Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2337
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: 69618
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:3243 original size:15 final size:15
Alignment explanation
Indices: 3225--3278 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
3215 CTTCTTCTCT
*
3225 CCTCCTCCTGTCATC
1 CCTCCTCCTATCATC
*
3240 CCTCCTCTCTCTATTATC
1 CCT-C-CTC-CTATCATC
*
3258 TCTCCTCCTATCATC
1 CCTCCTCCTATCATC
3273 CCTCCT
1 CCTCCT
3279 ATCTCTACTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 15 0.48
16 4 0.13
17 4 0.13
18 8 0.26
ACGTcount: A:0.09, C:0.50, G:0.02, T:0.39
Consensus pattern (15 bp):
CCTCCTCCTATCATC
Found at i:3262 original size:18 final size:18
Alignment explanation
Indices: 3241--3302 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
3231 CCTGTCATCC
3241 CTCCTCTCTCTATTATCT
1 CTCCTCTCTCTATTATCT
* *
3259 CT-C-CTC-CTATCATCC
1 CTCCTCTCTCTATTATCT
* *
3274 CTCCTATCTCTACTATCT
1 CTCCTCTCTCTATTATCT
*
3292 CTCCTGTCTCT
1 CTCCTCTCTCT
3303 CCTCCTATCA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
15 9 0.26
16 4 0.12
17 3 0.09
18 18 0.53
ACGTcount: A:0.11, C:0.44, G:0.02, T:0.44
Consensus pattern (18 bp):
CTCCTCTCTCTATTATCT
Found at i:3272 original size:33 final size:33
Alignment explanation
Indices: 3226--3296 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3216 TTCTTCTCTC
* * *
3226 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCT
3259 CTCCTCCTATCATCCCTCCTATCTCTACTATCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCT
3292 CTCCT
1 CTCCT
3297 GTCTCTCCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.46, G:0.01, T:0.41
Consensus pattern (33 bp):
CTCCTCCTATCATCCCTCCTATCTCTACTATCT
Found at i:3276 original size:12 final size:11
Alignment explanation
Indices: 3254--3325 Score: 53
Period size: 12 Copynumber: 6.5 Consensus size: 11
3244 CTCTCTCTAT
3254 TATCTCTCCTCC
1 TATCTC-CCTCC
3266 TATCATCCCTCC
1 TATC-TCCCTCC
*
3278 TATCT--CTAC
1 TATCTCCCTCC
3287 TATCT--CTCC
1 TATCTCCCTCC
*
3296 TGTCTCTCCTCC
1 TATCTC-CCTCC
3308 TATCATCCCTCC
1 TATC-TCCCTCC
*
3320 TCTCTC
1 TATCTC
3326 TTCTTTCTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
9 15 0.30
11 3 0.06
12 28 0.56
13 4 0.08
ACGTcount: A:0.11, C:0.47, G:0.01, T:0.40
Consensus pattern (11 bp):
TATCTCCCTCC
Found at i:3302 original size:42 final size:42
Alignment explanation
Indices: 3256--3335 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
3246 CTCTCTATTA
3256 TCTCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTG
1 TCTCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTG
* * *
3298 TCTCTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 TCTCTCCTCCTATCATCCCTCCTATCTCTACTATCTCT
3336 TTGAGGGCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.09, C:0.46, G:0.01, T:0.44
Consensus pattern (42 bp):
TCTCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTG
Found at i:5791 original size:20 final size:21
Alignment explanation
Indices: 5752--5792 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5742 TTTTTTTTAA
*
5752 TTTTTTTTTGTTGTCTTTCTT
1 TTTTTTTTTGTTGTCATTCTT
*
5773 TTTTTTTTTTTTGT-ATTCTT
1 TTTTTTTTTGTTGTCATTCTT
5793 GAAGAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.83
Consensus pattern (21 bp):
TTTTTTTTTGTTGTCATTCTT
Found at i:9794 original size:585 final size:587
Alignment explanation
Indices: 8679--9849 Score: 1829
Period size: 585 Copynumber: 2.0 Consensus size: 587
8669 TTTTTTTTTT
* *
8679 ATGACAACCATGATCCAAGGTTGCCTAAATAACAATCTTGAGATGGATTTCTAACAACAAACAGA
1 ATGACAACCATGAACCAAGGTTGCCAAAATAACAATCTTGAGATGGATTTCTAACAACAAACAGA
* *
8744 ATTATTAAAGGAAGAATAGAAATTGAAAAAAGCAAAAAAAATAATAAAACTGGAATAAAAGAGAG
66 ATTATTAAAGCAAGAATAGAAATTGAAAAAAGCAAAAAAAATAACAAAACTGGAATAAAAGAGAG
* * *
8809 ATGAAGGATGGCACCACAATCACAGGATTGATAAGCCAAAATGAATGATTGCCACAAGAGTCTCA
131 ATGAAGGATGGCACCACAATCACAAGATTGATAAGCCAAAAGGAATGATCGCCACAAGAGTCTCA
* * *
8874 ACCTTTTGATAAGATCTAAAAAAATGTTCTCACTCAAGAACCTAAGAATCACACTTGCACACAAA
196 ACCTCTTGATAAGATCCAAAAAAATGTGCTCACTCAAGAACCTAAGAATCACACTTGCACACAAA
* *
8939 ATGTGTTTAATCTGCAAATATCATTATCTGCCCCGTTCCAAATCTGTTTACAAGAGCTTATATAT
261 ATGTGTTT-ATCTGCAAATATCAATATCTGCCCCGCTCCAAATCTGTTTACAAGAGCTTATATAT
* *
9004 GCCTTCATAAGCCATAGTTAACACAAACCCTAAGGGGCTTATAGTGCTAACAAGCCCAATTCTTA
325 GCCCTCATAAGCCATAGTTAACACAAACCCTAAGGGGCTTATAGTGCTAACAAGCCCAACTCTTA
* * * *
9069 GTTAAACCCAAATAACAAGTTTTTATACTAAATAAAGCCCAAAGCAAGTCACAACCAGTAGGCCC
390 CTTAAACCCAAATAACAAGATTTTATACTAAATAAAACCCAAAGCAAGTCACAACCAGCAGGCCC
*
9134 TTTATTACAAAAAGACCCGAGTCCTAATTCAATCCATTGGAGCCCATATCTTCCAAATATATGCA
455 TTTATTACAAAAAGACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCTTCCAAATATATGCA
* * *
9199 ATTGACTAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAGGGCAGCAACCATCT
520 ATTAACTAGCTTGGGCTCTTCTAACTCCAAATTGAGTCTACTTTCAAATAGGCCAGCAACCATCT
9264 TTG
585 TTG
** *
9267 ATGACAACCATGAACCAAGGTTGCCAAAATAATGATCTTGAGATGGATTTCTAACAATAAACAGA
1 ATGACAACCATGAACCAAGGTTGCCAAAATAACAATCTTGAGATGGATTTCTAACAACAAACAGA
* * * *
9332 ATTATTGATGCAAGAATAGAAATTGAAAGAAGCAGAAAAAAATAACAAAA-TGGAATAGAATTG-
66 ATTATTAAAGCAAGAATAGAAATTGAAAAAAGCA-AAAAAAATAACAAAACTGGAATA-AA-AGA
* *
9395 GAGATGGAGGATGGCGCCACAATCACAAGATTGATAAGCCAAAAGGAATGATCGCCACAAGAGTC
128 GAGATGAAGGATGGCACCACAATCACAAGATTGATAAGCCAAAAGGAATGATCGCCACAAGAGTC
*** *
9460 TTGGCCTCTTGATAAGATCCAGAAAAAT-TGGCTCACTCAAGAACCTAAGAATCACACTCT-CAC
193 TCAACCTCTTGATAAGATCCAAAAAAATGT-GCTCACTCAAGAACCTAAGAATCACACT-TGCAC
* * *
9523 GCAAAATGTGTTT-TCTGCAAATATGAATGTCT-CCCC-CTCCAAATCTGTTTACAAGAGCTTAT
256 ACAAAATGTGTTTATCTGCAAATATCAATATCTGCCCCGCTCCAAATCTGTTTACAAGAGCTTAT
9585 ATATGCCCTCATAAGCCATAGTTAACACAAACCCTAAGGGGCTTATTA-TGCTAACAAGCCCAAC
321 ATATGCCCTCATAAGCCATAGTTAACACAAACCCTAAGGGGCTTA-TAGTGCTAACAAGCCCAAC
*
9649 TCTTACTTAAACCCAAATAACAAGATTTTATGCTAAATAAAACCCAAAGCAAGTCACAACCAGCA
385 TCTTACTTAAACCCAAATAACAAGATTTTATACTAAATAAAACCCAAAGCAAGTCACAACCAGCA
* *
9714 GGCCCTTTATTACAAAATA-ATCCAAGTCCTAATTGAATCCATTGGAGCCCATATCTTCCAAATA
450 GGCCCTTTATTACAAAA-AGACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCTTCCAAATA
*
9778 TATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAGATTGAGTCTACTTTCAAATAGGCCAGCAA
514 TATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAAATTGAGTCTACTTTCAAATAGGCCAGCAA
9843 CCATCTT
579 CCATCTT
9850 CTCTAGGTCT
Statistics
Matches: 534, Mismatches: 42, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
585 271 0.51
586 7 0.01
587 16 0.03
588 98 0.18
589 140 0.26
590 2 0.00
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (587 bp):
ATGACAACCATGAACCAAGGTTGCCAAAATAACAATCTTGAGATGGATTTCTAACAACAAACAGA
ATTATTAAAGCAAGAATAGAAATTGAAAAAAGCAAAAAAAATAACAAAACTGGAATAAAAGAGAG
ATGAAGGATGGCACCACAATCACAAGATTGATAAGCCAAAAGGAATGATCGCCACAAGAGTCTCA
ACCTCTTGATAAGATCCAAAAAAATGTGCTCACTCAAGAACCTAAGAATCACACTTGCACACAAA
ATGTGTTTATCTGCAAATATCAATATCTGCCCCGCTCCAAATCTGTTTACAAGAGCTTATATATG
CCCTCATAAGCCATAGTTAACACAAACCCTAAGGGGCTTATAGTGCTAACAAGCCCAACTCTTAC
TTAAACCCAAATAACAAGATTTTATACTAAATAAAACCCAAAGCAAGTCACAACCAGCAGGCCCT
TTATTACAAAAAGACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCTTCCAAATATATGCAA
TTAACTAGCTTGGGCTCTTCTAACTCCAAATTGAGTCTACTTTCAAATAGGCCAGCAACCATCTT
TG
Found at i:12774 original size:54 final size:54
Alignment explanation
Indices: 12715--12821 Score: 187
Period size: 54 Copynumber: 2.0 Consensus size: 54
12705 CTGATACCAA
*
12715 TTGATGACAACCATGATCCAAGGTTGCCTAAATAACGATCTTGAGATGGATTTT
1 TTGATGACAACCATGAACCAAGGTTGCCTAAATAACGATCTTGAGATGGATTTT
* *
12769 TTGATGACAACCATGAACCAAGGTTGCCTGAATAATGATCTTGAGATGGATTT
1 TTGATGACAACCATGAACCAAGGTTGCCTAAATAACGATCTTGAGATGGATTT
12822 CTAACAATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (54 bp):
TTGATGACAACCATGAACCAAGGTTGCCTAAATAACGATCTTGAGATGGATTTT
Found at i:15324 original size:12 final size:11
Alignment explanation
Indices: 15302--15377 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
15292 AGAGAAAGAA
*
15302 GAGAGAGGAGG
1 GAGATAGGAGG
15313 GATGATAGGAGG
1 GA-GATAGGAGG
*
15325 AGAGACAGGA--
1 -GAGATAGGAGG
*
15335 GAGATAGTA--
1 GAGATAGGAGG
15344 GAGATAGGAGG
1 GAGATAGGAGG
15355 GATGATAGGAGG
1 GA-GATAGGAGG
*
15367 AGAGACAGGAG
1 -GAGATAGGAG
15378 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:15334 original size:24 final size:24
Alignment explanation
Indices: 15301--15386 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
15291 AAGAGAAAGA
*
15301 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
15325 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
15343 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
15367 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
15387 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:15353 original size:42 final size:42
Alignment explanation
Indices: 15292--15410 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
15282 TAGCCCTCAA
* *
15292 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
15334 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
15376 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
15411 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:24516 original size:42 final size:42
Alignment explanation
Indices: 24461--24579 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
24451 TTCTTCTCTC
* *
24461 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
24503 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
24545 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
24580 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:24520 original size:12 final size:11
Alignment explanation
Indices: 24494--24569 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
24484 TCTATTATCT
*
24494 CTCCTGTCTCTC
1 CTCCTATCTC-C
24506 CTCCTATCATCC
1 CTCCTATC-TCC
24518 CTCCTATCT--
1 CTCCTATCTCC
*
24527 CTACTATCT--
1 CTCCTATCTCC
*
24536 CTCCTGTCTCTC
1 CTCCTATCTC-C
24548 CTCCTATCATCC
1 CTCCTATC-TCC
*
24560 CTCCTCTCTC
1 CTCCTATCTC
24570 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:24521 original size:24 final size:24
Alignment explanation
Indices: 24485--24570 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
24475 CCTCCTCTCT
* *
24485 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
24509 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
24530 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
24551 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
24571 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:24545 original size:18 final size:18
Alignment explanation
Indices: 24476--24546 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
24466 CCTGTCATCC
* *
24476 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
24494 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
24516 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
24536 CTCCTGTCTCT
1 CTCCTGTCTCT
24547 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:28243 original size:12 final size:12
Alignment explanation
Indices: 28223--28257 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
28213 AAATGAAAGA
28223 AGAGATAGGAGG
1 AGAGATAGGAGG
28235 -GATGATAGGAGG
1 AGA-GATAGGAGG
28247 AGAGATAGGAG
1 AGAGATAGGAG
28258 AGATAGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.40, C:0.00, G:0.49, T:0.11
Consensus pattern (12 bp):
AGAGATAGGAGG
Found at i:36742 original size:9 final size:9
Alignment explanation
Indices: 36730--36790 Score: 50
Period size: 9 Copynumber: 6.1 Consensus size: 9
36720 CTCTCTCTAT
36730 TATCTCTCC
1 TATCTCTCC
36739 TATCTCTTCTCC
1 TA--TC-TCTCC
36751 TATCATCCCTCC
1 TATC-T--CTCC
*
36763 TATCTCTAC
1 TATCTCTCC
36772 TATCTCTCC
1 TATCTCTCC
*
36781 TATTTCTCC
1 TATCTCTCC
36790 T
1 T
36791 CCTATCATCC
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 22 0.51
10 3 0.07
11 3 0.07
12 15 0.35
ACGTcount: A:0.13, C:0.41, G:0.00, T:0.46
Consensus pattern (9 bp):
TATCTCTCC
Found at i:36749 original size:42 final size:42
Alignment explanation
Indices: 36702--36811 Score: 175
Period size: 42 Copynumber: 2.6 Consensus size: 42
36692 TTCTTCTCTC
* * *
36702 CTTCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTATCT
1 CTTCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
*
36744 CTTCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATTT
1 CTTCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
*
36786 CTCCTCCTATCATCCCTCCTATCTCT
1 CTTCTCCTATCATCCCTCCTATCTCT
36812 TCTTTCTTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.12, C:0.44, G:0.01, T:0.44
Consensus pattern (42 bp):
CTTCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
Found at i:39725 original size:12 final size:11
Alignment explanation
Indices: 39703--39778 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
39693 AGAGAAAGAA
*
39703 GAGAGAGGAGG
1 GAGATAGGAGG
39714 GATGATAGGAGG
1 GA-GATAGGAGG
*
39726 AGAGACAGGA--
1 -GAGATAGGAGG
*
39736 GAGATAGTA--
1 GAGATAGGAGG
39745 GAGATAGGAGG
1 GAGATAGGAGG
39756 GATGATAGGAGG
1 GA-GATAGGAGG
*
39768 AGAGACAGGAG
1 -GAGATAGGAG
39779 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:39735 original size:24 final size:24
Alignment explanation
Indices: 39702--39787 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
39692 AAGAGAAAGA
*
39702 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
39726 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
39744 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
39768 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
39788 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:39754 original size:42 final size:42
Alignment explanation
Indices: 39693--39811 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
39683 TAGCCCTCAA
* *
39693 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
39735 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
39777 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
39812 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:45651 original size:18 final size:18
Alignment explanation
Indices: 45621--45667 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
45611 ATCTTCTTCT
45621 CTCCTC-CTCCTATCATCC
1 CTCCTCTCT-CTATCATCC
* *
45639 CTCCTCTCTCTATTATCT
1 CTCCTCTCTCTATCATCC
*
45657 CTCCTATCTCT
1 CTCCTCTCTCT
45668 TCTCCTATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 23 0.92
19 2 0.08
ACGTcount: A:0.11, C:0.47, G:0.00, T:0.43
Consensus pattern (18 bp):
CTCCTCTCTCTATCATCC
Found at i:45664 original size:9 final size:9
Alignment explanation
Indices: 45652--45712 Score: 59
Period size: 9 Copynumber: 6.1 Consensus size: 9
45642 CTCTCTCTAT
45652 TATCTCTCC
1 TATCTCTCC
45661 TATCTCTTCTCC
1 TA--TC-TCTCC
45673 TATCATCCCTCC
1 TATC-T--CTCC
*
45685 TATCTCTAC
1 TATCTCTCC
45694 TATCTCTCC
1 TATCTCTCC
45703 TATCTCTCC
1 TATCTCTCC
45712 T
1 T
45713 CCTATCATCC
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
9 23 0.52
10 3 0.07
11 3 0.07
12 15 0.34
ACGTcount: A:0.13, C:0.43, G:0.00, T:0.44
Consensus pattern (9 bp):
TATCTCTCC
Found at i:45678 original size:42 final size:42
Alignment explanation
Indices: 45624--45742 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
45614 TTCTTCTCTC
* *
45624 CTCCTCCTATCATCCCTCCTCTCTCTATTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
*
45666 CTTCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
* * *
45708 CTCCTCCTATCATCCCTCTTATCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCT
45743 TTAAGGGCTA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.12, C:0.44, G:0.00, T:0.45
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
Found at i:45704 original size:18 final size:18
Alignment explanation
Indices: 45639--45709 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 18
45629 CCTATCATCC
* *
45639 CTCCTCTCTCTATTATCT
1 CTCCTATCTCTACTATCT
*
45657 CTCCTATCTCTTCTCCTATCAT
1 CTCCTA--TC-TCTACTATC-T
45679 CCCTCCTATCTCTACTATCT
1 --CTCCTATCTCTACTATCT
45699 CTCCTATCTCT
1 CTCCTATCTCT
45710 CCTCCTATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
18 16 0.37
20 3 0.07
21 15 0.35
22 3 0.07
24 6 0.14
ACGTcount: A:0.13, C:0.42, G:0.00, T:0.45
Consensus pattern (18 bp):
CTCCTATCTCTACTATCT
Found at i:45716 original size:12 final size:12
Alignment explanation
Indices: 45657--45733 Score: 53
Period size: 12 Copynumber: 6.9 Consensus size: 12
45647 TCTATTATCT
*
45657 CTCCTATCTCTT
1 CTCCTATCTCTC
45669 CTCCTATCATC-C
1 CTCCTATC-TCTC
45681 CTCCTA--TCT-
1 CTCCTATCTCTC
*
45690 CTACTA--TCT-
1 CTCCTATCTCTC
45699 CTCCTATCTCTC
1 CTCCTATCTCTC
45711 CTCCTATCATC-C
1 CTCCTATC-TCTC
*
45723 CTCTTATCTCT
1 CTCCTATCTCT
45734 TCTTTCTCTT
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
9 15 0.28
11 5 0.09
12 30 0.56
13 4 0.07
ACGTcount: A:0.13, C:0.44, G:0.00, T:0.43
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:56144 original size:42 final size:42
Alignment explanation
Indices: 56097--56213 Score: 128
Period size: 42 Copynumber: 2.8 Consensus size: 42
56087 GAGAAAGAAG
*
56097 AGATAGGAGGAATGACATGAGGAGAGATAGAAGAGATAGTAC
1 AGATAGGAGGAATGACAGGAGGAGAGATAGAAGAGATAGTAC
* * * * *
56139 AGATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAATAG
1 AGATAGGAGGAATGACAGGAGGAGAGATAGAAGAGATAGTAC
* * * * *
56181 AGAGAGAAGGGATGATAGGAGGAG-GAGAGAAGA
1 AGATAGGAGGAATGACAGGAGGAGAGATAGAAGA
56214 AGATGGAAGA
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
41 7 0.11
42 58 0.89
ACGTcount: A:0.44, C:0.02, G:0.42, T:0.12
Consensus pattern (42 bp):
AGATAGGAGGAATGACAGGAGGAGAGATAGAAGAGATAGTAC
Found at i:56180 original size:12 final size:12
Alignment explanation
Indices: 56140--56187 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
56130 AGATAGTACA
*
56140 GATAGGAGGGAT
1 GATAGGAGAGAT
56152 GATAGGAGGAGA-
1 GATAGGA-GAGAT
56164 GATAGGAGAGAT
1 GATAGGAGAGAT
*
56176 AATAGAGAGAGA
1 GATAG-GAGAGA
56188 AGGGATGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 4 0.13
12 18 0.58
13 9 0.29
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12
Consensus pattern (12 bp):
GATAGGAGAGAT
Found at i:59412 original size:14 final size:13
Alignment explanation
Indices: 59408--59453 Score: 51
Period size: 14 Copynumber: 3.6 Consensus size: 13
59398 TATATTATAC
59408 TTATTTATACTTA
1 TTATTTATACTTA
59421 -T-TTTATACTTA
1 TTATTTATACTTA
*
59432 TTATATTATCCTTA
1 TTAT-TTATACTTA
*
59446 TTACTTAT
1 TTATTTAT
59454 TCTATTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 10 0.36
12 2 0.07
13 5 0.18
14 11 0.39
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATTTATACTTA
Found at i:59421 original size:21 final size:20
Alignment explanation
Indices: 59395--59454 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
59385 GTCCATTCCT
59395 TATTATATTATACTTATTTA
1 TATTATATTATACTTATTTA
*
59415 TACTTATTTTATACTTA-TTA
1 TA-TTATATTATACTTATTTA
*
59435 TATTATCCTTATTACTTATT
1 TATTAT-ATTA-TACTTATT
59455 CTATTATAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 4 0.12
20 10 0.29
21 19 0.56
22 1 0.03
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTATATTATACTTATTTA
Found at i:59425 original size:11 final size:11
Alignment explanation
Indices: 59397--59433 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
59387 CCATTCCTTA
*
59397 TTATATTATAC
1 TTATTTTATAC
59408 TTA-TTTATAC
1 TTATTTTATAC
59418 TTATTTTATAC
1 TTATTTTATAC
59429 TTATT
1 TTATT
59434 ATATTATCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTTATAC
Found at i:62519 original size:18 final size:18
Alignment explanation
Indices: 62498--62543 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
62488 CTGTCATCCC
* *
62498 TCCTCTCTCTATTATCTA
1 TCCTATCTCTACTATCTA
*
62516 TCCTATCTCTACTATCTC
1 TCCTATCTCTACTATCTA
*
62534 TGCTATCTCT
1 TCCTATCTCT
62544 CCTCCTATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.15, C:0.35, G:0.02, T:0.48
Consensus pattern (18 bp):
TCCTATCTCTACTATCTA
Found at i:65457 original size:9 final size:9
Alignment explanation
Indices: 65443--65502 Score: 63
Period size: 9 Copynumber: 7.0 Consensus size: 9
65433 CCTCTCTCAT
65443 TATCTCTCC
1 TATCTCTCC
65452 TATCTCTCC
1 TATCTCTCC
* *
65461 T-GCTAT-C
1 TATCTCTCC
*
65468 -ATCCCTCC
1 TATCTCTCC
*
65476 TATCTCTAC
1 TATCTCTCC
65485 TATCTCTCC
1 TATCTCTCC
65494 TATCTCTCC
1 TATCTCTCC
65503 ACCTATCATC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
7 3 0.08
8 4 0.10
9 33 0.82
ACGTcount: A:0.13, C:0.43, G:0.02, T:0.42
Consensus pattern (9 bp):
TATCTCTCC
Found at i:65466 original size:12 final size:12
Alignment explanation
Indices: 65448--65524 Score: 53
Period size: 12 Copynumber: 6.9 Consensus size: 12
65438 CTCATTATCT
65448 CTCCTATCTCTC
1 CTCCTATCTCTC
*
65460 CTGCTATCATC-C
1 CTCCTATC-TCTC
65472 CTCCTA--TCT-
1 CTCCTATCTCTC
*
65481 CTACTA--TCT-
1 CTCCTATCTCTC
65490 CTCCTATCTCTC
1 CTCCTATCTCTC
*
65502 CACCTATCATC-C
1 CTCCTATC-TCTC
65514 CTCCTATCTCT
1 CTCCTATCTCT
65525 TCTTTCTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
9 15 0.29
11 5 0.10
12 28 0.54
13 4 0.08
ACGTcount: A:0.14, C:0.45, G:0.01, T:0.39
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:65480 original size:24 final size:24
Alignment explanation
Indices: 65448--65524 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
65438 CTCATTATCT
*
65448 CTCCTATCTCTCCTGCTATCATCC
1 CTCCTATCTCTCCTACTATCATCC
65472 CTCCTA--TCT-CTACTATC-T--
1 CTCCTATCTCTCCTACTATCATCC
65490 CTCCTATCTCTCC-ACCTATCATCC
1 CTCCTATCTCTCCTA-CTATCATCC
65514 CTCCTATCTCT
1 CTCCTATCTCT
65525 TCTTTCTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
18 6 0.13
20 5 0.11
21 13 0.29
22 4 0.09
24 17 0.38
ACGTcount: A:0.14, C:0.45, G:0.01, T:0.39
Consensus pattern (24 bp):
CTCCTATCTCTCCTACTATCATCC
Found at i:65500 original size:42 final size:42
Alignment explanation
Indices: 65425--65524 Score: 157
Period size: 42 Copynumber: 2.4 Consensus size: 42
65415 CCTCCTCTTT
* * **
65425 TCATCCCTCCTCTCTC-ATTATCTCTCCTATCTCTCCTGCTA
1 TCATCCCTCCTATCTCTACTATCTCTCCTATCTCTCCACCTA
65466 TCATCCCTCCTATCTCTACTATCTCTCCTATCTCTCCACCTA
1 TCATCCCTCCTATCTCTACTATCTCTCCTATCTCTCCACCTA
65508 TCATCCCTCCTATCTCT
1 TCATCCCTCCTATCTCT
65525 TCTTTCTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
41 15 0.28
42 39 0.72
ACGTcount: A:0.14, C:0.45, G:0.01, T:0.40
Consensus pattern (42 bp):
TCATCCCTCCTATCTCTACTATCTCTCCTATCTCTCCACCTA
Done.