Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold494
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: 28234
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:888 original size:27 final size:27
Alignment explanation
Indices: 832--980 Score: 147
Period size: 27 Copynumber: 5.5 Consensus size: 27
822 ATTGTACAGC
*** *
832 CACTAAGTGTGCGAAAGGAATATG-ATG
1 CACTAAGTGTGCGATTTGACTATGTA-G
* * **
859 CACTAAGTGTGCGAATTGACCATGCGG
1 CACTAAGTGTGCGATTTGACTATGTAG
886 CACTAAGTGTGCGAGTTTGACTATGTAG
1 CACTAAGTGTGCGA-TTTGACTATGTAG
* *
914 CACTAAGTGTGCGATTTGATTACGTAG
1 CACTAAGTGTGCGATTTGACTATGTAG
* * *
941 CACTAAGTGTGCGAGTTGATTATATAG
1 CACTAAGTGTGCGATTTGACTATGTAG
*
968 CACTGAGTGTGCG
1 CACTAAGTGTGCG
981 GACTAATATA
Statistics
Matches: 105, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
27 82 0.78
28 23 0.22
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (27 bp):
CACTAAGTGTGCGATTTGACTATGTAG
Found at i:926 original size:55 final size:54
Alignment explanation
Indices: 832--980 Score: 156
Period size: 55 Copynumber: 2.7 Consensus size: 54
822 ATTGTACAGC
*** * * *
832 CACTAAGTGTGCGAAAGGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCGG
1 CACTAAGTGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCAG
* * ** *
886 CACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAG
1 CACTAAGTGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCAG
* *
941 CACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 CACTAAGTGTGCGAGTTGACTATATAGCACTAAGTGTGCG
981 GACTAATATA
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (54 bp):
CACTAAGTGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCAG
Found at i:8868 original size:27 final size:27
Alignment explanation
Indices: 8837--8987 Score: 187
Period size: 27 Copynumber: 5.6 Consensus size: 27
8827 TAAATTGTAC
8837 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
8864 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
8890 ATGCACTAAGTGTGCGAGTTTGACTATGT
1 A-GCACTAAGTGTGCGA-TTTGACTATGT
* *
8919 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
8946 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
8973 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
8988 GACTCAATAT
Statistics
Matches: 107, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
27 84 0.79
28 22 0.21
29 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:8924 original size:55 final size:55
Alignment explanation
Indices: 8837--8987 Score: 200
Period size: 55 Copynumber: 2.8 Consensus size: 55
8827 TAAATTGTAC
* *
8837 AGCACTAAGTGTGCGA-TTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGT
** *
8890 ATGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGT
1 A-GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGT
* * *
8946 AGCACTAAGTGTGCGAG-TTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCG
8988 GACTCAATAT
Statistics
Matches: 87, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
53 1 0.01
54 37 0.43
55 48 0.55
56 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGT
Found at i:8978 original size:82 final size:82
Alignment explanation
Indices: 8837--8987 Score: 223
Period size: 82 Copynumber: 1.8 Consensus size: 82
8827 TAAATTGTAC
* *
8837 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTG
1 AGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTG
8902 TGCGAGTTTGACTATGT
66 TGCGAGTTTGACTATGT
* ** * *
8919 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATTAT-ATAGCACTGAGT
1 AGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGT
8983 GTGCG
65 GTGCG
8988 GACTCAATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
81 2 0.03
82 59 0.97
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (82 bp):
AGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTG
TGCGAGTTTGACTATGT
Found at i:13467 original size:25 final size:24
Alignment explanation
Indices: 13439--13543 Score: 72
Period size: 25 Copynumber: 4.2 Consensus size: 24
13429 AAGCTCTTTC
**
13439 GAGCCATATAATAGGAAGCTCATGT
1 GAGCCATATAAT-GGAAGCTCATAA
* *
13464 GAGCCATGTAACGGGAAGCTCATAA
1 GAGCCATATAA-TGGAAGCTCATAA
13489 GAGCCATA-AATGAGAAGCTCA-AGA
1 GAGCCATATAATG-GAAGCTCATA-A
* * *
13513 GAGTCAAAT-ATCGGGAAGCTCATAC
1 GAGCCATATAAT--GGAAGCTCATAA
13538 GAGCCA
1 GAGCCA
13544 ATATCGGGAA
Statistics
Matches: 63, Mismatches: 10, Indels: 14
0.72 0.11 0.16
Matches are distributed among these distances:
23 2 0.03
24 19 0.30
25 40 0.63
26 2 0.03
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (24 bp):
GAGCCATATAATGGAAGCTCATAA
Found at i:13509 original size:49 final size:50
Alignment explanation
Indices: 13418--13568 Score: 139
Period size: 49 Copynumber: 3.1 Consensus size: 50
13408 CTCATACAAG
* * * * *
13418 CATGTAACGTGAAGCTCTTTCGAGCCATATAATAGGAAGCTCATGTGAGC
1 CATGTAACGGGAAGCTCATACGAGCCATATAATAGGAAGCTCAAGAGAGC
* *
13468 CATGTAACGGGAAGCTCATAAGAGCCATA-AAT-GAGAAGCTCAAGAGAGT
1 CATGTAACGGGAAGCTCATACGAGCCATATAATAG-GAAGCTCAAGAGAGC
** * * **
13517 CAAATATCGGGAAGCTCATACGAGCCA-AT-ATCGGGAAGCTCCGGAGAGC
1 CATGTAACGGGAAGCTCATACGAGCCATATAAT-AGGAAGCTCAAGAGAGC
13566 CAT
1 CAT
13569 TAATCAGAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 9
0.77 0.14 0.08
Matches are distributed among these distances:
48 4 0.05
49 52 0.63
50 26 0.32
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (50 bp):
CATGTAACGGGAAGCTCATACGAGCCATATAATAGGAAGCTCAAGAGAGC
Found at i:13531 original size:74 final size:74
Alignment explanation
Indices: 13452--13642 Score: 222
Period size: 74 Copynumber: 2.6 Consensus size: 74
13442 CCATATAATA
* * * * *
13452 GGAAGCTCATGTGAGCCATGTAACGGGAAGCTCATAAGAGCCATAAATGAG-AAGCTCAAGAGAG
1 GGAAGCTCATGCGAGCCA-ATAACGGGAAGCTCATGAGAGCCATAAATCAGAAAGCTCAAGAAAG
*
13516 TCAAATATCG
65 CCAAATATCG
* * ** * *
13526 GGAAGCTCATACGAGCCAATATCGGGAAGCTCCGGAGAGCCATTAATCAGAAAGCTCATGAAAGC
1 GGAAGCTCATGCGAGCCAATAACGGGAAGCTCATGAGAGCCATAAATCAGAAAGCTCAAGAAAGC
*
13591 CAATTATCG
66 CAAATATCG
* *
13600 GGAAGCTCGTGGGAGCCAAATAACGGGAAGCTCATGAGAGCCA
1 GGAAGCTCATGCGAGCC-AATAACGGGAAGCTCATGAGAGCCA
13643 AATATCGGGA
Statistics
Matches: 96, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
73 25 0.26
74 49 0.51
75 22 0.23
ACGTcount: A:0.36, C:0.20, G:0.28, T:0.16
Consensus pattern (74 bp):
GGAAGCTCATGCGAGCCAATAACGGGAAGCTCATGAGAGCCATAAATCAGAAAGCTCAAGAAAGC
CAAATATCG
Found at i:13605 original size:25 final size:25
Alignment explanation
Indices: 13452--13664 Score: 168
Period size: 25 Copynumber: 8.6 Consensus size: 25
13442 CCATATAATA
* *
13452 GGAAGCTCATGTGAGCC-ATGTAACG
1 GGAAGCTCATGAGAGCCAAT-TATCG
* *
13477 GGAAGCTCATAAGAGCC-ATAAAT-G
1 GGAAGCTCATGAGAGCCAAT-TATCG
* * * *
13501 AGAAGCTCAAGAGAGTCAAATATCG
1 GGAAGCTCATGAGAGCCAATTATCG
13526 GGAAGCTCAT-ACGAGCCAA-TATCG
1 GGAAGCTCATGA-GAGCCAATTATCG
** *
13550 GGAAGCTCCGGAGAGCC-ATTAATCA
1 GGAAGCTCATGAGAGCCAATT-ATCG
* *
13575 GAAAGCTCATGAAAGCCAATTATCG
1 GGAAGCTCATGAGAGCCAATTATCG
* * * *
13600 GGAAGCTCGTGGGAGCCAAATAACG
1 GGAAGCTCATGAGAGCCAATTATCG
*
13625 GGAAGCTCATGAGAGCCAAATATCG
1 GGAAGCTCATGAGAGCCAATTATCG
* *
13650 GGACGCTCATAAGAG
1 GGAAGCTCATGAGAG
13665 TTGTGGTGTG
Statistics
Matches: 148, Mismatches: 33, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
23 1 0.01
24 36 0.24
25 108 0.73
26 3 0.02
ACGTcount: A:0.36, C:0.20, G:0.28, T:0.16
Consensus pattern (25 bp):
GGAAGCTCATGAGAGCCAATTATCG
Found at i:14570 original size:17 final size:14
Alignment explanation
Indices: 14534--14563 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
14524 TATTATTTAA
14534 TTTA-TTTATCATC
1 TTTATTTTATCATC
14547 TTTATTTTATCATC
1 TTTATTTTATCATC
14561 TTT
1 TTT
14564 CCAATTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTTTATCATC
Found at i:17418 original size:29 final size:29
Alignment explanation
Indices: 17355--17422 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
17345 TAATCAACCA
17355 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
17384 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
17413 CGCACACTTA
1 CGCACACTTA
17423 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:17554 original size:174 final size:174
Alignment explanation
Indices: 17244--17571 Score: 550
Period size: 173 Copynumber: 1.9 Consensus size: 174
17234 AACTCAAGGT
* * *
17244 ACTTACCTTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCGTTCATGTAAATAATTTAT
1 ACTTACCTTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
* *
17309 AGAAAATATATATTGGGTTGCACACATAACGTTTAGTAATCAACCACGCACACTTAGTGCCATGC
66 AGAAAATATATATTGGGTTGCACACATAACGCTTAATAATCAACCACGCACACTTAGTGCCATGC
17374 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
17418 ACTTACC-TTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
1 ACTTACCTTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
** *
17482 AGAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATG
66 AGAAAATATATATTGGGTT-GCACACATAACGCTTAATAATCAACCACGCACACTTAGTGCCATG
* *
17547 TACTTTAAACTCGCACACTTAGTGC
130 CACTTTAAACTCACACACTTAGTGC
17572 TGTACAATTT
Statistics
Matches: 143, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
173 73 0.51
174 70 0.49
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
AGAAAATATATATTGGGTTGCACACATAACGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:17563 original size:29 final size:30
Alignment explanation
Indices: 17524--17602 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
17514 CTTAATAATC
17524 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
17554 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
17583 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
17603 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:17593 original size:174 final size:174
Alignment explanation
Indices: 17244--17596 Score: 530
Period size: 174 Copynumber: 2.0 Consensus size: 174
17234 AACTCAAGGT
* * *
17244 ACTTACCTTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCGTTCATGTAAATAATTTAT
1 ACTTACCTTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
* *
17309 AGAAAATATATATTGGGTTGCACACATAACGTTTAGTAATCAACCACGCACACTTAGTGCCATGC
66 AGAAAATATATATTGGGTTGCACACATAACGCTTAATAATCAACCACGCACACTTAGTGCCATGC
* ***
17374 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATACATTTCAAACCCGCAC
17418 ACTTACC-TTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
1 ACTTACCTTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
** *
17482 AGAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATG
66 AGAAAATATATATTGGGTT-GCACACATAACGCTTAATAATCAACCACGCACACTTAGTGCCATG
* * **
17547 TACTTTAAACTCGCACACTTAGTGCTGTACAATTT-AAACCCGCAC
130 CACTTTAAACTCACACACTTAGTGCCATAC-ATTTCAAACCCGCAC
17592 ACTTA
1 ACTTA
17597 GTGCCAATCT
Statistics
Matches: 161, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
173 73 0.45
174 84 0.52
175 4 0.02
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
AGAAAATATATATTGGGTTGCACACATAACGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATACATTTCAAACCCGCAC
Found at i:23150 original size:45 final size:44
Alignment explanation
Indices: 23086--23244 Score: 169
Period size: 45 Copynumber: 3.5 Consensus size: 44
23076 ATGCCTACAG
*
23086 ATGAGTAAGACCATAGTTGAAAGACGCTATGACATCACGCTATAA
1 ATGAGTAAGACCATAGTTGAAAGACGCTATGACATCAAG-TATAA
* ** * *
23131 ATGAGTAAGACCATAGTTGAAAGATGCTACAACGTCATGATATAA
1 ATGAGTAAGACCATAGTTGAAAGACGCTATGACATCAAG-TATAA
* * *
23176 ATGAGTAAAACCATAGCTGAAAGACG-TCATGACATCAAG-GTAA
1 ATGAGTAAGACCATAGTTGAAAGACGCT-ATGACATCAAGTATAA
*
23219 ATGGGACTAAGACCATAGTTGAAAGA
1 AT--GAGTAAGACCATAGTTGAAAGA
23245 AGATATGGCT
Statistics
Matches: 94, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
43 5 0.05
44 1 0.01
45 88 0.94
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.21
Consensus pattern (44 bp):
ATGAGTAAGACCATAGTTGAAAGACGCTATGACATCAAGTATAA
Found at i:23784 original size:325 final size:325
Alignment explanation
Indices: 23194--23847 Score: 1227
Period size: 325 Copynumber: 2.0 Consensus size: 325
23184 AACCATAGCT
23194 GAAAGACGTCATGACATCAAGGTAAATGGGACTAAGACCATAGTTGAAAGAAGATATGGCTTCCT
1 GAAAGACGTCATGACATCAAGGTAAATGGGACTAAGACCATAGTTGAAAGAAGATATGGCTTCCT
* * *
23259 AGTAGTCTACCGTGATAGTAAACATGGGAAATATAATGTGTAAAACCATATTTGGGATATGGCAA
66 AGTAGTCTACCGTAATAGTAAACATGGGAAATATAAGGTGTAAAACCATATTTAGGATATGGCAA
*
23324 CTCAAGTAGTCTAATGGGATGTTAAAAATAGATAGCCTTTCAAGATGATAAAAATGGAAAGTCCG
131 CTCAAGTAGTCTAATGGGATGTTAAAAATAGATAGCCTTTCAAGACGATAAAAATGGAAAGTCCG
*
23389 ATGGGACATTAAAGACGGGGTCATCTGCTAGGATGTTAAACATGGGGACTAGGGTGTATTAAGTT
196 ATGGGACATTAAAGACGGGGTCATCTGCTAGGATGTTAAACATAGGGACTAGGGTGTATTAAGTT
23454 AAAGTTTGGCTATGGAAATGAGTAGAAGTCCTTTAGGAAAAGGAACCTAGAAACTACCAGAATGA
261 AAAGTTTGGCTATGGAAATGAGTAGAAGTCCTTTAGGAAAAGGAACCTAGAAACTACCAGAATGA
23519 GAAAGACGTCATGACATCAAGGTAAATGGGACTAAGACCATAGTTGAAAGAAGATATGGCTTCCT
1 GAAAGACGTCATGACATCAAGGTAAATGGGACTAAGACCATAGTTGAAAGAAGATATGGCTTCCT
23584 AGTAGTCTACCGTAATAGTAAACATGGGAAATATAAGGTGTAAAACCATATTTAGGATATGGCAA
66 AGTAGTCTACCGTAATAGTAAACATGGGAAATATAAGGTGTAAAACCATATTTAGGATATGGCAA
* *
23649 CTCAAGTAGTCTGATGGGATGTTAAAAATAGATAGCCTTTCAAGACGATAAAAATGGGAAGTCCG
131 CTCAAGTAGTCTAATGGGATGTTAAAAATAGATAGCCTTTCAAGACGATAAAAATGGAAAGTCCG
* *
23714 ATGGGACATTAAAGACGGGGTCATCTGCTAGGATGTTAAATATAGGGACTGGGGTGTATTAAGTT
196 ATGGGACATTAAAGACGGGGTCATCTGCTAGGATGTTAAACATAGGGACTAGGGTGTATTAAGTT
23779 AAAGTTTGGCTATGGAAATGAGTAGAAGTCCTTTAGGAAAAGGAACCTAGAAACTACCAGAATGA
261 AAAGTTTGGCTATGGAAATGAGTAGAAGTCCTTTAGGAAAAGGAACCTAGAAACTACCAGAATGA
23844 GAAA
1 GAAA
23848 AGAGAATTTG
Statistics
Matches: 320, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
325 320 1.00
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (325 bp):
GAAAGACGTCATGACATCAAGGTAAATGGGACTAAGACCATAGTTGAAAGAAGATATGGCTTCCT
AGTAGTCTACCGTAATAGTAAACATGGGAAATATAAGGTGTAAAACCATATTTAGGATATGGCAA
CTCAAGTAGTCTAATGGGATGTTAAAAATAGATAGCCTTTCAAGACGATAAAAATGGAAAGTCCG
ATGGGACATTAAAGACGGGGTCATCTGCTAGGATGTTAAACATAGGGACTAGGGTGTATTAAGTT
AAAGTTTGGCTATGGAAATGAGTAGAAGTCCTTTAGGAAAAGGAACCTAGAAACTACCAGAATGA
Found at i:25968 original size:26 final size:27
Alignment explanation
Indices: 25893--25975 Score: 93
Period size: 26 Copynumber: 3.2 Consensus size: 27
25883 TTTCTTATTC
* *
25893 CAATTTTA-CTCTAGTAAAATTT-TGA
1 CAATTTTACCCCTAGTAAAATTTGAGA
* *
25918 CAATTTTACCCATAGTAAAA-ATGAGA
1 CAATTTTACCCCTAGTAAAATTTGAGA
25944 CAATTTTACCCCT-GTAAAATTTGAGA
1 CAATTTTACCCCTAGTAAAATTTGAGA
*
25970 AAATTT
1 CAATTT
25976 GTTCAATATA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
25 15 0.31
26 33 0.69
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (27 bp):
CAATTTTACCCCTAGTAAAATTTGAGA
Found at i:26528 original size:15 final size:16
Alignment explanation
Indices: 26508--26537 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26498 TGGTGCCTTG
26508 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
26523 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
26538 AGCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Done.