Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold919
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: 26962
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:1726 original size:114 final size:114
Alignment explanation
Indices: 1508--1914 Score: 654
Period size: 114 Copynumber: 3.6 Consensus size: 114
1498 ATTAAAAGAT
* * * * *
1508 TTTGAGATCGATTGTAACTACATTTAGATGTTGTTAGCGCCGCGTGTATGTGGACTGCAGTTGAA
1 TTTGCGATCGATTCTAATTACATTTAGATGTTGTTAGCGCCACGTGTATGTGGACTGCAGTGGAA
* * *
1573 TCTTTGTTCATAGCATAGTTGACGGTTAAAGGACTCATCATCCAATCGA
66 CCTTTGTTAATAGCATAGTTGACGGTTAAAGGACTCATCATCCAATCAA
* * *
1622 TTTGTGATAGATTCTAATTACATTTAGATGTTGTTAGTGCCACGTGTATGTGGACTGCAGTGGAA
1 TTTGCGATCGATTCTAATTACATTTAGATGTTGTTAGCGCCACGTGTATGTGGACTGCAGTGGAA
** *
1687 CCTTTGTTAATAGCGCAGTTGACGGTTAAGGGACTCATCATCCAATCAA
66 CCTTTGTTAATAGCATAGTTGACGGTTAAAGGACTCATCATCCAATCAA
1736 TTTGCGATCGATTCTAATTACATTTAGATGTTGTTAGCGCCACGTGTATGTGGACTGCAGTGGAA
1 TTTGCGATCGATTCTAATTACATTTAGATGTTGTTAGCGCCACGTGTATGTGGACTGCAGTGGAA
1801 CCTTTGTTAATAGCATAGTTGACGGTTAAAGGACTCATCA-CCAAATCAA
66 CCTTTGTTAATAGCATAGTTGACGGTTAAAGGACTCATCATCC-AATCAA
* *
1850 TTTGCGATCGATTCTAATTACATTTAGATGTTGTTAGAGCCACGTGTATGTGAACTGCAGTGGAA
1 TTTGCGATCGATTCTAATTACATTTAGATGTTGTTAGCGCCACGTGTATGTGGACTGCAGTGGAA
1915 TTGCGTAGTT
Statistics
Matches: 271, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
113 2 0.01
114 269 0.99
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (114 bp):
TTTGCGATCGATTCTAATTACATTTAGATGTTGTTAGCGCCACGTGTATGTGGACTGCAGTGGAA
CCTTTGTTAATAGCATAGTTGACGGTTAAAGGACTCATCATCCAATCAA
Found at i:4994 original size:3 final size:3
Alignment explanation
Indices: 4986--5016 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
4976 TGGTCTTTCT
4986 TTC TTC TTC TTTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC
5017 AAATTTGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:4997 original size:10 final size:10
Alignment explanation
Indices: 4982--5015 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
4972 GGTCTGGTCT
4982 TTCTTTCTTC
1 TTCTTTCTTC
4992 TTCTTTCTTC
1 TTCTTTCTTC
5002 TTC-TTCTTC
1 TTCTTTCTTC
5011 TTCTT
1 TTCTT
5016 CAAATTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (10 bp):
TTCTTTCTTC
Found at i:11362 original size:27 final size:27
Alignment explanation
Indices: 11332--11656 Score: 142
Period size: 27 Copynumber: 12.4 Consensus size: 27
11322 AGGGAAAGGA
11332 AGGAAGAGGAAGAAGCCAGGAGGAAAG
1 AGGAAGAGGAAGAAGCCAGGAGGAAAG
* * * * * *
11359 AGGAGGAAGAGGAGGCCAGAAAGAGAAG
1 AGGAAGAGGAAGAAGCCAGGAGGA-AAG
* * *
11387 A-GAGGAGGAAGAAGCTAAGAGGAAAG
1 AGGAAGAGGAAGAAGCCAGGAGGAAAG
* *
11413 AAGAAGAAGAGGCCCAA-AAG--AGAAGGGAAG
1 -AG--GAAGAGG---AAGAAGCCAGGAGGAAAG
* *
11443 AGGAAGAGG-AG--GCCAGAAGGAGAG
1 AGGAAGAGGAAGAAGCCAGGAGGAAAG
* * *
11467 AGGAAGACGAAGAAGCTAAGA-G-AAG
1 AGGAAGAGGAAGAAGCCAGGAGGAAAG
* * * * *
11492 -GGAAGAAGAGGAGGCCAGAAGGAGAG
1 AGGAAGAGGAAGAAGCCAGGAGGAAAG
* *
11518 AGGAAGAGGAAGAAGCTAAGA-G-AAG
1 AGGAAGAGGAAGAAGCCAGGAGGAAAG
** * *
11543 A-GAAGAAAAAGAGGCCAGGAGGAGAG
1 AGGAAGAGGAAGAAGCCAGGAGGAAAG
* * * *
11569 AGGAGGAAGAAGAAGCTAGGAGGAGAG
1 AGGAAGAGGAAGAAGCCAGGAGGAAAG
* * * *
11596 AGGAGGAAGAAGAAGCTAGGAGGGAAG
1 AGGAAGAGGAAGAAGCCAGGAGGAAAG
* *
11623 AGGAAGAGG-AG--GCCAGAAGGAGAG
1 AGGAAGAGGAAGAAGCCAGGAGGAAAG
11647 AGGAAGAGGA
1 AGGAAGAGGA
11657 TGCTCGGAGG
Statistics
Matches: 221, Mismatches: 56, Indels: 44
0.69 0.17 0.14
Matches are distributed among these distances:
22 1 0.00
23 1 0.00
24 62 0.28
25 9 0.04
26 12 0.05
27 112 0.51
28 4 0.02
29 2 0.01
30 13 0.06
32 3 0.01
33 2 0.01
ACGTcount: A:0.47, C:0.06, G:0.45, T:0.02
Consensus pattern (27 bp):
AGGAAGAGGAAGAAGCCAGGAGGAAAG
Found at i:11364 original size:24 final size:24
Alignment explanation
Indices: 11328--11607 Score: 73
Period size: 24 Copynumber: 10.8 Consensus size: 24
11318 TGAAAGGGAA
*
11328 AGGAAGGAAGAGGAAGAAGCCAGG
1 AGGAAAGAAGAGGAAGAAGCCAGG
* *
11352 AGGAAAGAGGAGGAAGAGGAGGCCAGAA
1 AGGAAAGAAGAGGAAGA--A-GCCAG-G
* * *
11380 AGAGAAGAGAGGAGGAAGAAGCTAAG
1 AG-GAA-AGAAGAGGAAGAAGCCAGG
* * **
11406 AGGAAAGAAGAAGAAGAGGCCCAAA
1 AGGAAAGAAGAGGAAGAAG-CCAGG
* *
11431 AGAGAAGGGAAGAGGAAGAGGAGGCCAGA
1 AG-GAA-AGAAGAGGAAGA--A-GCCAGG
* *
11460 AGGAGAGAGGAAGACGAAGAAGCTAAGAG
1 AGGA-A-A-GAAGAGGAAGAAGC-CAG-G
* *
11489 AAGGGAAGAAGAGG-AG--GCCAGA
1 -AGGAAAGAAGAGGAAGAAGCCAGG
* *
11511 AGGAGAGAGGAAGAGGAAGAAGCTAAG
1 AGGA-A-A-GAAGAGGAAGAAGCCAGG
** *
11538 A-GAAGAGAAGAAAAAGAGGCCAGG
1 AGGAA-AGAAGAGGAAGAAGCCAGG
* * *
11562 AGGAGAGAGGAGGAAGAAGAAGCTAGG
1 AGGA-A-A-GAAGAGGAAGAAGCCAGG
* *
11589 AGGAGAGAGGAGGAAGAAG
1 AGGAAAGAAGAGGAAGAAG
11608 AAGCTAGGAG
Statistics
Matches: 192, Mismatches: 38, Indels: 52
0.68 0.13 0.18
Matches are distributed among these distances:
21 3 0.02
22 1 0.01
23 3 0.02
24 61 0.32
25 16 0.08
26 13 0.07
27 48 0.25
28 9 0.05
29 12 0.06
30 26 0.14
ACGTcount: A:0.48, C:0.06, G:0.44, T:0.01
Consensus pattern (24 bp):
AGGAAAGAAGAGGAAGAAGCCAGG
Found at i:11391 original size:30 final size:29
Alignment explanation
Indices: 11357--11470 Score: 86
Period size: 30 Copynumber: 4.2 Consensus size: 29
11347 CCAGGAGGAA
11357 AGAGGAGGAAGAGGAGGCCAGAAAGAGAAG
1 AGAGGAGGAAGAGGAGGCCA-AAAGAGAAG
* *
11387 AGAGGAGGAAGA--A-GCTAAGAG-GAA-
1 AGAGGAGGAAGAGGAGGCCAAAAGAGAAG
*
11411 AGA--A-GAAGAAGAGGCCCAAAAGAGAAG
1 AGAGGAGGAAGAGGAGG-CCAAAAGAGAAG
* * *
11438 GGAAGAGGAAGAGGAGGCCAGAAG-G-AG
1 AGAGGAGGAAGAGGAGGCCAAAAGAGAAG
11465 AGAGGA
1 AGAGGA
11471 AGACGAAGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 21
0.69 0.09 0.22
Matches are distributed among these distances:
21 5 0.08
22 1 0.02
23 1 0.02
24 4 0.06
25 8 0.12
26 6 0.09
27 11 0.17
28 2 0.03
29 7 0.11
30 21 0.32
ACGTcount: A:0.48, C:0.07, G:0.44, T:0.01
Consensus pattern (29 bp):
AGAGGAGGAAGAGGAGGCCAAAAGAGAAG
Found at i:11419 original size:81 final size:81
Alignment explanation
Indices: 11324--11605 Score: 192
Period size: 81 Copynumber: 3.5 Consensus size: 81
11314 AAATTGAAAG
*
11324 GGAAAGGAAGGAAGAGGAAGAAGCCAGGAGGAAAGAGGAGGAAGAGGAGGCCAGAAAGAGAAGAG
1 GGAAA-GAA-GAAGAGGAAGAAGCCAGAAGGAAAGAGGAGGAAGAGGAGGCCAGAAAGAGAAGAG
* *
11389 AGGAGGAAGAAGCTAAGA
64 AAGAAGAAGAAGCTAAGA
* * * * *
11407 GGAAAGAAG-A-A-GAAGAGGCCCAAAAGAGAAGGGAAGAGGAAGAGGAGGCCAGAAGGAG-AGA
1 GGAAAGAAGAAGAGGAAGAAG-CCAGAAG-GAA-AGAGGAGGAAGAGGAGGCCAGAAAGAGAAGA
*
11468 GGAAGACGAAGAAGCTAAGA
63 -GAAGAAGAAGAAGCTAAGA
* * * *
11488 -GAAGGGAAGAAGAGG-AG--GCCAGAAGG--AGA-GAGGAAGAGGAAG-AAGCTAAGAGAAGAG
1 GGAA-AGAAGAAGAGGAAGAAGCCAGAAGGAAAGAGGAGGAAGAGGAGGCCAG-AAAGAGAAGAG
* * * *
11545 AAGAAAAAGAGGCCAGGA
64 AAGAAGAAGAAGCTAAGA
* * * * * * *
11563 GGAGAGAGGAGGAAGAAGAAGCTAGGAGGAGAGAGGAGGAAGA
1 GGAAAGAAGAAGAGGAAGAAGCCAGAAGGAAAGAGGAGGAAGA
11606 AGAAGCTAGG
Statistics
Matches: 155, Mismatches: 27, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
74 2 0.01
75 37 0.24
76 9 0.06
78 13 0.08
79 7 0.05
80 19 0.12
81 55 0.35
82 4 0.03
83 8 0.05
84 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.44, T:0.01
Consensus pattern (81 bp):
GGAAAGAAGAAGAGGAAGAAGCCAGAAGGAAAGAGGAGGAAGAGGAGGCCAGAAAGAGAAGAGAA
GAAGAAGAAGCTAAGA
Found at i:11425 original size:51 final size:53
Alignment explanation
Indices: 11325--11449 Score: 152
Period size: 51 Copynumber: 2.4 Consensus size: 53
11315 AATTGAAAGG
* *
11325 GAAAG-GAAGGAAGAGGAAGAAGCCAGGAGGAAAGAGGAGGAAGAGGAGG-CCA
1 GAAAGAGAAGGAAGAGGAAGAAGCCAAGAGGAAAGA-GAGGAAGAAGAGGCCCA
* *
11377 GAAAGAGAAGAGAGGAGGAAGAAGCTAAGAGGAAAGA-A-GAAGAAGAGGCCCA
1 GAAAGAGAAG-GAAGAGGAAGAAGCCAAGAGGAAAGAGAGGAAGAAGAGGCCCA
11429 -AAAGAGAAGGGAAGAGGAAGA
1 GAAAGAGAA-GGAAGAGGAAGA
11450 GGAGGCCAGA
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
51 27 0.42
52 10 0.16
53 4 0.06
54 23 0.36
ACGTcount: A:0.50, C:0.06, G:0.42, T:0.01
Consensus pattern (53 bp):
GAAAGAGAAGGAAGAGGAAGAAGCCAAGAGGAAAGAGAGGAAGAAGAGGCCCA
Found at i:11472 original size:30 final size:30
Alignment explanation
Indices: 11404--11653 Score: 107
Period size: 30 Copynumber: 9.3 Consensus size: 30
11394 GAAGAAGCTA
* *
11404 AGAGGAAAGAAGAAGAAGAGGCCCA-AAAGAG
1 AGAGG-AAGAAGAAGAGGAGG-CCAGAAGGAG
*
11435 A-AGGGAAGAGGAAGAGGAGGCCAGAAGGAG
1 AGA-GGAAGAAGAAGAGGAGGCCAGAAGGAG
* *
11465 AGAGGAAGACGAAGA--A-G-C-TAA-GAG
1 AGAGGAAGAAGAAGAGGAGGCCAGAAGGAG
11489 A-AGG--GAAGAAGAGGAGGCCAGAAGGAG
1 AGAGGAAGAAGAAGAGGAGGCCAGAAGGAG
* *
11516 AGAGGAAGAGGAAGA--A-G-C-TAA-GAG
1 AGAGGAAGAAGAAGAGGAGGCCAGAAGGAG
*
11540 A-AGAGAAGAA-AA-A-GAGGCCAGGAGGAG
1 AGAG-GAAGAAGAAGAGGAGGCCAGAAGGAG
* * *
11567 AGAGGAGGAAGAAGA--A-GCTAGGAGGAG
1 AGAGGAAGAAGAAGAGGAGGCCAGAAGGAG
* *
11594 AGAGGAGGAAGAAGA--A-G-C--TA-G-G
1 AGAGGAAGAAGAAGAGGAGGCCAGAAGGAG
*
11616 AG-GGAAGAGGAAGAGGAGGCCAGAAGGAG
1 AGAGGAAGAAGAAGAGGAGGCCAGAAGGAG
11645 AGAGGAAGA
1 AGAGGAAGA
11654 GGATGCTCGG
Statistics
Matches: 170, Mismatches: 19, Indels: 61
0.68 0.08 0.24
Matches are distributed among these distances:
21 17 0.10
22 4 0.02
23 11 0.06
24 17 0.10
25 7 0.04
26 5 0.03
27 43 0.25
28 11 0.06
29 7 0.04
30 44 0.26
31 4 0.02
ACGTcount: A:0.48, C:0.06, G:0.44, T:0.02
Consensus pattern (30 bp):
AGAGGAAGAAGAAGAGGAGGCCAGAAGGAG
Found at i:11473 original size:51 final size:49
Alignment explanation
Indices: 11430--11572 Score: 160
Period size: 51 Copynumber: 2.8 Consensus size: 49
11420 AGAGGCCCAA
* *
11430 AAGAGAAGGGAAGAGGAAGAGGAGGCCAGAAGGAGAGAGGAAGACGAAGAAGC
1 AAGAGAAGGG-A-A-GAAGAGGAGGCCAGAAGGAGAGAGGAAGAGGAACAA-C
*
11483 TAAGAGAAGGGAAGAAGAGGAGGCCAGAAGGAGAGAGGAAGAGGAAGAAGC
1 -AAGAGAAGGGAAGAAGAGGAGGCCAGAAGGAGAGAGGAAGAGGAACAA-C
* * * *
11534 TAAGAGAAGAGAAGAAAAAGAGGCCAGGAGGAGAGAGGA
1 -AAGAGAAGGGAAGAAGAGGAGGCCAGAAGGAGAGAGGA
11573 GGAAGAAGAA
Statistics
Matches: 84, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
51 72 0.86
52 1 0.01
53 1 0.01
54 10 0.12
ACGTcount: A:0.48, C:0.06, G:0.44, T:0.01
Consensus pattern (49 bp):
AAGAGAAGGGAAGAAGAGGAGGCCAGAAGGAGAGAGGAAGAGGAACAAC
Found at i:11581 original size:51 final size:51
Alignment explanation
Indices: 11451--11596 Score: 211
Period size: 51 Copynumber: 2.9 Consensus size: 51
11441 AGAGGAAGAG
* * * *
11451 GAGGCCAGAAGGAGAGAGGAAGACGAAGAAGCTAAGAGAAGGGAAGAAGAG
1 GAGGCCAGAAGGAGAGAGGAAGAAGAAGAAGCTAAGAGAAGAGAAGAAAAA
*
11502 GAGGCCAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGAAGAAAAA
1 GAGGCCAGAAGGAGAGAGGAAGAAGAAGAAGCTAAGAGAAGAGAAGAAAAA
* * * *
11553 GAGGCCAGGAGGAGAGAGGAGGAAGAAGAAGCTAGGAGGAGAGA
1 GAGGCCAGAAGGAGAGAGGAAGAAGAAGAAGCTAAGAGAAGAGA
11597 GGAGGAAGAA
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 86 1.00
ACGTcount: A:0.47, C:0.07, G:0.44, T:0.02
Consensus pattern (51 bp):
GAGGCCAGAAGGAGAGAGGAAGAAGAAGAAGCTAAGAGAAGAGAAGAAAAA
Found at i:11667 original size:24 final size:24
Alignment explanation
Indices: 11441--11688 Score: 120
Period size: 27 Copynumber: 9.7 Consensus size: 24
11431 AGAGAAGGGA
* * *
11441 AGAGGAAGAGGAGGCCAGAAGGAG
1 AGAGGAAGAGGAAGCTAGGAGGAG
* *
11465 AGAGGAAGACGAAGAAGCTAAGAGAAG
1 AGAGGAAGA-G--GAAGCTAGGAGGAG
* * * * *
11492 GGAAGAAGAGGAGGCCAGAAGGAG
1 AGAGGAAGAGGAAGCTAGGAGGAG
* *
11516 AGAGGAAGAGGAAGAAGCTAAGAGAAG
1 AGAGGAAGA-G--GAAGCTAGGAGGAG
* * * * *
11543 AGAAGAAAAAGAGGCCAGGAGGAGAG
1 AGAGGAAGAGGAAGCTAGGA-G-GAG
*
11569 AGGAGGAAGAAGAAGCTAGGAGGAGAG
1 A-GAGGAAGAGGAAGCTAGGA-G-GAG
*
11596 AGGAGGAAGAAGAAGCTAGGAGG-G
1 A-GAGGAAGAGGAAGCTAGGAGGAG
* * *
11620 AAGAGGAAGAGGAGGCCAGAAGGAG
1 -AGAGGAAGAGGAAGCTAGGAGGAG
* *
11645 AGAGGAAGAGGATGCTCGGAGGAGGG
1 AGAGGAAGAGGAAGCTAGGAGGA--G
*
11671 AAGAGGAAGAGGGAGCTA
1 -AGAGGAAGAGGAAGCTA
11689 CGAGAAGGGA
Statistics
Matches: 169, Mismatches: 41, Indels: 25
0.72 0.17 0.11
Matches are distributed among these distances:
24 69 0.41
25 6 0.04
26 6 0.04
27 88 0.52
ACGTcount: A:0.44, C:0.06, G:0.46, T:0.03
Consensus pattern (24 bp):
AGAGGAAGAGGAAGCTAGGAGGAG
Found at i:11697 original size:27 final size:26
Alignment explanation
Indices: 11616--11698 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 26
11606 AGAAGCTAGG
11616 AGGGAAGAGGAAGAGGAGGC-C-AGA
1 AGGGAAGAGGAAGAGGAGGCTCGAGA
* *
11640 A-GGAGAGAGGAAGAGGATGCTCGGAGG
1 AGGGA-AGAGGAAGAGGAGGCTC-GAGA
11667 AGGGAAGAGGAAGAGG-GAGCTACGAGA
1 AGGGAAGAGGAAGAGGAG-GCT-CGAGA
11694 AGGGA
1 AGGGA
11699 GACAAAGAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
23 3 0.06
24 15 0.31
25 1 0.02
27 25 0.52
28 4 0.08
ACGTcount: A:0.39, C:0.07, G:0.51, T:0.04
Consensus pattern (26 bp):
AGGGAAGAGGAAGAGGAGGCTCGAGA
Found at i:15144 original size:5 final size:5
Alignment explanation
Indices: 15134--15198 Score: 130
Period size: 5 Copynumber: 13.0 Consensus size: 5
15124 AAAATAGAGG
15134 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
15184 TATAT TATAT TATAT
1 TATAT TATAT TATAT
15199 GTATTATGTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 60 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:15927 original size:14 final size:14
Alignment explanation
Indices: 15910--15938 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
15900 CGGAGCTTCT
15910 TCTCTCCCTCTCCC
1 TCTCTCCCTCTCCC
15924 TCTCTCCCTCTCCC
1 TCTCTCCCTCTCCC
15938 T
1 T
15939 TCGGCTCTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (14 bp):
TCTCTCCCTCTCCC
Found at i:16589 original size:14 final size:14
Alignment explanation
Indices: 16566--16599 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
16556 TGGTATGAGT
16566 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
16579 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
16593 TTATAGG
1 TTATAGG
16600 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:21165 original size:22 final size:22
Alignment explanation
Indices: 21140--21189 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
21130 TTTATATACA
21140 GATAATTTGGCAATGTTATGTG
1 GATAATTTGGCAATGTTATGTG
21162 GATAATTTGGCAATGTTATGTG
1 GATAATTTGGCAATGTTATGTG
21184 GATAAT
1 GATAAT
21190 CTAGCTCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.30, C:0.04, G:0.26, T:0.40
Consensus pattern (22 bp):
GATAATTTGGCAATGTTATGTG
Found at i:24395 original size:3 final size:3
Alignment explanation
Indices: 24389--24425 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
24379 TGGTTTTTTT
24389 TTC TTC TTC TTC TTC TTC TTC -TC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
24426 GTTCCTAGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:24415 original size:17 final size:17
Alignment explanation
Indices: 24393--24425 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
24383 TTTTTTTTCT
24393 TCTTCTTCTTCTTCTTC
1 TCTTCTTCTTCTTCTTC
24410 TCTTCTTCTTCTTCTT
1 TCTTCTTCTTCTTCTT
24426 GTTCCTAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (17 bp):
TCTTCTTCTTCTTCTTC
Found at i:25833 original size:20 final size:20
Alignment explanation
Indices: 25810--25861 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
25800 AATCAAGTGC
25810 AAATGATTTTAACCAAGTCA
1 AAATGATTTTAACCAAGTCA
* * *
25830 AAATGATTTCAATCAAGTTA
1 AAATGATTTTAACCAAGTCA
*
25850 AAATCATTTTAA
1 AAATGATTTTAA
25862 ATGATTTTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.35
Consensus pattern (20 bp):
AAATGATTTTAACCAAGTCA
Found at i:26047 original size:20 final size:22
Alignment explanation
Indices: 26024--26063 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
26014 TATTTTCGGT
26024 ATCGATA-CTTT-TTAAAAATA
1 ATCGATACCTTTCTTAAAAATA
26044 ATCGATACCTTTCTTAAAAA
1 ATCGATACCTTTCTTAAAAA
26064 CGATACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 4 0.22
22 7 0.39
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (22 bp):
ATCGATACCTTTCTTAAAAATA
Done.