Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007518.1 Corchorus capsularis cultivar CVL-1 contig07539, 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: 42808
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3640 original size:31 final size:29
Alignment explanation
Indices: 3560--3658 Score: 110
Period size: 29 Copynumber: 3.3 Consensus size: 29
3550 TATTTCATTA
*
3560 AGGACGTTTTGTCCCCTGAACTTCAAATC
1 AGGACATTTTGTCCCCTGAACTTCAAATC
* * **
3589 AGGTCATCTTGTCCTTTGAACTTTCAAATCC
1 AGGACATTTTGTCCCCTGAAC-TTCAAAT-C
*
3620 AGGACCTTTTGTCCCCTGAACTTCAAATTC
1 AGGACATTTTGTCCCCTGAACTTCAAA-TC
3650 A-GACATTTT
1 AGGACATTTT
3659 ACCCCCTAAC
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
29 23 0.41
30 15 0.27
31 18 0.32
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.35
Consensus pattern (29 bp):
AGGACATTTTGTCCCCTGAACTTCAAATC
Found at i:6000 original size:31 final size:31
Alignment explanation
Indices: 5965--6027 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
5955 AATTTTATGT
*
5965 TTTCCGATTGTACCCTTATT-TTTAAAACATA
1 TTTCCAATTGTA-CCTTATTCTTTAAAACATA
*
5996 TTTCCAATTGTACCTTTTTCTTTAAAACATA
1 TTTCCAATTGTACCTTATTCTTTAAAACATA
6027 T
1 T
6028 CTCTAAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 6 0.21
31 23 0.79
ACGTcount: A:0.29, C:0.19, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCTTATTCTTTAAAACATA
Found at i:6163 original size:31 final size:31
Alignment explanation
Indices: 6128--6190 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
6118 AACTTTATGT
* *
6128 TTTCCGATTGTACCC-TTATTTTTAAAACATA
1 TTTCCAATTGTACCCATT-TCTTTAAAACATA
6159 TTTCCAATTGTACCCATTTCTTTAAAACATA
1 TTTCCAATTGTACCCATTTCTTTAAAACATA
6190 T
1 T
6191 CTCTAAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (31 bp):
TTTCCAATTGTACCCATTTCTTTAAAACATA
Found at i:6191 original size:163 final size:163
Alignment explanation
Indices: 5915--6252 Score: 615
Period size: 163 Copynumber: 2.1 Consensus size: 163
5905 ACCATCAAAC
* * *
5915 ATATTTATCTATACTATATATAAAAGTACGAATAAGGTGAAATTTTATGTTTTCCGATTGTACCC
1 ATATTAATCTATACTATATATAAAAGTACGAATAAGGGGAAACTTTATGTTTTCCGATTGTACCC
**
5980 TTATTTTTAAAACATATTTCCAATTGTACCTTTTTCTTTAAAACATATCTCTAAATTGCCATTAC
66 TTATTTTTAAAACATATTTCCAATTGTACCCATTTCTTTAAAACATATCTCTAAATTGCCATTAC
6045 TAAATAATATTTTAATTATTCCATTATTTTTTA
131 TAAATAATATTTTAATTATTCCATTATTTTTTA
6078 ATATTAATCTATACTATATATAAAAGTACGAATAAGGGGAAACTTTATGTTTTCCGATTGTACCC
1 ATATTAATCTATACTATATATAAAAGTACGAATAAGGGGAAACTTTATGTTTTCCGATTGTACCC
6143 TTATTTTTAAAACATATTTCCAATTGTACCCATTTCTTTAAAACATATCTCTAAATTGCCATTAC
66 TTATTTTTAAAACATATTTCCAATTGTACCCATTTCTTTAAAACATATCTCTAAATTGCCATTAC
*
6208 TAGATAATATTTTAATTATTCCATTATTTTTTA
131 TAAATAATATTTTAATTATTCCATTATTTTTTA
6241 ATATTAAT-TATA
1 ATATTAATCTATA
6253 TAATACGTGT
Statistics
Matches: 169, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
162 4 0.02
163 165 0.98
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.45
Consensus pattern (163 bp):
ATATTAATCTATACTATATATAAAAGTACGAATAAGGGGAAACTTTATGTTTTCCGATTGTACCC
TTATTTTTAAAACATATTTCCAATTGTACCCATTTCTTTAAAACATATCTCTAAATTGCCATTAC
TAAATAATATTTTAATTATTCCATTATTTTTTA
Found at i:6830 original size:24 final size:22
Alignment explanation
Indices: 6708--6869 Score: 116
Period size: 22 Copynumber: 7.3 Consensus size: 22
6698 TGTCTCTATG
* *
6708 TGGTTATCAAAATTTCATAAGA
1 TGGTTATTAAAATTTCATAGGA
* *
6730 TGGTTATTATAATTTCATGGGGA
1 TGGTTATTAAAATTTCAT-AGGA
* *
6753 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATTAAAATTTCATAG-GA
* **
6774 TGATTACCAAAATTTCATAGTG-
1 TGGTTATTAAAATTTCATAG-GA
*
6796 TGGTTACTAAAATTTCATAGGA
1 TGGTTATTAAAATTTCATAGGA
* *
6818 TCAGGTTATTAAAATCTCTTA-GA
1 T--GGTTATTAAAATTTCATAGGA
* *
6841 TTGGTTATTGAAATTTCATAGGG
1 -TGGTTATTAAAATTTCATAGGA
6864 TGGTTA
1 TGGTTA
6870 ATTATCACAA
Statistics
Matches: 112, Mismatches: 20, Indels: 16
0.76 0.14 0.11
Matches are distributed among these distances:
21 2 0.02
22 89 0.79
23 5 0.04
24 16 0.14
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAGGA
Found at i:6926 original size:22 final size:22
Alignment explanation
Indices: 6901--6963 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
6891 GGTTATCAAA
*
6901 GAGATTATCAAAATGTCATAGT
1 GAGATTATCAAAATTTCATAGT
6923 GAGATTAT-AAGAATTTCATAGT
1 GAGATTATCAA-AATTTCATAGT
* * *
6945 GTGGTTAACAAAATTTCAT
1 GAGATTATCAAAATTTCAT
6964 TAAATATTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (22 bp):
GAGATTATCAAAATTTCATAGT
Found at i:6951 original size:56 final size:56
Alignment explanation
Indices: 6891--7019 Score: 129
Period size: 56 Copynumber: 2.3 Consensus size: 56
6881 TTTATAGAAA
*
6891 GGTTATCAAAGAGATT-ATCAAA-ATGTCATAGTGAGATTAT-AAGAATTTCATAGTGT
1 GGTTATCAAA-A-ATTCATCAAATATGTCATAGGGAGATTATCAA-AATTTCATAGTGT
* * * * * * *
6947 GGTTAACAAAATTTCATTAAATATTTCATGGGGAGGTTATCAAAATTTTATAGTGT
1 GGTTATCAAAAATTCATCAAATATGTCATAGGGAGATTATCAAAATTTCATAGTGT
*
7003 GGTTATCAAAATTTCAT
1 GGTTATCAAAAATTCAT
7020 ATGAAGGTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
54 2 0.03
55 6 0.10
56 51 0.84
57 2 0.03
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (56 bp):
GGTTATCAAAAATTCATCAAATATGTCATAGGGAGATTATCAAAATTTCATAGTGT
Found at i:7028 original size:22 final size:21
Alignment explanation
Indices: 6980--7286 Score: 149
Period size: 22 Copynumber: 13.8 Consensus size: 21
6970 TTTCATGGGG
* *
6980 AGGTTATCAAAATTTTATAGTG
1 AGGTTATCAAAATTTCATAG-A
*
7002 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
* *
7024 AGGTTAT-AAAAGTCTCAATTTCATA
1 AGGTTATCAAAA-TTTC-A--T-AGA
* * *
7049 AGGAGTACCAAAATTTGATAGA
1 AGG-TTATCAAAATTTCATAGA
*
7071 AGGTTATC-AAATCTCATAG-
1 AGGTTATCAAAATTTCATAGA
*
7090 AGTGATTATCGAAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
7113 GATCGGATTATCAAAATTT-ATAGAA
1 -A--GG-TTATCAAAATTTCATAG-A
*
7138 AGATTATCAAAATTTCATAG-
1 AGGTTATCAAAATTTCATAGA
* * *
7158 TGTTGTTATCAAAATTTCAAAGTG
1 AG--GTTATCAAAATTTCATAG-A
*
7182 AGGTTATCAAAATTACATA-A
1 AGGTTATCAAAATTTCATAGA
* *
7202 TGTGATTATCAGAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
* * * * *
7225 GGGGTCAACAAAATTTTATAAA
1 -AGGTTATCAAAATTTCATAGA
*
7247 GAGGTTATCAAAATTTCATAAA
1 -AGGTTATCAAAATTTCATAGA
*
7269 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
7287 AAATGTGATT
Statistics
Matches: 221, Mismatches: 39, Indels: 50
0.71 0.13 0.16
Matches are distributed among these distances:
19 2 0.01
20 12 0.05
21 25 0.11
22 139 0.63
23 5 0.02
24 8 0.04
25 20 0.09
26 6 0.03
27 4 0.02
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:7211 original size:44 final size:44
Alignment explanation
Indices: 7074--7860 Score: 213
Period size: 44 Copynumber: 17.9 Consensus size: 44
7064 TGATAGAAGG
* * * *
7074 TTATC-AAATCTCATAGAGTGATTATCGAAATTTCATAGA-GATCGGA
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATA-ATG-T--GA
* * *
7120 TTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTTG-
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAATG-TGA
* * *
7163 TTATCAAAATTTCAAAGTGAGGTTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGTGA
* * * * * * * *
7207 TTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGTGA
* * *
7251 TTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGTGA
* * * * *
7295 TTA-CAAAAATTTCATAGTGGTCTTTCTGGGGAGGTTATCAAAATTCCATAGTATGG
1 TTATC-AAAATTTCATA------------GAGAGGTTATCAAAATTTCATAATGTGA
* * * * * *
7351 TTA-CCAAA-TT-A-GGA-AGGTTATTAAACTTTTATTATG-GA
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGTGA
* * **
7389 GTAATCAAAATTTCA-AG-GAGGGTATCAAAA-TTCAGGGA-GT-A
1 -TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCA-TAATGTGA
* *
7430 -TATCAAAATTTCACA-AGAGGGTTATCAAAATTACAT-A-GT-A
1 TTATCAAAATTTCATAGAGA-GGTTATCAAAATTTCATAATGTGA
* * * *
7470 TGTAGGTCAAAATTTCATAGGGAGATTAACAAAATTTCGTAGTATGT-A
1 T-TA--TCAAAATTTCATAGAGAGGTTATCAAAATTTCATA--ATGTGA
* * * * * *
7518 -GATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGG
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGTGA
* ** * *
7561 TTATAAAAAAAATCATAGGGAGGTTATCAAAATTT-GT-A---G-
1 TTAT-CAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGTGA
* * * *
7600 TTATCAAGATTTCATA-AGAATGTTATCAAAATTT--TATTGGGA
1 TTATCAAAATTTCATAGAG-AGGTTATCAAAATTTCATAATGTGA
* * * ****
7642 GGTTTATCAAAATTTTATAGAAAGATTTATCAAAATTTCATAGCAAGA
1 ---TTATCAAAATTTCATAGAGAG-GTTATCAAAATTTCATAATGTGA
* * * * * * *
7690 TTATCACAATTTCATAGTGTGATTATCAAAATTTTAGAGTGTGA
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGTGA
* * * * *
7734 TTA-CTAACAA-TTCATATG-GAGGTTTTTAAATTTTCATAACGTGG
1 TTATC-AA-AATTTCATA-GAGAGGTTATCAAAATTTCATAATGTGA
* * * * * * *
7778 TTATCAATATATCATATAGAGGTTATCAACATATCATAGTGTTGG
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAATG-TGA
* * * * *
7823 TCATTAAAATTTCATTGGGAAGTTATCAAAATTTCATA
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATA
7861 TTGAGGTCTT
Statistics
Matches: 540, Mismatches: 141, Indels: 121
0.67 0.18 0.15
Matches are distributed among these distances:
37 2 0.00
38 23 0.04
39 33 0.06
40 13 0.02
41 18 0.03
42 20 0.04
43 18 0.03
44 234 0.43
45 93 0.17
46 43 0.08
47 6 0.01
48 7 0.01
53 1 0.00
54 2 0.00
55 3 0.01
56 24 0.04
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (44 bp):
TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGTGA
Found at i:7422 original size:19 final size:20
Alignment explanation
Indices: 7392--7461 Score: 79
Period size: 19 Copynumber: 3.5 Consensus size: 20
7382 TTATGGAGTA
7392 ATCAAAATTTCAAGGAGGGT
1 ATCAAAATTTCAAGGAGGGT
* **
7412 ATCAAAA-TTCAGGGAGTAT
1 ATCAAAATTTCAAGGAGGGT
*
7431 ATCAAAATTTCACAAGAGGGTT
1 ATCAAAATTTCA-AGGAGGG-T
7453 ATCAAAATT
1 ATCAAAATT
7462 ACATAGTATG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 16 0.40
20 11 0.28
21 3 0.08
22 10 0.25
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGGT
Found at i:7436 original size:39 final size:40
Alignment explanation
Indices: 7386--7461 Score: 120
Period size: 39 Copynumber: 1.9 Consensus size: 40
7376 CTTTTATTAT
*
7386 GGAGTAATCAAAATTTCA-AGGAGGG-TATCAAAATTCAG
1 GGAGTAATCAAAATTTCACAAGAGGGTTATCAAAATTCAG
7424 GGAGTATATCAAAATTTCACAAGAGGGTTATCAAAATT
1 GGAGTA-ATCAAAATTTCACAAGAGGGTTATCAAAATT
7462 ACATAGTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
38 6 0.18
39 12 0.35
40 6 0.18
41 10 0.29
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (40 bp):
GGAGTAATCAAAATTTCACAAGAGGGTTATCAAAATTCAG
Found at i:7502 original size:22 final size:22
Alignment explanation
Indices: 7477--7595 Score: 91
Period size: 22 Copynumber: 5.4 Consensus size: 22
7467 GTATGTAGGT
7477 CAAAATTTCATAGGGAGATTAA
1 CAAAATTTCATAGGGAGATTAA
* *
7499 CAAAATTTCGTA--G-TATGTAGA
1 CAAAATTTCATAGGGAGAT-TA-A
7520 TCAAAATTTCATAGGGAGATTAA
1 -CAAAATTTCATAGGGAGATTAA
** *
7543 CAAAATTTCATAATGAGGTTATA
1 CAAAATTTCATAGGGAGATTA-A
* ** * *
7566 AAAAAAATCATAGGGAGGTTAT
1 CAAAATTTCATAGGGAGATTAA
7588 CAAAATTT
1 CAAAATTT
7596 GTAGTTATCA
Statistics
Matches: 74, Mismatches: 16, Indels: 14
0.71 0.15 0.13
Matches are distributed among these distances:
19 2 0.03
20 3 0.04
21 1 0.01
22 45 0.61
23 18 0.24
24 3 0.04
25 2 0.03
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (22 bp):
CAAAATTTCATAGGGAGATTAA
Found at i:7650 original size:23 final size:23
Alignment explanation
Indices: 7622--7725 Score: 95
Period size: 23 Copynumber: 4.6 Consensus size: 23
7612 CATAAGAATG
* ** *
7622 TTATCAAAATTTTATTGGGAGGT
1 TTATCAAAATTTTATAGAAAGAT
7645 TTATCAAAATTTTATAGAAAGAT
1 TTATCAAAATTTTATAGAAAGAT
* *
7668 TTATCAAAATTTCATAGCAAGA-
1 TTATCAAAATTTTATAGAAAGAT
* * ***
7690 TTATCACAATTTCATAGTGTGA-
1 TTATCAAAATTTTATAGAAAGAT
7712 TTATCAAAATTTTA
1 TTATCAAAATTTTA
7726 GAGTGTGATT
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
22 30 0.43
23 39 0.57
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGAAAGAT
Found at i:7700 original size:22 final size:23
Alignment explanation
Indices: 7600--7723 Score: 94
Period size: 22 Copynumber: 5.5 Consensus size: 23
7590 AAATTTGTAG
* *
7600 TTATCAAGATTTCATA-AGA-AT
1 TTATCAAAATTTCATAGAAAGAT
* * ** *
7621 GTTATCAAAATTTTATTGGGAGGT
1 -TTATCAAAATTTCATAGAAAGAT
*
7645 TTATCAAAATTTTATAGAAAGAT
1 TTATCAAAATTTCATAGAAAGAT
*
7668 TTATCAAAATTTCATAGCAAGA-
1 TTATCAAAATTTCATAGAAAGAT
* ***
7690 TTATCACAATTTCATAGTGTGA-
1 TTATCAAAATTTCATAGAAAGAT
7712 TTATCAAAATTT
1 TTATCAAAATTT
7724 TAGAGTGTGA
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
22 42 0.50
23 41 0.49
24 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTCATAGAAAGAT
Found at i:7730 original size:22 final size:22
Alignment explanation
Indices: 7668--7736 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
7658 ATAGAAAGAT
* ***
7668 TTATCAAAATTTCATAGCAAGA
1 TTATCAAAATTTCAGAGTGTGA
* *
7690 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
*
7712 TTATCAAAATTTTAGAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
7734 TTA
1 TTA
7737 CTAACAATTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTGA
Found at i:7969 original size:22 final size:22
Alignment explanation
Indices: 7938--7991 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
7928 AAGGTTCTCG
* * * *
7938 AAATTCCATAGTATCGTTATTA
1 AAATTTCATAGGAACGTTATCA
*
7960 AAATTTCATAGGAAGGTTATCA
1 AAATTTCATAGGAACGTTATCA
7982 AAATTTCATA
1 AAATTTCATA
7992 ATGGGATCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (22 bp):
AAATTTCATAGGAACGTTATCA
Found at i:30199 original size:23 final size:23
Alignment explanation
Indices: 30168--30224 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
30158 TTACTTGGCA
*
30168 CCCGACCACTTCCAAGTCT-AGCG
1 CCCGACCACTTCCAAGCCTGA-CG
*
30191 TCCGACCACTTCCAAGCCTGACG
1 CCCGACCACTTCCAAGCCTGACG
30214 CCCGACCACTT
1 CCCGACCACTT
30225 ACGACCATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.46, G:0.16, T:0.18
Consensus pattern (23 bp):
CCCGACCACTTCCAAGCCTGACG
Found at i:30357 original size:26 final size:27
Alignment explanation
Indices: 30313--30430 Score: 118
Period size: 26 Copynumber: 4.5 Consensus size: 27
30303 AGCTGGCACC
30313 CTACACGTGACCTCCAACGGACAACT-
1 CTACACGTGACCTCCAACGGACAACTA
* * * * *
30339 CTACACGTGATCTCTAACGTACGACTC
1 CTACACGTGACCTCCAACGGACAACTA
*
30366 CT-CACATGACCTCCAACGGACAACTA
1 CTACACGTGACCTCCAACGGACAACTA
* * *
30392 C-ACATGTGACCTCCAACGTACAAC-C
1 CTACACGTGACCTCCAACGGACAACTA
*
30417 CCACACGTGACCTC
1 CTACACGTGACCTC
30431 GCGCGTGCAA
Statistics
Matches: 74, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
25 1 0.01
26 71 0.96
27 2 0.03
ACGTcount: A:0.30, C:0.39, G:0.14, T:0.18
Consensus pattern (27 bp):
CTACACGTGACCTCCAACGGACAACTA
Found at i:30410 original size:52 final size:52
Alignment explanation
Indices: 30310--30430 Score: 145
Period size: 52 Copynumber: 2.3 Consensus size: 52
30300 GTCAGCTGGC
* * * * *
30310 ACCCTACACGTGACCTCCAACGGACAACTCTACACGTGATCTCTAACGTACG
1 ACCCCACACATGACCTCCAACGGACAACTCTACACGTGACCTCCAACGTACA
* * *
30362 ACTCCTCACATGACCTCCAACGGACAACTAC-ACATGTGACCTCCAACGTACA
1 ACCCCACACATGACCTCCAACGGACAACT-CTACACGTGACCTCCAACGTACA
*
30414 ACCCCACACGTGACCTC
1 ACCCCACACATGACCTC
30431 GCGCGTGCAA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
52 56 0.98
53 1 0.02
ACGTcount: A:0.30, C:0.40, G:0.13, T:0.17
Consensus pattern (52 bp):
ACCCCACACATGACCTCCAACGGACAACTCTACACGTGACCTCCAACGTACA
Found at i:39250 original size:42 final size:44
Alignment explanation
Indices: 39188--39270 Score: 143
Period size: 42 Copynumber: 1.9 Consensus size: 44
39178 AAGTTTGTTT
39188 TTTTTTGTTGTTTTTGTGAAAATATGAAAGATAAAGACTATTTG
1 TTTTTTGTTGTTTTTGTGAAAATATGAAAGATAAAGACTATTTG
*
39232 TTTTTT-TT-TTTTTGTGAAAATATGAAAGATAAAGGCTAT
1 TTTTTTGTTGTTTTTGTGAAAATATGAAAGATAAAGACTAT
39271 GAGGAAATTC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 30 0.79
43 2 0.05
44 6 0.16
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (44 bp):
TTTTTTGTTGTTTTTGTGAAAATATGAAAGATAAAGACTATTTG
Found at i:42340 original size:14 final size:15
Alignment explanation
Indices: 42321--42353 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
42311 AAAACTTACC
42321 TTCTTG-ACTTTGAA
1 TTCTTGTACTTTGAA
*
42335 TTCTTGTCCTTTGAA
1 TTCTTGTACTTTGAA
42350 TTCT
1 TTCT
42354 CCAACCAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.15, C:0.18, G:0.12, T:0.55
Consensus pattern (15 bp):
TTCTTGTACTTTGAA
Done.