Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold703
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: 67588
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:592 original size:24 final size:24
Alignment explanation
Indices: 564--609 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
554 AATAAAAATT
564 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
* * *
588 AGCCACCATTTTTTACATACAA
1 AGCCACCAATTTTGACAAACAA
610 AAATAACCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:635 original size:28 final size:28
Alignment explanation
Indices: 604--667 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
594 CATTTTTTAC
604 ATACAAA-AATAACCACCATATTTGACAA
1 ATACAAAGAA-AACCACCATATTTGACAA
*
632 ATACAAAGGAAACCACCATATTTGACAA
1 ATACAAAGAAAACCACCATATTTGACAA
660 ATACAAAG
1 ATACAAAG
668 GGTGACATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 33 0.97
29 1 0.03
ACGTcount: A:0.53, C:0.20, G:0.08, T:0.19
Consensus pattern (28 bp):
ATACAAAGAAAACCACCATATTTGACAA
Found at i:668 original size:28 final size:28
Alignment explanation
Indices: 614--668 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
604 ATACAAAAAT
614 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
642 AACCACCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
669 GTGACATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:1364 original size:3 final size:3
Alignment explanation
Indices: 1356--1402 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1346 CGAATTTAAC
1356 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1403 GAAAAAACAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2060 original size:22 final size:23
Alignment explanation
Indices: 2032--2085 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
2022 TTTGTAATAT
2032 TATTAAATAA-A-TTTAATATTA
1 TATTAAATAATAGTTTAATATTA
2053 CTATTAAATAATATGTTTAATATTA
1 -TATTAAATAATA-GTTTAATATTA
2078 TA-TAAATA
1 TATTAAATA
2086 GTATTATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 10 0.34
23 7 0.24
24 2 0.07
25 10 0.34
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
TATTAAATAATAGTTTAATATTA
Found at i:2083 original size:41 final size:36
Alignment explanation
Indices: 2032--2106 Score: 87
Period size: 37 Copynumber: 1.9 Consensus size: 36
2022 TTTGTAATAT
2032 TATTAAATAAATTTAATATTACTATTAAATAATATGTTTAA
1 TATTAAATAAA--TAATATTA-T-TTAAATAATA-GTTTAA
* *
2073 TATTATATAAATAGTATTATTTAAATAATAGTTT
1 TATTAAATAAATAATATTATTTAAATAATAGTTT
2107 TTTTAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 4 0.12
37 10 0.31
38 1 0.03
39 7 0.22
41 10 0.31
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (36 bp):
TATTAAATAAATAATATTATTTAAATAATAGTTTAA
Found at i:2099 original size:25 final size:25
Alignment explanation
Indices: 2037--2096 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
2027 AATATTATTA
*
2037 AATAAATTTAATATTACTATTAAAT
1 AATATATTTAATATTACTATTAAAT
*
2062 AATATGTTTAATATTA-TA-TAAAT
1 AATATATTTAATATTACTATTAAAT
*
2085 AGTATTATTTAA
1 AATA-TATTTAA
2097 ATAATAGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 8 0.27
24 8 0.27
25 14 0.47
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (25 bp):
AATATATTTAATATTACTATTAAAT
Found at i:3206 original size:91 final size:90
Alignment explanation
Indices: 3082--3262 Score: 326
Period size: 91 Copynumber: 2.0 Consensus size: 90
3072 AATTGTTTTC
*
3082 CCTTTCTGATACTACTTAATTATAAGTGAATAATAACTTTGTAATAAATTAATATTATATATTTT
1 CCTTTCTCATACTACTTAATTATAAGTGAATAATAACTTTGTAATAAATTAATATTATATATTTT
3147 CATAGAAAAATTTATAATTAAAATT
66 CATAGAAAAATTTATAATTAAAATT
* *
3172 CCTTTCTCATACTACTTAATTTTAAAGTGAATAATATCTTTGTAATAAATTAATATTATATATTT
1 CCTTTCTCATACTACTTAATTAT-AAGTGAATAATAACTTTGTAATAAATTAATATTATATATTT
3237 TCATAGAAAAATTTATAATTAAAATT
65 TCATAGAAAAATTTATAATTAAAATT
3263 TATTAGTTTA
Statistics
Matches: 87, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
90 21 0.24
91 66 0.76
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (90 bp):
CCTTTCTCATACTACTTAATTATAAGTGAATAATAACTTTGTAATAAATTAATATTATATATTTT
CATAGAAAAATTTATAATTAAAATT
Found at i:3418 original size:26 final size:27
Alignment explanation
Indices: 3362--3419 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
3352 TGAAATATAA
* * *
3362 TATTATTTAAATCAAATTAATTTGTAG
1 TATTATTTAAATAAAATTAATATGTAC
3389 TATTA-TTAAATAAAATTTAATAT-TAC
1 TATTATTTAAATAAAA-TTAATATGTAC
3415 TATTA
1 TATTA
3420 AATAATATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (27 bp):
TATTATTTAAATAAAATTAATATGTAC
Found at i:5513 original size:31 final size:29
Alignment explanation
Indices: 5475--5551 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 29
5465 GGTTGAAGAA
5475 TAAATTTGTCATTATACTATAGTTGGATATT
1 TAAATTTGTCATTATACTATA-TTGGA-ATT
* * **
5506 TAAATTTGTTATTATATTATATTTTAATT
1 TAAATTTGTCATTATACTATATTGGAATT
* *
5535 GATATTTGTCATTATAC
1 TAAATTTGTCATTATAC
5552 ATTTTTTATC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 16 0.42
30 3 0.08
31 19 0.50
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.53
Consensus pattern (29 bp):
TAAATTTGTCATTATACTATATTGGAATT
Found at i:10091 original size:3 final size:3
Alignment explanation
Indices: 10085--10124 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
10075 TAATTCCAAG
10085 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
10125 TTCAATACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16333 original size:20 final size:19
Alignment explanation
Indices: 16299--16354 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
16289 TATTTGCGAT
*
16299 TATAAAATAATAAAATATG
1 TATAAAATAATAAAAAATG
*
16318 TGTAAAATATATAAAAAATG
1 TATAAAATA-ATAAAAAATG
*
16338 TAAAAAATAAATAAAAA
1 TATAAAAT-AATAAAAA
16355 TAGACACAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 8 0.26
20 22 0.71
21 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
TATAAAATAATAAAAAATG
Found at i:16823 original size:2 final size:2
Alignment explanation
Indices: 16811--16854 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
16801 GAAATCTTTA
16811 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16854 A
1 A
16855 GAACTTCATT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18336 original size:2 final size:2
Alignment explanation
Indices: 18315--18352 Score: 51
Period size: 2 Copynumber: 18.5 Consensus size: 2
18305 TAAATTCAAG
18315 TA TA TA TGA TGA TA TA -A TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA T-A T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
18353 GCTCTAATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.82
3 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:20420 original size:2 final size:2
Alignment explanation
Indices: 20413--20450 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
20403 ACCATTCTTG
* *
20413 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20451 ACTTCATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20464 original size:69 final size:68
Alignment explanation
Indices: 20354--20482 Score: 215
Period size: 69 Copynumber: 1.9 Consensus size: 68
20344 GAAATCTTTA
*
20354 ATATGATATATATATATATATATGTAAAACTTCATTTTCTTCTCATTTTACCATTCTTGTATATA
1 ATATGATATATATATATATATATGTAAAACTTCATTTTCTTCGCATTTTACCATTCTTGTATATA
20419 TAT
66 TAT
*
20422 ATAT-ATATATATATATGTATATGTATATAACTTCATTTTCTTCGCATTTTACCATTCTTGT
1 ATATGATATATATATATATATATGTA-A-AACTTCATTTTCTTCGCATTTTACCATTCTTGT
20483 TCACTATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
67 20 0.35
68 5 0.09
69 32 0.56
ACGTcount: A:0.32, C:0.12, G:0.05, T:0.50
Consensus pattern (68 bp):
ATATGATATATATATATATATATGTAAAACTTCATTTTCTTCGCATTTTACCATTCTTGTATATA
TAT
Found at i:23515 original size:23 final size:24
Alignment explanation
Indices: 23462--23537 Score: 93
Period size: 23 Copynumber: 3.2 Consensus size: 24
23452 TTTTTAATTA
* *
23462 TAATATTATTTAAATGATAATATT
1 TAATATTATTTAAATAATATTATT
*
23486 GAA-ATTATTTAAA-AATATTATT
1 TAATATTATTTAAATAATATTATT
*
23508 TAATATTATGTAAATAATATTATT
1 TAATATTATTTAAATAATATTATT
23532 TCAATA
1 T-AATA
23538 AAAAATTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
22 9 0.20
23 19 0.43
24 12 0.27
25 4 0.09
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (24 bp):
TAATATTATTTAAATAATATTATT
Found at i:24119 original size:38 final size:38
Alignment explanation
Indices: 24038--24137 Score: 121
Period size: 38 Copynumber: 2.6 Consensus size: 38
24028 ATAATTAATA
* * *
24038 AATTTAATTTAAATTTAATT-GATGATTGGTTATTAAAG
1 AATTTAATTTAAATTTAATTAG-TAATTAGTGATTAAAG
* *
24076 TATTTAATTTAAATTTAATTAGTAATTAGTGATTAGAG
1 AATTTAATTTAAATTTAATTAGTAATTAGTGATTAAAG
* *
24114 AATTTAATTTGAATTTGATTAGTA
1 AATTTAATTTAAATTTAATTAGTA
24138 GTTAAAAAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 52 0.98
39 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (38 bp):
AATTTAATTTAAATTTAATTAGTAATTAGTGATTAAAG
Found at i:25817 original size:13 final size:13
Alignment explanation
Indices: 25799--25823 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25789 ACACAAAGTA
25799 TGTATCGATACAT
1 TGTATCGATACAT
25812 TGTATCGATACA
1 TGTATCGATACA
25824 CCATAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:25840 original size:33 final size:32
Alignment explanation
Indices: 25782--25846 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
25772 GCCAAACTTA
*
25782 TATCGATACACAAAGTATGTATCGATACATTG
1 TATCGATACACAAAGAATGTATCGATACATTG
25814 TATCGATACACCATAA-AATGTATCGATACATTG
1 TATCGATACA-CA-AAGAATGTATCGATACATTG
25847 GCTTGTAACG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 10 0.33
33 18 0.60
34 2 0.07
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (32 bp):
TATCGATACACAAAGAATGTATCGATACATTG
Found at i:26978 original size:5 final size:5
Alignment explanation
Indices: 26968--27001 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
26958 AAAAATTTTA
* *
26968 AAAAC AAAAC AAAAC AAATC AAACC AAAAC AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
27002 TACTATCCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.76, C:0.21, G:0.00, T:0.03
Consensus pattern (5 bp):
AAAAC
Found at i:28886 original size:31 final size:29
Alignment explanation
Indices: 28848--28924 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 29
28838 GGTTGAAGAA
28848 TAAATTTGTCATTATACTATAGTTGGATATT
1 TAAATTTGTCATTATACTATA-TTGGA-ATT
* * **
28879 TAAATTTGTTATTATATTATATTTTAATT
1 TAAATTTGTCATTATACTATATTGGAATT
* *
28908 GATATTTGTCATTATAC
1 TAAATTTGTCATTATAC
28925 ATTTTTTATC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 16 0.42
30 3 0.08
31 19 0.50
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.53
Consensus pattern (29 bp):
TAAATTTGTCATTATACTATATTGGAATT
Found at i:31198 original size:51 final size:50
Alignment explanation
Indices: 30963--31195 Score: 324
Period size: 50 Copynumber: 4.6 Consensus size: 50
30953 AGTTGTTGTC
* ** * *
30963 ATTGTTGACTA-TCTTTCACCAGTCTTTGACAATAGAGAGAGGTGGTCGTA
1 ATTGTTGACGATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
31013 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
31063 ATTGTTGACGATTTTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* * * *
31113 ATTGTTGACAATTCTTCACCAACCTTTGATAAATGGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGA-CAATAGAGAGAGGTGGCCATA
*
31164 ATTGTTGATGATTCTTCACCAACCTTTGACAA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAA
31196 ATGTGGCCAT
Statistics
Matches: 163, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
50 116 0.71
51 47 0.29
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:33205 original size:50 final size:50
Alignment explanation
Indices: 33130--33362 Score: 340
Period size: 50 Copynumber: 4.6 Consensus size: 50
33120 AGTTGTTGCC
* * * ** *
33130 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGGGAGAGGTGATCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
33180 ATTGTTGACGATTCTTTACCAACCTTTGACAATAGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
33230 ATTATTGACGATTCTTCACTAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* * *
33280 ATTGTTGACGATTCTTCACCAACCTTTGACAAATGGAGAGAGATGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGAC-AATAGAGAGAGGTGGCCATA
33331 ATTGTTGACGATTCTTCACCAACCTTTGACAA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAA
33363 ATGTGGCCAT
Statistics
Matches: 165, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
50 118 0.72
51 47 0.28
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:36261 original size:3 final size:3
Alignment explanation
Indices: 36253--36313 Score: 104
Period size: 3 Copynumber: 20.0 Consensus size: 3
36243 AATTGCAACG
*
36253 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
36301 ATA ATA ATCA ATA
1 ATA ATA AT-A ATA
36314 CTTGACAAAG
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:36348 original size:14 final size:14
Alignment explanation
Indices: 36329--36366 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
36319 CAAAGAGACT
36329 TACATAAGTATGAG
1 TACATAAGTATGAG
36343 TACATAAGTATGAG
1 TACATAAGTATGAG
36357 TACATAAGTA
1 TACATAAGTA
36367 AACCCTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (14 bp):
TACATAAGTATGAG
Found at i:41563 original size:3 final size:3
Alignment explanation
Indices: 41555--41598 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
41545 GAATTTTAAC
41555 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
41599 GAAAAAACAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:42261 original size:26 final size:27
Alignment explanation
Indices: 42202--42262 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
42192 TATTGAATTA
* *
42202 TAATATTATGTAAATCAAATTAATTTG
1 TAATATTATGTAAATAAAATTAATATG
42229 TAATATTAT-TAAATAAAATTTAATAT-
1 TAATATTATGTAAATAAAA-TTAATATG
*
42255 TACTATTA
1 TAATATTA
42263 AATAATATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 15 0.50
27 15 0.50
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (27 bp):
TAATATTATGTAAATAAAATTAATATG
Found at i:42269 original size:26 final size:24
Alignment explanation
Indices: 42240--42290 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
42230 AATATTATTA
42240 AATAAAATTTAATATTACTATTAAAT
1 AATAAAATTTAATATTA-TA-TAAAT
***
42266 AATATTGTTTAATATTATATAAAT
1 AATAAAATTTAATATTATATAAAT
42290 A
1 A
42291 GTATTATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 6 0.27
25 2 0.09
26 14 0.64
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (24 bp):
AATAAAATTTAATATTATATAAAT
Found at i:42295 original size:24 final size:26
Alignment explanation
Indices: 42235--42301 Score: 81
Period size: 24 Copynumber: 2.8 Consensus size: 26
42225 TTTGTAATAT
42235 TATTAAATAA-A--ATTTAATATTAC
1 TATTAAATAATATTATTTAATATTAC
*
42258 TATTAAATAATATTGTTTAATATTA-
1 TATTAAATAATATTATTTAATATTAC
*
42283 TA-TAAATAGTATTATTTAA
1 TATTAAATAATATTATTTAA
42302 ATAATAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
23 10 0.26
24 16 0.42
25 2 0.05
26 10 0.26
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (26 bp):
TATTAAATAATATTATTTAATATTAC
Found at i:44416 original size:31 final size:30
Alignment explanation
Indices: 44376--44439 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 30
44366 TTTACATTTA
*
44376 TTTTATTAAATTTTGTCACTAAATTTTAAT
1 TTTTATTAAATTTTATCACTAAATTTTAAT
*
44406 TTTTGATTAAATTTTATCACTCAATTTTAAT
1 TTTT-ATTAAATTTTATCACTAAATTTTAAT
44437 TTT
1 TTT
44440 GAATGGTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (30 bp):
TTTTATTAAATTTTATCACTAAATTTTAAT
Found at i:46282 original size:2 final size:2
Alignment explanation
Indices: 46275--46316 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
46265 TGAATATGAG
46275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46317 GTATGTATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46321 original size:4 final size:4
Alignment explanation
Indices: 46314--46340 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
46304 TATATATATA
46314 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
46341 ATGTAAAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:57231 original size:28 final size:27
Alignment explanation
Indices: 57184--57264 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 27
57174 TTTGACAAAT
* *
57184 AAATAAGCCTCCATATTTGACAAACACA
1 AAATAA-CCACCATTTTTGACAAACACA
57212 AAGGA-AACCACCATTTTTGACAAACACA
1 AA--ATAACCACCATTTTTGACAAACACA
*
57240 AAATAATCACCATTTTTGACAAACA
1 AAATAACCACCATTTTTGACAAACA
57265 AACGGGTGGC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
26 1 0.02
27 20 0.43
28 23 0.49
29 2 0.04
30 1 0.02
ACGTcount: A:0.47, C:0.23, G:0.07, T:0.22
Consensus pattern (27 bp):
AAATAACCACCATTTTTGACAAACACA
Found at i:57258 original size:27 final size:27
Alignment explanation
Indices: 57194--57264 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
57184 AAATAAGCCT
*
57194 CCATATTTGACAAACACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
*
57222 CCATTTTTGACAAACACAAA-ATAATCA
1 CCATTTTTGACAAACACAAAGA-AACCA
57249 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
57265 AACGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.50
28 19 0.47
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:58738 original size:21 final size:22
Alignment explanation
Indices: 58700--58745 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
58690 ATCTGTTGAA
* **
58700 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
58721 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
58743 ACT
1 ACT
58746 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:64384 original size:15 final size:15
Alignment explanation
Indices: 64360--64396 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
64350 AAAACTGATA
*
64360 TTATTATTATTATTG
1 TTATTATTATAATTG
*
64375 TTATTGTTATAATTG
1 TTATTATTATAATTG
64390 TTATTAT
1 TTATTAT
64397 GAAACTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (15 bp):
TTATTATTATAATTG
Found at i:65562 original size:22 final size:22
Alignment explanation
Indices: 65520--65560 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
65510 GCATATTTAA
65520 ATATATATATACTTATAAAATT
1 ATATATATATACTTATAAAATT
*
65542 ATATATATATAATT-TAAAA
1 ATATATATATACTTATAAAA
65561 ATAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATATATATACTTATAAAATT
Found at i:66175 original size:2 final size:2
Alignment explanation
Indices: 66170--66198 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
66160 TCAATTTGTT
66170 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 T
66199 GTTGAGCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66929 original size:11 final size:11
Alignment explanation
Indices: 66915--66951 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
66905 AGATTATATT
66915 TTATTTATAAA
1 TTATTTATAAA
* *
66926 TTATTTTTAAT
1 TTATTTATAAA
66937 TTATTTATAAA
1 TTATTTATAAA
66948 TTAT
1 TTAT
66952 ACAAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:67238 original size:20 final size:21
Alignment explanation
Indices: 67211--67260 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
67201 TACTTTTTAT
67211 TTAT-AATTATTTTTAACTTA
1 TTATAAATTATTTTTAACTTA
*
67231 -TATAAATTA-TTTTAATTTA
1 TTATAAATTATTTTTAACTTA
67250 TTATAAATTAT
1 TTATAAATTAT
67261 ACAAATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TTATAAATTATTTTTAACTTA
Found at i:67267 original size:309 final size:307
Alignment explanation
Indices: 66919--67559 Score: 918
Period size: 309 Copynumber: 2.1 Consensus size: 307
66909 TATATTTTAT
66919 TTATAAATTATTTTTAATTTATTTATAAATTATACAAATTTATTTGTATTAAAATTAATT-ATAT
1 TTATAAATTA-TTTTAATTTA-TTATAAATTATACAAATTTATTTGTATTAAAATTAATTAATAT
* * *
66983 TATACATATATTATTTTTATAATTGATAGAACTTAAATTTATGTTAGTCAACAATAAATTA-TTT
64 TATAAATATATTATTTTTATAATTGATAGAACTTAAATTTATGTGAGCCAACAA-AAATTACTTT
* * * *
67047 TTTTCGATAACTACTTATTTCGAATTATAGAAGCATATATTTATTTTTC-AGTAATGACTTAAAT
128 TTTT-GATAACGACTTATTTCAAATTATAGAAGCACACATTTATTTTTCGA-TAATGACTTAAAT
** * * *
67111 ATGAG-CTT-TTTTATCTGTAAAATGACCAAGAAAAAATTTATTGTACATGTCTTATTTTTATTA
191 ACAAGTCTTCTTTTATCTGTAAAATGACC---AAAAAATTTATTATACATATATTATTTTTATTA
* *
67174 AAATTAATTAATATTGTGCATGTA-TATTACTTTTTATTTATAATTATTTTTAACTTA
253 AAATTAA-T-ATATTGTACATATATTATTACTTTTTA-TTATAATTATTTTTAACTTA
* *
67231 -TATAAATTATTTTAATTTATTATAAATTATACAAATTTATTTTTATTAAAATTAATTAATATTG
1 TTATAAATTATTTTAATTTATTATAAATTATACAAATTTATTTGTATTAAAATTAATTAATATTA
*
67295 TAAATGTATTATTTTTATAATTGATAGAACTTAAATTTATGTGAGCCAACAAAAATTACTTTTTT
66 TAAATATATTATTTTTATAATTGATAGAACTTAAATTTATGTGAGCCAACAAAAATTACTTTTTT
*
67360 TGATAACGACTTATTTCAAATTATAGACGCACACATTTATTTTTCGATAATGACTTAAATACAAG
131 TGATAACGACTTATTTCAAATTATAGAAGCACACATTTATTTTTCGATAATGACTTAAATACAAG
* *
67425 TTTTCTTTTATCTGTAAAATGATCAAAAAATTTATTATACATATATTATTTTTATTAAAATTAAT
196 TCTTCTTTTATCTGTAAAATGACCAAAAAATTTATTATACATATATTATTTTTATTAAAATTAAT
*
67490 ATATTGTACATATATTATTACTTTTTATTATAATTATTTTTAATTTA
261 ATATTGTACATATATTATTACTTTTTATTATAATTATTTTTAACTTA
**
67537 TTTATAAATTATTCAAATTTATT
1 -TTATAAATTATTTTAATTTATT
67560 TTTATTAAAA
Statistics
Matches: 298, Mismatches: 23, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
306 31 0.10
307 13 0.04
308 56 0.19
309 98 0.33
310 73 0.24
311 27 0.09
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.49
Consensus pattern (307 bp):
TTATAAATTATTTTAATTTATTATAAATTATACAAATTTATTTGTATTAAAATTAATTAATATTA
TAAATATATTATTTTTATAATTGATAGAACTTAAATTTATGTGAGCCAACAAAAATTACTTTTTT
TGATAACGACTTATTTCAAATTATAGAAGCACACATTTATTTTTCGATAATGACTTAAATACAAG
TCTTCTTTTATCTGTAAAATGACCAAAAAATTTATTATACATATATTATTTTTATTAAAATTAAT
ATATTGTACATATATTATTACTTTTTATTATAATTATTTTTAACTTA
Found at i:67527 original size:22 final size:22
Alignment explanation
Indices: 67502--67549 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
67492 ATTGTACATA
* *
67502 TATTATTACTTTTTATTAT-AAT
1 TATTATTAATTTAT-TTATAAAT
*
67524 TATTTTTAATTTATTTATAAAT
1 TATTATTAATTTATTTATAAAT
67546 TATT
1 TATT
67550 CAAATTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
TATTATTAATTTATTTATAAAT
Done.