Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold758
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: 5854
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Found at i:700 original size:20 final size:20
Alignment explanation
Indices: 653--727 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
643 AAAAAAACAT
*
653 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
672 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
693 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
713 AATGTATCGATACAT
1 AATGTATCGATACAT
728 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:721 original size:40 final size:39
Alignment explanation
Indices: 650--727 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
640 GGTAAAAAAA
* *
650 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
689 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
728 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1357 original size:28 final size:28
Alignment explanation
Indices: 1238--2775 Score: 2256
Period size: 28 Copynumber: 55.3 Consensus size: 28
1228 ACAGTGGTGA
*
1238 TTTGAAAGG--GCCATTGACTTGCATGGGC
1 TTTGAAAGGATGCCACTGACTTG--TGGGC
* *
1266 TTTAAAAGGGTGCCACTGACTTGCGTGGGC
1 TTTGAAAGGATGCCACTGACTT--GTGGGC
* *
1296 TTTGAAAGAATGCCACT-ACTCGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
1323 TTTGAAAGGATGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
1351 TTTGAAA-GAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
*
1379 TTTGAAAAGGGTGCCACTGAC-TGTGGGC
1 TTTG-AAAGGATGCCACTGACTTGTGGGC
*
1407 TTTGAAA-GAGTGCCACTGAATTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
1435 -TTGAAAGG-TGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
1461 TTTGAAAGG--GCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
*
1487 TTTGAAAAGGGTGCCACTGACTTGTGGGC
1 TTTG-AAAGGATGCCACTGACTTGTGGGC
*
1516 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
*
1544 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
1572 TTTG-AA-GAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
* *
1599 TTTGAAAAGAGGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
1627 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
* *
1656 TTTGAAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
1684 TTTGAAA-GAGTGCCACTGA-TTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
1711 TTTGAAA-GAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
1739 TTTGAAAGG-TGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
1766 TTTGAAAGG-TGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
*
1793 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
*
1821 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
1849 TTTGAAA-GAGTGCCACTGA-TTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
*
1876 TTTGAAAAG-TGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
1903 TTTGAAA-GAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
*
1931 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
1959 TTTGAAAGG-TGCCACTGA-TTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
*
1985 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
2013 TTTGAAA-GAGTGCCACTGA-TTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
2040 TTTGAAA-GAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
*
2068 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
*
2096 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
2124 TTTGAAAGG-TGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
*
2151 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
*
2180 TTTGAAAAG-TGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
2207 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
*
2236 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
2264 TTTGAAA-GAGTGCCACTGA-TTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
2291 TTTGAAA-GAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
*
2319 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
*
2347 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
*
2375 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
*
2403 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
2431 TTTGAAA-GAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
2459 TTTGAAA-GAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
2487 TTTGAAA-GAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
2515 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
*
2544 TTTGAAAGGGTGCCACTGA-TTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
2571 TTTGAAAAGG-TGCCACTGACTTGTGGGC
1 TTTG-AAAGGATGCCACTGACTTGTGGGC
2599 TTTGAAA-GAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
2627 TTTGAAA-GAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
*
2655 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
2683 TTTGAAAGG-TGCCACTGACTTGTGGGC
1 TTTGAAAGGATGCCACTGACTTGTGGGC
*
2710 TTTGAAA-GAGTGCCACTGATTTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
2738 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGA-TGCCACTGACTTGTGGGC
2767 TTTGAAAGG
1 TTTGAAAGG
2776 GATGAACATT
Statistics
Matches: 1425, Mismatches: 34, Indels: 101
0.91 0.02 0.06
Matches are distributed among these distances:
26 69 0.05
27 368 0.26
28 774 0.54
29 183 0.13
30 30 0.02
32 1 0.00
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (28 bp):
TTTGAAAGGATGCCACTGACTTGTGGGC
Found at i:1404 original size:56 final size:56
Alignment explanation
Indices: 1238--2776 Score: 2577
Period size: 56 Copynumber: 27.7 Consensus size: 56
1228 ACAGTGGTGA
* *
1238 TTTGAAAG-G-GCCATTGACTTGCATGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGC
1 TTTGAAAGAGTGCCACTGACTTG--TGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGC
* * *
1296 TTTGAAAGAATGCCACT-ACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1351 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGAC-TGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC
*
1407 TTTGAAAGAGTGCCACTGAATTGTGGGC-TTGAAA-GGTGCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1461 TTTGAAAG-G-GCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC
*
1516 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
*
1572 TTTG-AAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAG-GCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC
*
1627 TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
*
1684 TTTGAAAGAGTGCCACTGA-TTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1739 TTTGAAAG-GTGCCACTGACTTGTGGGCTTTGAAA-GGTGCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
*
1793 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
*
1849 TTTGAAAGAGTGCCACTGA-TTGTGGGCTTTGAAA-AGTGCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1903 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1959 TTTGAAAG-GTGCCACTGA-TTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
*
2013 TTTGAAAGAGTGCCACTGA-TTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
*
2068 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
*
2124 TTTGAAAG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC
2180 TTTGAAA-AGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGC
* *
2236 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGA-TTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
2291 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
*
2347 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* *
2403 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
*
2459 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
2515 TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA-TTGTGGGC
1 TTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
*
2571 TTTGAAA-AGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGA-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
2627 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* *
2683 TTTGAAAG-GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
2738 TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGG
1 TTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAGGG
2777 ATGAACATTC
Statistics
Matches: 1411, Mismatches: 38, Indels: 65
0.93 0.03 0.04
Matches are distributed among these distances:
52 16 0.01
53 16 0.01
54 141 0.10
55 455 0.32
56 562 0.40
57 204 0.14
58 8 0.01
59 4 0.00
60 5 0.00
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (56 bp):
TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
Found at i:1549 original size:83 final size:84
Alignment explanation
Indices: 1238--2776 Score: 2557
Period size: 84 Copynumber: 18.5 Consensus size: 84
1228 ACAGTGGTGA
* *
1238 TTTGAAA-GG-GCCATTGACTTGCATGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGA
1 TTTGAAAGGGTGCCACTGACTTG--TGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGA
* *
1301 AAGAATGCCACT-ACTCGTGGGC
62 AAGAGTGCCACTGACTTGTGGGC
* *
1323 TTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAG
*
1388 GGTGCCACTGAC-TGTGGGC
65 AGTGCCACTGACTTGTGGGC
* *
1407 TTTGAAAGAGTGCCACTGAATTGTGGGC-TTGAAA-GGTGCCACTGACTTGTGGGCTTTGAAAG-
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGA
1469 G-GCCACTGACTTGTGGGC
66 GTGCCACTGACTTGTGGGC
1487 TTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
*
1552 GGTGCCACTGACTTGTGGGC
65 AGTGCCACTGACTTGTGGGC
* *
1572 TTTG-AAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAG-GCCACTGACTTGTGGGCTTTGAAAG
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAA-
1635 GAGTGCCACTGACTTGTGGGC
64 GAGTGCCACTGACTTGTGGGC
* *
1656 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGAGTGCCACTGA-TTGTGGGCTTTGAAAGA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGA
1720 GTGCCACTGACTTGTGGGC
66 GTGCCACTGACTTGTGGGC
*
1739 TTTGAAA-GGTGCCACTGACTTGTGGGCTTTGAAA-GGTGCCACTGACTTGTGGGCTTTGAAAGG
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGA
1802 GTGCCACTGACTTGTGGGC
66 GTGCCACTGACTTGTGGGC
*
1821 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGA-TTGTGGGCTTTGAAA-A
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGA
1884 GTGCCACTGACTTGTGGGC
66 GTGCCACTGACTTGTGGGC
*
1903 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG-
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGA
1967 GTGCCACTGA-TTGTGGGC
66 GTGCCACTGACTTGTGGGC
*
1985 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGA-TTGTGGGCTTTGAAAGA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGA
2049 GTGCCACTGACTTGTGGGC
66 GTGCCACTGACTTGTGGGC
2068 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG-
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGA
2132 GTGCCACTGACTTGTGGGC
66 GTGCCACTGACTTGTGGGC
* *
2151 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA-AGTGCCACTGACTTGTGGGCTTTGAAAG
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA-
2215 GAGTGCCACTGACTTGTGGGC
64 GAGTGCCACTGACTTGTGGGC
*
2236 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGA-TTGTGGGCTTTGAAAGA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGA
2300 GTGCCACTGACTTGTGGGC
66 GTGCCACTGACTTGTGGGC
*
2319 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGA
2384 GTGCCACTGACTTGTGGGC
66 GTGCCACTGACTTGTGGGC
*
2403 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGA
2468 GTGCCACTGACTTGTGGGC
66 GTGCCACTGACTTGTGGGC
*
2487 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAG
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAG
*
2552 GGTGCCACTGA-TTGTGGGC
65 AGTGCCACTGACTTGTGGGC
* *
2571 TTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGA
2636 GTGCCACTGACTTGTGGGC
66 GTGCCACTGACTTGTGGGC
2655 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA-GGTGCCACTGACTTGTGGGCTTTGAAAGA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGA
*
2719 GTGCCACTGATTTGTGGGC
66 GTGCCACTGACTTGTGGGC
2738 TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGG
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGG
2777 ATGAACATTC
Statistics
Matches: 1378, Mismatches: 45, Indels: 62
0.93 0.03 0.04
Matches are distributed among these distances:
79 9 0.01
80 12 0.01
81 52 0.04
82 224 0.16
83 451 0.33
84 457 0.33
85 161 0.12
86 1 0.00
87 11 0.01
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (84 bp):
TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGA
GTGCCACTGACTTGTGGGC
Found at i:4009 original size:1 final size:1
Alignment explanation
Indices: 4005--4055 Score: 57
Period size: 1 Copynumber: 51.0 Consensus size: 1
3995 TTTTTTGCTA
* * * * *
4005 TTTTTTCTTTTTTTTTGTTTTTTGTTTTGTTTTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4056 GGGTGTAAAG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (1 bp):
T
Found at i:4020 original size:12 final size:12
Alignment explanation
Indices: 4012--4055 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
4002 CTATTTTTTC
4012 TTTTTTTTTGTT
1 TTTTTTTTTGTT
*
4024 TTTTGTTTTGTT
1 TTTTTTTTTGTT
4036 TTTTTTTTTGTT
1 TTTTTTTTTGTT
4048 TTTTTTTT
1 TTTTTTTT
4056 GGGTGTAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:4025 original size:17 final size:16
Alignment explanation
Indices: 4005--4055 Score: 75
Period size: 17 Copynumber: 3.1 Consensus size: 16
3995 TTTTTTGCTA
*
4005 TTTTTTCTTTTTTTTT
1 TTTTTTGTTTTTTTTT
4021 GTTTTTTGTTTTGTTTTT
1 -TTTTTTGTTTT-TTTTT
4039 TTTTTTGTTTTTTTTT
1 TTTTTTGTTTTTTTTT
4055 T
1 T
4056 GGGTGTAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
16 6 0.19
17 21 0.66
18 5 0.16
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (16 bp):
TTTTTTGTTTTTTTTT
Done.