Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008314.1 Corchorus capsularis cultivar CVL-1 contig08335, 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: 96657
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2774 original size:17 final size:17
Alignment explanation
Indices: 2748--2785 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2738 TGTGAGATTG
2748 TGAGAGAGAGAAAAAGC
1 TGAGAGAGAGAAAAAGC
* *
2765 TGAGATAGAGAAAAAGT
1 TGAGAGAGAGAAAAAGC
2782 TGAG
1 TGAG
2786 TTTATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.34, T:0.13
Consensus pattern (17 bp):
TGAGAGAGAGAAAAAGC
Found at i:3083 original size:29 final size:31
Alignment explanation
Indices: 3050--3118 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 31
3040 GGTTCGGTCT
*
3050 GATTTGGGGTAAAACCTT-TT-AATTTTGTC
1 GATTTGGGGTAAAACCTTCTTAAATTGTGTC
* * *
3079 GATTTAGAGTAAAACGTTCTTAAATTGTGTC
1 GATTTGGGGTAAAACCTTCTTAAATTGTGTC
*
3110 AATTTGGGG
1 GATTTGGGG
3119 CAAGCGTCGT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
29 15 0.48
30 2 0.06
31 14 0.45
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.41
Consensus pattern (31 bp):
GATTTGGGGTAAAACCTTCTTAAATTGTGTC
Found at i:5999 original size:6 final size:6
Alignment explanation
Indices: 5988--6037 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
5978 CCCGAACTCG
* * * *
5988 CCCGAA CCCGAA CCCGAA CCC-AG CCTGAG CCCGAA CTCGAA CCCG-A
1 CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA
6034 CCCG
1 CCCG
6038 GGACCGAGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
5 8 0.22
6 29 0.78
ACGTcount: A:0.26, C:0.50, G:0.20, T:0.04
Consensus pattern (6 bp):
CCCGAA
Found at i:6351 original size:39 final size:35
Alignment explanation
Indices: 6272--6339 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
6262 CTAAAAAGTC
* * *
6272 TAAACAAATAAAGAGTCTAAAAAGAGGTTTATTAA
1 TAAAAAAACAAAGAGTCTAAAAAGAGGTTTACTAA
6307 TAAAAAAACAAAGAGTCTACAAAAGAGGTTTAC
1 TAAAAAAACAAAGAGTCTA-AAAAGAGGTTTAC
6340 GCCTAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 17 0.59
36 12 0.41
ACGTcount: A:0.54, C:0.09, G:0.15, T:0.22
Consensus pattern (35 bp):
TAAAAAAACAAAGAGTCTAAAAAGAGGTTTACTAA
Found at i:6764 original size:24 final size:23
Alignment explanation
Indices: 6720--6773 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 23
6710 TAAGCTCAAC
6720 TATATATATTTATGATTTTTTTAAG
1 TATATATATTTATGA-TTTTTT-AG
6745 TAATATATATTTATGA-TTTTTAG
1 T-ATATATATTTATGATTTTTTAG
6768 TATATA
1 TATATA
6774 ATAATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.18
23 3 0.11
24 5 0.18
25 1 0.04
26 14 0.50
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (23 bp):
TATATATATTTATGATTTTTTAG
Found at i:6779 original size:3 final size:3
Alignment explanation
Indices: 6771--6808 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
6761 TTTTTAGTAT
6771 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A
6809 GTCCAAGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:8521 original size:16 final size:16
Alignment explanation
Indices: 8467--8536 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 16
8457 AACCTAAATT
* *
8467 CGAACCCAACCTGGACC
1 CGAACCCAA-CAGAACC
* * *
8484 CGAACCCGATAGAACT
1 CGAACCCAACAGAACC
*
8500 CAAACCCAACAGAACC
1 CGAACCCAACAGAACC
* *
8516 CGAACCCGA-AGCACC
1 CGAACCCAACAGAACC
8531 CGAACC
1 CGAACC
8537 ACCCAATTGC
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
15 11 0.27
16 22 0.54
17 8 0.20
ACGTcount: A:0.37, C:0.43, G:0.16, T:0.04
Consensus pattern (16 bp):
CGAACCCAACAGAACC
Found at i:8717 original size:37 final size:38
Alignment explanation
Indices: 8659--8733 Score: 134
Period size: 37 Copynumber: 2.0 Consensus size: 38
8649 AAATCTATTG
8659 TCGTTTATTTTTTTCACATTTTAATTCCTCATTTCCGC
1 TCGTTTATTTTTTTCACATTTTAATTCCTCATTTCCGC
*
8697 TCGTTTA-TTTTTTCGCATTTTAATTCCTCATTTCCGC
1 TCGTTTATTTTTTTCACATTTTAATTCCTCATTTCCGC
8734 AATATTTGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 29 0.81
38 7 0.19
ACGTcount: A:0.15, C:0.24, G:0.07, T:0.55
Consensus pattern (38 bp):
TCGTTTATTTTTTTCACATTTTAATTCCTCATTTCCGC
Found at i:30921 original size:2 final size:2
Alignment explanation
Indices: 30914--30946 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
30904 TTTTGAATTA
*
30914 AT AT AT AT AT AT AT AT AT AT A- AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30947 TCTGTGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:33994 original size:26 final size:25
Alignment explanation
Indices: 33961--34009 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
33951 TGTCCCTCTT
* *
33961 AAAAAAAATGAGTGTTAGTAACCTC
1 AAAAAAAAAGAGCGTTAGTAACCTC
*
33986 AAAAGAAAAAGGGCGTTAGTAACC
1 AAAA-AAAAAGAGCGTTAGTAACC
34010 CCTAAATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.18
Consensus pattern (25 bp):
AAAAAAAAAGAGCGTTAGTAACCTC
Found at i:46636 original size:27 final size:27
Alignment explanation
Indices: 46604--46656 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
46594 AACCTTGATC
*
46604 TGAAATATCTAAAATATCATTTATAAT
1 TGAAATATCTAAAATACCATTTATAAT
*
46631 TGAAATATCTAAAATACCCTTTATAA
1 TGAAATATCTAAAATACCATTTATAA
46657 AATACTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (27 bp):
TGAAATATCTAAAATACCATTTATAAT
Found at i:57784 original size:22 final size:22
Alignment explanation
Indices: 57759--57990 Score: 69
Period size: 22 Copynumber: 10.8 Consensus size: 22
57749 ATGACGTTCG
57759 TATGAAATTTTGATAACATTCC
1 TATGAAATTTTGATAACATTCC
*
57781 TATGAAATTATGAT-A-ATTACAC
1 TATGAAATTTTGATAACATT-C-C
**
57803 TAT----TTTT--TATGATGTCC
1 TATGAAATTTTGATAACAT-TCC
*
57820 TTATGAAATTTTGATAACCTTCC
1 -TATGAAATTTTGATAACATTCC
** * *
57843 TATGAAATTTCAATAA-AGATAC
1 TATGAAATTTTGATAACA-TTCC
* * *
57865 TATGAAATTTCT-AGAACCTTTC
1 TATGAAATTT-TGATAACATTCC
* ** * *
57887 TAT-AATTTTTTTTAACCTTCT
1 TATGAAATTTTGATAACATTCC
* * *
57908 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACATTCC
* * *
57930 TAAGGAATTTTGA-AGAC-CTCAC
1 TATGAAATTTTGATA-ACATTC-C
57952 TATGAAATTTTGATAAC-TTCC
1 TATGAAATTTTGATAACATTCC
* *
57973 AAATGAAATTTTAATAAC
1 -TATGAAATTTTGATAAC
57991 CAACACTATA
Statistics
Matches: 154, Mismatches: 35, Indels: 42
0.67 0.15 0.18
Matches are distributed among these distances:
16 1 0.01
17 1 0.01
18 9 0.06
19 1 0.01
20 4 0.03
21 19 0.12
22 112 0.73
23 4 0.03
24 3 0.02
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACATTCC
Found at i:57797 original size:62 final size:62
Alignment explanation
Indices: 57723--57851 Score: 222
Period size: 62 Copynumber: 2.1 Consensus size: 62
57713 CATATATATT
*
57723 AAATTATGATAATTACACTATTTTTTATGACGTTCGTATGAAATTTTGATAACATTCCTATG
1 AAATTATGATAATTACACTATTTTTTATGACGTCCGTATGAAATTTTGATAACATTCCTATG
* * *
57785 AAATTATGATAATTACACTATTTTTTATGATGTCCTTATGAAATTTTGATAACCTTCCTATG
1 AAATTATGATAATTACACTATTTTTTATGACGTCCGTATGAAATTTTGATAACATTCCTATG
57847 AAATT
1 AAATT
57852 TCAATAAAGA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (62 bp):
AAATTATGATAATTACACTATTTTTTATGACGTCCGTATGAAATTTTGATAACATTCCTATG
Found at i:57867 original size:62 final size:62
Alignment explanation
Indices: 57723--57867 Score: 175
Period size: 62 Copynumber: 2.3 Consensus size: 62
57713 CATATATATT
* ** *
57723 AAATTATGATAATTACACTATTTTTTATGACGTTCGTATGAAATTTTGATAACATTCCTATG
1 AAATTATAATAAAGACACTATTTTTTATGACGTCCGTATGAAATTTTGATAACATTCCTATG
* ** * * *
57785 AAATTATGATAATTACACTATTTTTTATGATGTCCTTATGAAATTTTGATAACCTTCCTATG
1 AAATTATAATAAAGACACTATTTTTTATGACGTCCGTATGAAATTTTGATAACATTCCTATG
*
57847 AAATT-TCAATAAAGATACTAT
1 AAATTAT-AATAAAGACACTAT
57868 GAAATTTCTA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
61 1 0.01
62 73 0.99
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.43
Consensus pattern (62 bp):
AAATTATAATAAAGACACTATTTTTTATGACGTCCGTATGAAATTTTGATAACATTCCTATG
Found at i:58175 original size:45 final size:45
Alignment explanation
Indices: 58071--58175 Score: 115
Period size: 45 Copynumber: 2.3 Consensus size: 45
58061 TCACACTCTG
* * * *
58071 AAATTTTGATAATC-ACACTATGAAATTGTGATAACCTCGCTATG
1 AAATTTTGATAACCTACACTATAAAATTGTGATAACCTCCCTATA
* * *
58115 AAATTTTGATAAACCTTC-CTATAAAATTTTGATAAATCTCCCTATA
1 AAATTTTGAT-AACCTACACTATAAAATTGTGAT-AACCTCCCTATA
58161 AAATTTTGATAACCT
1 AAATTTTGATAACCT
58176 CCTTATGAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
44 10 0.20
45 21 0.41
46 20 0.39
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (45 bp):
AAATTTTGATAACCTACACTATAAAATTGTGATAACCTCCCTATA
Found at i:58186 original size:22 final size:21
Alignment explanation
Indices: 58069--58365 Score: 158
Period size: 22 Copynumber: 13.6 Consensus size: 21
58059 AATCACACTC
* *
58069 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAACCTC-CTA
*
58091 TGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAACCTC-CTA
58113 TGAAATTTTGATAAACCTTCCTA
1 TGAAATTTTGAT-AACC-TCCTA
* *
58136 TAAAATTTTGATAAATCTCCCTA
1 TGAAATTTTGAT-AACCT-CCTA
*
58159 TAAAATTTTGATAACCTCCTTA
1 TGAAATTTTGATAACCTCC-TA
** *
58181 TGAAATCCTGATGA----CTA
1 TGAAATTTTGATAACCTCCTA
* *
58198 -CAAATTTTGATAATCTCTCTA
1 TGAAATTTTGATAACCTC-CTA
** * * *
58219 TGATTTTTTTATTACCTCATTA
1 TGAAATTTTGATAACCTC-CTA
*
58241 TGAAATTTTG-TCAAACTCCTTA
1 TGAAATTTTGAT-AACCTCC-TA
* * *
58263 TGAAATTTTGATCTACATACTA
1 TGAAATTTTGAT-AACCTCCTA
* *
58285 TAAAATTTTGATAACCCTCTTA
1 TGAAATTTTGATAA-CCTCCTA
* *
58307 TGAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAACCT--CCTA
*
58329 TGAAATTTTGATAACCTTCATATA
1 TGAAATTTTGATAACC-TC--CTA
58353 TGAAATTTTGATA
1 TGAAATTTTGATA
58366 TGCTCCCTGA
Statistics
Matches: 209, Mismatches: 46, Indels: 38
0.71 0.16 0.13
Matches are distributed among these distances:
16 9 0.04
17 2 0.01
18 1 0.00
20 2 0.01
21 9 0.04
22 122 0.58
23 46 0.22
24 18 0.09
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (21 bp):
TGAAATTTTGATAACCTCCTA
Found at i:58578 original size:22 final size:22
Alignment explanation
Indices: 58465--58591 Score: 73
Period size: 22 Copynumber: 5.8 Consensus size: 22
58455 GAAATACCAC
*
58465 TATGAAATTTTCG-TAATCACAT
1 TATGAAATTTT-GATAACCACAT
* * ***
58487 TTTGAAAATTTGATAACCTTTT
1 TATGAAATTTTGATAACCACAT
* *
58509 TTTGAAATTTTGATAACCTC-T
1 TATGAAATTTTGATAACCACAT
* * *
58530 CTATAAAATTTTGTTGACGC-C-T
1 -TATGAAATTTTGATAAC-CACAT
*
58552 CTATGAAATTTTGATAATCACAT
1 -TATGAAATTTTGATAACCACAT
*
58575 TATGTAATTTTGATAAC
1 TATGAAATTTTGATAAC
58592 GTCGCTTTGA
Statistics
Matches: 82, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
21 3 0.04
22 77 0.94
23 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAT
Found at i:58603 original size:44 final size:44
Alignment explanation
Indices: 58467--58605 Score: 120
Period size: 44 Copynumber: 3.2 Consensus size: 44
58457 AATACCACTA
* * * * *
58467 TGAAATTTTCG-TAATCACATTTTGAAAATTTGATAACCTTTTTT
1 TGAAATTTT-GATAATCACATTATGAAATTTTGATAACGTCTCTT
* * * * * * *
58511 TGAAATTTTGATAACCTC-TCTATAAAATTTTGTTGACGCCTCTA
1 TGAAATTTTGATAATCACAT-TATGAAATTTTGATAACGTCTCTT
* *
58555 TGAAATTTTGATAATCACATTATGTAATTTTGATAACGTCGCTT
1 TGAAATTTTGATAATCACATTATGAAATTTTGATAACGTCTCTT
58599 TGAAATT
1 TGAAATT
58606 GGACCATCCA
Statistics
Matches: 71, Mismatches: 21, Indels: 6
0.72 0.21 0.06
Matches are distributed among these distances:
43 2 0.03
44 68 0.96
45 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.44
Consensus pattern (44 bp):
TGAAATTTTGATAATCACATTATGAAATTTTGATAACGTCTCTT
Found at i:58605 original size:22 final size:22
Alignment explanation
Indices: 58487--58605 Score: 80
Period size: 22 Copynumber: 5.4 Consensus size: 22
58477 GTAATCACAT
* * * *
58487 TTTGAAAATTTGATAACCTTTT
1 TTTGAAATTTTGATAACGTCTC
*
58509 TTTGAAATTTTGATAACCTCTC
1 TTTGAAATTTTGATAACGTCTC
* * * * *
58531 TATAAAATTTTGTTGACGCCTC
1 TTTGAAATTTTGATAACGTCTC
* *
58553 TATGAAATTTTGATAA--TCAC
1 TTTGAAATTTTGATAACGTCTC
* *
58573 ATTATGTAATTTTGATAACGTCGC
1 -TT-TGAAATTTTGATAACGTCTC
58597 TTTGAAATT
1 TTTGAAATT
58606 GGACCATCCA
Statistics
Matches: 75, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
20 2 0.03
21 1 0.01
22 67 0.89
23 2 0.03
24 3 0.04
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.45
Consensus pattern (22 bp):
TTTGAAATTTTGATAACGTCTC
Found at i:58752 original size:37 final size:37
Alignment explanation
Indices: 58659--58754 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 37
58649 ATCTAAGTCC
* * *
58659 AAATAGGACGTTGGAGACGAAGACAAAAAGCAAAATT
1 AAATAGGACGTTTGAAACAAAGACAAAAAGCAAAATT
** * *
58696 AAATACAACGATTGCAAACAAAGACAAAAGGCAAAATT
1 AAATAGGACGTTTG-AAACAAAGACAAAAAGCAAAATT
58734 AAATAGGACGTTTGAAACAAA
1 AAATAGGACGTTTGAAACAAA
58755 AAGTCAAATT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
37 17 0.35
38 31 0.65
ACGTcount: A:0.54, C:0.12, G:0.19, T:0.15
Consensus pattern (37 bp):
AAATAGGACGTTTGAAACAAAGACAAAAAGCAAAATT
Found at i:59046 original size:37 final size:37
Alignment explanation
Indices: 58953--59048 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 37
58943 ATCTAAGTCC
* * *
58953 AAATAGGACGTTGGAGACGAAGACAAAAAGCAAAATT
1 AAATAGGACGTTTGAAACAAAGACAAAAAGCAAAATT
** * *
58990 AAATACAACGATTGCAAACAAAGACAAAAGGCAAAATT
1 AAATAGGACGTTTG-AAACAAAGACAAAAAGCAAAATT
59028 AAATAGGACGTTTGAAACAAA
1 AAATAGGACGTTTGAAACAAA
59049 AAGTCAAATT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
37 17 0.35
38 31 0.65
ACGTcount: A:0.54, C:0.12, G:0.19, T:0.15
Consensus pattern (37 bp):
AAATAGGACGTTTGAAACAAAGACAAAAAGCAAAATT
Found at i:59063 original size:294 final size:294
Alignment explanation
Indices: 58534--59091 Score: 1107
Period size: 294 Copynumber: 1.9 Consensus size: 294
58524 ACCTCTCTAT
*
58534 AAAATTTTGTTGACGCCTCTATGAAATTTTGATAATCACATTATGTAATTTTGATAACGTCGCTT
1 AAAATTTTGTTGACACCTCTATGAAATTTTGATAATCACATTATGTAATTTTGATAACGTCGCTT
58599 TGAAATTGGACCATCCAAAGCAAAAACCCATTGCACATTTGTTTCAGATTATCTAAGTCCAAATA
66 TGAAATTGGACCATCCAAAGCAAAAACCCATTGCACATTTGTTTCAGATTATCTAAGTCCAAATA
58664 GGACGTTGGAGACGAAGACAAAAAGCAAAATTAAATACAACGATTGCAAACAAAGACAAAAGGCA
131 GGACGTTGGAGACGAAGACAAAAAGCAAAATTAAATACAACGATTGCAAACAAAGACAAAAGGCA
58729 AAATTAAATAGGACGTTTGAAACAAAAAGTCAAATTGACTTTTTTATAATTTAATATATGTATTA
196 AAATTAAATAGGACGTTTGAAACAAAAAGTCAAATTGACTTTTTTATAATTTAATATATGTATTA
58794 TATATTAATACATTATGTTTTGATAACAAAAAGC
261 TATATTAATACATTATGTTTTGATAACAAAAAGC
58828 AAAATTTTGTTGACACCTCTATGAAATTTTGATAATCACATTATGTAATTTTGATAACGTCGCTT
1 AAAATTTTGTTGACACCTCTATGAAATTTTGATAATCACATTATGTAATTTTGATAACGTCGCTT
58893 TGAAATTGGACCATCCAAAGCAAAAACCCATTGCACATTTGTTTCAGATTATCTAAGTCCAAATA
66 TGAAATTGGACCATCCAAAGCAAAAACCCATTGCACATTTGTTTCAGATTATCTAAGTCCAAATA
58958 GGACGTTGGAGACGAAGACAAAAAGCAAAATTAAATACAACGATTGCAAACAAAGACAAAAGGCA
131 GGACGTTGGAGACGAAGACAAAAAGCAAAATTAAATACAACGATTGCAAACAAAGACAAAAGGCA
59023 AAATTAAATAGGACGTTTGAAACAAAAAGTCAAATTGACTTTTTTATAATTTAATATATGTATTA
196 AAATTAAATAGGACGTTTGAAACAAAAAGTCAAATTGACTTTTTTATAATTTAATATATGTATTA
59088 TATA
261 TATA
59092 ATCTAATAAT
Statistics
Matches: 263, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
294 263 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (294 bp):
AAAATTTTGTTGACACCTCTATGAAATTTTGATAATCACATTATGTAATTTTGATAACGTCGCTT
TGAAATTGGACCATCCAAAGCAAAAACCCATTGCACATTTGTTTCAGATTATCTAAGTCCAAATA
GGACGTTGGAGACGAAGACAAAAAGCAAAATTAAATACAACGATTGCAAACAAAGACAAAAGGCA
AAATTAAATAGGACGTTTGAAACAAAAAGTCAAATTGACTTTTTTATAATTTAATATATGTATTA
TATATTAATACATTATGTTTTGATAACAAAAAGC
Found at i:59210 original size:30 final size:31
Alignment explanation
Indices: 59171--59235 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
59161 TGGCAATTTA
* * *
59171 GAAATATGTTTTTAAAA-AAGGGTACAATTG
1 GAAACATGTTTTAAAAATAAGGGTACAATCG
59201 GAAACATGTTTTAAAAATAAGGGTACAATCG
1 GAAACATGTTTTAAAAATAAGGGTACAATCG
59232 GAAA
1 GAAA
59236 ATATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (31 bp):
GAAACATGTTTTAAAAATAAGGGTACAATCG
Found at i:61446 original size:2 final size:2
Alignment explanation
Indices: 61439--61472 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
61429 CAAATAACCA
*
61439 AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61473 CGTTGCATCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:61707 original size:23 final size:26
Alignment explanation
Indices: 61647--61712 Score: 84
Period size: 23 Copynumber: 2.7 Consensus size: 26
61637 TTTAATGTTC
*
61647 AAACAAAATTTAAGTTGCCTTTAACA
1 AAACAAAATTTAAGTTGCCTCTAACA
*
61673 AAAAAAAATTTAAGTT-CC-CTAA-A
1 AAACAAAATTTAAGTTGCCTCTAACA
*
61696 AATCAAAATTTAAGTTG
1 AAACAAAATTTAAGTTG
61713 TTTTAAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 15 0.43
24 3 0.09
25 2 0.06
26 15 0.43
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.30
Consensus pattern (26 bp):
AAACAAAATTTAAGTTGCCTCTAACA
Found at i:64557 original size:24 final size:24
Alignment explanation
Indices: 64510--64566 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
64500 TCTAAAAGTT
64510 AAAAT-AAAATTATTATACCTAAA
1 AAAATAAAAATTATTATACCTAAA
64533 ATAAATAAAAATTATTAATA-C-AAA
1 A-AAATAAAAATTATT-ATACCTAAA
64557 AAGAATAAAA
1 AA-AATAAAA
64567 GAGTTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
23 2 0.07
24 15 0.50
25 10 0.33
26 3 0.10
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAAATTATTATACCTAAA
Found at i:65232 original size:28 final size:28
Alignment explanation
Indices: 65176--65233 Score: 100
Period size: 29 Copynumber: 2.1 Consensus size: 28
65166 TAACTATCCA
65176 TTTTTGGACAAATTGGTCCCTTAATCTT
1 TTTTTGGACAAATTGGTCCCTTAATCTT
65204 TTTTTGGGACAAATTGGTCCCTTAA-CTT
1 TTTTT-GGACAAATTGGTCCCTTAATCTT
65232 TT
1 TT
65234 AAAATCGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 10 0.34
29 19 0.66
ACGTcount: A:0.21, C:0.17, G:0.16, T:0.47
Consensus pattern (28 bp):
TTTTTGGACAAATTGGTCCCTTAATCTT
Found at i:66458 original size:11 final size:11
Alignment explanation
Indices: 66434--66468 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
66424 TTGACAGCGC
66434 AACAAAAACAA
1 AACAAAAACAA
* *
66445 AACGAAAACGA
1 AACAAAAACAA
66456 AACAAAAACAA
1 AACAAAAACAA
66467 AA
1 AA
66469 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:67712 original size:27 final size:27
Alignment explanation
Indices: 67674--67725 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
67664 TCTGAATTAA
* *
67674 TCGAGTCACAATGTGACTACGGATAAG
1 TCGAATCACAATGTAACTACGGATAAG
*
67701 TCGAATCACAATGTAACTATGGATA
1 TCGAATCACAATGTAACTACGGATA
67726 TACACATAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (27 bp):
TCGAATCACAATGTAACTACGGATAAG
Found at i:69023 original size:2 final size:2
Alignment explanation
Indices: 69016--69047 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
69006 GTAATTAAGC
69016 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69048 TACGTCTCAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70652 original size:12 final size:12
Alignment explanation
Indices: 70635--70684 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 12
70625 ACTTTTGCTT
70635 GAAAGAAAGGAA
1 GAAAGAAAGGAA
70647 GAAAGAAAGGAAA
1 GAAAGAAAGG-AA
* *
70660 AAAAGAAGAAGAA
1 GAAAGAA-AGGAA
70673 GAAA-AAA-GAA
1 GAAAGAAAGGAA
70683 GA
1 GA
70685 TATGGGTCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 5 0.15
11 1 0.03
12 12 0.36
13 13 0.39
14 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAAGAAAGGAA
Found at i:74630 original size:48 final size:48
Alignment explanation
Indices: 74574--74671 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
74564 TTTAAAGAAA
* *
74574 ACTTTAGATGAGAGGAGACTGCTTCAGTTCAGGAGATTAAGACATGTC
1 ACTTTAGATGAGAGGAGACGGCTTCAATTCAGGAGATTAAGACATGTC
*
74622 ACTTTAGATGAGAGGAGACGGCTTCAATTCAGGAGATTAAGGCATGTC
1 ACTTTAGATGAGAGGAGACGGCTTCAATTCAGGAGATTAAGACATGTC
74670 AC
1 AC
74672 AATCACAAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.26
Consensus pattern (48 bp):
ACTTTAGATGAGAGGAGACGGCTTCAATTCAGGAGATTAAGACATGTC
Found at i:80684 original size:4 final size:4
Alignment explanation
Indices: 80668--80698 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
80658 TAAACTAATT
80668 ACAA ACTAA ACAA ACAA ACAA ACAA ACAA AC
1 ACAA AC-AA ACAA ACAA ACAA ACAA ACAA AC
80699 TACTAAACCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.71, C:0.26, G:0.00, T:0.03
Consensus pattern (4 bp):
ACAA
Found at i:80692 original size:12 final size:13
Alignment explanation
Indices: 80668--80700 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
80658 TAAACTAATT
80668 ACAAACTAAACAA
1 ACAAACTAAACAA
80681 ACAAAC-AAACAA
1 ACAAACTAAACAA
80693 ACAAACTA
1 ACAAACTA
80701 CTAAACCCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.70, C:0.24, G:0.00, T:0.06
Consensus pattern (13 bp):
ACAAACTAAACAA
Found at i:84584 original size:35 final size:35
Alignment explanation
Indices: 84481--84587 Score: 178
Period size: 35 Copynumber: 3.1 Consensus size: 35
84471 TAATACAATA
*
84481 TTAAGGGTATTTTAGTAATTGACTAATTAAGATAT
1 TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
* * *
84516 TTAAGGATATTTTAATAATTGATTAATTAAGATTT
1 TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
84551 TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
1 TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
84586 TT
1 TT
84588 GAGTTCGTAC
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.36, C:0.02, G:0.15, T:0.47
Consensus pattern (35 bp):
TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
Found at i:86807 original size:16 final size:16
Alignment explanation
Indices: 86786--86857 Score: 94
Period size: 16 Copynumber: 4.6 Consensus size: 16
86776 GGCAATTGGG
86786 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
*
86802 CGGGTTCGGGT-TCTAT
1 CGGGTTCGGGTAT-TTT
86818 CGGGTTCGGGTA-TTT
1 CGGGTTCGGGTATTTT
*
86833 CAGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
*
86849 CGGGCTCGG
1 CGGGTTCGG
86858 ATCGGGTTCG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
15 14 0.29
16 34 0.71
ACGTcount: A:0.07, C:0.17, G:0.39, T:0.38
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:86840 original size:15 final size:15
Alignment explanation
Indices: 86786--86886 Score: 86
Period size: 16 Copynumber: 6.7 Consensus size: 15
86776 GGCAATTGGG
86786 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTA-TTT
86802 CGGGTTCGGGT-TCTAT
1 CGGGTTCGGGTAT-T-T
86818 CGGGTTCGGGTATTT
1 CGGGTTCGGGTATTT
*
86833 CAGGTTCGGGTATTTT
1 CGGGTTCGGGTA-TTT
*
86849 CGGGCTC-GG-A--T
1 CGGGTTCGGGTATTT
* *
86860 CGGGTTCGGGTCTGGT
1 CGGGTTCGGGTAT-TT
86876 CGGGTTCGGGT
1 CGGGTTCGGGT
86887 TCACTTTCGA
Statistics
Matches: 71, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
11 7 0.10
12 2 0.03
14 2 0.03
15 15 0.21
16 44 0.62
17 1 0.01
ACGTcount: A:0.06, C:0.17, G:0.42, T:0.36
Consensus pattern (15 bp):
CGGGTTCGGGTATTT
Found at i:87660 original size:16 final size:15
Alignment explanation
Indices: 87639--87680 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
87629 GTCGGGTTCA
87639 GGTTCGGGTTGTCTCG
1 GGTTCGGGTT-TCTCG
*
87655 GGTTCGGGTATTTTCG
1 GGTTCGGGT-TTCTCG
87671 GGTTCGGGTT
1 GGTTCGGGTT
87681 CGGGTTCGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 1 0.04
16 22 0.92
17 1 0.04
ACGTcount: A:0.02, C:0.14, G:0.43, T:0.40
Consensus pattern (15 bp):
GGTTCGGGTTTCTCG
Found at i:87661 original size:6 final size:6
Alignment explanation
Indices: 87619--87690 Score: 53
Period size: 6 Copynumber: 11.8 Consensus size: 6
87609 TATTTTGATC
* *
87619 TCGGGC TCGGG- TCGGGT TCAGGT TCGGGT T---GT CTCGGGT TCGGGTATTT
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT -TCGGGT TCGGG----T
87668 TCGGGT TCGGGT TCGGGT TCGGG
1 TCGGGT TCGGGT TCGGGT TCGGG
87691 ACGTTGACTT
Statistics
Matches: 55, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
3 2 0.04
4 1 0.02
5 5 0.09
6 39 0.71
7 2 0.04
10 6 0.11
ACGTcount: A:0.03, C:0.18, G:0.46, T:0.33
Consensus pattern (6 bp):
TCGGGT
Found at i:89585 original size:12 final size:12
Alignment explanation
Indices: 89568--89592 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
89558 GCCCAGACCT
89568 CTTGCAATATCC
1 CTTGCAATATCC
89580 CTTGCAATATCC
1 CTTGCAATATCC
89592 C
1 C
89593 ATGAGGCGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.08, T:0.32
Consensus pattern (12 bp):
CTTGCAATATCC
Found at i:95804 original size:21 final size:19
Alignment explanation
Indices: 95779--95836 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 19
95769 GCTGCTCTAA
95779 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* * *
95800 TAATCTAATCTGTATAGTG
1 TAATCTCATCTGTACAGTC
*
95819 TAATTTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
95837 TGCTAAATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:96403 original size:201 final size:200
Alignment explanation
Indices: 96051--96657 Score: 926
Period size: 201 Copynumber: 3.0 Consensus size: 200
96041 TTGGTTTAAA
* ** * * *
96051 ATAAGAAAATTTACACAATACACAATCAGTGGAGTTTAGCAGACTACATGTGCGGGGTTTAACTT
1 ATAAGAAAAATTATGCAATACACCATCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTT
* *
96116 TAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATAGA
66 TAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGG
* *
96181 GTATGTGTCAACTTTTTAACCCACTTATGGAGTTCAAAATTTATACTGATAGTGTATTGTATAAT
131 GTATGTGTCAAC-TTTTAACCCGCTTATGGAGTTCAAAATTTATACTGACAGTGTATTGTATAAT
96246 AATCCT
195 AATCCT
* * * *
96252 TTAAGAAAAATTATGCAATACGCCGTCCGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTT
1 ATAAGAAAAATTATGCAATACACCATCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTT
* * * * * *
96317 TAAGGGTTGAGATGTGTGCCTTTAGGGAATATATATTAATGTTAAATATTTAATCATGAAATGGG
66 TAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGG
*
96382 GTATGTGTCAACTTCTTAACCCGCTTATGGAGTTCAAAATTTATACTGACAGTGTATTGTATAGT
131 GTATGTGTCAACTT-TTAACCCGCTTATGGAGTTCAAAATTTATACTGACAGTGTATTGTATAAT
96447 AATCCT
195 AATCCT
* *
96453 ATAAGAAAAATTATGCAATACACCATTAGTGGAGTTTAGCAAACTGCACGTGCGGGGTTTAACTT
1 ATAAGAAAAATTATGCAATACACCATCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTT
* *
96518 TAAGGGTTGACATGTGTACCCTTAGGAAATATGTATTAATATTAAATATTTGATTATGAAATGGG
66 TAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGG
* * * * *
96583 ATATGTGTCAGCTTTTAACCCGCTTATAGAATCCAAAATTTATACTGACAGTGTATTGTATAATA
131 GTATGTGTCAACTTTTAACCCGCTTATGGAGTTCAAAATTTATACTGACAGTGTATTGTATAATA
96648 ATCCT
196 ATCCT
96653 ATAAG
1 ATAAG
Statistics
Matches: 364, Mismatches: 41, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
200 59 0.16
201 305 0.84
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.34
Consensus pattern (200 bp):
ATAAGAAAAATTATGCAATACACCATCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTT
TAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGG
GTATGTGTCAACTTTTAACCCGCTTATGGAGTTCAAAATTTATACTGACAGTGTATTGTATAATA
ATCCT
Done.