Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold391
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: 59996
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:4343 original size:14 final size:15
Alignment explanation
Indices: 4326--4363 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
4316 GTTTAGTCAC
*
4326 TAGGGTTTTT-GGTT
1 TAGGGTTTTTAGGGT
4340 TAGGGTTTTTAGGGT
1 TAGGGTTTTTAGGGT
4355 TAGGGTTTT
1 TAGGGTTTT
4364 GTTAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.11, C:0.00, G:0.37, T:0.53
Consensus pattern (15 bp):
TAGGGTTTTTAGGGT
Found at i:4531 original size:34 final size:32
Alignment explanation
Indices: 4414--4539 Score: 119
Period size: 34 Copynumber: 3.7 Consensus size: 32
4404 GAATAAATCA
4414 AGGTTTAGAGTTTTTTTAAAAAAATT-ATTAAATT
1 AGGTTTAGAG--TTTTT-AAAAAATTAATTAAATT
*
4448 AGGTTTTAGAGGTTTTAAATAAATTAATTAAATT
1 AGG-TTTAGAGTTTTTAAA-AAATTAATTAAATT
* *
4482 AGGGCTTAGAGTTTTTAAGAAAATTAACTAAATT
1 A-GGTTTAGAGTTTTTAA-AAAATTAATTAAATT
** *
4516 ATGGTTTAGTTTTTTTAAATAATT
1 A-GGTTTAGAGTTTTTAAAAAATT
4540 TTGTCTTTAG
Statistics
Matches: 78, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
32 3 0.04
33 14 0.18
34 51 0.65
35 10 0.13
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.45
Consensus pattern (32 bp):
AGGTTTAGAGTTTTTAAAAAATTAATTAAATT
Found at i:8760 original size:21 final size:19
Alignment explanation
Indices: 8711--8766 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 19
8701 AATTTTCGAG
8711 GATATACAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
8730 GATATGCAATCTTAGATAT
1 GATATACAATCTTAGATAT
8749 GATATATACAATCTTAGA
1 G--ATATACAATCTTAGA
8767 AGATACGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 19 0.58
21 14 0.42
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (19 bp):
GATATACAATCTTAGATAT
Found at i:11499 original size:140 final size:140
Alignment explanation
Indices: 11247--11527 Score: 562
Period size: 140 Copynumber: 2.0 Consensus size: 140
11237 TTTATTGTTT
11247 AATTTTTGTAATCGATCCAGCTAAACAAGATGTTTTGGATTGGAGAAAACGCTTCAACATTATTA
1 AATTTTTGTAATCGATCCAGCTAAACAAGATGTTTTGGATTGGAGAAAACGCTTCAACATTATTA
11312 AAGGGATTAAGCAAGGATTGCTTTATCTTCATAGAGATTCAAGACTAAGGATTATACATAGAGAT
66 AAGGGATTAAGCAAGGATTGCTTTATCTTCATAGAGATTCAAGACTAAGGATTATACATAGAGAT
11377 TTAAAAGTAA
131 TTAAAAGTAA
11387 AATTTTTGTAATCGATCCAGCTAAACAAGATGTTTTGGATTGGAGAAAACGCTTCAACATTATTA
1 AATTTTTGTAATCGATCCAGCTAAACAAGATGTTTTGGATTGGAGAAAACGCTTCAACATTATTA
11452 AAGGGATTAAGCAAGGATTGCTTTATCTTCATAGAGATTCAAGACTAAGGATTATACATAGAGAT
66 AAGGGATTAAGCAAGGATTGCTTTATCTTCATAGAGATTCAAGACTAAGGATTATACATAGAGAT
11517 TTAAAAGTAA
131 TTAAAAGTAA
11527 A
1 A
11528 TAATATTTTA
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 141 1.00
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (140 bp):
AATTTTTGTAATCGATCCAGCTAAACAAGATGTTTTGGATTGGAGAAAACGCTTCAACATTATTA
AAGGGATTAAGCAAGGATTGCTTTATCTTCATAGAGATTCAAGACTAAGGATTATACATAGAGAT
TTAAAAGTAA
Found at i:13395 original size:28 final size:30
Alignment explanation
Indices: 13355--13412 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
13345 AGACCCTAAG
13355 AGTCAATTTC-T-GTAGAAGGTCCTTTAAT
1 AGTCAATTTCGTAGTAGAAGGTCCTTTAAT
13383 AGTCAATTTCTGTAGTAGAAGGTCCTTTAA
1 AGTCAATTTC-GTAGTAGAAGGTCCTTTAA
13413 CTTCTCCCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 10 0.37
30 1 0.04
31 16 0.59
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (30 bp):
AGTCAATTTCGTAGTAGAAGGTCCTTTAAT
Found at i:13873 original size:20 final size:20
Alignment explanation
Indices: 13848--13897 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
13838 TGGCTTAAAA
13848 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
13868 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
13885 GTGGTAGTGGATT
1 TTGGTAGTGGATT
13898 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:18502 original size:20 final size:20
Alignment explanation
Indices: 18477--18526 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
18467 TGGCTTAAAA
18477 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
18497 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
18514 GTGGTAGTGGATT
1 TTGGTAGTGGATT
18527 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:23876 original size:34 final size:34
Alignment explanation
Indices: 23765--23882 Score: 105
Period size: 34 Copynumber: 3.5 Consensus size: 34
23755 AAATCAAGGT
** * * **
23765 TTAGAGTTTTT-TTTAAAATAATTAAATTAGGTT
1 TTAGAGTTTTTAAATAAATTAACTAAATTAGGGC
* *
23798 TTAGGGGTTTTAAATAAATTAACTAAATTAGGGC
1 TTAGAGTTTTTAAATAAATTAACTAAATTAGGGC
* *
23832 TTAGAGTTTTTAAGA-AAATTAACTAAATTATGGT
1 TTAGAGTTTTTAA-ATAAATTAACTAAATTAGGGC
**
23866 TTAGTTTTTTTAAATAA
1 TTAGAGTTTTTAAATAA
23883 TTTTGTGTTT
Statistics
Matches: 68, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
33 10 0.15
34 57 0.84
35 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.45
Consensus pattern (34 bp):
TTAGAGTTTTTAAATAAATTAACTAAATTAGGGC
Found at i:25060 original size:16 final size:16
Alignment explanation
Indices: 25036--25073 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
25026 ATCTAAACTC
* *
25036 AAATGATTCAAACTTG
1 AAATAATTCAAACTTA
25052 AAATAATTCAAACTTA
1 AAATAATTCAAACTTA
25068 AAATAA
1 AAATAA
25074 GTCGAATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (16 bp):
AAATAATTCAAACTTA
Found at i:27116 original size:40 final size:41
Alignment explanation
Indices: 27013--27125 Score: 106
Period size: 40 Copynumber: 2.8 Consensus size: 41
27003 CTAACAGTCG
* * * *
27013 AGCATTAGCGGCATTTTAC-GAAAAACGCCGCAAAATATCG
1 AGCATTAGCGGCGTTTTACAAAAAAACGCCGCAAAATACCA
** * * *
27053 AGCATTAGCGGCGTTACATAAAAAAACGCTGCTAAA-ACCA
1 AGCATTAGCGGCGTTTTACAAAAAAACGCCGCAAAATACCA
* *
27093 AGCATTAGTGGCGTTTTAC-AAAAAGCGCCGCAA
1 AGCATTAGCGGCGTTTTACAAAAAAACGCCGCAA
27126 TAGAGTAACA
Statistics
Matches: 56, Mismatches: 16, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
39 11 0.20
40 32 0.57
41 13 0.23
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.19
Consensus pattern (41 bp):
AGCATTAGCGGCGTTTTACAAAAAAACGCCGCAAAATACCA
Found at i:27476 original size:41 final size:40
Alignment explanation
Indices: 27384--27476 Score: 114
Period size: 41 Copynumber: 2.3 Consensus size: 40
27374 TATGGAGAAT
* * *
27384 CGCCGCTAATGTTCCGGTCTATAGCGGTGTTTGTGTAACAG
1 CGCCGCTAAT-TTCCGGTCTATAGCGGCGTTTGTGTAAAAA
* * *
27425 CACCGGTAATTCTTCGGTCTATAGCGGCGTTTGTGTAAAAA
1 CGCCGCTAATT-TCCGGTCTATAGCGGCGTTTGTGTAAAAA
27466 CGCCGCTAATT
1 CGCCGCTAATT
27477 AGAAAATCTA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 1 0.02
41 42 0.98
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.31
Consensus pattern (40 bp):
CGCCGCTAATTTCCGGTCTATAGCGGCGTTTGTGTAAAAA
Found at i:29654 original size:792 final size:793
Alignment explanation
Indices: 27943--30321 Score: 4348
Period size: 792 Copynumber: 3.0 Consensus size: 793
27933 CCGCAAAATG
* *
27943 TGTAACCGAAACGACTTCGTTTTTATACTGTTTATTGGTATTAGCGGCGTTTTTTGTAAAAACGC
1 TGTAACCGAAAAGACTTCGTTTTTATACTGTTTATTGGTATTAGCGGCATTTTTTGTAAAAACGC
* * * *
28008 CGCAAATGAAAGTTATGTATTTTAGGGTTTTGGGATTAATATTTAAGTTTTATTGTATACGGTTT
66 CGCAAATGAAAGTTATGTATTTTAGGGTATTGGGATTAATATTTAAGTTTTGTTGCATATGGTTT
** *
28073 GGGGTTTTAGGGTTTAATACATAATGTTTATTAATTTAGGATTACAATTTTATGTTTAGGGTTTT
131 GGGGTTTTAGGGTTCGATACATAATGTTTATTAATTTAGGATTATAATTTTATGTTTAGGGTTTT
*
28138 GGGTTTAGGTTTACAGCTTGAGGAATGGGGTTTAGGGTTTGAGTTTACATGTTAGTTTTAATGCG
196 GGGTTTAGGTTTACGGCTTGAGGAATGGGGTTTAGGGTTTGAGTTTACATGTTAGTTTTAATGCG
*
28203 AGGTTTACGGCTTATAAGATATATTAATGATCAAATTTATTGTTTTATGGCTTGATGTTTATGGT
261 AGGTTTACGGCTTATAAGATATATTAATGATCAAATTTATTGTTTTACGGCTTGATGTTTATGGT
28268 TTATGGTTTACCCTTATTGATTTGAATGTTACAATGCTTGGTTTTTGTGTTCGGATTTGCATGAA
326 TTATGGTTTACCCTTATTGATTTGAATGTTACAATGCTTGGTTTTTGTGTTCGGATTTGCATGAA
28333 GAATATGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATGTTTACGGGTTAT-AGGGATTAATAGC
391 GAATATGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATGTTTACGGGTTATAAGGGATTAATAGC
28397 TTCGGGTTTTAGGGTACAAAAGCAAAAAAAAAATTAAAATTCTTTCTGCTTTTTACTTCTTATTA
456 TTCGGGTTTTAGGGTACAAAAGCAAAAAAAAAATTAAAATTCTTTCTGCTTTTTACTTCTTATTA
*
28462 TGTCACTAGTATATAGGATTATAAGAGACAGGGTTATATATATATGTATATAATATGTCACGATA
521 TGTCACTAGTATATAGGATTATAAGAGACAGGG-T-TATATATA--TATAT-ATATGCCACGATA
28527 TATATCTATGCATATATGTTATATATTATACATACTGCATAAAATTGAAATAATTTTATAAATTC
581 TATATCTATGCATATATGTTATATATTATACATACTGCATAAAATTGAAATAATTTTATAAATTC
28592 ATATTAATGTATCAATTTAAAATAATGTCATAACAATTATCAAAATAAAAAATCTACTAAAAATC
646 ATATTAATGTATCAATTTAAAATAATGTCATAACAATTATCAAAATAAAAAATCTACTAAAAATC
28657 ATTAGACTTATAAATAAAGACAAATAAAATAAATTGAAAAATTAGCGGCGTTTATACAGAAAACG
711 ATTAGACTTATAAATAAAGACAAATAAAATAAATTGAAAAATTAGCGGCGTTTATACAGAAAACG
28722 CCGCTATAGAACAAGATT
776 CCGCTATAGAACAAGATT
28740 TGTAACCGAAAAGACTTCGTTTTTATACTGTTTATTGGTATTAGCGGCATTTTTTGTAAAAACGC
1 TGTAACCGAAAAGACTTCGTTTTTATACTGTTTATTGGTATTAGCGGCATTTTTTGTAAAAACGC
28805 CGCAAATGAAAGTTATGTATTTTAGGGTATTGGGATTAATATTTAAGTTTTGTTGCATATGGTTT
66 CGCAAATGAAAGTTATGTATTTTAGGGTATTGGGATTAATATTTAAGTTTTGTTGCATATGGTTT
28870 GGGGTTTTAGGGTTCGATACATAATGTTTATTAATTTAGGATTATAATTTTATGTTTAGGGTTTT
131 GGGGTTTTAGGGTTCGATACATAATGTTTATTAATTTAGGATTATAATTTTATGTTTAGGGTTTT
28935 GGGTTTAGGTTTACGGCTTGAGGAATGGGGTTTAGGGTTTGAGTTTACATGTTAGTTTTAATGCG
196 GGGTTTAGGTTTACGGCTTGAGGAATGGGGTTTAGGGTTTGAGTTTACATGTTAGTTTTAATGCG
29000 AGGTTTACGGCTTATAAGATATATTAATGATCAAATTTATTGTTTTACGGCTTGATGTTTATGGT
261 AGGTTTACGGCTTATAAGATATATTAATGATCAAATTTATTGTTTTACGGCTTGATGTTTATGGT
29065 TTATGGTTTACCCTTATTGATTTGAATGTTACAATGCTTGGTTTTTGTGTTCGGATTTGCATGAA
326 TTATGGTTTACCCTTATTGATTTGAATGTTACAATGCTTGGTTTTTGTGTTCGGATTTGCATGAA
29130 GAATATGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATGTTTACGGGTTATAAGGGATTAATAGC
391 GAATATGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATGTTTACGGGTTATAAGGGATTAATAGC
29195 TTCGGGTTTTAGGGTACAAAAGCAAAAAAAAAATTAAAATTCTTTCTGCTTTTTACTTCTTATTA
456 TTCGGGTTTTAGGGTACAAAAGCAAAAAAAAAATTAAAATTCTTTCTGCTTTTTACTTCTTATTA
29260 TGTCACTAGTATATAGGATTATAAGAGACAGGGTTATATATATATATATATG-CACGATATATAT
521 TGTCACTAGTATATAGGATTATAAGAGACAGGGTTATATATATATATATATGCCACGATATATAT
29324 CTATGCATATATGTTATATATTATACATACTGCATAAAATTGAAATAATTTTATAAATTCATATT
586 CTATGCATATATGTTATATATTATACATACTGCATAAAATTGAAATAATTTTATAAATTCATATT
29389 AATGTATCAATTTAAAATAATGTCATAACAATTATCAAAATAAAAAATCTACTAAAAATCATTAG
651 AATGTATCAATTTAAAATAATGTCATAACAATTATCAAAATAAAAAATCTACTAAAAATCATTAG
29454 ACTTATAAATAAAGACAAATAAAATAAATTGAAAAATTAGCGGCGTTTATACAGAAAACGCCGCT
716 ACTTATAAATAAAGACAAATAAAATAAATTGAAAAATTAGCGGCGTTTATACAGAAAACGCCGCT
29519 ATAGAACAAGATT
781 ATAGAACAAGATT
29532 TGTAACCGAAAAGACTTCGTTTTTATACTGTTTATTGGTATTAGCGGCATTTTTTGTAAAAACGC
1 TGTAACCGAAAAGACTTCGTTTTTATACTGTTTATTGGTATTAGCGGCATTTTTTGTAAAAACGC
*
29597 CGCAAATGAAAGTTATGTATTTTAGGGTATTGGGATTAATATTTAAGTTTCGTTGCATATGGTTT
66 CGCAAATGAAAGTTATGTATTTTAGGGTATTGGGATTAATATTTAAGTTTTGTTGCATATGGTTT
29662 GGGGTTTTAGGGTTCGATACATAATGTTTATTAATTTAGGATTATAATTTTATGTTTAGGGTTTT
131 GGGGTTTTAGGGTTCGATACATAATGTTTATTAATTTAGGATTATAATTTTATGTTTAGGGTTTT
29727 GGGTTTAGGTTTACGGCTTGAGGAATGGGGTTTAGGGTTTGAGTTTACATGTTAGTTTTAATGCG
196 GGGTTTAGGTTTACGGCTTGAGGAATGGGGTTTAGGGTTTGAGTTTACATGTTAGTTTTAATGCG
* * * *
29792 AGGTTTACAGCTTATAAG--AT-GTAATGATCAAATTTACTATTTTACGGCTTGATGTTTATGGT
261 AGGTTTACGGCTTATAAGATATATTAATGATCAAATTTATTGTTTTACGGCTTGATGTTTATGGT
* * *
29854 TTATGGTTCACCCTTATTGATTTGAATGTTACAATGCTTGGTTTTTGCGTTCGAATTTGCATGAA
326 TTATGGTTTACCCTTATTGATTTGAATGTTACAATGCTTGGTTTTTGTGTTCGGATTTGCATGAA
*
29919 GAATACGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATGTTTACGGGTTATAAGGGATTAATAGC
391 GAATATGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATGTTTACGGGTTATAAGGGATTAATAGC
29984 TTCGGGTTTTAGGGTACAAAAGCAAAAAAATTAAAATTAAAATTCTTTCTGCTTTTTACTTCTTA
456 TTCGGGTTTTAGGGTACAAAAGC-AAAAAA--AAAATTAAAATTCTTTCTGCTTTTTACTTCTTA
*
30049 TTATGTCACTAGTATATAGGATTATAAGTGACAGGG-T-TATATATATA-ATATGCCACGATATA
518 TTATGTCACTAGTATATAGGATTATAAGAGACAGGGTTATATATATATATATATGCCACGATATA
* *
30111 TATCTATGCATATATGTTATATATTATATATACTGCATAAAATTGAAATAATTTTATAAATGCAT
583 TATCTATGCATATATGTTATATATTATACATACTGCATAAAATTGAAATAATTTTATAAATTCAT
* *
30176 ATTAATGTATCAATTTAAAATAATGTCATAACAATTA-C-CAA-AAAAAATCTATTAAAAATCAT
648 ATTAATGTATCAATTTAAAATAATGTCATAACAATTATCAAAATAAAAAATCTACTAAAAATCAT
* * *
30238 TAAACTTATAAATAAAGACAAATAAAATAAATTGAAAAATTAGCGACGCTTATACAGAAAACGCC
713 TAGACTTATAAATAAAGACAAATAAAATAAATTGAAAAATTAGCGGCGTTTATACAGAAAACGCC
30303 GCTATAGAACAAGATT
778 GCTATAGAACAAGATT
30319 TGT
1 TGT
30322 GGCGTTTATT
Statistics
Matches: 1549, Mismatches: 28, Indels: 20
0.97 0.02 0.01
Matches are distributed among these distances:
787 101 0.07
788 2 0.00
789 194 0.13
790 127 0.08
791 1 0.00
792 564 0.36
793 5 0.00
794 5 0.00
796 8 0.01
797 431 0.28
798 111 0.07
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (793 bp):
TGTAACCGAAAAGACTTCGTTTTTATACTGTTTATTGGTATTAGCGGCATTTTTTGTAAAAACGC
CGCAAATGAAAGTTATGTATTTTAGGGTATTGGGATTAATATTTAAGTTTTGTTGCATATGGTTT
GGGGTTTTAGGGTTCGATACATAATGTTTATTAATTTAGGATTATAATTTTATGTTTAGGGTTTT
GGGTTTAGGTTTACGGCTTGAGGAATGGGGTTTAGGGTTTGAGTTTACATGTTAGTTTTAATGCG
AGGTTTACGGCTTATAAGATATATTAATGATCAAATTTATTGTTTTACGGCTTGATGTTTATGGT
TTATGGTTTACCCTTATTGATTTGAATGTTACAATGCTTGGTTTTTGTGTTCGGATTTGCATGAA
GAATATGAGTTAGCTAGGGTTTAGCCTTTAATTTTAATGTTTACGGGTTATAAGGGATTAATAGC
TTCGGGTTTTAGGGTACAAAAGCAAAAAAAAAATTAAAATTCTTTCTGCTTTTTACTTCTTATTA
TGTCACTAGTATATAGGATTATAAGAGACAGGGTTATATATATATATATATGCCACGATATATAT
CTATGCATATATGTTATATATTATACATACTGCATAAAATTGAAATAATTTTATAAATTCATATT
AATGTATCAATTTAAAATAATGTCATAACAATTATCAAAATAAAAAATCTACTAAAAATCATTAG
ACTTATAAATAAAGACAAATAAAATAAATTGAAAAATTAGCGGCGTTTATACAGAAAACGCCGCT
ATAGAACAAGATT
Found at i:30746 original size:16 final size:16
Alignment explanation
Indices: 30722--30752 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30712 ATTTTTCCTC
30722 TTCTAAAATCCCTAAG
1 TTCTAAAATCCCTAAG
*
30738 TTCTGAAATCCCTAA
1 TTCTAAAATCCCTAA
30753 CTCCATTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (16 bp):
TTCTAAAATCCCTAAG
Found at i:32749 original size:16 final size:17
Alignment explanation
Indices: 32712--32753 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
32702 CTAAGCTAGG
32712 TACA-ATAT-ATATGTA
1 TACATATATAATATGTA
32727 TACATATATAATATGT-
1 TACATATATAATATGTA
*
32743 TATATATATAA
1 TACATATATAA
32754 GTAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 14 0.58
17 6 0.25
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (17 bp):
TACATATATAATATGTA
Found at i:35052 original size:14 final size:15
Alignment explanation
Indices: 35035--35072 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
35025 GTTTAGTCAC
*
35035 TAGGGTTTTT-GGTT
1 TAGGGTTTTTAGGGT
35049 TAGGGTTTTTAGGGT
1 TAGGGTTTTTAGGGT
35064 TAGGGTTTT
1 TAGGGTTTT
35073 GTTAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.11, C:0.00, G:0.37, T:0.53
Consensus pattern (15 bp):
TAGGGTTTTTAGGGT
Found at i:35240 original size:34 final size:32
Alignment explanation
Indices: 35123--35248 Score: 119
Period size: 34 Copynumber: 3.7 Consensus size: 32
35113 GAATAAATCA
35123 AGGTTTAGAGTTTTTTTAAAAAAATT-ATTAAATT
1 AGGTTTAGAG--TTTTT-AAAAAATTAATTAAATT
*
35157 AGGTTTTAGAGGTTTTAAATAAATTAATTAAATT
1 AGG-TTTAGAGTTTTTAAA-AAATTAATTAAATT
* *
35191 AGGGCTTAGAGTTTTTAAGAAAATTAACTAAATT
1 A-GGTTTAGAGTTTTTAA-AAAATTAATTAAATT
** *
35225 ATGGTTTAGTTTTTTTAAATAATT
1 A-GGTTTAGAGTTTTTAAAAAATT
35249 TTGTCTTTAG
Statistics
Matches: 78, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
32 3 0.04
33 14 0.18
34 51 0.65
35 10 0.13
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.45
Consensus pattern (32 bp):
AGGTTTAGAGTTTTTAAAAAATTAATTAAATT
Found at i:39467 original size:21 final size:19
Alignment explanation
Indices: 39418--39473 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 19
39408 AATTTTCGAG
39418 GATATACAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
39437 GATATGCAATCTTAGATAT
1 GATATACAATCTTAGATAT
39456 GATATATACAATCTTAGA
1 G--ATATACAATCTTAGA
39474 AGATACGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 19 0.58
21 14 0.42
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (19 bp):
GATATACAATCTTAGATAT
Found at i:42207 original size:140 final size:140
Alignment explanation
Indices: 41955--42235 Score: 562
Period size: 140 Copynumber: 2.0 Consensus size: 140
41945 TTTATTGTTT
41955 AATTTTTGTAATCGATCCAGCTAAACAAGATGTTTTGGATTGGAGAAAACGCTTCAACATTATTA
1 AATTTTTGTAATCGATCCAGCTAAACAAGATGTTTTGGATTGGAGAAAACGCTTCAACATTATTA
42020 AAGGGATTAAGCAAGGATTGCTTTATCTTCATAGAGATTCAAGACTAAGGATTATACATAGAGAT
66 AAGGGATTAAGCAAGGATTGCTTTATCTTCATAGAGATTCAAGACTAAGGATTATACATAGAGAT
42085 TTAAAAGTAA
131 TTAAAAGTAA
42095 AATTTTTGTAATCGATCCAGCTAAACAAGATGTTTTGGATTGGAGAAAACGCTTCAACATTATTA
1 AATTTTTGTAATCGATCCAGCTAAACAAGATGTTTTGGATTGGAGAAAACGCTTCAACATTATTA
42160 AAGGGATTAAGCAAGGATTGCTTTATCTTCATAGAGATTCAAGACTAAGGATTATACATAGAGAT
66 AAGGGATTAAGCAAGGATTGCTTTATCTTCATAGAGATTCAAGACTAAGGATTATACATAGAGAT
42225 TTAAAAGTAA
131 TTAAAAGTAA
42235 A
1 A
42236 TAATATTTTA
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 141 1.00
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (140 bp):
AATTTTTGTAATCGATCCAGCTAAACAAGATGTTTTGGATTGGAGAAAACGCTTCAACATTATTA
AAGGGATTAAGCAAGGATTGCTTTATCTTCATAGAGATTCAAGACTAAGGATTATACATAGAGAT
TTAAAAGTAA
Found at i:44104 original size:28 final size:30
Alignment explanation
Indices: 44064--44121 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
44054 AGACCCTAAG
44064 AGTCAATTTC-T-GTAGAAGGTCCTTTAAT
1 AGTCAATTTCGTAGTAGAAGGTCCTTTAAT
44092 AGTCAATTTCTGTAGTAGAAGGTCCTTTAA
1 AGTCAATTTC-GTAGTAGAAGGTCCTTTAA
44122 CTTCTCCCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 10 0.37
30 1 0.04
31 16 0.59
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (30 bp):
AGTCAATTTCGTAGTAGAAGGTCCTTTAAT
Found at i:47132 original size:2 final size:2
Alignment explanation
Indices: 47125--47151 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47115 GTAAAATTAC
47125 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
47152 TCAATTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49498 original size:34 final size:34
Alignment explanation
Indices: 49387--49504 Score: 105
Period size: 34 Copynumber: 3.5 Consensus size: 34
49377 AAATCAAGGT
** * * **
49387 TTAGAGTTTTT-TTTAAAATAATTAAATTAGGTT
1 TTAGAGTTTTTAAATAAATTAACTAAATTAGGGC
* *
49420 TTAGGGGTTTTAAATAAATTAACTAAATTAGGGC
1 TTAGAGTTTTTAAATAAATTAACTAAATTAGGGC
* *
49454 TTAGAGTTTTTAAGA-AAATTAACTAAATTATGGT
1 TTAGAGTTTTTAA-ATAAATTAACTAAATTAGGGC
**
49488 TTAGTTTTTTTAAATAA
1 TTAGAGTTTTTAAATAA
49505 TTTTGTGTTT
Statistics
Matches: 68, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
33 10 0.15
34 57 0.84
35 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.45
Consensus pattern (34 bp):
TTAGAGTTTTTAAATAAATTAACTAAATTAGGGC
Found at i:50682 original size:16 final size:16
Alignment explanation
Indices: 50658--50695 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
50648 ATCTAAACTC
* *
50658 AAATGATTCAAACTTG
1 AAATAATTCAAACTTA
50674 AAATAATTCAAACTTA
1 AAATAATTCAAACTTA
50690 AAATAA
1 AAATAA
50696 GTCGAATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (16 bp):
AAATAATTCAAACTTA
Found at i:52738 original size:40 final size:41
Alignment explanation
Indices: 52635--52747 Score: 106
Period size: 40 Copynumber: 2.8 Consensus size: 41
52625 CTAACAGTCG
* * * *
52635 AGCATTAGCGGCATTTTAC-GAAAAACGCCGCAAAATATCG
1 AGCATTAGCGGCGTTTTACAAAAAAACGCCGCAAAATACCA
** * * *
52675 AGCATTAGCGGCGTTACATAAAAAAACGCTGCTAAA-ACCA
1 AGCATTAGCGGCGTTTTACAAAAAAACGCCGCAAAATACCA
* *
52715 AGCATTAGTGGCGTTTTAC-AAAAAGCGCCGCAA
1 AGCATTAGCGGCGTTTTACAAAAAAACGCCGCAA
52748 TAGAGTAACA
Statistics
Matches: 56, Mismatches: 16, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
39 11 0.20
40 32 0.57
41 13 0.23
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.19
Consensus pattern (41 bp):
AGCATTAGCGGCGTTTTACAAAAAAACGCCGCAAAATACCA
Found at i:53099 original size:41 final size:40
Alignment explanation
Indices: 53007--53099 Score: 123
Period size: 41 Copynumber: 2.3 Consensus size: 40
52997 TATGGAGAAT
* *
53007 CGCCGCTAATGTTCCGGTCTATAGCGGCGTTTGTGTAACAG
1 CGCCGCTAAT-TTCCGGTCTATAGCGGCGTTTGTGTAAAAA
* * *
53048 CACCGGTAATTCTTCGGTCTATAGCGGCGTTTGTGTAAAAA
1 CGCCGCTAATT-TCCGGTCTATAGCGGCGTTTGTGTAAAAA
53089 CGCCGCTAATT
1 CGCCGCTAATT
53100 AGAAAATCTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 1 0.02
41 43 0.98
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (40 bp):
CGCCGCTAATTTCCGGTCTATAGCGGCGTTTGTGTAAAAA
Found at i:55424 original size:19 final size:18
Alignment explanation
Indices: 55392--55427 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
55382 GAAACTTATT
55392 AAAAATAATAATTATAAA
1 AAAAATAATAATTATAAA
*
55410 AAAAATTATATATTATAA
1 AAAAATAATA-ATTATAA
55428 CAACTGAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAATAATAATTATAAA
Found at i:55570 original size:16 final size:16
Alignment explanation
Indices: 55546--55576 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55536 ATTTTTCCTC
55546 TTCTAAAATCCCTAAG
1 TTCTAAAATCCCTAAG
*
55562 TTCTGAAATCCCTAA
1 TTCTAAAATCCCTAA
55577 CTCCATTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (16 bp):
TTCTAAAATCCCTAAG
Found at i:57825 original size:34 final size:33
Alignment explanation
Indices: 57779--57904 Score: 112
Period size: 31 Copynumber: 3.8 Consensus size: 33
57769 AGGTTTAGGG
* *
57779 ATAAATCAAGGTTTAGAGTTTTTTTAAAAAAATTA
1 ATAAATTAGGGTTTAGAG--TTTTTAAAAAAATTA
* * * *
57814 TTAAATTAGGTTTTAG-G-TTTTAAATAAATAA
1 ATAAATTAGGGTTTAGAGTTTTTAAAAAAATTA
* *
57845 ATAAATTAGGGCTTAGAGTTTTTAAGAAAATTA
1 ATAAATTAGGGTTTAGAGTTTTTAAAAAAATTA
* **
57878 ACTAAATTATGGTTTAGTTTTTTTAAA
1 A-TAAATTAGGGTTTAGAGTTTTTAAA
57905 TAATTTTGTC
Statistics
Matches: 71, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
31 25 0.35
32 1 0.01
33 12 0.17
34 21 0.30
35 12 0.17
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.43
Consensus pattern (33 bp):
ATAAATTAGGGTTTAGAGTTTTTAAAAAAATTA
Done.