Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009049.1 Corchorus capsularis cultivar CVL-1 contig09070, whole genome shotgun sequence
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: 86233
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:282 original size:31 final size:31
Alignment explanation
Indices: 211--282 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
201 TTCTATCAGC
*
211 TTTTAATTTGTTTAATTTAAGGATTCCGTTT
1 TTTTAATTTGTTTAATTTAAGGATTCCATTT
* * *
242 TAATT-ATTTGTTTAATTTAATGCTT-CATTT
1 T-TTTAATTTGTTTAATTTAAGGATTCCATTT
272 GTTTTAATTTG
1 -TTTTAATTTG
283 CAATAATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
30 6 0.18
31 25 0.76
32 2 0.06
ACGTcount: A:0.24, C:0.06, G:0.11, T:0.60
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGGATTCCATTT
Found at i:763 original size:16 final size:16
Alignment explanation
Indices: 744--803 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
734 ACCTGAAAAT
*
744 ACCCGAATCCGACATA
1 ACCCGAACCCGACATA
*
760 ACCCGAACCCGA-AAA
1 ACCCGAACCCGACATA
*
775 TACCCGAACCCGACTTA
1 -ACCCGAACCCGACATA
* *
792 ACTCGAGCCCGA
1 ACCCGAACCCGA
804 AGATACCCGA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 2 0.06
16 33 0.92
17 1 0.03
ACGTcount: A:0.35, C:0.40, G:0.15, T:0.10
Consensus pattern (16 bp):
ACCCGAACCCGACATA
Found at i:774 original size:32 final size:32
Alignment explanation
Indices: 731--819 Score: 115
Period size: 32 Copynumber: 2.8 Consensus size: 32
721 CACCTGAAAT
* *
731 CGAACCTGAAAATACCCGAATCCGACATAACC
1 CGAACCCGAAAATACCCGAAACCGACATAACC
* * *
763 CGAACCCGAAAATACCCGAACCCGACTTAACT
1 CGAACCCGAAAATACCCGAAACCGACATAACC
* *
795 CGAGCCCGAAGATACCCGAAACCGA
1 CGAACCCGAAAATACCCGAAACCGA
820 AAAAGCCCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.38, C:0.36, G:0.16, T:0.10
Consensus pattern (32 bp):
CGAACCCGAAAATACCCGAAACCGACATAACC
Found at i:4596 original size:25 final size:23
Alignment explanation
Indices: 4548--4595 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 23
4538 GAATAATTAT
4548 AAAGAAAACAATTAAACTAAAAAC
1 AAAGAAAACAATTAAACT-AAAAC
4572 AAAGCAAAACAAATTAAATCTAAA
1 AAAG-AAAAC-AATTAAA-CTAAA
4596 CTATAGCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 4 0.19
25 5 0.24
26 10 0.48
27 2 0.10
ACGTcount: A:0.69, C:0.12, G:0.04, T:0.15
Consensus pattern (23 bp):
AAAGAAAACAATTAAACTAAAAC
Found at i:13932 original size:30 final size:30
Alignment explanation
Indices: 13898--13957 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
13888 AGACATCAAA
13898 GGATGGAGGAATCGCACCAAAGATGCCATT
1 GGATGGAGGAATCGCACCAAAGATGCCATT
13928 GGATGGAGGAATCGCACCAAAGATGCCATT
1 GGATGGAGGAATCGCACCAAAGATGCCATT
13958 TGATCCTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.20, G:0.30, T:0.17
Consensus pattern (30 bp):
GGATGGAGGAATCGCACCAAAGATGCCATT
Found at i:17683 original size:25 final size:26
Alignment explanation
Indices: 17649--17703 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
17639 TCCTTCTCAA
17649 GGACTGACAAGCTAAAAT-GGGTGGT
1 GGACTGACAAGCTAAAATGGGGTGGT
* *
17674 GGACTTACAAGCTAAATTGGGGTGGT
1 GGACTGACAAGCTAAAATGGGGTGGT
17700 GGAC
1 GGAC
17704 ATATCGATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.29, C:0.13, G:0.36, T:0.22
Consensus pattern (26 bp):
GGACTGACAAGCTAAAATGGGGTGGT
Found at i:20315 original size:34 final size:34
Alignment explanation
Indices: 20277--20344 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
20267 ATCATTTTGT
* * *
20277 AAAGGCGTGATGAAGGCCTGTTTAAATTCATTGG
1 AAAGGCGTGATGAAGACCCGTGTAAATTCATTGG
*
20311 AAAGGCGTGATGAAGACCCGTGTAACTTCATTGG
1 AAAGGCGTGATGAAGACCCGTGTAAATTCATTGG
20345 TGTAAGAGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.26
Consensus pattern (34 bp):
AAAGGCGTGATGAAGACCCGTGTAAATTCATTGG
Found at i:23334 original size:2 final size:2
Alignment explanation
Indices: 23327--23358 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
23317 TTGCAAGATT
23327 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
23359 AAAGGAGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:24157 original size:30 final size:31
Alignment explanation
Indices: 24123--24200 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 31
24113 CAAACAATCT
*
24123 ATCAATCAATTAACAA-ATAATTGCAATTC-A
1 ATCAATCAATTAACAAGAT-ATGGCAATTCAA
*
24153 ATCAATCAA-TAGCAAGATATGGCAATTCAA
1 ATCAATCAATTAACAAGATATGGCAATTCAA
*
24183 ATCAAT-AATTGA-AAGATA
1 ATCAATCAATTAACAAGATA
24201 GAATAAGCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
29 22 0.54
30 19 0.46
ACGTcount: A:0.50, C:0.14, G:0.09, T:0.27
Consensus pattern (31 bp):
ATCAATCAATTAACAAGATATGGCAATTCAA
Found at i:30472 original size:115 final size:114
Alignment explanation
Indices: 30235--30506 Score: 318
Period size: 115 Copynumber: 2.4 Consensus size: 114
30225 TCTGGGATCC
* * * * * **
30235 CAGACGCCGCCATTTAGCAGCGTTTTGCG-TCAAGACGCCTCGATTTTTTAGGCTTCATTTTTGG
1 CAGACGCCACCATTTAGCAGCGTTTAG-GTTCAAGACGCCGCTATTTGTTAGGCTTCATTTTTAC
* * * * * *
30299 TTTTTTCATTTCTCTGAATACATAAATTATATGGCGGCGTTTTGATCCTT
65 TATCTACATTTCTCCGAATAAATAAATTATATGGCGGCGTTTTGATACTT
* **
30349 -AGATGCCACCATTTAGTGGCGTTTAGGTTCAAGACGCCGCTATTTGTTAGGCTTCATTTTTACT
1 CAGACGCCACCATTTAGCAGCGTTTAGGTTCAAGACGCCGCTATTTGTTAGGCTTCATTTTTACT
30413 CAATCTACATTTCTCCGAATAAATAAATTATATGGCGGCGTTTTG-TACTT
66 --ATCTACATTTCTCCGAATAAATAAATTATATGGCGGCGTTTTGATACTT
* *
30463 CAGACGCCACCATTTAGCAGTGTTTA-TTGTCAAGACGCCGCTAT
1 CAGACGCCACCATTTAGCAGCGTTTAGGT-TCAAGACGCCGCTAT
30507 ATTCAATTTT
Statistics
Matches: 132, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
112 1 0.01
113 52 0.39
114 5 0.04
115 74 0.56
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (114 bp):
CAGACGCCACCATTTAGCAGCGTTTAGGTTCAAGACGCCGCTATTTGTTAGGCTTCATTTTTACT
ATCTACATTTCTCCGAATAAATAAATTATATGGCGGCGTTTTGATACTT
Found at i:39679 original size:2 final size:2
Alignment explanation
Indices: 39672--39762 Score: 75
Period size: 2 Copynumber: 48.0 Consensus size: 2
39662 GTTATATTAC
* * * * *
39672 AT AT AT AT AT AT AT AT -T AT TT AG AA AT A- AT AT AG AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
39712 AT -T AC AT -T AT AT AT AT AT AT AT AT AT TT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39752 AT A- AT AT AT AT
1 AT AT AT AT AT AT
39763 TACATAGTAA
Statistics
Matches: 69, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
1 5 0.07
2 64 0.93
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39703 original size:22 final size:25
Alignment explanation
Indices: 39664--39768 Score: 91
Period size: 24 Copynumber: 4.5 Consensus size: 25
39654 ATTGTGATGT
39664 TATA-TTACAT-ATATATATATATA
1 TATATTTACATAATATATATATATA
* *
39687 T-TATTTAGA-AATA-ATATAGATA
1 TATATTTACATAATATATATATATA
* *
39709 TGTA-TTACATTATATATATATATA
1 TATATTTACATAATATATATATATA
* *
39733 TATATTTATAT-TTATATATATA-A
1 TATATTTACATAATATATATATATA
39756 TATATATTACATA
1 TATAT-TTACATA
39769 GTAATTCGGG
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
22 15 0.23
23 19 0.29
24 26 0.40
25 5 0.08
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (25 bp):
TATATTTACATAATATATATATATA
Found at i:41076 original size:30 final size:31
Alignment explanation
Indices: 41025--41086 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
41015 GGAAGGTTGT
*
41025 TGCTGAAGGTGGCACCGTGAATCAAGGAAGTAG
1 TGCTGAAGGTGG--CCGTGAATCAAGAAAGTAG
41058 TGCTGAAGGTGG-CGTGAATCAAGAAAGTA
1 TGCTGAAGGTGGCCGTGAATCAAGAAAGTA
41087 AATCAATGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 16 0.57
33 12 0.43
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.19
Consensus pattern (31 bp):
TGCTGAAGGTGGCCGTGAATCAAGAAAGTAG
Found at i:42406 original size:15 final size:15
Alignment explanation
Indices: 42388--42418 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42378 TTTAAGTTTC
42388 AGGGACTTAATTGAA
1 AGGGACTTAATTGAA
*
42403 AGGGACTTATTTGAA
1 AGGGACTTAATTGAA
42418 A
1 A
42419 AGAAAAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (15 bp):
AGGGACTTAATTGAA
Found at i:50566 original size:2 final size:2
Alignment explanation
Indices: 50559--50590 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
50549 AATTCTAATT
*
50559 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
50591 AGTTAATCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:51165 original size:20 final size:20
Alignment explanation
Indices: 51116--51158 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
51106 GGATTGATAG
* *
51116 AATAGTAGAAGGGGGTGAGA
1 AATAGAAGAAGGGGATGAGA
51136 AATAGAAGAAGGGGATGAGA
1 AATAGAAGAAGGGGATGAGA
51156 AAT
1 AAT
51159 TAGAGAATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.40, T:0.14
Consensus pattern (20 bp):
AATAGAAGAAGGGGATGAGA
Found at i:51878 original size:19 final size:18
Alignment explanation
Indices: 51854--51893 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
51844 TTGAAGATTT
*
51854 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
51873 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
51891 ATT
1 ATT
51894 ATTTCAAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:56443 original size:19 final size:18
Alignment explanation
Indices: 56410--56446 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
56400 TCGAAATAAT
56410 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
56428 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
56447 AAATTTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:59231 original size:3 final size:3
Alignment explanation
Indices: 59223--59261 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
59213 TTAATTGATA
59223 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
59262 ATATATTGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:62546 original size:1 final size:1
Alignment explanation
Indices: 62540--62583 Score: 88
Period size: 1 Copynumber: 44.0 Consensus size: 1
62530 AGAGAGAGAG
62540 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
62584 CTATACGAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:70072 original size:11 final size:11
Alignment explanation
Indices: 70048--70082 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
70038 TTGACAGCGC
70048 AACAAAAACAA
1 AACAAAAACAA
* *
70059 AACGAAAACGA
1 AACAAAAACAA
70070 AACAAAAACAA
1 AACAAAAACAA
70081 AA
1 AA
70083 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:70452 original size:356 final size:352
Alignment explanation
Indices: 69756--70455 Score: 962
Period size: 357 Copynumber: 2.0 Consensus size: 352
69746 CGTTTGGCAT
* * * * *
69756 TGTTTTTGTTTTCTGTTTTCTGTTGTCAATTTCCTGTTTTTGGAAACAAAACAGTGAAAACATGT
1 TGTTTTTGTTGTCTGTCTTCTATTGTCAATTTCATGTTTTAGGAAACAAAACAGTGAAAACATGT
** * * *
69821 TTGGCAGACTGTTTCCGCTTTCAAAAATTTTGGAAACAGAAGCAGTGTTTTGGAAAAAAGTGGAA
66 TTGGCAGACTGCATCCGCTTTCAAAAATTTTGAAAACAGAAGCAATATTTTGGAAAAAAGTGGAA
* ** * *
69886 GCAAGAATTTTGTGTTTTCATGTTTTTCCAAAACACATAAGTAGAATGATGAATAGTAACTCACA
131 GCAAGAATTTTGTGTTTTCATGTTTTTCCAAAACACAGAAACACAATGATGAACAGTAACTCACA
*** *
69951 TACTTTTTAACCATTTTTTCTTTTACTTTTTTTATTTAAAAACATACAACCAAATTGTATATCCA
196 TACTTTTTAACCATTTTTTCTAAAACTTTTTTTATTTAAAAACATACAACAAAATTGTATATCCA
*
70016 AACATGTTTTTGTTTTCAAAAATTGACAGCGCAACAAAAACAAAACGAAAACGAAACAAAAACAA
261 AACATGTTTTTGTTTTCAAAAATTGACAACGCAACAAAAACAAAACGAAAACGAAACAAAAACAA
70081 AAAACAGAAAAACGAAAACAATGCCAC
326 AAAACAGAAAAACGAAAACAATGCCAC
* * *
70108 TGTTTTTGTTGTCTGTCTTCTATTG-CTAATTTTATGTTTTAGGAAGCAAAATAGTGAAAACATG
1 TGTTTTTGTTGTCTGTCTTCTATTGTC-AATTTCATGTTTTAGGAAACAAAACAGTGAAAACATG
* * *
70172 TTTGGCATG-CTGCATCTG-TTTCAAGAATTTTGAAAACAGAATCAATATTTTGGAAAAAAAAAA
65 TTTGGCA-GACTGCATCCGCTTTCAAAAATTTTGAAAACAGAAGCAATATTTTGG------AAAA
* *
70235 AAGTGGAAGTAAGAATTTTGTGTTTTCATGTTTTTCCAAAACACAGAAACACAGTGATGAACAGT
123 AAGTGGAAGCAAGAATTTTGTGTTTTCATGTTTTTCCAAAACACAGAAACACAATGATGAACAGT
* *
70300 ATCTCATATACATTTTT-ACCATTTTTT-TAAAAC-TTTTTTATTTAAAAACATACAACAAAATT
188 AACTCACATAC-TTTTTAACCATTTTTTCTAAAACTTTTTTTATTTAAAAACATACAACAAAATT
* * *
70362 GTATATTCAAACATGTTTTTGTTTTCAAAAAATTGACAACGCCACAAAAATAAAACGAAAACGAA
252 GTATATCCAAACATGTTTTTGTTTTC-AAAAATTGACAACGCAACAAAAACAAAACGAAAACGAA
*
70427 ACAAAAGCAAAAAACAGAAAAACGAAAAC
316 ACAAAAACAAAAAACAGAAAAACGAAAAC
70456 GATTCCCAAC
Statistics
Matches: 304, Mismatches: 34, Indels: 16
0.86 0.10 0.05
Matches are distributed among these distances:
351 31 0.10
352 67 0.22
353 1 0.00
355 53 0.17
356 66 0.22
357 81 0.27
358 5 0.02
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (352 bp):
TGTTTTTGTTGTCTGTCTTCTATTGTCAATTTCATGTTTTAGGAAACAAAACAGTGAAAACATGT
TTGGCAGACTGCATCCGCTTTCAAAAATTTTGAAAACAGAAGCAATATTTTGGAAAAAAGTGGAA
GCAAGAATTTTGTGTTTTCATGTTTTTCCAAAACACAGAAACACAATGATGAACAGTAACTCACA
TACTTTTTAACCATTTTTTCTAAAACTTTTTTTATTTAAAAACATACAACAAAATTGTATATCCA
AACATGTTTTTGTTTTCAAAAATTGACAACGCAACAAAAACAAAACGAAAACGAAACAAAAACAA
AAAACAGAAAAACGAAAACAATGCCAC
Found at i:71442 original size:30 final size:30
Alignment explanation
Indices: 71406--71465 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
71396 GACATCTTAA
*
71406 TGGCATCTCCATGAGGCTTTGCGATTCCAT
1 TGGCATCTCCATGAGACTTTGCGATTCCAT
71436 TGGCATCTCCATGAGACTTTGCGATTCCAT
1 TGGCATCTCCATGAGACTTTGCGATTCCAT
71466 CCTCTCCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.18, C:0.27, G:0.22, T:0.33
Consensus pattern (30 bp):
TGGCATCTCCATGAGACTTTGCGATTCCAT
Found at i:74252 original size:3 final size:3
Alignment explanation
Indices: 74244--74273 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
74234 ACAGTTATAT
74244 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
74274 TACAAGAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:75436 original size:2 final size:2
Alignment explanation
Indices: 75423--75459 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
75413 AGTAGTTGTG
*
75423 TA TA TG TA TA 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 TA TA TA TA TA T
75460 TATGTTTGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:80803 original size:15 final size:16
Alignment explanation
Indices: 80783--80823 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
80773 AATAGAGAAG
80783 TTTGTTTTTTG-TTCT
1 TTTGTTTTTTGTTTCT
*
80798 TTTGTTTTTTGTTTTT
1 TTTGTTTTTTGTTTCT
80814 TTTGTTTTTT
1 TTTGTTTTTT
80824 TACAGGCTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.85
Consensus pattern (16 bp):
TTTGTTTTTTGTTTCT
Found at i:80815 original size:8 final size:8
Alignment explanation
Indices: 80783--80824 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
80773 AATAGAGAAG
80783 TTTG-TTT
1 TTTGTTTT
*
80790 TTTGTTCT
1 TTTGTTTT
80798 TTTG-TTT
1 TTTGTTTT
80805 TTTGTTTTT
1 TTTG-TTTT
80814 TTTGTTTT
1 TTTGTTTT
80822 TTT
1 TTT
80825 ACAGGCTCGG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
7 10 0.33
8 13 0.43
9 7 0.23
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (8 bp):
TTTGTTTT
Found at i:80823 original size:7 final size:7
Alignment explanation
Indices: 80783--80814 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
80773 AATAGAGAAG
80783 TTTGTTT
1 TTTGTTT
80790 TTTGTTCT
1 TTTGTT-T
80798 TTTGTTT
1 TTTGTTT
80805 TTTGTTT
1 TTTGTTT
80812 TTT
1 TTT
80815 TTGTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.84
Consensus pattern (7 bp):
TTTGTTT
Done.