Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 332 of 332
Found at i:109033291 original size:16 final size:18
Alignment explanation
Indices: 109033258--109033291 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
109033248 GTATAAAGAT
109033258 AATTATTATACAAATTAA
1 AATTATTATACAAATTAA
109033276 AATTA-TATAC-AATTAA
1 AATTATTATACAAATTAA
109033292 CTTAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTATTATACAAATTAA
Found at i:109040167 original size:30 final size:30
Alignment explanation
Indices: 109040131--109040230 Score: 94
Period size: 30 Copynumber: 3.2 Consensus size: 30
109040121 ATTTTTACAG
* * *
109040131 ATCTTTTAAAAATATATGAATATATTATAT
1 ATCTTTTAAATATTTAAGAATATATTATAT
109040161 ATCTTTTAGGCATATATTTAAGAATATATTATAT
1 ATCTTTTA---A-ATATTTAAGAATATATTATAT
** *
109040195 AT-TTTTCTGATATTTAGGAATATATTATAT
1 ATCTTTT-AAATATTTAAGAATATATTATAT
109040225 ATCTTT
1 ATCTTT
109040231 CTTATTTCTG
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
30 30 0.52
31 3 0.05
33 5 0.09
34 20 0.34
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (30 bp):
ATCTTTTAAATATTTAAGAATATATTATAT
Found at i:109040232 original size:30 final size:32
Alignment explanation
Indices: 109040148--109040232 Score: 104
Period size: 30 Copynumber: 2.7 Consensus size: 32
109040138 AAAAATATAT
109040148 GAATATATTATATATCTTT-TAGGCATATATTTAA
1 GAATATATTATATATCTTTCTA-G-A-ATATTTAA
* *
109040182 GAATATATTATATATTTTTCT-G-ATATTTAG
1 GAATATATTATATATCTTTCTAGAATATTTAA
109040212 GAATATATTATATATCTTTCT
1 GAATATATTATATATCTTTCT
109040233 TATTTCTGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
30 27 0.57
33 1 0.02
34 18 0.38
35 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (32 bp):
GAATATATTATATATCTTTCTAGAATATTTAA
Found at i:109044230 original size:48 final size:50
Alignment explanation
Indices: 109044172--109044271 Score: 150
Period size: 48 Copynumber: 2.0 Consensus size: 50
109044162 GTATATATTA
*
109044172 ATTTTTAATTTTGATTCAATTTTATATCTT-TA-TTTTATATTAGATAGT
1 ATTTCTAATTTTGATTCAATTTTATATCTTATATTTTTATATTAGATAGT
* * *
109044220 ATTTCTAATTTTGATTTAATTTTATATTTTATATTTTTATATTGGATAGT
1 ATTTCTAATTTTGATTCAATTTTATATCTTATATTTTTATATTAGATAGT
109044270 AT
1 AT
109044272 GATGTAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 27 0.59
49 2 0.04
50 17 0.37
ACGTcount: A:0.29, C:0.03, G:0.07, T:0.61
Consensus pattern (50 bp):
ATTTCTAATTTTGATTCAATTTTATATCTTATATTTTTATATTAGATAGT
Found at i:109048981 original size:48 final size:48
Alignment explanation
Indices: 109048920--109049019 Score: 173
Period size: 48 Copynumber: 2.1 Consensus size: 48
109048910 AAAAATCTAA
*
109048920 AACAAAAAATTAATATGAAAAAATCGAGAATCAAATCAAATTATGAAG
1 AACAAAAAATTAATATGAAAAAATCGAGAACCAAATCAAATTATGAAG
* *
109048968 AACACAAAGTTAATATGAAAAAATCGAGAACCAAATCAAATTATGAAG
1 AACAAAAAATTAATATGAAAAAATCGAGAACCAAATCAAATTATGAAG
109049016 AACA
1 AACA
109049020 GTTTAAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (48 bp):
AACAAAAAATTAATATGAAAAAATCGAGAACCAAATCAAATTATGAAG
Found at i:109067772 original size:7 final size:7
Alignment explanation
Indices: 109067760--109067802 Score: 86
Period size: 7 Copynumber: 6.1 Consensus size: 7
109067750 AGTTTAGTTA
109067760 AGAATAT
1 AGAATAT
109067767 AGAATAT
1 AGAATAT
109067774 AGAATAT
1 AGAATAT
109067781 AGAATAT
1 AGAATAT
109067788 AGAATAT
1 AGAATAT
109067795 AGAATAT
1 AGAATAT
109067802 A
1 A
109067803 TGATCGAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.58, C:0.00, G:0.14, T:0.28
Consensus pattern (7 bp):
AGAATAT
Found at i:109074731 original size:17 final size:17
Alignment explanation
Indices: 109074681--109074734 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
109074671 TTAAAACTGT
109074681 AAAATTATATTTAGG-AA
1 AAAATTA-ATTTAGGAAA
* *
109074698 AAAAGT-A-TTAGATAAA
1 AAAATTAATTTAG-GAAA
109074714 AAAATTAATTTAGGAAA
1 AAAATTAATTTAGGAAA
109074731 AAAA
1 AAAA
109074735 ATACTCCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
14 4 0.14
15 1 0.03
16 7 0.24
17 13 0.45
18 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (17 bp):
AAAATTAATTTAGGAAA
Found at i:109090820 original size:46 final size:45
Alignment explanation
Indices: 109090770--109090945 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 45
109090760 TGGTTGAGCA
109090770 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *** * *
109090816 TCCGAACTCGTTGAGTTGAGTCCGGGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
109090863 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
109090909 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
109090946 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 68 0.62
47 31 0.28
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:109090926 original size:93 final size:93
Alignment explanation
Indices: 109090767--109090937 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
109090757 GGATGGTTGA
* *
109090767 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
109090832 TGAGTCCGGGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
109090860 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
109090925 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
109090938 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:109092259 original size:14 final size:14
Alignment explanation
Indices: 109092240--109092266 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
109092230 TTTAAAATTT
109092240 TTTAGAAAACTTCA
1 TTTAGAAAACTTCA
109092254 TTTAGAAAACTTC
1 TTTAGAAAACTTC
109092267 GCTGAAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (14 bp):
TTTAGAAAACTTCA
Found at i:109100866 original size:12 final size:12
Alignment explanation
Indices: 109100846--109100885 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
109100836 ATTGCATAAG
*
109100846 TGTATGTATATA
1 TGTAAGTATATA
109100858 TGTAAGTATATA
1 TGTAAGTATATA
109100870 TGTAAGTATATA
1 TGTAAGTATATA
109100882 TGTA
1 TGTA
109100886 TTATGATAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (12 bp):
TGTAAGTATATA
Found at i:109102809 original size:25 final size:25
Alignment explanation
Indices: 109102781--109102831 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
109102771 CGTAATTCAA
109102781 TTTAATGAAATTTCTTTTACAATGC
1 TTTAATGAAATTTCTTTTACAATGC
109102806 TTTAATGAAATTTCTTTTACAATGC
1 TTTAATGAAATTTCTTTTACAATGC
109102831 T
1 T
109102832 ATAAATCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (25 bp):
TTTAATGAAATTTCTTTTACAATGC
Found at i:109111137 original size:18 final size:18
Alignment explanation
Indices: 109111114--109111206 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
109111104 CCCAACTACT
*
109111114 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
109111132 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
109111150 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
* * *
109111168 ATATACGTAAATAGTGCC
1 GTATACGTGAATAGTACC
* *
109111186 ATATACGTGAATAGTATC
1 GTATACGTGAATAGTACC
109111204 GTA
1 GTA
109111207 AACGGTCGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:109111166 original size:36 final size:36
Alignment explanation
Indices: 109111114--109111206 Score: 141
Period size: 36 Copynumber: 2.6 Consensus size: 36
109111104 CCCAACTACT
* *
109111114 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
*
109111150 GTATACGTGAATAGTACCATATACGTAAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
* *
109111186 ATATACGTGAATAGTATCGTA
1 GTATACGTGAATAGTACCGTA
109111207 AACGGTCGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
Found at i:109112636 original size:5 final size:6
Alignment explanation
Indices: 109112607--109112634 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
109112597 ATCAAAGGTA
109112607 AAAAAC AAAAAC AAAAAC AAAAAC AAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAA
109112635 CATGAGGCAT
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:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:109128049 original size:3 final size:3
Alignment explanation
Indices: 109128041--109128075 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
109128031 GGTACTGCAC
* *
109128041 ATT ATT ATT ATT ATT ACT ATT ACT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
109128076 CATCATCCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:109128478 original size:3 final size:3
Alignment explanation
Indices: 109128472--109128501 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
109128462 TTAATATTCC
109128472 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
109128502 TTGCCTCCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
CTG
Found at i:109132992 original size:16 final size:17
Alignment explanation
Indices: 109132963--109133000 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
109132953 TCTATTTAAC
* *
109132963 ATAAAAATATACAACAA
1 ATAAAAATAAACAAAAA
109132980 ATAAAAA-AAACAAAAA
1 ATAAAAATAAACAAAAA
109132996 ATAAA
1 ATAAA
109133001 TTTTTTACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (17 bp):
ATAAAAATAAACAAAAA
Found at i:109133044 original size:6 final size:6
Alignment explanation
Indices: 109133033--109133057 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
109133023 GCGTGCGGTG
109133033 GCCGGC GCCGGC GCCGGC GCCGGC G
1 GCCGGC GCCGGC GCCGGC GCCGGC G
109133058 AGCCTCCGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.48, G:0.52, T:0.00
Consensus pattern (6 bp):
GCCGGC
Found at i:109133616 original size:6 final size:6
Alignment explanation
Indices: 109133616--109133649 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
109133606 TTATTAGTAT
109133616 TATTAG TATTAG TATTAG TATTATG TATTAG TAT
1 TATTAG TATTAG TATTAG TATTA-G TATTAG TAT
109133650 ATATTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (6 bp):
TATTAG
Found at i:109133778 original size:3 final size:3
Alignment explanation
Indices: 109133765--109133812 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
109133755 TATTCCAATG
* *
109133765 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
109133813 GTTTATGCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:109134090 original size:64 final size:64
Alignment explanation
Indices: 109134016--109134147 Score: 164
Period size: 64 Copynumber: 2.1 Consensus size: 64
109134006 GTCGTATTAT
*
109134016 TATATTTTAATATTA-TA-TTATATAATTATA-TA-TACATATATCTTTTATATATATTATCATT
1 TATATTTTAATATTATTAGTTATAT-ATTACACTATTACATATAT-TTTTATA-ATATTAT-ATT
109134077 GTA
62 GTA
* * *
109134080 TATATTTTAATATTATTAGTTATATTTTACACTATTATATATATTTTTCTAATATTATATTGTA
1 TATATTTTAATATTATTAGTTATATATTACACTATTACATATATTTTTATAATATTATATTGTA
109134144 TATA
1 TATA
109134148 CTGTCGTTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
64 25 0.42
65 13 0.22
66 14 0.23
67 8 0.13
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (64 bp):
TATATTTTAATATTATTAGTTATATATTACACTATTACATATATTTTTATAATATTATATTGTA
Found at i:109134122 original size:19 final size:18
Alignment explanation
Indices: 109134078--109134137 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 18
109134068 ATTATCATTG
109134078 TATATATTTTAATATTAT
1 TATATATTTTAATATTAT
109134096 TAGTTATATTTTACACTATTAT
1 TA--TATATTTTA-A-TATTAT
*
109134118 ATATATTTTTCTAATATTAT
1 -TATATATTT-TAATATTAT
109134138 ATTGTATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
18 2 0.06
20 15 0.43
21 8 0.23
22 8 0.23
23 2 0.06
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (18 bp):
TATATATTTTAATATTAT
Found at i:109134579 original size:38 final size:37
Alignment explanation
Indices: 109134495--109134589 Score: 97
Period size: 38 Copynumber: 2.5 Consensus size: 37
109134485 TATACGTACT
*
109134495 TATACATACTTAAATATATTTTTCATATTTCATAATTC
1 TATACATACTTAAATATATTTTGCATATTT-ATAATTC
* *
109134533 T-TATATACTTACATATATTTATGCATATTT-TACA-TC
1 TATACATACTTAAATATATTT-TGCATATTTATA-ATTC
*
109134569 ATATACATACTTATATATATT
1 -TATACATACTTAAATATATT
109134590 CTTTATATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
36 4 0.08
37 19 0.40
38 25 0.52
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.49
Consensus pattern (37 bp):
TATACATACTTAAATATATTTTGCATATTTATAATTC
Found at i:109151379 original size:30 final size:30
Alignment explanation
Indices: 109151343--109151410 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
109151333 TATCTATATA
*
109151343 ATTTTTAAAGAGTTA-AATCA-AATTTTTATT
1 ATTTTTAAAGAATTAGAAT-ATAA-TTTTATT
*
109151373 ATTTTTAATGAATTAGAATATAATTTTATT
1 ATTTTTAAAGAATTAGAATATAATTTTATT
*
109151403 ATTATTAA
1 ATTTTTAA
109151411 TTTAAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 28 0.85
31 5 0.15
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.51
Consensus pattern (30 bp):
ATTTTTAAAGAATTAGAATATAATTTTATT
Found at i:109158931 original size:13 final size:13
Alignment explanation
Indices: 109158913--109158937 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
109158903 ACTAATCCAA
109158913 AAGAGAGAGAGAT
1 AAGAGAGAGAGAT
109158926 AAGAGAGAGAGA
1 AAGAGAGAGAGA
109158938 GAGACTTGGA
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:0.56, C:0.00, G:0.40, T:0.04
Consensus pattern (13 bp):
AAGAGAGAGAGAT
Found at i:109164969 original size:18 final size:18
Alignment explanation
Indices: 109164946--109165031 Score: 127
Period size: 18 Copynumber: 4.8 Consensus size: 18
109164936 CGTTTACAGT
109164946 ACTATTCACGTATACGGC
1 ACTATTCACGTATACGGC
* *
109164964 ACTATTTACGTATACGGT
1 ACTATTCACGTATACGGC
109164982 ACTATTCACGTATACGGC
1 ACTATTCACGTATACGGC
* *
109165000 ACTATTCACATATACGGT
1 ACTATTCACGTATACGGC
*
109165018 ACTGTTCACGTATA
1 ACTATTCACGTATA
109165032 TAGTAGTTGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 60 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (18 bp):
ACTATTCACGTATACGGC
Found at i:109164991 original size:36 final size:36
Alignment explanation
Indices: 109164944--109165031 Score: 149
Period size: 36 Copynumber: 2.4 Consensus size: 36
109164934 ACCGTTTACA
* *
109164944 GTACTATTCACGTATACGGCACTATTTACGTATACG
1 GTACTATTCACGTATACGGCACTATTCACATATACG
109164980 GTACTATTCACGTATACGGCACTATTCACATATACG
1 GTACTATTCACGTATACGGCACTATTCACATATACG
*
109165016 GTACTGTTCACGTATA
1 GTACTATTCACGTATA
109165032 TAGTAGTTGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (36 bp):
GTACTATTCACGTATACGGCACTATTCACATATACG
Found at i:109184212 original size:17 final size:19
Alignment explanation
Indices: 109184192--109184233 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
109184182 AATAAAATAT
109184192 AAATAT-AAAT-AATAGAG
1 AAATATCAAATAAATAGAG
109184209 AAATATCACAAATAAATAGAG
1 AAATAT--CAAATAAATAGAG
109184230 AAAT
1 AAAT
109184234 TAAGCACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
20 4 0.19
21 11 0.52
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (19 bp):
AAATATCAAATAAATAGAG
Found at i:109188171 original size:15 final size:15
Alignment explanation
Indices: 109188151--109188179 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
109188141 AAATGAGTCC
109188151 AATTTATTAAAAAGA
1 AATTTATTAAAAAGA
109188166 AATTTATTAAAAAG
1 AATTTATTAAAAAG
109188180 TTAGAAGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (15 bp):
AATTTATTAAAAAGA
Found at i:109191322 original size:59 final size:58
Alignment explanation
Indices: 109191258--109191382 Score: 180
Period size: 59 Copynumber: 2.1 Consensus size: 58
109191248 CTACATTATA
* * *
109191258 AACTATTGATAAATT-TTATTTTAATCATTTAATTATAAAAAATTATAAAATAATTACTC
1 AACTATTAATAAATTATT-TTTT-ATAATTTAACTATAAAAAATTATAAAATAATTACTC
*
109191317 AACTATTAATAAATTCATTTTTTATAATTTAACTATAAAAAATTATAAAATAATTACTT
1 AACTATTAATAAATT-ATTTTTTATAATTTAACTATAAAAAATTATAAAATAATTACTC
109191376 AACTATT
1 AACTATT
109191383 CAAACTTTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
59 54 0.90
60 4 0.07
61 2 0.03
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.44
Consensus pattern (58 bp):
AACTATTAATAAATTATTTTTTATAATTTAACTATAAAAAATTATAAAATAATTACTC
Found at i:109196765 original size:18 final size:19
Alignment explanation
Indices: 109196733--109196770 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
109196723 ACGTAAGGTT
*
109196733 TAAAATATTTTAAAATAAA
1 TAAAATATTTAAAAATAAA
109196752 TAAAA-ATTTAAAAATAAA
1 TAAAATATTTAAAAATAAA
109196770 T
1 T
109196771 TGCACGTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAAATATTTAAAAATAAA
Found at i:109196995 original size:17 final size:18
Alignment explanation
Indices: 109196961--109196996 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
109196951 GCTTGGATGC
*
109196961 TTTATTTACTTATTTAAA
1 TTTATTTACTTATATAAA
109196979 TTTATTTA-TTATATAAA
1 TTTATTTACTTATATAAA
109196996 T
1 T
109196997 AGTAAATCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTATTTACTTATATAAA
Found at i:109199028 original size:26 final size:26
Alignment explanation
Indices: 109198992--109199051 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
109198982 GCTAAGGTGG
*
109198992 TGCATATTAGTCAGTCCATGGATCAA
1 TGCATATTAGTCAGCCCATGGATCAA
109199018 TGCATATTAGTCAGCCCATGGATCAA
1 TGCATATTAGTCAGCCCATGGATCAA
109199044 TGCATATT
1 TGCATATT
109199052 CAGTTTTCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (26 bp):
TGCATATTAGTCAGCCCATGGATCAA
Found at i:109199864 original size:52 final size:52
Alignment explanation
Indices: 109199781--109199882 Score: 159
Period size: 52 Copynumber: 2.0 Consensus size: 52
109199771 AATTTTGCTT
* ** *
109199781 CATGCATCTGTAAGTGAAATGTGTTTGTATATATATTCTTTTGATATATTTG
1 CATGCATCCGTAAGTGAAATGTGCATCTATATATATTCTTTTGATATATTTG
*
109199833 CATGCATCCGTAAGTGAAATTTGCATCTATATATATTCTTTTGATATATT
1 CATGCATCCGTAAGTGAAATGTGCATCTATATATATTCTTTTGATATATT
109199883 CTTTCTATCT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (52 bp):
CATGCATCCGTAAGTGAAATGTGCATCTATATATATTCTTTTGATATATTTG
Found at i:109199868 original size:116 final size:113
Alignment explanation
Indices: 109199653--109199873 Score: 352
Period size: 116 Copynumber: 1.9 Consensus size: 113
109199643 GCACATTCCA
* * *
109199653 TATAAATTTTGCTTCCTGCATCTGTAAGTGAAATGTGTGTTTATATATTCTTTTTATATATTTGC
1 TATAAATTTTGCTTCATGCATCTGTAAGTGAAATGTGTGTATATATATTCTTTTGATATATTTGC
* *
109199718 ATTCATCCATAAATGAAATTTGCATGTATATATATTTCTTTCTATCTGT
66 ATGCATCCATAAATGAAATTTGCATCTATATATA-TTCTTTCTATCTGT
109199767 TATAAATTTTGCTTCATGCATCTGTAAGTGAAATGTGTTTGTATATATATTCTTTTGATATATTT
1 TATAAATTTTGCTTCATGCATCTGTAAGTGAAATGTG--TGTATATATATTCTTTTGATATATTT
* *
109199832 GCATGCATCCGTAAGTGAAATTTGCATCTATATATATTCTTT
64 GCATGCATCCATAAATGAAATTTGCATCTATATATATTCTTT
109199874 TGATATATTC
Statistics
Matches: 98, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
114 36 0.37
115 6 0.06
116 56 0.57
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.48
Consensus pattern (113 bp):
TATAAATTTTGCTTCATGCATCTGTAAGTGAAATGTGTGTATATATATTCTTTTGATATATTTGC
ATGCATCCATAAATGAAATTTGCATCTATATATATTCTTTCTATCTGT
Found at i:109199908 original size:27 final size:27
Alignment explanation
Indices: 109199876--109199927 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
109199866 TATTCTTTTG
* *
109199876 ATATATTCTTTCTATCTGTTTGTGTAT
1 ATATATCCTTTCTATCTGTATGTGTAT
109199903 ATATATCCTTTCTATCTGTATGTGT
1 ATATATCCTTTCTATCTGTATGTGT
109199928 GTGTGTCACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.13, G:0.12, T:0.56
Consensus pattern (27 bp):
ATATATCCTTTCTATCTGTATGTGTAT
Found at i:109202815 original size:42 final size:42
Alignment explanation
Indices: 109202763--109202930 Score: 223
Period size: 43 Copynumber: 3.9 Consensus size: 42
109202753 GATATCCCCG
109202763 TCAATAAAAAAAA-AAAGAAGAAAAAGTACTGGGTTAATTGCCT
1 TCAA-AAAAAAAAGAAA-AAGAAAAAGTACTGGGTTAATTGCCT
*
109202806 T-AAAGAAAAAAAGAAAAAGAAAAAGTACTGGGTTTATTGCCT
1 TCAAA-AAAAAAAGAAAAAGAAAAAGTACTGGGTTAATTGCCT
*
109202848 TCAAAAAGAAAAAGGAAAAGAAAAAGTACTGGGTTAATTGCCT
1 TCAAAAA-AAAAAGAAAAAGAAAAAGTACTGGGTTAATTGCCT
* * *
109202891 TCAAAAAAAAAAAAGAATAAGAAAAAGTACAGGGTAAATT
1 TC--AAAAAAAAAAGAAAAAGAAAAAGTACTGGGTTAATT
109202931 TTCATTCTTC
Statistics
Matches: 112, Mismatches: 7, Indels: 11
0.86 0.05 0.08
Matches are distributed among these distances:
41 1 0.01
42 37 0.33
43 42 0.38
44 27 0.24
45 5 0.04
ACGTcount: A:0.55, C:0.08, G:0.18, T:0.19
Consensus pattern (42 bp):
TCAAAAAAAAAAGAAAAAGAAAAAGTACTGGGTTAATTGCCT
Found at i:109203053 original size:21 final size:21
Alignment explanation
Indices: 109203019--109203074 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
109203009 TTCCCGTTCT
** *
109203019 GGTTCAGTACTTTTAGTCCCC
1 GGTTCAGTTGTTTTAGTACCC
* *
109203040 GGTTCAGTTGTTTTTGTATCC
1 GGTTCAGTTGTTTTAGTACCC
109203061 GGTTCAGTTGTTTT
1 GGTTCAGTTGTTTT
109203075 TACATGTCTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (21 bp):
GGTTCAGTTGTTTTAGTACCC
Found at i:109209748 original size:18 final size:18
Alignment explanation
Indices: 109209727--109209785 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
109209717 TAAGAAGACG
109209727 AAGTATGCCTTGAAGGCT
1 AAGTATGCCTTGAAGGCT
* * * * *
109209745 AAGTGT-CATAGAAGACG
1 AAGTATGCCTTGAAGGCT
*
109209762 AAGCATGCCTTGAAGGCT
1 AAGTATGCCTTGAAGGCT
109209780 AAGTAT
1 AAGTAT
109209786 TTGAGAAGAC
Statistics
Matches: 28, Mismatches: 12, Indels: 2
0.67 0.29 0.05
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (18 bp):
AAGTATGCCTTGAAGGCT
Found at i:109209758 original size:35 final size:36
Alignment explanation
Indices: 109209693--109209848 Score: 189
Period size: 35 Copynumber: 4.5 Consensus size: 36
109209683 TTGAGAAGTT
109209693 GAAGTATGCCTTGAAGGCT--GTGTC-TAAGAAGAC
1 GAAGTATGCCTTGAAGGCTAAGTGTCATAAGAAGAC
109209726 GAAGTATGCCTTGAAGGCTAAGTGTCAT-AGAAGAC
1 GAAGTATGCCTTGAAGGCTAAGTGTCATAAGAAGAC
* * * *
109209761 GAAGCATGCCTTGAAGGCTAAGTAT-TTGAGAAGAC
1 GAAGTATGCCTTGAAGGCTAAGTGTCATAAGAAGAC
* * ** *
109209796 GAAGTTTGCCTTAAAGGCTAAGTG-CCGAAGAAGAT
1 GAAGTATGCCTTGAAGGCTAAGTGTCATAAGAAGAC
109209831 GAAGTATGCCTTGAAGGC
1 GAAGTATGCCTTGAAGGC
109209849 GGTGTCTAAG
Statistics
Matches: 105, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
33 19 0.18
34 1 0.01
35 84 0.80
36 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (36 bp):
GAAGTATGCCTTGAAGGCTAAGTGTCATAAGAAGAC
Found at i:109209813 original size:70 final size:68
Alignment explanation
Indices: 109209693--109209860 Score: 212
Period size: 70 Copynumber: 2.4 Consensus size: 68
109209683 TTGAGAAGTT
* * *
109209693 GAAGTATGCCTTGAAGGCTGTGTCTAAGAAGACGAAGTATGCCTTGAAGGCTAAGTGTC-ATAGA
1 GAAGTATGCCTTGAAGGCTGTATCTAAGAAGACGAAGTATGCCTTAAAGGCTAAGTGCCGA-AGA
109209757 AGAC
65 AGAC
* * * *
109209761 GAAGCATGCCTTGAAGGCTAAGTATTTGAGAAGACGAAGTTTGCCTTAAAGGCTAAGTGCCGAAG
1 GAAGTATGCCTTGAAGGCT--GTATCTAAGAAGACGAAGTATGCCTTAAAGGCTAAGTGCCGAAG
*
109209826 AAGAT
64 AAGAC
* *
109209831 GAAGTATGCCTTGAAGGCGGTGTCTAAGAA
1 GAAGTATGCCTTGAAGGCTGTATCTAAGAA
109209861 TAGAAAGTAT
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
68 26 0.31
70 57 0.68
71 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (68 bp):
GAAGTATGCCTTGAAGGCTGTATCTAAGAAGACGAAGTATGCCTTAAAGGCTAAGTGCCGAAGAA
GAC
Found at i:109209886 original size:103 final size:103
Alignment explanation
Indices: 109209682--109209921 Score: 247
Period size: 103 Copynumber: 2.3 Consensus size: 103
109209672 AGTTTAGTTG
* * * *
109209682 TTTGAGAAGTTGAAGTATGCCTTGAAGGCT--GTGTCTAAGAAGACGAAGTATGCCTTGAAGGCT
1 TTTGAGAAG-AGAAGTATGCCTTAAAGGCTAAGTGCCGAAGAAGACGAAGTATGCCTTGAAGGC-
*
109209745 AAGTGTCATAGAAGACGAAGCATGCCTTGAAGGCTAAGTA
64 AAGTGTCATAGAAGACGAAGCATGCCTCGAAGGCTAAGTA
* *
109209785 TTTGAGAAGACGAAGTTTGCCTTAAAGGCTAAGTGCCGAAGAAGATGAAGTATGCCTTGAAGGC-
1 TTTGAGAAGA-GAAGTATGCCTTAAAGGCTAAGTGCCGAAGAAGACGAAGTATGCCTTGAAGGCA
* * * * * * *
109209849 GGTGTC-TAAGAATA-GAAAGTATGTCTCGTAGGTTAAGTG
65 AGTGTCAT-AGAAGACG-AAGCATGCCTCGAAGGCTAAGTA
* *
109209888 TTTGAGAAGTAGAAGTATGCATTAAAAGCTAAGT
1 TTTGAGAAG-AGAAGTATGCCTTAAAGGCTAAGT
109209922 TCCTGGAAAT
Statistics
Matches: 114, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
102 2 0.02
103 82 0.72
104 1 0.01
105 29 0.25
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (103 bp):
TTTGAGAAGAGAAGTATGCCTTAAAGGCTAAGTGCCGAAGAAGACGAAGTATGCCTTGAAGGCAA
GTGTCATAGAAGACGAAGCATGCCTCGAAGGCTAAGTA
Found at i:109213568 original size:16 final size:16
Alignment explanation
Indices: 109213547--109213581 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
109213537 GTAAGTACTG
*
109213547 TGTTATTTGGTTAGCT
1 TGTTATTGGGTTAGCT
*
109213563 TGTTATTGGGTTGGCT
1 TGTTATTGGGTTAGCT
109213579 TGT
1 TGT
109213582 GTCTGAGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.06, G:0.31, T:0.54
Consensus pattern (16 bp):
TGTTATTGGGTTAGCT
Found at i:109223724 original size:31 final size:31
Alignment explanation
Indices: 109223686--109223755 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
109223676 CACACTTTTC
*
109223686 CAAGTTTCATCGGTAGAGGAGAGCACCTATA
1 CAAGTTTCATCAGTAGAGGAGAGCACCTATA
109223717 CAAGTTTCATCAGTAGAGGAGAGCACCTATA
1 CAAGTTTCATCAGTAGAGGAGAGCACCTATA
109223748 CAAGTTTC
1 CAAGTTTC
109223756 TTTCTTTCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (31 bp):
CAAGTTTCATCAGTAGAGGAGAGCACCTATA
Found at i:109229525 original size:155 final size:155
Alignment explanation
Indices: 109229243--109229555 Score: 626
Period size: 155 Copynumber: 2.0 Consensus size: 155
109229233 TGATCGAGGA
109229243 AAATCGAGGGTAATTTATATCAAACTTGACATTAGTCCTTGTTCTTTTTAAATAATTCCTGATTC
1 AAATCGAGGGTAATTTATATCAAACTTGACATTAGTCCTTGTTCTTTTTAAATAATTCCTGATTC
109229308 ACCTGTGAGTTGGCAAATTCTGTTCATCCTGCATTTTCCCGGAAGTCAAACAGGAGACTTAAATG
66 ACCTGTGAGTTGGCAAATTCTGTTCATCCTGCATTTTCCCGGAAGTCAAACAGGAGACTTAAATG
109229373 TTTTTAATATCTTAAAGGGGGAATC
131 TTTTTAATATCTTAAAGGGGGAATC
109229398 AAATCGAGGGTAATTTATATCAAACTTGACATTAGTCCTTGTTCTTTTTAAATAATTCCTGATTC
1 AAATCGAGGGTAATTTATATCAAACTTGACATTAGTCCTTGTTCTTTTTAAATAATTCCTGATTC
109229463 ACCTGTGAGTTGGCAAATTCTGTTCATCCTGCATTTTCCCGGAAGTCAAACAGGAGACTTAAATG
66 ACCTGTGAGTTGGCAAATTCTGTTCATCCTGCATTTTCCCGGAAGTCAAACAGGAGACTTAAATG
109229528 TTTTTAATATCTTAAAGGGGGAATC
131 TTTTTAATATCTTAAAGGGGGAATC
109229553 AAA
1 AAA
109229556 ATAAAATACT
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
155 158 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (155 bp):
AAATCGAGGGTAATTTATATCAAACTTGACATTAGTCCTTGTTCTTTTTAAATAATTCCTGATTC
ACCTGTGAGTTGGCAAATTCTGTTCATCCTGCATTTTCCCGGAAGTCAAACAGGAGACTTAAATG
TTTTTAATATCTTAAAGGGGGAATC
Done.