGGTG
*
106967601 TTTAAATGCTGTAAATTGAAGTG
1 -TTAAATGCTGTAAATTGAGGTG
*
106967624 TTTAATTGCTGTAAATTGAGGTG
1 -TTAAATGCTGTAAATTGAGGTG
* * *
106967647 CTCAAATGATGTAAATTGAAGTG
1 -TTAAATGCTGTAAATTGAGGTG
* * *
106967670 TTTAAGTGCTGCAAATTGTGGTG
1 -TTAAATGCTGTAAATTGAGGTG
106967693 T
1 T
106967694 ACAAATGAGT
Statistics
Matches: 192, Mismatches: 50, Indels: 24
0.72 0.19 0.09
Matches are distributed among these distances:
21 11 0.06
22 22 0.11
23 115 0.60
24 38 0.20
25 6 0.03
ACGTcount: A:0.29, C:0.05, G:0.26, T:0.39
Consensus pattern (22 bp):
TTAAATGCTGTAAATTGAGGTG
Found at i:106967686 original size:46 final size:46
Alignment explanation
Indices: 106967397--106967693 Score: 237
Period size: 46 Copynumber: 6.5 Consensus size: 46
106967387 AGCCCTATTC
* * ** * *
106967397 AAGTGTTGCAAATTGAAGAATTTAAATGCTGTGAATTGAAGTG-TT
1 AAGTGCTGCAAATTGAGGTGTTTAAATGTTGTAAATTGAAGTGTTT
*
106967442 AACGTGCTGCAAATTGAAGTGTTTTAAATGTTGTAAATTGAAGTGTTTT
1 AA-GTGCTGCAAATTGAGGTG-TTTAAATGTTGTAAATTGAAGTG-TTT
* ** ** *
106967491 AAGTACTGCAAATTGAATTGTTTAGTTGTTGGAAATTG-AGATGTTT
1 AAGTGCTGCAAATTGAGGTGTTTAAATGTTGTAAATTGAAG-TGTTT
* * * * * *
106967537 -A-TCGCTG-TAATTGAGGTGTATAAACGTTGTTAATTG-GGATGTTA
1 AAGT-GCTGCAAATTGAGGTGTTTAAATGTTGTAAATTGAAG-TGTTT
* * * *
106967581 AAGTGTTGTAAGTTGAGGTGTTTAAATGCTGTAAATTGAAGTGTTT
1 AAGTGCTGCAAATTGAGGTGTTTAAATGTTGTAAATTGAAGTGTTT
* * * * *
106967627 AATTGCTGTAAATTGAGGTGCTCAAATGATGTAAATTGAAGTGTTT
1 AAGTGCTGCAAATTGAGGTGTTTAAATGTTGTAAATTGAAGTGTTT
*
106967673 AAGTGCTGCAAATTGTGGTGT
1 AAGTGCTGCAAATTGAGGTGT
106967694 ACAAATGAGT
Statistics
Matches: 201, Mismatches: 41, Indels: 19
0.77 0.16 0.07
Matches are distributed among these distances:
44 27 0.13
45 10 0.05
46 105 0.52
47 39 0.19
48 16 0.08
49 4 0.02
ACGTcount: A:0.30, C:0.05, G:0.26, T:0.39
Consensus pattern (46 bp):
AAGTGCTGCAAATTGAGGTGTTTAAATGTTGTAAATTGAAGTGTTT
Found at i:106974841 original size:268 final size:268
Alignment explanation
Indices: 106974364--106974897 Score: 1005
Period size: 268 Copynumber: 2.0 Consensus size: 268
106974354 ACTATATGTT
106974364 TTTTGTTTTTGAATTGTCTGTTCCGCTTTGCTCATATTATATCTATCTTGCTTTATATTTGTTAT
1 TTTTGTTTTTGAATTGTCTGTTCCGCTTTGCTCATATTATATCTATCTTGCTTTATATTTGTTAT
* * *
106974429 TTTTCCTTCGCAAAATACTGTTGGGGTTTCTGTTTGTTTCTCTTCTACTTTCGTGAGGTAGATAA
66 TTTTCCTTCGCAAAATACTGTTGGGGTTTCTGTTTGTTTCTCGTCTACGTTCGTGAGGTAGAGAA
106974494 ATTCTAAGTTTTCTCTTTCGTTTCTATTTTGTGTGTTTTTTGAAATCCCCGATTGAGGGTACTTT
131 ATTCTAAGTTTTCTCTTTCGTTTCTATTTTGTGTGTTTTTTGAAATCCCCGATTGAGGGTACTTT
* *
106974559 TGGTGGCTATGGTTTTGGTGTTGGTGCTCGCGATTCTTTCGGCATTCACATGTATTTTTTTACTT
196 TGGTGGCTATGGTTTTGGTGTTGGTGCTCGCGATTCTTTCGGCATTCACATGTATTCTTTTAATT
106974624 TTTTTTTA
261 TTTTTTTA
* *
106974632 TTTTGTTTTTGAATTGTCTGTTTCGCTTTGCTCATATTGTATCTATCTTGCTTTATATTTGTTAT
1 TTTTGTTTTTGAATTGTCTGTTCCGCTTTGCTCATATTATATCTATCTTGCTTTATATTTGTTAT
106974697 TTTTCCTTCGCAAAATACTGTTGGGGTTTCTGTTTGTTTCTCGTCTACGTTCGTGAGGTAGAGAA
66 TTTTCCTTCGCAAAATACTGTTGGGGTTTCTGTTTGTTTCTCGTCTACGTTCGTGAGGTAGAGAA
106974762 ATTCTAAGTTTTCTCTTTCGTTTCTATTTTGTGTGTTTTTTGAAATCCCCGATTGAGGGTACTTT
131 ATTCTAAGTTTTCTCTTTCGTTTCTATTTTGTGTGTTTTTTGAAATCCCCGATTGAGGGTACTTT
106974827 TGGTGGCTATGGTTTTGGTGTTGGTGCTCGCGATTCTTTCGGCATTCACATGTATTCTTTTAATT
196 TGGTGGCTATGGTTTTGGTGTTGGTGCTCGCGATTCTTTCGGCATTCACATGTATTCTTTTAATT
106974892 TTTTTT
261 TTTTTT
106974898 AAAATTTTTT
Statistics
Matches: 259, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
268 259 1.00
ACGTcount: A:0.14, C:0.15, G:0.19, T:0.52
Consensus pattern (268 bp):
TTTTGTTTTTGAATTGTCTGTTCCGCTTTGCTCATATTATATCTATCTTGCTTTATATTTGTTAT
TTTTCCTTCGCAAAATACTGTTGGGGTTTCTGTTTGTTTCTCGTCTACGTTCGTGAGGTAGAGAA
ATTCTAAGTTTTCTCTTTCGTTTCTATTTTGTGTGTTTTTTGAAATCCCCGATTGAGGGTACTTT
TGGTGGCTATGGTTTTGGTGTTGGTGCTCGCGATTCTTTCGGCATTCACATGTATTCTTTTAATT
TTTTTTTA
Found at i:106975484 original size:16 final size:16
Alignment explanation
Indices: 106975463--106975504 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
106975453 TCCCGGATAG
106975463 GGATATCCCG-TCCTTA
1 GGATATCCCGCT-CTTA
106975479 GGATATCCCGCTCTTA
1 GGATATCCCGCTCTTA
*
106975495 GGGTATCCCG
1 GGATATCCCG
106975505 GCTCAATGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 23 0.96
17 1 0.04
ACGTcount: A:0.17, C:0.31, G:0.24, T:0.29
Consensus pattern (16 bp):
GGATATCCCGCTCTTA
Found at i:106975746 original size:29 final size:29
Alignment explanation
Indices: 106975703--106975758 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
106975693 CAAATAATAA
* *
106975703 TATATATTTGTTATAACTAATGTATATTT
1 TATACATTTGGTATAACTAATGTATATTT
*
106975732 TATACATTTGGTATAATTAATGTATAT
1 TATACATTTGGTATAACTAATGTATAT
106975759 ATTTGTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.52
Consensus pattern (29 bp):
TATACATTTGGTATAACTAATGTATATTT
Found at i:106975757 original size:22 final size:22
Alignment explanation
Indices: 106975732--106975775 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
106975722 ATGTATATTT
106975732 TATACATTTGGTATAATTAATG
1 TATACATTTGGTATAATTAATG
* * *
106975754 TATATATTTGTTTTAATTAATG
1 TATACATTTGGTATAATTAATG
106975776 CATATTTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.52
Consensus pattern (22 bp):
TATACATTTGGTATAATTAATG
Found at i:106980962 original size:25 final size:25
Alignment explanation
Indices: 106980933--106980982 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
106980923 AAAAAAAAGA
106980933 GTCAAACATACCCATATAAGATGCG
1 GTCAAACATACCCATATAAGATGCG
*
106980958 GTCAAACATACCCATATAAGGTGCG
1 GTCAAACATACCCATATAAGATGCG
106980983 TGCGTGTCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (25 bp):
GTCAAACATACCCATATAAGATGCG
Found at i:106982065 original size:19 final size:20
Alignment explanation
Indices: 106982041--106982079 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
106982031 CAATTGTTTT
106982041 AAAA-TTAA-ATAAGTTTAAA
1 AAAATTTAATATAA-TTTAAA
106982060 AAAATTTAATATAATTTAAA
1 AAAATTTAATATAATTTAAA
106982080 TTTTTAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
AAAATTTAATATAATTTAAA
Found at i:106987208 original size:2 final size:2
Alignment explanation
Indices: 106987203--106987228 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
106987193 TCGTTCGCCG
106987203 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
106987229 AGTATCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:106988275 original size:32 final size:32
Alignment explanation
Indices: 106988234--106988304 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
106988224 CAGGTAGGGA
*
106988234 TATCCCATTCTGTC-GATATCCCGGTTTAGATT
1 TATCCCATTC-GGCGGATATCCCGGTTTAGATT
*
106988266 TATCCCATTCGGCGGTTATCCCGGTTTAGATT
1 TATCCCATTCGGCGGATATCCCGGTTTAGATT
106988298 TATCCCA
1 TATCCCA
106988305 CTTGAAGGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 2 0.06
32 34 0.94
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.38
Consensus pattern (32 bp):
TATCCCATTCGGCGGATATCCCGGTTTAGATT
Found at i:106988318 original size:32 final size:32
Alignment explanation
Indices: 106988248--106988320 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
106988238 CCATTCTGTC
**
106988248 GATATCCCGGTTTAGATTTATCCCATTCGGCG
1 GATATCCCGGTTTAGATTTATCCCATTCGAAG
*
106988280 GTTATCCCGGTTTAGATTTATCCCACTT-GAAG
1 GATATCCCGGTTTAGATTTATCCCA-TTCGAAG
106988312 GATATCCCG
1 GATATCCCG
106988321 TTTTTGAGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
32 34 0.94
33 2 0.06
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (32 bp):
GATATCCCGGTTTAGATTTATCCCATTCGAAG
Done.