Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold197
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: 573162
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.31
Warning! 46325 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:559096 original size:16 final size:16
Alignment explanation
Indices: 559058--559088 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
559048 CCTTCTCTTC
559058 AAAAAAAAAGCAAAAG
1 AAAAAAAAAGCAAAAG
*
559074 AAAAAAAAAGGAAAA
1 AAAAAAAAAGCAAAA
559089 AAACAAAACA
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:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGCAAAAG
Found at i:559112 original size:12 final size:11
Alignment explanation
Indices: 559057--559108 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
559047 ACCTTCTCTT
*
559057 CAAAAAAAAAG
1 CAAAAAAAAAA
559068 CAAAAGAAAAAA
1 CAAAA-AAAAAA
559080 -AAAGGAAAAAAA
1 CAAA--AAAAAAA
559092 CAAAACAAAAAA
1 CAAAA-AAAAAA
559104 CAAAA
1 CAAAA
559109 CAAAGAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
11 9 0.26
12 22 0.63
13 4 0.11
ACGTcount: A:0.83, C:0.10, G:0.08, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:560245 original size:59 final size:58
Alignment explanation
Indices: 560102--560637 Score: 613
Period size: 59 Copynumber: 9.3 Consensus size: 58
560092 TCCGCTTTTT
* * * * **
560102 AGTCCTCAGAGAGCAGGATGCCTTTTCCTTTTAAAAGCCCCCACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACG-CTTTT-CTCTT-AAAGCCCACACAAGTTGGTGGCACCTT-C
*
560164 AGTCCTCAAAGAGCATGACGCTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGC-TTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
*
560223 AGTCCTCAAAGAGCGGGACGCTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGC-TTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
560282 AGTCCTCAAAGAGCGGGACACCTTTTCTCTTAAAGCCCACACAAGTTGGTAGGCACCTTC
1 AGTCCTCAAAGAGCAGGAC-GCTTTTCTCTTAAAGCCCACACAAGTTGGT-GGCACCTTC
560342 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACG-CTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
** **
560401 AGTCCTCAAAGAGCAGGAC-CCCTT-TC--AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTT-C
* * **
560456 AGTCCTCAAAGAGCAGGACAC-CTT-TC--AAAGCCCACACAAGTTGGTGGCATTTTTCC
1 AGTCCTCAAAGAGCAGGACGCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCA-CCTT-C
*
560512 AGTCCTC-AAGAGCAGGACAC----CTCTT-AAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACC-TTC
* * * *
560565 AGTCCTCAAAGAGCAGGACGC-CTT-TC--AAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACGCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCAC-CTTC
560620 AGTCCTCAAAGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
560638 TACACTTTAT
Statistics
Matches: 435, Mismatches: 22, Indels: 41
0.87 0.04 0.08
Matches are distributed among these distances:
53 10 0.02
54 61 0.14
55 103 0.24
56 18 0.04
57 3 0.01
59 133 0.31
60 81 0.19
61 5 0.01
62 21 0.05
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (58 bp):
AGTCCTCAAAGAGCAGGACGCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:560272 original size:119 final size:116
Alignment explanation
Indices: 560102--560637 Score: 631
Period size: 119 Copynumber: 4.7 Consensus size: 116
560092 TCCGCTTTTT
* * * *
560102 AGTCCTCAGAGAGCAGGATGCCTTTTCCTTTTAAAAGCCCCCACAAGTTGGTGGCATTTTCCAGT
1 AGTCCTCAAAGAGCAGGACG-CTTTT-CTCTT-AAAGCCCACACAAGTTGGTGGCATTTT-CAGT
* *
560167 CCTCAAAGAGCATGACGCTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
62 CCTCAAAGAGCAGGACAC-TTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
* **
560223 AGTCCTCAAAGAGCGGGACGCTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCT
1 AGTCCTCAAAGAGCAGGACGC-TTTTCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCT
*
560288 CAAAGAGCGGGACACCTTTTCTCTTAAAGCCCACACAAGTTGGTAGGCACCTTC
65 CAAAGAGCAGGACA-CTTTTCTCTTAAAGCCCACACAAGTTGGT-GGCACCTTC
**
560342 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCT
1 AGTCCTCAAAGAGCAGGACG-CTTTTCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCT
** **
560407 CAAAGAGCAGGAC-CCCTT-TC--AAAGCCCACACAAGTTGGTGGCATTTTCC
65 CAAAGAGCAGGACACTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTT-C
* *
560456 AGTCCTCAAAGAGCAGGACAC-CTT-TC--AAAGCCCACACAAGTTGGTGGCATTTTTCCAGTCC
1 AGTCCTCAAAGAGCAGGACGCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTT-CAGTCC
560517 TC-AAGAGCAGGACAC----CTCTT-AAGCCCACACAAGTTGGTGGCACCTTTC
64 TCAAAGAGCAGGACACTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACC-TTC
* * *
560565 AGTCCTCAAAGAGCAGGACGC-CTT-TC--AAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCT
1 AGTCCTCAAAGAGCAGGACGCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCT
560626 CAAAGAGCAGGA
65 CAAAGAGCAGGA
560638 TACACTTTAT
Statistics
Matches: 376, Mismatches: 26, Indels: 38
0.85 0.06 0.09
Matches are distributed among these distances:
108 9 0.02
109 107 0.28
110 15 0.04
111 11 0.03
112 2 0.01
113 7 0.02
114 39 0.10
116 2 0.01
117 3 0.01
118 46 0.12
119 108 0.29
120 6 0.02
121 21 0.06
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (116 bp):
AGTCCTCAAAGAGCAGGACGCTTTTCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTC
AAAGAGCAGGACACTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:561414 original size:19 final size:21
Alignment explanation
Indices: 561368--561417 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
561358 AAAAAATTCA
561368 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
561389 AATGTATCGATACATTTGT-G
1 AATGTATCGATACATTTGTAG
561409 -ATGTATCGA
1 AATGTATCGA
561418 CACAAGGTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 9 0.31
20 1 0.03
21 19 0.66
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:561485 original size:19 final size:18
Alignment explanation
Indices: 561455--561524 Score: 60
Period size: 19 Copynumber: 4.1 Consensus size: 18
561445 GAAATTCAAC
*
561455 AATTTATATCGATACATA
1 AATTTGTATCGATACATA
561473 AATTTTGTATCGATAC---
1 AA-TTTGTATCGATACATA
561489 AA--TGTATCGATACATA
1 AATTTGTATCGATACATA
* *
561505 AGTATTGTATCAATACATA
1 AAT-TTGTATCGATACATA
561524 A
1 A
561525 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
13 11 0.26
16 3 0.07
18 2 0.05
19 26 0.62
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.37
Consensus pattern (18 bp):
AATTTGTATCGATACATA
Found at i:561496 original size:13 final size:13
Alignment explanation
Indices: 561478--561502 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
561468 ACATAAATTT
561478 TGTATCGATACAA
1 TGTATCGATACAA
561491 TGTATCGATACA
1 TGTATCGATACA
561503 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:561502 original size:32 final size:32
Alignment explanation
Indices: 561461--561521 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
561451 CAACAATTTA
* *
561461 TATCGATACATAAATTTTGTATCGATACAATG
1 TATCGATACATAAATATTGTATCAATACAATG
*
561493 TATCGATACATAAGTATTGTATCAATACA
1 TATCGATACATAAATATTGTATCAATACA
561522 TAATTAGCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.36
Consensus pattern (32 bp):
TATCGATACATAAATATTGTATCAATACAATG
Found at i:561582 original size:13 final size:13
Alignment explanation
Indices: 561564--561589 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
561554 CATTTTTCTG
561564 TGTATCGATACAT
1 TGTATCGATACAT
561577 TGTATCGATACAT
1 TGTATCGATACAT
561590 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:561583 original size:33 final size:33
Alignment explanation
Indices: 561544--561610 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
561534 GCCAAGGAAA
***
561544 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
561577 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
561610 T
1 T
561611 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:564183 original size:52 final size:53
Alignment explanation
Indices: 563957--564239 Score: 208
Period size: 52 Copynumber: 5.4 Consensus size: 53
563947 CAATTCTCCA
* * * *
563957 CAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAATTTTCTAT
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACCAATTTTCTTT
* *
564009 -AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAA-TTTCTTT
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAAACACCAATTTTCTTT
* * ** ** * * ** *
564061 ACAATCGGGGACACTCCAACCCCG--TTAATCATCGGGATACTCCAACCCCGTTATTT
1 -CAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAAACACCAA---TTTTCTTT
*
564117 C--TGAGGGGATACTCCAACCCC-AGTTTTATTTTC-AAAACACCAATTTTCTTT
1 CAAT-CGGGGATACTCCAACCCCGA-TTTTATTTTCAAAAACACCAATTTTCTTT
* * * **
564168 CAATCGGGGATACTCCAACACCGATTTTATTTCCAAAAATACCAATTTT-TCA
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACCAATTTTCTTT
*
564220 CAATCGAGGATACTCCAACC
1 CAATCGGGGATACTCCAACC
564240 TCGTTATTTC
Statistics
Matches: 179, Mismatches: 36, Indels: 32
0.72 0.15 0.13
Matches are distributed among these distances:
51 37 0.21
52 62 0.35
53 25 0.14
54 43 0.24
55 1 0.01
56 11 0.06
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.31
Consensus pattern (53 bp):
CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACCAATTTTCTTT
Found at i:564212 original size:159 final size:159
Alignment explanation
Indices: 563962--564315 Score: 491
Period size: 160 Copynumber: 2.2 Consensus size: 159
563952 CTCCACAATC
* * *
563962 GGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCG-TTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAAC
* * *
564027 TCCGATTTTATTTCCAAAAAACACCAATTTCTTTACAATCGGGGACACTCCAACCCCGTTA-ATC
65 ACCGATTTTATTTCCAAAAAACACCAATTT-TTCACAATCGAGGACACTCCAACCCCGTTATATC
564091 ATC-GGGATACTCCAACCCCGTTA-TTTCTGA
129 ATCGGGGATACTCCAACCCCGTTACTTT-TGA
*
564121 GGGGATACTCCAACCCCAGTTTTATTTTCAAAACACCAATTTTCTTTCAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCC-GTTTTATTTTCAAAACACCAATTTTCTAT-AATCGGGGATACTCCAA
* * * *
564186 CACCGATTTTATTTCC-AAAAATACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTATTTC
64 CACCGATTTTATTTCCAAAAAACACCAATTTTTCACAATCGAGGACACTCCAACCCCGTTATATC
564250 ATCGGGGATACTCCAACCCCGTTACTTTTGA
129 ATCGGGGATACTCCAACCCCGTTACTTTTGA
* * * *
564281 GGGAACACTCCAACCCCGTTATTATCTCCAAAACA
1 GGGGATACTCCAACCCCGTT-TTATTTTCAAAACA
564316 TTAAATTTCT
Statistics
Matches: 174, Mismatches: 15, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
158 26 0.15
159 62 0.36
160 83 0.48
161 3 0.02
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (159 bp):
GGGGATACTCCAACCCCGTTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAACA
CCGATTTTATTTCCAAAAAACACCAATTTTTCACAATCGAGGACACTCCAACCCCGTTATATCAT
CGGGGATACTCCAACCCCGTTACTTTTGA
Found at i:564250 original size:31 final size:28
Alignment explanation
Indices: 564222--564303 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 28
564212 ATTTTTCACA
*
564222 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
*
564250 ATCGGGGATACTCCAACCCCGTTACTTT-
1 ATCGAGGATACTCCAACCCCGTTA-TTTC
*
564278 -T-GAGGGAACACTCCAACCCCGTTATT
1 ATCGA-GG-ATACTCCAACCCCGTTATT
564304 ATCTCCAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
26 1 0.02
27 5 0.11
28 38 0.81
29 3 0.06
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.28
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTATTTC
Found at i:565998 original size:19 final size:19
Alignment explanation
Indices: 565974--566038 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
565964 GTCAATGATT
565974 TGTATCGATACATAAGTGC
1 TGTATCGATACATAAGTGC
565993 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGC
566006 TGTATCGATACATAAGTGC
1 TGTATCGATACATAAGTGC
566025 TGTATCGATACATA
1 TGTATCGATACATA
566039 TGAAGCTACT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
19 25 0.62
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (19 bp):
TGTATCGATACATAAGTGC
Found at i:566011 original size:13 final size:13
Alignment explanation
Indices: 565993--566017 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
565983 ACATAAGTGC
565993 TGTATCGATACAA
1 TGTATCGATACAA
566006 TGTATCGATACA
1 TGTATCGATACA
566018 TAAGTGCTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:566015 original size:32 final size:32
Alignment explanation
Indices: 565974--566036 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
565964 GTCAATGATT
565974 TGTATCGATACATAAGTGCTGTATCGATACAA
1 TGTATCGATACATAAGTGCTGTATCGATACAA
566006 TGTATCGATACATAAGTGCTGTATCGATACA
1 TGTATCGATACATAAGTGCTGTATCGATACA
566037 TATGAAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (32 bp):
TGTATCGATACATAAGTGCTGTATCGATACAA
Found at i:566084 original size:20 final size:19
Alignment explanation
Indices: 566059--566112 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
566049 GCCAAGAAAA
*
566059 TGTATCGATACATTACTCAT
1 TGTATCGATACATGA-TCAT
*
566079 TGTATCGATACACTGATCTT
1 TGTATCGATACA-TGATCAT
566099 TGTATCGATACATG
1 TGTATCGATACATG
566113 CAGGCAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATGATCAT
Found at i:567070 original size:20 final size:20
Alignment explanation
Indices: 567033--567071 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
567023 ACAACCTTGA
*
567033 TCATGCATTTTTACCATGTT
1 TCATGCATTTATACCATGTT
*
567053 TCATGCATTTATAGCATGT
1 TCATGCATTTATACCATGT
567072 CCAGCACCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (20 bp):
TCATGCATTTATACCATGTT
Found at i:570211 original size:200 final size:200
Alignment explanation
Indices: 569847--570246 Score: 685
Period size: 200 Copynumber: 2.0 Consensus size: 200
569837 TATATCTTTT
*
569847 TACAATTGGGTCCACAATATGAAAATAAGTGGATAGGTATTTTTGAACAAATAAGAAGCTTTTTA
1 TACAATTGGGTCCACAATATGAAAATAACTGGATAGGTATTTTTGAACAAATAAGAAGCTTTTTA
* *
569912 AAAAGTATCAAAATAAATTTGGGGAGCATCAACTTGTTTCATCTAGTGATGTTGAAAGAAATAGT
66 AAAAGTATCAAAATAAATTTGGGGAGCATCAACTTGCTTCATCTAGTGATGCTGAAAGAAATAGT
* *
569977 CAAAGAGAAATTTGTCAAGGAATGAGAATAAGTTATATTTGTTTACATTTTTATTAAATTATTAA
131 CAAAGAAAAATTTCTCAAGGAATGAGAATAAGTTATATTTGTTTACATTTTTATTAAATTATTAA
570042 TTAAA
196 TTAAA
* *
570047 TACAATTGGGTTCACAATATGAAAATAACTGGGTAGGTATTTTTGAACAAATGAAGAAGCTTTTT
1 TACAATTGGGTCCACAATATGAAAATAACTGGATAGGTATTTTTGAACAAAT-AAGAAGCTTTTT
* *
570112 GAAAAGTATCGAAATAAA-TTGGGGAGCATCAACTTGCTTCATCTAGTGATGCTGAAAGAAATAG
65 AAAAAGTATCAAAATAAATTTGGGGAGCATCAACTTGCTTCATCTAGTGATGCTGAAAGAAATAG
* *
570176 TCAAAGAAAAATTTCTCAAGGCATGAGAGTAAGTTATATTTGTTTACATTTTTATTAAATTATTA
130 TCAAAGAAAAATTTCTCAAGGAATGAGAATAAGTTATATTTGTTTACATTTTTATTAAATTATTA
570241 ATTAAA
195 ATTAAA
570247 GATTTTAATA
Statistics
Matches: 188, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
200 160 0.85
201 28 0.15
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (200 bp):
TACAATTGGGTCCACAATATGAAAATAACTGGATAGGTATTTTTGAACAAATAAGAAGCTTTTTA
AAAAGTATCAAAATAAATTTGGGGAGCATCAACTTGCTTCATCTAGTGATGCTGAAAGAAATAGT
CAAAGAAAAATTTCTCAAGGAATGAGAATAAGTTATATTTGTTTACATTTTTATTAAATTATTAA
TTAAA
Found at i:571241 original size:21 final size:22
Alignment explanation
Indices: 571202--571244 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
571192 TAAAGCTCAT
571202 GATATAATTCACTTTTTGATAA
1 GATATAATTCACTTTTTGATAA
571224 GATATAATTCAC-TTTTGATAA
1 GATATAATTCACTTTTTGATAA
571245 ATTATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (22 bp):
GATATAATTCACTTTTTGATAA
Found at i:571508 original size:16 final size:16
Alignment explanation
Indices: 571483--571525 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
571473 ATTCGGTTTC
*
571483 TTTCGGGTTTGAGCTA
1 TTTCGAGTTTGAGCTA
571499 TTTCGAGTTTGAGCTA
1 TTTCGAGTTTGAGCTA
*
571515 TTTCAAGTTTG
1 TTTCGAGTTTG
571526 GATTTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.16, C:0.12, G:0.26, T:0.47
Consensus pattern (16 bp):
TTTCGAGTTTGAGCTA
Found at i:572520 original size:19 final size:20
Alignment explanation
Indices: 572494--572539 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
572484 CAATGCTTCA
572494 ATTGATTACCTACTAATTAG
1 ATTGATTACCTACTAATTAG
* *
572514 A-TGATTATCTATTAATTAG
1 ATTGATTACCTACTAATTAG
572533 ATTGATT
1 ATTGATT
572540 TGATAATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.46
Consensus pattern (20 bp):
ATTGATTACCTACTAATTAG
Done.