Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2631
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: 14021
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Found at i:563 original size:16 final size:15
Alignment explanation
Indices: 541--589 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
531 TAATGATGTG
541 AATA-AAAATA-TATA
1 AATATAAAATATTA-A
555 AATATAAAATATTAA
1 AATATAAAATATTAA
*
570 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
586 AATA
1 AATA
590 ATAATTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 4 0.13
15 12 0.39
16 15 0.48
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:579 original size:8 final size:7
Alignment explanation
Indices: 541--582 Score: 50
Period size: 8 Copynumber: 5.7 Consensus size: 7
531 TAATGATGTG
541 AATA-AA
1 AATATAA
547 AATATATA
1 AATATA-A
555 AATATAA
1 AATATAA
562 AATATTAA
1 AATA-TAA
570 AATATCAA
1 AATAT-AA
578 AATAT
1 AATAT
583 TAGAATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 4 0.12
7 7 0.22
8 21 0.66
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (7 bp):
AATATAA
Found at i:821 original size:27 final size:26
Alignment explanation
Indices: 791--853 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
781 TAGTTAAGAT
791 ATATACATAAGATAACATGTAAAAAAA
1 ATATACATAAGATAACAT-TAAAAAAA
* * * * *
818 ATATAAATAATATAATATTAAAGATA
1 ATATACATAAGATAACATTAAAAAAA
844 ATATACATAA
1 ATATACATAA
854 AATAGTATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 15 0.50
27 15 0.50
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (26 bp):
ATATACATAAGATAACATTAAAAAAA
Found at i:872 original size:25 final size:24
Alignment explanation
Indices: 737--873 Score: 91
Period size: 25 Copynumber: 5.5 Consensus size: 24
727 GTGATAATAT
* *
737 TAAAAATATGTACATAATATAGTGT
1 TAAAAATATATACATAATATAGT-A
*
762 TAAAAATACATACATAATATAGT-
1 TAAAAATATATACATAATATAGTA
* *
785 T-AAGATATATACATAAGATAACATGTA
1 TAAAAATATATACAT-A-AT-ATA-GTA
* * *
812 -AAAAAAATATAAATAATATAATA
1 TAAAAATATATACATAATATAGTA
* *
835 TTAAAGATAATATACATAAAATAGTA
1 -TAAAAAT-ATATACATAATATAGTA
861 TAAAATATATATA
1 TAAAA-ATATATA
874 TATACGTAAT
Statistics
Matches: 86, Mismatches: 16, Indels: 20
0.70 0.13 0.16
Matches are distributed among these distances:
22 11 0.13
23 4 0.05
24 4 0.05
25 38 0.44
26 19 0.22
27 10 0.12
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (24 bp):
TAAAAATATATACATAATATAGTA
Found at i:950 original size:23 final size:25
Alignment explanation
Indices: 907--952 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
897 TATACCTAAT
907 ATATTAAAAGAATATATATAATATA
1 ATATTAAAAGAATATATATAATATA
*
932 ATATTAAGA-AATATA-ATAATA
1 ATATTAAAAGAATATATATAATA
953 ACAAAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATTAAAAGAATATATATAATATA
Found at i:1482 original size:27 final size:28
Alignment explanation
Indices: 1432--1586 Score: 186
Period size: 28 Copynumber: 5.8 Consensus size: 28
1422 GGTACAAGTG
* *
1432 GTGGTGGAGAAGTGTGGCTAGTGGAGTT
1 GTGGTGGAAAAGAGTGGCTAGTGGAGTT
1460 GTGGTGGAAAAGAGT-GCTAGTGGA---
1 GTGGTGGAAAAGAGTGGCTAGTGGAGTT
*
1484 ---GTGG-AAAGTGTGGCTAGTGGAGTT
1 GTGGTGGAAAAGAGTGGCTAGTGGAGTT
1508 GGTGGTGG-AAAGAGTGGCTAGTGGAGTT
1 -GTGGTGGAAAAGAGTGGCTAGTGGAGTT
1536 GTGG-GGAAAAGAGTGGCTAGTGGAGTT
1 GTGGTGGAAAAGAGTGGCTAGTGGAGTT
1563 GGTGGTGGAAAAGGAGTGGCTAGT
1 -GTGGTGGAAAA-GAGTGGCTAGT
1587 TGAGAAAAGT
Statistics
Matches: 111, Mismatches: 4, Indels: 22
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.05
21 13 0.12
26 2 0.02
27 33 0.30
28 40 0.36
29 6 0.05
30 11 0.10
ACGTcount: A:0.23, C:0.04, G:0.48, T:0.25
Consensus pattern (28 bp):
GTGGTGGAAAAGAGTGGCTAGTGGAGTT
Found at i:1487 original size:21 final size:21
Alignment explanation
Indices: 1463--1506 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1453 TGGAGTTGTG
1463 GTGGAAAAGAGT-GCTAGTGGA
1 GTGG-AAAGAGTGGCTAGTGGA
*
1484 GTGGAAAGTGTGGCTAGTGGA
1 GTGGAAAGAGTGGCTAGTGGA
1505 GT
1 GT
1507 TGGTGGTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.27, C:0.05, G:0.45, T:0.23
Consensus pattern (21 bp):
GTGGAAAGAGTGGCTAGTGGA
Found at i:1502 original size:16 final size:16
Alignment explanation
Indices: 1483--1532 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
1473 GTGCTAGTGG
1483 AGTGGAAAGTGTGGCT
1 AGTGGAAAGTGTGGCT
1499 AGTGG--AGT-TGG-T
1 AGTGGAAAGTGTGGCT
* *
1511 GGTGGAAAGAGTGGCT
1 AGTGGAAAGTGTGGCT
1527 AGTGGA
1 AGTGGA
1533 GTTGTGGGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
12 5 0.19
13 3 0.11
14 5 0.19
15 3 0.11
16 11 0.41
ACGTcount: A:0.24, C:0.04, G:0.48, T:0.24
Consensus pattern (16 bp):
AGTGGAAAGTGTGGCT
Found at i:1559 original size:55 final size:50
Alignment explanation
Indices: 1435--1586 Score: 193
Period size: 55 Copynumber: 2.9 Consensus size: 50
1425 ACAAGTGGTG
*
1435 GTGGAGAAGTGTGGCTAGTGGAGTT-GTGGTGGAAAAGAGT-GCTAGTGGA
1 GTGGA-AAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAGAGTGGCTAGTGGA
*
1484 GTGGAAAGTGTGGCTAGTGGAGTTGGTGGTGG-AAAGAGTGGCTAGTGGA
1 GTGGAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAGAGTGGCTAGTGGA
1533 GTTGTGGGGAAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAGGAGTGGCTAGT
1 ---GT--GG-AAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAA-GAGTGGCTAGT
1587 TGAGAAAAGT
Statistics
Matches: 92, Mismatches: 1, Indels: 12
0.88 0.01 0.11
Matches are distributed among these distances:
48 26 0.28
49 21 0.23
52 2 0.02
54 2 0.02
55 27 0.29
56 3 0.03
57 11 0.12
ACGTcount: A:0.24, C:0.04, G:0.48, T:0.24
Consensus pattern (50 bp):
GTGGAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAGAGTGGCTAGTGGA
Found at i:2298 original size:14 final size:14
Alignment explanation
Indices: 2262--2312 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
2252 GAGTTGATTT
* *
2262 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
2276 TTGAAAAAAACAGAAA
1 TTG--AAAAACAGAAA
*
2292 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
2306 TT-AAAAA
1 TTGAAAAA
2313 GACCTCAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
16 12 0.39
ACGTcount: A:0.65, C:0.04, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:2366 original size:104 final size:104
Alignment explanation
Indices: 2178--2385 Score: 267
Period size: 104 Copynumber: 2.0 Consensus size: 104
2168 ATTGACTCTG
* * * * *
2178 AAAACTAGACATTAAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCT
1 AAAACTAGAAATTAAAAACAGAAATTAAAAAGACCTCAGCACGTGAGCCAAGACTCAACTCACCT
* * *
2243 CTCGCAAAAGAGTTGATTTTTGAAAAATATAAATTGAAA
66 CTCGCAAAAGAGTTAATTTTTGAAAAACAGAAATTGAAA
* * *
2282 AAAAC-AGAAATTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACC
1 AAAACTAGAAATT-AAAAACAGAAATTAAAAAGACCTCAGCACGTGAGCCAAGACTCAACTCACC
* *
2346 TCTCGCAATATG-GTTAATTTTTGACAAACAGAAATTGAAA
65 TCTCGCAA-AAGAGTTAATTTTTGAAAAACAGAAATTGAAA
2386 TTACCTCAGC
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
103 6 0.07
104 81 0.91
105 2 0.02
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.22
Consensus pattern (104 bp):
AAAACTAGAAATTAAAAACAGAAATTAAAAAGACCTCAGCACGTGAGCCAAGACTCAACTCACCT
CTCGCAAAAGAGTTAATTTTTGAAAAACAGAAATTGAAA
Found at i:2424 original size:72 final size:74
Alignment explanation
Indices: 2329--3283 Score: 473
Period size: 72 Copynumber: 12.5 Consensus size: 74
2319 AGCATGTGAG
*
2329 CCGAGACTCAACTCACCTCTCGCAATATG-GTT-AATTTTTGACAAACAGAAATTGAAATTACCT
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTGACAAACAGAAATTGAAATTACCT
2392 CAGCGTGTC
66 CAGCGTGTC
* * * * *
2401 CCGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAAAAATACC
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTGACAAACAGAAA-TTGAAATTACC
2466 TCAGCGTGTC
65 TCAGCGTGTC
* * * *
2476 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTACGAACAGAAATTGAAGAACA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--ATTTTTGACAAACAGAAATT---G---A
*** * *
2541 GAATTGA-AAAAACCTCAG-C
58 -AATT-ACCTCAGCGT--GTC
** *
2560 ATGTGAACTAAGGCTCAACTCACCTCTCGCAATATGAGTT-AA-TTTTGACAAACAG-AATTGAA
1 --CCG-A-G---GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTGACAAACAGAAATTGAA
*
2622 ATTACCTCAGC-TATC
59 ATTACCTCAGCGTGTC
* * *
2637 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTGAAAAACAGAAATTTAAAATACCT
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTGACAAACAGAAATTGAAATTACCT
*
2701 CAACGTGT-
66 CAGCGTGTC
* * * * *
2709 CCTAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTTTACGAACAGAAATTGAAGA--ACA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTGACAAACAGAAATTGAA-ATTAC-
*** *** *
2772 GAAATTGAAAAGAC
64 CTCA--G-CGTGTC
* * * * * * * ***
2786 CTCAGCATGTAAGC-CGAGGCTCAACTCAC-C--TCTCGCAATATGAGTTAATT--TTGACA-AA
1 C-C-G-A-G---GCTC-A-ACTCACCTCTCGCAATAT-G-AGT-TGAATT-TTTGACAAACAGAA
2844 CA--GAAATTGAAATACCTCAGCGTGTC
53 -ATTGAAA-T----TACCTCAGCGTGTC
* * * *
2870 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-A-TTTTGAAAAACAGAAATTTAAAATACCT
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTGACAAACAGAAATTGAAATTACCT
2933 CAGCGTGTC
66 CAGCGTGTC
** * * *
2942 TTGAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTTTTTTACGAACAGAAATTAAAAATGA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--ATTTTTGACAAACAGAAA-T-----TGA
* *
3006 AATTGAAAAGACCTCAGCATGTGA
58 AATT------ACCTCAGCGTGT-C
* *
3030 GCGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTGAAAAACAGAAATTGAAA-TACCT
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTGACAAACAGAAATTGAAATTACCT
3093 CAGCGT-TC
66 CAGCGTGTC
** *
3101 TTGAGGCTCAACTCACCTATCGCAATATGAGTTG-ATTTTTGA-AAACAGAAATTGAAATTACCT
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTGACAAACAGAAATTGAAATTACCT
3164 CAGCGTGTC
66 CAGCGTGTC
* * * * * * *
3173 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTG-A--TTTGAAAAACAAAAAATTAAAAGTATC
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTGACAAAC-AGAAATTGAAATTACC
**
3235 TCAATGTGTC
65 TCAGCGTGTC
** * *
3245 TTGAGGCTCAACTCATCGCTCGCAATATGAGTTG-ATTTT
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTT
3284 CCTTGAAAAG
Statistics
Matches: 678, Mismatches: 116, Indels: 176
0.70 0.12 0.18
Matches are distributed among these distances:
70 49 0.07
71 84 0.12
72 190 0.28
73 35 0.05
74 22 0.03
75 70 0.10
76 16 0.02
77 26 0.04
78 5 0.01
79 9 0.01
80 8 0.01
81 8 0.01
82 7 0.01
83 11 0.02
84 15 0.02
85 15 0.02
86 22 0.03
87 24 0.04
88 15 0.02
89 18 0.03
90 1 0.00
91 28 0.04
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (74 bp):
CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTGACAAACAGAAATTGAAATTACCT
CAGCGTGTC
Found at i:2595 original size:91 final size:91
Alignment explanation
Indices: 2440--2605 Score: 246
Period size: 91 Copynumber: 1.8 Consensus size: 91
2430 AGTTGATTTT
* ** *
2440 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTGAAAAATACCTCAGCGTGAACTAAGGCTCAACTCACCTCTCGCAATATG
*
2505 AGTTGATTTTTTTTTACGAACAGAAA
66 AGTTAATTTTTTTTTACGAACAGAAA
*
2531 TTGAAGAACAG-AATTGAAAAA-ACCTCAGCATGTGAACTAAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTGAAAAATACCTCAGC--GTGAACTAAGGCTCAACTCACCTCTCGCAATA
2594 TGAGTTAATTTT
64 TGAGTTAATTTT
2606 GACAAACAGA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
89 8 0.12
90 9 0.13
91 50 0.75
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (91 bp):
TTGAAAAACAGAAATTGAAAAATACCTCAGCGTGAACTAAGGCTCAACTCACCTCTCGCAATATG
AGTTAATTTTTTTTTACGAACAGAAA
Found at i:2772 original size:14 final size:14
Alignment explanation
Indices: 2753--2780 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2743 ATTTTTTTAC
2753 GAACAGAAATTGAA
1 GAACAGAAATTGAA
2767 GAACAGAAATTGAA
1 GAACAGAAATTGAA
2781 AAGACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:3166 original size:231 final size:237
Alignment explanation
Indices: 2284--3210 Score: 1485
Period size: 232 Copynumber: 4.0 Consensus size: 237
2274 AATTGAAAAA
* *
2284 AACAGAAATTGAA-AAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTC
1 AACAGAAATTGAAGAA-CAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTC
2348 TCGCAATATG-GTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAA
65 TCGCAATATGAGTTAA-TTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAA
*
2412 CTCACCTTTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCC
129 CTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTT-AAAATACCTCAGCGTGTCC
2477 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTACG
192 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTACG
* * **
2523 AACAGAAATTGAAGAACAG-AATTGAAAAAACCTCAGCATGTGAACTAAGGCTCAACTCACCTCT
1 AACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCT
*
2587 CGCAATATGAGTTAATTTTGACAAACAG-AATTGAAATTACCTCAGC-TATCCCGAGGCTCAACT
66 CGCAATATGAGTTAATTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACT
*
2650 CACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAACGTGTCCT-AG
131 CACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGTCCTGAG
*
2714 GCTCAACTTACCTCTCGCAATATGAGTTGA--TTTTTTTACG
196 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTACG
*
2754 AACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTAAGCCGAGGCTCAACTCACCTCT
1 AACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCT
*
2819 CGCAATATGAGTTAATTTTGACAAACAGAAATTGAAA-TACCTCAGCGTGTCCTGAGGCTCAACT
66 CGCAATATGAGTTAATTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACT
*
2883 CACCTCTCGCAATATGAGTTGA-TTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGTCTTGAG
131 CACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGTCCTGAG
2947 GCTCAACTCA-CTCTCGCAATATGAGTTGATTTTTTTTTACG
196 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTACG
2988 AACAGAAATT-AA-AA-ATGAAATTGAAAAGACCTCAGCATGTGAG-CGAGGCTCAACTCACCTC
1 AACAGAAATTGAAGAACA-GAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTC
* * **
3049 TCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAA-TACCTCAGCGT-TCTTGAGGCTCAA
65 TCGCAATATGAGTT-AATTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAA
* * *
3112 CTCACCTATCGCAATATGAGTTGATTTTTG-AAAACAGAAATTGAAATTACCTCAGCGTGTCCTG
129 CTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGTCCTG
*
3176 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTT
194 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
3211 GAAAAACAAA
Statistics
Matches: 647, Mismatches: 29, Indels: 31
0.92 0.04 0.04
Matches are distributed among these distances:
231 140 0.22
232 220 0.34
233 89 0.14
234 39 0.06
235 20 0.03
236 37 0.06
237 18 0.03
238 61 0.09
239 21 0.03
240 2 0.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (237 bp):
AACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCT
CGCAATATGAGTTAATTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACT
CACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAATACCTCAGCGTGTCCTGAG
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTACG
Found at i:11286 original size:12 final size:12
Alignment explanation
Indices: 11266--11301 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
11256 TGGGATATGC
*
11266 AATGTATGAATG
1 AATGCATGAATG
11278 AATGCATGAATG
1 AATGCATGAATG
11290 AATGCATGAATG
1 AATGCATGAATG
11302 TCAAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:12840 original size:16 final size:15
Alignment explanation
Indices: 12819--12866 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
12809 GATGTGAATA
12819 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
12835 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
12850 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
12866 A
1 A
12867 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:12842 original size:24 final size:24
Alignment explanation
Indices: 12815--12870 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
12805 TAATGATGTG
*
12815 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
12839 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
12863 AATAATAA
1 AATAATAA
12871 TAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:12849 original size:8 final size:8
Alignment explanation
Indices: 12815--12866 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
12805 TAATGATGTG
*
12815 AATAATAA
1 AATATTAA
12823 AATATATAA
1 AATAT-TAA
12832 AATA-TAA
1 AATATTAA
12839 AATATTAA
1 AATATTAA
*
12847 AATATCAA
1 AATATTAA
*
12855 AATATTAG
1 AATATTAA
12863 AATA
1 AATA
12867 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:13112 original size:15 final size:14
Alignment explanation
Indices: 13091--13137 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
13081 ATAACATGTA
13091 AAAAATATATATAT
1 AAAAATATATATAT
13105 AAATAATATA-ATATT
1 AAA-AATATATATA-T
* *
13120 AAAGATATATACAT
1 AAAAATATATATAT
13134 AAAA
1 AAAA
13138 TAGTATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (14 bp):
AAAAATATATATAT
Found at i:13130 original size:31 final size:31
Alignment explanation
Indices: 13068--13145 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
13058 TATAGTTAAG
* *
13068 ATATATACATAAGATAACATGTAAAAAATAT
1 ATATATAAATAATATAACATGTAAAAAATAT
* *
13099 ATATATAAATAATATAATAT-T-AAAGATAT
1 ATATATAAATAATATAACATGTAAAAAATAT
* *
13128 ATACATAAAATAGTATAA
1 ATATAT-AAATAATATAA
13146 AATATATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 12 0.30
30 11 0.28
31 17 0.43
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.32
Consensus pattern (31 bp):
ATATATAAATAATATAACATGTAAAAAATAT
Found at i:13135 original size:25 final size:25
Alignment explanation
Indices: 13009--13230 Score: 115
Period size: 25 Copynumber: 9.0 Consensus size: 25
12999 TAAATACGTG
* *
13009 ATAATATTAAAAATATGTACATAAT
1 ATAATATTAAAGATATATACATAAT
* * * *
13034 ATAGTGTTAAAAATACATACATAAT
1 ATAATATTAAAGATATATACATAAT
* *
13059 AT-A-GTT-AAGATATATACATAAG
1 ATAATATTAAAGATATATACATAAT
* * *
13081 ATAACATGTAAAAAATATATATATAAATAAT
1 ATAATAT-T----AA-AGATATATACATAAT
*
13112 ATAATATTAAAGATATATACATAAA
1 ATAATATTAAAGATATATACATAAT
* * * *
13137 ATAGTATAAAATATATATACGTAAT
1 ATAATATTAAAGATATATACATAAT
* *
13162 ATAGA-ATTTAA-A-ATATACCTAAT
1 ATA-ATATTAAAGATATATACATAAT
* *
13185 AT-AT-TAAAAGA-ATATATATAAT
1 ATAATATTAAAGATATATACATAAT
*
13207 ATAATATT-AAGAAATATA-ATAAT
1 ATAATATTAAAGATATATACATAAT
13230 A
1 A
13231 ACAAAAAAGG
Statistics
Matches: 152, Mismatches: 30, Indels: 32
0.71 0.14 0.15
Matches are distributed among these distances:
21 4 0.03
22 27 0.18
23 28 0.18
24 8 0.05
25 63 0.41
26 2 0.01
30 2 0.01
31 18 0.12
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (25 bp):
ATAATATTAAAGATATATACATAAT
Found at i:13212 original size:50 final size:50
Alignment explanation
Indices: 13009--13213 Score: 127
Period size: 50 Copynumber: 4.0 Consensus size: 50
12999 TAAATACGTG
* * * ** * *
13009 ATAATATTAAAAATATGTACATAATATAGTGTTAAAA-ATACATACATAAT
1 ATAATATTAAAGATATATACATAAAATAGT-AAAAAATATATATAAATAAT
* *
13059 AT-A-GTT-AAGATATATACATAAGATAACATGTAAAAAATATATATATAAATAAT
1 ATAATATTAAAGATATATACAT-A-A-AATA-GT-AAAAA-ATATATATAAATAAT
* **
13112 ATAATATTAAAGATATATACATAAAATAGTATAAAATATATATACGTAAT
1 ATAATATTAAAGATATATACATAAAATAGTAAAAAATATATATAAATAAT
* * * *
13162 ATAGA-ATTTAA-A-ATATACCTAATATATTAAAAGAATATATATAATATAAT
1 ATA-ATATTAAAGATATATACATAAAATAGTAAAA-AATATATATAA-ATAAT
13212 AT
1 AT
13214 TAAGAAATAT
Statistics
Matches: 121, Mismatches: 22, Indels: 24
0.72 0.13 0.14
Matches are distributed among these distances:
47 11 0.09
48 19 0.16
49 13 0.11
50 31 0.26
51 10 0.08
52 3 0.02
53 16 0.13
54 2 0.02
55 3 0.02
56 13 0.11
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (50 bp):
ATAATATTAAAGATATATACATAAAATAGTAAAAAATATATATAAATAAT
Found at i:13762 original size:29 final size:30
Alignment explanation
Indices: 13708--13820 Score: 194
Period size: 29 Copynumber: 3.8 Consensus size: 30
13698 TAGGTACAAG
*
13708 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
13738 TGGTGGTGGAAAA-GAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
13767 TGGT-GTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
13796 TGGTGGTGGAAAAGGTGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGT
13821 TGAGAAAAGT
Statistics
Matches: 78, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
28 8 0.10
29 38 0.49
30 32 0.41
ACGTcount: A:0.20, C:0.04, G:0.50, T:0.27
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Done.