Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2564
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: 69127
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1364 original size:40 final size:40
Alignment explanation
Indices: 1235--1490 Score: 366
Period size: 39 Copynumber: 6.6 Consensus size: 40
1225 AAACCAAGTA
** * *
1235 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
1274 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC-AATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1313 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1353 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
1393 CCTTC-GGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
** * *
1432 CCTTCGGG-CTTAGCCCGAAT-TA-TCACTAGCAC-AATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1468 CCTTCGGGACTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
1491 CATCCGAATA
Statistics
Matches: 201, Mismatches: 10, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
36 12 0.06
37 18 0.09
38 3 0.01
39 101 0.50
40 67 0.33
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:1365 original size:79 final size:79
Alignment explanation
Indices: 1235--1486 Score: 372
Period size: 79 Copynumber: 3.2 Consensus size: 79
1225 AAACCAAGTA
** *
1235 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATA
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATA
1298 GTAACTCGCACAATG
65 GTAACTCGCACAATG
*
1313 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG
1378 TAACTCGCACAAATG
66 TAACTCGCAC-AATG
**
1393 CCTTC-GGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGAAT-TA-
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG
* *
1454 TCACTAGCACAATG
66 TAACTCGCACAATG
1468 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
1487 TTATCATCCG
Statistics
Matches: 161, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
75 9 0.06
76 21 0.13
77 2 0.01
78 23 0.14
79 97 0.60
80 9 0.06
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG
TAACTCGCACAATG
Found at i:9344 original size:40 final size:40
Alignment explanation
Indices: 9267--9527 Score: 352
Period size: 40 Copynumber: 6.6 Consensus size: 40
9257 AAACCAAGTA
** * *
9267 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
9306 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
9346 CCTTCGGGACTTAGCCCGGTTATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
9386 CCTTCGGGACTTAGCCCGGTTATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* *
9426 CCTTCAGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* *
9466 CCTTCGGG-CTTAGCCCGGAATTAT--TCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGG--TTATAGTAACTCGCACAAATG
* *
9505 CTTTCGGGACTTAGCTCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
9528 CATCCGAATA
Statistics
Matches: 201, Mismatches: 16, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
38 4 0.02
39 43 0.21
40 151 0.75
41 3 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:14363 original size:26 final size:26
Alignment explanation
Indices: 14327--14428 Score: 107
Period size: 31 Copynumber: 3.7 Consensus size: 26
14317 CTTTGTTTTT
14327 AGGGGATTGTTTTTTGTTTTTTGGAGG
1 AGGGG-TTGTTTTTTGTTTTTTGGAGG
14354 AGGGGTTGTTTTTTTTTTTGTTTTTTGGAGG
1 AGGGGTTG-----TTTTTTGTTTTTTGGAGG
* **
14385 A-GTGTTGTTTTTTGTTTTTTGGAAT
1 AGGGGTTGTTTTTTGTTTTTTGGAGG
*
14410 AGGGGTTGTTTTTTATTTT
1 AGGGGTTGTTTTTTGTTTT
14429 GGAAAGGCTA
Statistics
Matches: 64, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
25 17 0.27
26 18 0.28
27 5 0.08
30 5 0.08
31 19 0.30
ACGTcount: A:0.10, C:0.00, G:0.30, T:0.60
Consensus pattern (26 bp):
AGGGGTTGTTTTTTGTTTTTTGGAGG
Found at i:14374 original size:31 final size:30
Alignment explanation
Indices: 14336--14403 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 30
14326 TAGGGGATTG
14336 TTTTTTGTTTTTTGGAGGAGGGGTTGTTTTT
1 TTTTTTGTTTTTTGGAGGA-GGGTTGTTTTT
*
14367 TTTTTTGTTTTTTGGAGGAGTGTTGTTTTT
1 TTTTTTGTTTTTTGGAGGAGGGTTGTTTTT
14397 TGTTTTT
1 T-TTTTT
14404 TGGAATAGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.06, C:0.00, G:0.28, T:0.66
Consensus pattern (30 bp):
TTTTTTGTTTTTTGGAGGAGGGTTGTTTTT
Found at i:14584 original size:24 final size:24
Alignment explanation
Indices: 14555--14619 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 24
14545 AAACTAGCCT
14555 TTCC-AAAACAAAAAACAACCCCTA
1 TTCCAAAAACAAAAAACAA-CCCTA
*
14579 TTCCAAAAAACAAAAAACAACCCTC
1 TTCC-AAAAACAAAAAACAACCCTA
*
14604 CTCCAAAAACAAAAAA
1 TTCCAAAAACAAAAAA
14620 AAAAAAAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
24 16 0.43
25 7 0.19
26 14 0.38
ACGTcount: A:0.58, C:0.31, G:0.00, T:0.11
Consensus pattern (24 bp):
TTCCAAAAACAAAAAACAACCCTA
Found at i:14592 original size:26 final size:24
Alignment explanation
Indices: 14559--14619 Score: 86
Period size: 26 Copynumber: 2.5 Consensus size: 24
14549 TAGCCTTTCC
*
14559 AAAACAAAAAACAACCCCTATTCCAA
1 AAAACAAAAAACAA-CCCTACTCC-A
*
14585 AAAACAAAAAACAACCCTCCTCCA
1 AAAACAAAAAACAACCCTACTCCA
14609 AAAACAAAAAA
1 AAAACAAAAAA
14620 AAAAAAAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 12 0.36
25 7 0.21
26 14 0.42
ACGTcount: A:0.62, C:0.30, G:0.00, T:0.08
Consensus pattern (24 bp):
AAAACAAAAAACAACCCTACTCCA
Found at i:14593 original size:25 final size:24
Alignment explanation
Indices: 14542--14618 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
14532 GATTAATCTT
* * *
14542 CAAAAACTAGCCT-TTCCAAAACA
1 CAAAAACAACCCTATTCCAAAAAA
14565 -AAAAACAACCCCTATTCCAAAAAA
1 CAAAAACAA-CCCTATTCCAAAAAA
**
14589 CAAAAAACAACCCTCCTCC-AAAAA
1 C-AAAAACAACCCTATTCCAAAAAA
14613 CAAAAA
1 CAAAAA
14619 AAAAAAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
22 7 0.16
23 8 0.18
24 15 0.33
25 7 0.16
26 8 0.18
ACGTcount: A:0.56, C:0.31, G:0.01, T:0.12
Consensus pattern (24 bp):
CAAAAACAACCCTATTCCAAAAAA
Found at i:14619 original size:25 final size:26
Alignment explanation
Indices: 14559--14620 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 26
14549 TAGCCTTTCC
*
14559 AAAAC-AAAAAACAACCCCTATTCCA
1 AAAACAAAAAAACAACCCCTACTCCA
*
14584 AAAA-ACAAAAAACAA-CCCTCCTCCA
1 AAAACA-AAAAAACAACCCCTACTCCA
14609 AAAACAAAAAAA
1 AAAACAAAAAAA
14621 AAAAAAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 22 0.69
26 10 0.31
ACGTcount: A:0.63, C:0.29, G:0.00, T:0.08
Consensus pattern (26 bp):
AAAACAAAAAAACAACCCCTACTCCA
Found at i:14628 original size:34 final size:34
Alignment explanation
Indices: 14583--14653 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
14573 CCCCTATTCC
* *
14583 AAAAAACAAAAAACAA-CCCTCCTCCAAAAACAA
1 AAAAAAAAAAAAACAAGCCCTCCTCAAAAAACAA
14616 AAAAAAAAAAAAACAAGCCCTCCTCAAAAAACAA
1 AAAAAAAAAAAAACAAGCCCTCCTCAAAAAACAA
14650 AAAA
1 AAAA
14654 CAACCTCCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 15 0.43
34 20 0.57
ACGTcount: A:0.68, C:0.25, G:0.01, T:0.06
Consensus pattern (34 bp):
AAAAAAAAAAAAACAAGCCCTCCTCAAAAAACAA
Found at i:17263 original size:20 final size:20
Alignment explanation
Indices: 17238--17279 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
17228 TCATTTTGAT
*
17238 TTACATTAGTACACAAGTGG
1 TTACATCAGTACACAAGTGG
17258 TTACATCAGTACACAAGTGG
1 TTACATCAGTACACAAGTGG
17278 TT
1 TT
17280 CCATATCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (20 bp):
TTACATCAGTACACAAGTGG
Found at i:21538 original size:28 final size:29
Alignment explanation
Indices: 21472--21539 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 29
21462 GCGGTGTGAG
**
21472 AAATCTCCAAAATTGGAAACCCTAAACAA
1 AAATCTCCAAAATTCAAAACCCTAAACAA
* * *
21501 AAAT-TCCCAAAA-TCAAAACCCTTACCCA
1 AAATCT-CCAAAATTCAAAACCCTAAACAA
21529 AAATCTCCAAA
1 AAATCTCCAAA
21540 TTATACCACC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 21 0.66
29 11 0.34
ACGTcount: A:0.50, C:0.29, G:0.03, T:0.18
Consensus pattern (29 bp):
AAATCTCCAAAATTCAAAACCCTAAACAA
Found at i:24123 original size:20 final size:18
Alignment explanation
Indices: 24098--24149 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 18
24088 TTATTTGAAT
24098 TATTAAATATAATTCAAAAA
1 TATTAAATATAATTC--AAA
*
24118 TATTAATTTATAAATTCAAA
1 TATTAA-ATAT-AATTCAAA
24138 TATTATAATATA
1 TATTA-AATATA
24150 CAATTTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
19 1 0.04
20 17 0.63
21 4 0.15
22 5 0.19
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
TATTAAATATAATTCAAA
Found at i:24332 original size:36 final size:36
Alignment explanation
Indices: 24280--24351 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
24270 AAATAAATGA
*
24280 TATTTTATAAACTAAAA-GATAATTATAGTACAAGTT
1 TATTTTATAAACTAAAATG-TAATTATACTACAAGTT
*
24316 TATTTTATAAATTAAAATGTAATTATACTACAAGTT
1 TATTTTATAAACTAAAATGTAATTATACTACAAGTT
24352 CTATAATATG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 32 0.97
37 1 0.03
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.42
Consensus pattern (36 bp):
TATTTTATAAACTAAAATGTAATTATACTACAAGTT
Found at i:31674 original size:20 final size:19
Alignment explanation
Indices: 31630--31678 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
31620 TTTTCTACAA
*
31630 TTTTTATATATATTTTATC
1 TTTTTATAAATATTTTATC
31649 TATTTTATAAATAATTTTAAT-
1 T-TTTTATAAAT-ATTTT-ATC
31670 TTTTTATAA
1 TTTTTATAA
31679 TTTTTATACA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.04
20 17 0.65
21 6 0.23
22 2 0.08
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTATAAATATTTTATC
Found at i:33991 original size:19 final size:19
Alignment explanation
Indices: 33964--34000 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
33954 TTGGTAAGAT
*
33964 ATATATTTTTTGTACTATG
1 ATATATTTTTTGCACTATG
*
33983 ATATTTTTTTTGCACTAT
1 ATATATTTTTTGCACTAT
34001 TTGTTTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.59
Consensus pattern (19 bp):
ATATATTTTTTGCACTATG
Found at i:34553 original size:24 final size:24
Alignment explanation
Indices: 34530--34577 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
34520 ATTGAAGTTA
34530 AAATT-TTTTTTTTTGTTATGGTT
1 AAATTATTTTTTTTTGTTATGGTT
*
34553 -AGTTAATTTTTTTTTGTTATGGTT
1 AAATT-ATTTTTTTTTGTTATGGTT
34577 A
1 A
34578 TATATTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 3 0.14
24 18 0.86
ACGTcount: A:0.19, C:0.00, G:0.15, T:0.67
Consensus pattern (24 bp):
AAATTATTTTTTTTTGTTATGGTT
Found at i:36404 original size:2 final size:2
Alignment explanation
Indices: 36399--36426 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36389 AATATATATA
36399 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
36427 AATGAGATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:36612 original size:15 final size:15
Alignment explanation
Indices: 36589--36638 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
36579 TTTATTAAAT
36589 TTATATTGATTGAAA
1 TTATATTGATTGAAA
* *
36604 TTATTTTGATTGAAT
1 TTATATTGATTGAAA
36619 TTATATTGATTG-AA
1 TTATATTGATTGAAA
36633 TTATAT
1 TTATAT
36639 AATATATATG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 7 0.23
15 24 0.77
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:36620 original size:30 final size:28
Alignment explanation
Indices: 36578--36636 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 28
36568 TGAATATATG
36578 TTTTATTAAATTTATATTGATTGAAATTA
1 TTTTATTAAATTTATATTGATTG-AATTA
*
36607 TTTTGATTGAATTTATATTGATTGAATTA
1 TTTT-ATTAAATTTATATTGATTGAATTA
36636 T
1 T
36637 ATAATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (28 bp):
TTTTATTAAATTTATATTGATTGAATTA
Found at i:36961 original size:23 final size:23
Alignment explanation
Indices: 36935--37009 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 23
36925 AGGCACTTTA
36935 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
36958 TGTGTCGTA--TCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
* **
36979 TGTGTCGT-TTT-AGGCACTTTA
1 TGTGTCGTATTTCAGGCACCTCG
37000 TGTGTCGTAT
1 TGTGTCGTAT
37010 ACTGATAAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
21 35 0.76
22 2 0.04
23 9 0.20
ACGTcount: A:0.13, C:0.21, G:0.27, T:0.39
Consensus pattern (23 bp):
TGTGTCGTATTTCAGGCACCTCG
Found at i:41160 original size:15 final size:15
Alignment explanation
Indices: 41142--41190 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 15
41132 GTTATTTTCC
41142 TATTATTTATTATAT
1 TATTATTTATTATAT
* *
41157 TA-T-TTT-TTACAC
1 TATTATTTATTATAT
41169 TATTATTTATTATACT
1 TATTATTTATTATA-T
41185 TATTAT
1 TATTAT
41191 ATCATTTTCG
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
12 6 0.23
13 4 0.15
14 4 0.15
15 6 0.23
16 6 0.23
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTATTTATTATAT
Found at i:47762 original size:6 final size:6
Alignment explanation
Indices: 47739--47876 Score: 79
Period size: 6 Copynumber: 22.7 Consensus size: 6
47729 AAAAAAGAGA
* *
47739 AAAAGG AAAGAGAA AAAAGG AAAAGG AAAA-- ATAAGAG AAAA-- -AAAGG
1 AAAAGG AAA-AG-G AAAAGG AAAAGG AAAAGG AAAAG-G AAAAGG AAAAGG
* * * * *
47785 AAAAGG AAAAGG AAAAAG AATAGA AAAAGG AAAGAGAA AAAAAG AAAAGG
1 AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAA-AG-G AAAAGG AAAAGG
* * * *
47835 AAAAAG AAGAGA AAAAGG AAAGGG AAAAAAGG AAAAGG AAAA
1 AAAAGG AAAAGG AAAAGG AAAAGG --AAAAGG AAAAGG AAAA
47877 AGAAGAGAAA
Statistics
Matches: 98, Mismatches: 22, Indels: 24
0.68 0.15 0.17
Matches are distributed among these distances:
3 3 0.03
4 3 0.03
6 71 0.72
7 10 0.10
8 11 0.11
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (6 bp):
AAAAGG
Found at i:47778 original size:38 final size:38
Alignment explanation
Indices: 47727--47888 Score: 237
Period size: 38 Copynumber: 4.4 Consensus size: 38
47717 CTTCACTTTC
*
47727 AAAAAAAAGAGAAAAAGGAAAGAGAAAAAAGGAAAAGG
1 AAAAAGAAGAGAAAAAGGAAAGAGAAAAAAGGAAAAGG
*
47765 AAAAATAAGAG-AAAA--AAAG-G--AAAAGGAAAAGG
1 AAAAAGAAGAGAAAAAGGAAAGAGAAAAAAGGAAAAGG
* *
47797 AAAAAGAATAGAAAAAGGAAAGAGAAAAAAAGAAAAGG
1 AAAAAGAAGAGAAAAAGGAAAGAGAAAAAAGGAAAAGG
*
47835 AAAAAGAAGAGAAAAAGGAAAGGGAAAAAAGGAAAAGG
1 AAAAAGAAGAGAAAAAGGAAAGAGAAAAAAGGAAAAGG
47873 AAAAAGAAGAGAAAAA
1 AAAAAGAAGAGAAAAA
47889 CAAAAAAGAG
Statistics
Matches: 111, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
32 21 0.19
33 4 0.04
34 1 0.01
35 8 0.07
36 1 0.01
37 4 0.04
38 72 0.65
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.01
Consensus pattern (38 bp):
AAAAAGAAGAGAAAAAGGAAAGAGAAAAAAGGAAAAGG
Found at i:47845 original size:70 final size:74
Alignment explanation
Indices: 47727--47912 Score: 245
Period size: 70 Copynumber: 2.5 Consensus size: 74
47717 CTTCACTTTC
* * *
47727 AAAAAAAAGAGAAAAAGGAAAGAGAAAAAAGGAAAAGGAAAAATAAGAG-AAAA-AAA-GG-AAA
1 AAAAAGAAGAGAAAAAGGAAAGAGAAAAAAAGAAAAGGAAAAAGAAGAGAAAAAGAAAGGGAAAA
47788 AGGAAAAGG
66 AGGAAAAGG
*
47797 AAAAAGAATAGAAAAAGGAAAGAGAAAAAAAGAAAAGGAAAAAGAAGAGAAAAAGGAAAGGGAAA
1 AAAAAGAAGAGAAAAAGGAAAGAGAAAAAAAGAAAAGGAAAAAGAAGAGAAAAA-GAAAGGG-AA
47862 AAAGGAAAAGG
64 AAAGGAAAAGG
**
47873 AAAAAGAAGAGAAAAACAAAAAAGAGAAAGAAAAGAAAAG
1 AAAAAGAAGAG-AAAA-AGGAAAGAGAAA-AAAAGAAAAG
47913 CAAATGAGAG
Statistics
Matches: 100, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
70 45 0.45
71 4 0.04
73 3 0.03
74 2 0.02
76 22 0.22
77 4 0.04
78 10 0.10
79 10 0.10
ACGTcount: A:0.73, C:0.01, G:0.25, T:0.01
Consensus pattern (74 bp):
AAAAAGAAGAGAAAAAGGAAAGAGAAAAAAAGAAAAGGAAAAAGAAGAGAAAAAGAAAGGGAAAA
AGGAAAAGG
Found at i:47895 original size:32 final size:32
Alignment explanation
Indices: 47819--47901 Score: 78
Period size: 38 Copynumber: 2.4 Consensus size: 32
47809 AAAAGGAAAG
*
47819 AGAAAAAAAGAAAAGGAAAAAGAAGAGAAAAAGGAA
1 AGAAAAAAGGAAAAGGAAAAAGAAGAG--AAA--AA
47855 AGGGAAAAAAGGAAAAGGAAAAAGAAGAG-AAAA
1 A--GAAAAAAGGAAAAGGAAAAAGAAGAGAAAAA
*
47888 ACAAAAAAGAGAAA
1 AGAAAAAAG-GAAA
47902 GAAAAGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
31 7 0.17
32 4 0.10
33 3 0.07
35 2 0.05
36 1 0.02
38 25 0.60
ACGTcount: A:0.73, C:0.01, G:0.25, T:0.00
Consensus pattern (32 bp):
AGAAAAAAGGAAAAGGAAAAAGAAGAGAAAAA
Found at i:47902 original size:6 final size:5
Alignment explanation
Indices: 47739--47912 Score: 56
Period size: 5 Copynumber: 33.0 Consensus size: 5
47729 AAAAAAGAGA
* * *
47739 AAAAG GAAAG AGAAA- AAAGG AAAAGG AAAA- ATAAGAG AAAA- AAAGG
1 AAAAG AAAAG A-AAAG AAAAG AAAA-G AAAAG A-AA-AG AAAAG AAAAG
* *
47785 AAAAGG AAAAGG AAAAAG AATAG AAAAAG GAAAG AGAAA- AAAAG AAAAGG
1 AAAA-G AAAA-G -AAAAG AAAAG -AAAAG AAAAG A-AAAG AAAAG AAAA-G
* * * * *
47835 AAAAAG AAGAG AAAAAGG AAAGG GAAA- AAAGG AAAAGG AAAAAG AAGAG
1 -AAAAG AAAAG -AAAA-G AAAAG AAAAG AAAAG AAAA-G -AAAAG AAAAG
*
47884 AAAA- ACAA- AAAAG AGAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG A-AAAG AAAAG AAAAG
47913 CAAATGAGAG
Statistics
Matches: 126, Mismatches: 22, Indels: 42
0.66 0.12 0.22
Matches are distributed among these distances:
4 17 0.13
5 54 0.43
6 41 0.33
7 14 0.11
ACGTcount: A:0.72, C:0.01, G:0.26, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:49392 original size:133 final size:133
Alignment explanation
Indices: 49153--49770 Score: 950
Period size: 133 Copynumber: 4.6 Consensus size: 133
49143 CAGATATCAT
* * * * *
49153 CAGCCTTATCTTCACTGAGTAGGAGTGGAGTAGGCTAAATATTAGATCTTATCTTTACTGAGCAG
1 CAGCCTTATCTTCACTGAGCAAGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCACTGAGCAG
*
49218 GAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTATCAGCAATGGAGCAGATTTCAGC
66 GAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTATCGGCAATGGAGCAGATTTCAGC
49283 CAC
131 CAC
*
49286 CAGCCTTATCTTCACTGAGCAAGAGTGGAGTAGGCTAAATACTAGATCTTATCTTCACTGAGCAG
1 CAGCCTTATCTTCACTGAGCAAGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCACTGAGCAG
*
49351 GAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCTATGTATCGGCAATGGAGCAGATTTCAGC
66 GAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTATCGGCAATGGAGCAGATTTCAGC
49416 CAC
131 CAC
*
49419 CAGCCTTATCTTCACTGAGCAAGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCACTGAGCAA
1 CAGCCTTATCTTCACTGAGCAAGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCACTGAGCAG
49484 GAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTATCGGCAATGGAGCAGATTTCAGC
66 GAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTATCGGCAATGGAGCAGATTTCAGC
*
49549 CAT
131 CAC
* *
49552 CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCGCTGAGCAG
1 CAGCCTTATCTTCACTGAGCAAGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCACTGAGCAG
* * * * * * *
49617 GAGCGGAGCAGATCAAATTTTGGTGAA-TCTTATCTCCATGAATTGGCAATGGAGCAGATTCCAA
66 GAGTGAAGCAGATCAAATTTTGG-CAAGTCTTATCTCCATGTATCGGCAATGGAGCAGATTTCAG
* *
49681 TCAT
130 CCAC
* * * * *
49685 CAGCCTTATCTTCACCGAGCATGAGTAGAGCAGGCTAAACATACCAGATCTTATCTTTACTGAGC
1 CAGCCTTATCTTCACTGAGCAAGAGTGGAGCAGGCT-AA-ATACTAGATCTTATCTTCACTGAGC
* *
49750 AGGAGTAAAGCAGATTAAATT
64 AGGAGTGAAGCAGATCAAATT
49771 ACAGCAGATC
Statistics
Matches: 451, Mismatches: 31, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
133 408 0.90
134 4 0.01
135 39 0.09
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (133 bp):
CAGCCTTATCTTCACTGAGCAAGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCACTGAGCAG
GAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTATCGGCAATGGAGCAGATTTCAGC
CAC
Found at i:51039 original size:16 final size:16
Alignment explanation
Indices: 50992--51041 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
50982 GTTATTTTCC
*
50992 TATTGTTTATTATA-T
1 TATTATTTATTATACT
*
51007 TATT-TTT-TTACAC-
1 TATTATTTATTATACT
51020 TATTATTTATTATACT
1 TATTATTTATTATACT
51036 TATTAT
1 TATTAT
51042 ATCATTTTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 8 0.28
14 6 0.21
15 9 0.31
16 6 0.21
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (16 bp):
TATTATTTATTATACT
Found at i:58067 original size:24 final size:24
Alignment explanation
Indices: 57991--58067 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
57981 TCATGTACAC
57991 ATTATT-TATATTATT-TTA-TGATT
1 ATTATTGTAT-TTATTATTACT-ATT
* * *
58014 ATTATTGTGTTTATTTTTACTACT
1 ATTATTGTATTTATTATTACTATT
*
58038 ATTATTGTATTTATTATTAGTATT
1 ATTATTGTATTTATTATTACTATT
*
58062 AGTATT
1 ATTATT
58068 ATAATTACTA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
23 11 0.25
24 32 0.73
25 1 0.02
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.62
Consensus pattern (24 bp):
ATTATTGTATTTATTATTACTATT
Found at i:58195 original size:14 final size:14
Alignment explanation
Indices: 58173--58202 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
58163 TATTTTTAAC
58173 ATATATATGTATAT
1 ATATATATGTATAT
*
58187 ATATGTATGTATAT
1 ATATATATGTATAT
58201 AT
1 AT
58203 TTATGAAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (14 bp):
ATATATATGTATAT
Found at i:58300 original size:11 final size:11
Alignment explanation
Indices: 58259--58336 Score: 58
Period size: 11 Copynumber: 7.3 Consensus size: 11
58249 TTCTAATGTG
58259 TATATATTATA
1 TATATATTATA
*
58270 TATAT-TTTTAA
1 TATATATTAT-A
*
58281 TACTATATTATG
1 TA-TATATTATA
58293 TATATATTATA
1 TATATATTATA
58304 T-TATA-TATA
1 TATATATTATA
58313 T-T-TATTATA
1 TATATATTATA
* *
58322 TTTTTATGTATA
1 TATATAT-TATA
58334 TAT
1 TAT
58337 TTTTAATATC
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
8 2 0.04
9 11 0.20
10 8 0.15
11 20 0.36
12 11 0.20
13 3 0.05
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (11 bp):
TATATATTATA
Found at i:58312 original size:25 final size:23
Alignment explanation
Indices: 58259--58336 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 23
58249 TTCTAATGTG
58259 TATATATTA-TATATATTT-TTAA
1 TATATATTATTATATATTTATT-A
58281 TACTATATTATGTATATATTATATTA
1 TA-TATATTAT-TATATATT-TATTA
*
58307 TATATATTTATTATATTTTTATGTA
1 TATATA-TTATTATATATTTAT-TA
58332 TATAT
1 TATAT
58337 TTTTAATATC
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.04
23 7 0.15
24 3 0.06
25 26 0.54
26 8 0.17
27 2 0.04
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (23 bp):
TATATATTATTATATATTTATTA
Found at i:58329 original size:37 final size:39
Alignment explanation
Indices: 58261--58337 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 39
58251 CTAATGTGTA
58261 TATATTATATATATTTTTAATACTATATTATGTATATAT
1 TATATTATATATATTTTTAATACTATATTATGTATATAT
*
58300 TATATTATATATATTTATT-ATA-T-TTTTATGTATATAT
1 TATATTATATATATTT-TTAATACTATATTATGTATATAT
58337 T
1 T
58338 TTTAATATCA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
37 14 0.39
38 1 0.03
39 19 0.53
40 2 0.06
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (39 bp):
TATATTATATATATTTTTAATACTATATTATGTATATAT
Found at i:58338 original size:23 final size:23
Alignment explanation
Indices: 58259--58337 Score: 83
Period size: 23 Copynumber: 3.3 Consensus size: 23
58249 TTCTAATGTG
58259 TATATATTATATATATTTTTA-A
1 TATATATTATATATATTTTTATA
58281 TACTATATTATGTATATATTATATTATA
1 TA-TATATTA--TATATATT-T-TTATA
*
58309 TATAT-TTAT-TATATTTTTATG
1 TATATATTATATATATTTTTATA
58330 TATATATT
1 TATATATT
58338 TTTAATATCA
Statistics
Matches: 49, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
21 9 0.18
22 5 0.10
23 13 0.27
24 1 0.02
25 8 0.16
26 4 0.08
27 6 0.12
28 3 0.06
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (23 bp):
TATATATTATATATATTTTTATA
Found at i:58519 original size:3 final size:3
Alignment explanation
Indices: 58513--58565 Score: 54
Period size: 3 Copynumber: 17.0 Consensus size: 3
58503 TTTTTTCATA
* *
58513 TAT TAT TAT CAT TAT TTT CTACGT TAT -AT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT -TA--T TAT TAT TAT TAT TAT TAT TAT TAT
58560 TAT TAT
1 TAT TAT
58566 CATTTTCATT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 2 0.05
3 36 0.86
4 1 0.02
5 2 0.05
6 1 0.02
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Done.