Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2193
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: 41383
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Found at i:406 original size:9 final size:8
Alignment explanation
Indices: 384--472 Score: 53
Period size: 8 Copynumber: 11.0 Consensus size: 8
374 GTTTGATTCA
384 TTGATTTT
1 TTGATTTT
392 TT--TTATT
1 TTGATT-TT
399 TTGATTATT
1 TTGATT-TT
*
408 ATGA-TTT
1 TTGATTTT
* *
415 TTCA-TAT
1 TTGATTTT
422 TTGATTTT
1 TTGATTTT
*
430 TTTATTATTAT
1 TTGA-T-TT-T
441 TTGA-TTT
1 TTGATTTT
448 TTGATTTT
1 TTGATTTT
456 TTGATTTTT
1 TTGA-TTTT
465 TTGATTTT
1 TTGATTTT
473 GTTATTTTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
6 2 0.03
7 18 0.28
8 21 0.33
9 17 0.27
10 2 0.03
11 4 0.06
ACGTcount: A:0.18, C:0.01, G:0.09, T:0.72
Consensus pattern (8 bp):
TTGATTTT
Found at i:440 original size:31 final size:33
Alignment explanation
Indices: 397--466 Score: 90
Period size: 34 Copynumber: 2.2 Consensus size: 33
387 ATTTTTTTTA
*
397 TTTTGATTATTA-TGATTTTTCA-TATTTGATT
1 TTTTTATTATTATTGATTTTTCATTATTTGATT
* *
428 TTTTTATTATTATTTGATTTTTGATTTTTTGATT
1 TTTTTATTATTA-TTGATTTTTCATTATTTGATT
462 TTTTT
1 TTTTT
467 GATTTTGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 11 0.33
33 9 0.27
34 13 0.39
ACGTcount: A:0.19, C:0.01, G:0.09, T:0.71
Consensus pattern (33 bp):
TTTTTATTATTATTGATTTTTCATTATTTGATT
Found at i:473 original size:6 final size:7
Alignment explanation
Indices: 397--464 Score: 52
Period size: 7 Copynumber: 9.6 Consensus size: 7
387 ATTTTTTTTA
397 TTTTGAT
1 TTTTGAT
404 TATTATGAT
1 T-TT-TGAT
*
413 TTTTCAT
1 TTTTGAT
*
420 ATTTGAT
1 TTTTGAT
427 TTTT--T
1 TTTTGAT
*
432 TATT-AT
1 TTTTGAT
438 TATTTGAT
1 T-TTTGAT
446 TTTTGATT
1 TTTTGA-T
454 TTTTGAT
1 TTTTGAT
461 TTTT
1 TTTT
465 TTGATTTTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
5 4 0.08
6 2 0.04
7 24 0.49
8 14 0.29
9 5 0.10
ACGTcount: A:0.19, C:0.01, G:0.09, T:0.71
Consensus pattern (7 bp):
TTTTGAT
Found at i:817 original size:2 final size:2
Alignment explanation
Indices: 750--801 Score: 95
Period size: 2 Copynumber: 25.5 Consensus size: 2
740 ATTAAGTGTC
750 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
793 TA TA TA TA T
1 TA TA TA TA T
802 TACCTATTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 47 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:829 original size:8 final size:7
Alignment explanation
Indices: 750--830 Score: 65
Period size: 8 Copynumber: 10.4 Consensus size: 7
740 ATTAAGTGTC
*
750 TATACTA
1 TATATTA
757 TATATATA
1 TATAT-TA
765 TATATATA
1 TATAT-TA
773 TATATATA
1 TATAT-TA
781 TATATATA
1 TATAT-TA
789 TATATATA
1 TATAT-TA
797 TATATTA
1 TATATTA
804 CCTAT-TTGA
1 --TATATT-A
813 TATATTA
1 TATATTA
820 TATCATTA
1 TAT-ATTA
828 TAT
1 TAT
831 TGTATTAATA
Statistics
Matches: 67, Mismatches: 1, Indels: 11
0.85 0.01 0.14
Matches are distributed among these distances:
7 13 0.19
8 50 0.75
9 4 0.06
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (7 bp):
TATATTA
Found at i:902 original size:23 final size:24
Alignment explanation
Indices: 876--928 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
866 AGTTGTATAA
*
876 ATATTATTACTT-TATAT-ATATTT
1 ATATTATTA-TTGAATATAATATTT
*
899 ATATAATTATTGAATATAATATTT
1 ATATTATTATTGAATATAATATTT
923 -TATTAT
1 ATATTAT
929 ATTATAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 2 0.08
23 17 0.68
24 6 0.24
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
ATATTATTATTGAATATAATATTT
Found at i:2574 original size:93 final size:94
Alignment explanation
Indices: 2458--2653 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 94
2448 GGAAAAATTG
* * *
2458 AAAAATTAAGTGCTAAAACATTAAATACCTAATTTTTAGTACTAAATTTATAAGCATTGAATTTG
1 AAAAATTAAGTGCTAAAAAATTAAATACCTAATTTTTAGTACTAAATTTAAAAGCATCGAATTTG
* * *
2523 TATTA-TAAAAATTGTTTAATATATTATT
66 TATTACAAAAAATTGCTTAATATATTACT
* * * *
2551 AAAAATTAGGTGTTAAAAAATTAAATACTTAATTTTTAGTATTAAATTTAAAAGCATCGAATTTG
1 AAAAATTAAGTGCTAAAAAATTAAATACCTAATTTTTAGTACTAAATTTAAAAGCATCGAATTTG
*
2616 TATTACAAAAAATTGCTTGATATATTACT
66 TATTACAAAAAATTGCTTAATATATTACT
2645 AAAAATTAA
1 AAAAATTAA
2654 ATACTGAATA
Statistics
Matches: 90, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
93 63 0.70
94 27 0.30
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (94 bp):
AAAAATTAAGTGCTAAAAAATTAAATACCTAATTTTTAGTACTAAATTTAAAAGCATCGAATTTG
TATTACAAAAAATTGCTTAATATATTACT
Found at i:2719 original size:7 final size:7
Alignment explanation
Indices: 2704--2744 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
2694 GAATTTTGAA
*
2704 AATTGTT
1 AATTTTT
*
2711 AACTTTT
1 AATTTTT
2718 AATTTTT
1 AATTTTT
2725 AATTTTT
1 AATTTTT
2732 AATTTTT
1 AATTTTT
2739 AATTTT
1 AATTTT
2745 AATAGCATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (7 bp):
AATTTTT
Found at i:3205 original size:15 final size:16
Alignment explanation
Indices: 3187--3216 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3177 TTACTTTTTC
3187 TTTTTT-AAAACATTT
1 TTTTTTCAAAACATTT
3202 TTTTTTCAAAACATT
1 TTTTTTCAAAACATT
3217 CATATAGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTTTCAAAACATTT
Found at i:13680 original size:2 final size:2
Alignment explanation
Indices: 13673--13716 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
13663 TTCCTCTTTC
13673 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13715 TA
1 TA
13717 CAATCTAGCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15536 original size:2 final size:2
Alignment explanation
Indices: 15523--15571 Score: 80
Period size: 2 Copynumber: 24.0 Consensus size: 2
15513 GATACCATCG
15523 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
15566 TT TA TA
1 TA TA TA
15572 AAGTCTCTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18944 original size:12 final size:12
Alignment explanation
Indices: 18922--18954 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
18912 GAAGTATGTC
18922 TAAACATAAAATA
1 TAAA-ATAAAATA
18935 TAAAATAAAATA
1 TAAAATAAAATA
18947 TAAAATAA
1 TAAAATAA
18955 CAAAACATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (12 bp):
TAAAATAAAATA
Found at i:19816 original size:2 final size:2
Alignment explanation
Indices: 19809--19833 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19799 ACATACATAC
19809 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
19834 GGATAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22537 original size:130 final size:130
Alignment explanation
Indices: 22402--22650 Score: 462
Period size: 130 Copynumber: 1.9 Consensus size: 130
22392 TGTTTGTTAA
*
22402 TAATAAACTAATATTTATTAATAATAAATATTTTTGAAAAATTTTAAAAATCACAAATTTTGCAT
1 TAATAAACTAATATTTATTAATAATAAATATCTTTGAAAAATTTTAAAAATCACAAATTTTGCAT
* *
22467 TTTATTTAATAAGGTAATTTCAAAAATTACCATCATATTCCTGTATAGTATTTATTAATATTTAT
66 TTTATTTAATAAGGTAATTTCAAAAAATACCATCACATTCCTGTATAGTATTTATTAATATTTAT
*
22532 TAATAAACTAATATTTATTAATAATAAATATCTTTGAAAAATTTTAAAAATCATAAATTTTGCAT
1 TAATAAACTAATATTTATTAATAATAAATATCTTTGAAAAATTTTAAAAATCACAAATTTTGCAT
22597 TTTATTTAATAAGGTAATTTCAAAAAATACCATCACATTCCTGTATAGTATTTA
66 TTTATTTAATAAGGTAATTTCAAAAAATACCATCACATTCCTGTATAGTATTTA
22651 ATAAACCACA
Statistics
Matches: 115, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
130 115 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (130 bp):
TAATAAACTAATATTTATTAATAATAAATATCTTTGAAAAATTTTAAAAATCACAAATTTTGCAT
TTTATTTAATAAGGTAATTTCAAAAAATACCATCACATTCCTGTATAGTATTTATTAATATTTAT
Found at i:25156 original size:9 final size:9
Alignment explanation
Indices: 25144--25194 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
25134 TTTTTAAATT
25144 TTTTTCTTA
1 TTTTTCTTA
25153 TTTTTCTTA
1 TTTTTCTTA
25162 TTTTT-TGTA
1 TTTTTCT-TA
25171 TTTTT-TTAAA
1 TTTTTCTT--A
*
25181 TTTTTCTAA
1 TTTTTCTTA
25190 TTTTT
1 TTTTT
25195 TTGTTATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
8 2 0.05
9 28 0.76
10 6 0.16
11 1 0.03
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (9 bp):
TTTTTCTTA
Found at i:25164 original size:29 final size:28
Alignment explanation
Indices: 25125--25195 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 28
25115 TGCGTTTGTA
* **
25125 TTTTCTCATTTTTTAAATTTTTTTCTTAT
1 TTTTCTAATTTTTTAAATTTTTTT-AAAT
* **
25154 TTTTCTTATTTTTTGTATTTTTTTAAAT
1 TTTTCTAATTTTTTAAATTTTTTTAAAT
25182 TTTTCTAATTTTTT
1 TTTTCTAATTTTTT
25196 TGTTATTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 15 0.42
29 21 0.58
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.75
Consensus pattern (28 bp):
TTTTCTAATTTTTTAAATTTTTTTAAAT
Found at i:27637 original size:28 final size:27
Alignment explanation
Indices: 27576--27638 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
27566 GAATATTTTT
* * *
27576 TTATATTTTATTAAAAATGTTATTATA
1 TTATATTTTAATAAAAATATTATTAAA
27603 TTAATATTTTAATAATAAATATGTA-TAAA
1 TT-ATATTTTAATAA-AAATAT-TATTAAA
27632 TTATATT
1 TTATATT
27639 GTATAAAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 2 0.07
28 16 0.53
29 10 0.33
30 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (27 bp):
TTATATTTTAATAAAAATATTATTAAA
Found at i:28706 original size:155 final size:155
Alignment explanation
Indices: 28454--28738 Score: 369
Period size: 155 Copynumber: 1.8 Consensus size: 155
28444 AAATCTCCTA
* * ** *
28454 TTTTTAAAATACAAAGTTTTCTACCCCGTAAATTTTTTCGGAGGATTTTTCTTGGCTTTTAATTT
1 TTTTCAAAATACAAAGTTTTCTACCCCGTAAATTTTTACGGAAAATTTTTCTCGGCTTTTAATTT
* * *
28519 TTAAAATTAATCAAATATTATTATTTATTTCATATTAAATCAGTTTTCAAAAATTCATTCATTTT
66 TTAAAATTAATCAAATATCATCATTTAATTCATATTAAATCAGTTTTCAAAAATTCATTCATTTT
28584 TCATTTTTTTCTTGAATTTTTCATG
131 TCATTTTTTTCTTGAATTTTTCATG
* * *
28609 TTTTCAAAATACAGAA-TTTTCTACTCCGTAAATGTTTTAGGGAAAATTTTTCTCGGTTTTTAAT
1 TTTTCAAAATACA-AAGTTTTCTACCCCGTAAAT-TTTTACGGAAAATTTTTCTCGGCTTTTAAT
* * * * * *
28673 TTTT-TAATTCA-CAAAATATCATCATTTAATTCATATTAAATTATTTTTGAAAAATTCATTTAT
64 TTTTAAAATTAATC-AAATATCATCATTTAATTCATATTAAATCAGTTTTCAAAAATTCATTCAT
28736 TTT
128 TTT
28739 CATGAGTTTT
Statistics
Matches: 110, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
154 1 0.01
155 79 0.72
156 30 0.27
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.50
Consensus pattern (155 bp):
TTTTCAAAATACAAAGTTTTCTACCCCGTAAATTTTTACGGAAAATTTTTCTCGGCTTTTAATTT
TTAAAATTAATCAAATATCATCATTTAATTCATATTAAATCAGTTTTCAAAAATTCATTCATTTT
TCATTTTTTTCTTGAATTTTTCATG
Found at i:29271 original size:10 final size:11
Alignment explanation
Indices: 29242--29266 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29232 GATTAGCAAA
29242 AAAAAAAAGAG
1 AAAAAAAAGAG
29253 AAAAAAAAGAG
1 AAAAAAAAGAG
29264 AAA
1 AAA
29267 GAAAGGCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:29271 original size:21 final size:20
Alignment explanation
Indices: 29247--29309 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
29237 GCAAAAAAAA
29247 AAAGAGAAAAAAAAGAGAAAG
1 AAAG-GAAAAAAAAGAGAAAG
29268 AAAGGCAAGAAAAATAGA-AAAG
1 AAAGG-AA-AAAAA-AGAGAAAG
* *
29290 AATAGGTAAAAAAATAGAAA
1 AA-AGGAAAAAAAAGAGAAA
29310 AACTAAACTA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
20 3 0.09
21 14 0.40
22 12 0.34
23 6 0.17
ACGTcount: A:0.71, C:0.02, G:0.21, T:0.06
Consensus pattern (20 bp):
AAAGGAAAAAAAAGAGAAAG
Found at i:29289 original size:22 final size:22
Alignment explanation
Indices: 29253--29310 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
29243 AAAAAAAGAG
29253 AAAAAAA-AGAGAAAGAA-AGGC
1 AAAAAAATAGA-AAAGAATAGGC
*
29274 AAGAAAAATAGAAAAGAATAGGT
1 AA-AAAAATAGAAAAGAATAGGC
29297 AAAAAAATAGAAAA
1 AAAAAAATAGAAAA
29311 ACTAAACTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
21 2 0.06
22 23 0.70
23 8 0.24
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.07
Consensus pattern (22 bp):
AAAAAAATAGAAAAGAATAGGC
Found at i:30349 original size:155 final size:155
Alignment explanation
Indices: 30076--30509 Score: 442
Period size: 155 Copynumber: 2.8 Consensus size: 155
30066 AATATTAATC
* *** *
30076 ATTTTTTAATCTTTTATATTCCTATGACCATCCGTAGGGGTATAAAAGATTTTAAAACTTTTTGT
1 ATTTTTT-ATCTTTTATA-TACTATGGGGATCCGTAGGGGTATAAAAGATTTCAAAACTTTTTGT
* * * * *
30141 AT-TTTTTAGGTTTCCAATAAGGTACG-AAATGGTGTTTTTCAAAAATAAATAAATTAAATTAA-
64 ATCTTTTTGGGTTTCCATTAAGGTACGAAAATGGTATTTTTCAAAAACAAATAAATAAAATTAAG
* *
30203 C-ACTTTCATAATTGAAATAAATATTAATA
129 CAACTTTCATAACTGAAAGAAA-ATT--TA
* * *
30232 ATTTTTCTAATCTTTTA-A-ACTATGGGG-TCCGTAGAGGAATAAAAGATTTCAAAAACTTTTCG
1 ATTTTT-T-ATCTTTTATATACTATGGGGATCCGTAGGGGTATAAAAGATTTC-AAAACTTTTTG
* *
30294 TATCTTTTCGGGTTTCCATTAAGGTACGAAAAT-GTATTTATT-GAAAACAAATAAATAAAATTA
63 TATCTTTTTGGGTTTCCATTAAGGTACGAAAATGGTATTT-TTCAAAAACAAATAAATAAAATTA
* * *
30357 AGCTAATACTTTCATAACTGAGAGGAACTTTA
127 AGC--A-ACTTTCATAACTGAAAGAAAATTTA
*
30389 ATTTTTTATCTTTTATATTCCTATGGGGATCCGTAGGGGTATAAAAGATTTCAAAACTTTTTGTA
1 ATTTTTTATCTTTTATA-TACTATGGGGATCCGTAGGGGTATAAAAGATTTCAAAACTTTTTGTA
* * * *
30454 TCTTTTTGGGTTTCCATTAAGGTATG-AAAT-GAAATTTTCAAAAATAAA-AAATAAAA
65 TCTTTTTGGGTTTCCATTAAGGTACGAAAATGGTATTTTTCAAAAACAAATAAATAAAA
30510 AATAAAAAAT
Statistics
Matches: 233, Mismatches: 30, Indels: 30
0.80 0.10 0.10
Matches are distributed among these distances:
153 20 0.09
154 18 0.08
155 53 0.23
156 26 0.11
157 33 0.14
158 44 0.19
159 23 0.10
160 16 0.07
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.39
Consensus pattern (155 bp):
ATTTTTTATCTTTTATATACTATGGGGATCCGTAGGGGTATAAAAGATTTCAAAACTTTTTGTAT
CTTTTTGGGTTTCCATTAAGGTACGAAAATGGTATTTTTCAAAAACAAATAAATAAAATTAAGCA
ACTTTCATAACTGAAAGAAAATTTA
Found at i:30505 original size:7 final size:7
Alignment explanation
Indices: 30493--30535 Score: 68
Period size: 7 Copynumber: 5.9 Consensus size: 7
30483 TGAAATTTTC
30493 AAAAATA
1 AAAAATA
30500 AAAAATA
1 AAAAATA
30507 AAAAATA
1 AAAAATA
30514 AAAAATA
1 AAAAATA
30521 AAATAATA
1 AAA-AATA
30529 AATAAAT
1 AA-AAAT
30536 TCTTTTTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
7 24 0.71
8 9 0.26
9 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (7 bp):
AAAAATA
Found at i:30512 original size:158 final size:154
Alignment explanation
Indices: 30066--30509 Score: 483
Period size: 156 Copynumber: 2.9 Consensus size: 154
30056 AAGATATTTC
* *** *
30066 AATATTAATCATTTTTTAATCTTTTATATTCCTATGACCATCCGTAGGGGTATAAAAGATTTTAA
1 AATATT-ATAATTTTTTAATCTTTTATATTCCTATGGGGATCCGTAGGGGTATAAAAGATTTCAA
* * *
30131 AACTTTTTGTAT-TTTTTAGGTTTCCAATAAGGTACGAAATGGTGTTTTTCAAAAATAAATAAAT
65 AACTTTTTGTATCTTTTTGGGTTTCCATTAAGGTACGAAAT-GTATTTTTCAAAAATAAA-AAAT
* * *
30195 TAAATTAACACTTTCATAATTGAAATA
128 AAAATTAACACTTTCATAACTGAAAGA
* * *
30222 AATATTAATAATTTTTCTAATCTTTTA-A--ACTATGGGG-TCCGTAGAGGAATAAAAGATTTCA
1 AATATT-ATAATTTTT-TAATCTTTTATATTCCTATGGGGATCCGTAGGGGTATAAAAGATTTC-
* * * *
30283 AAAACTTTTCGTATCTTTTCGGGTTTCCATTAAGGTACGAAAATGTATTTATTGAAAACA-AATA
63 AAAACTTTTTGTATCTTTTTGGGTTTCCATTAAGGTACG-AAATGTATTT-TTCAAAA-ATAAAA
* *
30347 AATAAAATTAAGCTAATACTTTCATAACTGAGAGG
125 AATAAAATTAA-C----ACTTTCATAACTGAAAGA
*
30382 AA-CTT-TAATTTTTT-ATCTTTTATATTCCTATGGGGATCCGTAGGGGTATAAAAGATTTCAAA
1 AATATTATAATTTTTTAATCTTTTATATTCCTATGGGGATCCGTAGGGGTATAAAAGATTTCAAA
* * *
30444 ACTTTTTGTATCTTTTTGGGTTTCCATTAAGGTATGAAATGAAATTTTCAAAAATAAAAAATAAA
66 ACTTTTTGTATCTTTTTGGGTTTCCATTAAGGTACGAAATGTATTTTTCAAAAATAAAAAATAAA
30509 A
131 A
30510 AATAAAAAAT
Statistics
Matches: 241, Mismatches: 31, Indels: 32
0.79 0.10 0.11
Matches are distributed among these distances:
153 20 0.08
154 18 0.07
155 46 0.19
156 47 0.20
157 27 0.11
158 44 0.18
159 23 0.10
160 16 0.07
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.39
Consensus pattern (154 bp):
AATATTATAATTTTTTAATCTTTTATATTCCTATGGGGATCCGTAGGGGTATAAAAGATTTCAAA
ACTTTTTGTATCTTTTTGGGTTTCCATTAAGGTACGAAATGTATTTTTCAAAAATAAAAAATAAA
ATTAACACTTTCATAACTGAAAGA
Found at i:31090 original size:155 final size:151
Alignment explanation
Indices: 30907--31469 Score: 556
Period size: 155 Copynumber: 3.6 Consensus size: 151
30897 TATCATCTTT
* * **
30907 TTTTTAAGTCCTTTAGGGGTATCGGGTACTTCTATTTCGAAGGTATCCCTCAAGGGTATTTTCGT
1 TTTTTAAGTCCTTTAAGGGTATCAGGTACTT-TACGTCGAAGGTATCCCT-AAGGGTATTTTCGT
* * * * * *
30972 AATTTTTTAGAACCAACTCTTAGGTCGTCACCAGGT-TCGCTTTTATGCTAAAGGTGGGTATTTA
64 AATTTTTTAGAATCGAGTCTTAGGTTGTCACCAGGTCT-GCTTTTATGCTGAAGGTGGGCATTTA
*
31036 GGATGGGTTCATCCCGTCTTAAACC
128 GGATAGGTTCATCCC-TCTTAAACC
* * * * *
31061 TTTTTTAAGTCTTTTAAGGGTATCAGGTACTTTACATCGACGGTATACCTATATGGGTATTTTTG
1 -TTTTTAAGTCCTTTAAGGGTATCAGGTACTTTACGTCGAAGGTATCCCTA-A-GGGTATTTTCG
* * * * * *
31126 TAATTTCTTAGAGTCGAGTCTTAGGTTGTCATCGGGTCTGCTTTTATGCTGAAGATGGGCAATTA
63 TAATTTTTTAGAATCGAGTCTTAGGTTGTCACCAGGTCTGCTTTTATGCTGAAGGTGGGCATTTA
** *
31191 GGATAGGTTCATCCCATCTTTTATC
128 GGATAGGTTCATCCC-TCTTAAACC
** * *
31216 TTTTTAAGTCCTTT-AGGGTTATTGGGATACTTTCATGTCAAAGGTATACCCATAAGGGTATTTT
1 TTTTTAAGTCCTTTAAGGG-TATCAGG-TACTTT-ACGTCGAAGGTAT-CCC-TAAGGGTATTTT
* * * * *
31280 CGTAATTTTTTAGAGTTGAGTCCTAGGTTGTCACTAGGTCTACTTTTATGCTGAAGGTGGGCATT
61 CGTAATTTTTTAGAATCGAGTCTTAGGTTGTCACCAGGTCTGCTTTTATGCTGAAGGTGGGCATT
*
31345 TAGGATAGGTTCATCCCTTTTAAAATCC
126 TAGGATAGGTTCATCCCTCTT-AAA-CC
* * * * *
31373 TTTTTAAATCCTTTAAGGGTATTAGGTACTTTTACGTCGAAGGTATCATCT-AGTGGCATTTTCA
1 TTTTTAAGTCCTTTAAGGGTATCAGGTAC-TTTACGTCGAAGGTATC-CCTAAG-GGTATTTTCG
* * *
31437 TAATTTTTTAGAATCGAATCCTAGATTGTCACC
63 TAATTTTTTAGAATCGAGTCTTAGGTTGTCACC
31470 GAATCCGTTT
Statistics
Matches: 335, Mismatches: 59, Indels: 28
0.79 0.14 0.07
Matches are distributed among these distances:
153 5 0.01
154 35 0.10
155 156 0.47
156 107 0.32
157 26 0.08
158 6 0.02
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (151 bp):
TTTTTAAGTCCTTTAAGGGTATCAGGTACTTTACGTCGAAGGTATCCCTAAGGGTATTTTCGTAA
TTTTTTAGAATCGAGTCTTAGGTTGTCACCAGGTCTGCTTTTATGCTGAAGGTGGGCATTTAGGA
TAGGTTCATCCCTCTTAAACC
Found at i:36435 original size:20 final size:20
Alignment explanation
Indices: 36410--36463 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
36400 TTTTACCCAG
***
36410 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATGGATCA
* *
36430 ATGTATCAATACATGGATGA
1 ATGTATCGATACATGGATCA
36450 ATGTATCGATACAT
1 ATGTATCGATACAT
36464 CTAGTTAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATGGATCA
Done.