Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3484
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: 35274
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:1079 original size:27 final size:26
Alignment explanation
Indices: 1048--1224 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 26
1038 TAAATTGTAC
1048 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
1075 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
*
1101 ATGCACTAAGTGTGCGAATTGACCATG-
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
1128 CGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
1156 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
1183 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
1210 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
1225 GGCTCATATA
Statistics
Matches: 129, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
25 1 0.01
26 14 0.11
27 97 0.75
28 17 0.13
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:1163 original size:81 final size:80
Alignment explanation
Indices: 1049--1203 Score: 222
Period size: 81 Copynumber: 1.9 Consensus size: 80
1039 AAATTGTACA
* *
1049 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
1113 TGCGAATTGACCATGC
65 TGCGAATTGACCATGC
* ** *
1129 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
1194 TGCGAGTTGA
65 TGCGAATTGA
1204 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
80 15 0.23
81 50 0.76
82 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (80 bp):
GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGC
Found at i:2927 original size:16 final size:17
Alignment explanation
Indices: 2906--2938 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2896 ATGATGGTGC
2906 ATGAAAT-ACTGATATA
1 ATGAAATGACTGATATA
*
2922 ATGAAATGATTGATATA
1 ATGAAATGACTGATATA
2939 TACTTATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.33
Consensus pattern (17 bp):
ATGAAATGACTGATATA
Found at i:9571 original size:14 final size:14
Alignment explanation
Indices: 9554--9590 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
9544 AACACTATCA
9554 AATTTTTCAAAAAT
1 AATTTTTCAAAAAT
*
9568 AATTTTTCTAAAAT
1 AATTTTTCAAAAAT
*
9582 ACTTTTTCA
1 AATTTTTCA
9591 CAACACTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.49
Consensus pattern (14 bp):
AATTTTTCAAAAAT
Found at i:9699 original size:20 final size:19
Alignment explanation
Indices: 9676--9721 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
9666 TTTTTAGGGC
*
9676 TTTTTAGAATTTTTATGAT
1 TTTTTAGAATTTTAATGAT
*
9695 ATTTTAGGAATTTTAATGAT
1 TTTTTA-GAATTTTAATGAT
9715 TTTTTAG
1 TTTTTAG
9722 TTTTTATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (19 bp):
TTTTTAGAATTTTAATGAT
Found at i:9850 original size:20 final size:19
Alignment explanation
Indices: 9807--9850 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
9797 AGTTTTCAAT
*
9807 TTTTTTAGATTTTTTTGGA
1 TTTTTTAGATTTCTTTGGA
* *
9826 ATTTTTATGATTTCTTTGTA
1 TTTTTTA-GATTTCTTTGGA
9846 TTTTT
1 TTTTT
9851 AATAATTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.16, C:0.02, G:0.11, T:0.70
Consensus pattern (19 bp):
TTTTTTAGATTTCTTTGGA
Found at i:12115 original size:24 final size:24
Alignment explanation
Indices: 12088--12185 Score: 69
Period size: 24 Copynumber: 4.2 Consensus size: 24
12078 CTACGAATTG
12088 TATTTATAGAAATGTCGCAAACTA
1 TATTTATAGAAATGTCGCAAACTA
* * * *
12112 TA-TTATAAAATATTTTGCGAACTA
1 TATTTATAGAA-ATGTCGCAAACTA
* *
12136 TATTTACAGAAATG-CTGCTAACTA
1 TATTTATAGAAATGTC-GCAAACTA
* * *
12160 TA-TTGTAG-AATGTCACAAACTG
1 TATTTATAGAAATGTCGCAAACTA
12182 TATT
1 TATT
12186 GTAGAATTAC
Statistics
Matches: 55, Mismatches: 14, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
22 11 0.20
23 13 0.24
24 25 0.45
25 6 0.11
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (24 bp):
TATTTATAGAAATGTCGCAAACTA
Found at i:12292 original size:23 final size:23
Alignment explanation
Indices: 12217--12299 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 23
12207 GAAATATTGT
* *
12217 GAATTGTGTTGTAGAATTACTAC
1 GAATTGTATTGTAGAATTACTGC
* * * * * * *
12240 AAACTGTATTTATAAAAATAATGT
1 GAATTGTA-TTGTAGAATTACTGC
12264 GAATTGTATTGTAGAATTACTGC
1 GAATTGTATTGTAGAATTACTGC
12287 GAATTGTATTGTA
1 GAATTGTATTGTA
12300 ATACATAAGA
Statistics
Matches: 43, Mismatches: 16, Indels: 2
0.70 0.26 0.03
Matches are distributed among these distances:
23 28 0.65
24 15 0.35
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.40
Consensus pattern (23 bp):
GAATTGTATTGTAGAATTACTGC
Found at i:12402 original size:54 final size:53
Alignment explanation
Indices: 12307--12675 Score: 272
Period size: 54 Copynumber: 6.8 Consensus size: 53
12297 GTAATACATA
* * * * * * *
12307 AGATTC-TAAAAATCTTGTATGCAAAAGATCCTGATCATAAATCAACGGACCGCG
1 AGATTCAT-AAAATC-TGTAAGTAAAAGGTCATGATCGTAAATCAGCGGACCGTG
** * * * *
12361 AGATTCATAAAATCATGTAAGTGGAAGGTCGTGATTGTAAATCAGCTGACCATG
1 AGATTCATAAAATC-TGTAAGTAAAAGGTCATGATCGTAAATCAGCGGACCGTG
* * ** ** * *
12415 AAATTCATAAAATCTGTAAGTAAAATGTCATGATTTTAAATCAGTTGACTGTA
1 AGATTCATAAAATCTGTAAGTAAAAGGTCATGATCGTAAATCAGCGGACCGTG
* * * * *
12468 AGATTCGTAAAATCTCTAAGTAAAAGGTCATGATCGTGAATCAGTGGACCGTA
1 AGATTCATAAAATCTGTAAGTAAAAGGTCATGATCGTAAATCAGCGGACCGTG
* ** * * * *
12521 AGATTCGTAAAATCTCGTAAGTAAAAGGTTGTGATCATAAATCAACGGACTGCG
1 AGATTCATAAAATCT-GTAAGTAAAAGGTCATGATCGTAAATCAGCGGACCGTG
* * * * * * *
12575 AGATTCGTTAAATCTCGCATGTAAAAAAGGTCATGATTGTAAATCAGTGGATCGTG
1 AGATTCATAAAATCT-GTAAGT--AAAAGGTCATGATCGTAAATCAGCGGACCGTG
* **
12631 AGATTCGTAAAATCCCATAAGTAAAAGGTCATGATCGTAAATCAG
1 AGATTCATAAAAT-CTGTAAGTAAAAGGTCATGATCGTAAATCAG
12676 TAGACCGTAA
Statistics
Matches: 250, Mismatches: 60, Indels: 10
0.78 0.19 0.03
Matches are distributed among these distances:
53 89 0.36
54 121 0.48
55 1 0.00
56 38 0.15
57 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (53 bp):
AGATTCATAAAATCTGTAAGTAAAAGGTCATGATCGTAAATCAGCGGACCGTG
Found at i:12456 original size:53 final size:52
Alignment explanation
Indices: 12361--12681 Score: 222
Period size: 53 Copynumber: 5.9 Consensus size: 52
12351 ACGGACCGCG
** *
12361 AGATTCATAAAATCATGTAAGTGGAAGGTCGTGATTGTAAATCAGCTGACCATGA
1 AGATTCATAAAATC-TGTAAGTAAAAGGTCATGATTGTAAATCAG-TGACC-TGA
* *
12416 A-ATTCATAAAATCTGTAAGTAAAATGTCATGATTTTAAATCAGTTGA-CTGTA
1 AGATTCATAAAATCTGTAAGTAAAAGGTCATGATTGTAAATCAG-TGACCTG-A
* * * *
12468 AGATTCGTAAAATCTCTAAGTAAAAGGTCATGATCGTGAATCAGTGGACC-GTA
1 AGATTCATAAAATCTGTAAGTAAAAGGTCATGATTGTAAATCAGT-GACCTG-A
* ** ** *
12521 AGATTCGTAAAATCTCGTAAGTAAAAGGTTGTGATCATAAATCAACG-GA-CTGCG
1 AGATTCATAAAATCT-GTAAGTAAAAGGTCATGATTGTAAATC-A-GTGACCTG-A
* * * * *
12575 AGATTCGTTAAATCTCGCATGTAAAAAAGGTCATGATTGTAAATCAGTGGATCGTG-
1 AGATTCATAAAATCT-GTAAGT--AAAAGGTCATGATTGTAAATCAGT-GA-CCTGA
* ** *
12631 AGATTCGTAAAATCCCATAAGTAAAAGGTCATGATCGTAAATCAGTAGACC
1 AGATTCATAAAAT-CTGTAAGTAAAAGGTCATGATTGTAAATCAGT-GACC
12682 GTAAGAAAGC
Statistics
Matches: 216, Mismatches: 35, Indels: 32
0.76 0.12 0.11
Matches are distributed among these distances:
51 2 0.01
52 4 0.02
53 86 0.40
54 83 0.38
55 3 0.01
56 35 0.16
57 1 0.00
58 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (52 bp):
AGATTCATAAAATCTGTAAGTAAAAGGTCATGATTGTAAATCAGTGACCTGA
Found at i:17715 original size:47 final size:47
Alignment explanation
Indices: 17606--17716 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
17596 TCGGGATAAG
*
17606 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
17653 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
17700 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
17717 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:18488 original size:4 final size:4
Alignment explanation
Indices: 18479--18535 Score: 114
Period size: 4 Copynumber: 14.2 Consensus size: 4
18469 CCCTTTTCTA
18479 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
18527 TTTC TTTC T
1 TTTC TTTC T
18536 CACGTTTGCT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:24978 original size:46 final size:45
Alignment explanation
Indices: 24872--24979 Score: 123
Period size: 46 Copynumber: 2.4 Consensus size: 45
24862 CCGGGATAAG
*
24872 CACATAGTGCTTCATCGGAAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAAAATCCGGAACTTTAACAGTATAGTA
* * *
24917 CACAAAGTACTTCATCGGAACAAATCC-GAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGG-A-AAATCCGGAACTTTAACAGTA-TAGTA
24963 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
24980 ACTCAATGTC
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
45 17 0.32
46 28 0.53
47 8 0.15
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (45 bp):
CACATAGTGCTTCATCGGAAAATCCGGAACTTTAACAGTATAGTA
Found at i:25749 original size:4 final size:4
Alignment explanation
Indices: 25740--25771 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
25730 CCCTTTTCTA
25740 TTTC TTTC TTTC TTTC -TTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
25772 CACGTTGCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:25759 original size:15 final size:15
Alignment explanation
Indices: 25741--25771 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
25731 CCTTTTCTAT
25741 TTCTTTCTTTCTTTC
1 TTCTTTCTTTCTTTC
25756 TTCTTTCTTTCTTTC
1 TTCTTTCTTTCTTTC
25771 T
1 T
25772 CACGTTGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TTCTTTCTTTCTTTC
Found at i:26120 original size:12 final size:14
Alignment explanation
Indices: 26103--26138 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
26093 ACTATAATTC
26103 ATAAATATTC-T-A
1 ATAAATATTCATGA
26115 ATAAATATTCATGA
1 ATAAATATTCATGA
26129 ATAAAT-TTCA
1 ATAAATATTCA
26139 CGGAAACAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.45
13 5 0.23
14 7 0.32
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (14 bp):
ATAAATATTCATGA
Found at i:32777 original size:26 final size:27
Alignment explanation
Indices: 32741--32834 Score: 95
Period size: 29 Copynumber: 3.4 Consensus size: 27
32731 ATTTGTAGAA
* *
32741 TTACCATCGATTTACAGAA-TACTGTT
1 TTACCCTCGATTTACAAAATTACTGTT
32767 TTACCCTCGA-TTACAAAATTACCAT-TT
1 TTACCCTCGATTTACAAAATTA-C-TGTT
* *
32794 TTACCCTCAGTTTTACAAAATTACCGTTT
1 TTACCCTC-GATTTACAAAATTACTG-TT
32823 TTACCCTCGATT
1 TTACCCTCGATT
32835 GTGTAAATTA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
25 7 0.12
26 11 0.20
27 11 0.20
28 6 0.11
29 21 0.38
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.39
Consensus pattern (27 bp):
TTACCCTCGATTTACAAAATTACTGTT
Found at i:32815 original size:29 final size:27
Alignment explanation
Indices: 32765--32834 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 27
32755 CAGAATACTG
32765 TTTTACCCTCGATTACAAAATTACCAT
1 TTTTACCCTCGATTACAAAATTACCAT
* *
32792 TTTTACCCTCAGTTTTACAAAATTACCGT
1 TTTTACCCTC-G-ATTACAAAATTACCAT
32821 TTTTACCCTCGATT
1 TTTTACCCTCGATT
32835 GTGTAAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 12 0.32
28 2 0.05
29 24 0.63
ACGTcount: A:0.27, C:0.26, G:0.06, T:0.41
Consensus pattern (27 bp):
TTTTACCCTCGATTACAAAATTACCAT
Found at i:32896 original size:26 final size:29
Alignment explanation
Indices: 32867--32990 Score: 95
Period size: 27 Copynumber: 4.6 Consensus size: 29
32857 GTAGGATTAG
32867 AATTACCAAAA-ACCCCTAGTTT-TT-AA
1 AATTACCAAAATACCCCTAGTTTGTTAAA
*
32893 AATT-CCAAAATACCCTTAGTTTGTTAAA
1 AATTACCAAAATACCCCTAGTTTGTTAAA
* * * * *
32921 AATTACCGAAATA-CCATTGTTTGCT-GA
1 AATTACCAAAATACCCCTAGTTTGTTAAA
* * *
32948 AATTATCGAAATA-CCCTCAATTTG-T-AA
1 AATTACCAAAATACCCCT-AGTTTGTTAAA
32975 AATTACCAAAATACCC
1 AATTACCAAAATACCC
32991 TAATTTACAA
Statistics
Matches: 79, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
25 6 0.08
26 14 0.18
27 31 0.39
28 21 0.27
29 7 0.09
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.31
Consensus pattern (29 bp):
AATTACCAAAATACCCCTAGTTTGTTAAA
Found at i:32977 original size:27 final size:26
Alignment explanation
Indices: 32947--33044 Score: 81
Period size: 27 Copynumber: 3.7 Consensus size: 26
32937 TTGTTTGCTG
*
32947 AAATTATCGAAATACCCTCAATTTGTA
1 AAATTATCGAAATACCCT-AATTTATA
* * *
32974 AAATTACCAAAATACCCTAATTTACA
1 AAATTATCGAAATACCCTAATTTATA
* * * *
33000 AAATTAACAGAAATACCTTGACTTTCTA
1 AAATTATC-GAAATACCCT-AATTTATA
*
33028 AAATT-TTGAAATACCCT
1 AAATTATCGAAATACCCT
33045 TGGTTTGTAG
Statistics
Matches: 56, Mismatches: 13, Indels: 5
0.76 0.18 0.07
Matches are distributed among these distances:
26 22 0.39
27 24 0.43
28 10 0.18
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (26 bp):
AAATTATCGAAATACCCTAATTTATA
Found at i:33144 original size:25 final size:27
Alignment explanation
Indices: 33110--33169 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 27
33100 TACATAGTAA
* *
33110 AAAAAGACCGTAA-GCCCCTGTA-GGT
1 AAAATGACCGTAATACCCCTGTATGGT
*
33135 AAAGTGACCGTAATACCCCTGTATGGT
1 AAAATGACCGTAATACCCCTGTATGGT
33162 AAAATGAC
1 AAAATGAC
33170 GAATATGCCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 11 0.38
26 8 0.28
27 10 0.34
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (27 bp):
AAAATGACCGTAATACCCCTGTATGGT
Found at i:34056 original size:25 final size:26
Alignment explanation
Indices: 33988--34056 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 26
33978 AAGTTGCTTA
33988 AAAAGGGCTTATGCCCCAG-TCTAGCG
1 AAAAGGGCTT-TGCCCCAGTTCTAGCG
* * *
34014 AAAA-GGTTTTG-CCCAGTTTTATC-
1 AAAAGGGCTTTGCCCCAGTTCTAGCG
34037 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
34057 AATTAAAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
23 9 0.25
24 12 0.33
25 11 0.31
26 4 0.11
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTTGCCCCAGTTCTAGCG
Found at i:34064 original size:24 final size:24
Alignment explanation
Indices: 33988--34084 Score: 65
Period size: 24 Copynumber: 4.0 Consensus size: 24
33978 AAGTTGCTTA
*
33988 AAAAGGGCTTATGCCCCAGTCT-AGC
1 AAAAGGGCTT-TGCCCCAGT-TAATC
* *
34013 GAAAA-GGTTTTG-CCCAGTTTTATC
1 -AAAAGGGCTTTGCCCCAG-TTAATC
*
34037 AAAAGGGCTTTGCCCCAGTTAATT
1 AAAAGGGCTTTGCCCCAGTTAATC
* **
34061 AAAAGAGCTAGGCCTCCAGTTAAT
1 AAAAGGGCTTTGCC-CCAGTTAAT
34085 ATGATAAAGC
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
23 10 0.17
24 26 0.45
25 18 0.31
26 4 0.07
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTAATC
Found at i:34327 original size:31 final size:31
Alignment explanation
Indices: 34292--34356 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
34282 GCTGTCGGCT
*
34292 AGTGAT-TGAT-TTATGGAAAAGGCTTTGGCCC
1 AGTGATATGATGTTAT-GAAAA-GCTTCGGCCC
34323 AGTGATATGATGTTATGAAAAGCTTCGGCCC
1 AGTGATATGATGTTATGAAAAGCTTCGGCCC
34354 AGT
1 AGT
34357 ATAGTCGCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 18 0.58
32 9 0.29
33 4 0.13
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (31 bp):
AGTGATATGATGTTATGAAAAGCTTCGGCCC
Done.