Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2431
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: 44568
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2774 original size:24 final size:26
Alignment explanation
Indices: 2718--2775 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
2708 AATCCTTTTC
*
2718 TCTCTTCTTCTTCCTCCTCCTCTTCTT
1 TCTCTTCTTCTTCCTCCT-CTCTTCCT
* *
2745 TTTCTTCTTCTTCCTCGT-TC-TCCT
1 TCTCTTCTTCTTCCTCCTCTCTTCCT
2769 TCTCTTC
1 TCTCTTC
2776 AACTTCCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 9 0.33
25 2 0.07
27 16 0.59
ACGTcount: A:0.00, C:0.41, G:0.02, T:0.57
Consensus pattern (26 bp):
TCTCTTCTTCTTCCTCCTCTCTTCCT
Found at i:3397 original size:7 final size:7
Alignment explanation
Indices: 3380--3416 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
3370 AAATATGGAC
3380 TAAATTAT
1 TAAA-TAT
3388 TAAATAT
1 TAAATAT
3395 TAAATAT
1 TAAATAT
3402 TAAATAT
1 TAAATAT
3409 TAAATAT
1 TAAATAT
3416 T
1 T
3417 TAAGTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 25 0.86
8 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TAAATAT
Found at i:3695 original size:7 final size:7
Alignment explanation
Indices: 3683--3722 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
3673 CTAAGCCTTA
3683 AACCCCT
1 AACCCCT
3690 AACCCCT
1 AACCCCT
*
3697 ACCCCCT
1 AACCCCT
*
3704 AACCCTT
1 AACCCCT
*
3711 AAACCCT
1 AACCCCT
3718 AACCC
1 AACCC
3723 TTAAACCGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.30, C:0.55, G:0.00, T:0.15
Consensus pattern (7 bp):
AACCCCT
Found at i:3723 original size:14 final size:14
Alignment explanation
Indices: 3673--3770 Score: 70
Period size: 14 Copynumber: 6.9 Consensus size: 14
3663 ATTAATTAAT
*
3673 CTAAGCCTTAAACCC
1 CTAACCCTTAAA-CC
* **
3688 CTAACCCCTACCCC
1 CTAACCCTTAAACC
3702 CTAACCCTTAAACC
1 CTAACCCTTAAACC
3716 CTAACCCTTAAACC
1 CTAACCCTTAAACC
* * * *
3730 GTAATCCATAATCC
1 CTAACCCTTAAACC
* *
3744 CTAAACCCATAATCC
1 CT-AACCCTTAAACC
* *
3759 ATAAACCTTAAA
1 CTAACCCTTAAA
3771 ATAGTAAATC
Statistics
Matches: 65, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
14 45 0.69
15 20 0.31
ACGTcount: A:0.37, C:0.40, G:0.02, T:0.21
Consensus pattern (14 bp):
CTAACCCTTAAACC
Found at i:3745 original size:22 final size:22
Alignment explanation
Indices: 3717--3770 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
3707 CCTTAAACCC
*
3717 TAACCCTTAAA-CCGTAATCCA
1 TAACCCTTAAACCCATAATCCA
3738 TAATCCC-TAAACCCATAATCCA
1 TAA-CCCTTAAACCCATAATCCA
*
3760 TAAACCTTAAA
1 TAACCCTTAAA
3771 ATAGTAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.43, C:0.31, G:0.02, T:0.24
Consensus pattern (22 bp):
TAACCCTTAAACCCATAATCCA
Found at i:3755 original size:15 final size:15
Alignment explanation
Indices: 3735--3765 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3725 AAACCGTAAT
*
3735 CCATAATCCCTAAAC
1 CCATAATCCATAAAC
3750 CCATAATCCATAAAC
1 CCATAATCCATAAAC
3765 C
1 C
3766 TTAAAATAGT
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:0.42, C:0.39, G:0.00, T:0.19
Consensus pattern (15 bp):
CCATAATCCATAAAC
Found at i:3801 original size:21 final size:21
Alignment explanation
Indices: 3775--3820 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3765 CTTAAAATAG
**
3775 TAAATCATACACTTTAAACCC
1 TAAATCATACACCCTAAACCC
*
3796 TAAATCATATACCCTAAACCC
1 TAAATCATACACCCTAAACCC
3817 TAAA
1 TAAA
3821 CTATAAAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAATCATACACCCTAAACCC
Found at i:3961 original size:22 final size:20
Alignment explanation
Indices: 3919--3980 Score: 52
Period size: 22 Copynumber: 2.9 Consensus size: 20
3909 ACTAATTAAT
* *
3919 CTAAACCTTAAACTCTTAATCC
1 CTAAACCATAAAC-CTGAAT-C
*
3941 CTAAACCCTAAACCATGAATC
1 CTAAACCATAAACC-TGAATC
*
3962 CTAAAACATAAACCCTGAA
1 CTAAACCATAAA-CCTGAA
3981 CCATGAACCA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
21 16 0.47
22 18 0.53
ACGTcount: A:0.44, C:0.31, G:0.03, T:0.23
Consensus pattern (20 bp):
CTAAACCATAAACCTGAATC
Found at i:3966 original size:14 final size:14
Alignment explanation
Indices: 3944--3994 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
3934 TTAATCCCTA
3944 AACCCTAAACCATG
1 AACCCTAAACCATG
* * *
3958 AATCCTAAAACATA
1 AACCCTAAACCATG
*
3972 AACCCTGAACCATG
1 AACCCTAAACCATG
3986 AACCACTAA
1 AACC-CTAA
3995 CCCTTAACCC
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
14 25 0.89
15 3 0.11
ACGTcount: A:0.47, C:0.31, G:0.06, T:0.16
Consensus pattern (14 bp):
AACCCTAAACCATG
Found at i:3966 original size:21 final size:21
Alignment explanation
Indices: 3940--3980 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3930 ACTCTTAATC
* *
3940 CCTAAACCCTAAACCATGAAT
1 CCTAAAACATAAACCATGAAT
*
3961 CCTAAAACATAAACCCTGAA
1 CCTAAAACATAAACCATGAA
3981 CCATGAACCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.32, G:0.05, T:0.17
Consensus pattern (21 bp):
CCTAAAACATAAACCATGAAT
Found at i:4015 original size:21 final size:21
Alignment explanation
Indices: 3972--4046 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 21
3962 CTAAAACATA
* * * *
3972 AACCCTGAACCATGAACCACT
1 AACCCTTAACCCTTAACCCCT
3993 AACCCTTAACCCTTAACCCCT
1 AACCCTTAACCCTTAACCCCT
*
4014 AACACCTAAACGACCTTAAACCCC-
1 AAC-CCTTAAC--CCTT-AACCCCT
4038 AACCCTTAA
1 AACCCTTAA
4047 ACCACCCTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
21 20 0.45
22 6 0.14
23 5 0.11
24 7 0.16
25 6 0.14
ACGTcount: A:0.37, C:0.41, G:0.04, T:0.17
Consensus pattern (21 bp):
AACCCTTAACCCTTAACCCCT
Found at i:4055 original size:25 final size:26
Alignment explanation
Indices: 4001--4060 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
3991 CTAACCCTTA
*
4001 ACCCTT-AACCCCTAACACCTAAACG
1 ACCCTTAAACCCCTAACACCTAAACC
4026 A-CCTTAAACCCC-AAC-CCTTAAACC
1 ACCCTTAAACCCCTAACACC-TAAACC
4050 ACCCTTAAACC
1 ACCCTTAAACC
4061 ATAATCCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
23 2 0.06
24 13 0.42
25 16 0.52
ACGTcount: A:0.37, C:0.45, G:0.02, T:0.17
Consensus pattern (26 bp):
ACCCTTAAACCCCTAACACCTAAACC
Found at i:4511 original size:79 final size:81
Alignment explanation
Indices: 4411--4560 Score: 205
Period size: 79 Copynumber: 1.9 Consensus size: 81
4401 TTAATTTTTT
* *
4411 GCGGCGTTTTTTAAAAGGCGCCGCTAATACTTGATCTTTAGTGGTGCTTTTCA-AAAAACGCCGC
1 GCGGCATTTTTTAAAAGGCGCCGCTAATACTTGATCTTTAGCGGTGCTTTTCATAAAAACGCCGC
4475 TAAAAATGAACCTATA
66 TAAAAATGAACCTATA
* * * * ** *
4491 GCGGCATTTTTTGAAA-GCGCCGCTAGTGCTTGATCTTTAGCGGTGTTTTTCATTCAATCGCCGC
1 GCGGCATTTTTTAAAAGGCGCCGCTAATACTTGATCTTTAGCGGTGCTTTTCATAAAAACGCCGC
4555 TAAAAA
66 TAAAAA
4561 CGCCGCTAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
79 32 0.53
80 28 0.47
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (81 bp):
GCGGCATTTTTTAAAAGGCGCCGCTAATACTTGATCTTTAGCGGTGCTTTTCATAAAAACGCCGC
TAAAAATGAACCTATA
Found at i:4566 original size:12 final size:12
Alignment explanation
Indices: 4549--4573 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4539 TTCATTCAAT
4549 CGCCGCTAAAAA
1 CGCCGCTAAAAA
4561 CGCCGCTAAAAA
1 CGCCGCTAAAAA
4573 C
1 C
4574 CTGTTTTGCT
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:0.40, C:0.36, G:0.16, T:0.08
Consensus pattern (12 bp):
CGCCGCTAAAAA
Found at i:7841 original size:10 final size:10
Alignment explanation
Indices: 7822--7853 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
7812 AATTATTTCA
*
7822 AAAAGGTTTG
1 AAAAGATTTG
7832 AAAAGATTTG
1 AAAAGATTTG
7842 AAAAGATTTG
1 AAAAGATTTG
7852 AA
1 AA
7854 GTATTTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28
Consensus pattern (10 bp):
AAAAGATTTG
Found at i:9599 original size:26 final size:27
Alignment explanation
Indices: 9569--9636 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 27
9559 GGAGGCTAGT
**
9569 ATTACTGAAATACCTTTGAAGGGTA-A
1 ATTACTGAAATACCCCTGAAGGGTAGA
* * *
9595 GTTACTGAAATGCCCCTGTAGGGTAGA
1 ATTACTGAAATACCCCTGAAGGGTAGA
9622 ATTACTGAAATACCC
1 ATTACTGAAATACCC
9637 TTGGTTTACA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 20 0.59
27 14 0.41
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (27 bp):
ATTACTGAAATACCCCTGAAGGGTAGA
Found at i:9651 original size:27 final size:27
Alignment explanation
Indices: 9621--9959 Score: 178
Period size: 27 Copynumber: 12.6 Consensus size: 27
9611 TGTAGGGTAG
*
9621 AATTACTGAAATACCCTTGGTTTACAA
1 AATTACTGAAATACCCTTGATTTACAA
**
9648 AATTGTTG-AATACCCTTTG-TTTACAA
1 AATTACTGAAATACCC-TTGATTTACAA
** * *
9674 AATTACCAAAATACCCTCGA-TTAGTAA
1 AATTACTGAAATACCCTTGATTTA-CAA
** * ***
9701 AATTACCAAAATACCCCTGATTTGTGA
1 AATTACTGAAATACCCTTGATTTACAA
* * * **
9728 AATTATTGAAATACCCTCGACTTGTAA
1 AATTACTGAAATACCCTTGATTTACAA
9755 AATTACTGAAATA-CCTTCGAATTGTA-AA
1 AATTACTGAAATACCCTT-G-ATT-TACAA
* * * *
9783 ACTT-TTGAAATACCCTTAATTTATAA
1 AATTACTGAAATACCCTTGATTTACAA
* * **
9809 AATTAC-CAGAATACCCCTGATTTGGAA
1 AATTACTGA-AATACCCTTGATTTACAA
* * **
9836 AATTAC-CAAATTACCCCTGATTTGGAA
1 AATTACTGAAA-TACCCTTGATTTACAA
***
9863 AATTAAAAAAATACCCTTGATTTACAA
1 AATTACTGAAATACCCTTGATTTACAA
*
9890 AATTACAGAAATACCCTTGACTTT-CAAA
1 AATTACTGAAATACCCTTGA-TTTAC-AA
* *
9918 AATTA-TAGAAATACCCTTGGTTTGCAA
1 AATTACT-GAAATACCCTTGATTTACAA
9945 AATTA-TCGAAATACC
1 AATTACT-GAAATACC
9960 ATTGGTTTGT
Statistics
Matches: 251, Mismatches: 43, Indels: 36
0.76 0.13 0.11
Matches are distributed among these distances:
25 2 0.01
26 37 0.15
27 172 0.69
28 39 0.16
29 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.32
Consensus pattern (27 bp):
AATTACTGAAATACCCTTGATTTACAA
Found at i:10274 original size:41 final size:41
Alignment explanation
Indices: 10227--10351 Score: 196
Period size: 41 Copynumber: 3.0 Consensus size: 41
10217 GGAGGAAGAA
*
10227 ATTGAGGATCACATGGTTGCTTGATGACCGTGGATCCACCG
1 ATTGAGGATCACATGGTTGCTTGACGACCGTGGATCCACCG
** * *
10268 ATTGAGGATTGCATGGTTTCTTGACGACCGTGGATCTACCG
1 ATTGAGGATCACATGGTTGCTTGACGACCGTGGATCCACCG
*
10309 ATTAAGGATCACATGGTTGCTTGACGACCGTGGATCCACCG
1 ATTGAGGATCACATGGTTGCTTGACGACCGTGGATCCACCG
10350 AT
1 AT
10352 GGCTTTTAAG
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (41 bp):
ATTGAGGATCACATGGTTGCTTGACGACCGTGGATCCACCG
Found at i:14842 original size:39 final size:39
Alignment explanation
Indices: 14788--14866 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
14778 TTTATGAAAA
14788 CTTAAAGACAATTAAGAGAAAAGTGATGGCTAAAAATTG
1 CTTAAAGACAATTAAGAGAAAAGTGATGGCTAAAAATTG
*
14827 CTTAAAGATAATTAAGAGAAAAGTGATGGCTAAAAATTG
1 CTTAAAGACAATTAAGAGAAAAGTGATGGCTAAAAATTG
14866 C
1 C
14867 AAAGGTTCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (39 bp):
CTTAAAGACAATTAAGAGAAAAGTGATGGCTAAAAATTG
Found at i:16147 original size:24 final size:24
Alignment explanation
Indices: 16120--16266 Score: 152
Period size: 24 Copynumber: 5.8 Consensus size: 24
16110 AACCAAAATG
16120 AGAATCAGAATCAGAATCAGTAAC
1 AGAATCAGAATCAGAATCAGTAAC
*
16144 AGAATCAGAATCA-ATATTAGTAAC
1 AGAATCAGAATCAGA-ATCAGTAAC
*
16168 AGAATCAGAATCAAAATCAGAATTAGGTGAC
1 AGAATCAGAATCAGAATCAG---TA----AC
16199 AGAATCAGAATCAGAATCAGTAAC
1 AGAATCAGAATCAGAATCAGTAAC
* * *
16223 AGAATTAGAATCAGTATTAGTAAC
1 AGAATCAGAATCAGAATCAGTAAC
* *
16247 ATAATTAGAATCAGAATCAG
1 AGAATCAGAATCAGAATCAG
16267 AATTAGGTGA
Statistics
Matches: 105, Mismatches: 9, Indels: 18
0.80 0.07 0.14
Matches are distributed among these distances:
23 1 0.01
24 78 0.74
25 1 0.01
27 2 0.02
28 2 0.02
31 21 0.20
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.22
Consensus pattern (24 bp):
AGAATCAGAATCAGAATCAGTAAC
Found at i:16204 original size:31 final size:31
Alignment explanation
Indices: 16143--16218 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
16133 GAATCAGTAA
16143 CAGAATCAGAATCA-ATATTAGTAACAGAAT
1 CAGAATCAGAATCAGATATTAGTAACAGAAT
* *
16173 CAGAATCAAAATCAGA-ATTAGGTGACAGAAT
1 CAGAATCAGAATCAGATATTA-GTAACAGAAT
16204 CAGAATCAGAATCAG
1 CAGAATCAGAATCAG
16219 TAACAGAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
30 17 0.41
31 24 0.59
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (31 bp):
CAGAATCAGAATCAGATATTAGTAACAGAAT
Found at i:16214 original size:79 final size:79
Alignment explanation
Indices: 16120--16294 Score: 296
Period size: 79 Copynumber: 2.2 Consensus size: 79
16110 AACCAAAATG
16120 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAATATTAGTAACAGAATCAGAATCAAAAT
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAATATTAGTAACAGAATCAGAATCAAAAT
16185 CAGAATTAGGTGAC
66 CAGAATTAGGTGAC
* * * * *
16199 AGAATCAGAATCAGAATCAGTAACAGAATTAGAATCAGTATTAGTAACATAATTAGAATCAGAAT
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAATATTAGTAACAGAATCAGAATCAAAAT
16264 CAGAATTAGGTGAC
66 CAGAATTAGGTGAC
*
16278 AGAATCAGAATTAGAAT
1 AGAATCAGAATCAGAAT
16295 ATGAATGCAA
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 90 1.00
ACGTcount: A:0.49, C:0.12, G:0.17, T:0.22
Consensus pattern (79 bp):
AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAATATTAGTAACAGAATCAGAATCAAAAT
CAGAATTAGGTGAC
Found at i:16288 original size:6 final size:6
Alignment explanation
Indices: 16120--16269 Score: 114
Period size: 6 Copynumber: 24.8 Consensus size: 6
16110 AACCAAAATG
*
16120 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC A-ATATT AGTAA-C
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGA-ATC AG-AATC
* * *
16168 AGAATC AGAATC AAAATC AGAATT AG-GTGAC AGAATC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC
* * * * *
16217 AGTAA-C AGAATT AGAATC AGTATT AGTAA-C ATAATT AGAATC AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC
16265 AGAAT
1 AGAAT
16270 TAGGTGACAG
Statistics
Matches: 113, Mismatches: 18, Indels: 26
0.72 0.11 0.17
Matches are distributed among these distances:
5 10 0.09
6 93 0.82
7 8 0.07
8 2 0.02
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.22
Consensus pattern (6 bp):
AGAATC
Found at i:16477 original size:27 final size:27
Alignment explanation
Indices: 16413--16469 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
16403 GCATGGCTGT
* * *
16413 CAGA-ACAGATATCGTGACAGAGTCAC
1 CAGATACAGATATAGTGGCAGAGCCAC
16439 CAGATACAGATATAGTGGCAGAGCCAC
1 CAGATACAGATATAGTGGCAGAGCCAC
16466 CAGA
1 CAGA
16470 ATTAGATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.14
Consensus pattern (27 bp):
CAGATACAGATATAGTGGCAGAGCCAC
Found at i:16698 original size:22 final size:22
Alignment explanation
Indices: 16650--16708 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
16640 GTAAATACGT
*
16650 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
16672 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
16694 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
16709 TAATAGCGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:16875 original size:27 final size:26
Alignment explanation
Indices: 16796--16878 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 26
16786 TCAATCGGTC
* * *
16796 AACAGATATTGTGACAGAGTCACCAA
1 AACAGATATTGTGGCAGAGCCACCAG
*
16822 ATACAGATATTGTGGCAGGGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
16849 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
16876 AAC
1 AAC
16879 GCTTCCTTCG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
26 8 0.16
27 41 0.84
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:17221 original size:81 final size:81
Alignment explanation
Indices: 17079--17265 Score: 232
Period size: 81 Copynumber: 2.3 Consensus size: 81
17069 GGCAAAATGG
* * * * * * *
17079 TAATTTTACCCCACAAGGGTATCTCGATAATTCTACCGTATAGGGGTATTTCGGTATTTCTACCC
1 TAATTCTACCCTACAGGGGTATTTCGATAATTCTACCGTATAAGGGTATTTCAGTAATTCTACCC
*
17144 TACAAGGGTATTTCGA
66 TACAAGGGTATTTCAA
* *
17160 TAATTCTACCCTACAGGGGTATTTTGGTAATTCTATCC-TATAAGGGTATTTCAGTAATTCTACC
1 TAATTCTACCCTACAGGGGTATTTCGATAATTCTA-CCGTATAAGGGTATTTCAGTAATTCTACC
* * *
17224 CTATAGGGGTATTTTAA
65 CTACAAGGGTATTTCAA
*
17241 AAATTCTACCCTACAGGGGTATTTC
1 TAATTCTACCCTACAGGGGTATTTC
17266 AGTAATTTCA
Statistics
Matches: 90, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
81 88 0.98
82 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (81 bp):
TAATTCTACCCTACAGGGGTATTTCGATAATTCTACCGTATAAGGGTATTTCAGTAATTCTACCC
TACAAGGGTATTTCAA
Found at i:17272 original size:27 final size:27
Alignment explanation
Indices: 17078--17272 Score: 196
Period size: 27 Copynumber: 7.2 Consensus size: 27
17068 GGGCAAAATG
* * * *
17078 GTAATTTTACCCCACAAGGGTATCTC-
1 GTAATTCTACCCTACAGGGGTATTTCA
* * *
17104 GATAATTCTACCGTATAGGGGTATTTCG
1 G-TAATTCTACCCTACAGGGGTATTTCA
* *
17132 GTATTTCTACCCTACAAGGGTATTTC-
1 GTAATTCTACCCTACAGGGGTATTTCA
**
17158 GATAATTCTACCCTACAGGGGTATTTTG
1 G-TAATTCTACCCTACAGGGGTATTTCA
* * *
17186 GTAATTCTATCCTATAAGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
17213 GTAATTCTACCCTATAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCA
**
17240 AAAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
17267 GTAATT
1 GTAATT
17273 TCACAATCGA
Statistics
Matches: 138, Mismatches: 27, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
26 2 0.01
27 134 0.97
28 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCA
Found at i:17272 original size:54 final size:54
Alignment explanation
Indices: 17076--17265 Score: 247
Period size: 54 Copynumber: 3.5 Consensus size: 54
17066 AGGGGCAAAA
* * * *
17076 TGGTAATTTTACCCCACAAGGGTATCTCGATAATTCTACCGTATAGGGGTATTT
1 TGGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTATAGGGGTATTT
* * *
17130 CGGTATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTATAGGGGTATTT
* *
17184 TGGTAATTCTATCCTATAAGGGTATTTC-AGTAATTCTACCCTATAGGGGTATTT
1 TGGTAATTCTACCCTACAAGGGTATTTCGA-TAATTCTACCCTATAGGGGTATTT
*** *
17238 TAAAAATTCTACCCTACAGGGGTATTTC
1 TGGTAATTCTACCCTACAAGGGTATTTC
17266 AGTAATTTCA
Statistics
Matches: 117, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
53 1 0.01
54 116 0.99
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.36
Consensus pattern (54 bp):
TGGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTATAGGGGTATTT
Found at i:17307 original size:27 final size:27
Alignment explanation
Indices: 17277--17759 Score: 564
Period size: 27 Copynumber: 17.9 Consensus size: 27
17267 GTAATTTCAC
17277 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
17304 AATCGAGGGTAAAATGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
17331 AA-CTGAGGAT-AAACTAGTAATTCTGTA
1 AATC-GAGGGTAAAAC-GGTAATTCTGTA
* * **
17358 AATCAAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
17385 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
17412 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
17439 AA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
*
17466 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
17493 AA-CTGAGGGTAAAATGGTAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* * * **
17520 AATCGAGGGTAAAATGATAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
17547 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* **
17574 AATTGAGGGTAAAACAATAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
17601 AA-CTGAGGGTAAAATGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
17628 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
17655 AA-CTAAGGGTAAAACGATAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* **
17682 AATCGAGGGTAAAACGGTAATTTTAAA
1 AATCGAGGGTAAAACGGTAATTCTGTA
17709 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
17736 AATCAAGGGTAAAACGGTAATTCT
1 AATCGAGGGTAAAACGGTAATTCT
17760 ATAATTCGGG
Statistics
Matches: 387, Mismatches: 57, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
26 7 0.02
27 371 0.96
28 9 0.02
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:21314 original size:68 final size:65
Alignment explanation
Indices: 21100--21321 Score: 211
Period size: 67 Copynumber: 3.4 Consensus size: 65
21090 CATAATTTTG
* *
21100 GCTCTCTTGTACACATGGTGTACACATAGTATCACCCATGTGACCTAGCCACT--TTATCTCGTA
1 GCTCTCTTGTACACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACTCATTATCTCGTA
** * * * * * * *
21163 GCTCTCTTGTTTACATGGTGTTCTTCACCTGGAACCACACATGCAACCTAGCTA--CATCTATCT
1 GCTCTCTTGTACACATGGTG---TACACATAGTATCACCCATGCGACCTAGCTACTCAT-TATCT
21226 CGTA
62 CGTA
*
21230 GCTCTCTTGT-CTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACCTCATAATATAT
1 GCTCTCTTGTAC-ACATGGTGTACACATAGTATCACCCATGCGACCTAGCTA-CTCAT--TATCT
21294 CGTA
62 CGTA
* *
21298 GCTCTCTTATACACATGGTATACA
1 GCTCTCTTGTACACATGGTGTACA
21322 TCCCGTATTA
Statistics
Matches: 124, Mismatches: 23, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
63 18 0.15
64 24 0.19
66 23 0.19
67 30 0.24
68 28 0.23
69 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (65 bp):
GCTCTCTTGTACACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACTCATTATCTCGTA
Found at i:27184 original size:53 final size:54
Alignment explanation
Indices: 27101--27309 Score: 210
Period size: 53 Copynumber: 3.9 Consensus size: 54
27091 TGGATTCTTT
* * *
27101 TGAAACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTA
1 TGAAACCTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA
* * **
27155 TG-AACCAACCAATGCCATGCCTTGGCATGGTCTTACATGG-GGCCTTTGCCTTA
1 TGAAACCTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTA
* * * * * * * *
27208 TGGTAACTTATCAATGCCATGTCTTGACATGGTCTTACGTGATTTCCTTTCCTTA
1 T-GAAACCTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA
* *
27263 -GAAACCTTACC-ATGTCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 TGAAACC-TACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
27310 AAACCCTAAT
Statistics
Matches: 124, Mismatches: 26, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
52 2 0.02
53 76 0.61
54 6 0.05
55 38 0.31
56 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (54 bp):
TGAAACCTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA
Found at i:27256 original size:108 final size:108
Alignment explanation
Indices: 27104--27302 Score: 294
Period size: 108 Copynumber: 1.8 Consensus size: 108
27094 ATTCTTTTGA
* *
27104 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AACC-AACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTAACC-A
27167 TGCCATGCCTTGGCATGGTCTTACATGGGGCCTTTGCCTTATGGT
64 TGCCATGCCTTGGCATGGTCTTACATGGGGCCTTTGCCTTATGGT
* * * * *
27212 AACTTATCAATGCCATGTCTTGACATGGTCTTACGTGATTTCCTTTCCTTAGAAACCTTACCATG
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTAACCATG
*
27277 TCATGCCTTGGCATGGTCTTACATGG
66 CCATGCCTTGGCATGGTCTTACATGG
27303 TATCCTTAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 1 0.01
108 77 0.95
109 3 0.04
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (108 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTAACCATG
CCATGCCTTGGCATGGTCTTACATGGGGCCTTTGCCTTATGGT
Found at i:27262 original size:55 final size:52
Alignment explanation
Indices: 27058--27309 Score: 192
Period size: 53 Copynumber: 4.8 Consensus size: 52
27048 ACGCGGGTAC
* * * * * * *
27058 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGATTCTTT--TGA--AA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGTATCCTTTCCTTATGAA
* *
27106 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACAT-GTATCCTTTCCTTATGAA
** * * ***
27159 CCAACCAATGCCATGCCTTGGCATGGTCTTACATGGGGCCTTTGCCTTATGGTAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGTATCCTTT-CCTTAT-G-AA
* * *
27214 CTTATCAATGCCATGTCTTGACATGGTCTTACGTGATTTCCTTTCCTTA-GAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATG-TATCCTTTCCTTATG-AA
* * *
27267 CCTTACC-ATGTCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAATGCCATGTCTTGACATGGTCTTACAT-GTATCCTT
27310 AAACCCTAAT
Statistics
Matches: 161, Mismatches: 32, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
48 31 0.19
49 6 0.04
51 2 0.01
52 5 0.03
53 69 0.43
54 7 0.04
55 36 0.22
56 5 0.03
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.37
Consensus pattern (52 bp):
CTTACCAATGCCATGTCTTGACATGGTCTTACATGTATCCTTTCCTTATGAA
Found at i:34603 original size:39 final size:40
Alignment explanation
Indices: 34533--34701 Score: 287
Period size: 39 Copynumber: 4.4 Consensus size: 40
34523 TATGTGCATA
34533 GCATTCGTGC--GTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
34571 GCATTCGTGCGGGTTATTATAA-CGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
34610 GCA-TCGTG-GGGTTATTATAACCGGGTTAAGT-CCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
34647 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
34687 GCATTCGTGCTGGTT
1 GCATTCGTGCGGGTT
34702 GTTACATCCG
Statistics
Matches: 124, Mismatches: 1, Indels: 10
0.92 0.01 0.07
Matches are distributed among these distances:
37 21 0.17
38 30 0.24
39 43 0.35
40 30 0.24
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:34634 original size:77 final size:78
Alignment explanation
Indices: 34533--34695 Score: 287
Period size: 77 Copynumber: 2.1 Consensus size: 78
34523 TATGTGCATA
*
34533 GCATTCGT-GCGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAA-CGG
1 GCATTCGTGGGGTTATTATAACCGGGTTAAGT-CCGAAGGCATTCGTGCGGGTTATTATAACCGG
34596 GTTAAGTCCCGAAG
65 GTTAAGTCCCGAAG
34610 GCA-TCGTGGGGTTATTATAACCGGGTTAAGTCCGAAGGCATTCGTGCGGGTTATTATAACCGGG
1 GCATTCGTGGGGTTATTATAACCGGGTTAAGTCCGAAGGCATTCGTGCGGGTTATTATAACCGGG
34674 TTAAGTCCCGAAG
66 TTAAGTCCCGAAG
34687 GCATTCGTG
1 GCATTCGTG
34696 CTGGTTGTTA
Statistics
Matches: 82, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
76 32 0.39
77 45 0.55
78 5 0.06
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (78 bp):
GCATTCGTGGGGTTATTATAACCGGGTTAAGTCCGAAGGCATTCGTGCGGGTTATTATAACCGGG
TTAAGTCCCGAAG
Found at i:34725 original size:40 final size:40
Alignment explanation
Indices: 34565--34725 Score: 114
Period size: 40 Copynumber: 4.1 Consensus size: 40
34555 GGGTTAAGTC
* * ** * *
34565 CCGAAGGCATTCGTGCGGGTTATTATAA-CGGGTTAAGTC
1 CCGAAGGCATTCGTGCGGGTTATTACAACCGAGCCAAATT
* *** *
34604 CCGAAGGCA-TCGTG-GGGTTATTATAACCG-GGTTAAGT
1 CCGAAGGCATTCGTGCGGGTTATTACAACCGAGCCAAATT
* * ** * *
34641 CCGAAGGCATTCGTGCGGGTTATTATAACCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGGGTTATTACAACCGAGCCAAATT
* * *
34681 CCGAAGGCATTCGTGCTGGTTGTTACATCCGAGCCAAATT
1 CCGAAGGCATTCGTGCGGGTTATTACAACCGAGCCAAATT
34721 CCGAA
1 CCGAA
34726 AGTATTTATG
Statistics
Matches: 99, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
37 24 0.24
38 12 0.12
39 24 0.24
40 39 0.39
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGGGTTATTACAACCGAGCCAAATT
Found at i:43089 original size:39 final size:39
Alignment explanation
Indices: 43005--43173 Score: 272
Period size: 39 Copynumber: 4.4 Consensus size: 39
42995 TATGTGCATA
43005 GCATTCGTGCGGG-T-TTA-AACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGT-CCGAAG
* *
43042 GCATTCGTGCGGGTTATTATAATCGAGTTAAGTCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCGAAG
*
43081 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCAAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCGAAG
43120 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCGAAG
*
43159 GCATTCGTGCTGGTT
1 GCATTCGTGCGGGTT
43174 GTTACATCCG
Statistics
Matches: 122, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
37 13 0.11
38 1 0.01
39 97 0.80
40 11 0.09
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.29
Consensus pattern (39 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCGAAG
Done.