Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3354
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: 38529
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Found at i:351 original size:25 final size:25
Alignment explanation
Indices: 321--370 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
311 GAGCTAAAAC
321 ATACAGGAACAAGCTCAGTTAACAT
1 ATACAGGAACAAGCTCAGTTAACAT
346 ATACAGGAACAAGCTCAGTTAACAT
1 ATACAGGAACAAGCTCAGTTAACAT
371 CTGTAGATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (25 bp):
ATACAGGAACAAGCTCAGTTAACAT
Found at i:7293 original size:14 final size:14
Alignment explanation
Indices: 7276--7306 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
7266 TTAGATTAAT
7276 CTATTTAGGACTGC
1 CTATTTAGGACTGC
7290 CTATTTAGGACTGC
1 CTATTTAGGACTGC
7304 CTA
1 CTA
7307 GAACTGCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (14 bp):
CTATTTAGGACTGC
Found at i:9489 original size:30 final size:30
Alignment explanation
Indices: 9453--9510 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
9443 AAAGAATGTT
9453 TTAATCACAATAAATGTTACCGTTGACATC
1 TTAATCACAATAAATGTTACCGTTGACATC
*
9483 TTAATCACCATAAATGTTACCGTTGACA
1 TTAATCACAATAAATGTTACCGTTGACA
9511 CCTATCTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (30 bp):
TTAATCACAATAAATGTTACCGTTGACATC
Found at i:9903 original size:18 final size:18
Alignment explanation
Indices: 9858--9950 Score: 96
Period size: 18 Copynumber: 4.7 Consensus size: 18
9848 TCTTTTATAT
9858 CCCGGTTCCGGTTTTTTGGGAC
1 CCCGGTT-CGG-TTTTT--GAC
*
9880 CCCGGTTCGGTTTTTGAT
1 CCCGGTTCGGTTTTTGAC
*
9898 CCCGGTTCGGTTTTTTAC
1 CCCGGTTCGGTTTTTGAC
9916 CCCGGTTCGGTTTTTTTATGAC
1 CCCGGTTCGG---TTTT-TGAC
9938 CCCGGTTCGGTTT
1 CCCGGTTCGGTTT
9951 GAGTTGGCAA
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
18 28 0.44
19 3 0.05
20 5 0.08
21 7 0.11
22 20 0.32
ACGTcount: A:0.05, C:0.26, G:0.27, T:0.42
Consensus pattern (18 bp):
CCCGGTTCGGTTTTTGAC
Found at i:9925 original size:36 final size:38
Alignment explanation
Indices: 9856--9930 Score: 118
Period size: 36 Copynumber: 2.0 Consensus size: 38
9846 ATTCTTTTAT
9856 ATCCCGGTTCCGGTTTTTTGGGACCCCGGTTCGGTTTTTG
1 ATCCCGGTTCCGGTTTTTT--GACCCCGGTTCGGTTTTTG
9896 ATCCCGGTT-CGGTTTTTT-ACCCCGGTTCGGTTTTT
1 ATCCCGGTTCCGGTTTTTTGACCCCGGTTCGGTTTTT
9931 TTATGACCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
36 17 0.49
39 9 0.26
40 9 0.26
ACGTcount: A:0.05, C:0.25, G:0.27, T:0.43
Consensus pattern (38 bp):
ATCCCGGTTCCGGTTTTTTGACCCCGGTTCGGTTTTTG
Found at i:9942 original size:40 final size:38
Alignment explanation
Indices: 9850--9950 Score: 118
Period size: 40 Copynumber: 2.6 Consensus size: 38
9840 TATCCCATTC
9850 TTTTAT-ATCCCGGTTCCGGTTTTTTGGGACCCCGGTTCGG
1 TTTTATGATCCCGGTT-CGGTTTTTT--GACCCCGGTTCGG
9890 TTTT-TGATCCCGGTTCGGTTTTTT-ACCCCGGTTCGG
1 TTTTATGATCCCGGTTCGGTTTTTTGACCCCGGTTCGG
*
9926 TTTTTTTATGACCCCGGTTCGGTTT
1 ---TTTTATGATCCCGGTTCGGTTT
9951 GAGTTGGCAA
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
36 12 0.22
39 14 0.25
40 29 0.53
ACGTcount: A:0.07, C:0.24, G:0.25, T:0.45
Consensus pattern (38 bp):
TTTTATGATCCCGGTTCGGTTTTTTGACCCCGGTTCGG
Found at i:11926 original size:14 final size:14
Alignment explanation
Indices: 11909--11936 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11899 TATGACATTT
11909 TTGTTTTGACCATG
1 TTGTTTTGACCATG
11923 TTGTTTTGACCATG
1 TTGTTTTGACCATG
11937 ACACTCATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.50
Consensus pattern (14 bp):
TTGTTTTGACCATG
Found at i:19083 original size:51 final size:51
Alignment explanation
Indices: 19018--19121 Score: 156
Period size: 51 Copynumber: 2.0 Consensus size: 51
19008 CCTTAATTTT
* *
19018 TTTCTAACGCCTTTTTTCCTTTACT-GGTTGTTAATTTTCTTTCTTATTCTG
1 TTTCTAACGCCTTTTTTCATTT-CTCGGATGTTAATTTTCTTTCTTATTCTG
* *
19069 TTTCTAACGTCTTTTTTCATTTTTCGGATGTTAATTTTCTTTCTTATTCTG
1 TTTCTAACGCCTTTTTTCATTTCTCGGATGTTAATTTTCTTTCTTATTCTG
19120 TT
1 TT
19122 CCGGCTTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
50 1 0.02
51 47 0.98
ACGTcount: A:0.12, C:0.17, G:0.10, T:0.61
Consensus pattern (51 bp):
TTTCTAACGCCTTTTTTCATTTCTCGGATGTTAATTTTCTTTCTTATTCTG
Found at i:25925 original size:43 final size:44
Alignment explanation
Indices: 25864--25957 Score: 147
Period size: 43 Copynumber: 2.2 Consensus size: 44
25854 ATCCTAATTG
*
25864 AGAAAATAGTTCTCTTATTCTAATAAACTACTAAAACATAAAA-
1 AGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAT
* *
25907 AGAAAATAGTTCCCTTATTCTAGTAAACTACTAAAAGATAAAAT
1 AGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAT
25951 A-AAAATA
1 AGAAAATA
25958 TTTCTAGAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (44 bp):
AGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAT
Found at i:26001 original size:19 final size:18
Alignment explanation
Indices: 25979--26018 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
25969 TGAATAAAAC
25979 TTATCTATCC-AAATAAGAT
1 TTATCTA-CCTAAATAA-AT
25998 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
26016 TTA
1 TTA
26019 AAATATATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:26404 original size:3 final size:3
Alignment explanation
Indices: 26396--26430 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
26386 ATCACATGTT
26396 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
26431 TGGATGTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:26550 original size:73 final size:73
Alignment explanation
Indices: 26431--26616 Score: 354
Period size: 73 Copynumber: 2.5 Consensus size: 73
26421 TATTATTATT
*
26431 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
26496 ATTTTAAG
66 ATTTTAAG
26504 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
26569 ATTTTAAG
66 ATTTTAAG
*
26577 TGTATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
26617 GTCAAGTTGT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 111 1.00
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.41
Consensus pattern (73 bp):
TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
ATTTTAAG
Found at i:30839 original size:3 final size:3
Alignment explanation
Indices: 30825--30856 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
30815 ATCACATGTT
*
30825 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
30857 TGGATGTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:30976 original size:73 final size:73
Alignment explanation
Indices: 30857--31042 Score: 345
Period size: 73 Copynumber: 2.5 Consensus size: 73
30847 TATTATTATT
* *
30857 TGGATGTAATGATGTAATTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
30922 ATTTTAAG
66 ATTTTAAG
30930 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
30995 ATTTTAAG
66 ATTTTAAG
*
31003 TGTATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
31043 GTCAAGTTGT
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 110 1.00
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.42
Consensus pattern (73 bp):
TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
ATTTTAAG
Found at i:32845 original size:31 final size:31
Alignment explanation
Indices: 32807--32872 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
32797 CTTTTCCAAC
32807 TTTCATCAGTAGAGGAGAGCACCTATACAAG
1 TTTCATCAGTAGAGGAGAGCACCTATACAAG
32838 TTTCATCAGTAGAGGAGAGCACCTATACAAG
1 TTTCATCAGTAGAGGAGAGCACCTATACAAG
32869 TTTC
1 TTTC
32873 TTTCTTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (31 bp):
TTTCATCAGTAGAGGAGAGCACCTATACAAG
Found at i:37418 original size:7 final size:7
Alignment explanation
Indices: 37402--37489 Score: 59
Period size: 7 Copynumber: 12.1 Consensus size: 7
37392 GGTTTGGGAG
*
37402 TTAGGTT
1 TTAGGGT
37409 TTAGGGT
1 TTAGGGT
*
37416 TTAAGGT
1 TTAGGGT
37423 TTAGGGT
1 TTAGGGT
*
37430 TCAGGGCT
1 TTAGGG-T
* **
37438 TAAGATT
1 TTAGGGT
*
37445 TTAGGGC
1 TTAGGGT
*
37452 TAAGGGTT
1 TTAGGG-T
37460 TTAGGGT
1 TTAGGGT
*
37467 TGAGGGTT
1 TTAGGG-T
37475 TTAGGGT
1 TTAGGGT
*
37482 TCAGGGT
1 TTAGGGT
37489 T
1 T
37490 CAAGGTTCAG
Statistics
Matches: 61, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
7 46 0.75
8 15 0.25
ACGTcount: A:0.18, C:0.05, G:0.38, T:0.40
Consensus pattern (7 bp):
TTAGGGT
Found at i:37481 original size:15 final size:15
Alignment explanation
Indices: 37443--37489 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
37433 GGGCTTAAGA
*
37443 TTTTAGGGCTAAGGG
1 TTTTAGGGTTAAGGG
*
37458 TTTTAGGGTTGAGGG
1 TTTTAGGGTTAAGGG
*
37473 TTTTAGGGTTCAGGG
1 TTTTAGGGTTAAGGG
37488 TT
1 TT
37490 CAAGGTTCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.15, C:0.04, G:0.40, T:0.40
Consensus pattern (15 bp):
TTTTAGGGTTAAGGG
Found at i:37549 original size:7 final size:7
Alignment explanation
Indices: 37529--37566 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
37519 GGGTCAGGCT
37529 CTCAA-G
1 CTCAAGG
*
37535 CTCCAGG
1 CTCAAGG
37542 CTCAAGG
1 CTCAAGG
*
37549 CTCAGGG
1 CTCAAGG
37556 CTCAAGG
1 CTCAAGG
37563 CTCA
1 CTCA
37567 GGGTTCAGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
6 4 0.15
7 23 0.85
ACGTcount: A:0.24, C:0.34, G:0.26, T:0.16
Consensus pattern (7 bp):
CTCAAGG
Found at i:37558 original size:21 final size:21
Alignment explanation
Indices: 37534--37576 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
37524 AGGCTCTCAA
*
37534 GCTCCAGGCTCAAGGCTCAGG
1 GCTCAAGGCTCAAGGCTCAGG
* *
37555 GCTCAAGGCTCAGGGTTCAGG
1 GCTCAAGGCTCAAGGCTCAGG
37576 G
1 G
37577 TTTTAGGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.28, G:0.37, T:0.16
Consensus pattern (21 bp):
GCTCAAGGCTCAAGGCTCAGG
Found at i:37574 original size:7 final size:7
Alignment explanation
Indices: 37566--38517 Score: 685
Period size: 7 Copynumber: 135.1 Consensus size: 7
37556 CTCAAGGCTC
*
37566 AGGGTTC
1 AGGGTTT
37573 AGGGTTTT
1 AGGG-TTT
*
37581 AGGGTTC
1 AGGGTTT
37588 AGGGTTT
1 AGGGTTT
*
37595 ATGGTTTT
1 A-GGGTTT
37603 AGGGTTT
1 AGGGTTT
37610 AGGG-TT
1 AGGGTTT
37616 AGGGTTT
1 AGGGTTT
37623 AGGGGTTT
1 A-GGGTTT
*
37631 AAGGTTT
1 AGGGTTT
37638 AGAGGTTT
1 AG-GGTTT
37646 AGGGTTT
1 AGGGTTT
*
37653 AAGGTTT
1 AGGGTTT
37660 AGGGTTTT
1 AGGG-TTT
*
37668 GGGGTTT
1 AGGGTTT
37675 AGGGTTT
1 AGGGTTT
37682 AGGG-TT
1 AGGGTTT
37688 AGGGTTT
1 AGGGTTT
37695 A-GGTTT
1 AGGGTTT
*
37701 TGGGTTT
1 AGGGTTT
*
37708 GGGGTTTT
1 AGGG-TTT
37716 AGGGTTT
1 AGGGTTT
*
37723 -GGGGTT
1 AGGGTTT
* *
37729 CGAGGTTC
1 AG-GGTTT
37737 AGGG-TT
1 AGGGTTT
* *
37743 CGAGGTTC
1 AG-GGTTT
* *
37751 GGGGTTC
1 AGGGTTT
*
37758 AGGTTTT
1 AGGGTTT
37765 AGGGTTT
1 AGGGTTT
37772 AGGGTTT
1 AGGGTTT
37779 -GGGTTT
1 AGGGTTT
37785 AGGGTTT
1 AGGGTTT
37792 -GGG-TT
1 AGGGTTT
*
37797 -GGGGTT
1 AGGGTTT
37803 AGGG-TT
1 AGGGTTT
* *
37809 GGGGGTT
1 AGGGTTT
*
37816 -GGGTTG
1 AGGGTTT
*
37822 AGGGCTT
1 AGGGTTT
*
37829 AGGGCTT
1 AGGGTTT
*
37836 AGGGCTT
1 AGGGTTT
*
37843 AGGGGTT
1 AGGGTTT
*
37850 -GGG-GT
1 AGGGTTT
37855 -GGGTCTCT
1 AGGGT-T-T
*
37863 -GGAG-CT
1 AGG-GTTT
*
37869 AGGGTCT
1 AGGGTTT
*
37876 GGGGTTTT
1 AGGG-TTT
*
37884 GGGGTTTTT
1 AGGG--TTT
37893 AGGG-TT
1 AGGGTTT
37899 -GGGTTT
1 AGGGTTT
37905 AGGGTTT
1 AGGGTTT
*
37912 GGGGTTT
1 AGGGTTT
*
37919 GGGGTTT
1 AGGGTTT
*
37926 GGGGTTTT
1 AGGG-TTT
*
37934 AGGTGTCT
1 AGG-GTTT
*
37942 AGGGTCT
1 AGGGTTT
*
37949 AGGGTCCT
1 AGGGT-TT
37957 AGGGTTTT
1 AGGG-TTT
*
37965 AGGGTCT
1 AGGGTTT
37972 AGGGTTT
1 AGGGTTT
37979 AGGGTTTT
1 AGGG-TTT
37987 AGGGTTTT
1 AGGG-TTT
37995 AGGGTTTT
1 AGGG-TTT
* *
38003 AAGTTTT
1 AGGGTTT
38010 AGGGTTTT
1 AGGG-TTT
*
38018 AGGTTTT
1 AGGGTTT
38025 AGGGTTT
1 AGGGTTT
38032 A-GG-TT
1 AGGGTTT
*
38037 ATGGTTTT
1 A-GGGTTT
38045 AGGG-TT
1 AGGGTTT
38051 AGGGTTT
1 AGGGTTT
38058 AGGTGTTTT
1 AGG-G-TTT
38067 AGGGTTT
1 AGGGTTT
38074 AGGG-TT
1 AGGGTTT
38080 AGGGTTT
1 AGGGTTT
38087 AGGG-TT
1 AGGGTTT
38093 AGGGTTT
1 AGGGTTT
38100 AGGGTTT
1 AGGGTTT
*
38107 CA-GTTTT
1 -AGGGTTT
38114 AGGGTTTT
1 AGGG-TTT
38122 AGGG-TT
1 AGGGTTT
38128 AGGGTTT
1 AGGGTTT
38135 AGGGTTTT
1 AGGG-TTT
38143 AGGGTTT
1 AGGGTTT
38150 A--G-TT
1 AGGGTTT
38154 AGGTGTTTTT
1 AGG-G--TTT
* *
38164 ATGTTATT
1 AGGGT-TT
38172 AGGG-TT
1 AGGGTTT
*
38178 AGTGTTT
1 AGGGTTT
38185 A-GGTTT
1 AGGGTTT
38191 AGGG-TT
1 AGGGTTT
*
38197 A-GG-AT
1 AGGGTTT
38202 AGGGTTT
1 AGGGTTT
38209 AGGGTTT
1 AGGGTTT
38216 AGGGTTTT
1 AGGG-TTT
*
38224 AGGGTTG
1 AGGGTTT
38231 AGGGTTT
1 AGGGTTT
38238 AGGG-TT
1 AGGGTTT
38244 AGGGTTT
1 AGGGTTT
38251 AGGGTTT
1 AGGGTTT
38258 AGGGTTTT
1 AGGG-TTT
38266 AGGGTTT
1 AGGGTTT
38273 AGGG-TT
1 AGGGTTT
38279 AGGGTTT
1 AGGGTTT
38286 AGGGTTT
1 AGGGTTT
*
38293 AGGGGTT
1 AGGGTTT
38300 -GGGTTT
1 AGGGTTT
38306 AGGGTTT
1 AGGGTTT
38313 A-GGTTT
1 AGGGTTT
38319 AGGGTTT
1 AGGGTTT
*
38326 GGGGTTT
1 AGGGTTT
*
38333 AGGGTAT
1 AGGGTTT
38340 AGGGTTT
1 AGGGTTT
38347 AGGGTTT
1 AGGGTTT
38354 AGGG-TT
1 AGGGTTT
38360 AGGGTTT
1 AGGGTTT
38367 AGGGTTT
1 AGGGTTT
38374 AGGGCGTTT
1 A-GG-GTTT
38383 AGGGTTT
1 AGGGTTT
38390 AGGGTGTTT
1 A-GG-GTTT
*
38399 GGTGGGTTT
1 --AGGGTTT
38408 -GGGTTT
1 AGGGTTT
38414 AGGGTTT
1 AGGGTTT
38421 -GGGTTT
1 AGGGTTT
38427 AGGGTTT
1 AGGGTTT
* *
38434 ATAGG-TA
1 A-GGGTTT
38441 AGGGTTT
1 AGGGTTT
38448 AGGCGGGTTT
1 A---GGGTTT
38458 AGGCGTTTT
1 AGG-G-TTT
38467 AGGTTGGTTT
1 A-G--GGTTT
*
38477 A-CGTTT
1 AGGGTTT
38483 AGGGTTT
1 AGGGTTT
38490 AGGGTTT
1 AGGGTTT
38497 -GGGTTT
1 AGGGTTT
38503 AGGGTTT
1 AGGGTTT
38510 AGGGTTT
1 AGGGTTT
38517 A
1 A
38518 ATGCTCCTCT
Statistics
Matches: 783, Mismatches: 77, Indels: 170
0.76 0.07 0.17
Matches are distributed among these distances:
4 3 0.00
5 20 0.03
6 149 0.19
7 410 0.52
8 148 0.19
9 33 0.04
10 18 0.02
11 1 0.00
12 1 0.00
ACGTcount: A:0.13, C:0.03, G:0.43, T:0.42
Consensus pattern (7 bp):
AGGGTTT
Found at i:37586 original size:15 final size:14
Alignment explanation
Indices: 37566--38517 Score: 685
Period size: 13 Copynumber: 67.6 Consensus size: 14
37556 CTCAAGGCTC
*
37566 AGGGTTCAGGGTTTT
1 AGGGTTTAGGG-TTT
*
37581 AGGGTTCAGGGTTT
1 AGGGTTTAGGGTTT
*
37595 ATGGTTTTAGGGTTT
1 A-GGGTTTAGGGTTT
37610 AGGG-TTAGGGTTT
1 AGGGTTTAGGGTTT
*
37623 AGGGGTTTAAGGTTT
1 A-GGGTTTAGGGTTT
37638 AGAGGTTTAGGGTTT
1 AG-GGTTTAGGGTTT
*
37653 AAGGTTTAGGGTTTT
1 AGGGTTTAGGG-TTT
*
37668 GGGGTTTAGGGTTT
1 AGGGTTTAGGGTTT
37682 AGGG-TTAGGGTTT
1 AGGGTTTAGGGTTT
*
37695 A-GGTTTTGGGTTT
1 AGGGTTTAGGGTTT
*
37708 GGGGTTTTAGGGTTT
1 AGGG-TTTAGGGTTT
* * *
37723 -GGGGTTCGAGGTTC
1 AGGGTTTAG-GGTTT
* *
37737 AGGG-TTCGAGGTTC
1 AGGGTTTAG-GGTTT
* * *
37751 GGGGTTCAGGTTTT
1 AGGGTTTAGGGTTT
37765 AGGGTTTAGGGTTT
1 AGGGTTTAGGGTTT
37779 -GGGTTTAGGGTTT
1 AGGGTTTAGGGTTT
*
37792 -GGG-TT-GGGGTT
1 AGGGTTTAGGGTTT
* *
37803 AGGG-TTGGGGGTT
1 AGGGTTTAGGGTTT
* *
37816 -GGGTTGAGGGCTT
1 AGGGTTTAGGGTTT
* *
37829 AGGGCTTAGGGCTT
1 AGGGTTTAGGGTTT
* *
37843 AGGGGTT-GGG-GT
1 AGGGTTTAGGGTTT
*
37855 -GGGTCTCT-GGAG-CT
1 AGGGT-T-TAGG-GTTT
* *
37869 AGGGTCTGGGGTTTT
1 AGGGTTTAGGG-TTT
*
37884 GGGGTTTTTAGGG-TT
1 AGGG--TTTAGGGTTT
37899 -GGGTTTAGGGTTT
1 AGGGTTTAGGGTTT
* *
37912 GGGGTTTGGGGTTT
1 AGGGTTTAGGGTTT
* *
37926 GGGGTTTTAGGTGTCT
1 AGGG-TTTAGG-GTTT
* *
37942 AGGGTCTAGGGTCCT
1 AGGGTTTAGGGT-TT
*
37957 AGGGTTTTAGGGTCT
1 AGGG-TTTAGGGTTT
37972 AGGGTTTAGGGTTTT
1 AGGGTTTAGGG-TTT
37987 AGGGTTTTAGGGTTTT
1 AGGG-TTTAGGG-TTT
* *
38003 AAGTTTTAGGGTTTT
1 AGGGTTTAGGG-TTT
*
38018 AGGTTTTAGGGTTT
1 AGGGTTTAGGGTTT
*
38032 A-GG-TTATGGTTTT
1 AGGGTTTA-GGGTTT
38045 AGGG-TTAGGGTTT
1 AGGGTTTAGGGTTT
38058 AGGTGTTTTAGGGTTT
1 AGG-G-TTTAGGGTTT
38074 AGGG-TTAGGGTTT
1 AGGGTTTAGGGTTT
38087 AGGG-TTAGGGTTT
1 AGGGTTTAGGGTTT
*
38100 AGGGTTTCA-GTTTT
1 AGGGTTT-AGGGTTT
38114 AGGGTTTTAGGG-TT
1 AGGG-TTTAGGGTTT
38128 AGGGTTTAGGGTTTT
1 AGGGTTTAGGG-TTT
38143 AGGGTTTA--G-TT
1 AGGGTTTAGGGTTT
* *
38154 AGGTGTTTTTATGTTATT
1 AGG-G--TTTAGGGT-TT
*
38172 AGGG-TTAGTGTTT
1 AGGGTTTAGGGTTT
38185 A-GGTTTAGGG-TT
1 AGGGTTTAGGGTTT
*
38197 A-GG-ATAGGGTTT
1 AGGGTTTAGGGTTT
38209 AGGGTTTAGGGTTTT
1 AGGGTTTAGGG-TTT
*
38224 AGGGTTGAGGGTTT
1 AGGGTTTAGGGTTT
38238 AGGG-TTAGGGTTT
1 AGGGTTTAGGGTTT
38251 AGGGTTTAGGGTTTT
1 AGGGTTTAGGG-TTT
38266 AGGGTTTAGGG-TT
1 AGGGTTTAGGGTTT
38279 AGGGTTTAGGGTTT
1 AGGGTTTAGGGTTT
*
38293 AGGGGTT-GGGTTT
1 AGGGTTTAGGGTTT
38306 AGGGTTTA-GGTTT
1 AGGGTTTAGGGTTT
*
38319 AGGGTTTGGGGTTT
1 AGGGTTTAGGGTTT
*
38333 AGGGTATAGGGTTT
1 AGGGTTTAGGGTTT
38347 AGGGTTTAGGG-TT
1 AGGGTTTAGGGTTT
38360 AGGGTTTAGGGTTT
1 AGGGTTTAGGGTTT
38374 AGGGCGTTTAGGGTTT
1 A-GG-GTTTAGGGTTT
*
38390 AGGGTGTTTGGTGGGTTT
1 A-GG-GTTT--AGGGTTT
38408 -GGGTTTAGGGTTT
1 AGGGTTTAGGGTTT
38421 -GGGTTTAGGGTTT
1 AGGGTTTAGGGTTT
* *
38434 ATAGG-TAAGGGTTT
1 A-GGGTTTAGGGTTT
38448 AGGCGGGTTTAGGCGTTTT
1 A---GGGTTTAGG-G-TTT
*
38467 AGGTTGGTTTA-CGTTT
1 A-G--GGTTTAGGGTTT
38483 AGGGTTTAGGGTTT
1 AGGGTTTAGGGTTT
38497 -GGGTTTAGGGTTT
1 AGGGTTTAGGGTTT
38510 AGGGTTTA
1 AGGGTTTA
38518 ATGCTCCTCT
Statistics
Matches: 782, Mismatches: 79, Indels: 153
0.77 0.08 0.15
Matches are distributed among these distances:
11 18 0.02
12 35 0.04
13 228 0.29
14 221 0.28
15 181 0.23
16 65 0.08
17 12 0.02
18 12 0.02
19 10 0.01
ACGTcount: A:0.13, C:0.03, G:0.43, T:0.42
Consensus pattern (14 bp):
AGGGTTTAGGGTTT
Found at i:37591 original size:22 final size:22
Alignment explanation
Indices: 37566--38516 Score: 560
Period size: 20 Copynumber: 44.6 Consensus size: 22
37556 CTCAAGGCTC
* *
37566 AGGGTTCAGGGTTTTAGGGTTC
1 AGGGTTTAGGGTTTTAGGGTTT
*
37588 AGGGTTTATGGTTTTAGGGTTT
1 AGGGTTTAGGGTTTTAGGGTTT
37610 AGGG-TTAGGG-TTTAGGGGTTT
1 AGGGTTTAGGGTTTTA-GGGTTT
*
37631 AAGGTTTAGAGG-TTTAGGGTTT
1 AGGGTTTAG-GGTTTTAGGGTTT
* *
37653 AAGGTTTAGGGTTTTGGGGTTT
1 AGGGTTTAGGGTTTTAGGGTTT
37675 AGGGTTTAGGG--TTAGGGTTT
1 AGGGTTTAGGGTTTTAGGGTTT
* *
37695 A-GGTTTTGGG-TTTGGGGTTTT
1 AGGGTTTAGGGTTTTAGGG-TTT
* ** *
37716 AGGGTTTGGGGTTCGA-GGTTC
1 AGGGTTTAGGGTTTTAGGGTTT
* ** *
37737 AGGG-TTCGAGG-TTCGGGGTTC
1 AGGGTTTAG-GGTTTTAGGGTTT
*
37758 AGGTTTTAGGG-TTTAGGGTTT
1 AGGGTTTAGGGTTTTAGGGTTT
37779 -GGGTTTAGGG-TTT-GGG-TT
1 AGGGTTTAGGGTTTTAGGGTTT
* * *
37797 -GGGGTTAGGG--TTGGGGGTT
1 AGGGTTTAGGGTTTTAGGGTTT
* * *
37816 -GGGTTGAGGG-CTTAGGGCTT
1 AGGGTTTAGGGTTTTAGGGTTT
* * *
37836 AGGGCTTAGGG-GTT-GGG-GT
1 AGGGTTTAGGGTTTTAGGGTTT
* ** *** *
37855 -GGGTCTCTGGAGCTAGGGTCT
1 AGGGTTTAGGGTTTTAGGGTTT
* *
37876 GGGGTTTTGGGGTTTTTAGGG-TT
1 AGGG-TTTAGGG-TTTTAGGGTTT
*
37899 -GGGTTTAGGG-TTTGGGGTTT
1 AGGGTTTAGGGTTTTAGGGTTT
* * *
37919 GGGGTTTGGGGTTTTAGGTGTCT
1 AGGGTTTAGGGTTTTAGG-GTTT
* **
37942 AGGGTCTAGGGTCCTAGGGTTTT
1 AGGGTTTAGGGTTTTAGGG-TTT
*
37965 AGGGTCTAGGG-TTTAGGGTTTT
1 AGGGTTTAGGGTTTTAGGG-TTT
* *
37987 AGGGTTTTAGGGTTTTAAGTTTT
1 AGGG-TTTAGGGTTTTAGGGTTT
38010 AGGGTTTTA-GGTTTTAGGGTTT
1 AGGG-TTTAGGGTTTTAGGGTTT
*
38032 A-GG-TTATGGTTTTAGGG-TT
1 AGGGTTTAGGGTTTTAGGGTTT
38051 AGGGTTTAGGTGTTTTAGGGTTT
1 AGGGTTTAGG-GTTTTAGGGTTT
38074 AGGG-TTAGGG-TTTAGGG-TT
1 AGGGTTTAGGGTTTTAGGGTTT
* *
38093 AGGGTTTAGGGTTTCA-GTTTT
1 AGGGTTTAGGGTTTTAGGGTTT
38114 AGGGTTTTAGGG--TTAGGGTTT
1 AGGG-TTTAGGGTTTTAGGGTTT
38135 AGGGTTTTAGGG-TTTA--G-TT
1 AGGG-TTTAGGGTTTTAGGGTTT
*
38154 AGGTGTTTTTA-TGTTATTAGGG-TT
1 AGG-G--TTTAGGGTT-TTAGGGTTT
*
38178 AGTGTTTA-GG-TTTAGGGTTAGGAT
1 AGGGTTTAGGGTTTTAGGGTT----T
38202 AGGGTTTAGGG-TTTAGGGTTTT
1 AGGGTTTAGGGTTTTAGGG-TTT
*
38224 AGGGTTGAGGG-TTTAGGG-TT
1 AGGGTTTAGGGTTTTAGGGTTT
38244 AGGGTTTAGGG-TTTAGGGTTTT
1 AGGGTTTAGGGTTTTAGGG-TTT
38266 AGGGTTTAGGG--TTAGGGTTT
1 AGGGTTTAGGGTTTTAGGGTTT
*
38286 AGGGTTTAGGG-GTT-GGGTTT
1 AGGGTTTAGGGTTTTAGGGTTT
38306 AGGGTTTA-GG-TTTAGGGTTT
1 AGGGTTTAGGGTTTTAGGGTTT
* *
38326 GGGGTTTAGGG-TATAGGGTTT
1 AGGGTTTAGGGTTTTAGGGTTT
38347 AGGGTTTAGGG--TTAGGGTTT
1 AGGGTTTAGGGTTTTAGGGTTT
*
38367 AGGGTTTAGGGCGTTTAGGGTTT
1 AGGGTTTAGGG-TTTTAGGGTTT
* *
38390 AGGGTGTTTGGTGGGTTT-GGGTTT
1 A-GG-GTTTAG-GGTTTTAGGGTTT
38414 AGGGTTT-GGG-TTTAGGGTTT
1 AGGGTTTAGGGTTTTAGGGTTT
* *
38434 ATAGG-TAAGGG-TTTAGGCGGGTTT
1 A-GGGTTTAGGGTTTTA---GGGTTT
* *
38458 AGGCGTTTTAGGTTGGTTTA-CGTTT
1 AGG-G-TTTAGG--GTTTTAGGGTTT
38483 AGGGTTTAGGG-TTT-GGGTTT
1 AGGGTTTAGGGTTTTAGGGTTT
38503 AGGGTTTAGGGTTT
1 AGGGTTTAGGGTTT
38517 AATGCTCCTC
Statistics
Matches: 764, Mismatches: 88, Indels: 155
0.76 0.09 0.15
Matches are distributed among these distances:
17 2 0.00
18 20 0.03
19 60 0.08
20 189 0.25
21 156 0.20
22 173 0.23
23 85 0.11
24 41 0.05
25 25 0.03
26 8 0.01
28 1 0.00
29 4 0.01
ACGTcount: A:0.13, C:0.03, G:0.43, T:0.42
Consensus pattern (22 bp):
AGGGTTTAGGGTTTTAGGGTTT
Found at i:37974 original size:30 final size:30
Alignment explanation
Indices: 37927--37999 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
37917 TTGGGGTTTG
37927 GGGTTTTAGGTGTCTAGGGTCTAGGGTCCTA
1 GGGTTTTAGG-GTCTAGGGTCTAGGGTCCTA
* **
37958 GGGTTTTAGGGTCTAGGGTTTAGGGTTTTA
1 GGGTTTTAGGGTCTAGGGTCTAGGGTCCTA
37988 GGGTTTTAGGGT
1 GGGTTTTAGGGT
38000 TTTAAGTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 29 0.74
31 10 0.26
ACGTcount: A:0.12, C:0.07, G:0.41, T:0.40
Consensus pattern (30 bp):
GGGTTTTAGGGTCTAGGGTCTAGGGTCCTA
Done.